[chronojump] Windows: Updated R to 2.15.2
- From: Xavier de Blas <xaviblas src gnome org>
- To: commits-list gnome org
- Cc:
- Subject: [chronojump] Windows: Updated R to 2.15.2
- Date: Fri, 8 Feb 2013 15:09:23 +0000 (UTC)
commit d0716d1b6939495a0b046385397ddd15704f32ab
Author: Xavier de Blas <xaviblas gmail com>
Date: Fri Feb 8 16:00:11 2013 +0100
Windows: Updated R to 2.15.2
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win32/deps/library/survival/tests/r_donnell.R | 60 +
.../library/survival/tests/r_donnell.Rout.save | 114 +
win32/deps/library/survival/tests/r_lung.R | 49 +
win32/deps/library/survival/tests/r_lung.Rout.save | 165 +
win32/deps/library/survival/tests/r_peterson.R | 44 +
.../library/survival/tests/r_peterson.Rout.save | 117 +
win32/deps/library/survival/tests/r_resid.R | 109 +
.../deps/library/survival/tests/r_resid.Rout.save | 348 ++
win32/deps/library/survival/tests/r_sas.R | 259 +
win32/deps/library/survival/tests/r_sas.Rout.save | 438 ++
win32/deps/library/survival/tests/r_scale.R | 30 +
.../deps/library/survival/tests/r_scale.Rout.save | 55 +
win32/deps/library/survival/tests/r_stanford.R | 71 +
.../library/survival/tests/r_stanford.Rout.save | 111 +
win32/deps/library/survival/tests/r_strata.R | 60 +
.../deps/library/survival/tests/r_strata.Rout.save | 148 +
win32/deps/library/survival/tests/r_tdist.R | 41 +
.../deps/library/survival/tests/r_tdist.Rout.save | 200 +
win32/deps/library/survival/tests/r_user.R | 29 +
win32/deps/library/survival/tests/r_user.Rout.save | 53 +
win32/deps/library/survival/tests/ratetable.R | 63 +
.../library/survival/tests/ratetable.Rout.save | 164 +
win32/deps/library/survival/tests/rounding.R | 14 +
.../deps/library/survival/tests/rounding.Rout.save | 34 +
win32/deps/library/survival/tests/singtest.R | 22 +
.../deps/library/survival/tests/singtest.Rout.save | 50 +
win32/deps/library/survival/tests/strata2.R | 17 +
.../deps/library/survival/tests/strata2.Rout.save | 45 +
win32/deps/library/survival/tests/stratatest.R | 43 +
.../library/survival/tests/stratatest.Rout.save | 68 +
.../deps/library/survival/tests/summary_survfit.R | 5 +
.../survival/tests/summary_survfit.Rout.save | 54 +
win32/deps/library/survival/tests/surv.R | 23 +
win32/deps/library/survival/tests/surv.Rout.save | 59 +
win32/deps/library/survival/tests/survfit2.R | 13 +
.../deps/library/survival/tests/survfit2.Rout.save | 33 +
win32/deps/library/survival/tests/survreg2.R | 62 +
.../deps/library/survival/tests/survreg2.Rout.save | 87 +
win32/deps/library/survival/tests/survtest.R | 60 +
.../deps/library/survival/tests/survtest.Rout.save | 99 +
win32/deps/library/survival/tests/testci.R | 67 +
win32/deps/library/survival/tests/testci.Rout.save | 91 +
win32/deps/library/survival/tests/testci2.R | 52 +
.../deps/library/survival/tests/testci2.Rout.save | 72 +
win32/deps/library/survival/tests/testnull.R | 19 +
.../deps/library/survival/tests/testnull.Rout.save | 42 +
win32/deps/library/survival/tests/testreg.R | 79 +
.../deps/library/survival/tests/testreg.Rout.save | 301 ++
win32/deps/library/survival/tests/tiedtime.R | 23 +
.../deps/library/survival/tests/tiedtime.Rout.save | 44 +
win32/deps/library/survival/tests/ties.rda | Bin 0 -> 6060 bytes
win32/deps/library/survival/tests/tt.R | 38 +
win32/deps/library/survival/tests/turnbull.R | 156 +
.../deps/library/survival/tests/turnbull.Rout.save | 194 +
win32/deps/library/tcltk/DESCRIPTION | 8 +-
win32/deps/library/tcltk/Meta/Rd.rds | Bin 2342 -> 2336 bytes
win32/deps/library/tcltk/Meta/demo.rds | Bin 266 -> 266 bytes
win32/deps/library/tcltk/Meta/hsearch.rds | Bin 2401 -> 2399 bytes
win32/deps/library/tcltk/Meta/links.rds | Bin 0 -> 2034 bytes
win32/deps/library/tcltk/Meta/nsInfo.rds | Bin 464 -> 464 bytes
win32/deps/library/tcltk/Meta/package.rds | Bin 503 -> 490 bytes
win32/deps/library/tcltk/NAMESPACE | 1 +
win32/deps/library/tcltk/R-ex/Rex.zip | Bin 4703 -> 0 bytes
win32/deps/library/tcltk/R/tcltk | 2 +-
win32/deps/library/tcltk/R/tcltk.rdb | Bin 43108 -> 77227 bytes
win32/deps/library/tcltk/R/tcltk.rdx | Bin 3337 -> 3483 bytes
win32/deps/library/tcltk/demo/tkcanvas.R | 2 +
win32/deps/library/tcltk/demo/tkdensity.R | 6 +-
win32/deps/library/tcltk/demo/tkfaq.R | 2 +
win32/deps/library/tcltk/demo/tkttest.R | 2 +
win32/deps/library/tcltk/exec/Tk-frontend.R | 20 +-
win32/deps/library/tcltk/exec/console.tcl | 2 +-
win32/deps/library/tcltk/help/AnIndex | 2 +
win32/deps/library/tcltk/help/Rhelp.zip | Bin 15191 -> 0 bytes
win32/deps/library/tcltk/help/aliases.rds | Bin 0 -> 2030 bytes
win32/deps/library/tcltk/help/paths.rds | Bin 0 -> 254 bytes
win32/deps/library/tcltk/help/tcltk.rdb | Bin 0 -> 50332 bytes
win32/deps/library/tcltk/help/tcltk.rdx | Bin 0 -> 491 bytes
win32/deps/library/tcltk/html/00Index.html | 664 +++
win32/deps/library/tcltk/html/R.css | 57 +
win32/deps/library/tcltk/libs/i386/tcltk.dll | Bin 0 -> 25600 bytes
win32/deps/library/tcltk/libs/tcltk.dll | Bin 34816 -> 0 bytes
.../library/tcltk/po/da/LC_MESSAGES/R-tcltk.mo | Bin 0 -> 2388 bytes
.../deps/library/tcltk/po/da/LC_MESSAGES/tcltk.mo | Bin 0 -> 1353 bytes
.../library/tcltk/po/de/LC_MESSAGES/R-tcltk.mo | Bin 0 -> 2370 bytes
.../deps/library/tcltk/po/de/LC_MESSAGES/tcltk.mo | Bin 0 -> 1394 bytes
.../tcltk/po/en quot/LC_MESSAGES/R-tcltk.mo | Bin 0 -> 2284 bytes
.../library/tcltk/po/en quot/LC_MESSAGES/tcltk.mo | Bin 0 -> 1288 bytes
.../library/tcltk/po/fr/LC_MESSAGES/R-tcltk.mo | Bin 0 -> 2522 bytes
.../deps/library/tcltk/po/fr/LC_MESSAGES/tcltk.mo | Bin 0 -> 1474 bytes
.../library/tcltk/po/it/LC_MESSAGES/R-tcltk.mo | Bin 0 -> 916 bytes
.../library/tcltk/po/ja/LC_MESSAGES/R-tcltk.mo | Bin 0 -> 2861 bytes
.../deps/library/tcltk/po/ja/LC_MESSAGES/tcltk.mo | Bin 0 -> 1533 bytes
.../library/tcltk/po/ko/LC_MESSAGES/R-tcltk.mo | Bin 0 -> 2769 bytes
.../deps/library/tcltk/po/ko/LC_MESSAGES/tcltk.mo | Bin 0 -> 1516 bytes
.../library/tcltk/po/pl/LC_MESSAGES/R-tcltk.mo | Bin 0 -> 2592 bytes
.../deps/library/tcltk/po/pl/LC_MESSAGES/tcltk.mo | Bin 0 -> 1519 bytes
.../library/tcltk/po/pt_BR/LC_MESSAGES/R-tcltk.mo | Bin 0 -> 2534 bytes
.../library/tcltk/po/pt_BR/LC_MESSAGES/tcltk.mo | Bin 0 -> 1440 bytes
.../library/tcltk/po/ru/LC_MESSAGES/R-tcltk.mo | Bin 0 -> 2468 bytes
.../deps/library/tcltk/po/ru/LC_MESSAGES/tcltk.mo | Bin 0 -> 1442 bytes
.../library/tcltk/po/zh_CN/LC_MESSAGES/R-tcltk.mo | Bin 0 -> 2239 bytes
.../library/tcltk/po/zh_CN/LC_MESSAGES/tcltk.mo | Bin 0 -> 1285 bytes
win32/deps/library/tools/DESCRIPTION | 11 +-
win32/deps/library/tools/INDEX | 34 +-
win32/deps/library/tools/Meta/Rd.rds | Bin 1755 -> 2586 bytes
win32/deps/library/tools/Meta/hsearch.rds | Bin 1721 -> 2540 bytes
win32/deps/library/tools/Meta/links.rds | Bin 0 -> 1299 bytes
win32/deps/library/tools/Meta/nsInfo.rds | Bin 904 -> 1375 bytes
win32/deps/library/tools/Meta/package.rds | Bin 519 -> 495 bytes
win32/deps/library/tools/NAMESPACE | 119 +-
win32/deps/library/tools/R-ex/Rex.zip | Bin 6174 -> 0 bytes
win32/deps/library/tools/R/tools | 2 +-
win32/deps/library/tools/R/tools.rdb | Bin 250107 -> 1089871 bytes
win32/deps/library/tools/R/tools.rdx | Bin 4668 -> 8703 bytes
win32/deps/library/tools/help/AnIndex | 48 +-
win32/deps/library/tools/help/Rhelp.zip | Bin 33103 -> 0 bytes
win32/deps/library/tools/help/aliases.rds | Bin 0 -> 1054 bytes
win32/deps/library/tools/help/paths.rds | Bin 0 -> 599 bytes
win32/deps/library/tools/help/tools.rdb | Bin 0 -> 168932 bytes
win32/deps/library/tools/help/tools.rdx | Bin 0 -> 1345 bytes
win32/deps/library/tools/html/00Index.html | 363 ++
win32/deps/library/tools/html/R.css | 57 +
win32/deps/library/tools/libs/i386/tools.dll | Bin 0 -> 23040 bytes
win32/deps/library/tools/libs/tools.dll | Bin 12800 -> 0 bytes
.../library/tools/po/da/LC_MESSAGES/R-tools.mo | Bin 0 -> 7100 bytes
.../deps/library/tools/po/da/LC_MESSAGES/tools.mo | Bin 0 -> 977 bytes
.../library/tools/po/de/LC_MESSAGES/R-tools.mo | Bin 0 -> 37421 bytes
.../deps/library/tools/po/de/LC_MESSAGES/tools.mo | Bin 0 -> 985 bytes
.../tools/po/en quot/LC_MESSAGES/R-tools.mo | Bin 0 -> 35950 bytes
.../library/tools/po/en quot/LC_MESSAGES/tools.mo | Bin 0 -> 914 bytes
.../library/tools/po/fr/LC_MESSAGES/R-tools.mo | Bin 0 -> 38744 bytes
.../deps/library/tools/po/fr/LC_MESSAGES/tools.mo | Bin 0 -> 1038 bytes
.../library/tools/po/it/LC_MESSAGES/R-tools.mo | Bin 0 -> 5734 bytes
.../deps/library/tools/po/it/LC_MESSAGES/tools.mo | Bin 0 -> 661 bytes
.../library/tools/po/ja/LC_MESSAGES/R-tools.mo | Bin 0 -> 44108 bytes
.../deps/library/tools/po/ja/LC_MESSAGES/tools.mo | Bin 0 -> 1111 bytes
.../library/tools/po/ko/LC_MESSAGES/R-tools.mo | Bin 0 -> 40547 bytes
.../deps/library/tools/po/ko/LC_MESSAGES/tools.mo | Bin 0 -> 1167 bytes
.../library/tools/po/pl/LC_MESSAGES/R-tools.mo | Bin 0 -> 38844 bytes
.../deps/library/tools/po/pl/LC_MESSAGES/tools.mo | Bin 0 -> 1103 bytes
.../library/tools/po/pt_BR/LC_MESSAGES/R-tools.mo | Bin 0 -> 2446 bytes
.../library/tools/po/pt_BR/LC_MESSAGES/tools.mo | Bin 0 -> 809 bytes
.../library/tools/po/ru/LC_MESSAGES/R-tools.mo | Bin 0 -> 36732 bytes
.../deps/library/tools/po/ru/LC_MESSAGES/tools.mo | Bin 0 -> 1086 bytes
.../library/tools/po/tr/LC_MESSAGES/R-tools.mo | Bin 0 -> 522 bytes
.../library/tools/po/zh_CN/LC_MESSAGES/R-tools.mo | Bin 0 -> 33382 bytes
.../library/tools/po/zh_CN/LC_MESSAGES/tools.mo | Bin 0 -> 874 bytes
win32/deps/library/tools/tests/undoc.R | 4 +
win32/deps/library/utils/DESCRIPTION | 8 +-
win32/deps/library/utils/INDEX | 64 +-
win32/deps/library/utils/Meta/Rd.rds | Bin 5561 -> 6170 bytes
win32/deps/library/utils/Meta/hsearch.rds | Bin 5437 -> 5992 bytes
win32/deps/library/utils/Meta/links.rds | Bin 0 -> 3110 bytes
win32/deps/library/utils/Meta/nsInfo.rds | Bin 1911 -> 2141 bytes
win32/deps/library/utils/Meta/package.rds | Bin 489 -> 470 bytes
win32/deps/library/utils/Meta/vignette.rds | Bin 0 -> 208 bytes
win32/deps/library/utils/NAMESPACE | 103 +-
win32/deps/library/utils/R-ex/Rex.zip | Bin 31361 -> 0 bytes
win32/deps/library/utils/R/utils | 2 +-
win32/deps/library/utils/R/utils.rdb | Bin 186059 -> 632254 bytes
win32/deps/library/utils/R/utils.rdx | Bin 4780 -> 6157 bytes
win32/deps/library/utils/Sweave/Sweave-test-1.Rnw | 20 +-
win32/deps/library/utils/Sweave/example-1.Rnw | 29 +
win32/deps/library/utils/doc/Sweave.R | 39 +
win32/deps/library/utils/doc/Sweave.Rnw | 814 +++
win32/deps/library/utils/doc/Sweave.pdf | Bin 0 -> 321092 bytes
win32/deps/library/utils/doc/index.html | 27 +
win32/deps/library/utils/help/AnIndex | 71 +-
win32/deps/library/utils/help/Rhelp.zip | Bin 154521 -> 0 bytes
win32/deps/library/utils/help/aliases.rds | Bin 0 -> 2584 bytes
win32/deps/library/utils/help/paths.rds | Bin 0 -> 1276 bytes
win32/deps/library/utils/help/utils.rdb | Bin 0 -> 594322 bytes
win32/deps/library/utils/help/utils.rdx | Bin 0 -> 3183 bytes
win32/deps/library/utils/html/00Index.html | 670 +++
win32/deps/library/utils/html/R.css | 57 +
.../library/utils/po/da/LC_MESSAGES/R-utils.mo | Bin 0 -> 6289 bytes
.../library/utils/po/de/LC_MESSAGES/R-utils.mo | Bin 0 -> 38513 bytes
.../utils/po/en quot/LC_MESSAGES/R-utils.mo | Bin 0 -> 37238 bytes
.../library/utils/po/fr/LC_MESSAGES/R-utils.mo | Bin 0 -> 40117 bytes
.../library/utils/po/ja/LC_MESSAGES/R-utils.mo | Bin 0 -> 45377 bytes
.../library/utils/po/ko/LC_MESSAGES/R-utils.mo | Bin 0 -> 43182 bytes
.../library/utils/po/pl/LC_MESSAGES/R-utils.mo | Bin 0 -> 40363 bytes
.../library/utils/po/pt_BR/LC_MESSAGES/R-utils.mo | Bin 0 -> 1407 bytes
.../library/utils/po/ru/LC_MESSAGES/R-utils.mo | Bin 0 -> 38036 bytes
.../library/utils/po/tr/LC_MESSAGES/R-utils.mo | Bin 0 -> 999 bytes
.../library/utils/po/zh_CN/LC_MESSAGES/R-utils.mo | Bin 0 -> 33846 bytes
win32/deps/library/utils/tests/Sexpr-verb-ex.Rnw | 44 +
win32/deps/library/utils/tests/Sweave-tst.R | 84 +
win32/deps/library/utils/tests/completion.R | 29 +
win32/deps/library/utils/tests/customgraphics.Rnw | 20 +
win32/deps/library/utils/tests/keepsource.Rnw | 12 +
win32/deps/library/utils/tests/swv-keepSrc-1.Rnw | 47 +
1799 files changed, 87462 insertions(+), 20119 deletions(-)
---
diff --git a/win32/deps/bin/R.exe b/win32/deps/bin/R.exe
index e2c6803..43731fa 100644
Binary files a/win32/deps/bin/R.exe and b/win32/deps/bin/R.exe differ
diff --git a/win32/deps/bin/Rscript.exe b/win32/deps/bin/Rscript.exe
index 0d37a50..43731fa 100644
Binary files a/win32/deps/bin/Rscript.exe and b/win32/deps/bin/Rscript.exe differ
diff --git a/win32/deps/bin/i386/R.dll b/win32/deps/bin/i386/R.dll
new file mode 100644
index 0000000..ba7b61a
Binary files /dev/null and b/win32/deps/bin/i386/R.dll differ
diff --git a/win32/deps/bin/i386/R.exe b/win32/deps/bin/i386/R.exe
new file mode 100644
index 0000000..6697c70
Binary files /dev/null and b/win32/deps/bin/i386/R.exe differ
diff --git a/win32/deps/bin/i386/RSetReg.exe b/win32/deps/bin/i386/RSetReg.exe
new file mode 100644
index 0000000..3e5eea2
Binary files /dev/null and b/win32/deps/bin/i386/RSetReg.exe differ
diff --git a/win32/deps/bin/i386/Rblas.dll b/win32/deps/bin/i386/Rblas.dll
new file mode 100644
index 0000000..6dd7a92
Binary files /dev/null and b/win32/deps/bin/i386/Rblas.dll differ
diff --git a/win32/deps/bin/i386/Rcmd.exe b/win32/deps/bin/i386/Rcmd.exe
new file mode 100644
index 0000000..6aca7db
Binary files /dev/null and b/win32/deps/bin/i386/Rcmd.exe differ
diff --git a/win32/deps/bin/i386/Rgraphapp.dll b/win32/deps/bin/i386/Rgraphapp.dll
new file mode 100644
index 0000000..c17e5c7
Binary files /dev/null and b/win32/deps/bin/i386/Rgraphapp.dll differ
diff --git a/win32/deps/bin/i386/Rgui.exe b/win32/deps/bin/i386/Rgui.exe
new file mode 100644
index 0000000..b0757cd
Binary files /dev/null and b/win32/deps/bin/i386/Rgui.exe differ
diff --git a/win32/deps/bin/i386/Riconv.dll b/win32/deps/bin/i386/Riconv.dll
new file mode 100644
index 0000000..4bc6323
Binary files /dev/null and b/win32/deps/bin/i386/Riconv.dll differ
diff --git a/win32/deps/bin/i386/Rlapack.dll b/win32/deps/bin/i386/Rlapack.dll
new file mode 100644
index 0000000..b96ad74
Binary files /dev/null and b/win32/deps/bin/i386/Rlapack.dll differ
diff --git a/win32/deps/bin/i386/Rscript.exe b/win32/deps/bin/i386/Rscript.exe
new file mode 100644
index 0000000..fd03c0a
Binary files /dev/null and b/win32/deps/bin/i386/Rscript.exe differ
diff --git a/win32/deps/bin/i386/Rterm.exe b/win32/deps/bin/i386/Rterm.exe
new file mode 100644
index 0000000..1efc779
Binary files /dev/null and b/win32/deps/bin/i386/Rterm.exe differ
diff --git a/win32/deps/bin/i386/Rzlib.dll b/win32/deps/bin/i386/Rzlib.dll
new file mode 100644
index 0000000..133975c
Binary files /dev/null and b/win32/deps/bin/i386/Rzlib.dll differ
diff --git a/win32/deps/bin/i386/open.exe b/win32/deps/bin/i386/open.exe
new file mode 100644
index 0000000..24aa7ae
Binary files /dev/null and b/win32/deps/bin/i386/open.exe differ
diff --git a/win32/deps/etc/Rcmd_environ b/win32/deps/etc/Rcmd_environ
index 8276a97..e308ee5 100644
--- a/win32/deps/etc/Rcmd_environ
+++ b/win32/deps/etc/Rcmd_environ
@@ -2,40 +2,35 @@
R_SHARE_DIR=${R_HOME}/share
R_INCLUDE_DIR=${R_HOME}/include
R_DOC_DIR=${R_HOME}/doc
-R_LIBS=${R_HOME}/lib/R/library
R_ARCH=
## from Rcmd
R_OSTYPE=windows
-PERL5LIB=${R_SHARE_DIR}/perl;${PERL5LIB}
-TEXINPUTS=.;${TEXINPUTS};${R_SHARE_DIR}/texmf;
+TEXINPUTS=.;${TEXINPUTS};${R_SHARE_DIR}/texmf/tex/latex;
+BIBINPUTS=.;${BIBINPUTS};${R_SHARE_DIR}/texmf/bibtex/bib;
+BSTINPUTS=.;${BSTINPUTS};${R_SHARE_DIR}/texmf/bibtex/bst;
## from etc/Renviron
-R_PLAFORM='i386-pc-mingw32'
+# R_PLATFORM='i386-pc-mingw32'
R_PAPERSIZE_USER=${R_PAPERSIZE}
R_PAPERSIZE=${R_PAPERSIZE-'a4'}
-## Default TeXMF stuff
-R_LATEXCMD=${R_LATEXCMD-${LATEX-'latex'}}
-R_PDFLATEXCMD=${R_PDFLATEXCMD-${PDFLATEX-'pdflatex'}}
-R_DVIPSCMD=${R_DVIPSCMD-${DVIPS-'dvips'}}
-R_MAKEINDEXCMD=${R_MAKEINDEX-${MAKEINDEX-'makeindex'}}
-R_RD4DVI=${R_RD4DVI-'ae'}
-R_RD4PDF=${R_RD4PDF-'times,hyper'}
+# for Rd2dpf, reference manual
+R_RD4PDF=${R_RD4PDF-'times,inconsolata,hyper'}
+## used for options("texi2dvi")
+# R_TEXI2DVICMD=${R_TEXI2DVICMD-${TEXI2DVI-'texi2dvi'}}
+## used by INSTALL, check, build
+R_GZIPCMD=${R_GZIPCMD-'gzip'}
## Default zip/unzip commands
R_UNZIPCMD=${R_UNZIPCMD-'unzip'}
R_ZIPCMD=${R_ZIPCMD-'zip'}
+R_BZIPCMD=${R_BZIPCMD-'bzip2'}
## Default browser
-R_BROWSER=${R_BROWSER-'open'}
+# R_BROWSER=${R_BROWSER-'open'}
## Default editor
-#EDITOR=${EDITOR-${VISUAL-vi}}
+# EDITOR=${EDITOR-${VISUAL-vi}}
## Default pager
-#PAGER=${PAGER-''}
+# PAGER=${PAGER-''}
## Default PDF viewer
-R_PDFVIEWER=${R_PDFVIEWER-'open'}
-## Use configure values
-AWK=gawk
-GREP='grep -E'
-#MAKE=${MAKE-make'}
-#PERL=${PERL-perl}
+# R_PDFVIEWER=${R_PDFVIEWER-'open'}
+# MAKE=${MAKE-make}
SED=${SED-sed}
-#TAR=${TAR-tar}
diff --git a/win32/deps/etc/Rdevga b/win32/deps/etc/Rdevga
index cb361fb..c2d2dcb 100644
--- a/win32/deps/etc/Rdevga
+++ b/win32/deps/etc/Rdevga
@@ -4,9 +4,9 @@
# Format is
# [TT] face:style
# where style is plain, bold, italic or bold&italic.
-# If 'TT' is present, only True Type fonts are searched.
+# If 'TT' is present, only TrueType/OpenType fonts are searched.
# Remarks:
-# (a) Windows graphics engine can only rotate True Type fonts;
+# (a) Windows graphics engine can only rotate TrueType fonts;
# (b) Only the first 32 fonts will be used.
TT Arial : plain
diff --git a/win32/deps/etc/Rprofile.site b/win32/deps/etc/Rprofile.site
new file mode 100644
index 0000000..f909b59
--- /dev/null
+++ b/win32/deps/etc/Rprofile.site
@@ -0,0 +1,23 @@
+# Things you might want to change
+
+# options(papersize="a4")
+# options(editor="notepad")
+# options(pager="internal")
+
+# set the default help type
+# options(help_type="text")
+ options(help_type="html")
+
+# set a site library
+# .Library.site <- file.path(chartr("\\", "/", R.home()), "site-library")
+
+# set a CRAN mirror
+# local({r <- getOption("repos")
+# r["CRAN"] <- "http://my.local.cran";
+# options(repos=r)})
+
+# Give a fortune cookie, but only to interactive sessions
+# (This would need the fortunes package to be installed.)
+# if (interactive())
+# fortunes::fortune()
+
diff --git a/win32/deps/etc/i386/Makeconf b/win32/deps/etc/i386/Makeconf
new file mode 100644
index 0000000..e9ad4d4
--- /dev/null
+++ b/win32/deps/etc/i386/Makeconf
@@ -0,0 +1,219 @@
+#-*- Makefile -*-
+# $(R_HOME}/etc$(R_ARCH)/Makeconf
+
+# Hand-edited version for gnuwin32.
+
+ifdef DEBUG
+ DLLFLAGS=
+ DEBUGFLAG=-gdwarf-2
+else
+ DLLFLAGS=-s
+ DEBUGFLAG=
+endif
+
+DLLFLAGS+= -static-libgcc
+LINKFLAGS+= -static-libgcc
+
+## Things which are substituted by fixed/Makefile (and also -O3 -> -O2)
+WIN = 32
+BINPREF =
+# SYMPAT = 's/^.* [BCDRT] _/ /p' for 32-bit
+# SYMPAT = 's/^.* [BCDRT] / /p' for 64-bit
+SYMPAT = 's/^.* [BCDRT] _/ /p'
+IMPDIR = bin/i386
+# flags for multilib builds, for compilers, dlltool and windres
+M_ARCH =
+DT_ARCH =
+RC_ARCH =
+# Used by packages tcltk and tkrplot
+TCL_HOME = $(R_HOME)/Tcl
+LOCAL_SOFT =
+
+ifneq ($(strip $(LOCAL_SOFT)),)
+LOCAL_CPPFLAGS = -I"$(LOCAL_SOFT)/include"
+LOCAL_LIBS = -L"$(LOCAL_SOFT)/lib$(R_ARCH)" -L"$(LOCAL_SOFT)/lib"
+endif
+
+DLLTOOL = $(BINPREF)dlltool --as $(BINPREF)as $(DT_ARCH)
+DLLTOOLFLAGS = -k
+NM = $(BINPREF)nm
+RESCOMP = $(BINPREF)windres $(RC_ARCH)
+## MAIN_LD needs to be set by the package
+LINKER = $(MAIN_LD)
+## as a default
+DLL = $(CC)
+
+## Things defined in Renviron on Unix
+SED = sed
+TAR = tar
+
+## Things defined in MkRules
+CAT = cat
+CP = cp
+MKDIR = mkdir
+RM = rm -f
+SORT = sort
+
+## For use in packages
+GRAPHAPP_LIB = -lRgraphapp
+TCL_VERSION = 85
+ZLIB_LIBS = -lRzlib
+
+AR = $(BINPREF)ar
+## Used by packages 'maps' and 'mapdata'
+AWK = gawk
+BLAS_LIBS = -L"$(R_HOME)/$(IMPDIR)" -lRblas
+C_VISIBILITY =
+CC = $(BINPREF)gcc $(M_ARCH)
+CFLAGS = -O3 -Wall $(DEBUGFLAG) -std=gnu99 -mtune=core2
+CPICFLAGS =
+CPPFLAGS =
+CXX = $(BINPREF)g++ $(M_ARCH)
+CXXCPP = $(CXX) -E
+CXXFLAGS = -O2 -Wall $(DEBUGFLAG) -mtune=core2
+CXXPICFLAGS =
+DYLIB_EXT = .dll
+DYLIB_LD = $(DLL)
+DYLIB_LDFLAGS = -shared
+DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
+ECHO = echo
+ECHO_C =
+ECHO_N = -n
+ECHO_T =
+FC = $(BINPREF)gfortran $(M_ARCH)
+FCFLAGS = -O3 $(DEBUGFLAG) -mtune=core2
+# additional libs needed when linking with $(FC), e.g. on Solaris
+FCLIBS =
+F77 = $(BINPREF)gfortran $(M_ARCH)
+F77_VISIBILITY =
+FFLAGS = -O3 $(DEBUGFLAG) -mtune=core2
+FLIBS = -lgfortran
+FCPICFLAGS =
+FPICFLAGS =
+FOUNDATION_CPPFLAGS =
+FOUNDATION_LIBS =
+JAR =
+JAVA =
+JAVAC =
+JAVAH =
+# JAVA_HOME =
+# JAVA_LD_LIBRARY_PATH =
+JAVA_LIBS = -L"$(JAVA_HOME)/bin/client" -ljvm -ljvm-w32
+JAVA_CPPFLAGS = -I"$(JAVA_HOME)/../include" -I"$(JAVA_HOME)/../include/win32"
+LAPACK_LIBS = -L"$(R_HOME)/$(IMPDIR)" -lRlapack
+## we only need this is if it is external, as otherwise link to R
+LIBINTL=
+LIBM = -lm
+LIBR = -L"$(R_HOME)/$(IMPDIR)" -lR
+LIBS = -lm
+## needed by R CMD config
+LIBnn = lib
+LIBTOOL =
+LDFLAGS =
+## needed to build applications linking to static libR
+# MAIN_LD =
+# MAIN_LDFLAGS =
+# MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS)
+# don't have this: would 'mkdir -p' do?
+# MKINSTALLDIRS = $(R_HOME)/bin/mkinstalldirs
+OBJC = $(CC)
+OBJCFLAGS = -O2
+OBJC_LIBS = -lobjc
+OBJCXX =
+R_ARCH = /i386
+RANLIB = $(BINPREF)ranlib
+SAFE_FFLAGS = -O3 -ffloat-store
+SED = sed
+## it seems some makes (but not ours) get upset if SHELL is set.
+# SHELL = /bin/sh
+SHLIB_CFLAGS =
+SHLIB_CXXFLAGS =
+SHLIB_CXXLD = $(CXX)
+## ideally -shared -static-libstdc++, but not for gcc 4.2.1
+SHLIB_CXXLDFLAGS = -shared
+SHLIB_EXT = .dll
+SHLIB_FCLD = $(FC)
+## ideally -shared -static-libgfortran, but not for gcc 4.2.1
+SHLIB_FCLDFLAGS = -shared
+SHLIB_FFLAGS =
+SHLIB_LD = $(CC)
+SHLIB_LDFLAGS = -shared
+SHLIB_LIBADD =
+SHLIB_LINK = $(SHLIB_LD) -Wl,--export-all-symbols $(SHLIB_LDFLAGS) $(LDFLAGS)
+SHLIB_OPENMP_CFLAGS = -fopenmp
+SHLIB_OPENMP_CXXFLAGS = -fopenmp
+SHLIB_OPENMP_FCFLAGS = -fopenmp
+SHLIB_OPENMP_FFLAGS = -fopenmp
+SHLIB_PTHREAD_FLAGS = -pthread
+STRIP_LIBS = $(BINPREF)strip --strip-unneeded
+STRIP_STATIC_LIBS = $(BINPREF)strip --strip-debug
+TCLTK_CPPFLAGS = -I "$(TCL_HOME)/include" -DWin32
+TCLTK_LIBS = -L"$(TCL_HOME)/bin" -ltcl$(TCL_VERSION) -ltk$(TCL_VERSION)
+
+STATIC_LIBR =
+
+R_XTRA_CFLAGS =
+R_XTRA_CPPFLAGS = -I"$(R_HOME)/include" -DNDEBUG
+R_XTRA_CXXFLAGS =
+R_XTRA_FFLAGS =
+
+ALL_CFLAGS = $(R_XTRA_CFLAGS) $(PKG_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS)
+ALL_CPPFLAGS = $(R_XTRA_CPPFLAGS) $(PKG_CPPFLAGS) $(CPPFLAGS) $($*-CPPFLAGS) $(CLINK_CPPFLAGS) $(LOCAL_CPPFLAGS)
+ALL_CXXFLAGS = $(R_XTRA_CXXFLAGS) $(PKG_CXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(CXXFLAGS)
+ALL_OBJCFLAGS = $(PKG_OBJCFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(OBJCFLAGS)
+ALL_OBJCXXFLAGS = $(PKG_OBJCXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(OBJCXXFLAGS)
+ALL_FFLAGS = $(R_XTRA_FFLAGS) $(PKG_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS)
+ALL_LIBS = $(PKG_LIBS) $(LOCAL_LIBS) $(SHLIB_LIBADD) $(LIBR) $(LIBINTL)
+
+.SUFFIXES:
+.SUFFIXES: .c .cc .cpp .d .f .f90 .f95 .m .mm .M .o .a .def .dll .exe .rc
+
+.c.o:
+ $(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -c $< -o $@
+.c.d:
+ @echo "making $@ from $<"
+ @$(CC) -std=gnu99 -MM $(ALL_CPPFLAGS) $< > $@
+.cc.o:
+ $(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
+.cpp.o:
+ $(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
+.cc.d:
+ @echo "making $@ from $<"
+ @$(CXX) -M $(ALL_CPPFLAGS) $< > $@
+.cpp.d:
+ @echo "making $@ from $<"
+ @$(CXX) -M $(ALL_CPPFLAGS) $< > $@
+.m.o:
+ $(OBJC) $(ALL_CPPFLAGS) $(ALL_OBJCFLAGS) -c $< -o $@
+.m.d:
+ @echo "making $@ from $<"
+ @$(OBJC) -MM $(ALL_CPPFLAGS) $< > $@
+.mm.o:
+ $(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
+.M.o:
+ $(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
+.f.o:
+ $(F77) $(ALL_FFLAGS) -c $< -o $@
+.f95.o:
+ $(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c $< -o $@
+.f90.o:
+ $(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c $< -o $@
+
+%.exe:
+ $(LINKER) $(LINKFLAGS) $($*-LINKFLAGS) -o $@ $^ $($*-LIBS) $(LOCAL_LIBS) $(LIBS)
+
+%.dll:
+ @echo EXPORTS > $*.def
+ @$(NM) $^ | $(SED) -n $(SYMPAT) >> $*.def
+ $(SHLIB_LD) -shared $(DLLFLAGS) -o $@ $*.def $^ $(ALL_LIBS)
+ @$(RM) $*.def
+
+lib%.dll.a: %.def
+ $(DLLTOOL) $(DLLTOOLFLAGS) $($*-DLLTOOLFLAGS) --dllname $*.dll --input-def $*.def --output-lib $@
+
+%.a:
+ @$(RM) $@
+ $(AR) crs $@ $^
+
+%.o: %.rc
+ $(RESCOMP) $(RESFLAGS) -i $< -o $@
diff --git a/win32/deps/etc/repositories b/win32/deps/etc/repositories
new file mode 100644
index 0000000..440c10b
--- /dev/null
+++ b/win32/deps/etc/repositories
@@ -0,0 +1,20 @@
+## The fields here are tab-delimited: there is a row name
+## menu_name is the name to be used in setRepositories()
+## URL is the base URL (see R-admin.texi)
+## default is whether this should be a default choice
+## source, win.binary, mac.binary indicate if the corresponding type is present
+##
+## BioC entries are version-specific, with %v getting expanded to the
+## BioC version associated with the current R version.
+## Also, %bm is substituted from the setting of getOption("BioC_mirror")
+##
+menu_name URL default source win.binary mac.binary
+CRAN CRAN @CRAN@ TRUE TRUE TRUE TRUE
+CRANextra CRAN (extras) "http://www.stats.ox.ac.uk/pub/RWin"; TRUE FALSE TRUE TRUE
+BioCsoft "BioC software" %bm/packages/%v/bioc FALSE TRUE TRUE TRUE
+BioCann "BioC annotation" %bm/packages/%v/data/annotation FALSE TRUE TRUE TRUE
+BioCexp "BioC experiment" %bm/packages/%v/data/experiment FALSE TRUE TRUE TRUE
+BioCextra "BioC extra" %bm/packages/%v/extra FALSE TRUE TRUE TRUE
+Omegahat Omegahat http://www.omegahat.org/R FALSE TRUE TRUE FALSE
+R-Forge R-Forge http://R-Forge.R-project.org FALSE TRUE TRUE TRUE
+rforge.net rforge.net http://www.rforge.net FALSE TRUE TRUE TRUE
diff --git a/win32/deps/library/Cairo/DESCRIPTION b/win32/deps/library/Cairo/DESCRIPTION
new file mode 100644
index 0000000..ef681dc
--- /dev/null
+++ b/win32/deps/library/Cairo/DESCRIPTION
@@ -0,0 +1,32 @@
+Package: Cairo
+Version: 1.5-2
+Title: R graphics device using cairo graphics library for creating
+ high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG,
+ PostScript) and display (X11 and Win32) output.
+Author: Simon Urbanek <Simon Urbanek r-project org>, Jeffrey Horner
+ <jeff horner vanderbilt edu>
+Maintainer: Simon Urbanek <Simon Urbanek r-project org>
+Depends: R (>= 2.4.0)
+Suggests: png
+Enhances: FastRWeb
+Description: This package provides a Cairo graphics device that can be
+ use to create high-quality vector (PDF, PostScript and SVG) and
+ bitmap output (PNG,JPEG,TIFF), and high-quality rendering in
+ displays (X11 and Win32). Since it uses the same back-end for
+ all output, copying across formats is WYSIWYG. Files are
+ created without the dependence on X11 or other external
+ programs. This device supports alpha channel (semi-transparent
+ drawing) and resulting images can contain transparent and
+ semi-transparent regions. It is ideal for use in server
+ environemnts (file output) and as a replacement for other
+ devices that don't have Cairo's capabilities such as alpha
+ support or anti-aliasing. Backends are modular such that any
+ subset of backends is supported.
+License: GPL-2
+SystemRequirements: cairo (>= 1.2 http://www.cairographics.org/)
+URL: http://www.rforge.net/Cairo/
+Packaged: 2012-11-05 18:22:35 UTC; svnuser
+Repository: CRAN
+Date/Publication: 2012-11-05 19:46:52
+Built: R 2.15.2; i386-w64-mingw32; 2013-01-03 17:06:29 UTC; windows
+Archs: i386, x64
diff --git a/win32/deps/library/Cairo/INDEX b/win32/deps/library/Cairo/INDEX
new file mode 100644
index 0000000..1708875
--- /dev/null
+++ b/win32/deps/library/Cairo/INDEX
@@ -0,0 +1,10 @@
+Cairo Create a new Cairo-based graphics device
+Cairo.capabilities Reports which output types are supported by
+ this Cairo build
+Cairo.capture Capture contents of an image backend.
+Cairo.onSave Cairo callbacks
+Cairo.serial Check for changes in the graphics state of
+ Cairo devices.
+CairoFontMatch Find installed fonts with a fontconfig pattern
+CairoFonts Set the fonts used for all Cairo graphics
+ devices.
diff --git a/win32/deps/library/Cairo/MD5 b/win32/deps/library/Cairo/MD5
new file mode 100644
index 0000000..395e2d2
--- /dev/null
+++ b/win32/deps/library/Cairo/MD5
@@ -0,0 +1,23 @@
+367e1d046a1b3bcc1bd575b171b84a48 *DESCRIPTION
+fc2c0a74538e45f22ff465b0e64fafec *INDEX
+e3e837c005b332a79b709a50da125b2e *Meta/Rd.rds
+4db599095e401fe2698de6ec03c1bc55 *Meta/hsearch.rds
+62f4a47498cb94c97fdefef3dbb5ae37 *Meta/links.rds
+f0fe1e54466b28647836b904a036c97c *Meta/nsInfo.rds
+2711cfe07728704728dc42b4fca35826 *Meta/package.rds
+a4757769cbeeb852905ad940c7ac7029 *NAMESPACE
+3b624acf7084dcf42766ad70a70644af *NEWS
+240d28d145138a75831809e31a480bad *R/Cairo
+9a22fef89f7d92813d04c9f689d7374f *R/Cairo.rdb
+1d82db82df08a0dde48e4496fc390431 *R/Cairo.rdx
+87c65a40e4a86e4ef484df5260fb21df *help/AnIndex
+cc9130832b75b9d47cd1c34820a8c1ff *help/Cairo.rdb
+ff518ffddf788112cb32d7b0b1527544 *help/Cairo.rdx
+59e0de616bb718ce1a5023e0c84b637b *help/aliases.rds
+913c51196267929a30ef2de38f9d8889 *help/paths.rds
+8cc3b6376814258a0c58e2cb4443edfc *html/00Index.html
+444535b9cb76ddff1bab1e1865a3fb14 *html/R.css
+470c7f09a7bf4dc3a363e555443a8bf6 *libs/i386/Cairo.dll
+3ed973be2396fc83baea840e8bb59c24 *libs/i386/symbols.rds
+3a9c89cbe58b07e653a6b938d0c0a63d *libs/x64/Cairo.dll
+9a6cbf714e835eacd7ac8b19d633c197 *libs/x64/symbols.rds
diff --git a/win32/deps/library/Cairo/Meta/Rd.rds b/win32/deps/library/Cairo/Meta/Rd.rds
new file mode 100644
index 0000000..e610773
Binary files /dev/null and b/win32/deps/library/Cairo/Meta/Rd.rds differ
diff --git a/win32/deps/library/Cairo/Meta/hsearch.rds b/win32/deps/library/Cairo/Meta/hsearch.rds
new file mode 100644
index 0000000..4fe8318
Binary files /dev/null and b/win32/deps/library/Cairo/Meta/hsearch.rds differ
diff --git a/win32/deps/library/Cairo/Meta/links.rds b/win32/deps/library/Cairo/Meta/links.rds
new file mode 100644
index 0000000..40cf766
Binary files /dev/null and b/win32/deps/library/Cairo/Meta/links.rds differ
diff --git a/win32/deps/library/Cairo/Meta/nsInfo.rds b/win32/deps/library/Cairo/Meta/nsInfo.rds
new file mode 100644
index 0000000..6248edd
Binary files /dev/null and b/win32/deps/library/Cairo/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/Cairo/Meta/package.rds b/win32/deps/library/Cairo/Meta/package.rds
new file mode 100644
index 0000000..143bed0
Binary files /dev/null and b/win32/deps/library/Cairo/Meta/package.rds differ
diff --git a/win32/deps/library/Cairo/NAMESPACE b/win32/deps/library/Cairo/NAMESPACE
new file mode 100644
index 0000000..0af3d7e
--- /dev/null
+++ b/win32/deps/library/Cairo/NAMESPACE
@@ -0,0 +1 @@
+exportPattern("^Cairo")
diff --git a/win32/deps/library/Cairo/NEWS b/win32/deps/library/Cairo/NEWS
new file mode 100644
index 0000000..5da0c42
--- /dev/null
+++ b/win32/deps/library/Cairo/NEWS
@@ -0,0 +1,224 @@
+NEWS/Changelog
+
+1.5-2 (2012-11-05)
+ o added Cairo.onSave() callback which allows R code to be run
+ when Cairo finishes a page
+
+ o added Cairo.serial() function which allows user code to check
+ whether the graphics have been updated
+
+ o bugfix/update in Cairo connection patch (by Karl Millar)
+
+
+1.5-1 (2011-12-10)
+ o add support for dev.hold()/dev.flush()
+
+ o use new R 2.14.0 device capabilities advertizing feature
+
+ o fix memory leak when setting fonts via CairoFonts()
+
+ o explicitly request font anti-aliasing even if it is not the
+ surface default - in particular Windows has disabled font
+ anti-aliasing by default
+
+
+1.5-0 (2011-09-30)
+ o fix swapped bold vs italic traits if freetype is not available
+
+ o use Times font for symbols on Windows because Symbol font
+ doesn't seem to support Unicode
+
+ o add support for poly-paths
+
+ o add support for dev.capture()/grid.cap()
+
+ o added new type "raster" that creates an image back-end without
+ any output file. It can be used in conjunction with
+ dev.capture() to create in-memory image representations, e.g.:
+ Cairo(type='raster')
+ plot(1:10, col=2)
+ p = writePNG(dev.capture(native=TRUE), raw())
+ will create a raw vector containg a PNG image.
+
+
+1.4-9 (2011-04-06)
+ o force static built-in libraries on Windows to prevent Cairo
+ from picking up broken system libraries
+
+1.4-8 (2011-03-07)
+ o spurious character in the 1.4-7 w32-backed source has made it
+ unusable on Windows. This is a re-packaging of 1.4-7 without
+ that spurious character.
+
+1.4-7 (2011-03-07)
+ o fix a bug in raster support causing raster to be usable only
+ once
+
+ o win backend: release and re-get DC on resize -- fixes resizing
+ issues in CairoWin() for some Windows versions
+
+1.4-6 (2011-02-10)
+ o adds raster image support (courtesy of R core)
+
+ o update Windows libcairo binary to cairo 1.10.2, use static
+ build to avoid DLL issues and add 64-bit binary
+
+1.4-5 (2009-07-16)
+ o minor Windows configuration change
+
+ o fix SET_VECTOR_ELT issue for R 2.9.0+
+
+1.4-4 (2008-10-17)
+ o adapt to changes in R-devel (2.9.0-to-be), clean up warnings
+
+1.4-3 (2008-07-21)
+ o make the use of an invalid font non-fatal
+
+ o allow Cairo to compile on some older systems that don't have
+ trunc()
+
+ o updated libcairo binary for Windows to 1.6.4 (from GTK+)
+
+1.4-2 (2008-04-03)
+ o adapt to even more changes in R 2.7
+
+1.4-1 (2008-03-14)
+ o adapt to R 2.7 changes
+
+1.4-0
+ o fix DPI detection in X11 back-end and use 90dpi as a fallback
+
+ o fix cra settings to be closer to what other devices use
+
+ o CairoX11 no longer fixes DPI to 72, "auto" is now the default.
+ In addition, CairoWin and CairoX11 allow additional arguments
+ to ba passed to Cairo.
+
+1.3-5 (2007-08-27)
+ o adapt to const char* CHARs in R-devel
+
+ o fix a bug in CairoSVG (wrong argument name)
+
+ o fix a bug in CairoPS (units were not set to "in" and
+ width/height had no defaults)
+
+ o fix unintentional doubling of the .ps suffix
+
+1.3-4 (2007-05-10)
+ o more fixes in flag-guessing
+
+ o some vector backends (e.g. PDF, SVG) were falling back to
+ bitamp rasterization, we try to prevent this
+
+ o address expose issues with some X11 servers
+
+ o add CairoSVG wrapper
+
+ o add an unified way to register back-ends and get a list of all
+ supported types.
+
+ o add Cairo.capabilities() function
+
+1.3-3 2007-04-25
+ o improve detection of cairo and its dependencies
+
+ o work around missing API such that cairo 1.0 can be used.
+ However, it is strongly encouraged to use cairo 1.2 or
+ possibly 1.4 as they contain important bugfixes.
+
+ o fix page numbering to start at 1 (was 0) and update
+ documentation correspondingly
+
+1.3-2 2007-04-18
+ o added format autodetection for tiff and png. The 32-bit
+ version of either format is used if the background
+ is not opaque.
+
+ o fixed bug in the value returned by Cairo
+
+ o added type and file attributes to the Cairo object
+
+ o added (hidden, experimental) functions that allow direct
+ modification of image content in Cairo (.image, .ptr.to.raw
+ and .raw.to.ptr)
+
+1.3-1
+ o change semantics of canvas and bg to match other devices:
+ canvas is used by devices that don't support any kind
+ of transparency in case bg is translucent
+
+ o fixed data ordering issues in TIFF and JPEG output
+
+ o added "compression" parameter to TIFF back-end which
+ now defaults to LZW compression
+
+1.3-0
+ o add support for canvas and dpi specification
+
+ o allow backends to detect native resolution
+
+ o add support for custom parameters (e.g. quality for jpeg)
+
+1.2-1
+ o improve rendering on bitmap devices by aligning straight lines
+ to the pixel grid and adding bleed to such fills.
+
+ o added wrappers that take exactly the same parameters as
+ existing devices such as png, jpeg, pdf, postscript, X11 or
+ windows and map them to calls to Cairo. They can be used to
+ replace native devices by Cairo without the need to change
+ existing code.
+
+ o added namespace
+
+1.2-0
+ o additional interactive back ends: X11 (XLib) and win (Win32)
+
+ o enhanced back-end API to support interactive back-ends
+
+ o change default backgroud color to "white", because
+ alpha-blending doesn't work properly in cairo when painting on
+ purely transparent background.
+
+ o change the way filenames are interpreted, use multi-file
+ printf convention as other devices do.
+
+ o added support for jpeg and tiff image formats
+
+1.1-0
+ o additional file/stream back-ends: svg, ps
+
+ o enhanced back-end API
+
+1.0-0
+ o fixed function names to not conflict with GDD
+
+0.1-5
+ o added R connections patch support at config time.
+ see
+ http://wiki.r-project.org/rwiki/doku.php?id=developers:r_connections_api
+
+0.1-4 (2006-12-07)
+ o add pdf backend (Jeff Horner)
+
+ o fix up backend infrastructure (Jeff Horner)
+
+0.1-3 (2006-12-06)
+ o add freetype and fontconfig support (Jeff Horner)
+
+ o fix memory leaks (Jeff Horner)
+
+ o make transparent background default with bg="transparent"
+
+0.1-2 (2006-12-05)
+ o add support for caps/joints (patch by Jeff Horner)
+
+ o make rectangels to snap to grid (patch by Jeff Horner)
+
+ o use transparent image background by default
+
+
+0.1-1 (2005-12-23)
+ o first official release, image backend works, others are
+ waiting to be implemented by volunteers
+
diff --git a/win32/deps/library/Cairo/R/Cairo b/win32/deps/library/Cairo/R/Cairo
new file mode 100644
index 0000000..ac8cebe
--- /dev/null
+++ b/win32/deps/library/Cairo/R/Cairo
@@ -0,0 +1,9 @@
+local({
+ info <- loadingNamespaceInfo()
+ ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
+ if (is.null(ns))
+ stop("cannot find namespace environment");
+ barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
+ dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
+ lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
+})
diff --git a/win32/deps/library/Cairo/R/Cairo.rdb b/win32/deps/library/Cairo/R/Cairo.rdb
new file mode 100644
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index 0000000..84252c7
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diff --git a/win32/deps/library/Cairo/help/AnIndex b/win32/deps/library/Cairo/help/AnIndex
new file mode 100644
index 0000000..606aac8
--- /dev/null
+++ b/win32/deps/library/Cairo/help/AnIndex
@@ -0,0 +1,15 @@
+Cairo Cairo
+Cairo.capabilities Cairo.capabilities
+Cairo.capture Cairo.capture
+Cairo.onSave Cairo.onSave
+Cairo.serial Cairo.serial
+CairoFontMatch CairoFontMatch
+CairoFonts CairoFonts
+CairoJPEG Cairo
+CairoPDF Cairo
+CairoPNG Cairo
+CairoPS Cairo
+CairoSVG Cairo
+CairoTIFF Cairo
+CairoWin Cairo
+CairoX11 Cairo
diff --git a/win32/deps/library/Cairo/help/Cairo.rdb b/win32/deps/library/Cairo/help/Cairo.rdb
new file mode 100644
index 0000000..1155c10
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index 0000000..6ed70c9
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diff --git a/win32/deps/library/Cairo/help/aliases.rds b/win32/deps/library/Cairo/help/aliases.rds
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index 0000000..79a01c7
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diff --git a/win32/deps/library/Cairo/help/paths.rds b/win32/deps/library/Cairo/help/paths.rds
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index 0000000..697d544
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diff --git a/win32/deps/library/Cairo/html/00Index.html b/win32/deps/library/Cairo/html/00Index.html
new file mode 100644
index 0000000..35e57ec
--- /dev/null
+++ b/win32/deps/library/Cairo/html/00Index.html
@@ -0,0 +1,58 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: R graphics device using cairo graphics library for creating
+high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG,
+PostScript) and display (X11 and Win32) output.</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> R graphics device using cairo graphics library for creating
+high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG,
+PostScript) and display (X11 and Win32) output.
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘Cairo’ version 1.5-2</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+<li><a href="../NEWS">Package NEWS</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<table width="100%">
+<tr><td width="25%"><a href="Cairo.html">Cairo</a></td>
+<td>Create a new Cairo-based graphics device</td></tr>
+<tr><td width="25%"><a href="Cairo.capabilities.html">Cairo.capabilities</a></td>
+<td>Reports which output types are supported by this Cairo build</td></tr>
+<tr><td width="25%"><a href="Cairo.capture.html">Cairo.capture</a></td>
+<td>Capture contents of an image backend.</td></tr>
+<tr><td width="25%"><a href="Cairo.onSave.html">Cairo.onSave</a></td>
+<td>Cairo callbacks</td></tr>
+<tr><td width="25%"><a href="Cairo.serial.html">Cairo.serial</a></td>
+<td>Check for changes in the graphics state of Cairo devices.</td></tr>
+<tr><td width="25%"><a href="CairoFontMatch.html">CairoFontMatch</a></td>
+<td>Find installed fonts with a fontconfig pattern</td></tr>
+<tr><td width="25%"><a href="CairoFonts.html">CairoFonts</a></td>
+<td>Set the fonts used for all Cairo graphics devices.</td></tr>
+<tr><td width="25%"><a href="Cairo.html">CairoJPEG</a></td>
+<td>Create a new Cairo-based graphics device</td></tr>
+<tr><td width="25%"><a href="Cairo.html">CairoPDF</a></td>
+<td>Create a new Cairo-based graphics device</td></tr>
+<tr><td width="25%"><a href="Cairo.html">CairoPNG</a></td>
+<td>Create a new Cairo-based graphics device</td></tr>
+<tr><td width="25%"><a href="Cairo.html">CairoPS</a></td>
+<td>Create a new Cairo-based graphics device</td></tr>
+<tr><td width="25%"><a href="Cairo.html">CairoSVG</a></td>
+<td>Create a new Cairo-based graphics device</td></tr>
+<tr><td width="25%"><a href="Cairo.html">CairoTIFF</a></td>
+<td>Create a new Cairo-based graphics device</td></tr>
+<tr><td width="25%"><a href="Cairo.html">CairoWin</a></td>
+<td>Create a new Cairo-based graphics device</td></tr>
+<tr><td width="25%"><a href="Cairo.html">CairoX11</a></td>
+<td>Create a new Cairo-based graphics device</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/Cairo/html/R.css b/win32/deps/library/Cairo/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/Cairo/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/Cairo/libs/i386/Cairo.dll b/win32/deps/library/Cairo/libs/i386/Cairo.dll
new file mode 100644
index 0000000..a2561b7
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diff --git a/win32/deps/library/Cairo/libs/i386/symbols.rds b/win32/deps/library/Cairo/libs/i386/symbols.rds
new file mode 100644
index 0000000..370f74b
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diff --git a/win32/deps/library/Cairo/libs/x64/Cairo.dll b/win32/deps/library/Cairo/libs/x64/Cairo.dll
new file mode 100644
index 0000000..b61e06b
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diff --git a/win32/deps/library/Cairo/libs/x64/symbols.rds b/win32/deps/library/Cairo/libs/x64/symbols.rds
new file mode 100644
index 0000000..f8b09cd
Binary files /dev/null and b/win32/deps/library/Cairo/libs/x64/symbols.rds differ
diff --git a/win32/deps/library/EMD/DESCRIPTION b/win32/deps/library/EMD/DESCRIPTION
index fbb73ac..02e30f7 100644
--- a/win32/deps/library/EMD/DESCRIPTION
+++ b/win32/deps/library/EMD/DESCRIPTION
@@ -1,14 +1,19 @@
Package: EMD
+Version: 1.5.2
+Date: 2013-01-18
Title: Empirical Mode Decomposition and Hilbert Spectral Analysis
-Version: 1.2.0
-Date: 2008-11-08
-Author: Donghoh Kim <donghoh kim gmail com>, Hee-Seok Oh
- <heeseok stats snu ac kr>
+Author: Donghoh Kim and Hee-Seok Oh
Maintainer: Donghoh Kim <donghoh kim gmail com>
-Depends: R (>= 2.6), fields (>= 4.1)
-Description: This package carries out empirical mode decompostion and
- Hilbert spectral analysis.
-License: GPL version 2 or newer
+Depends: R (>= 2.11), fields (>= 6.3), locfit (>= 1.5-8)
+Description: This package carries out empirical mode decomposition and
+ Hilbert spectral analysis. For usage of EMD, see Kim and Oh,
+ 2009 (Kim, D and Oh, H.-S. (2009) EMD: A Package for Empirical
+ Mode Decomposition and Hilbert Spectrum, The R Journal, 1,
+ 40-46).
+License: GPL (>= 2)
URL: http://dasan.sejong.ac.kr/~dhkim/software_emd.html
-Packaged: Fri Nov 28 13:13:50 2008; Administrator
-Built: R 2.9.2; i386-pc-mingw32; 2010-01-13 23:31:11 UTC; windows
+Packaged: 2013-01-18 01:48:24 UTC; donghohkim
+Repository: CRAN
+Date/Publication: 2013-01-18 06:42:37
+Built: R 2.15.2; x86_64-w64-mingw32; 2013-02-07 02:53:10 UTC; windows
+Archs: i386, x64
diff --git a/win32/deps/library/EMD/INDEX b/win32/deps/library/EMD/INDEX
index 699dfea..0425bf6 100644
--- a/win32/deps/library/EMD/INDEX
+++ b/win32/deps/library/EMD/INDEX
@@ -1,18 +1,22 @@
+cvimpute.by.mean Imputation by the mean of the two adjacent
+ values
cvtype Generating test dataset index for
cross-validation
emd Empirical Mode Decomposition
emd.pred Prediction by EMD and VAR model
-emd2d Two dimensional Empirical Mode Decomposition
-emddenoise Denoising by EMD and Cross-Validation
+emd2d Bidimenasional Empirical Mode Decomposition
+emddenoise Denoising by EMD and Thresholding
extractimf Intrinsic Mode Function
-extractimf2d Two dimensional Intrinsic Mode Function
+extractimf2d Bidimensional Intrinsic Mode Function
extrema Finding Local Extrema and Zero-crossings
extrema2dC Finding Local Extrema
hilbertspec Hilbert Transform and Instantaneous Frequency
-imageEMD Plot of Two Dimensional Decomposition Result
+imageEMD Plot of Bidimenasional Empirical Mode
+ Decomposition Result
kospi200 Korea Stock Price Index 200
lena Gray Lena image
lennon Gray John Lennon image
+semd Statistical Empirical Mode Decomposition
solar irradiance Solar Irradiance Proxy Data
spectrogram Spectrogram
sunspot Sunspot Data
diff --git a/win32/deps/library/EMD/MD5 b/win32/deps/library/EMD/MD5
index 175aec5..25e3f33 100644
--- a/win32/deps/library/EMD/MD5
+++ b/win32/deps/library/EMD/MD5
@@ -1,87 +1,31 @@
-607fe7c20cc6198d4769db1077b5f775 *CONTENTS
-4579c9a462f562c374ade65ee2d5ec90 *DESCRIPTION
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-b5d136ef6ad10c2f783510373a367076 *Meta/package.rds
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-40c9a3f0f3e9b73396429898758c42f9 *R-ex/emd.R
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-b9a944848f99bcbd5df8cbf732d37b52 *R-ex/emddenoise.R
-fe686fb4eef8b49fa81f9a0e8285c773 *R-ex/extractimf.R
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-b9dd6c73cd45735ff2f4be573935fa12 *R-ex/extrema.R
-eb85b6674792136c8d9f4de52a4139d8 *R-ex/extrema2dC.R
-61d84dc0c28537466e226efffdc0715f *R-ex/hilbertspec.R
-77d9aca0f0bf3ed3f2cdba4cc15d29dd *R-ex/imageEMD.R
-5a1db4a8943c8f343942e07027310694 *R-ex/kospi200.R
-5661cc4325d2005e66dcd576ca9ce3f0 *R-ex/lena.R
-c45960f72dbe9e594f944954d1871fd6 *R-ex/lennon.R
-4aec27ed4df85d77ac5d872a242702d3 *R-ex/solar.R
-3aecd6626321a98ba0ebb026208fbb8e *R-ex/spectrogram.R
-5195cb2eeeb0b33fa24e9c3cd57648be *R-ex/sunspot.R
-6e60a4480e0345d65902fc23b54bffd6 *R/EMD
-bb7b8ce8e83c89ac52f5ef40ffc49fd9 *R/EMD.rdb
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-5c898f6852de9c9675db44004c3dd255 *data/filelist
-217d6b7da68b6e0617548e655b4b6269 *help/AnIndex
-897aa2e6df4561402044718bbce5f421 *help/EMD-internal
-2f2439a0c0888a08c0e87565d2d101db *help/cvtype
-0b534fecfa97a2261d18d294de4064ef *help/emd
-2666f26afd90ddd3a3c9e67f74afc1a5 *help/emd.pred
-c37771d3ad1d972c4fe38c820f14000f *help/emd2d
-aba8d28fd62e9f8ca37943b043792f54 *help/emddenoise
-0ceed4cfcda07658b73b4d04f13f628a *help/extractimf
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-dc1a34c082ad9d4c56af8429c0a9d2f6 *help/kospi200
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-a3af05fd46524eb62ee787576bc3a311 *help/lennon
-bb001b996d6451f8d3a2667d65c81aa1 *help/solar
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-1e160762f17eab3d7c97e9e13e22db11 *help/sunspot
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-486f919fd81b7f163eb386e45477b65a *html/sunspot.html
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-1994b554962ed5a28a9a47cf8550c845 *latex/sunspot.tex
-1d8088e0e2cbb72a9eaea539530f85d8 *libs/EMD.dll
-ebdea9070fe291a3164c1465e3011260 *man/EMD.Rd.gz
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+240d28d145138a75831809e31a480bad *R/EMD
+6ce426beb884abcff567512a7a48fc87 *R/EMD.rdb
+5e94892b2d1179e2c4f0ff8e300f4913 *R/EMD.rdx
+a101e733a90cbb1bbf82848273f91983 *data/beryllium.rda
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+f588d89cb0247e7592c955545be5bbab *data/solar.lean.rda
+c8e09219747bd132c5d706d69a2b795f *data/sunspot.rda
+4f46211dbfe73e7d13b6d4fa282c583c *help/AnIndex
+289c7c7c619a19c5eb751c761a53b230 *help/EMD.rdb
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+fffddfd179844861217ca3958304c206 *help/aliases.rds
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index 2e9759c..eb64c90 100644
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index 41179ae..441a179 100644
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diff --git a/win32/deps/library/EMD/NAMESPACE b/win32/deps/library/EMD/NAMESPACE
new file mode 100644
index 0000000..8bf7cb5
--- /dev/null
+++ b/win32/deps/library/EMD/NAMESPACE
@@ -0,0 +1,10 @@
+# Export all names
+exportPattern(".")
+
+# Import all packages listed as Imports or Depends
+import(
+ fields,
+ locfit
+)
+
+useDynLib(EMD)
diff --git a/win32/deps/library/EMD/R/EMD b/win32/deps/library/EMD/R/EMD
index be99e29..ac8cebe 100644
--- a/win32/deps/library/EMD/R/EMD
+++ b/win32/deps/library/EMD/R/EMD
@@ -1,18 +1,9 @@
-.First.lib <- function(libname, pkgname)
-{
- fullName <- paste("package", pkgname, sep=":")
- myEnv <- as.environment(match(fullName, search()))
- barepackage <- sub("([^-]+)_.*", "\\1", pkgname)
- dbbase <- file.path(libname, pkgname, "R", barepackage)
- rm(.First.lib, envir = myEnv)
- lazyLoad(dbbase, myEnv)
- if(exists(".First.lib", envir = myEnv, inherits = FALSE)) {
- f <- get(".First.lib", envir = myEnv, inherits = FALSE)
- if(is.function(f))
- f(libname, pkgname)
- else
- stop(gettextf("package '%s' has a non-function '.First.lib'",
- pkgname),
- domain = NA)
- }
-}
+local({
+ info <- loadingNamespaceInfo()
+ ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
+ if (is.null(ns))
+ stop("cannot find namespace environment");
+ barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
+ dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
+ lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
+})
diff --git a/win32/deps/library/EMD/R/EMD.rdb b/win32/deps/library/EMD/R/EMD.rdb
index e992a9d..54b4a28 100644
Binary files a/win32/deps/library/EMD/R/EMD.rdb and b/win32/deps/library/EMD/R/EMD.rdb differ
diff --git a/win32/deps/library/EMD/R/EMD.rdx b/win32/deps/library/EMD/R/EMD.rdx
index 92e1d10..4b1669a 100644
Binary files a/win32/deps/library/EMD/R/EMD.rdx and b/win32/deps/library/EMD/R/EMD.rdx differ
diff --git a/win32/deps/library/EMD/data/beryllium.rda b/win32/deps/library/EMD/data/beryllium.rda
new file mode 100644
index 0000000..40dbb10
Binary files /dev/null and b/win32/deps/library/EMD/data/beryllium.rda differ
diff --git a/win32/deps/library/EMD/data/datalist b/win32/deps/library/EMD/data/datalist
new file mode 100644
index 0000000..7b62ea9
--- /dev/null
+++ b/win32/deps/library/EMD/data/datalist
@@ -0,0 +1,7 @@
+beryllium
+kospi200
+lena
+lennon
+solar.hs
+solar.lean
+sunspot
diff --git a/win32/deps/library/EMD/data/kospi200.rda b/win32/deps/library/EMD/data/kospi200.rda
new file mode 100644
index 0000000..1a9ef7b
Binary files /dev/null and b/win32/deps/library/EMD/data/kospi200.rda differ
diff --git a/win32/deps/library/EMD/data/lena.rda b/win32/deps/library/EMD/data/lena.rda
new file mode 100644
index 0000000..17905b7
Binary files /dev/null and b/win32/deps/library/EMD/data/lena.rda differ
diff --git a/win32/deps/library/EMD/data/lennon.rda b/win32/deps/library/EMD/data/lennon.rda
new file mode 100644
index 0000000..416e00f
Binary files /dev/null and b/win32/deps/library/EMD/data/lennon.rda differ
diff --git a/win32/deps/library/EMD/data/solar.hs.rda b/win32/deps/library/EMD/data/solar.hs.rda
new file mode 100644
index 0000000..0b5dc17
Binary files /dev/null and b/win32/deps/library/EMD/data/solar.hs.rda differ
diff --git a/win32/deps/library/EMD/data/solar.lean.rda b/win32/deps/library/EMD/data/solar.lean.rda
new file mode 100644
index 0000000..a8bf629
Binary files /dev/null and b/win32/deps/library/EMD/data/solar.lean.rda differ
diff --git a/win32/deps/library/EMD/data/sunspot.rda b/win32/deps/library/EMD/data/sunspot.rda
new file mode 100644
index 0000000..45dc1c1
Binary files /dev/null and b/win32/deps/library/EMD/data/sunspot.rda differ
diff --git a/win32/deps/library/EMD/help/AnIndex b/win32/deps/library/EMD/help/AnIndex
index 706911e..0c1bfb6 100644
--- a/win32/deps/library/EMD/help/AnIndex
+++ b/win32/deps/library/EMD/help/AnIndex
@@ -1,4 +1,5 @@
beryllium solar
+cvimpute.by.mean cvimpute.by.mean
cvtype cvtype
emd emd
EMD-internal EMD-internal
@@ -9,6 +10,7 @@ extractimf extractimf
extractimf2d extractimf2d
extrema extrema
extrema2dC extrema2dC
+extrema2dVC EMD-internal
hilbert EMD-internal
hilbertspec hilbertspec
image.plot.ts EMD-internal
@@ -16,6 +18,7 @@ imageEMD imageEMD
kospi200 kospi200
lena lena
lennon lennon
+semd semd
solar irradiance solar
solar.hs solar
solar.lean solar
diff --git a/win32/deps/library/EMD/help/EMD.rdb b/win32/deps/library/EMD/help/EMD.rdb
new file mode 100644
index 0000000..f0aa687
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diff --git a/win32/deps/library/EMD/help/EMD.rdx b/win32/deps/library/EMD/help/EMD.rdx
new file mode 100644
index 0000000..ab30a2e
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diff --git a/win32/deps/library/EMD/help/aliases.rds b/win32/deps/library/EMD/help/aliases.rds
new file mode 100644
index 0000000..b27a529
Binary files /dev/null and b/win32/deps/library/EMD/help/aliases.rds differ
diff --git a/win32/deps/library/EMD/help/paths.rds b/win32/deps/library/EMD/help/paths.rds
new file mode 100644
index 0000000..e8effc1
Binary files /dev/null and b/win32/deps/library/EMD/help/paths.rds differ
diff --git a/win32/deps/library/EMD/html/00Index.html b/win32/deps/library/EMD/html/00Index.html
index ac35dcc..203c874 100644
--- a/win32/deps/library/EMD/html/00Index.html
+++ b/win32/deps/library/EMD/html/00Index.html
@@ -1,19 +1,19 @@
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html><head><title>R: Empirical Mode Decomposition and Hilbert Spectral Analysis</title>
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><link rel="stylesheet" type="text/css" href="../../R.css">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
</head><body>
-<h1>Empirical Mode Decomposition and Hilbert Spectral Analysis <img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]"></h1>
-
+<h1> Empirical Mode Decomposition and Hilbert Spectral Analysis
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
<hr>
-
<div align="center">
-<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg"
-alt="[Package List]" width="30" height="30" border="0"></a>
-<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg"
-alt="[Top]" width="30" height="30" border="0"></a>
-</div>
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘EMD’ version 1.5.2</h2>
-<h2>Documentation for package ‘EMD’ version 1.2.0</h2>
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+</ul>
<h2>Help Pages</h2>
@@ -21,6 +21,8 @@ alt="[Top]" width="30" height="30" border="0"></a>
<table width="100%">
<tr><td width="25%"><a href="solar.html">beryllium</a></td>
<td>Solar Irradiance Proxy Data</td></tr>
+<tr><td width="25%"><a href="cvimpute.by.mean.html">cvimpute.by.mean</a></td>
+<td>Imputation by the mean of the two adjacent values</td></tr>
<tr><td width="25%"><a href="cvtype.html">cvtype</a></td>
<td>Generating test dataset index for cross-validation</td></tr>
<tr><td width="25%"><a href="emd.html">emd</a></td>
@@ -28,13 +30,13 @@ alt="[Top]" width="30" height="30" border="0"></a>
<tr><td width="25%"><a href="emd.pred.html">emd.pred</a></td>
<td>Prediction by EMD and VAR model</td></tr>
<tr><td width="25%"><a href="emd2d.html">emd2d</a></td>
-<td>Two dimensional Empirical Mode Decomposition</td></tr>
+<td>Bidimenasional Empirical Mode Decomposition</td></tr>
<tr><td width="25%"><a href="emddenoise.html">emddenoise</a></td>
-<td>Denoising by EMD and Cross-Validation</td></tr>
+<td>Denoising by EMD and Thresholding</td></tr>
<tr><td width="25%"><a href="extractimf.html">extractimf</a></td>
<td>Intrinsic Mode Function</td></tr>
<tr><td width="25%"><a href="extractimf2d.html">extractimf2d</a></td>
-<td>Two dimensional Intrinsic Mode Function</td></tr>
+<td>Bidimensional Intrinsic Mode Function</td></tr>
<tr><td width="25%"><a href="extrema.html">extrema</a></td>
<td>Finding Local Extrema and Zero-crossings</td></tr>
<tr><td width="25%"><a href="extrema2dC.html">extrema2dC</a></td>
@@ -42,13 +44,15 @@ alt="[Top]" width="30" height="30" border="0"></a>
<tr><td width="25%"><a href="hilbertspec.html">hilbertspec</a></td>
<td>Hilbert Transform and Instantaneous Frequency</td></tr>
<tr><td width="25%"><a href="imageEMD.html">imageEMD</a></td>
-<td>Plot of Two Dimensional Decomposition Result</td></tr>
+<td>Plot of Bidimenasional Empirical Mode Decomposition Result</td></tr>
<tr><td width="25%"><a href="kospi200.html">kospi200</a></td>
<td>Korea Stock Price Index 200</td></tr>
<tr><td width="25%"><a href="lena.html">lena</a></td>
<td>Gray Lena image</td></tr>
<tr><td width="25%"><a href="lennon.html">lennon</a></td>
<td>Gray John Lennon image</td></tr>
+<tr><td width="25%"><a href="semd.html">semd</a></td>
+<td>Statistical Empirical Mode Decomposition</td></tr>
<tr><td width="25%"><a href="solar.html">solar irradiance</a></td>
<td>Solar Irradiance Proxy Data</td></tr>
<tr><td width="25%"><a href="solar.html">solar.hs</a></td>
diff --git a/win32/deps/library/EMD/html/R.css b/win32/deps/library/EMD/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/EMD/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/EMD/libs/i386/EMD.dll b/win32/deps/library/EMD/libs/i386/EMD.dll
new file mode 100644
index 0000000..a8e5896
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diff --git a/win32/deps/library/EMD/libs/i386/symbols.rds b/win32/deps/library/EMD/libs/i386/symbols.rds
new file mode 100644
index 0000000..46466df
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diff --git a/win32/deps/library/EMD/libs/x64/EMD.dll b/win32/deps/library/EMD/libs/x64/EMD.dll
new file mode 100644
index 0000000..46f7fe3
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diff --git a/win32/deps/library/EMD/libs/x64/symbols.rds b/win32/deps/library/EMD/libs/x64/symbols.rds
new file mode 100644
index 0000000..2bcfda7
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diff --git a/win32/deps/library/KernSmooth/DESCRIPTION b/win32/deps/library/KernSmooth/DESCRIPTION
index c7ce18a..9036db2 100644
--- a/win32/deps/library/KernSmooth/DESCRIPTION
+++ b/win32/deps/library/KernSmooth/DESCRIPTION
@@ -1,18 +1,22 @@
-Package: KernSmooth
-Priority: recommended
-Version: 2.23-2
-Date: 2009-05-22
-Title: Functions for kernel smoothing for Wand & Jones (1995)
-Author: S original by Matt Wand. R port by Brian Ripley
- <ripley stats ox ac uk>.
-Maintainer: Brian Ripley <ripley stats ox ac uk>
-Depends: R (>= 2.5.0), stats
-Suggests: MASS
-Description: functions for kernel smoothing (and density estimation)
- corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
- "Kernel Smoothing".
-License: Unlimited
-Packaged: 2009-05-22 13:00:56 UTC; ripley
-Repository: CRAN
-Date/Publication: 2009-05-24 08:45:58
-Built: R 2.9.2; i386-pc-mingw32; 2009-08-24 13:04:08 UTC; windows
+Package: KernSmooth
+Priority: recommended
+Version: 2.23-8
+Date: 2012-06-27
+Title: Functions for kernel smoothing for Wand & Jones (1995)
+Authors R: c(person("Matt", "Wand", role = "aut", email =
+ "Matt Wand uts edu au"), person("Brian", "Ripley", role =
+ c("trl", "cre", "ctb"), email = "ripley stats ox ac uk"))
+Author: Matt Wand <Matt Wand uts edu au> R port and updates by Brian
+ Ripley <ripley stats ox ac uk>.
+Maintainer: Brian Ripley <ripley stats ox ac uk>
+Depends: R (>= 2.5.0), stats
+Suggests: MASS
+Description: functions for kernel smoothing (and density estimation)
+ corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
+ "Kernel Smoothing".
+License: Unlimited
+Packaged: 2012-06-27 09:44:29 UTC; ripley
+Repository: CRAN
+Date/Publication: 2012-06-27 09:57:46
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:15:03 UTC; windows
+Archs: i386, x64
diff --git a/win32/deps/library/KernSmooth/INDEX b/win32/deps/library/KernSmooth/INDEX
index 2d524a4..9a10490 100644
--- a/win32/deps/library/KernSmooth/INDEX
+++ b/win32/deps/library/KernSmooth/INDEX
@@ -1,7 +1,8 @@
-bkde Compute a Binned Kernel Density Estimate
-bkde2D Compute a 2D Binned Kernel Density Estimate
-bkfe Compute a Binned Kernel Functional Estimate
-dpih Select a Histogram Bin Width
-dpik Select a Bandwidth for Kernel Density Estimation
-dpill Select a Bandwidth for Local Linear Regression
-locpoly Estimate Functions Using Local Polynomials
+bkde Compute a Binned Kernel Density Estimate
+bkde2D Compute a 2D Binned Kernel Density Estimate
+bkfe Compute a Binned Kernel Functional Estimate
+dpih Select a Histogram Bin Width
+dpik Select a Bandwidth for Kernel Density
+ Estimation
+dpill Select a Bandwidth for Local Linear Regression
+locpoly Estimate Functions Using Local Polynomials
diff --git a/win32/deps/library/KernSmooth/LICENCE b/win32/deps/library/KernSmooth/LICENCE
index 3daadbb..f25e338 100644
--- a/win32/deps/library/KernSmooth/LICENCE
+++ b/win32/deps/library/KernSmooth/LICENCE
@@ -2,4 +2,4 @@ By agreement with Dr Wand (1998-June-22), the R port can be used and
distributed freely, superseding the comments in orig/KernSmooth.tex.
The original S code is copyright Matt Wand, the R port copyright
-Brian Ripley
\ No newline at end of file
+Brian Ripley
diff --git a/win32/deps/library/KernSmooth/Meta/Rd.rds b/win32/deps/library/KernSmooth/Meta/Rd.rds
index b53465b..1c8ea5b 100644
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diff --git a/win32/deps/library/KernSmooth/Meta/hsearch.rds b/win32/deps/library/KernSmooth/Meta/hsearch.rds
index 81a09fb..f6c3189 100644
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diff --git a/win32/deps/library/KernSmooth/Meta/links.rds b/win32/deps/library/KernSmooth/Meta/links.rds
new file mode 100644
index 0000000..f47f8aa
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diff --git a/win32/deps/library/KernSmooth/Meta/nsInfo.rds b/win32/deps/library/KernSmooth/Meta/nsInfo.rds
index c355055..b89c026 100644
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diff --git a/win32/deps/library/KernSmooth/Meta/package.rds b/win32/deps/library/KernSmooth/Meta/package.rds
index 6eec3d7..bd6ee61 100644
Binary files a/win32/deps/library/KernSmooth/Meta/package.rds and b/win32/deps/library/KernSmooth/Meta/package.rds differ
diff --git a/win32/deps/library/KernSmooth/R/KernSmooth b/win32/deps/library/KernSmooth/R/KernSmooth
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/KernSmooth/R/KernSmooth
+++ b/win32/deps/library/KernSmooth/R/KernSmooth
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/KernSmooth/R/KernSmooth.rdb b/win32/deps/library/KernSmooth/R/KernSmooth.rdb
index e116e42..906e4cf 100644
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diff --git a/win32/deps/library/KernSmooth/R/KernSmooth.rdx b/win32/deps/library/KernSmooth/R/KernSmooth.rdx
index 0a1b7d5..f63b753 100644
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diff --git a/win32/deps/library/KernSmooth/help/KernSmooth.rdb b/win32/deps/library/KernSmooth/help/KernSmooth.rdb
new file mode 100644
index 0000000..be8cd2a
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new file mode 100644
index 0000000..a0104db
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diff --git a/win32/deps/library/KernSmooth/help/aliases.rds b/win32/deps/library/KernSmooth/help/aliases.rds
new file mode 100644
index 0000000..fce3a9a
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diff --git a/win32/deps/library/KernSmooth/help/paths.rds b/win32/deps/library/KernSmooth/help/paths.rds
new file mode 100644
index 0000000..9e1d180
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diff --git a/win32/deps/library/KernSmooth/html/00Index.html b/win32/deps/library/KernSmooth/html/00Index.html
new file mode 100644
index 0000000..5768c31
--- /dev/null
+++ b/win32/deps/library/KernSmooth/html/00Index.html
@@ -0,0 +1,37 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Functions for kernel smoothing for Wand & Jones (1995)</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Functions for kernel smoothing for Wand & Jones (1995)
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘KernSmooth’ version 2.23-8</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<table width="100%">
+<tr><td width="25%"><a href="bkde.html">bkde</a></td>
+<td>Compute a Binned Kernel Density Estimate</td></tr>
+<tr><td width="25%"><a href="bkde2D.html">bkde2D</a></td>
+<td>Compute a 2D Binned Kernel Density Estimate</td></tr>
+<tr><td width="25%"><a href="bkfe.html">bkfe</a></td>
+<td>Compute a Binned Kernel Functional Estimate</td></tr>
+<tr><td width="25%"><a href="dpih.html">dpih</a></td>
+<td>Select a Histogram Bin Width</td></tr>
+<tr><td width="25%"><a href="dpik.html">dpik</a></td>
+<td>Select a Bandwidth for Kernel Density Estimation</td></tr>
+<tr><td width="25%"><a href="dpill.html">dpill</a></td>
+<td>Select a Bandwidth for Local Linear Regression</td></tr>
+<tr><td width="25%"><a href="locpoly.html">locpoly</a></td>
+<td>Estimate Functions Using Local Polynomials</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/KernSmooth/html/R.css b/win32/deps/library/KernSmooth/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/KernSmooth/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/KernSmooth/libs/i386/KernSmooth.dll b/win32/deps/library/KernSmooth/libs/i386/KernSmooth.dll
new file mode 100644
index 0000000..143a1cf
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diff --git a/win32/deps/library/KernSmooth/po/de/LC_MESSAGES/R-KernSmooth.mo b/win32/deps/library/KernSmooth/po/de/LC_MESSAGES/R-KernSmooth.mo
new file mode 100644
index 0000000..616386a
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diff --git a/win32/deps/library/KernSmooth/po/en quot/LC_MESSAGES/R-KernSmooth.mo b/win32/deps/library/KernSmooth/po/en quot/LC_MESSAGES/R-KernSmooth.mo
new file mode 100644
index 0000000..d31a14e
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diff --git a/win32/deps/library/KernSmooth/po/pl/LC_MESSAGES/R-KernSmooth.mo b/win32/deps/library/KernSmooth/po/pl/LC_MESSAGES/R-KernSmooth.mo
new file mode 100644
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diff --git a/win32/deps/library/KernSmooth/tests/bkfe.R b/win32/deps/library/KernSmooth/tests/bkfe.R
new file mode 100644
index 0000000..aa576c0
--- /dev/null
+++ b/win32/deps/library/KernSmooth/tests/bkfe.R
@@ -0,0 +1,8 @@
+## failed in bkfe with exaxt powers of 2 prior to 2.23-5
+library(KernSmooth)
+x <- 1:100
+dpik(x, gridsize = 256)
+## and for bkde for some x.
+x <- c(0.036, 0.042, 0.052, 0.216, 0.368, 0.511, 0.705, 0.753, 0.776, 0.84)
+bkde(x, gridsize = 256, range.x = range(x))
+
diff --git a/win32/deps/library/MASS/CITATION b/win32/deps/library/MASS/CITATION
index f6a6566..a0a7f2b 100644
--- a/win32/deps/library/MASS/CITATION
+++ b/win32/deps/library/MASS/CITATION
@@ -1,4 +1,4 @@
-citHeader("To cite the VR bundle (MASS, class, nnet, spatial) in publications use:")
+citHeader("To cite the MASS package in publications use:")
citEntry(entry="Book",
title = "Modern Applied Statistics with S",
diff --git a/win32/deps/library/MASS/DESCRIPTION b/win32/deps/library/MASS/DESCRIPTION
index ddbdc31..78a75d2 100644
--- a/win32/deps/library/MASS/DESCRIPTION
+++ b/win32/deps/library/MASS/DESCRIPTION
@@ -1,24 +1,28 @@
-Bundle: VR
-Contains: MASS class nnet spatial
-Priority: recommended
-Version: 7.2-48
-Date: 2009-07-29
-Depends: R (>= 2.5.0), grDevices, graphics, stats, utils
-Suggests: lattice, nlme, survival
-Author: S original by Venables & Ripley. R port by Brian Ripley
- <ripley stats ox ac uk>, following earlier work by Kurt Hornik
- and Albrecht Gebhardt.
-Maintainer: Brian Ripley <ripley stats ox ac uk>
-BundleDescription: Functions and datasets to support Venables and
- Ripley, 'Modern Applied Statistics with S' (4th edition).
-License: GPL-2 | GPL-3
-URL: http://www.stats.ox.ac.uk/pub/MASS4/
-Packaged: 2009-07-31 13:56:57 UTC; ripley
-Repository: CRAN
-Date/Publication: 2009-08-05 11:20:53
-Package: MASS
-Description: The main library and the datasets
-Title: Main Package of Venables and Ripley's MASS
-LazyLoad: yes
-LazyData: yes
-Built: R 2.9.2; i386-pc-mingw32; 2009-08-24 12:59:32 UTC; windows
+Package: MASS
+Priority: recommended
+Version: 7.3-22
+Date: 2012-10-08
+Revision: $Rev: 3252 $
+Depends: R (>= 2.14.0), grDevices, graphics, stats, utils
+Suggests: lattice, nlme, nnet, survival
+Authors R: c(person("Brian", "Ripley", role = c("aut", "cre", "cph"),
+ email = "ripley stats ox ac uk"), person("Bill", "Venables",
+ role = "ctb"), person("Kurt", "Hornik", role = "trl", comment =
+ "partial port ca 1998"), person("Albrecht", "Gebhardt", role =
+ "trl", comment = "partial port ca 1998"), person("David",
+ "Firth", role = "ctb"))
+Description: Functions and datasets to support Venables and Ripley,
+ 'Modern Applied Statistics with S' (4th edition, 2002).
+Title: Support Functions and Datasets for Venables and Ripley's MASS
+License: GPL-2 | GPL-3
+URL: http://www.stats.ox.ac.uk/pub/MASS4/
+LazyData: yes
+Packaged: 2012-10-08 10:07:18 UTC; ripley
+Author: Brian Ripley [aut, cre, cph],
+ Bill Venables [ctb],
+ Kurt Hornik [trl] (partial port ca 1998),
+ Albrecht Gebhardt [trl] (partial port ca 1998),
+ David Firth [ctb]
+Maintainer: Brian Ripley <ripley stats ox ac uk>
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:10:20 UTC; windows
+Archs: i386, x64
diff --git a/win32/deps/library/MASS/INDEX b/win32/deps/library/MASS/INDEX
index 2495c26..01f1fb9 100644
--- a/win32/deps/library/MASS/INDEX
+++ b/win32/deps/library/MASS/INDEX
@@ -9,7 +9,7 @@ bandwidth.nrd Bandwidth for density() via Normal Reference
Distribution
bcv Biased Cross-Validation for Bandwidth Selection
boxcox Box-Cox Transformations for Linear Models
-con2tr Convert Lists to Data Frames for use by Trellis
+con2tr Convert Lists to Data Frames for use by lattice
confint-MASS Confidence Intervals for Model Parameters
contr.sdif Successive Differences Contrast Coding
corresp Simple Correspondence Analysis
@@ -56,9 +56,10 @@ plot.mca Plot Method for Objects of Class 'mca'
polr Proportional Odds Logistic Regression
predict.lda Classify Multivariate Observations by Linear
Discrimination
-predict.lqs Predict from an lqs Fit
+predict.lqs Predict from an lqs Fit
predict.mca Predict Method for Class 'mca'
predict.qda Classify from Quadratic Discriminant Analysis
+profile.glm Method for Profiling glm Objects
qda Quadratic Discriminant Analysis
rational Rational Approximation
renumerate Convert a Formula Transformed by 'denumerate'
@@ -72,7 +73,6 @@ studres Extract Studentized Residuals from a Linear Model
summary.loglm Summary Method Function for Objects of Class 'loglm'
summary.negbin Summary Method Function for Objects of Class 'negbin'
summary.rlm Summary Method for Robust Linear Models
-synth.tr Synthetic Classification Problem
theta.md Estimate theta of the Negative Binomial by Deviance
theta.ml Estimate theta of the Negative Binomial by Maximum
Likelihood
@@ -88,7 +88,6 @@ Datasets:
Aids2 Australian AIDS Survival Data
Animals Brain and Body Weights for 28 Species
-Belgian-phones Belgium Phone Calls 1950-1973
Boston Housing Values in Suburbs of Boston
Cars93 Data from 93 Cars on Sale in the USA in 1993
Cushings Diagnostic Tests on Patients with Cushing's Syndrome
@@ -124,6 +123,7 @@ chem Copper in Wholemeal Flour
coop Co-operative Trial in Analytical Chemistry
cpus Performance of Computer CPUs
crabs Morphological Measurements on Leptograpsus Crabs
+deaths Monthly Deaths from Lung Diseases in the UK
drivers Deaths of Car Drivers in Great Britain 1969-84
eagles Foraging Ecology of Bald Eagles
epil Seizure Counts for Epileptics
@@ -143,18 +143,20 @@ leuk Survival Times and White Blood Counts for
Leukaemia Patients
mammals Brain and Body Weights for 62 Species of Land Mammals
mcycle Data from a Simulated Motorcycle Accident
-menarche Age of Menarche data
+menarche Age of Menarche in Warsaw
michelson Michelson's Speed of Light Data
minn38 Minnesota High School Graduates of 1938
motors Accelerated Life Testing of Motorettes
muscle Effect of Calcium Chloride on Muscle Contraction
in Rat Hearts
+newcomb Newcomb's Measurements of the Passage Time of Light
nlschools Eighth-Grade Pupils in the Netherlands
npk Classical N, P, K Factorial Experiment
npr1 US Naval Petroleum Reserve No. 1 data
oats Data from an Oats Field Trial
painters The Painter's Data of de Piles
petrol N. L. Prater's Petrol Refinery Data
+phones Belgium Phone Calls 1950-1973
quine Absenteeism from School in Rural New South Wales
road Road Accident Deaths in US States
rotifer Numbers of Rotifers by Fluid Density
@@ -166,6 +168,7 @@ snails Snail Mortality Data
steam The Saturated Steam Pressure Data
stormer The Stormer Viscometer Data
survey Student Survey Data
+synth.tr Synthetic Classification Problem
topo Spatial Topographic Data
waders Counts of Waders at 15 Sites in South Africa
whiteside House Insulation: Whiteside's Data
diff --git a/win32/deps/library/MASS/LICENCE b/win32/deps/library/MASS/LICENCE
index e694c08..9f0d123 100644
--- a/win32/deps/library/MASS/LICENCE
+++ b/win32/deps/library/MASS/LICENCE
@@ -21,10 +21,7 @@ File MASS/R/profiles.R copyright (C) 1996 D. M. Bates and W. N. Venables.
Our understanding is that the dataset files MASS/data/*.rda are not copyright.
-Files spatial/data/*.dat were generated or digitized by B. D. Ripley: no
-copyright is asserted.
-
-All other files are copyright (C) 1994-2007 W. N. Venables and
+All other files are copyright (C) 1994-2009 W. N. Venables and
B. D. Ripley. Those parts which were distributed with the first
edition are also copyright (C) 1994 Springer-Verlag New York Inc, with
all rights assigned to W. N. Venables and B. D. Ripley.
diff --git a/win32/deps/library/MASS/Meta/Rd.rds b/win32/deps/library/MASS/Meta/Rd.rds
index 32d5a0b..2c8596c 100644
Binary files a/win32/deps/library/MASS/Meta/Rd.rds and b/win32/deps/library/MASS/Meta/Rd.rds differ
diff --git a/win32/deps/library/MASS/Meta/data.rds b/win32/deps/library/MASS/Meta/data.rds
index 06f82c1..dad9d2c 100644
Binary files a/win32/deps/library/MASS/Meta/data.rds and b/win32/deps/library/MASS/Meta/data.rds differ
diff --git a/win32/deps/library/MASS/Meta/hsearch.rds b/win32/deps/library/MASS/Meta/hsearch.rds
index ebf14f5..52b966b 100644
Binary files a/win32/deps/library/MASS/Meta/hsearch.rds and b/win32/deps/library/MASS/Meta/hsearch.rds differ
diff --git a/win32/deps/library/MASS/Meta/links.rds b/win32/deps/library/MASS/Meta/links.rds
new file mode 100644
index 0000000..fde6ca4
Binary files /dev/null and b/win32/deps/library/MASS/Meta/links.rds differ
diff --git a/win32/deps/library/MASS/Meta/nsInfo.rds b/win32/deps/library/MASS/Meta/nsInfo.rds
index f1f27d9..1052867 100644
Binary files a/win32/deps/library/MASS/Meta/nsInfo.rds and b/win32/deps/library/MASS/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/MASS/Meta/package.rds b/win32/deps/library/MASS/Meta/package.rds
index 55e96a4..15bd788 100644
Binary files a/win32/deps/library/MASS/Meta/package.rds and b/win32/deps/library/MASS/Meta/package.rds differ
diff --git a/win32/deps/library/MASS/NAMESPACE b/win32/deps/library/MASS/NAMESPACE
index e37e843..6012139 100644
--- a/win32/deps/library/MASS/NAMESPACE
+++ b/win32/deps/library/MASS/NAMESPACE
@@ -37,7 +37,7 @@ export(denumerate.formula, renumerate.formula)
importFrom(graphics, pairs, plot)
importFrom(stats, anova, biplot, coef, confint, extractAIC, family, fitted,
- logLik, model.frame, predict, profile, residuals, se.contrast,
+ logLik, model.frame, nobs, predict, profile, residuals, se.contrast,
simulate, terms, update, vcov)
@@ -108,6 +108,8 @@ S3method(Math, fractions)
S3method(model.frame, lda)
S3method(model.frame, polr)
S3method(model.frame, qda)
+S3method(nobs, loglm)
+S3method(nobs, polr)
S3method(Ops, fractions)
S3method(pairs, lda)
S3method(pairs, profile)
@@ -156,6 +158,7 @@ S3method(rlm, formula)
S3method(se.contrast, rlm)
S3method(select, ridgelm)
S3method(simulate, negbin)
+S3method(simulate, polr)
S3method(Summary, fractions)
S3method(summary, loglm)
S3method(summary, negbin)
@@ -165,6 +168,7 @@ S3method(t, fractions)
S3method(terms, gls)
S3method(terms, lme)
S3method(update, loglm)
+S3method(vcov, fitdistr)
S3method(vcov, negbin)
S3method(vcov, polr)
S3method(vcov, rlm)
diff --git a/win32/deps/library/MASS/NEWS b/win32/deps/library/MASS/NEWS
index 9d2aa46..f7a2c65 100644
--- a/win32/deps/library/MASS/NEWS
+++ b/win32/deps/library/MASS/NEWS
@@ -153,9 +153,37 @@ This file documents software changes since the third edition.
- removed unused argument 'nseg' to plot.profile.
- 'alpha' in the "glm" and "polr" methods for profile() is now interpreted
as two-tailed univariate for consistency with other profile methods.
-- 'mammals': corrected typos in names, some thanks to Arni Magnusson
+- 'mammals': corrected typos in names, some thanks to Arni Magnusson.
- profile.glm() now works for binomial glm specified with a matrix response
and a cmpletely zero row.
- there is a "negbin" method for simulate()
- the use of package mclust has been removed from the ch11.R script
because of the change of licence conditions for that package.
+- change ch13.R script for change in package 'survival' 2.35-x.
+- glmmPQL looks up variables in its 'correlation' argument (if a formula)
+ in the usual scope (wish of Ben Bolker: such arguments are unsupported).
+- added a simulate() method for unweighted polr() fits.
+- kde2d() allows a length-2 argument 'n'.
+- the default for truehist(col=) is now set to a colour, not a colour number.
+- the returned fitted values and (undocumented) linear predictor for
+ polr() did not take any offset into account (reported by Ioannis Kosmides).
+- the vcov() method for polr() now returns on the zeta scale (suggested by
+ Achim Zeileis).
+- fitdistr() gains a vcov() method (suggested by Achim Zeileis).
+- ch06.R has R alternatives to fac.design.
+- ch11.R has R alternatives for ggobi and factor rotation.
+- hubers() copes in extreme cases when middle 50% of data is constant.
+- tests/ now includes dataset for polr.R, so checking depends only on
+ base packages and lattice.
+- The "glm" method for profile() failed when given a binomial model
+ with a two-column response.
+- fitdistr() works harder to rescale the problem when fitting a gamma.
+- cov.trob() handles zero weights without giving a warning (reported by
+ John Fox).
+- boxcox() works better when 'y' is very badly scaled, e.g. around 1e-16
+ (patch by Martin Maechler).
+- mvrnorm() no longer defaults to the deprecated EISPACK=TRUE (and
+ hence changes the results). It gains an argument 'EISPACK' for
+ back-compatibility.
+- the "polr" method for profile() could lose dimensions in its return object
+ (reported by Joris Meys)
diff --git a/win32/deps/library/MASS/R/MASS b/win32/deps/library/MASS/R/MASS
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/MASS/R/MASS
+++ b/win32/deps/library/MASS/R/MASS
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/MASS/R/MASS.rdb b/win32/deps/library/MASS/R/MASS.rdb
index 7e2141a..7c3922d 100644
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diff --git a/win32/deps/library/MASS/R/MASS.rdx b/win32/deps/library/MASS/R/MASS.rdx
index 73254dd..3d0998d 100644
Binary files a/win32/deps/library/MASS/R/MASS.rdx and b/win32/deps/library/MASS/R/MASS.rdx differ
diff --git a/win32/deps/library/MASS/data/Rdata.rdb b/win32/deps/library/MASS/data/Rdata.rdb
index cfbfe66..e51620e 100644
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diff --git a/win32/deps/library/MASS/data/Rdata.rds b/win32/deps/library/MASS/data/Rdata.rds
index c3af8f5..4a64627 100644
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diff --git a/win32/deps/library/MASS/data/Rdata.rdx b/win32/deps/library/MASS/data/Rdata.rdx
index 005608f..fabbbfc 100644
Binary files a/win32/deps/library/MASS/data/Rdata.rdx and b/win32/deps/library/MASS/data/Rdata.rdx differ
diff --git a/win32/deps/library/MASS/help/AnIndex b/win32/deps/library/MASS/help/AnIndex
index f72f9fe..b7eb220 100644
--- a/win32/deps/library/MASS/help/AnIndex
+++ b/win32/deps/library/MASS/help/AnIndex
@@ -30,7 +30,6 @@ Cars93 Cars93
cats cats
cement cement
chem chem
-coef.fitdistr fitdistr
coef.lda lda
con2tr con2tr
confint.glm confint
@@ -112,7 +111,6 @@ lm.gls lm.gls
lm.ridge lm.ridge
lmsreg lqs
lmwork stdres
-logLik.fitdistr fitdistr
logLik.negbin glm.nb
loglm loglm
loglm1 loglm1
@@ -172,7 +170,6 @@ predict.lqs predict.lqs
predict.mca predict.mca
predict.qda predict.qda
predict.rlm rlm
-print.fitdistr fitdistr
print.fractions fractions
print.gamma.shape gamma.shape.glm
print.glm.dose dose.p
diff --git a/win32/deps/library/MASS/help/MASS.rdb b/win32/deps/library/MASS/help/MASS.rdb
new file mode 100644
index 0000000..1a4898d
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diff --git a/win32/deps/library/MASS/help/MASS.rdx b/win32/deps/library/MASS/help/MASS.rdx
new file mode 100644
index 0000000..80f1b77
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diff --git a/win32/deps/library/MASS/help/aliases.rds b/win32/deps/library/MASS/help/aliases.rds
new file mode 100644
index 0000000..12ce6a2
Binary files /dev/null and b/win32/deps/library/MASS/help/aliases.rds differ
diff --git a/win32/deps/library/MASS/help/paths.rds b/win32/deps/library/MASS/help/paths.rds
new file mode 100644
index 0000000..e7cbe02
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diff --git a/win32/deps/library/MASS/html/00Index.html b/win32/deps/library/MASS/html/00Index.html
new file mode 100644
index 0000000..fe6b1cc
--- /dev/null
+++ b/win32/deps/library/MASS/html/00Index.html
@@ -0,0 +1,645 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Support Functions and Datasets for Venables and Ripley's MASS</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Support Functions and Datasets for Venables and Ripley's MASS
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘MASS’ version 7.3-22</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+<li><a href="../NEWS">Package NEWS</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<p align="center">
+<a href="#A">A</a>
+<a href="#B">B</a>
+<a href="#C">C</a>
+<a href="#D">D</a>
+<a href="#E">E</a>
+<a href="#F">F</a>
+<a href="#G">G</a>
+<a href="#H">H</a>
+<a href="#I">I</a>
+<a href="#K">K</a>
+<a href="#L">L</a>
+<a href="#M">M</a>
+<a href="#N">N</a>
+<a href="#O">O</a>
+<a href="#P">P</a>
+<a href="#Q">Q</a>
+<a href="#R">R</a>
+<a href="#S">S</a>
+<a href="#T">T</a>
+<a href="#U">U</a>
+<a href="#V">V</a>
+<a href="#W">W</a>
+<a href="#misc">misc</a>
+</p>
+
+
+<h2><a name="A">-- A --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="abbey.html">abbey</a></td>
+<td>Determinations of Nickel Content</td></tr>
+<tr><td width="25%"><a href="accdeaths.html">accdeaths</a></td>
+<td>Accidental Deaths in the US 1973-1978</td></tr>
+<tr><td width="25%"><a href="addterm.html">addterm</a></td>
+<td>Try All One-Term Additions to a Model</td></tr>
+<tr><td width="25%"><a href="addterm.html">addterm.default</a></td>
+<td>Try All One-Term Additions to a Model</td></tr>
+<tr><td width="25%"><a href="addterm.html">addterm.glm</a></td>
+<td>Try All One-Term Additions to a Model</td></tr>
+<tr><td width="25%"><a href="addterm.html">addterm.lm</a></td>
+<td>Try All One-Term Additions to a Model</td></tr>
+<tr><td width="25%"><a href="Aids2.html">Aids2</a></td>
+<td>Australian AIDS Survival Data</td></tr>
+<tr><td width="25%"><a href="Animals.html">Animals</a></td>
+<td>Brain and Body Weights for 28 Species</td></tr>
+<tr><td width="25%"><a href="anorexia.html">anorexia</a></td>
+<td>Anorexia Data on Weight Change</td></tr>
+<tr><td width="25%"><a href="anova.negbin.html">anova.negbin</a></td>
+<td>Likelihood Ratio Tests for Negative Binomial GLMs</td></tr>
+<tr><td width="25%"><a href="area.html">area</a></td>
+<td>Adaptive Numerical Integration</td></tr>
+<tr><td width="25%"><a href="fractions.html">as.character.fractions</a></td>
+<td>Rational Approximation</td></tr>
+<tr><td width="25%"><a href="fractions.html">as.fractions</a></td>
+<td>Rational Approximation</td></tr>
+</table>
+
+<h2><a name="B">-- B --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="bacteria.html">bacteria</a></td>
+<td>Presence of Bacteria after Drug Treatments</td></tr>
+<tr><td width="25%"><a href="bandwidth.nrd.html">bandwidth.nrd</a></td>
+<td>Bandwidth for density() via Normal Reference Distribution</td></tr>
+<tr><td width="25%"><a href="bcv.html">bcv</a></td>
+<td>Biased Cross-Validation for Bandwidth Selection</td></tr>
+<tr><td width="25%"><a href="beav1.html">beav1</a></td>
+<td>Body Temperature Series of Beaver 1</td></tr>
+<tr><td width="25%"><a href="beav2.html">beav2</a></td>
+<td>Body Temperature Series of Beaver 2</td></tr>
+<tr><td width="25%"><a href="biopsy.html">biopsy</a></td>
+<td>Biopsy Data on Breast Cancer Patients</td></tr>
+<tr><td width="25%"><a href="birthwt.html">birthwt</a></td>
+<td>Risk Factors Associated with Low Infant Birth Weight</td></tr>
+<tr><td width="25%"><a href="Boston.html">Boston</a></td>
+<td>Housing Values in Suburbs of Boston</td></tr>
+<tr><td width="25%"><a href="boxcox.html">boxcox</a></td>
+<td>Box-Cox Transformations for Linear Models</td></tr>
+<tr><td width="25%"><a href="boxcox.html">boxcox.default</a></td>
+<td>Box-Cox Transformations for Linear Models</td></tr>
+<tr><td width="25%"><a href="boxcox.html">boxcox.formula</a></td>
+<td>Box-Cox Transformations for Linear Models</td></tr>
+<tr><td width="25%"><a href="boxcox.html">boxcox.lm</a></td>
+<td>Box-Cox Transformations for Linear Models</td></tr>
+</table>
+
+<h2><a name="C">-- C --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="cabbages.html">cabbages</a></td>
+<td>Data from a cabbage field trial</td></tr>
+<tr><td width="25%"><a href="caith.html">caith</a></td>
+<td>Colours of Eyes and Hair of People in Caithness</td></tr>
+<tr><td width="25%"><a href="Cars93.html">Cars93</a></td>
+<td>Data from 93 Cars on Sale in the USA in 1993</td></tr>
+<tr><td width="25%"><a href="cats.html">cats</a></td>
+<td>Anatomical Data from Domestic Cats</td></tr>
+<tr><td width="25%"><a href="cement.html">cement</a></td>
+<td>Heat Evolved by Setting Cements</td></tr>
+<tr><td width="25%"><a href="chem.html">chem</a></td>
+<td>Copper in Wholemeal Flour</td></tr>
+<tr><td width="25%"><a href="lda.html">coef.lda</a></td>
+<td>Linear Discriminant Analysis</td></tr>
+<tr><td width="25%"><a href="con2tr.html">con2tr</a></td>
+<td>Convert Lists to Data Frames for use by lattice</td></tr>
+<tr><td width="25%"><a href="confint.html">confint.glm</a></td>
+<td>Confidence Intervals for Model Parameters</td></tr>
+<tr><td width="25%"><a href="confint.html">confint.nls</a></td>
+<td>Confidence Intervals for Model Parameters</td></tr>
+<tr><td width="25%"><a href="confint.html">confint.profile.glm</a></td>
+<td>Confidence Intervals for Model Parameters</td></tr>
+<tr><td width="25%"><a href="confint.html">confint.profile.nls</a></td>
+<td>Confidence Intervals for Model Parameters</td></tr>
+<tr><td width="25%"><a href="contr.sdif.html">contr.sdif</a></td>
+<td>Successive Differences Contrast Coding</td></tr>
+<tr><td width="25%"><a href="coop.html">coop</a></td>
+<td>Co-operative Trial in Analytical Chemistry</td></tr>
+<tr><td width="25%"><a href="corresp.html">corresp</a></td>
+<td>Simple Correspondence Analysis</td></tr>
+<tr><td width="25%"><a href="corresp.html">corresp.data.frame</a></td>
+<td>Simple Correspondence Analysis</td></tr>
+<tr><td width="25%"><a href="corresp.html">corresp.default</a></td>
+<td>Simple Correspondence Analysis</td></tr>
+<tr><td width="25%"><a href="corresp.html">corresp.factor</a></td>
+<td>Simple Correspondence Analysis</td></tr>
+<tr><td width="25%"><a href="corresp.html">corresp.formula</a></td>
+<td>Simple Correspondence Analysis</td></tr>
+<tr><td width="25%"><a href="corresp.html">corresp.matrix</a></td>
+<td>Simple Correspondence Analysis</td></tr>
+<tr><td width="25%"><a href="corresp.html">corresp.xtabs</a></td>
+<td>Simple Correspondence Analysis</td></tr>
+<tr><td width="25%"><a href="cov.rob.html">cov.mcd</a></td>
+<td>Resistant Estimation of Multivariate Location and Scatter</td></tr>
+<tr><td width="25%"><a href="cov.rob.html">cov.mve</a></td>
+<td>Resistant Estimation of Multivariate Location and Scatter</td></tr>
+<tr><td width="25%"><a href="cov.rob.html">cov.rob</a></td>
+<td>Resistant Estimation of Multivariate Location and Scatter</td></tr>
+<tr><td width="25%"><a href="cov.trob.html">cov.trob</a></td>
+<td>Covariance Estimation for Multivariate t Distribution</td></tr>
+<tr><td width="25%"><a href="cpus.html">cpus</a></td>
+<td>Performance of Computer CPUs</td></tr>
+<tr><td width="25%"><a href="crabs.html">crabs</a></td>
+<td>Morphological Measurements on Leptograpsus Crabs</td></tr>
+<tr><td width="25%"><a href="Cushings.html">Cushings</a></td>
+<td>Diagnostic Tests on Patients with Cushing's Syndrome</td></tr>
+</table>
+
+<h2><a name="D">-- D --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="DDT.html">DDT</a></td>
+<td>DDT in Kale</td></tr>
+<tr><td width="25%"><a href="deaths.html">deaths</a></td>
+<td>Monthly Deaths from Lung Diseases in the UK</td></tr>
+<tr><td width="25%"><a href="denumerate.html">denumerate</a></td>
+<td>Transform an Allowable Formula for 'loglm' into one for 'terms'</td></tr>
+<tr><td width="25%"><a href="denumerate.html">denumerate.formula</a></td>
+<td>Transform an Allowable Formula for 'loglm' into one for 'terms'</td></tr>
+<tr><td width="25%"><a href="dose.p.html">dose.p</a></td>
+<td>Predict Doses for Binomial Assay model</td></tr>
+<tr><td width="25%"><a href="drivers.html">drivers</a></td>
+<td>Deaths of Car Drivers in Great Britain 1969-84</td></tr>
+<tr><td width="25%"><a href="dropterm.html">dropterm</a></td>
+<td>Try All One-Term Deletions from a Model</td></tr>
+<tr><td width="25%"><a href="dropterm.html">dropterm.default</a></td>
+<td>Try All One-Term Deletions from a Model</td></tr>
+<tr><td width="25%"><a href="dropterm.html">dropterm.glm</a></td>
+<td>Try All One-Term Deletions from a Model</td></tr>
+<tr><td width="25%"><a href="dropterm.html">dropterm.lm</a></td>
+<td>Try All One-Term Deletions from a Model</td></tr>
+</table>
+
+<h2><a name="E">-- E --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="eagles.html">eagles</a></td>
+<td>Foraging Ecology of Bald Eagles</td></tr>
+<tr><td width="25%"><a href="epil.html">epil</a></td>
+<td>Seizure Counts for Epileptics</td></tr>
+<tr><td width="25%"><a href="eqscplot.html">eqscplot</a></td>
+<td>Plots with Geometrically Equal Scales</td></tr>
+<tr><td width="25%"><a href="stepAIC.html">extractAIC.gls</a></td>
+<td>Choose a model by AIC in a Stepwise Algorithm</td></tr>
+<tr><td width="25%"><a href="stepAIC.html">extractAIC.lme</a></td>
+<td>Choose a model by AIC in a Stepwise Algorithm</td></tr>
+</table>
+
+<h2><a name="F">-- F --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="glm.nb.html">family.negbin</a></td>
+<td>Fit a Negative Binomial Generalized Linear Model</td></tr>
+<tr><td width="25%"><a href="farms.html">farms</a></td>
+<td>Ecological Factors in Farm Management</td></tr>
+<tr><td width="25%"><a href="fgl.html">fgl</a></td>
+<td>Measurements of Forensic Glass Fragments</td></tr>
+<tr><td width="25%"><a href="fitdistr.html">fitdistr</a></td>
+<td>Maximum-likelihood Fitting of Univariate Distributions</td></tr>
+<tr><td width="25%"><a href="forbes.html">forbes</a></td>
+<td>Forbes' Data on Boiling Points in the Alps</td></tr>
+<tr><td width="25%"><a href="fractions.html">fractions</a></td>
+<td>Rational Approximation</td></tr>
+</table>
+
+<h2><a name="G">-- G --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="GAGurine.html">GAGurine</a></td>
+<td>Level of GAG in Urine of Children</td></tr>
+<tr><td width="25%"><a href="galaxies.html">galaxies</a></td>
+<td>Velocities for 82 Galaxies</td></tr>
+<tr><td width="25%"><a href="gamma.dispersion.html">gamma.dispersion</a></td>
+<td>Calculate the MLE of the Gamma Dispersion Parameter in a GLM Fit</td></tr>
+<tr><td width="25%"><a href="gamma.shape.glm.html">gamma.shape</a></td>
+<td>Estimate the Shape Parameter of the Gamma Distribution in a GLM Fit</td></tr>
+<tr><td width="25%"><a href="gamma.shape.glm.html">gamma.shape.glm</a></td>
+<td>Estimate the Shape Parameter of the Gamma Distribution in a GLM Fit</td></tr>
+<tr><td width="25%"><a href="gehan.html">gehan</a></td>
+<td>Remission Times of Leukaemia Patients</td></tr>
+<tr><td width="25%"><a href="genotype.html">genotype</a></td>
+<td>Rat Genotype Data</td></tr>
+<tr><td width="25%"><a href="geyser.html">geyser</a></td>
+<td>Old Faithful Geyser Data</td></tr>
+<tr><td width="25%"><a href="gilgais.html">gilgais</a></td>
+<td>Line Transect of Soil in Gilgai Territory</td></tr>
+<tr><td width="25%"><a href="ginv.html">ginv</a></td>
+<td>Generalized Inverse of a Matrix</td></tr>
+<tr><td width="25%"><a href="glm.convert.html">glm.convert</a></td>
+<td>Change a Negative Binomial fit to a GLM fit</td></tr>
+<tr><td width="25%"><a href="glm.nb.html">glm.nb</a></td>
+<td>Fit a Negative Binomial Generalized Linear Model</td></tr>
+<tr><td width="25%"><a href="glmmPQL.html">glmmPQL</a></td>
+<td>Fit Generalized Linear Mixed Models via PQL</td></tr>
+</table>
+
+<h2><a name="H">-- H --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="hills.html">hills</a></td>
+<td>Record Times in Scottish Hill Races</td></tr>
+<tr><td width="25%"><a href="hist.scott.html">hist.FD</a></td>
+<td>Plot a Histogram with Automatic Bin Width Selection</td></tr>
+<tr><td width="25%"><a href="hist.scott.html">hist.scott</a></td>
+<td>Plot a Histogram with Automatic Bin Width Selection</td></tr>
+<tr><td width="25%"><a href="housing.html">housing</a></td>
+<td>Frequency Table from a Copenhagen Housing Conditions Survey</td></tr>
+<tr><td width="25%"><a href="huber.html">huber</a></td>
+<td>Huber M-estimator of Location with MAD Scale</td></tr>
+<tr><td width="25%"><a href="hubers.html">hubers</a></td>
+<td>Huber Proposal 2 Robust Estimator of Location and/or Scale</td></tr>
+</table>
+
+<h2><a name="I">-- I --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="immer.html">immer</a></td>
+<td>Yields from a Barley Field Trial</td></tr>
+<tr><td width="25%"><a href="Insurance.html">Insurance</a></td>
+<td>Numbers of Car Insurance claims</td></tr>
+<tr><td width="25%"><a href="fractions.html">is.fractions</a></td>
+<td>Rational Approximation</td></tr>
+<tr><td width="25%"><a href="isoMDS.html">isoMDS</a></td>
+<td>Kruskal's Non-metric Multidimensional Scaling</td></tr>
+</table>
+
+<h2><a name="K">-- K --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="kde2d.html">kde2d</a></td>
+<td>Two-Dimensional Kernel Density Estimation</td></tr>
+</table>
+
+<h2><a name="L">-- L --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="lda.html">lda</a></td>
+<td>Linear Discriminant Analysis</td></tr>
+<tr><td width="25%"><a href="lda.html">lda.data.frame</a></td>
+<td>Linear Discriminant Analysis</td></tr>
+<tr><td width="25%"><a href="lda.html">lda.default</a></td>
+<td>Linear Discriminant Analysis</td></tr>
+<tr><td width="25%"><a href="lda.html">lda.formula</a></td>
+<td>Linear Discriminant Analysis</td></tr>
+<tr><td width="25%"><a href="lda.html">lda.matrix</a></td>
+<td>Linear Discriminant Analysis</td></tr>
+<tr><td width="25%"><a href="ldahist.html">ldahist</a></td>
+<td>Histograms or Density Plots of Multiple Groups</td></tr>
+<tr><td width="25%"><a href="leuk.html">leuk</a></td>
+<td>Survival Times and White Blood Counts for Leukaemia Patients</td></tr>
+<tr><td width="25%"><a href="lm.gls.html">lm.gls</a></td>
+<td>Fit Linear Models by Generalized Least Squares</td></tr>
+<tr><td width="25%"><a href="lm.ridge.html">lm.ridge</a></td>
+<td>Ridge Regression</td></tr>
+<tr><td width="25%"><a href="lqs.html">lmsreg</a></td>
+<td>Resistant Regression</td></tr>
+<tr><td width="25%"><a href="stdres.html">lmwork</a></td>
+<td>Extract Standardized Residuals from a Linear Model</td></tr>
+<tr><td width="25%"><a href="glm.nb.html">logLik.negbin</a></td>
+<td>Fit a Negative Binomial Generalized Linear Model</td></tr>
+<tr><td width="25%"><a href="loglm.html">loglm</a></td>
+<td>Fit Log-Linear Models by Iterative Proportional Scaling</td></tr>
+<tr><td width="25%"><a href="logtrans.html">logtrans</a></td>
+<td>Estimate log Transformation Parameter</td></tr>
+<tr><td width="25%"><a href="logtrans.html">logtrans.default</a></td>
+<td>Estimate log Transformation Parameter</td></tr>
+<tr><td width="25%"><a href="logtrans.html">logtrans.formula</a></td>
+<td>Estimate log Transformation Parameter</td></tr>
+<tr><td width="25%"><a href="logtrans.html">logtrans.lm</a></td>
+<td>Estimate log Transformation Parameter</td></tr>
+<tr><td width="25%"><a href="lqs.html">lqs</a></td>
+<td>Resistant Regression</td></tr>
+<tr><td width="25%"><a href="lqs.html">lqs.default</a></td>
+<td>Resistant Regression</td></tr>
+<tr><td width="25%"><a href="lqs.html">lqs.formula</a></td>
+<td>Resistant Regression</td></tr>
+<tr><td width="25%"><a href="lqs.html">ltsreg</a></td>
+<td>Resistant Regression</td></tr>
+</table>
+
+<h2><a name="M">-- M --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="mammals.html">mammals</a></td>
+<td>Brain and Body Weights for 62 Species of Land Mammals</td></tr>
+<tr><td width="25%"><a href="fractions.html">Math.fractions</a></td>
+<td>Rational Approximation</td></tr>
+<tr><td width="25%"><a href="mca.html">mca</a></td>
+<td>Multiple Correspondence Analysis</td></tr>
+<tr><td width="25%"><a href="mcycle.html">mcycle</a></td>
+<td>Data from a Simulated Motorcycle Accident</td></tr>
+<tr><td width="25%"><a href="Melanoma.html">Melanoma</a></td>
+<td>Survival from Malignant Melanoma</td></tr>
+<tr><td width="25%"><a href="menarche.html">menarche</a></td>
+<td>Age of Menarche in Warsaw</td></tr>
+<tr><td width="25%"><a href="michelson.html">michelson</a></td>
+<td>Michelson's Speed of Light Data</td></tr>
+<tr><td width="25%"><a href="minn38.html">minn38</a></td>
+<td>Minnesota High School Graduates of 1938</td></tr>
+<tr><td width="25%"><a href="lda.html">model.frame.lda</a></td>
+<td>Linear Discriminant Analysis</td></tr>
+<tr><td width="25%"><a href="qda.html">model.frame.qda</a></td>
+<td>Quadratic Discriminant Analysis</td></tr>
+<tr><td width="25%"><a href="motors.html">motors</a></td>
+<td>Accelerated Life Testing of Motorettes</td></tr>
+<tr><td width="25%"><a href="muscle.html">muscle</a></td>
+<td>Effect of Calcium Chloride on Muscle Contraction in Rat Hearts</td></tr>
+<tr><td width="25%"><a href="mvrnorm.html">mvrnorm</a></td>
+<td>Simulate from a Multivariate Normal Distribution</td></tr>
+</table>
+
+<h2><a name="N">-- N --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="negative.binomial.html">negative.binomial</a></td>
+<td>Family function for Negative Binomial GLMs</td></tr>
+<tr><td width="25%"><a href="newcomb.html">newcomb</a></td>
+<td>Newcomb's Measurements of the Passage Time of Light</td></tr>
+<tr><td width="25%"><a href="nlschools.html">nlschools</a></td>
+<td>Eighth-Grade Pupils in the Netherlands</td></tr>
+<tr><td width="25%"><a href="npk.html">npk</a></td>
+<td>Classical N, P, K Factorial Experiment</td></tr>
+<tr><td width="25%"><a href="npr1.html">npr1</a></td>
+<td>US Naval Petroleum Reserve No. 1 data</td></tr>
+<tr><td width="25%"><a href="Null.html">Null</a></td>
+<td>Null Spaces of Matrices</td></tr>
+</table>
+
+<h2><a name="O">-- O --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="oats.html">oats</a></td>
+<td>Data from an Oats Field Trial</td></tr>
+<tr><td width="25%"><a href="OME.html">OME</a></td>
+<td>Tests of Auditory Perception in Children with OME</td></tr>
+<tr><td width="25%"><a href="fractions.html">Ops.fractions</a></td>
+<td>Rational Approximation</td></tr>
+</table>
+
+<h2><a name="P">-- P --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="painters.html">painters</a></td>
+<td>The Painter's Data of de Piles</td></tr>
+<tr><td width="25%"><a href="pairs.lda.html">pairs.lda</a></td>
+<td>Produce Pairwise Scatterplots from an 'lda' Fit</td></tr>
+<tr><td width="25%"><a href="plot.profile.html">pairs.profile</a></td>
+<td>Plotting Functions for 'profile' Objects</td></tr>
+<tr><td width="25%"><a href="parcoord.html">parcoord</a></td>
+<td>Parallel Coordinates Plot</td></tr>
+<tr><td width="25%"><a href="petrol.html">petrol</a></td>
+<td>N. L. Prater's Petrol Refinery Data</td></tr>
+<tr><td width="25%"><a href="phones.html">phones</a></td>
+<td>Belgium Phone Calls 1950-1973</td></tr>
+<tr><td width="25%"><a href="Pima.tr.html">Pima.te</a></td>
+<td>Diabetes in Pima Indian Women</td></tr>
+<tr><td width="25%"><a href="Pima.tr.html">Pima.tr</a></td>
+<td>Diabetes in Pima Indian Women</td></tr>
+<tr><td width="25%"><a href="Pima.tr.html">Pima.tr2</a></td>
+<td>Diabetes in Pima Indian Women</td></tr>
+<tr><td width="25%"><a href="plot.lda.html">plot.lda</a></td>
+<td>Plot Method for Class 'lda'</td></tr>
+<tr><td width="25%"><a href="plot.mca.html">plot.mca</a></td>
+<td>Plot Method for Objects of Class 'mca'</td></tr>
+<tr><td width="25%"><a href="plot.profile.html">plot.profile</a></td>
+<td>Plotting Functions for 'profile' Objects</td></tr>
+<tr><td width="25%"><a href="lm.ridge.html">plot.ridgelm</a></td>
+<td>Ridge Regression</td></tr>
+<tr><td width="25%"><a href="polr.html">polr</a></td>
+<td>Ordered Logistic or Probit Regression</td></tr>
+<tr><td width="25%"><a href="predict.glmmPQL.html">predict.glmmPQL</a></td>
+<td>Predict Method for glmmPQL Fits</td></tr>
+<tr><td width="25%"><a href="predict.lda.html">predict.lda</a></td>
+<td>Classify Multivariate Observations by Linear Discrimination</td></tr>
+<tr><td width="25%"><a href="predict.lqs.html">predict.lqs</a></td>
+<td>Predict from an lqs Fit</td></tr>
+<tr><td width="25%"><a href="predict.mca.html">predict.mca</a></td>
+<td>Predict Method for Class 'mca'</td></tr>
+<tr><td width="25%"><a href="predict.qda.html">predict.qda</a></td>
+<td>Classify from Quadratic Discriminant Analysis</td></tr>
+<tr><td width="25%"><a href="rlm.html">predict.rlm</a></td>
+<td>Robust Fitting of Linear Models</td></tr>
+<tr><td width="25%"><a href="fractions.html">print.fractions</a></td>
+<td>Rational Approximation</td></tr>
+<tr><td width="25%"><a href="gamma.shape.glm.html">print.gamma.shape</a></td>
+<td>Estimate the Shape Parameter of the Gamma Distribution in a GLM Fit</td></tr>
+<tr><td width="25%"><a href="dose.p.html">print.glm.dose</a></td>
+<td>Predict Doses for Binomial Assay model</td></tr>
+<tr><td width="25%"><a href="lda.html">print.lda</a></td>
+<td>Linear Discriminant Analysis</td></tr>
+<tr><td width="25%"><a href="mca.html">print.mca</a></td>
+<td>Multiple Correspondence Analysis</td></tr>
+<tr><td width="25%"><a href="qda.html">print.qda</a></td>
+<td>Quadratic Discriminant Analysis</td></tr>
+<tr><td width="25%"><a href="lm.ridge.html">print.ridgelm</a></td>
+<td>Ridge Regression</td></tr>
+<tr><td width="25%"><a href="rlm.html">print.rlm</a></td>
+<td>Robust Fitting of Linear Models</td></tr>
+<tr><td width="25%"><a href="rms.curv.html">print.rms.curv</a></td>
+<td>Relative Curvature Measures for Non-Linear Regression</td></tr>
+<tr><td width="25%"><a href="summary.loglm.html">print.summary.loglm</a></td>
+<td>Summary Method Function for Objects of Class 'loglm'</td></tr>
+<tr><td width="25%"><a href="summary.negbin.html">print.summary.negbin</a></td>
+<td>Summary Method Function for Objects of Class 'negbin'</td></tr>
+<tr><td width="25%"><a href="summary.rlm.html">print.summary.rlm</a></td>
+<td>Summary Method for Robust Linear Models</td></tr>
+<tr><td width="25%"><a href="profile.glm.html">profile.glm</a></td>
+<td>Method for Profiling glm Objects</td></tr>
+<tr><td width="25%"><a href="rlm.html">psi.bisquare</a></td>
+<td>Robust Fitting of Linear Models</td></tr>
+<tr><td width="25%"><a href="rlm.html">psi.hampel</a></td>
+<td>Robust Fitting of Linear Models</td></tr>
+<tr><td width="25%"><a href="rlm.html">psi.huber</a></td>
+<td>Robust Fitting of Linear Models</td></tr>
+</table>
+
+<h2><a name="Q">-- Q --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="qda.html">qda</a></td>
+<td>Quadratic Discriminant Analysis</td></tr>
+<tr><td width="25%"><a href="qda.html">qda.data.frame</a></td>
+<td>Quadratic Discriminant Analysis</td></tr>
+<tr><td width="25%"><a href="qda.html">qda.default</a></td>
+<td>Quadratic Discriminant Analysis</td></tr>
+<tr><td width="25%"><a href="qda.html">qda.formula</a></td>
+<td>Quadratic Discriminant Analysis</td></tr>
+<tr><td width="25%"><a href="qda.html">qda.matrix</a></td>
+<td>Quadratic Discriminant Analysis</td></tr>
+<tr><td width="25%"><a href="quine.html">quine</a></td>
+<td>Absenteeism from School in Rural New South Wales</td></tr>
+</table>
+
+<h2><a name="R">-- R --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Rabbit.html">Rabbit</a></td>
+<td>Blood Pressure in Rabbits</td></tr>
+<tr><td width="25%"><a href="rational.html">rational</a></td>
+<td>Rational Approximation</td></tr>
+<tr><td width="25%"><a href="renumerate.html">renumerate</a></td>
+<td>Convert a Formula Transformed by 'denumerate'</td></tr>
+<tr><td width="25%"><a href="renumerate.html">renumerate.formula</a></td>
+<td>Convert a Formula Transformed by 'denumerate'</td></tr>
+<tr><td width="25%"><a href="rlm.html">rlm</a></td>
+<td>Robust Fitting of Linear Models</td></tr>
+<tr><td width="25%"><a href="rlm.html">rlm.default</a></td>
+<td>Robust Fitting of Linear Models</td></tr>
+<tr><td width="25%"><a href="rlm.html">rlm.formula</a></td>
+<td>Robust Fitting of Linear Models</td></tr>
+<tr><td width="25%"><a href="rms.curv.html">rms.curv</a></td>
+<td>Relative Curvature Measures for Non-Linear Regression</td></tr>
+<tr><td width="25%"><a href="rnegbin.html">rnegbin</a></td>
+<td>Simulate Negative Binomial Variates</td></tr>
+<tr><td width="25%"><a href="road.html">road</a></td>
+<td>Road Accident Deaths in US States</td></tr>
+<tr><td width="25%"><a href="rotifer.html">rotifer</a></td>
+<td>Numbers of Rotifers by Fluid Density</td></tr>
+<tr><td width="25%"><a href="Rubber.html">Rubber</a></td>
+<td>Accelerated Testing of Tyre Rubber</td></tr>
+</table>
+
+<h2><a name="S">-- S --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="sammon.html">sammon</a></td>
+<td>Sammon's Non-Linear Mapping</td></tr>
+<tr><td width="25%"><a href="lm.ridge.html">select</a></td>
+<td>Ridge Regression</td></tr>
+<tr><td width="25%"><a href="lm.ridge.html">select.ridgelm</a></td>
+<td>Ridge Regression</td></tr>
+<tr><td width="25%"><a href="isoMDS.html">Shepard</a></td>
+<td>Kruskal's Non-metric Multidimensional Scaling</td></tr>
+<tr><td width="25%"><a href="ships.html">ships</a></td>
+<td>Ships Damage Data</td></tr>
+<tr><td width="25%"><a href="shoes.html">shoes</a></td>
+<td>Shoe wear data of Box, Hunter and Hunter</td></tr>
+<tr><td width="25%"><a href="shrimp.html">shrimp</a></td>
+<td>Percentage of Shrimp in Shrimp Cocktail</td></tr>
+<tr><td width="25%"><a href="shuttle.html">shuttle</a></td>
+<td>Space Shuttle Autolander Problem</td></tr>
+<tr><td width="25%"><a href="Sitka.html">Sitka</a></td>
+<td>Growth Curves for Sitka Spruce Trees in 1988</td></tr>
+<tr><td width="25%"><a href="Sitka89.html">Sitka89</a></td>
+<td>Growth Curves for Sitka Spruce Trees in 1989</td></tr>
+<tr><td width="25%"><a href="Skye.html">Skye</a></td>
+<td>AFM Compositions of Aphyric Skye Lavas</td></tr>
+<tr><td width="25%"><a href="snails.html">snails</a></td>
+<td>Snail Mortality Data</td></tr>
+<tr><td width="25%"><a href="SP500.html">SP500</a></td>
+<td>Returns of the Standard and Poors 500</td></tr>
+<tr><td width="25%"><a href="stdres.html">stdres</a></td>
+<td>Extract Standardized Residuals from a Linear Model</td></tr>
+<tr><td width="25%"><a href="steam.html">steam</a></td>
+<td>The Saturated Steam Pressure Data</td></tr>
+<tr><td width="25%"><a href="stepAIC.html">stepAIC</a></td>
+<td>Choose a model by AIC in a Stepwise Algorithm</td></tr>
+<tr><td width="25%"><a href="stormer.html">stormer</a></td>
+<td>The Stormer Viscometer Data</td></tr>
+<tr><td width="25%"><a href="studres.html">studres</a></td>
+<td>Extract Studentized Residuals from a Linear Model</td></tr>
+<tr><td width="25%"><a href="fractions.html">Summary.fractions</a></td>
+<td>Rational Approximation</td></tr>
+<tr><td width="25%"><a href="summary.loglm.html">summary.loglm</a></td>
+<td>Summary Method Function for Objects of Class 'loglm'</td></tr>
+<tr><td width="25%"><a href="summary.negbin.html">summary.negbin</a></td>
+<td>Summary Method Function for Objects of Class 'negbin'</td></tr>
+<tr><td width="25%"><a href="summary.rlm.html">summary.rlm</a></td>
+<td>Summary Method for Robust Linear Models</td></tr>
+<tr><td width="25%"><a href="survey.html">survey</a></td>
+<td>Student Survey Data</td></tr>
+<tr><td width="25%"><a href="synth.tr.html">synth.te</a></td>
+<td>Synthetic Classification Problem</td></tr>
+<tr><td width="25%"><a href="synth.tr.html">synth.tr</a></td>
+<td>Synthetic Classification Problem</td></tr>
+</table>
+
+<h2><a name="T">-- T --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="fractions.html">t.fractions</a></td>
+<td>Rational Approximation</td></tr>
+<tr><td width="25%"><a href="stepAIC.html">terms.gls</a></td>
+<td>Choose a model by AIC in a Stepwise Algorithm</td></tr>
+<tr><td width="25%"><a href="stepAIC.html">terms.lme</a></td>
+<td>Choose a model by AIC in a Stepwise Algorithm</td></tr>
+<tr><td width="25%"><a href="theta.md.html">theta.md</a></td>
+<td>Estimate theta of the Negative Binomial</td></tr>
+<tr><td width="25%"><a href="theta.md.html">theta.ml</a></td>
+<td>Estimate theta of the Negative Binomial</td></tr>
+<tr><td width="25%"><a href="theta.md.html">theta.mm</a></td>
+<td>Estimate theta of the Negative Binomial</td></tr>
+<tr><td width="25%"><a href="topo.html">topo</a></td>
+<td>Spatial Topographic Data</td></tr>
+<tr><td width="25%"><a href="Traffic.html">Traffic</a></td>
+<td>Effect of Swedish Speed Limits on Accidents</td></tr>
+<tr><td width="25%"><a href="truehist.html">truehist</a></td>
+<td>Plot a Histogram</td></tr>
+</table>
+
+<h2><a name="U">-- U --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="ucv.html">ucv</a></td>
+<td>Unbiased Cross-Validation for Bandwidth Selection</td></tr>
+<tr><td width="25%"><a href="UScereal.html">UScereal</a></td>
+<td>Nutritional and Marketing Information on US Cereals</td></tr>
+<tr><td width="25%"><a href="UScrime.html">UScrime</a></td>
+<td>The Effect of Punishment Regimes on Crime Rates</td></tr>
+</table>
+
+<h2><a name="V">-- V --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="VA.html">VA</a></td>
+<td>Veteran's Administration Lung Cancer Trial</td></tr>
+</table>
+
+<h2><a name="W">-- W --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="waders.html">waders</a></td>
+<td>Counts of Waders at 15 Sites in South Africa</td></tr>
+<tr><td width="25%"><a href="whiteside.html">whiteside</a></td>
+<td>House Insulation: Whiteside's Data</td></tr>
+<tr><td width="25%"><a href="width.SJ.html">width.SJ</a></td>
+<td>Bandwidth Selection by Pilot Estimation of Derivatives</td></tr>
+<tr><td width="25%"><a href="write.matrix.html">write.matrix</a></td>
+<td>Write a Matrix or Data Frame</td></tr>
+<tr><td width="25%"><a href="wtloss.html">wtloss</a></td>
+<td>Weight Loss Data from an Obese Patient</td></tr>
+</table>
+
+<h2><a name="misc">-- misc --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="rational.html">.rat</a></td>
+<td>Rational Approximation</td></tr>
+<tr><td width="25%"><a href="fractions.html">[.fractions</a></td>
+<td>Rational Approximation</td></tr>
+<tr><td width="25%"><a href="fractions.html">[<-.fractions</a></td>
+<td>Rational Approximation</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/MASS/html/R.css b/win32/deps/library/MASS/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/MASS/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/MASS/libs/i386/MASS.dll b/win32/deps/library/MASS/libs/i386/MASS.dll
new file mode 100644
index 0000000..17a89c4
Binary files /dev/null and b/win32/deps/library/MASS/libs/i386/MASS.dll differ
diff --git a/win32/deps/library/MASS/po/de/LC_MESSAGES/R-MASS.mo b/win32/deps/library/MASS/po/de/LC_MESSAGES/R-MASS.mo
new file mode 100644
index 0000000..99db4f6
Binary files /dev/null and b/win32/deps/library/MASS/po/de/LC_MESSAGES/R-MASS.mo differ
diff --git a/win32/deps/library/MASS/po/en quot/LC_MESSAGES/R-MASS.mo b/win32/deps/library/MASS/po/en quot/LC_MESSAGES/R-MASS.mo
new file mode 100644
index 0000000..14f1590
Binary files /dev/null and b/win32/deps/library/MASS/po/en quot/LC_MESSAGES/R-MASS.mo differ
diff --git a/win32/deps/library/MASS/po/fr/LC_MESSAGES/R-MASS.mo b/win32/deps/library/MASS/po/fr/LC_MESSAGES/R-MASS.mo
new file mode 100644
index 0000000..0b8e29e
Binary files /dev/null and b/win32/deps/library/MASS/po/fr/LC_MESSAGES/R-MASS.mo differ
diff --git a/win32/deps/library/MASS/po/pl/LC_MESSAGES/R-MASS.mo b/win32/deps/library/MASS/po/pl/LC_MESSAGES/R-MASS.mo
new file mode 100644
index 0000000..4c38eed
Binary files /dev/null and b/win32/deps/library/MASS/po/pl/LC_MESSAGES/R-MASS.mo differ
diff --git a/win32/deps/library/MASS/scripts/ch01.R b/win32/deps/library/MASS/scripts/ch01.R
index a21c0a8..0c6a900 100644
--- a/win32/deps/library/MASS/scripts/ch01.R
+++ b/win32/deps/library/MASS/scripts/ch01.R
@@ -2,8 +2,8 @@
## Script from Fourth Edition of `Modern Applied Statistics with S'
-options(echo = T, width=65, digits=5, height=9999)
-postscript(file="ch01.ps", width=8, height=6, pointsize=9)
+options(width=65, digits=5, height=9999)
+pdf(file="ch01.pdf", width=8, height=6, pointsize=9)
# Chapter 1 Introduction
diff --git a/win32/deps/library/MASS/scripts/ch02.R b/win32/deps/library/MASS/scripts/ch02.R
index fff2212..066aea7 100644
--- a/win32/deps/library/MASS/scripts/ch02.R
+++ b/win32/deps/library/MASS/scripts/ch02.R
@@ -5,7 +5,7 @@
# Chapter 2 Data Manipulation
library(MASS)
-options(echo = T, width=65, digits=5, height=9999)
+options(width=65, digits=5, height=9999)
-2:2
@@ -105,7 +105,7 @@ names(longitude) <- state.name
longitude[c("Hawaii", "Alaska")]
myarr[1, 2:4, ]
-myarr[1, 2:4, , drop = F]
+myarr[1, 2:4, , drop = FALSE]
attach(painters)
painters[Colour >= 17, ]
@@ -138,7 +138,7 @@ lcrabs[, 4:8] <- log(crabs[, 4:8])
scrabs <- crabs # make a copy
scrabs[, 4:8] <- lapply(scrabs[, 4:8], scale)
## or to just centre the variables
-scrabs[, 4:8] <- lapply(scrabs[, 4:8], scale, scale = F)
+scrabs[, 4:8] <- lapply(scrabs[, 4:8], scale, scale = FALSE)
scrabs <- crabs # make a copy
scrabs[ ] <- lapply(scrabs,
diff --git a/win32/deps/library/MASS/scripts/ch03.R b/win32/deps/library/MASS/scripts/ch03.R
index 3b5253c..51446e3 100644
--- a/win32/deps/library/MASS/scripts/ch03.R
+++ b/win32/deps/library/MASS/scripts/ch03.R
@@ -5,7 +5,7 @@
# Chapter 3 S Language
library(MASS)
-options(echo = T, width=65, digits=5, height=9999)
+options(width=65, digits=5, height=9999)
# from Chapter 2
@@ -112,7 +112,7 @@ paste(c("X", "Y"), 1:4, sep = "", collapse = " + ")
substring(state.name[44:50], 1, 4)
as.vector(abbreviate(state.name[44:50]))
-as.vector(abbreviate(state.name[44:50], use.classes = F))
+as.vector(abbreviate(state.name[44:50], use.classes = FALSE))
grep("na$", state.name)
regexpr("na$", state.name)
diff --git a/win32/deps/library/MASS/scripts/ch04.R b/win32/deps/library/MASS/scripts/ch04.R
index a6d5bf2..c3d4c22 100644
--- a/win32/deps/library/MASS/scripts/ch04.R
+++ b/win32/deps/library/MASS/scripts/ch04.R
@@ -6,9 +6,8 @@
library(MASS)
library(lattice)
-trellis.device(postscript, file="ch04.ps", width=8, height=6,
- pointsize=9)
-options(echo=T, width=65, digits=5)
+pdf(file="ch04.pdf", width=8, height=6, pointsize=9)
+options(width=65, digits=5)
# 4.2 Basic plotting functions
@@ -21,7 +20,7 @@ if(interactive())
loc <- barplot(t(lung.deaths), names = dimnames(lung.deaths)[[1]],
angle = c(45, 135), density = 10, col = 1)
total <- rowSums(lung.deaths)
-text(loc, total + par("cxy")[2], total, cex = 0.7, xpd = T)
+text(loc, total + par("cxy")[2], total, cex = 0.7, xpd = TRUE)
# S: if(interactive()) brush(hills)
@@ -82,7 +81,7 @@ qqline(Infant.Mortality)
samp <- cbind(Infant.Mortality, matrix(rnorm(47*19), 47, 19))
samp <- apply(scale(samp), 2, sort)
rs <- samp[, 1]
-xs <- qqnorm(rs, plot = F)$x
+xs <- qqnorm(rs, plot = FALSE)$x
env <- t(apply(samp[, -1], 1, range))
matplot(xs, cbind(rs, env), type = "pnn",
@@ -187,11 +186,11 @@ bwplot(Age ~ Days | Sex*Lrn*Eth, data = Quine, layout = c(4, 2),
strip = function(...) strip.default(..., style = 1))
stripplot(Age ~ Days | Sex*Lrn*Eth, data = Quine,
- jitter = T, layout = c(4, 2))
+ jitter = TRUE, layout = c(4, 2))
stripplot(Age ~ Days | Eth*Sex, data = Quine,
groups = Lrn, jitter = TRUE,
- panel = function(x, y, subscripts, jitter.data = F, ...) {
+ panel = function(x, y, subscripts, jitter.data = FALSE, ...) {
if(jitter.data) y <- jitter(as.numeric(y))
panel.superpose(x, y, subscripts, ...)
},
@@ -212,11 +211,11 @@ stripplot(type ~ y | meas, data = fgl.df,
scales = list(x = "free"), xlab = "", cex = 0.5,
strip = function(...) strip.default(style = 1, ...))
-if(F) { # no data supplied
+if(FALSE) { # no data supplied
xyplot(ratio ~ scant | subject, data = A5,
xlab = "scan interval (years)",
ylab = "ventricle/brain volume normalized to 1 at start",
- subscripts = T, ID = A5$ID,
+ subscripts = TRUE, ID = A5$ID,
strip = function(factor, ...)
strip.default(..., factor.levels = labs, style = 1),
layout = c(8, 5, 1),
diff --git a/win32/deps/library/MASS/scripts/ch05.R b/win32/deps/library/MASS/scripts/ch05.R
index b35d23a..f61852f 100644
--- a/win32/deps/library/MASS/scripts/ch05.R
+++ b/win32/deps/library/MASS/scripts/ch05.R
@@ -24,14 +24,14 @@ perm.t.test <- function(d) {
x <- d * 2 * (binary.v(1:n, digits) - 0.5)
mx <- matrix(1/digits, 1, digits) %*% x
s <- matrix(1/(digits - 1), 1, digits)
- vx <- s %*% (x - matrix(mx, digits, n, byrow=T))^2
+ vx <- s %*% (x - matrix(mx, digits, n, byrow=TRUE))^2
as.vector(mx/sqrt(vx/digits))
}
library(MASS)
-options(echo = T,width=65, digits=5, height=9999)
+options(width=65, digits=5, height=9999)
library(lattice)
-trellis.device(postscript, file="ch05.ps", width=8, height=6, pointsize=9)
+pdf(file="ch05.pdf", width=8, height=6, pointsize=9)
rm(A, B) # precautionary clear-out
attach(shoes)
@@ -106,15 +106,15 @@ wilcox.test(A, mu = 10)
var.test(A, B)
-t.test(A, B, var.equal = T)
+t.test(A, B, var.equal = TRUE)
-t.test(A, B, var.equal = F)
+t.test(A, B, var.equal = FALSE)
wilcox.test(A, B)
-t.test(A, B, paired = T)
+t.test(A, B, paired = TRUE)
-wilcox.test(A, B, paired = T)
+wilcox.test(A, B, paired = TRUE)
detach()
par(mfrow = c(1, 2))
@@ -230,7 +230,7 @@ density(gal, n = 1, from = 20.833, to = 20.834, width = "SJ")$y
set.seed(101)
m <- 1000
res <- numeric(m)
-for (i in 1:m) res[i] <- median(sample(gal, replace = T))
+for (i in 1:m) res[i] <- median(sample(gal, replace = TRUE))
mean(res - median(gal))
sqrt(var(res))
@@ -249,7 +249,7 @@ boot.ci(gal.boot, conf = c(0.90, 0.95),
type = c("norm","basic","perc","bca"))
plot(gal.boot)
-if(F){ # bootstrap() is an S-PLUS function
+if(FALSE) { # bootstrap() is an S-PLUS function
gal.bt <- bootstrap(gal, median, seed = 101, B = 1000)
summary(gal.bt)
plot(gal.bt)
@@ -261,7 +261,7 @@ limits.bca(gal.bt)
sim.gen <- function(data, mle) {
n <- length(data)
- data[sample(n, replace = T)] + mle*rnorm(n)
+ data[sample(n, replace = TRUE)] + mle*rnorm(n)
}
gal.boot2 <- boot(gal, median, R = 1000,
sim = "parametric", ran.gen = sim.gen, mle = 0.5)
diff --git a/win32/deps/library/MASS/scripts/ch06.R b/win32/deps/library/MASS/scripts/ch06.R
index 854d349..aaea793 100644
--- a/win32/deps/library/MASS/scripts/ch06.R
+++ b/win32/deps/library/MASS/scripts/ch06.R
@@ -6,8 +6,8 @@
library(MASS)
library(lattice)
-options(echo = T,width=65, digits=5, height=9999)
-trellis.device(postscript, file="ch06.ps", width=8, height=6, pointsize=9)
+options(width=65, digits=5, height=9999)
+pdf(file="ch06.pdf", width=8, height=6, pointsize=9)
options(contrasts = c("contr.helmert", "contr.poly"))
@@ -137,18 +137,17 @@ abline(lqs(calls ~ year, phones), lty =3, col = 3)
# legend(locator(1), lty = 1:3, col = 1:3,
# legend = c("least squares", "M-estimate", "LTS"))
-summary(lm(calls ~ year, data = phones), cor = F)
-summary(rlm(calls ~ year, maxit = 50, data = phones), cor = F)
-summary(rlm(calls ~ year, scale.est = "proposal 2",
- data = phones), cor = F)
-summary(rlm(calls ~ year, data = phones, psi = psi.bisquare),
- cor = F)
+## cor = FALSE is the default in R
+summary(lm(calls ~ year, data = phones))
+summary(rlm(calls ~ year, maxit = 50, data = phones))
+summary(rlm(calls ~ year, scale.est = "proposal 2", data = phones))
+summary(rlm(calls ~ year, data = phones, psi = psi.bisquare))
lqs(calls ~ year, data = phones)
lqs(calls ~ year, data = phones, method = "lms")
lqs(calls ~ year, data = phones, method = "S")
-summary(rlm(calls ~ year, data = phones, method = "MM"), cor = F)
+summary(rlm(calls ~ year, data = phones, method = "MM"))
# library(robust) # S-PLUS only
# phones.lmr <- lmRob(calls ~ year, data = phones)
@@ -159,11 +158,11 @@ hills.lm
hills1.lm # omitting Knock Hill
rlm(time ~ dist + climb, data = hills)
summary(rlm(time ~ dist + climb, data = hills,
- weights = 1/dist^2, method = "MM"), cor = F)
+ weights = 1/dist^2, method = "MM"))
lqs(time ~ dist + climb, data = hills, nsamp = "exact")
summary(hills2.lm) # omitting Knock Hill
-summary(rlm(ispeed ~ grad, data = hills), cor = F)
-summary(rlm(ispeed ~ grad, data = hills, method="MM"), cor=F)
+summary(rlm(ispeed ~ grad, data = hills))
+summary(rlm(ispeed ~ grad, data = hills, method="MM"))
# summary(lmRob(ispeed ~ grad, data = hills))
lqs(ispeed ~ grad, data = hills)
@@ -199,12 +198,12 @@ options(contrasts=c("contr.treatment", "contr.poly"))
npk.aov1 <- aov(yield ~ block + N + K, data = npk)
summary.lm(npk.aov1)
se.contrast(npk.aov1, list(N == "0", N == "1"), data = npk)
-model.tables(npk.aov1, type = "means", se = T)
+model.tables(npk.aov1, type = "means", se = TRUE)
mp <- c("-", "+")
(NPK <- expand.grid(N = mp, P = mp, K = mp))
-if(F) {
+if(FALSE) { ## fac.design is part of S-PLUS.
blocks13 <- fac.design(levels = c(2, 2, 2),
factor= list(N=mp, P=mp, K=mp), rep = 3, fraction = 1/2)
@@ -223,6 +222,16 @@ factors <- list(S=mp, D=mp, H=mp, G=mp, R=mp, B=mp, P=mp)
replications(~ .^2, data=Bike)
}
+if(require("FrF2")) {
+NPK <- FrF2(8, factor.names = c("N", "P", "K"), default.levels = 0:1,
+ blocks = 2, replications = 3)
+print(NPK)
+print(as.data.frame(NPK))
+
+print(Bike <- FrF2(factor.names = c("S", "D", "H", "G", "R", "B", "P"),
+ default.levels = c("+", "-"), resolution = 3))
+print(replications(~ .^2, data=Bike))
+}
# 6.8 An unbalanced four-way layout
@@ -237,11 +246,12 @@ plot(Means, Vars, xlab = "Cell Means", ylab = "Cell Variances")
plot(Means, SD, xlab = "Cell Means", ylab = "Cell Std Devn.")
detach()
-boxcox(Days+1 ~ Eth*Sex*Age*Lrn, data = quine, singular.ok = T,
+## singular.ok = TRUE is the default in R
+boxcox(Days+1 ~ Eth*Sex*Age*Lrn, data = quine, singular.ok = TRUE,
lambda = seq(-0.05, 0.45, len = 20))
logtrans(Days ~ Age*Sex*Eth*Lrn, data = quine,
- alpha = seq(0.75, 6.5, len = 20), singular.ok = T)
+ alpha = seq(0.75, 6.5, len = 20), singular.ok = TRUE)
quine.hi <- aov(log(Days + 2.5) ~ .^4, quine)
quine.nxt <- update(quine.hi, . ~ . - Eth:Sex:Age:Lrn)
@@ -252,7 +262,7 @@ addterm(quine.lo, quine.hi, test = "F")
quine.stp <- stepAIC(quine.nxt,
scope = list(upper = ~Eth*Sex*Age*Lrn, lower = ~1),
- trace = F)
+ trace = FALSE)
quine.stp$anova
dropterm(quine.stp, test = "F")
@@ -273,7 +283,7 @@ cpus1 <- cpus
attach(cpus)
for(v in names(cpus)[2:7])
cpus1[[v]] <- cut(cpus[[v]], unique(quantile(cpus[[v]])),
- include.lowest = T)
+ include.lowest = TRUE)
detach()
boxcox(perf ~ syct + mmin + mmax + cach + chmin + chmax,
data = cpus1, lambda = seq(-0.25, 1, 0.1))
@@ -297,7 +307,7 @@ test.cpus <- function(fit)
sqrt(sum((log10(cpus2[-cpus.samp, "perf"]) -
predict(fit, cpus2[-cpus.samp,]))^2)/109)
test.cpus(cpus.lm)
-cpus.lm2 <- stepAIC(cpus.lm, trace=F)
+cpus.lm2 <- stepAIC(cpus.lm, trace=FALSE)
cpus.lm2$anova
test.cpus(cpus.lm2)
@@ -307,10 +317,10 @@ test.cpus(cpus.lm2)
immer.aov <- aov((Y1 + Y2)/2 ~ Var + Loc, data = immer)
summary(immer.aov)
-model.tables(immer.aov, type = "means", se = T, cterms = "Var")
+model.tables(immer.aov, type = "means", se = TRUE, cterms = "Var")
-if(F) {
-multicomp(immer.aov, plot = T)
+if(FALSE) {
+multicomp(immer.aov, plot = TRUE)
oats1 <- aov(Y ~ N + V + B, data = oats)
summary(oats1)
diff --git a/win32/deps/library/MASS/scripts/ch07.R b/win32/deps/library/MASS/scripts/ch07.R
index 9da4466..483bea9 100644
--- a/win32/deps/library/MASS/scripts/ch07.R
+++ b/win32/deps/library/MASS/scripts/ch07.R
@@ -5,8 +5,8 @@
# Chapter 7 Generalized Linear Models
library(MASS)
-options(echo = T,width=65, digits=5, height=9999)
-postscript(file="ch07.ps", width=8, height=6, pointsize=9)
+options(width=65, digits=5, height=9999)
+pdf(file="ch07.pdf", width=8, height=6, pointsize=9)
options(contrasts = c("contr.treatment", "contr.poly"))
ax.1 <- glm(Postwt ~ Prewt + Treat + offset(Prewt),
@@ -21,7 +21,7 @@ numdead <- c(1, 4, 9, 13, 18, 20, 0, 2, 6, 10, 12, 16)
sex <- factor(rep(c("M", "F"), c(6, 6)))
SF <- cbind(numdead, numalive = 20 - numdead)
budworm.lg <- glm(SF ~ sex*ldose, family = binomial)
-summary(budworm.lg, cor = F)
+summary(budworm.lg)
plot(c(1,32), c(0,1), type = "n", xlab = "dose",
ylab = "prob", log = "x")
@@ -60,28 +60,29 @@ bwt <- data.frame(low = factor(low), age, lwt, race,
detach(); rm(race, ptd, ftv)
birthwt.glm <- glm(low ~ ., family = binomial, data = bwt)
-summary(birthwt.glm, cor = F)
-birthwt.step <- stepAIC(birthwt.glm, trace = F)
+summary(birthwt.glm)
+birthwt.step <- stepAIC(birthwt.glm, trace = FALSE)
birthwt.step$anova
birthwt.step2 <- stepAIC(birthwt.glm, ~ .^2 + I(scale(age)^2)
- + I(scale(lwt)^2), trace = F)
+ + I(scale(lwt)^2), trace = FALSE)
birthwt.step2$anova
-summary(birthwt.step2, cor = F)$coef
+summary(birthwt.step2)$coef
table(bwt$low, predict(birthwt.step2) > 0)
## R has a similar gam() in package gam and a different gam() in package mgcv
-library(gam)
-attach(bwt)
-age1 <- age*(ftv=="1"); age2 <- age*(ftv=="2+")
-birthwt.gam <- gam(low ~ s(age) + s(lwt) + smoke + ptd +
- ht + ui + ftv + s(age1) + s(age2) + smoke:ui, binomial,
- bwt, bf.maxit=25)
-summary(birthwt.gam)
-table(low, predict(birthwt.gam) > 0)
-par(mfrow = c(2, 2))
-if(interactive()) plot(birthwt.gam, ask = TRUE, se = TRUE)
-par(mfrow = c(1, 1))
-detach()
+if(require(gam)) {
+ attach(bwt)
+ age1 <- age*(ftv=="1"); age2 <- age*(ftv=="2+")
+ birthwt.gam <- gam(low ~ s(age) + s(lwt) + smoke + ptd +
+ ht + ui + ftv + s(age1) + s(age2) + smoke:ui, binomial,
+ bwt, bf.maxit=25)
+ print(summary(birthwt.gam))
+ print(table(low, predict(birthwt.gam) > 0))
+ par(mfrow = c(2, 2))
+ if(interactive()) plot(birthwt.gam, ask = TRUE, se = TRUE)
+ par(mfrow = c(1, 1))
+ detach()
+}
library(mgcv)
attach(bwt)
@@ -99,12 +100,12 @@ detach()
names(housing)
house.glm0 <- glm(Freq ~ Infl*Type*Cont + Sat,
family = poisson, data = housing)
-summary(house.glm0, cor = F)
+summary(house.glm0)
addterm(house.glm0, ~. + Sat:(Infl+Type+Cont), test = "Chisq")
house.glm1 <- update(house.glm0, . ~ . + Sat:(Infl+Type+Cont))
-summary(house.glm1, cor = F)
+summary(house.glm1)
1 - pchisq(deviance(house.glm1), house.glm1$df.resid)
dropterm(house.glm1, test = "Chisq")
@@ -114,7 +115,7 @@ addterm(house.glm1, ~. + Sat:(Infl+Type+Cont)^2, test = "Chisq")
hnames <- lapply(housing[, -5], levels) # omit Freq
house.pm <- predict(house.glm1, expand.grid(hnames),
type = "response") # poisson means
-house.pm <- matrix(house.pm, ncol = 3, byrow = T,
+house.pm <- matrix(house.pm, ncol = 3, byrow = TRUE,
dimnames = list(NULL, hnames[[1]]))
house.pr <- house.pm/drop(house.pm %*% rep(1, 3))
cbind(expand.grid(hnames[-1]), round(house.pr, 2))
@@ -147,7 +148,7 @@ house.pr1 <- predict(house.plr, expand.grid(hnames[-1]),
type = "probs")
cbind(expand.grid(hnames[-1]), round(house.pr1, 2))
-Fr <- matrix(housing$Freq, ncol = 3, byrow = T)
+Fr <- matrix(housing$Freq, ncol = 3, byrow = TRUE)
2 * sum(Fr * log(house.pr/house.pr1))
house.plr2 <- stepAIC(house.plr, ~.^2)
diff --git a/win32/deps/library/MASS/scripts/ch08.R b/win32/deps/library/MASS/scripts/ch08.R
index beafe82..4647707 100644
--- a/win32/deps/library/MASS/scripts/ch08.R
+++ b/win32/deps/library/MASS/scripts/ch08.R
@@ -6,8 +6,8 @@
library(MASS)
library(lattice)
-options(echo = T, width=65, digits=5, height=9999)
-trellis.device(postscript, file="ch08.ps", width=8, height=6, pointsize=9)
+options(width=65, digits=5, height=9999)
+pdf(file="ch08.pdf", width=8, height=6, pointsize=9)
# From Chapter 6, for comparisons
@@ -25,10 +25,10 @@ cpus1 <- cpus
attach(cpus)
for(v in names(cpus)[2:7])
cpus1[[v]] <- cut(cpus[[v]], unique(quantile(cpus[[v]])),
- include.lowest = T)
+ include.lowest = TRUE)
detach()
cpus.lm <- lm(log10(perf) ~ ., data=cpus1[cpus.samp, 2:8])
-cpus.lm2 <- stepAIC(cpus.lm, trace=F)
+cpus.lm2 <- stepAIC(cpus.lm, trace=FALSE)
res2 <- log10(cpus1[-cpus.samp, "perf"]) -
predict(cpus.lm2, cpus1[-cpus.samp,])
cpus2 <- cpus[, 2:8] # excludes names, authors' predictions
@@ -55,7 +55,7 @@ detach()
wtloss.st <- c(b0 = 90, b1 = 95, th = 120)
wtloss.fm <- nls(Weight ~ b0 + b1*2^(-Days/th),
- data = wtloss, start = wtloss.st, trace = T)
+ data = wtloss, start = wtloss.st, trace = TRUE)
wtloss.fm
expn <- function(b0, b1, th, x) {
@@ -68,7 +68,7 @@ expn <- function(b0, b1, th, x) {
}
wtloss.gr <- nls(Weight ~ expn(b0, b1, th, Days),
- data = wtloss, start = wtloss.st, trace = T)
+ data = wtloss, start = wtloss.st, trace = TRUE)
expn1 <- deriv(y ~ b0 + b1 * 2^(-x/th), c("b0", "b1", "th"),
function(b0, b1, th, x) {})
@@ -79,7 +79,7 @@ negexp <- selfStart(model = ~ b0 + b1*exp(-x/th),
template = function(x, b0, b1, th) {})
wtloss.ss <- nls(Weight ~ negexp(Days, B0, B1, theta),
- data = wtloss, trace = T)
+ data = wtloss, trace = TRUE)
# 8.3 Non-linear fitted model objects and method functions
@@ -109,7 +109,7 @@ detach()
xyplot(Yhat ~ Conc | Strip, Muscle, as.table = TRUE,
ylim = range(c(Muscle$Yhat, Muscle$logLength), na.rm = TRUE),
- subscripts = T, xlab = "Calcium Chloride concentration (mM)",
+ subscripts = TRUE, xlab = "Calcium Chloride concentration (mM)",
ylab = "log(Length in mm)", panel =
function(x, y, subscripts, ...) {
lines(spline(x, y))
@@ -143,7 +143,7 @@ b0 <- coef(fm0)
names(b0) <- c("b1", "b2")
b0
storm.fm <- nls(Time ~ b1*Viscosity/(Wt-b2), data = stormer,
- start = b0, trace = T)
+ start = b0, trace = TRUE)
bc <- coef(storm.fm)
se <- sqrt(diag(vcov(storm.fm)))
@@ -169,8 +169,8 @@ qf(0.95, 2, 21)
plot(b1, b2, type = "n")
lev <- c(1, 2, 5, 7, 10, 15, 20)
-contour(b1, b2, fstat, levels = lev, labex = 0.75, lty = 2, add = T)
-contour(b1, b2, fstat, levels = qf(0.95,2,21), add = T, labex = 0)
+contour(b1, b2, fstat, levels = lev, labex = 0.75, lty = 2, add = TRUE)
+contour(b1, b2, fstat, levels = qf(0.95,2,21), add = TRUE, labex = 0)
text(31.6, 0.3, labels = "95% CR", adj = 0, cex = 0.75)
points(bc[1], bc[2], pch = 3, mkh = 0.1)
detach()
@@ -283,7 +283,7 @@ cpus.bruto$type
cpus.bruto$df
# examine the fitted functions
par(mfrow = c(3, 2))
-Xp <- matrix(sapply(cpus2[cpus.samp, 1:6], mean), 100, 6, byrow = T)
+Xp <- matrix(sapply(cpus2[cpus.samp, 1:6], mean), 100, 6, byrow = TRUE)
for(i in 1:6) {
xr <- sapply(cpus2, range)
Xp1 <- Xp; Xp1[, i] <- seq(xr[1, i], xr[2, i], len = 100)
@@ -301,7 +301,7 @@ showcuts <- function(obj)
showcuts(cpus.mars)
test2(cpus.mars)
# examine the fitted functions
-Xp <- matrix(sapply(cpus2[cpus.samp, 1:6], mean), 100, 6, byrow = T)
+Xp <- matrix(sapply(cpus2[cpus.samp, 1:6], mean), 100, 6, byrow = TRUE)
for(i in 1:6) {
xr <- sapply(cpus2, range)
Xp1 <- Xp; Xp1[, i] <- seq(xr[1, i], xr[2, i], len = 100)
@@ -373,7 +373,7 @@ cpus.ppr2 <- ppr(log10(perf) ~ ., data = cpus2[cpus.samp,],
test.cpus(cpus.ppr2)
res3 <- log10(cpus2[-cpus.samp, "perf"]) -
predict(cpus.ppr, cpus2[-cpus.samp,])
-wilcox.test(res2^2, res3^2, paired = T, alternative = "greater")
+wilcox.test(res2^2, res3^2, paired = TRUE, alternative = "greater")
# 8.10 Neural networks
@@ -383,11 +383,11 @@ attach(rock)
area1 <- area/10000; peri1 <- peri/10000
rock1 <- data.frame(perm, area = area1, peri = peri1, shape)
rock.nn <- nnet(log(perm) ~ area + peri + shape, rock1,
- size = 3, decay = 1e-3, linout = T, skip = T,
- maxit = 1000, Hess = T)
+ size = 3, decay = 1e-3, linout = TRUE, skip = TRUE,
+ maxit = 1000, Hess = TRUE)
sum((log(perm) - predict(rock.nn))^2)
detach()
-eigen(rock.nn$Hessian, T)$values # rock.nn$Hessian in R
+eigen(rock.nn$Hessian, TRUE)$values # rock.nn$Hessian in R
Xp <- expand.grid(area = seq(0.1, 1.2, 0.05),
peri = seq(0, 0.5, 0.02), shape = 0.2)
@@ -408,17 +408,17 @@ test.cpus <- function(fit)
sqrt(sum((log10(cpus3[-cpus.samp, "perf"]) -
predict(fit, cpus3[-cpus.samp,]))^2)/109)
cpus.nn1 <- nnet(log10(perf) ~ ., cpus3[cpus.samp,],
- linout = T, skip = T, size = 0)
+ linout = TRUE, skip = TRUE, size = 0)
test.cpus(cpus.nn1)
-cpus.nn2 <- nnet(log10(perf) ~ ., cpus3[cpus.samp,], linout = T,
- skip = T, size = 4, decay = 0.01, maxit = 1000)
+cpus.nn2 <- nnet(log10(perf) ~ ., cpus3[cpus.samp,], linout = TRUE,
+ skip = TRUE, size = 4, decay = 0.01, maxit = 1000)
test.cpus(cpus.nn2)
-cpus.nn3 <- nnet(log10(perf) ~ ., cpus3[cpus.samp,], linout = T,
- skip = T, size = 10, decay = 0.01, maxit = 1000)
+cpus.nn3 <- nnet(log10(perf) ~ ., cpus3[cpus.samp,], linout = TRUE,
+ skip = TRUE, size = 10, decay = 0.01, maxit = 1000)
test.cpus(cpus.nn3)
-cpus.nn4 <- nnet(log10(perf) ~ ., cpus3[cpus.samp,], linout = T,
- skip = T, size = 25, decay = 0.01, maxit = 1000)
+cpus.nn4 <- nnet(log10(perf) ~ ., cpus3[cpus.samp,], linout = TRUE,
+ skip = TRUE, size = 25, decay = 0.01, maxit = 1000)
test.cpus(cpus.nn4)
CVnn.cpus <- function(formula, data = cpus3[cpus.samp, ],
@@ -434,7 +434,7 @@ CVnn.cpus <- function(formula, data = cpus3[cpus.samp, ],
for (i in sort(unique(ri))) {
cat(" ", i, sep="")
for(rep in 1:nreps) {
- learn <- nnet(formula, data[ri !=i,], trace=F, ...)
+ learn <- nnet(formula, data[ri !=i,], trace=FALSE, ...)
res[ri == i] <- res[ri == i] +
predict(learn, data[ri == i,])
}
@@ -452,6 +452,6 @@ CVnn.cpus <- function(formula, data = cpus3[cpus.samp, ],
cbind(size=size, decay=lambda, fit=sqrt(choice/100))
}
CVnn.cpus(log10(perf) ~ ., data = cpus3[cpus.samp,],
- linout = T, skip = T, maxit = 1000)
+ linout = TRUE, skip = TRUE, maxit = 1000)
# End of ch08
diff --git a/win32/deps/library/MASS/scripts/ch09.R b/win32/deps/library/MASS/scripts/ch09.R
index 1b9b122..d22f7ed 100644
--- a/win32/deps/library/MASS/scripts/ch09.R
+++ b/win32/deps/library/MASS/scripts/ch09.R
@@ -5,8 +5,8 @@
# Chapter 9 Tree-based Methods
library(MASS)
-postscript(file="ch09.ps", width=8, height=6, pointsize=9)
-options(echo = TRUE, digits=5)
+pdf(file="ch09.pdf", width=8, height=6, pointsize=9)
+options(digits=5)
library(rpart)
diff --git a/win32/deps/library/MASS/scripts/ch10.R b/win32/deps/library/MASS/scripts/ch10.R
index c7c70cc..defcfad 100644
--- a/win32/deps/library/MASS/scripts/ch10.R
+++ b/win32/deps/library/MASS/scripts/ch10.R
@@ -6,8 +6,8 @@
library(MASS)
library(lattice)
-trellis.device(postscript, file="ch10.ps", width=8, height=6, pointsize=9)
-options(echo=T, width=65, digits=5)
+pdf(file="ch10.pdf", width=8, height=6, pointsize=9)
+options(width=65, digits=5)
library(nlme)
# 10.1 Linear models
@@ -23,9 +23,9 @@ xyplot(Y ~ EP | No, data = petrol,
Petrol <- petrol
names(Petrol)
-Petrol[, 2:5] <- scale(Petrol[, 2:5], scale = F)
+Petrol[, 2:5] <- scale(Petrol[, 2:5], scale = FALSE)
pet1.lm <- lm(Y ~ No/EP - 1, Petrol)
-matrix(round(coef(pet1.lm), 2), 2, 10, byrow = T,
+matrix(round(coef(pet1.lm), 2), 2, 10, byrow = TRUE,
dimnames = list(c("b0", "b1"), levels(Petrol$No)))
pet2.lm <- lm(Y ~ No - 1 + EP, Petrol)
@@ -57,20 +57,19 @@ classMeans <- tapply(IQ, class, mean)
nl1$IQave <- classMeans[as.character(class)]
detach()
cen <- c("IQ", "IQave", "SES")
-nl1[cen] <- scale(nl1[cen], center = T, scale = F)
+nl1[cen] <- scale(nl1[cen], center = TRUE, scale = FALSE)
options(contrasts = c("contr.treatment", "contr.poly"))
nl.lme <- lme(lang ~ IQ*COMB + IQave + SES,
random = ~ IQ | class, data = nl1)
summary(nl.lme)
-summary(lm(lang ~ IQ*COMB + SES + class, data = nl1,
- singular.ok = T), cor = F)
+## singular.ok = TRUE is the default in R
+summary(lm(lang ~ IQ*COMB + SES + class, data = nl1, singular.ok = TRUE))
nl2 <- cbind(aggregate(nl1[c(1,7)], list(class = nl1$class), mean),
unique(nl1[c("class", "COMB", "GS")]))
-summary(lm(lang ~ IQave + COMB, data = nl2, weights = GS),
- cor = F)
+summary(lm(lang ~ IQave + COMB, data = nl2, weights = GS))
sitka.lme <- lme(size ~ treat*ordered(Time),
random = ~1 | tree, data = Sitka, method = "ML")
@@ -84,13 +83,13 @@ anova(sitka.lme, sitka.lme2)
# fitted curves
matrix(fitted(sitka.lme2, level = 0)[c(301:305, 1:5)],
- 2, 5, byrow = T,
+ 2, 5, byrow = TRUE,
dimnames = list(c("control", "ozone"), unique(Sitka$Time)))
# 10.2 Classic nested designs
-if(F) {
+if(FALSE) {
summary(raov(Conc ~ Lab/Bat, data = coop, subset = Spc=="S1"))
is.random(coop) <- T
@@ -106,7 +105,7 @@ varcomp(Conc ~ Lab/Bat, data = coop, subset = Spc=="S1",
#oats <- oats # make a local copy: needed in S-PLUS
oats$Nf <- ordered(oats$N, levels = sort(levels(oats$N)))
-oats.aov <- aov(Y ~ Nf*V + Error(B/V), data = oats, qr = T)
+oats.aov <- aov(Y ~ Nf*V + Error(B/V), data = oats, qr = TRUE)
summary(oats.aov)
summary(oats.aov, split = list(Nf = list(L = 1, Dev = 2:3)))
@@ -116,8 +115,8 @@ oats.pr <- proj(oats.aov)
qqnorm(oats.pr[[4]][,"Residuals"], ylab = "Stratum 4 residuals")
qqline(oats.pr[[4]][,"Residuals"])
-oats.aov <- aov(Y ~ N + V + Error(B/V), data = oats, qr = T)
-model.tables(oats.aov, type = "means", se = T)
+oats.aov <- aov(Y ~ N + V + Error(B/V), data = oats, qr = TRUE)
+model.tables(oats.aov, type = "means", se = TRUE)
# we can get the unimplemented standard errors from
se.contrast(oats.aov, list(N == "0.0cwt", N == "0.2cwt"), data=oats)
se.contrast(oats.aov, list(V == "Golden.rain", V == "Victory"), data=oats)
@@ -139,7 +138,7 @@ options(contrasts = c("contr.treatment", "contr.poly"))
sitka.nlme <- nlme(size ~ A + B * (1 - exp(-(Time-100)/C)),
fixed = list(A ~ treat, B ~ treat, C ~ 1),
random = A + B ~ 1 | tree, data = Sitka,
- start = list(fixed = c(2, 0, 4, 0, 100)), verbose = T)
+ start = list(fixed = c(2, 0, 4, 0, 100)), verbose = TRUE)
summary(sitka.nlme)
@@ -185,7 +184,7 @@ summary(R.nlme2)
xyplot(BPchange ~ log(Dose) | Animal * Treatment, Rabbit,
xlab = "log(Dose) of Phenylbiguanide",
ylab = "Change in blood pressure (mm Hg)",
- subscripts = T, aspect = "xy", panel =
+ subscripts = TRUE, aspect = "xy", panel =
function(x, y, subscripts) {
panel.grid()
panel.xyplot(x, y)
@@ -196,18 +195,13 @@ xyplot(BPchange ~ log(Dose) | Animal * Treatment, Rabbit,
# 10.4 Generalized linear mixed models
-# bacteria <- bacteria # needed in S-PLUS
contrasts(bacteria$trt) <- structure(contr.sdif(3),
dimnames = list(NULL, c("drug", "encourage")))
-summary(glm(y ~ trt * week, binomial, data = bacteria),
- cor = F)
-summary(glm(y ~ trt + week, binomial, data = bacteria),
- cor = F)
+summary(glm(y ~ trt * week, binomial, data = bacteria))
+summary(glm(y ~ trt + week, binomial, data = bacteria))
-summary(glm(y ~ lbase*trt + lage + V4, family = poisson,
- data = epil), cor = F)
+summary(glm(y ~ lbase*trt + lage + V4, family = poisson, data = epil))
-# epil <- epil # needed in S-PLUS
epil2 <- epil[epil$period == 1, ]
epil2["period"] <- rep(0, 59); epil2["y"] <- epil2["base"]
epil["time"] <- 1; epil2["time"] <- 4
@@ -221,7 +215,7 @@ epil3$pred <- factor(epil3$pred, labels = c("base", "placebo", "drug"))
contrasts(epil3$pred) <- structure(contr.sdif(3),
dimnames = list(NULL, c("placebo-base", "drug-placebo")))
summary(glm(y ~ pred + factor(subject) + offset(log(time)),
- family = poisson, data = epil3), cor = F)
+ family = poisson, data = epil3))
glm(y ~ factor(subject), family = poisson, data = epil)
@@ -235,10 +229,10 @@ coxph(Surv(Time, unclass(y)) ~ I(week > 2) + strata(ID),
data = bacteria, method = "exact")
fit <- glm(y ~ trt + I(week> 2), binomial, data = bacteria)
-summary(fit, cor = F)
+summary(fit)
sum(residuals(fit, type = "pearson")^2)
-if(F) { # very slow
+if(FALSE) { # very slow
library(GLMMGibbs)
# declare a random intercept for each subject
epil$subject <- Ra(data = factor(epil$subject))
@@ -262,6 +256,7 @@ summary(glmmPQL(y ~ pred, random = ~1 | subject,
# 10.5 GEE models
+if(FALSE) {
## modified for YAGS 3.21-3
library(yags)
attach(bacteria)
@@ -273,6 +268,7 @@ attach(epil)
yags(y ~ lbase*trt + lage + V4, family = poisson, alphainit=0,
id = subject, corstr = "exchangeable")
detach("epil")
+}
options(contrasts = c("contr.sum", "contr.poly"))
library(gee)
diff --git a/win32/deps/library/MASS/scripts/ch11.R b/win32/deps/library/MASS/scripts/ch11.R
index 4679164..a324e44 100644
--- a/win32/deps/library/MASS/scripts/ch11.R
+++ b/win32/deps/library/MASS/scripts/ch11.R
@@ -5,8 +5,8 @@
# Chapter 11 Exploratory Multivariate Analysis
library(MASS)
-postscript(file="ch11.ps", width=8, height=6, pointsize=9)
-options(echo=T, width=65, digits=5)
+pdf(file="ch11.pdf", width=8, height=6, pointsize=9)
+options(width=65, digits=5)
# 11.1 Visualization methods
@@ -14,7 +14,7 @@ options(echo=T, width=65, digits=5)
# ir <- rbind(iris[,,1], iris[,,2], iris[,,3])
ir <- rbind(iris3[,,1], iris3[,,2], iris3[,,3])
ir.species <- factor(c(rep("s", 50), rep("c", 50), rep("v", 50)))
-(ir.pca <- princomp(log(ir), cor = T))
+(ir.pca <- princomp(log(ir), cor = TRUE))
summary(ir.pca)
plot(ir.pca)
ir.pc <- predict(ir.pca)
@@ -31,14 +31,22 @@ loadings(lcrabs.pca)
lcrabs.pc <- predict(lcrabs.pca)
dimnames(lcrabs.pc) <- list(NULL, paste("PC", 1:5, sep = ""))
-if(F) { # needs interaction with XGobi
+if(FALSE) { # needs interaction with XGobi, or, better, rggobi
library(xgobi)
xgobi(lcrabs, colors = c("SkyBlue", "SlateBlue", "Orange",
"Red")[rep(1:4, each = 50)])
xgobi(lcrabs, glyphs = 12 + 5*rep(0:3, each = 50, 4))
+
+library(rggobi)
+g <- ggobi(lcrabs)
+d <- displays(g)[[1]]
+pmode(d) <- "2D Tour"
+crabs.grp <- factor(c("B", "b", "O", "o")[rep(1:4, each = 50)])
+glyph_colour(g$lcrabs) <- crabs.grp
+colorscheme(g) <- "Paired 4"
}
-ir.scal <- cmdscale(dist(ir), k = 2, eig = T)
+ir.scal <- cmdscale(dist(ir), k = 2, eig = TRUE)
ir.scal$points[, 2] <- -ir.scal$points[, 2]
eqscplot(ir.scal$points, type = "n")
text(ir.scal$points, labels = as.character(ir.species),
@@ -69,7 +77,7 @@ eqscplot(lcrabs.sam$points, type = "n", xlab = "", ylab = "")
text(lcrabs.sam$points, labels = as.character(crabs.grp))
fgl.iso <- isoMDS(dist(as.matrix(fgl[-40, -10])))
-eqscplot(fgl.iso$points, type = "n", xlab = "", ylab = "", axes = F)
+eqscplot(fgl.iso$points, type = "n", xlab = "", ylab = "", axes = FALSE)
# either
# for(i in seq(along = levels(fgl$type))) {
# set <- fgl$type[-40] == levels(fgl$type)[i]
@@ -93,14 +101,14 @@ plot(crabs.som)
bins <- as.numeric(knn1(crabs.som$code, lcrabs, 0:47))
plot(crabs.som$grid, type = "n")
symbols(crabs.som$grid$pts[, 1], crabs.som$grid$pts[, 2],
- circles = rep(0.4, 48), inches = F, add = T)
+ circles = rep(0.4, 48), inches = FALSE, add = TRUE)
text(crabs.som$grid$pts[bins, ] + rnorm(400, 0, 0.1),
as.character(crabs.grp))
crabs.som2 <- SOM(lcrabs, gr); plot(crabs.som2)
state <- state.x77[, 2:7]; row.names(state) <- state.abb
-biplot(princomp(state, cor = T), pc.biplot = T, cex = 0.7,
+biplot(princomp(state, cor = TRUE), pc.biplot = TRUE, cex = 0.7,
expand = 0.8)
library(fastICA)
@@ -112,7 +120,7 @@ for(i in 1:nICA) boxplot(Z[, i] ~ crabs.grp)
par(mfrow = c(1, 1))
-# S: stars(state.x77[, c(7, 4, 6, 2, 5, 3)], byrow = T)
+# S: stars(state.x77[, c(7, 4, 6, 2, 5, 3)], byrow = TRUE)
stars(state.x77[, c(7, 4, 6, 2, 5, 3)])
parcoord(state.x77[, c(7, 4, 6, 2, 5, 3)])
@@ -165,25 +173,9 @@ fanny(swiss.px, 3)
## use, and the code given in the first printing does not work in R's
## mclust-2.x.'
##
-## And now mclust has been given a more restrictive licence, so
-## this code is not run by default.
-if(FALSE) {
-library(mclust) # 2.x equivalent commands
-h <- hc(modelName = "VVV", swiss.x)
-print(mh <- as.vector(hclass(h, 3)))
-z <- me(modelName = "VVV", swiss.x, z = 0.5*(unmap(mh)+1/3))
-eqscplot(swiss.px[, 1:2], type = "n",
- xlab = "first principal component",
- ylab = "second principal component")
-text(swiss.px[, 1:2], labels = max.col(z$z))
-vals <- EMclust(swiss.x) # all possible models, 0:9 clusters.
-print(sm <- summary(vals, swiss.x))
-eqscplot(swiss.px[, 1:2], type = "n",
- xlab = "first principal component",
- ylab = "second principal component")
-text(swiss.px[, 1:2], labels = sm$classification)
-}
+## And later mclust was given a restrictive licence, so this example
+## has been removed.
# 11.3 Factor analysis
@@ -194,16 +186,16 @@ ability.FA
#summary(ability.FA)
round(loadings(ability.FA) %*% t(loadings(ability.FA)) +
diag(ability.FA$uniq), 3)
-# loadings(rotate(ability.FA, rotation = "oblimin"))
-if(FALSE) {
-par(pty = "s")
-L <- loadings(ability.FA)
-eqscplot(L, xlim = c(0,1), ylim = c(0,1))
-if(interactive()) identify(L, dimnames(L)[[1]])
-oblirot <- rotate(loadings(ability.FA), rotation = "oblimin")
-naxes <- solve(oblirot$tmat)
-arrows(rep(0, 2), rep(0, 2), naxes[,1], naxes[,2])
+if(require("GPArotation")) {
+# loadings(rotate(ability.FA, rotation = "oblimin"))
+ L <- loadings(ability.FA)
+ print(oblirot <- oblimin(L))
+ par(pty = "s")
+ eqscplot(L, xlim = c(0,1), ylim = c(0,1))
+ if(interactive()) identify(L, dimnames(L)[[1]])
+ naxes <- oblirot$Th
+ arrows(rep(0, 2), rep(0, 2), naxes[,1], naxes[,2])
}
@@ -211,9 +203,9 @@ arrows(rep(0, 2), rep(0, 2), naxes[,1], naxes[,2])
caith <- as.matrix(caith)
names(dimnames(caith)) <- c("eyes", "hair")
-mosaicplot(caith, color = T)
+mosaicplot(caith, color = TRUE)
House <- xtabs(Freq ~ Type + Infl + Cont + Sat, housing)
-mosaicplot(House, color = T)
+mosaicplot(House, color = TRUE)
corresp(caith)
@@ -225,7 +217,7 @@ plot(corresp(caith2, nf = 2), type = "rows"); title("rows")
plot(corresp(caith2, nf = 2), type = "col"); title("columns")
par(mfrow = c(1, 1))
-farms.mca <- mca(farms, abbrev = T) # Use levels as names
+farms.mca <- mca(farms, abbrev = TRUE) # Use levels as names
plot(farms.mca, cex = rep(0.7, 2))
# End of ch11
diff --git a/win32/deps/library/MASS/scripts/ch12.R b/win32/deps/library/MASS/scripts/ch12.R
index f42c811..863843e 100644
--- a/win32/deps/library/MASS/scripts/ch12.R
+++ b/win32/deps/library/MASS/scripts/ch12.R
@@ -5,8 +5,8 @@
# Chapter 12 Classification
library(MASS)
-postscript(file="ch12.ps", width=8, height=6, pointsize=9)
-options(echo=T, width=65, digits=5)
+pdf(file="ch12.pdf", width=8, height=6, pointsize=9)
+options(width=65, digits=5)
library(class)
library(nnet)
@@ -46,7 +46,6 @@ perp <- function(x, y) {
abline(c(m[2] - s*m[1], s))
invisible()
}
-# For R replace @means by $means
cr.m <- lda(cr.t, crabs$sex)$means
points(cr.m, pch = 3, mkh = 0.3)
perp(cr.m[1, ], cr.m[2, ])
@@ -58,7 +57,7 @@ Xcon <- matrix(c(rep(x,length(y)),
rep(y, rep(length(x), length(y)))),,2)
cr.pr <- predict(cr.lda, Xcon)$post[, c("B", "O")] %*% c(1,1)
contour(x, y, matrix(cr.pr, length(x), length(y)),
- levels = 0.5, labex = 0, add = T, lty= 3)
+ levels = 0.5, labex = 0, add = TRUE, lty= 3)
for(i in c("O", "o", "B", "b"))
print(var(lcrabs[crabs.grp == i, ]))
@@ -104,10 +103,10 @@ predplot <- function(object, main="", len = 100, ...)
Z <- predict(object, cushT, ...); zp <- as.numeric(Z$class)
zp <- Z$post[,3] - pmax(Z$post[,2], Z$post[,1])
contour(exp(xp), exp(yp), matrix(zp, len),
- add = T, levels = 0, labex = 0)
+ add = TRUE, levels = 0, labex = 0)
zp <- Z$post[,1] - pmax(Z$post[,2], Z$post[,3])
contour(exp(xp), exp(yp), matrix(zp, len),
- add = T, levels = 0, labex = 0)
+ add = TRUE, levels = 0, labex = 0)
invisible()
}
@@ -121,15 +120,15 @@ cushplot <- function(xp, yp, Z)
labels = as.character(Cushings$Type[set]), col = 2 + il) }
zp <- Z[, 3] - pmax(Z[, 2], Z[, 1])
contour(exp(xp), exp(yp), matrix(zp, np),
- add = T, levels = 0, labex = 0)
+ add = TRUE, levels = 0, labex = 0)
zp <- Z[, 1] - pmax(Z[, 2], Z[, 3])
contour(exp(xp), exp(yp), matrix(zp, np),
- add = T, levels = 0, labex = 0)
+ add = TRUE, levels = 0, labex = 0)
invisible()
}
cush <- log(as.matrix(Cushings[, -3]))
-tp <- Cushings$Type[1:21, drop = T]
+tp <- Cushings$Type[1:21, drop = TRUE]
cush.lda <- lda(cush[1:21,], tp); predplot(cush.lda, "LDA")
cush.qda <- qda(cush[1:21,], tp); predplot(cush.qda, "QDA")
predplot(cush.qda, "QDA (predictive)", method = "predictive")
@@ -155,16 +154,16 @@ for(il in 1:4) {
set <- Cushings$Type==levels(Cushings$Type)[il]
text(cush[set, 1], cush[set, 2],
labels = as.character(Cushings$Type[set]), col = 2 + il) }
-par(cex = 1.5); partition.tree(cush.tr, add = T); par(cex = 1)
+par(cex = 1.5); partition.tree(cush.tr, add = TRUE); par(cex = 1)
# 12.3 Non-parametric rules
-Z <- knn(scale(cush[1:21, ], F, c(3.4, 5.7)),
- scale(cushT, F, c(3.4, 5.7)), tp)
+Z <- knn(scale(cush[1:21, ], FALSE, c(3.4, 5.7)),
+ scale(cushT, FALSE, c(3.4, 5.7)), tp)
cushplot(xp, yp, class.ind(Z))
-Z <- knn(scale(cush[1:21, ], F, c(3.4, 5.7)),
- scale(cushT, F, c(3.4, 5.7)), tp, k = 3)
+Z <- knn(scale(cush[1:21, ], FALSE, c(3.4, 5.7)),
+ scale(cushT, FALSE, c(3.4, 5.7)), tp, k = 3)
cushplot(xp, yp, class.ind(Z))
@@ -181,7 +180,7 @@ pltnn <- function(main, ...) {
plt.bndry <- function(size=0, decay=0, ...)
{
- cush.nn <- nnet(cush, tpi, skip=T, softmax=T, size=size,
+ cush.nn <- nnet(cush, tpi, skip=TRUE, softmax=TRUE, size=size,
decay=decay, maxit=1000)
invisible(b1(predict(cush.nn, cushT), ...))
}
@@ -190,10 +189,10 @@ b1 <- function(Z, ...)
{
zp <- Z[,3] - pmax(Z[,2], Z[,1])
contour(exp(xp), exp(yp), matrix(zp, np),
- add=T, levels=0, labex=0, ...)
+ add=TRUE, levels=0, labex=0, ...)
zp <- Z[,1] - pmax(Z[,3], Z[,2])
contour(exp(xp), exp(yp), matrix(zp, np),
- add=T, levels=0, labex=0, ...)
+ add=TRUE, levels=0, labex=0, ...)
}
cush <- cush[1:21,]; tpi <- class.ind(tp)
@@ -221,10 +220,9 @@ pltnn("Many local maxima")
Z <- matrix(0, nrow(cushT), ncol(tpi))
for(iter in 1:20) {
set.seed(iter)
- cush.nn <- nnet(cush, tpi, skip = T, softmax = T, size = 3,
- decay = 0.01, maxit = 1000, trace = F)
+ cush.nn <- nnet(cush, tpi, skip = TRUE, softmax = TRUE, size = 3,
+ decay = 0.01, maxit = 1000, trace = FALSE)
Z <- Z + predict(cush.nn, cushT)
-# In R replace @ by $ in next line.
cat("final value", format(round(cush.nn$value,3)), "\n")
b1(predict(cush.nn, cushT), col = 2, lwd = 0.5)
}
@@ -278,7 +276,7 @@ CVtest <- function(fitfn, predfn, ...)
res.multinom <- CVtest(
function(x, ...) multinom(type ~ ., fgl[x, ], ...),
function(obj, x) predict(obj, fgl[x, ], type = "class"),
- maxit = 1000, trace = F )
+ maxit = 1000, trace = FALSE)
con(true = fgl$type, predicted = res.multinom)
@@ -298,7 +296,7 @@ fgl0 <- fgl[ , -10] # drop type
res } -> res.knn1
con(true = fgl$type, predicted = res.knn1)
-res.lb <- knn(fgl0, fgl0, fgl$type, k = 3, prob = T, use.all = F)
+res.lb <- knn(fgl0, fgl0, fgl$type, k = 3, prob = TRUE, use.all = FALSE)
table(attr(res.lb, "prob"))
library(rpart)
@@ -334,7 +332,7 @@ CVnn2 <- function(formula, data,
for (i in sort(unique(ri))) {
if(verbose > 20) cat(" ", i, sep="")
for(rep in 1:nreps) {
- learn <- nnet(formula, data[ri !=i,], trace = F, ...)
+ learn <- nnet(formula, data[ri !=i,], trace = FALSE, ...)
res[ri == i,] <- res[ri == i,] +
predict(learn, data[ri == i,])
}
@@ -347,7 +345,7 @@ CVnn2 <- function(formula, data,
choice <- numeric(length(lambda))
for (i in sort(unique(rand))) {
if(verbose > 0) cat("fold ", i,"\n", sep="")
- ri <- sample(nifold, sum(rand!=i), replace=T)
+ ri <- sample(nifold, sum(rand!=i), replace=TRUE)
for(j in seq(along=lambda)) {
if(verbose > 10)
cat(" size =", size[j], "decay =", lambda[j], "\n")
@@ -361,7 +359,7 @@ CVnn2 <- function(formula, data,
if(verbose > 1) cat("chosen size = ", csize,
" decay = ", decay, "\n", sep="")
for(rep in 1:nreps) {
- learn <- nnet(formula, data[rand != i,], trace=F,
+ learn <- nnet(formula, data[rand != i,], trace=FALSE,
size=csize, decay=decay, ...)
res[rand == i,] <- res[rand == i,] +
predict(learn, data[rand == i,])
@@ -370,8 +368,8 @@ CVnn2 <- function(formula, data,
factor(levels(truth)[max.col(res/nreps)], levels = levels(truth))
}
-if(F) { # only run this if you have time to wait
-res.nn2 <- CVnn2(type ~ ., fgl1, skip = T, maxit = 500, nreps = 10)
+if(FALSE) { # only run this if you have time to wait
+res.nn2 <- CVnn2(type ~ ., fgl1, skip = TRUE, maxit = 500, nreps = 10)
con(true = fgl$type, predicted = res.nn2)
}
@@ -420,7 +418,7 @@ CVprobs <- function(fitfn, predfn, ...)
probs.multinom <- CVprobs(
function(x, ...) multinom(type ~ ., fgl[x, ], ...),
function(obj, x) predict(obj, fgl[x, ], type = "probs"),
- maxit = 1000, trace = F )
+ maxit = 1000, trace = FALSE)
probs.yes <- as.vector(class.ind(fgl$type))
probs <- as.vector(probs.multinom)
diff --git a/win32/deps/library/MASS/scripts/ch13.R b/win32/deps/library/MASS/scripts/ch13.R
index b20999d..fbce974 100644
--- a/win32/deps/library/MASS/scripts/ch13.R
+++ b/win32/deps/library/MASS/scripts/ch13.R
@@ -5,9 +5,9 @@
# Chapter 13 Survival Analysis
library(MASS)
-options(echo=T, width=65, digits=5, height=9999)
+options(width=65, digits=5, height=9999)
options(contrasts=c("contr.treatment", "contr.poly"))
-postscript("ch13.ps", width=8, height=6, pointsize=9)
+pdf("ch13.pdf", width=8, height=6, pointsize=9)
library(survival)
@@ -23,7 +23,7 @@ plot(log(time) ~ pair)
gehan.surv <- survfit(Surv(time, cens) ~ treat, data = gehan,
conf.type = "log-log")
summary(gehan.surv)
-plot(gehan.surv, conf.int = T, lty = 3:2, log = T,
+plot(gehan.surv, conf.int = TRUE, lty = 3:2, log = TRUE,
xlab = "time of remission (weeks)", ylab = "survival")
lines(gehan.surv, lty = 3:2, lwd = 2, cex = 2)
legend(25, 0.1 , c("control", "6-MP"), lty = 2:3, lwd = 2)
@@ -43,32 +43,31 @@ survreg(Surv(time) ~ ag*log(wbc), leuk, dist = "exponential")
summary(survreg(Surv(time) ~ ag + log(wbc), leuk, dist = "exponential"))
summary(survreg(Surv(time) ~ ag + log(wbc), leuk)) # Weibull
summary(survreg(Surv(time) ~ ag + log(wbc), leuk,
- dist="loglogistic"))
+ dist="loglogistic"))
anova(survreg(Surv(time) ~ log(wbc), data = leuk),
survreg(Surv(time) ~ ag + log(wbc), data = leuk))
summary(survreg(Surv(time) ~ strata(ag) + log(wbc), data=leuk))
leuk.wei <- survreg(Surv(time) ~ ag + log(wbc), leuk)
ntimes <- leuk$time * exp(-leuk.wei$linear.predictors)
-plot(survfit(Surv(ntimes) ~ 1), log = T)
+plot(survfit(Surv(ntimes) ~ 1), log = TRUE)
survreg(Surv(time, cens) ~ factor(pair) + treat, gehan,
- dist = "exponential")
+ dist = "exponential")
summary(survreg(Surv(time, cens) ~ treat, gehan, dist = "exponential"))
summary(survreg(Surv(time, cens) ~ treat, gehan))
-plot(survfit(Surv(time, cens) ~ factor(temp), motors),
- conf.int = F)
+plot(survfit(Surv(time, cens) ~ factor(temp), motors), conf.int = FALSE)
motor.wei <- survreg(Surv(time, cens) ~ temp, motors)
summary(motor.wei)
-unlist(predict(motor.wei, data.frame(temp=130), se.fit = T))
+unlist(predict(motor.wei, data.frame(temp=130), se.fit = TRUE))
predict(motor.wei, data.frame(temp=130), type = "quantile",
p = c(0.5, 0.1))
t1 <- predict(motor.wei, data.frame(temp=130),
- type = "uquantile", p = 0.5, se = T)
+ type = "uquantile", p = 0.5, se = TRUE)
exp(c(LL=t1$fit - 2*t1$se, UL=t1$fit + 2*t1$se))
t1 <- predict(motor.wei, data.frame(temp=130),
- type = "uquantile", p = 0.1, se = T)
+ type = "uquantile", p = 0.1, se = TRUE)
exp(c(LL=t1$fit - 2*t1$se, UL=t1$fit + 2*t1$se))
# summary(censorReg(censor(time, cens) ~ treat, gehan))
@@ -83,7 +82,7 @@ update(leuk.cox, ~ . -ag)
(leuk.coxs <- coxph(Surv(time) ~ strata(ag) + log(wbc), data = leuk))
(leuk.coxs1 <- update(leuk.coxs, . ~ . + ag:log(wbc)))
-plot(survfit(Surv(time) ~ ag), lty = 2:3, log = T)
+plot(survfit(Surv(time) ~ ag), lty = 2:3, log = TRUE)
lines(survfit(leuk.coxs), lty = 2:3, lwd = 3)
legend(80, 0.8, c("ag absent", "ag present"), lty = 2:3)
leuk.cox <- coxph(Surv(time) ~ ag, leuk)
@@ -121,7 +120,7 @@ summary( survfit(motor.cox, newdata = data.frame(temp=130)) )
diag.time + strata(cell) + prior, data = VA))
par(mfrow=c(1,2), pty="s")
-plot(survfit(VA.coxs), log = T, lty = 1:4, col = 2:5)
+plot(survfit(VA.coxs), log = TRUE, lty = 1:4, col = 2:5)
#legend(locator(1), c("squamous", "small", "adeno", "large"), lty = 1:4, col = 2:5)
plot(survfit(VA.coxs), fun = "cloglog", lty = 1:4, col = 2:5)
cKarn <- factor(cut(VA$Karn, 5))
@@ -132,11 +131,11 @@ scatter.smooth(VA$Karn, residuals(VA.cox2))
VA.wei <- survreg(Surv(stime, status) ~ treat + age + Karn +
diag.time + cell + prior, data = VA)
-summary(VA.wei, cor = F)
+summary(VA.wei, cor = FALSE)
VA.exp <- survreg(Surv(stime, status) ~ Karn + cell,
data = VA, dist = "exponential")
-summary(VA.exp, cor = F)
+summary(VA.exp, cor = FALSE)
cox.zph(VA.coxs)
@@ -166,7 +165,7 @@ coxph(Surv(start, stop, event) ~ transplant*
stan1 <- coxph(Surv(start, stop, event) ~ strata(transplant) +
year + year:transplant + age + surgery, heart)
par(mfrow=c(1,2), pty="s")
-plot(survfit(stan1), conf.int = T, log = T, lty = c(1, 3), col = 2:3)
+plot(survfit(stan1), conf.int = TRUE, log = TRUE, lty = c(1, 3), col = 2:3)
#legend(locator(1), c("before", "after"), lty = c(1, 3), col= 2:3)
attach(heart)
@@ -184,16 +183,15 @@ summary(survfit(stan))
# follow-up for two years
stan2 <- data.frame(start = c(0, 183), stop= c(183, 2*365),
event = c(0, 0), year = c(4, 4), age = c(50, 50) - 48,
- surgery = c(1, 1), transplant = c(0, 1))
-summary(survfit(stan, stan2, individual = T,
- conf.type = "log-log"))
+ surgery = c(1, 1), transplant = as.factor(c(0, 1)))
+summary(survfit(stan, stan2, individual = TRUE, conf.type = "log-log"))
# Aids analysis
time.depend.covar <- function(data) {
id <- row.names(data); n <- length(id)
events <- c(0, 10043, 11139, 12053) # julian days
- crit1 <- matrix(events[1:3], n, 3 ,byrow = T)
- crit2 <- matrix(events[2:4], n, 3, byrow = T)
+ crit1 <- matrix(events[1:3], n, 3 ,byrow = TRUE)
+ crit2 <- matrix(events[2:4], n, 3, byrow = TRUE)
diag <- matrix(data$diag,n,3); death <- matrix(data$death,n,3)
incid <- (diag < crit2) & (death >= crit1); incid <- t(incid)
indr <- col(incid)[incid]; indc <- row(incid)[incid]
@@ -222,7 +220,7 @@ summary(aids.cox)
aids1.cox <- coxph(Surv(start, stop, status)
~ zid + strata(state) + T.categ + age, data = Aids3)
(aids1.surv <- survfit(aids1.cox))
-plot(aids1.surv, mark.time = F, lty = 1:4, col = 2:5,
+plot(aids1.surv, mark.time = FALSE, lty = 1:4, col = 2:5,
xscale = 365.25/12, xlab = "months since diagnosis")
#legend(locator(1), levels(state), lty = 1:4, col = 2:5)
@@ -231,11 +229,11 @@ aids2.cox <- coxph(Surv(start, stop, status)
(aids2.surv <- survfit(aids2.cox))
par(mfrow = c(1, 2), pty="s")
-plot(aids2.surv[1:4], mark.time = F, lty = 1:4, col = 2:5,
+plot(aids2.surv[1:4], mark.time = FALSE, lty = 1:4, col = 2:5,
xscale=365.25/12, xlab="months since diagnosis")
#legend(locator(1), levels(T.categ)[1:4], lty = 1:4, col = 2:5)
-plot(aids2.surv[c(1, 5, 6, 8)], mark.time = F, lty = 1:4, col = 2:5,
+plot(aids2.surv[c(1, 5, 6, 8)], mark.time = FALSE, lty = 1:4, col = 2:5,
xscale=365.25/12, xlab="months since diagnosis")
#legend(locator(1), levels(T.categ)[c(1, 5, 6, 8)], lty = 1:4, col = 2:5)
par(mfrow=c(1,1), pty="m")
@@ -267,7 +265,7 @@ make.aidsp <- function(){
Aidsp <- make.aidsp()
aids.wei <- survreg(Surv(survtime + 0.9, status) ~ state
+ T.categ + sex + age, data = Aidsp)
-summary(aids.wei, cor = F)
+summary(aids.wei, cor = FALSE)
survreg(Surv(survtime + 0.9, status) ~ state + T.categ
+ age, data = Aidsp)
diff --git a/win32/deps/library/MASS/scripts/ch14.R b/win32/deps/library/MASS/scripts/ch14.R
index c0820bb..ffe8566 100644
--- a/win32/deps/library/MASS/scripts/ch14.R
+++ b/win32/deps/library/MASS/scripts/ch14.R
@@ -5,8 +5,8 @@
# Chapter 14 Time Series
library(MASS)
-postscript(file="ch14.ps", width=8, height=6, pointsize=9)
-options(width=65, digits=5, echo = T)
+pdf(file="ch14.pdf", width=8, height=6, pointsize=9)
+options(width=65, digits=5)
lh
deaths
@@ -60,7 +60,7 @@ par(mfrow = c(1, 1))
acf(lh, type = "partial")
acf(deaths, type = "partial")
-lh.ar1 <- ar(lh, F, 1)
+lh.ar1 <- ar(lh, FALSE, 1)
cpgram(lh.ar1$resid, main = "AR(1) fit to lh")
lh.ar <- ar(lh, order.max = 9)
lh.ar$order
@@ -241,18 +241,18 @@ plot(density(SP500, width = "sj", n = 256), type = "l", xlab = "", ylab = "")
par(pty = "s")
qqnorm(SP500)
qqline(SP500)
-if(F) {
-module(garch)
-summary(garch(SP500 ~ 1, ~garch(1,1)))
+if(FALSE) {
+ module(garch)
+ summary(garch(SP500 ~ 1, ~garch(1,1)))
-fit <- garch(SP500 ~ 1, ~garch(1,1), cond.dist = "t")
-summary(fit)
-plot(fit)
+ fit <- garch(SP500 ~ 1, ~garch(1,1), cond.dist = "t")
+ summary(fit)
+ plot(fit)
-summary(garch(SP500 ~ 1, ~egarch(1,1), cond.dist = "t", leverage = T))
+ summary(garch(SP500 ~ 1, ~egarch(1,1), cond.dist = "t", leverage = TRUE))
}
-library(tseries)
-summary(garch(x = SP500 - median(SP500), order = c(1, 1)))
+if(require(tseries))
+ print(summary(garch(x = SP500 - median(SP500), order = c(1, 1))))
# End of ch14
diff --git a/win32/deps/library/MASS/scripts/ch15.R b/win32/deps/library/MASS/scripts/ch15.R
index 8995d80..9fe0a99 100644
--- a/win32/deps/library/MASS/scripts/ch15.R
+++ b/win32/deps/library/MASS/scripts/ch15.R
@@ -5,8 +5,8 @@
# Chapter 15 Spatial Statistics
library(MASS)
-postscript(file="ch15.ps", width=8, height=8, pointsize=9)
-options(echo = TRUE, width=65, digits=5)
+pdf(file="ch15.pdf", width=8, height=8, pointsize=9)
+options(width=65, digits=5)
library(spatial)
@@ -16,25 +16,25 @@ par(mfrow=c(2,2), pty = "s")
topo.ls <- surf.ls(2, topo)
trsurf <- trmat(topo.ls, 0, 6.5, 0, 6.5, 30)
eqscplot(trsurf, , xlab = "", ylab = "", type = "n")
-contour(trsurf, levels = seq(600, 1000, 25), add = T)
+contour(trsurf, levels = seq(600, 1000, 25), add = TRUE)
points(topo)
title("Degree=2")
topo.ls <- surf.ls(3, topo)
trsurf <- trmat(topo.ls, 0, 6.5, 0, 6.5, 30)
eqscplot(trsurf, , xlab = "", ylab = "", type = "n")
-contour(trsurf, levels = seq(600, 1000, 25), add = T)
+contour(trsurf, levels = seq(600, 1000, 25), add = TRUE)
points(topo)
title("Degree=3")
topo.ls <- surf.ls(4, topo)
trsurf <- trmat(topo.ls, 0, 6.5, 0, 6.5, 30)
eqscplot(trsurf, , xlab = "", ylab = "", type = "n")
-contour(trsurf, levels = seq(600, 1000, 25), add = T)
+contour(trsurf, levels = seq(600, 1000, 25), add = TRUE)
points(topo)
title("Degree=4")
topo.ls <- surf.ls(6, topo)
trsurf <- trmat(topo.ls, 0, 6.5, 0, 6.5, 30)
eqscplot(trsurf, , xlab = "", ylab = "", type = "n")
-contour(trsurf, levels = seq(600, 1000, 25), add = T)
+contour(trsurf, levels = seq(600, 1000, 25), add = TRUE)
points(topo)
title("Degree=6")
@@ -46,33 +46,33 @@ plt1 <- levelplot(z ~ x * y, trsurf, aspect=1,
at = seq(650, 1000, 10), xlab = "", ylab = "")
plt2 <- wireframe(z ~ x * y, trsurf, aspect=c(1, 0.5),
screen = list(z = -30, x = -60))
-print(plt1, position = c(0, 0, 0.5, 1), more=T)
+print(plt1, position = c(0, 0, 0.5, 1), more=TRUE)
print(plt2, position = c(0.45, 0, 1, 1))
par(mfcol = c(2, 2), pty = "s")
topo.loess <- loess(z ~ x * y, topo, degree = 2, span = 0.25,
- normalize = F)
+ normalize = FALSE)
topo.mar <- list(x = seq(0, 6.5, 0.1), y = seq(0, 6.5, 0.1))
-topo.lo <- predict(topo.loess, expand.grid(topo.mar), se = T)
+topo.lo <- predict(topo.loess, expand.grid(topo.mar), se = TRUE)
eqscplot(topo.mar, xlab = "fit", ylab = "", type = "n")
contour(topo.mar$x, topo.mar$y, topo.lo$fit,
- levels = seq(700, 1000, 25), add = T)
+ levels = seq(700, 1000, 25), add = TRUE)
points(topo)
eqscplot(topo.mar, xlab = "standard error", ylab = "", type = "n")
contour(topo.mar$x,topo.mar$y,topo.lo$se.fit,
- levels = seq(5, 25, 5), add = T)
+ levels = seq(5, 25, 5), add = TRUE)
title("Loess degree = 2")
points(topo)
-topo.loess <- loess(z ~ x * y, topo, degree = 1, span = 0.25, normalize = F)
-topo.lo <- predict(topo.loess, expand.grid(topo.mar), se=T)
+topo.loess <- loess(z ~ x * y, topo, degree = 1, span = 0.25, normalize = FALSE)
+topo.lo <- predict(topo.loess, expand.grid(topo.mar), se=TRUE)
eqscplot(topo.mar, xlab = "fit", ylab = "", type = "n")
contour(topo.mar$x,topo.mar$y,topo.lo$fit, levels = seq(700, 1000, 25),
- add = T)
+ add = TRUE)
points(topo)
eqscplot(topo.mar, xlab = "standard error", ylab = "", type = "n")
contour(topo.mar$x,topo.mar$y,topo.lo$se.fit, levels = seq(5, 25, 5),
- add = T)
+ add = TRUE)
title("Loess degree = 1")
points(topo)
@@ -80,13 +80,13 @@ library(akima)
par(mfrow = c(1, 2), pty= "s")
topo.int <- interp.old(topo$x, topo$y, topo$z)
eqscplot(topo.int, xlab = "interp default", ylab = "", type = "n")
-contour(topo.int, levels = seq(600, 1000, 25), add = T)
+contour(topo.int, levels = seq(600, 1000, 25), add = TRUE)
points(topo)
topo.mar <- list(x = seq(0, 6.5, 0.1), y = seq(0, 6.5, 0.1))
topo.int2 <- interp.old(topo$x, topo$y, topo$z, topo.mar$x, topo.mar$y,
- ncp = 4, extrap = T)
+ ncp = 4, extrap = TRUE)
eqscplot(topo.int2, xlab = "interp", ylab = "", type = "n")
-contour(topo.int2, levels = seq(600, 1000, 25), add = T)
+contour(topo.int2, levels = seq(600, 1000, 25), add = TRUE)
points(topo)
@@ -97,25 +97,25 @@ par(mfrow = c(2, 2), pty = "s")
topo.ls <- surf.ls(2, topo)
trsurf <- trmat(topo.ls, 0, 6.5, 0, 6.5, 30)
eqscplot(trsurf, , xlab = "", ylab = "", type = "n")
-contour(trsurf, levels = seq(600, 1000, 25), add = T)
+contour(trsurf, levels = seq(600, 1000, 25), add = TRUE)
points(topo)
title("LS trend surface")
topo.gls <- surf.gls(2, expcov, topo, d = 0.7)
trsurf <- trmat(topo.gls, 0, 6.5, 0, 6.5, 30)
eqscplot(trsurf, , xlab = "", ylab = "", type = "n")
-contour(trsurf, levels = seq(600, 1000, 25), add = T)
+contour(trsurf, levels = seq(600, 1000, 25), add = TRUE)
points(topo)
title("GLS trend surface")
prsurf <- prmat(topo.gls, 0, 6.5, 0, 6.5, 50)
eqscplot(prsurf, , xlab = "", ylab = "", type = "n")
-contour(prsurf, levels = seq(600, 1000, 25), add = T)
+contour(prsurf, levels = seq(600, 1000, 25), add = TRUE)
points(topo)
title("Kriging prediction")
sesurf <- semat(topo.gls, 0, 6.5, 0, 6.5, 30)
eqscplot(sesurf, , xlab = "", ylab = "", type = "n")
-contour(sesurf, levels = c(20, 25), add = T)
+contour(sesurf, levels = c(20, 25), add = TRUE)
points(topo)
title("Kriging s.e.")
@@ -142,11 +142,11 @@ par(mfrow = c(2, 2), pty = "s")
topo.kr <- surf.gls(2, gaucov, topo, d = 1, alph = 0.3)
prsurf <- prmat(topo.kr, 0, 6.5, 0, 6.5, 50)
eqscplot(prsurf, , xlab = "fit", ylab = "", type = "n")
-contour(prsurf, levels = seq(600, 1000, 25), add = T)
+contour(prsurf, levels = seq(600, 1000, 25), add = TRUE)
points(topo)
sesurf <- semat(topo.kr, 0, 6.5, 0, 6.5, 25)
eqscplot(sesurf, , xlab = "standard error", ylab = "", type = "n")
-contour(sesurf, levels = c(15, 20, 25), add = T)
+contour(sesurf, levels = c(15, 20, 25), add = TRUE)
points(topo)
## bottom row of Figure 15.8
@@ -154,11 +154,11 @@ topo.kr <- surf.gls(0, gaucov, topo, d = 2, alph = 0.05,
nx = 10000)
prsurf <- prmat(topo.kr, 0, 6.5, 0, 6.5, 50)
eqscplot(prsurf, , xlab = "fit", ylab = "", type = "n")
-contour(prsurf, levels = seq(600, 1000, 25), add = T)
+contour(prsurf, levels = seq(600, 1000, 25), add = TRUE)
points(topo)
sesurf <- semat(topo.kr, 0, 6.5, 0, 6.5, 25)
eqscplot(sesurf, , xlab = "standard error", ylab = "", type = "n")
-contour(sesurf, levels = c(15, 20, 25), add = T)
+contour(sesurf, levels = c(15, 20, 25), add = TRUE)
points(topo)
diff --git a/win32/deps/library/MASS/scripts/ch16.R b/win32/deps/library/MASS/scripts/ch16.R
index a552451..9ae2079 100644
--- a/win32/deps/library/MASS/scripts/ch16.R
+++ b/win32/deps/library/MASS/scripts/ch16.R
@@ -5,8 +5,8 @@
# Chapter 16 Optimization and Mazimum Likelihood Estimation
library(MASS)
-postscript(file="ch16.ps", width=8, height=8, pointsize=9)
-options(echo = T, width=65, digits=5)
+pdf(file="ch16.pdf", width=8, height=8, pointsize=9)
+options(width=65, digits=5)
# 16.3 General optimization
@@ -47,7 +47,7 @@ mix.gr <- function(p, x) {
optim(p0, mix.obj, mix.gr, x = waiting, method = "BFGS",
control = list(parscale= c(0.1, rep(1, 4))))$par
-mix.nl0 <- optim(p0, mix.obj, mix.gr, method = "L-BFGS-B", hessian = T,
+mix.nl0 <- optim(p0, mix.obj, mix.gr, method = "L-BFGS-B", hessian = TRUE,
lower = c(0, -Inf, 0, -Inf, 0),
upper = c(1, rep(Inf, 4)), x = waiting)
rbind(est = mix.nl0$par, se = sqrt(diag(solve(mix.nl0$hessian))))
@@ -93,7 +93,7 @@ p1 <- mix.nl0$par; tmp <- as.vector(p1[1])
p2 <- c(a = log(tmp/(1-tmp)), b = 0, p1[-1])
mix.nl1 <- optim(p2, mix1.obj, method = "L-BFGS-B",
lower = c(-Inf, -Inf, -Inf, 0, -Inf, 0),
- upper = rep(Inf, 6), hessian = T,
+ upper = rep(Inf, 6), hessian = TRUE,
x = waiting[-1], y = duration[-299])
rbind(est = mix.nl1$par, se = sqrt(diag(solve(mix.nl1$hessian))))
@@ -109,7 +109,7 @@ if(!exists("bwt")) {
}
logitreg <- function(x, y, wt = rep(1, length(y)),
- intercept = T, start = rep(0, p), ...)
+ intercept = TRUE, start = rep(0, p), ...)
{
fmin <- function(beta, X, y, w) {
p <- plogis(X %*% beta)
diff --git a/win32/deps/library/MASS/tests/BankWages.rda b/win32/deps/library/MASS/tests/BankWages.rda
new file mode 100644
index 0000000..75dbd05
Binary files /dev/null and b/win32/deps/library/MASS/tests/BankWages.rda differ
diff --git a/win32/deps/library/MASS/tests/Examples/MASS-Ex.Rout.save b/win32/deps/library/MASS/tests/Examples/MASS-Ex.Rout.save
new file mode 100644
index 0000000..90c808f
--- /dev/null
+++ b/win32/deps/library/MASS/tests/Examples/MASS-Ex.Rout.save
@@ -0,0 +1,5231 @@
+
+R Under development (unstable) (2012-05-26 r59449) -- "Unsuffered Consequences"
+Copyright (C) 2012 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+ Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> pkgname <- "MASS"
+> source(file.path(R.home("share"), "R", "examples-header.R"))
+> options(warn = 1)
+> library('MASS')
+>
+> assign(".oldSearch", search(), pos = 'CheckExEnv')
+> cleanEx()
+> nameEx("Insurance")
+> ### * Insurance
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: Insurance
+> ### Title: Numbers of Car Insurance claims
+> ### Aliases: Insurance
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> ## main-effects fit as Poisson GLM with offset
+> glm(Claims ~ District + Group + Age + offset(log(Holders)),
++ data = Insurance, family = poisson)
+
+Call: glm(formula = Claims ~ District + Group + Age + offset(log(Holders)),
+ family = poisson, data = Insurance)
+
+Coefficients:
+(Intercept) District2 District3 District4 Group.L Group.Q
+ -1.810508 0.025868 0.038524 0.234205 0.429708 0.004632
+ Group.C Age.L Age.Q Age.C
+ -0.029294 -0.394432 -0.000355 -0.016737
+
+Degrees of Freedom: 63 Total (i.e. Null); 54 Residual
+Null Deviance: 236.3
+Residual Deviance: 51.42 AIC: 388.7
+>
+> # same via loglm
+> loglm(Claims ~ District + Group + Age + offset(log(Holders)),
++ data = Insurance)
+Call:
+loglm(formula = Claims ~ District + Group + Age + offset(log(Holders)),
+ data = Insurance)
+
+Statistics:
+ X^2 df P(> X^2)
+Likelihood Ratio 51.42003 54 0.5745071
+Pearson 48.62933 54 0.6809086
+>
+>
+>
+> cleanEx()
+> nameEx("Null")
+> ### * Null
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: Null
+> ### Title: Null Spaces of Matrices
+> ### Aliases: Null
+> ### Keywords: algebra
+>
+> ### ** Examples
+>
+> # The function is currently defined as
+> function(M)
++ {
++ tmp <- qr(M)
++ set <- if(tmp$rank == 0) 1:ncol(M) else - (1:tmp$rank)
++ qr.Q(tmp, complete = TRUE)[, set, drop = FALSE]
++ }
+function (M)
+{
+ tmp <- qr(M)
+ set <- if (tmp$rank == 0)
+ 1:ncol(M)
+ else -(1:tmp$rank)
+ qr.Q(tmp, complete = TRUE)[, set, drop = FALSE]
+}
+>
+>
+>
+> cleanEx()
+> nameEx("OME")
+> ### * OME
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: OME
+> ### Title: Tests of Auditory Perception in Children with OME
+> ### Aliases: OME
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> # Fit logistic curve from p = 0.5 to p = 1.0
+> fp1 <- deriv(~ 0.5 + 0.5/(1 + exp(-(x-L75)/scal)),
++ c("L75", "scal"),
++ function(x,L75,scal)NULL)
+> nls(Correct/Trials ~ fp1(Loud, L75, scal), data = OME,
++ start = c(L75=45, scal=3))
+Nonlinear regression model
+ model: Correct/Trials ~ fp1(Loud, L75, scal)
+ data: OME
+ L75 scal
+44.149 3.775
+ residual sum-of-squares: 69.88
+
+Number of iterations to convergence: 4
+Achieved convergence tolerance: 7.016e-06
+> nls(Correct/Trials ~ fp1(Loud, L75, scal),
++ data = OME[OME$Noise == "coherent",],
++ start=c(L75=45, scal=3))
+Nonlinear regression model
+ model: Correct/Trials ~ fp1(Loud, L75, scal)
+ data: OME[OME$Noise == "coherent", ]
+ L75 scal
+47.993 1.259
+ residual sum-of-squares: 30.35
+
+Number of iterations to convergence: 5
+Achieved convergence tolerance: 4.895e-06
+> nls(Correct/Trials ~ fp1(Loud, L75, scal),
++ data = OME[OME$Noise == "incoherent",],
++ start = c(L75=45, scal=3))
+Nonlinear regression model
+ model: Correct/Trials ~ fp1(Loud, L75, scal)
+ data: OME[OME$Noise == "incoherent", ]
+ L75 scal
+38.87 2.17
+ residual sum-of-squares: 23.73
+
+Number of iterations to convergence: 11
+Achieved convergence tolerance: 3.846e-06
+>
+> # individual fits for each experiment
+>
+> aa <- factor(OME$Age)
+> ab <- 10*OME$ID + unclass(aa)
+> ac <- unclass(factor(ab))
+> OME$UID <- as.vector(ac)
+> OME$UIDn <- OME$UID + 0.1*(OME$Noise == "incoherent")
+> rm(aa, ab, ac)
+> OMEi <- OME
+>
+> library(nlme)
+> fp2 <- deriv(~ 0.5 + 0.5/(1 + exp(-(x-L75)/2)),
++ "L75", function(x,L75) NULL)
+> dec <- getOption("OutDec")
+> options(show.error.messages = FALSE, OutDec=".")
+> OMEi.nls <- nlsList(Correct/Trials ~ fp2(Loud, L75) | UIDn,
++ data = OMEi, start = list(L75=45), control = list(maxiter=100))
+> options(show.error.messages = TRUE, OutDec=dec)
+> tmp <- sapply(OMEi.nls, function(X)
++ {if(is.null(X)) NA else as.vector(coef(X))})
+> OMEif <- data.frame(UID = round(as.numeric((names(tmp)))),
++ Noise = rep(c("coherent", "incoherent"), 110),
++ L75 = as.vector(tmp), stringsAsFactors = TRUE)
+> OMEif$Age <- OME$Age[match(OMEif$UID, OME$UID)]
+> OMEif$OME <- OME$OME[match(OMEif$UID, OME$UID)]
+> OMEif <- OMEif[OMEif$L75 > 30,]
+> summary(lm(L75 ~ Noise/Age, data = OMEif, na.action = na.omit))
+
+Call:
+lm(formula = L75 ~ Noise/Age, data = OMEif, na.action = na.omit)
+
+Residuals:
+ Min 1Q Median 3Q Max
+-13.0022 -1.9878 0.3346 2.0229 16.3260
+
+Coefficients:
+ Estimate Std. Error t value Pr(>|t|)
+(Intercept) 47.73580 0.76456 62.435 < 2e-16 ***
+Noiseincoherent -4.87352 1.11247 -4.381 1.92e-05 ***
+Noisecoherent:Age -0.02785 0.02349 -1.186 0.237
+Noiseincoherent:Age -0.12219 0.02589 -4.719 4.50e-06 ***
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+Residual standard error: 3.774 on 196 degrees of freedom
+ (17 observations deleted due to missingness)
+Multiple R-squared: 0.5246, Adjusted R-squared: 0.5173
+F-statistic: 72.09 on 3 and 196 DF, p-value: < 2.2e-16
+
+> summary(lm(L75 ~ Noise/(Age + OME), data = OMEif,
++ subset = (Age >= 30 & Age <= 60),
++ na.action = na.omit), cor = FALSE)
+
+Call:
+lm(formula = L75 ~ Noise/(Age + OME), data = OMEif, subset = (Age >=
+ 30 & Age <= 60), na.action = na.omit)
+
+Residuals:
+ Min 1Q Median 3Q Max
+-10.4514 -2.0588 0.0194 1.6827 15.9738
+
+Coefficients:
+ Estimate Std. Error t value Pr(>|t|)
+(Intercept) 50.21090 1.74482 28.777 < 2e-16 ***
+Noiseincoherent -5.97491 2.70148 -2.212 0.02890 *
+Noisecoherent:Age -0.09358 0.03586 -2.609 0.01023 *
+Noiseincoherent:Age -0.15155 0.04151 -3.651 0.00039 ***
+Noisecoherent:OMElow 0.45103 1.07594 0.419 0.67583
+Noiseincoherent:OMElow -0.14075 1.24537 -0.113 0.91021
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+Residual standard error: 3.7 on 119 degrees of freedom
+ (17 observations deleted due to missingness)
+Multiple R-squared: 0.6073, Adjusted R-squared: 0.5908
+F-statistic: 36.81 on 5 and 119 DF, p-value: < 2.2e-16
+
+>
+> # Or fit by weighted least squares
+> fpl75 <- deriv(~ sqrt(n)*(r/n - 0.5 - 0.5/(1 + exp(-(x-L75)/scal))),
++ c("L75", "scal"),
++ function(r,n,x,L75,scal) NULL)
+> nls(0 ~ fpl75(Correct, Trials, Loud, L75, scal),
++ data = OME[OME$Noise == "coherent",],
++ start = c(L75=45, scal=3))
+Nonlinear regression model
+ model: 0 ~ fpl75(Correct, Trials, Loud, L75, scal)
+ data: OME[OME$Noise == "coherent", ]
+ L75 scal
+47.798 1.296
+ residual sum-of-squares: 91.72
+
+Number of iterations to convergence: 5
+Achieved convergence tolerance: 9.302e-06
+> nls(0 ~ fpl75(Correct, Trials, Loud, L75, scal),
++ data = OME[OME$Noise == "incoherent",],
++ start = c(L75=45, scal=3))
+Nonlinear regression model
+ model: 0 ~ fpl75(Correct, Trials, Loud, L75, scal)
+ data: OME[OME$Noise == "incoherent", ]
+ L75 scal
+38.553 2.078
+ residual sum-of-squares: 60.19
+
+Number of iterations to convergence: 8
+Achieved convergence tolerance: 4.55e-06
+>
+> # Test to see if the curves shift with age
+> fpl75age <- deriv(~sqrt(n)*(r/n - 0.5 - 0.5/(1 +
++ exp(-(x-L75-slope*age)/scal))),
++ c("L75", "slope", "scal"),
++ function(r,n,x,age,L75,slope,scal) NULL)
+> OME.nls1 <-
++ nls(0 ~ fpl75age(Correct, Trials, Loud, Age, L75, slope, scal),
++ data = OME[OME$Noise == "coherent",],
++ start = c(L75=45, slope=0, scal=2))
+> sqrt(diag(vcov(OME.nls1)))
+ L75 slope scal
+0.61091761 0.01665916 0.17566450
+>
+> OME.nls2 <-
++ nls(0 ~ fpl75age(Correct, Trials, Loud, Age, L75, slope, scal),
++ data = OME[OME$Noise == "incoherent",],
++ start = c(L75=45, slope=0, scal=2))
+> sqrt(diag(vcov(OME.nls2)))
+ L75 slope scal
+0.49553854 0.01348281 0.24453836
+>
+> # Now allow random effects by using NLME
+> OMEf <- OME[rep(1:nrow(OME), OME$Trials),]
+> OMEf$Resp <- with(OME, rep(rep(c(1,0), length(Trials)),
++ t(cbind(Correct, Trials-Correct))))
+> OMEf <- OMEf[, -match(c("Correct", "Trials"), names(OMEf))]
+>
+> ## Not run:
+> ##D ## this fails in R on some platforms
+> ##D fp2 <- deriv(~ 0.5 + 0.5/(1 + exp(-(x-L75)/exp(lsc))),
+> ##D c("L75", "lsc"),
+> ##D function(x, L75, lsc) NULL)
+> ##D G1.nlme <- nlme(Resp ~ fp2(Loud, L75, lsc),
+> ##D fixed = list(L75 ~ Age, lsc ~ 1),
+> ##D random = L75 + lsc ~ 1 | UID,
+> ##D data = OMEf[OMEf$Noise == "coherent",], method = "ML",
+> ##D start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verbose = TRUE)
+> ##D summary(G1.nlme)
+> ##D
+> ##D G2.nlme <- nlme(Resp ~ fp2(Loud, L75, lsc),
+> ##D fixed = list(L75 ~ Age, lsc ~ 1),
+> ##D random = L75 + lsc ~ 1 | UID,
+> ##D data = OMEf[OMEf$Noise == "incoherent",], method="ML",
+> ##D start = list(fixed=c(L75=c(41.5, -0.1), lsc=0)), verbose = TRUE)
+> ##D summary(G2.nlme)
+> ## End(Not run)
+>
+>
+> cleanEx()
+
+detaching âpackage:nlmeâ
+
+> nameEx("Skye")
+> ### * Skye
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: Skye
+> ### Title: AFM Compositions of Aphyric Skye Lavas
+> ### Aliases: Skye
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> # ternary() is from the on-line answers.
+> ternary <- function(X, pch = par("pch"), lcex = 1,
++ add = FALSE, ord = 1:3, ...)
++ {
++ X <- as.matrix(X)
++ if(any(X < 0)) stop("X must be non-negative")
++ s <- drop(X %*% rep(1, ncol(X)))
++ if(any(s<=0)) stop("each row of X must have a positive sum")
++ if(max(abs(s-1)) > 1e-6) {
++ warning("row(s) of X will be rescaled")
++ X <- X / s
++ }
++ X <- X[, ord]
++ s3 <- sqrt(1/3)
++ if(!add)
++ {
++ oldpty <- par("pty")
++ on.exit(par(pty=oldpty))
++ par(pty="s")
++ plot(c(-s3, s3), c(0.5-s3, 0.5+s3), type="n", axes=FALSE,
++ xlab="", ylab="")
++ polygon(c(0, -s3, s3), c(1, 0, 0), density=0)
++ lab <- NULL
++ if(!is.null(dn <- dimnames(X))) lab <- dn[[2]]
++ if(length(lab) < 3) lab <- as.character(1:3)
++ eps <- 0.05 * lcex
++ text(c(0, s3+eps*0.7, -s3-eps*0.7),
++ c(1+eps, -0.1*eps, -0.1*eps), lab, cex=lcex)
++ }
++ points((X[,2] - X[,3])*s3, X[,1], ...)
++ }
+>
+> ternary(Skye/100, ord=c(1,3,2))
+>
+>
+>
+> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
+> cleanEx()
+> nameEx("addterm")
+> ### * addterm
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: addterm
+> ### Title: Try All One-Term Additions to a Model
+> ### Aliases: addterm addterm.default addterm.glm addterm.lm
+> ### Keywords: models
+>
+> ### ** Examples
+>
+> quine.hi <- aov(log(Days + 2.5) ~ .^4, quine)
+> quine.lo <- aov(log(Days+2.5) ~ 1, quine)
+> addterm(quine.lo, quine.hi, test="F")
+Single term additions
+
+Model:
+log(Days + 2.5) ~ 1
+ Df Sum of Sq RSS AIC F Value Pr(F)
+<none> 106.787 -43.664
+Eth 1 10.6820 96.105 -57.052 16.0055 0.0001006 ***
+Sex 1 0.5969 106.190 -42.483 0.8094 0.3698057
+Age 3 4.7469 102.040 -44.303 2.2019 0.0904804 .
+Lrn 1 0.0043 106.783 -41.670 0.0058 0.9392083
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+>
+> house.glm0 <- glm(Freq ~ Infl*Type*Cont + Sat, family=poisson,
++ data=housing)
+> addterm(house.glm0, ~. + Sat:(Infl+Type+Cont), test="Chisq")
+Single term additions
+
+Model:
+Freq ~ Infl * Type * Cont + Sat
+ Df Deviance AIC LRT Pr(Chi)
+<none> 217.46 610.43
+Infl:Sat 4 111.08 512.05 106.371 < 2.2e-16 ***
+Type:Sat 6 156.79 561.76 60.669 3.292e-11 ***
+Cont:Sat 2 212.33 609.30 5.126 0.07708 .
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+> house.glm1 <- update(house.glm0, . ~ . + Sat*(Infl+Type+Cont))
+> addterm(house.glm1, ~. + Sat:(Infl+Type+Cont)^2, test = "Chisq")
+Single term additions
+
+Model:
+Freq ~ Infl + Type + Cont + Sat + Infl:Type + Infl:Cont + Type:Cont +
+ Infl:Sat + Type:Sat + Cont:Sat + Infl:Type:Cont
+ Df Deviance AIC LRT Pr(Chi)
+<none> 38.662 455.63
+Infl:Type:Sat 12 16.107 457.08 22.5550 0.03175 *
+Infl:Cont:Sat 4 37.472 462.44 1.1901 0.87973
+Type:Cont:Sat 6 28.256 457.23 10.4064 0.10855
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+>
+>
+>
+> cleanEx()
+> nameEx("anova.negbin")
+> ### * anova.negbin
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: anova.negbin
+> ### Title: Likelihood Ratio Tests for Negative Binomial GLMs
+> ### Aliases: anova.negbin
+> ### Keywords: regression
+>
+> ### ** Examples
+>
+> m1 <- glm.nb(Days ~ Eth*Age*Lrn*Sex, quine, link = log)
+> m2 <- update(m1, . ~ . - Eth:Age:Lrn:Sex)
+> anova(m2, m1)
+Likelihood ratio tests of Negative Binomial Models
+
+Response: Days
+ Model
+1 Eth + Age + Lrn + Sex + Eth:Age + Eth:Lrn + Age:Lrn + Eth:Sex + Age:Sex + Lrn:Sex + Eth:Age:Lrn + Eth:Age:Sex + Eth:Lrn:Sex + Age:Lrn:Sex
+2 Eth * Age * Lrn * Sex
+ theta Resid. df 2 x log-lik. Test df LR stat. Pr(Chi)
+1 1.90799 120 -1040.728
+2 1.92836 118 -1039.324 1 vs 2 2 1.403843 0.4956319
+> anova(m2)
+Warning in anova.negbin(m2) : tests made without re-estimating 'theta'
+Analysis of Deviance Table
+
+Model: Negative Binomial(1.908), link: log
+
+Response: Days
+
+Terms added sequentially (first to last)
+
+
+ Df Deviance Resid. Df Resid. Dev Pr(>Chi)
+NULL 145 270.03
+Eth 1 19.0989 144 250.93 1.241e-05 ***
+Age 3 16.3483 141 234.58 0.000962 ***
+Lrn 1 3.5449 140 231.04 0.059730 .
+Sex 1 0.3989 139 230.64 0.527666
+Eth:Age 3 14.6030 136 216.03 0.002189 **
+Eth:Lrn 1 0.0447 135 215.99 0.832601
+Age:Lrn 2 1.7482 133 214.24 0.417240
+Eth:Sex 1 1.1470 132 213.09 0.284183
+Age:Sex 3 21.9746 129 191.12 6.603e-05 ***
+Lrn:Sex 1 0.0277 128 191.09 0.867712
+Eth:Age:Lrn 2 9.0099 126 182.08 0.011054 *
+Eth:Age:Sex 3 4.8218 123 177.26 0.185319
+Eth:Lrn:Sex 1 3.3160 122 173.94 0.068608 .
+Age:Lrn:Sex 2 6.3941 120 167.55 0.040882 *
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+>
+>
+>
+> cleanEx()
+> nameEx("area")
+> ### * area
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: area
+> ### Title: Adaptive Numerical Integration
+> ### Aliases: area
+> ### Keywords: nonlinear
+>
+> ### ** Examples
+>
+> area(sin, 0, pi) # integrate the sin function from 0 to pi.
+[1] 2
+>
+>
+>
+> cleanEx()
+> nameEx("bacteria")
+> ### * bacteria
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: bacteria
+> ### Title: Presence of Bacteria after Drug Treatments
+> ### Aliases: bacteria
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> contrasts(bacteria$trt) <- structure(contr.sdif(3),
++ dimnames = list(NULL, c("drug", "encourage")))
+> ## fixed effects analyses
+> summary(glm(y ~ trt * week, binomial, data = bacteria))
+
+Call:
+glm(formula = y ~ trt * week, family = binomial, data = bacteria)
+
+Deviance Residuals:
+ Min 1Q Median 3Q Max
+-2.2144 0.4245 0.5373 0.6750 1.0697
+
+Coefficients:
+ Estimate Std. Error z value Pr(>|z|)
+(Intercept) 1.97548 0.30053 6.573 4.92e-11 ***
+trtdrug -0.99848 0.69490 -1.437 0.15075
+trtencourage 0.83865 0.73482 1.141 0.25374
+week -0.11814 0.04460 -2.649 0.00807 **
+trtdrug:week -0.01722 0.10570 -0.163 0.87061
+trtencourage:week -0.07043 0.10964 -0.642 0.52060
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+(Dispersion parameter for binomial family taken to be 1)
+
+ Null deviance: 217.38 on 219 degrees of freedom
+Residual deviance: 203.12 on 214 degrees of freedom
+AIC: 215.12
+
+Number of Fisher Scoring iterations: 4
+
+> summary(glm(y ~ trt + week, binomial, data = bacteria))
+
+Call:
+glm(formula = y ~ trt + week, family = binomial, data = bacteria)
+
+Deviance Residuals:
+ Min 1Q Median 3Q Max
+-2.2899 0.3885 0.5400 0.7027 1.1077
+
+Coefficients:
+ Estimate Std. Error z value Pr(>|z|)
+(Intercept) 1.96018 0.29705 6.599 4.15e-11 ***
+trtdrug -1.10667 0.42519 -2.603 0.00925 **
+trtencourage 0.45502 0.42766 1.064 0.28735
+week -0.11577 0.04414 -2.623 0.00872 **
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+(Dispersion parameter for binomial family taken to be 1)
+
+ Null deviance: 217.38 on 219 degrees of freedom
+Residual deviance: 203.81 on 216 degrees of freedom
+AIC: 211.81
+
+Number of Fisher Scoring iterations: 4
+
+> summary(glm(y ~ trt + I(week > 2), binomial, data = bacteria))
+
+Call:
+glm(formula = y ~ trt + I(week > 2), family = binomial, data = bacteria)
+
+Deviance Residuals:
+ Min 1Q Median 3Q Max
+-2.4043 0.3381 0.5754 0.6237 1.0051
+
+Coefficients:
+ Estimate Std. Error z value Pr(>|z|)
+(Intercept) 2.2479 0.3560 6.315 2.71e-10 ***
+trtdrug -1.1187 0.4288 -2.609 0.00909 **
+trtencourage 0.4815 0.4330 1.112 0.26614
+I(week > 2)TRUE -1.2949 0.4104 -3.155 0.00160 **
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+(Dispersion parameter for binomial family taken to be 1)
+
+ Null deviance: 217.38 on 219 degrees of freedom
+Residual deviance: 199.18 on 216 degrees of freedom
+AIC: 207.18
+
+Number of Fisher Scoring iterations: 5
+
+>
+> # conditional random-effects analysis
+> library(survival)
+Loading required package: splines
+> bacteria$Time <- rep(1, nrow(bacteria))
+> coxph(Surv(Time, unclass(y)) ~ week + strata(ID),
++ data = bacteria, method = "exact")
+Call:
+coxph(formula = Surv(Time, unclass(y)) ~ week + strata(ID), data = bacteria,
+ method = "exact")
+
+
+ coef exp(coef) se(coef) z p
+week -0.163 0.85 0.0547 -2.97 0.003
+
+Likelihood ratio test=9.85 on 1 df, p=0.0017 n= 220, number of events= 177
+> coxph(Surv(Time, unclass(y)) ~ factor(week) + strata(ID),
++ data = bacteria, method = "exact")
+Call:
+coxph(formula = Surv(Time, unclass(y)) ~ factor(week) + strata(ID),
+ data = bacteria, method = "exact")
+
+
+ coef exp(coef) se(coef) z p
+factor(week)2 0.198 1.219 0.724 0.274 0.780
+factor(week)4 -1.421 0.242 0.667 -2.131 0.033
+factor(week)6 -1.661 0.190 0.682 -2.434 0.015
+factor(week)11 -1.675 0.187 0.678 -2.471 0.013
+
+Likelihood ratio test=15.4 on 4 df, p=0.00385 n= 220, number of events= 177
+> coxph(Surv(Time, unclass(y)) ~ I(week > 2) + strata(ID),
++ data = bacteria, method = "exact")
+Call:
+coxph(formula = Surv(Time, unclass(y)) ~ I(week > 2) + strata(ID),
+ data = bacteria, method = "exact")
+
+
+ coef exp(coef) se(coef) z p
+I(week > 2)TRUE -1.67 0.188 0.482 -3.47 0.00053
+
+Likelihood ratio test=15.2 on 1 df, p=9.93e-05 n= 220, number of events= 177
+>
+> # PQL glmm analysis
+> library(nlme)
+> summary(glmmPQL(y ~ trt + I(week > 2), random = ~ 1 | ID,
++ family = binomial, data = bacteria))
+iteration 1
+iteration 2
+iteration 3
+iteration 4
+iteration 5
+iteration 6
+Linear mixed-effects model fit by maximum likelihood
+ Data: bacteria
+ AIC BIC logLik
+ NA NA NA
+
+Random effects:
+ Formula: ~1 | ID
+ (Intercept) Residual
+StdDev: 1.410637 0.7800511
+
+Variance function:
+ Structure: fixed weights
+ Formula: ~invwt
+Fixed effects: y ~ trt + I(week > 2)
+ Value Std.Error DF t-value p-value
+(Intercept) 2.7447864 0.3784193 169 7.253294 0.0000
+trtdrug -1.2473553 0.6440635 47 -1.936696 0.0588
+trtencourage 0.4930279 0.6699339 47 0.735935 0.4654
+I(week > 2)TRUE -1.6072570 0.3583379 169 -4.485311 0.0000
+ Correlation:
+ (Intr) trtdrg trtncr
+trtdrug 0.009
+trtencourage 0.036 -0.518
+I(week > 2)TRUE -0.710 0.047 -0.046
+
+Standardized Within-Group Residuals:
+ Min Q1 Med Q3 Max
+-5.1985361 0.1572336 0.3513075 0.4949482 1.7448845
+
+Number of Observations: 220
+Number of Groups: 50
+>
+>
+>
+> cleanEx()
+
+detaching âpackage:nlmeâ, âpackage:survivalâ, âpackage:splinesâ
+
+> nameEx("bandwidth.nrd")
+> ### * bandwidth.nrd
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: bandwidth.nrd
+> ### Title: Bandwidth for density() via Normal Reference Distribution
+> ### Aliases: bandwidth.nrd
+> ### Keywords: dplot
+>
+> ### ** Examples
+>
+> # The function is currently defined as
+> function(x)
++ {
++ r <- quantile(x, c(0.25, 0.75))
++ h <- (r[2] - r[1])/1.34
++ 4 * 1.06 * min(sqrt(var(x)), h) * length(x)^(-1/5)
++ }
+function (x)
+{
+ r <- quantile(x, c(0.25, 0.75))
+ h <- (r[2] - r[1])/1.34
+ 4 * 1.06 * min(sqrt(var(x)), h) * length(x)^(-1/5)
+}
+>
+>
+>
+> cleanEx()
+> nameEx("bcv")
+> ### * bcv
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: bcv
+> ### Title: Biased Cross-Validation for Bandwidth Selection
+> ### Aliases: bcv
+> ### Keywords: dplot
+>
+> ### ** Examples
+>
+> bcv(geyser$duration)
+[1] 0.8940809
+>
+>
+>
+> cleanEx()
+> nameEx("beav1")
+> ### * beav1
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: beav1
+> ### Title: Body Temperature Series of Beaver 1
+> ### Aliases: beav1
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> attach(beav1)
+> beav1$hours <- 24*(day-346) + trunc(time/100) + (time%%100)/60
+> plot(beav1$hours, beav1$temp, type="l", xlab="time",
++ ylab="temperature", main="Beaver 1")
+> usr <- par("usr"); usr[3:4] <- c(-0.2, 8); par(usr=usr)
+> lines(beav1$hours, beav1$activ, type="s", lty=2)
+> temp <- ts(c(beav1$temp[1:82], NA, beav1$temp[83:114]),
++ start = 9.5, frequency = 6)
+> activ <- ts(c(beav1$activ[1:82], NA, beav1$activ[83:114]),
++ start = 9.5, frequency = 6)
+>
+> acf(temp[1:53])
+> acf(temp[1:53], type = "partial")
+> ar(temp[1:53])
+
+Call:
+ar(x = temp[1:53])
+
+Coefficients:
+ 1
+0.8222
+
+Order selected 1 sigma^2 estimated as 0.01011
+> act <- c(rep(0, 10), activ)
+> X <- cbind(1, act = act[11:125], act1 = act[10:124],
++ act2 = act[9:123], act3 = act[8:122])
+> alpha <- 0.80
+> stemp <- as.vector(temp - alpha*lag(temp, -1))
+> sX <- X[-1, ] - alpha * X[-115,]
+> beav1.ls <- lm(stemp ~ -1 + sX, na.action = na.omit)
+> summary(beav1.ls, cor = FALSE)
+
+Call:
+lm(formula = stemp ~ -1 + sX, na.action = na.omit)
+
+Residuals:
+ Min 1Q Median 3Q Max
+-0.21317 -0.04317 0.00683 0.05483 0.37683
+
+Coefficients:
+ Estimate Std. Error t value Pr(>|t|)
+sX 36.85587 0.03922 939.833 < 2e-16 ***
+sXact 0.25400 0.03930 6.464 3.37e-09 ***
+sXact1 0.17096 0.05100 3.352 0.00112 **
+sXact2 0.16202 0.05147 3.148 0.00215 **
+sXact3 0.10548 0.04310 2.448 0.01605 *
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+Residual standard error: 0.08096 on 104 degrees of freedom
+ (5 observations deleted due to missingness)
+Multiple R-squared: 0.9999, Adjusted R-squared: 0.9999
+F-statistic: 1.81e+05 on 5 and 104 DF, p-value: < 2.2e-16
+
+> detach("beav1"); rm(temp, activ)
+>
+>
+>
+> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
+> cleanEx()
+> nameEx("beav2")
+> ### * beav2
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: beav2
+> ### Title: Body Temperature Series of Beaver 2
+> ### Aliases: beav2
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> attach(beav2)
+> beav2$hours <- 24*(day-307) + trunc(time/100) + (time%%100)/60
+> plot(beav2$hours, beav2$temp, type = "l", xlab = "time",
++ ylab = "temperature", main = "Beaver 2")
+> usr <- par("usr"); usr[3:4] <- c(-0.2, 8); par(usr = usr)
+> lines(beav2$hours, beav2$activ, type = "s", lty = 2)
+>
+> temp <- ts(temp, start = 8+2/3, frequency = 6)
+> activ <- ts(activ, start = 8+2/3, frequency = 6)
+> acf(temp[activ == 0]); acf(temp[activ == 1]) # also look at PACFs
+> ar(temp[activ == 0]); ar(temp[activ == 1])
+
+Call:
+ar(x = temp[activ == 0])
+
+Coefficients:
+ 1
+0.7392
+
+Order selected 1 sigma^2 estimated as 0.02011
+
+Call:
+ar(x = temp[activ == 1])
+
+Coefficients:
+ 1
+0.7894
+
+Order selected 1 sigma^2 estimated as 0.01792
+>
+> arima(temp, order = c(1,0,0), xreg = activ)
+
+Call:
+arima(x = temp, order = c(1, 0, 0), xreg = activ)
+
+Coefficients:
+ ar1 intercept activ
+ 0.8733 37.1920 0.6139
+s.e. 0.0684 0.1187 0.1381
+
+sigma^2 estimated as 0.01518: log likelihood = 66.78, aic = -125.55
+> dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*beav2$hours/24))
+> arima(temp, order = c(1,0,0), xreg = cbind(active=activ, dreg))
+
+Call:
+arima(x = temp, order = c(1, 0, 0), xreg = cbind(active = activ, dreg))
+
+Coefficients:
+ ar1 intercept active dreg.sin dreg.cos
+ 0.7905 37.1674 0.5322 -0.282 0.1201
+s.e. 0.0681 0.0939 0.1282 0.105 0.0997
+
+sigma^2 estimated as 0.01434: log likelihood = 69.83, aic = -127.67
+>
+> library(nlme)
+> beav2.gls <- gls(temp ~ activ, data = beav2, corr = corAR1(0.8),
++ method = "ML")
+> summary(beav2.gls)
+Generalized least squares fit by maximum likelihood
+ Model: temp ~ activ
+ Data: beav2
+ AIC BIC logLik
+ -125.5505 -115.1298 66.77523
+
+Correlation Structure: AR(1)
+ Formula: ~1
+ Parameter estimate(s):
+ Phi
+0.8731771
+
+Coefficients:
+ Value Std.Error t-value p-value
+(Intercept) 37.19195 0.1131328 328.7460 0
+activ 0.61418 0.1087286 5.6487 0
+
+ Correlation:
+ (Intr)
+activ -0.582
+
+Standardized residuals:
+ Min Q1 Med Q3 Max
+-2.42080780 -0.61510520 -0.03573836 0.81641138 2.15153499
+
+Residual standard error: 0.2527856
+Degrees of freedom: 100 total; 98 residual
+> summary(update(beav2.gls, subset = 6:100))
+Generalized least squares fit by maximum likelihood
+ Model: temp ~ activ
+ Data: beav2
+ Subset: 6:100
+ AIC BIC logLik
+ -124.981 -114.7654 66.49048
+
+Correlation Structure: AR(1)
+ Formula: ~1
+ Parameter estimate(s):
+ Phi
+0.8380448
+
+Coefficients:
+ Value Std.Error t-value p-value
+(Intercept) 37.25001 0.09634047 386.6496 0
+activ 0.60277 0.09931904 6.0690 0
+
+ Correlation:
+ (Intr)
+activ -0.657
+
+Standardized residuals:
+ Min Q1 Med Q3 Max
+-2.0231494 -0.8910348 -0.1497564 0.7640939 2.2719468
+
+Residual standard error: 0.2188542
+Degrees of freedom: 95 total; 93 residual
+> detach("beav2"); rm(temp, activ)
+>
+>
+>
+> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
+> cleanEx()
+
+detaching âpackage:nlmeâ
+
+> nameEx("birthwt")
+> ### * birthwt
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: birthwt
+> ### Title: Risk Factors Associated with Low Infant Birth Weight
+> ### Aliases: birthwt
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> attach(birthwt)
+> race <- factor(race, labels = c("white", "black", "other"))
+> ptd <- factor(ptl > 0)
+> ftv <- factor(ftv)
+> levels(ftv)[-(1:2)] <- "2+"
+> bwt <- data.frame(low = factor(low), age, lwt, race,
++ smoke = (smoke > 0), ptd, ht = (ht > 0), ui = (ui > 0), ftv)
+> detach("birthwt")
+> options(contrasts = c("contr.treatment", "contr.poly"))
+> glm(low ~ ., binomial, bwt)
+
+Call: glm(formula = low ~ ., family = binomial, data = bwt)
+
+Coefficients:
+(Intercept) age lwt raceblack raceother smokeTRUE
+ 0.82302 -0.03723 -0.01565 1.19241 0.74068 0.75553
+ ptdTRUE htTRUE uiTRUE ftv1 ftv2+
+ 1.34376 1.91317 0.68020 -0.43638 0.17901
+
+Degrees of Freedom: 188 Total (i.e. Null); 178 Residual
+Null Deviance: 234.7
+Residual Deviance: 195.5 AIC: 217.5
+>
+>
+>
+> options(contrasts = c(unordered = "contr.treatment",ordered = "contr.poly"))
+> cleanEx()
+> nameEx("boxcox")
+> ### * boxcox
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: boxcox
+> ### Title: Box-Cox Transformations for Linear Models
+> ### Aliases: boxcox boxcox.default boxcox.formula boxcox.lm
+> ### Keywords: regression models hplot
+>
+> ### ** Examples
+>
+> boxcox(Volume ~ log(Height) + log(Girth), data = trees,
++ lambda = seq(-0.25, 0.25, length = 10))
+>
+> boxcox(Days+1 ~ Eth*Sex*Age*Lrn, data = quine,
++ lambda = seq(-0.05, 0.45, len = 20))
+>
+>
+>
+> cleanEx()
+> nameEx("caith")
+> ### * caith
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: caith
+> ### Title: Colours of Eyes and Hair of People in Caithness
+> ### Aliases: caith
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> corresp(caith)
+First canonical correlation(s): 0.4463684
+
+ Row scores:
+ blue light medium dark
+-0.89679252 -0.98731818 0.07530627 1.57434710
+
+ Column scores:
+ fair red medium dark black
+-1.21871379 -0.52257500 -0.09414671 1.31888486 2.45176017
+> dimnames(caith)[[2]] <- c("F", "R", "M", "D", "B")
+> par(mfcol=c(1,3))
+> plot(corresp(caith, nf=2)); title("symmetric")
+> plot(corresp(caith, nf=2), type="rows"); title("rows")
+> plot(corresp(caith, nf=2), type="col"); title("columns")
+> par(mfrow=c(1,1))
+>
+>
+>
+> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
+> cleanEx()
+> nameEx("cement")
+> ### * cement
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: cement
+> ### Title: Heat Evolved by Setting Cements
+> ### Aliases: cement
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> lm(y ~ x1 + x2 + x3 + x4, cement)
+
+Call:
+lm(formula = y ~ x1 + x2 + x3 + x4, data = cement)
+
+Coefficients:
+(Intercept) x1 x2 x3 x4
+ 62.4054 1.5511 0.5102 0.1019 -0.1441
+
+>
+>
+>
+> cleanEx()
+> nameEx("confint")
+> ### * confint
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: confint-MASS
+> ### Title: Confidence Intervals for Model Parameters
+> ### Aliases: confint.glm confint.nls confint.profile.glm
+> ### confint.profile.nls
+> ### Keywords: models
+>
+> ### ** Examples
+>
+> expn1 <- deriv(y ~ b0 + b1 * 2^(-x/th), c("b0", "b1", "th"),
++ function(b0, b1, th, x) {})
+>
+> wtloss.gr <- nls(Weight ~ expn1(b0, b1, th, Days),
++ data = wtloss, start = c(b0=90, b1=95, th=120))
+>
+> expn2 <- deriv(~b0 + b1*((w0 - b0)/b1)^(x/d0),
++ c("b0","b1","d0"), function(b0, b1, d0, x, w0) {})
+>
+> wtloss.init <- function(obj, w0) {
++ p <- coef(obj)
++ d0 <- - log((w0 - p["b0"])/p["b1"])/log(2) * p["th"]
++ c(p[c("b0", "b1")], d0 = as.vector(d0))
++ }
+>
+> out <- NULL
+> w0s <- c(110, 100, 90)
+> for(w0 in w0s) {
++ fm <- nls(Weight ~ expn2(b0, b1, d0, Days, w0),
++ wtloss, start = wtloss.init(wtloss.gr, w0))
++ out <- rbind(out, c(coef(fm)["d0"], confint(fm, "d0")))
++ }
+Waiting for profiling to be done...
+Waiting for profiling to be done...
+Waiting for profiling to be done...
+> dimnames(out) <- list(paste(w0s, "kg:"), c("d0", "low", "high"))
+> out
+ d0 low high
+110 kg: 261.5132 256.2303 267.5009
+100 kg: 349.4979 334.7293 368.0151
+90 kg: 507.0941 457.2637 594.8745
+>
+> ldose <- rep(0:5, 2)
+> numdead <- c(1, 4, 9, 13, 18, 20, 0, 2, 6, 10, 12, 16)
+> sex <- factor(rep(c("M", "F"), c(6, 6)))
+> SF <- cbind(numdead, numalive = 20 - numdead)
+> budworm.lg0 <- glm(SF ~ sex + ldose - 1, family = binomial)
+> confint(budworm.lg0)
+Waiting for profiling to be done...
+ 2.5 % 97.5 %
+sexF -4.4581438 -2.613610
+sexM -3.1728745 -1.655117
+ldose 0.8228708 1.339058
+> confint(budworm.lg0, "ldose")
+Waiting for profiling to be done...
+ 2.5 % 97.5 %
+0.8228708 1.3390581
+>
+>
+>
+> cleanEx()
+> nameEx("contr.sdif")
+> ### * contr.sdif
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: contr.sdif
+> ### Title: Successive Differences Contrast Coding
+> ### Aliases: contr.sdif
+> ### Keywords: models
+>
+> ### ** Examples
+>
+> contr.sdif(6)
+ 2-1 3-2 4-3 5-4 6-5
+1 -0.8333333 -0.6666667 -0.5 -0.3333333 -0.1666667
+2 0.1666667 -0.6666667 -0.5 -0.3333333 -0.1666667
+3 0.1666667 0.3333333 -0.5 -0.3333333 -0.1666667
+4 0.1666667 0.3333333 0.5 -0.3333333 -0.1666667
+5 0.1666667 0.3333333 0.5 0.6666667 -0.1666667
+6 0.1666667 0.3333333 0.5 0.6666667 0.8333333
+> zapsmall(ginv(contr.sdif(6)))
+ [,1] [,2] [,3] [,4] [,5] [,6]
+[1,] -1 1 0 0 0 0
+[2,] 0 -1 1 0 0 0
+[3,] 0 0 -1 1 0 0
+[4,] 0 0 0 -1 1 0
+[5,] 0 0 0 0 -1 1
+>
+>
+>
+> cleanEx()
+> nameEx("corresp")
+> ### * corresp
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: corresp
+> ### Title: Simple Correspondence Analysis
+> ### Aliases: corresp corresp.xtabs corresp.data.frame corresp.default
+> ### corresp.factor corresp.formula corresp.matrix
+> ### Keywords: category multivariate
+>
+> ### ** Examples
+>
+> (ct <- corresp(~ Age + Eth, data = quine))
+First canonical correlation(s): 0.05317534
+
+ Age scores:
+ F0 F1 F2 F3
+-0.3344445 1.4246090 -1.0320002 -0.4612728
+
+ Eth scores:
+ A N
+-1.0563816 0.9466276
+> ## Not run: plot(ct)
+>
+> corresp(caith)
+First canonical correlation(s): 0.4463684
+
+ Row scores:
+ blue light medium dark
+-0.89679252 -0.98731818 0.07530627 1.57434710
+
+ Column scores:
+ fair red medium dark black
+-1.21871379 -0.52257500 -0.09414671 1.31888486 2.45176017
+> biplot(corresp(caith, nf = 2))
+>
+>
+>
+> cleanEx()
+> nameEx("cov.rob")
+> ### * cov.rob
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: cov.rob
+> ### Title: Resistant Estimation of Multivariate Location and Scatter
+> ### Aliases: cov.rob cov.mve cov.mcd
+> ### Keywords: robust multivariate
+>
+> ### ** Examples
+>
+> set.seed(123)
+> cov.rob(stackloss)
+$center
+ Air.Flow Water.Temp Acid.Conc. stack.loss
+ 56.3750 20.0000 85.4375 13.0625
+
+$cov
+ Air.Flow Water.Temp Acid.Conc. stack.loss
+Air.Flow 23.050000 6.666667 16.625000 19.308333
+Water.Temp 6.666667 5.733333 5.333333 7.733333
+Acid.Conc. 16.625000 5.333333 34.395833 13.837500
+stack.loss 19.308333 7.733333 13.837500 18.462500
+
+$msg
+[1] "20 singular samples of size 5 out of 2500"
+
+$crit
+[1] 19.89056
+
+$best
+ [1] 5 6 7 8 9 10 11 12 15 16 18 19 20
+
+$n.obs
+[1] 21
+
+> cov.rob(stack.x, method = "mcd", nsamp = "exact")
+$center
+ Air.Flow Water.Temp Acid.Conc.
+ 56.70588 20.23529 85.52941
+
+$cov
+ Air.Flow Water.Temp Acid.Conc.
+Air.Flow 23.470588 7.573529 16.102941
+Water.Temp 7.573529 6.316176 5.367647
+Acid.Conc. 16.102941 5.367647 32.389706
+
+$msg
+[1] "266 singular samples of size 4 out of 5985"
+
+$crit
+[1] 5.472581
+
+$best
+ [1] 4 5 6 7 8 9 10 11 12 13 14 20
+
+$n.obs
+[1] 21
+
+>
+>
+>
+> cleanEx()
+> nameEx("cov.trob")
+> ### * cov.trob
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: cov.trob
+> ### Title: Covariance Estimation for Multivariate t Distribution
+> ### Aliases: cov.trob
+> ### Keywords: multivariate
+>
+> ### ** Examples
+>
+> cov.trob(stackloss)
+$cov
+ Air.Flow Water.Temp Acid.Conc. stack.loss
+Air.Flow 60.47035 17.027203 18.554452 62.28032
+Water.Temp 17.02720 8.085857 5.604132 20.50469
+Acid.Conc. 18.55445 5.604132 24.404633 16.91085
+stack.loss 62.28032 20.504687 16.910855 72.80743
+
+$center
+ Air.Flow Water.Temp Acid.Conc. stack.loss
+ 58.96905 20.79263 86.05588 16.09028
+
+$n.obs
+[1] 21
+
+$call
+cov.trob(x = stackloss)
+
+$iter
+[1] 5
+
+>
+>
+>
+> cleanEx()
+> nameEx("denumerate")
+> ### * denumerate
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: denumerate
+> ### Title: Transform an Allowable Formula for 'loglm' into one for 'terms'
+> ### Aliases: denumerate denumerate.formula
+> ### Keywords: models
+>
+> ### ** Examples
+>
+> denumerate(~(1+2+3)^3 + a/b)
+~(.v1 + .v2 + .v3)^3 + a/b
+> ## Not run: ~ (.v1 + .v2 + .v3)^3 + a/b
+>
+>
+>
+> cleanEx()
+> nameEx("dose.p")
+> ### * dose.p
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: dose.p
+> ### Title: Predict Doses for Binomial Assay model
+> ### Aliases: dose.p print.glm.dose
+> ### Keywords: regression models
+>
+> ### ** Examples
+>
+> ldose <- rep(0:5, 2)
+> numdead <- c(1, 4, 9, 13, 18, 20, 0, 2, 6, 10, 12, 16)
+> sex <- factor(rep(c("M", "F"), c(6, 6)))
+> SF <- cbind(numdead, numalive = 20 - numdead)
+> budworm.lg0 <- glm(SF ~ sex + ldose - 1, family = binomial)
+>
+> dose.p(budworm.lg0, cf = c(1,3), p = 1:3/4)
+ Dose SE
+p = 0.25: 2.231265 0.2499089
+p = 0.50: 3.263587 0.2297539
+p = 0.75: 4.295910 0.2746874
+> dose.p(update(budworm.lg0, family = binomial(link=probit)),
++ cf = c(1,3), p = 1:3/4)
+ Dose SE
+p = 0.25: 2.191229 0.2384478
+p = 0.50: 3.257703 0.2240685
+p = 0.75: 4.324177 0.2668745
+>
+>
+>
+> cleanEx()
+> nameEx("dropterm")
+> ### * dropterm
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: dropterm
+> ### Title: Try All One-Term Deletions from a Model
+> ### Aliases: dropterm dropterm.default dropterm.glm dropterm.lm
+> ### Keywords: models
+>
+> ### ** Examples
+>
+> quine.hi <- aov(log(Days + 2.5) ~ .^4, quine)
+> quine.nxt <- update(quine.hi, . ~ . - Eth:Sex:Age:Lrn)
+> dropterm(quine.nxt, test= "F")
+Single term deletions
+
+Model:
+log(Days + 2.5) ~ Eth + Sex + Age + Lrn + Eth:Sex + Eth:Age +
+ Eth:Lrn + Sex:Age + Sex:Lrn + Age:Lrn + Eth:Sex:Age + Eth:Sex:Lrn +
+ Eth:Age:Lrn + Sex:Age:Lrn
+ Df Sum of Sq RSS AIC F Value Pr(F)
+<none> 64.099 -68.184
+Eth:Sex:Age 3 0.97387 65.073 -71.982 0.60773 0.61125
+Eth:Sex:Lrn 1 1.57879 65.678 -66.631 2.95567 0.08816 .
+Eth:Age:Lrn 2 2.12841 66.227 -67.415 1.99230 0.14087
+Sex:Age:Lrn 2 1.46623 65.565 -68.882 1.37247 0.25743
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+> quine.stp <- stepAIC(quine.nxt,
++ scope = list(upper = ~Eth*Sex*Age*Lrn, lower = ~1),
++ trace = FALSE)
+> dropterm(quine.stp, test = "F")
+Single term deletions
+
+Model:
+log(Days + 2.5) ~ Eth + Sex + Age + Lrn + Eth:Sex + Eth:Age +
+ Eth:Lrn + Sex:Age + Sex:Lrn + Age:Lrn + Eth:Sex:Lrn + Eth:Age:Lrn
+ Df Sum of Sq RSS AIC F Value Pr(F)
+<none> 66.600 -72.597
+Sex:Age 3 10.7959 77.396 -56.663 6.7542 0.0002933 ***
+Eth:Sex:Lrn 1 3.0325 69.632 -68.096 5.6916 0.0185476 *
+Eth:Age:Lrn 2 2.0960 68.696 -72.072 1.9670 0.1441822
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+> quine.3 <- update(quine.stp, . ~ . - Eth:Age:Lrn)
+> dropterm(quine.3, test = "F")
+Single term deletions
+
+Model:
+log(Days + 2.5) ~ Eth + Sex + Age + Lrn + Eth:Sex + Eth:Age +
+ Eth:Lrn + Sex:Age + Sex:Lrn + Age:Lrn + Eth:Sex:Lrn
+ Df Sum of Sq RSS AIC F Value Pr(F)
+<none> 68.696 -72.072
+Eth:Age 3 3.0312 71.727 -71.768 1.8679 0.1383323
+Sex:Age 3 11.4272 80.123 -55.607 7.0419 0.0002037 ***
+Age:Lrn 2 2.8149 71.511 -70.209 2.6020 0.0780701 .
+Eth:Sex:Lrn 1 4.6956 73.391 -64.419 8.6809 0.0038268 **
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+> quine.4 <- update(quine.3, . ~ . - Eth:Age)
+> dropterm(quine.4, test = "F")
+Single term deletions
+
+Model:
+log(Days + 2.5) ~ Eth + Sex + Age + Lrn + Eth:Sex + Eth:Lrn +
+ Sex:Age + Sex:Lrn + Age:Lrn + Eth:Sex:Lrn
+ Df Sum of Sq RSS AIC F Value Pr(F)
+<none> 71.727 -71.768
+Sex:Age 3 11.5656 83.292 -55.942 6.9873 0.0002147 ***
+Age:Lrn 2 2.9118 74.639 -69.959 2.6387 0.0752793 .
+Eth:Sex:Lrn 1 6.8181 78.545 -60.511 12.3574 0.0006052 ***
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+> quine.5 <- update(quine.4, . ~ . - Age:Lrn)
+> dropterm(quine.5, test = "F")
+Single term deletions
+
+Model:
+log(Days + 2.5) ~ Eth + Sex + Age + Lrn + Eth:Sex + Eth:Lrn +
+ Sex:Age + Sex:Lrn + Eth:Sex:Lrn
+ Df Sum of Sq RSS AIC F Value Pr(F)
+<none> 74.639 -69.959
+Sex:Age 3 9.9002 84.539 -57.774 5.8362 0.0008944 ***
+Eth:Sex:Lrn 1 6.2988 80.937 -60.130 11.1396 0.0010982 **
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+>
+> house.glm0 <- glm(Freq ~ Infl*Type*Cont + Sat, family=poisson,
++ data = housing)
+> house.glm1 <- update(house.glm0, . ~ . + Sat*(Infl+Type+Cont))
+> dropterm(house.glm1, test = "Chisq")
+Single term deletions
+
+Model:
+Freq ~ Infl + Type + Cont + Sat + Infl:Type + Infl:Cont + Type:Cont +
+ Infl:Sat + Type:Sat + Cont:Sat + Infl:Type:Cont
+ Df Deviance AIC LRT Pr(Chi)
+<none> 38.662 455.63
+Infl:Sat 4 147.780 556.75 109.117 < 2.2e-16 ***
+Type:Sat 6 100.889 505.86 62.227 1.586e-11 ***
+Cont:Sat 2 54.722 467.69 16.060 0.0003256 ***
+Infl:Type:Cont 6 43.952 448.92 5.290 0.5072454
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+>
+>
+>
+> cleanEx()
+> nameEx("eagles")
+> ### * eagles
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: eagles
+> ### Title: Foraging Ecology of Bald Eagles
+> ### Aliases: eagles
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> eagles.glm <- glm(cbind(y, n - y) ~ P*A + V, data = eagles,
++ family = binomial)
+> dropterm(eagles.glm)
+Single term deletions
+
+Model:
+cbind(y, n - y) ~ P * A + V
+ Df Deviance AIC
+<none> 0.333 23.073
+V 1 53.737 74.478
+P:A 1 6.956 27.696
+> prof <- profile(eagles.glm)
+> plot(prof)
+> pairs(prof)
+>
+>
+>
+> cleanEx()
+> nameEx("epil")
+> ### * epil
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: epil
+> ### Title: Seizure Counts for Epileptics
+> ### Aliases: epil
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> summary(glm(y ~ lbase*trt + lage + V4, family = poisson,
++ data = epil), cor = FALSE)
+
+Call:
+glm(formula = y ~ lbase * trt + lage + V4, family = poisson,
+ data = epil)
+
+Deviance Residuals:
+ Min 1Q Median 3Q Max
+-5.0915 -1.4126 -0.2739 0.7580 10.7711
+
+Coefficients:
+ Estimate Std. Error z value Pr(>|z|)
+(Intercept) 1.89791 0.04260 44.552 < 2e-16 ***
+lbase 0.94862 0.04360 21.759 < 2e-16 ***
+trtprogabide -0.34588 0.06100 -5.670 1.42e-08 ***
+lage 0.88760 0.11650 7.619 2.56e-14 ***
+V4 -0.15977 0.05458 -2.927 0.00342 **
+lbase:trtprogabide 0.56154 0.06352 8.841 < 2e-16 ***
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+(Dispersion parameter for poisson family taken to be 1)
+
+ Null deviance: 2517.83 on 235 degrees of freedom
+Residual deviance: 869.07 on 230 degrees of freedom
+AIC: 1647
+
+Number of Fisher Scoring iterations: 5
+
+> epil2 <- epil[epil$period == 1, ]
+> epil2["period"] <- rep(0, 59); epil2["y"] <- epil2["base"]
+> epil["time"] <- 1; epil2["time"] <- 4
+> epil2 <- rbind(epil, epil2)
+> epil2$pred <- unclass(epil2$trt) * (epil2$period > 0)
+> epil2$subject <- factor(epil2$subject)
+> epil3 <- aggregate(epil2, list(epil2$subject, epil2$period > 0),
++ function(x) if(is.numeric(x)) sum(x) else x[1])
+> epil3$pred <- factor(epil3$pred,
++ labels = c("base", "placebo", "drug"))
+>
+> contrasts(epil3$pred) <- structure(contr.sdif(3),
++ dimnames = list(NULL, c("placebo-base", "drug-placebo")))
+> summary(glm(y ~ pred + factor(subject) + offset(log(time)),
++ family = poisson, data = epil3), cor = FALSE)
+
+Call:
+glm(formula = y ~ pred + factor(subject) + offset(log(time)),
+ family = poisson, data = epil3)
+
+Deviance Residuals:
+ Min 1Q Median 3Q Max
+-5.2928 -0.7350 0.0000 0.6997 4.7145
+
+Coefficients:
+ Estimate Std. Error z value Pr(>|z|)
+(Intercept) 1.122e+00 2.008e-01 5.590 2.28e-08 ***
+predplacebo-base 1.087e-01 4.691e-02 2.318 0.020474 *
+preddrug-placebo -1.016e-01 6.507e-02 -1.561 0.118431
+factor(subject)2 -2.300e-15 2.828e-01 0.000 1.000000
+factor(subject)3 -3.857e-01 3.144e-01 -1.227 0.219894
+factor(subject)4 -1.744e-01 2.960e-01 -0.589 0.555847
+factor(subject)5 1.577e+00 2.197e-01 7.178 7.08e-13 ***
+factor(subject)6 6.729e-01 2.458e-01 2.738 0.006182 **
+factor(subject)7 -4.082e-02 2.858e-01 -0.143 0.886411
+factor(subject)8 1.758e+00 2.166e-01 8.117 4.77e-16 ***
+factor(subject)9 5.878e-01 2.494e-01 2.356 0.018454 *
+factor(subject)10 5.423e-01 2.515e-01 2.156 0.031060 *
+factor(subject)11 1.552e+00 2.202e-01 7.048 1.81e-12 ***
+factor(subject)12 9.243e-01 2.364e-01 3.910 9.22e-05 ***
+factor(subject)13 3.075e-01 2.635e-01 1.167 0.243171
+factor(subject)14 1.212e+00 2.278e-01 5.320 1.04e-07 ***
+factor(subject)15 1.765e+00 2.164e-01 8.153 3.54e-16 ***
+factor(subject)16 9.708e-01 2.348e-01 4.134 3.57e-05 ***
+factor(subject)17 -4.082e-02 2.858e-01 -0.143 0.886411
+factor(subject)18 2.236e+00 2.104e-01 10.629 < 2e-16 ***
+factor(subject)19 2.776e-01 2.651e-01 1.047 0.295060
+factor(subject)20 3.646e-01 2.603e-01 1.401 0.161324
+factor(subject)21 3.922e-02 2.801e-01 0.140 0.888645
+factor(subject)22 -8.338e-02 2.889e-01 -0.289 0.772894
+factor(subject)23 1.823e-01 2.708e-01 0.673 0.500777
+factor(subject)24 8.416e-01 2.393e-01 3.517 0.000436 ***
+factor(subject)25 2.069e+00 2.123e-01 9.750 < 2e-16 ***
+factor(subject)26 -5.108e-01 3.266e-01 -1.564 0.117799
+factor(subject)27 -2.231e-01 3.000e-01 -0.744 0.456990
+factor(subject)28 1.386e+00 2.236e-01 6.200 5.66e-10 ***
+factor(subject)29 1.604e+00 2.227e-01 7.203 5.90e-13 ***
+factor(subject)30 1.023e+00 2.372e-01 4.313 1.61e-05 ***
+factor(subject)31 9.149e-02 2.821e-01 0.324 0.745700
+factor(subject)32 -3.111e-02 2.909e-01 -0.107 0.914822
+factor(subject)33 4.710e-01 2.597e-01 1.814 0.069736 .
+factor(subject)34 3.887e-01 2.640e-01 1.473 0.140879
+factor(subject)35 1.487e+00 2.250e-01 6.609 3.87e-11 ***
+factor(subject)36 3.598e-01 2.656e-01 1.355 0.175551
+factor(subject)37 -1.221e-01 2.979e-01 -0.410 0.681943
+factor(subject)38 1.344e+00 2.283e-01 5.889 3.90e-09 ***
+factor(subject)39 1.082e+00 2.354e-01 4.596 4.30e-06 ***
+factor(subject)40 -7.687e-01 3.634e-01 -2.116 0.034384 *
+factor(subject)41 1.656e-01 2.772e-01 0.597 0.550234
+factor(subject)42 5.227e-02 2.848e-01 0.184 0.854388
+factor(subject)43 1.543e+00 2.239e-01 6.891 5.54e-12 ***
+factor(subject)44 9.605e-01 2.393e-01 4.014 5.96e-05 ***
+factor(subject)45 1.177e+00 2.326e-01 5.061 4.18e-07 ***
+factor(subject)46 -5.275e-01 3.355e-01 -1.572 0.115840
+factor(subject)47 1.053e+00 2.363e-01 4.456 8.35e-06 ***
+factor(subject)48 -5.275e-01 3.355e-01 -1.572 0.115840
+factor(subject)49 2.949e+00 2.082e-01 14.168 < 2e-16 ***
+factor(subject)50 3.887e-01 2.640e-01 1.473 0.140879
+factor(subject)51 1.038e+00 2.367e-01 4.385 1.16e-05 ***
+factor(subject)52 5.711e-01 2.548e-01 2.241 0.025023 *
+factor(subject)53 1.670e+00 2.215e-01 7.538 4.76e-14 ***
+factor(subject)54 4.443e-01 2.611e-01 1.702 0.088759 .
+factor(subject)55 2.674e-01 2.709e-01 0.987 0.323618
+factor(subject)56 1.124e+00 2.341e-01 4.800 1.59e-06 ***
+factor(subject)57 2.674e-01 2.709e-01 0.987 0.323618
+factor(subject)58 -6.017e-01 3.436e-01 -1.751 0.079911 .
+factor(subject)59 -7.556e-02 2.942e-01 -0.257 0.797331
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+(Dispersion parameter for poisson family taken to be 1)
+
+ Null deviance: 3180.82 on 117 degrees of freedom
+Residual deviance: 303.16 on 57 degrees of freedom
+AIC: 1003.5
+
+Number of Fisher Scoring iterations: 5
+
+>
+> summary(glmmPQL(y ~ lbase*trt + lage + V4,
++ random = ~ 1 | subject,
++ family = poisson, data = epil))
+Loading required package: nlme
+iteration 1
+iteration 2
+iteration 3
+iteration 4
+iteration 5
+Linear mixed-effects model fit by maximum likelihood
+ Data: epil
+ AIC BIC logLik
+ NA NA NA
+
+Random effects:
+ Formula: ~1 | subject
+ (Intercept) Residual
+StdDev: 0.4442704 1.400807
+
+Variance function:
+ Structure: fixed weights
+ Formula: ~invwt
+Fixed effects: y ~ lbase * trt + lage + V4
+ Value Std.Error DF t-value p-value
+(Intercept) 1.8696677 0.1055620 176 17.711554 0.0000
+lbase 0.8818228 0.1292834 54 6.820849 0.0000
+trtprogabide -0.3095253 0.1490438 54 -2.076740 0.0426
+lage 0.5335460 0.3463119 54 1.540652 0.1292
+V4 -0.1597696 0.0774521 176 -2.062819 0.0406
+lbase:trtprogabide 0.3415425 0.2033325 54 1.679725 0.0988
+ Correlation:
+ (Intr) lbase trtprg lage V4
+lbase -0.126
+trtprogabide -0.691 0.089
+lage -0.103 -0.038 0.088
+V4 -0.162 0.000 0.000 0.000
+lbase:trtprogabide 0.055 -0.645 -0.184 0.267 0.000
+
+Standardized Within-Group Residuals:
+ Min Q1 Med Q3 Max
+-2.13240534 -0.63871136 -0.08486339 0.41960195 4.97872138
+
+Number of Observations: 236
+Number of Groups: 59
+> summary(glmmPQL(y ~ pred, random = ~1 | subject,
++ family = poisson, data = epil3))
+iteration 1
+iteration 2
+iteration 3
+iteration 4
+iteration 5
+iteration 6
+iteration 7
+iteration 8
+Linear mixed-effects model fit by maximum likelihood
+ Data: epil3
+ AIC BIC logLik
+ NA NA NA
+
+Random effects:
+ Formula: ~1 | subject
+ (Intercept) Residual
+StdDev: 0.7257895 2.16629
+
+Variance function:
+ Structure: fixed weights
+ Formula: ~invwt
+Fixed effects: y ~ pred
+ Value Std.Error DF t-value p-value
+(Intercept) 3.213631 0.10569117 58 30.405865 0.0000
+predplacebo-base 0.110855 0.09989089 57 1.109763 0.2718
+preddrug-placebo -0.105613 0.13480483 57 -0.783450 0.4366
+ Correlation:
+ (Intr) prdpl-
+predplacebo-base 0.081
+preddrug-placebo -0.010 -0.700
+
+Standardized Within-Group Residuals:
+ Min Q1 Med Q3 Max
+-2.0446864 -0.4765135 -0.1975651 0.3145761 2.6532834
+
+Number of Observations: 118
+Number of Groups: 59
+>
+>
+>
+> cleanEx()
+
+detaching âpackage:nlmeâ
+
+> nameEx("farms")
+> ### * farms
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: farms
+> ### Title: Ecological Factors in Farm Management
+> ### Aliases: farms
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> farms.mca <- mca(farms, abbrev = TRUE) # Use levels as names
+> eqscplot(farms.mca$cs, type = "n")
+> text(farms.mca$rs, cex = 0.7)
+> text(farms.mca$cs, labels = dimnames(farms.mca$cs)[[1]], cex = 0.7)
+>
+>
+>
+> cleanEx()
+> nameEx("fitdistr")
+> ### * fitdistr
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: fitdistr
+> ### Title: Maximum-likelihood Fitting of Univariate Distributions
+> ### Aliases: fitdistr
+> ### Keywords: distribution htest
+>
+> ### ** Examples
+>
+> ## avoid spurious accuracy
+> op <- options(digits = 3)
+> set.seed(123)
+> x <- rgamma(100, shape = 5, rate = 0.1)
+> fitdistr(x, "gamma")
+ shape rate
+ 6.4870 0.1365
+ (0.8946) (0.0196)
+> ## now do this directly with more control.
+> fitdistr(x, dgamma, list(shape = 1, rate = 0.1), lower = 0.001)
+ shape rate
+ 6.4869 0.1365
+ (0.8944) (0.0196)
+>
+> set.seed(123)
+> x2 <- rt(250, df = 9)
+> fitdistr(x2, "t", df = 9)
+ m s
+ -0.0107 1.0441
+ ( 0.0722) ( 0.0543)
+> ## allow df to vary: not a very good idea!
+> fitdistr(x2, "t")
+Warning in dt((x - m)/s, df, log = TRUE) : NaNs produced
+ m s df
+ -0.00965 1.00617 6.62729
+ ( 0.07147) ( 0.07707) ( 2.71033)
+> ## now do fixed-df fit directly with more control.
+> mydt <- function(x, m, s, df) dt((x-m)/s, df)/s
+> fitdistr(x2, mydt, list(m = 0, s = 1), df = 9, lower = c(-Inf, 0))
+ m s
+ -0.0107 1.0441
+ ( 0.0722) ( 0.0543)
+>
+> set.seed(123)
+> x3 <- rweibull(100, shape = 4, scale = 100)
+> fitdistr(x3, "weibull")
+ shape scale
+ 4.080 99.984
+ ( 0.313) ( 2.582)
+>
+> set.seed(123)
+> x4 <- rnegbin(500, mu = 5, theta = 4)
+> fitdistr(x4, "Negative Binomial")
+ size mu
+ 4.216 4.945
+ (0.504) (0.147)
+> options(op)
+>
+>
+>
+> cleanEx()
+> nameEx("fractions")
+> ### * fractions
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: fractions
+> ### Title: Rational Approximation
+> ### Aliases: fractions Math.fractions Ops.fractions Summary.fractions
+> ### [.fractions [<-.fractions as.character.fractions as.fractions
+> ### is.fractions print.fractions t.fractions
+> ### Keywords: math
+>
+> ### ** Examples
+>
+> X <- matrix(runif(25), 5, 5)
+> zapsmall(solve(X, X/5)) # print near-zeroes as zero
+ [,1] [,2] [,3] [,4] [,5]
+[1,] 0.2 0.0 0.0 0.0 0.0
+[2,] 0.0 0.2 0.0 0.0 0.0
+[3,] 0.0 0.0 0.2 0.0 0.0
+[4,] 0.0 0.0 0.0 0.2 0.0
+[5,] 0.0 0.0 0.0 0.0 0.2
+> fractions(solve(X, X/5))
+ [,1] [,2] [,3] [,4] [,5]
+[1,] 1/5 0 0 0 0
+[2,] 0 1/5 0 0 0
+[3,] 0 0 1/5 0 0
+[4,] 0 0 0 1/5 0
+[5,] 0 0 0 0 1/5
+> fractions(solve(X, X/5)) + 1
+ [,1] [,2] [,3] [,4] [,5]
+[1,] 6/5 1 1 1 1
+[2,] 1 6/5 1 1 1
+[3,] 1 1 6/5 1 1
+[4,] 1 1 1 6/5 1
+[5,] 1 1 1 1 6/5
+>
+>
+>
+> cleanEx()
+> nameEx("galaxies")
+> ### * galaxies
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: galaxies
+> ### Title: Velocities for 82 Galaxies
+> ### Aliases: galaxies
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> gal <- galaxies/1000
+> c(width.SJ(gal, method = "dpi"), width.SJ(gal))
+[1] 3.256151 2.566423
+> plot(x = c(0, 40), y = c(0, 0.3), type = "n", bty = "l",
++ xlab = "velocity of galaxy (1000km/s)", ylab = "density")
+> rug(gal)
+> lines(density(gal, width = 3.25, n = 200), lty = 1)
+> lines(density(gal, width = 2.56, n = 200), lty = 3)
+>
+>
+>
+> cleanEx()
+> nameEx("gamma.shape.glm")
+> ### * gamma.shape.glm
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: gamma.shape
+> ### Title: Estimate the Shape Parameter of the Gamma Distribution in a GLM
+> ### Fit
+> ### Aliases: gamma.shape gamma.shape.glm print.gamma.shape
+> ### Keywords: models
+>
+> ### ** Examples
+>
+> clotting <- data.frame(
++ u = c(5,10,15,20,30,40,60,80,100),
++ lot1 = c(118,58,42,35,27,25,21,19,18),
++ lot2 = c(69,35,26,21,18,16,13,12,12))
+> clot1 <- glm(lot1 ~ log(u), data = clotting, family = Gamma)
+> gamma.shape(clot1)
+
+Alpha: 538.1315
+SE: 253.5991
+>
+> gm <- glm(Days + 0.1 ~ Age*Eth*Sex*Lrn,
++ quasi(link=log, variance="mu^2"), quine,
++ start = c(3, rep(0,31)))
+> gamma.shape(gm, verbose = TRUE)
+Initial estimate: 1.060344
+Iter. 1 Alpha: 1.238408
+Iter. 2 Alpha: 1.276997
+Iter. 3 Alpha: 1.278343
+Iter. 4 Alpha: 1.278345
+
+Alpha: 1.2783449
+SE: 0.1345175
+> summary(gm, dispersion = gamma.dispersion(gm)) # better summary
+
+Call:
+glm(formula = Days + 0.1 ~ Age * Eth * Sex * Lrn, family = quasi(link = log,
+ variance = "mu^2"), data = quine, start = c(3, rep(0, 31)))
+
+Deviance Residuals:
+ Min 1Q Median 3Q Max
+-3.0385 -0.7164 -0.1532 0.3863 1.3087
+
+Coefficients: (4 not defined because of singularities)
+ Estimate Std. Error z value Pr(>|z|)
+(Intercept) 3.06105 0.44223 6.922 4.46e-12 ***
+AgeF1 -0.61870 0.59331 -1.043 0.297041
+AgeF2 -2.31911 0.98885 -2.345 0.019014 *
+AgeF3 -0.37623 0.53149 -0.708 0.479020
+EthN -0.13789 0.62540 -0.220 0.825496
+SexM -0.48844 0.59331 -0.823 0.410369
+LrnSL -1.92965 0.98885 -1.951 0.051009 .
+AgeF1:EthN 0.10249 0.82338 0.124 0.900942
+AgeF2:EthN -0.50874 1.39845 -0.364 0.716017
+AgeF3:EthN 0.06314 0.74584 0.085 0.932534
+AgeF1:SexM 0.40695 0.94847 0.429 0.667884
+AgeF2:SexM 3.06173 1.11626 2.743 0.006091 **
+AgeF3:SexM 1.10841 0.74208 1.494 0.135267
+EthN:SexM -0.74217 0.82338 -0.901 0.367394
+AgeF1:LrnSL 2.60967 1.10114 2.370 0.017789 *
+AgeF2:LrnSL 4.78434 1.36304 3.510 0.000448 ***
+AgeF3:LrnSL NA NA NA NA
+EthN:LrnSL 2.22936 1.39845 1.594 0.110899
+SexM:LrnSL 1.56531 1.18112 1.325 0.185077
+AgeF1:EthN:SexM -0.30235 1.32176 -0.229 0.819065
+AgeF2:EthN:SexM 0.29742 1.57035 0.189 0.849780
+AgeF3:EthN:SexM 0.82215 1.03277 0.796 0.425995
+AgeF1:EthN:LrnSL -3.50803 1.54655 -2.268 0.023311 *
+AgeF2:EthN:LrnSL -3.33529 1.92481 -1.733 0.083133 .
+AgeF3:EthN:LrnSL NA NA NA NA
+AgeF1:SexM:LrnSL -2.39791 1.51050 -1.587 0.112400
+AgeF2:SexM:LrnSL -4.12161 1.60698 -2.565 0.010323 *
+AgeF3:SexM:LrnSL NA NA NA NA
+EthN:SexM:LrnSL -0.15305 1.66253 -0.092 0.926653
+AgeF1:EthN:SexM:LrnSL 2.13480 2.08685 1.023 0.306317
+AgeF2:EthN:SexM:LrnSL 2.11886 2.27882 0.930 0.352473
+AgeF3:EthN:SexM:LrnSL NA NA NA NA
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+(Dispersion parameter for quasi family taken to be 0.7822615)
+
+ Null deviance: 190.40 on 145 degrees of freedom
+Residual deviance: 128.36 on 118 degrees of freedom
+AIC: NA
+
+Number of Fisher Scoring iterations: 7
+
+>
+>
+>
+> cleanEx()
+> nameEx("gehan")
+> ### * gehan
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: gehan
+> ### Title: Remission Times of Leukaemia Patients
+> ### Aliases: gehan
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> library(survival)
+Loading required package: splines
+> gehan.surv <- survfit(Surv(time, cens) ~ treat, data = gehan,
++ conf.type = "log-log")
+> summary(gehan.surv)
+Call: survfit(formula = Surv(time, cens) ~ treat, data = gehan, conf.type = "log-log")
+
+ treat=6-MP
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 6 21 3 0.857 0.0764 0.620 0.952
+ 7 17 1 0.807 0.0869 0.563 0.923
+ 10 15 1 0.753 0.0963 0.503 0.889
+ 13 12 1 0.690 0.1068 0.432 0.849
+ 16 11 1 0.627 0.1141 0.368 0.805
+ 22 7 1 0.538 0.1282 0.268 0.747
+ 23 6 1 0.448 0.1346 0.188 0.680
+
+ treat=control
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 1 21 2 0.9048 0.0641 0.67005 0.975
+ 2 19 2 0.8095 0.0857 0.56891 0.924
+ 3 17 1 0.7619 0.0929 0.51939 0.893
+ 4 16 2 0.6667 0.1029 0.42535 0.825
+ 5 14 2 0.5714 0.1080 0.33798 0.749
+ 8 12 4 0.3810 0.1060 0.18307 0.578
+ 11 8 2 0.2857 0.0986 0.11656 0.482
+ 12 6 2 0.1905 0.0857 0.05948 0.377
+ 15 4 1 0.1429 0.0764 0.03566 0.321
+ 17 3 1 0.0952 0.0641 0.01626 0.261
+ 22 2 1 0.0476 0.0465 0.00332 0.197
+ 23 1 1 0.0000 NaN NA NA
+
+> survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist = "exponential")
+Call:
+survreg(formula = Surv(time, cens) ~ factor(pair) + treat, data = gehan,
+ dist = "exponential")
+
+Coefficients:
+ (Intercept) factor(pair)2 factor(pair)3 factor(pair)4 factor(pair)5
+ 2.0702861 2.1476909 1.8329493 1.7718527 1.4682566
+ factor(pair)6 factor(pair)7 factor(pair)8 factor(pair)9 factor(pair)10
+ 1.8954775 0.5583010 2.5187140 2.2970513 2.4862208
+factor(pair)11 factor(pair)12 factor(pair)13 factor(pair)14 factor(pair)15
+ 1.0524472 1.8270477 1.6772567 1.7778672 2.0859913
+factor(pair)16 factor(pair)17 factor(pair)18 factor(pair)19 factor(pair)20
+ 3.0634288 0.7996252 1.5855018 1.4083884 0.4023946
+factor(pair)21 treatcontrol
+ 1.9698390 -1.7671562
+
+Scale fixed at 1
+
+Loglik(model)= -101.6 Loglik(intercept only)= -116.8
+ Chisq= 30.27 on 21 degrees of freedom, p= 0.087
+n= 42
+> summary(survreg(Surv(time, cens) ~ treat, gehan, dist = "exponential"))
+
+Call:
+survreg(formula = Surv(time, cens) ~ treat, data = gehan, dist = "exponential")
+ Value Std. Error z p
+(Intercept) 3.69 0.333 11.06 2.00e-28
+treatcontrol -1.53 0.398 -3.83 1.27e-04
+
+Scale fixed at 1
+
+Exponential distribution
+Loglik(model)= -108.5 Loglik(intercept only)= -116.8
+ Chisq= 16.49 on 1 degrees of freedom, p= 4.9e-05
+Number of Newton-Raphson Iterations: 4
+n= 42
+
+> summary(survreg(Surv(time, cens) ~ treat, gehan))
+
+Call:
+survreg(formula = Surv(time, cens) ~ treat, data = gehan)
+ Value Std. Error z p
+(Intercept) 3.516 0.252 13.96 2.61e-44
+treatcontrol -1.267 0.311 -4.08 4.51e-05
+Log(scale) -0.312 0.147 -2.12 3.43e-02
+
+Scale= 0.732
+
+Weibull distribution
+Loglik(model)= -106.6 Loglik(intercept only)= -116.4
+ Chisq= 19.65 on 1 degrees of freedom, p= 9.3e-06
+Number of Newton-Raphson Iterations: 5
+n= 42
+
+> gehan.cox <- coxph(Surv(time, cens) ~ treat, gehan)
+> summary(gehan.cox)
+Call:
+coxph(formula = Surv(time, cens) ~ treat, data = gehan)
+
+ n= 42, number of events= 30
+
+ coef exp(coef) se(coef) z Pr(>|z|)
+treatcontrol 1.5721 4.8169 0.4124 3.812 0.000138 ***
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+ exp(coef) exp(-coef) lower .95 upper .95
+treatcontrol 4.817 0.2076 2.147 10.81
+
+Concordance= 0.69 (se = 0.053 )
+Rsquare= 0.322 (max possible= 0.988 )
+Likelihood ratio test= 16.35 on 1 df, p=5.261e-05
+Wald test = 14.53 on 1 df, p=0.0001378
+Score (logrank) test = 17.25 on 1 df, p=3.283e-05
+
+>
+>
+>
+> cleanEx()
+
+detaching âpackage:survivalâ, âpackage:splinesâ
+
+> nameEx("ginv")
+> ### * ginv
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: ginv
+> ### Title: Generalized Inverse of a Matrix
+> ### Aliases: ginv
+> ### Keywords: algebra
+>
+> ### ** Examples
+>
+> ## Not run:
+> ##D # The function is currently defined as
+> ##D function(X, tol = sqrt(.Machine$double.eps))
+> ##D {
+> ##D ## Generalized Inverse of a Matrix
+> ##D dnx <- dimnames(X)
+> ##D if(is.null(dnx)) dnx <- vector("list", 2)
+> ##D s <- svd(X)
+> ##D nz <- s$d > tol * s$d[1]
+> ##D structure(
+> ##D if(any(nz)) s$v[, nz] %*% (t(s$u[, nz])/s$d[nz]) else X,
+> ##D dimnames = dnx[2:1])
+> ##D }
+> ## End(Not run)
+>
+>
+> cleanEx()
+> nameEx("glm.convert")
+> ### * glm.convert
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: glm.convert
+> ### Title: Change a Negative Binomial fit to a GLM fit
+> ### Aliases: glm.convert
+> ### Keywords: regression models
+>
+> ### ** Examples
+>
+> quine.nb1 <- glm.nb(Days ~ Sex/(Age + Eth*Lrn), data = quine)
+> quine.nbA <- glm.convert(quine.nb1)
+> quine.nbB <- update(quine.nb1, . ~ . + Sex:Age:Lrn)
+> anova(quine.nbA, quine.nbB)
+Analysis of Deviance Table
+
+Model 1: Days ~ Sex/(Age + Eth * Lrn)
+Model 2: Days ~ Sex + Sex:Age + Sex:Eth + Sex:Lrn + Sex:Eth:Lrn + Sex:Age:Lrn
+ Resid. Df Resid. Dev Df Deviance
+1 132 167.56
+2 128 166.83 4 0.723
+>
+>
+>
+> cleanEx()
+> nameEx("glm.nb")
+> ### * glm.nb
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: glm.nb
+> ### Title: Fit a Negative Binomial Generalized Linear Model
+> ### Aliases: glm.nb family.negbin logLik.negbin
+> ### Keywords: regression models
+>
+> ### ** Examples
+>
+> quine.nb1 <- glm.nb(Days ~ Sex/(Age + Eth*Lrn), data = quine)
+> quine.nb2 <- update(quine.nb1, . ~ . + Sex:Age:Lrn)
+> quine.nb3 <- update(quine.nb2, Days ~ .^4)
+> anova(quine.nb1, quine.nb2, quine.nb3)
+Likelihood ratio tests of Negative Binomial Models
+
+Response: Days
+ Model
+1 Sex/(Age + Eth * Lrn)
+2 Sex + Sex:Age + Sex:Eth + Sex:Lrn + Sex:Eth:Lrn + Sex:Age:Lrn
+3 Sex + Sex:Age + Sex:Eth + Sex:Lrn + Sex:Eth:Lrn + Sex:Age:Lrn + Sex:Age:Eth + Sex:Age:Eth:Lrn
+ theta Resid. df 2 x log-lik. Test df LR stat. Pr(Chi)
+1 1.597991 132 -1063.025
+2 1.686899 128 -1055.398 1 vs 2 4 7.627279 0.10622602
+3 1.928360 118 -1039.324 2 vs 3 10 16.073723 0.09754136
+> ## Don't show:
+> ## PR#1695
+> y <- c(7, 5, 4, 7, 5, 2, 11, 5, 5, 4, 2, 3, 4, 3, 5, 9, 6, 7, 10, 6, 12,
++ 6, 3, 5, 3, 9, 13, 0, 6, 1, 2, 0, 1, 0, 0, 4, 5, 1, 5, 3, 3, 4)
+>
+> lag1 <- c(0, 7, 5, 4, 7, 5, 2, 11, 5, 5, 4, 2, 3, 4, 3, 5, 9, 6, 7, 10,
++ 6, 12, 6, 3, 5, 3, 9, 13, 0, 6, 1, 2, 0, 1, 0, 0, 4, 5, 1, 5, 3, 3)
+>
+> lag2 <- c(0, 0, 7, 5, 4, 7, 5, 2, 11, 5, 5, 4, 2, 3, 4, 3, 5, 9, 6, 7,
++ 10, 6, 12, 6, 3, 5, 3, 9, 13, 0, 6, 1, 2, 0, 1, 0, 0, 4, 5, 1, 5, 3)
+>
+> lag3 <- c(0, 0, 0, 7, 5, 4, 7, 5, 2, 11, 5, 5, 4, 2, 3, 4, 3, 5, 9, 6,
++ 7, 10, 6, 12, 6, 3, 5, 3, 9, 13, 0, 6, 1, 2, 0, 1, 0, 0, 4, 5, 1, 5)
+>
+> (fit <- glm(y ~ lag1+lag2+lag3, family=poisson(link=identity),
++ start=c(2, 0.1, 0.1, 0.1)))
+
+Call: glm(formula = y ~ lag1 + lag2 + lag3, family = poisson(link = identity),
+ start = c(2, 0.1, 0.1, 0.1))
+
+Coefficients:
+(Intercept) lag1 lag2 lag3
+ 2.6609 0.1573 0.1424 0.1458
+
+Degrees of Freedom: 41 Total (i.e. Null); 38 Residual
+Null Deviance: 100.2
+Residual Deviance: 90.34 AIC: 225.6
+> try(glm.nb(y ~ lag1+lag2+lag3, link=identity))
+Warning in log(ifelse(y == 0, 1, y/mu)) : NaNs produced
+Error : no valid set of coefficients has been found: please supply starting values
+> glm.nb(y ~ lag1+lag2+lag3, link=identity, start=c(2, 0.1, 0.1, 0.1))
+
+Call: glm.nb(formula = y ~ lag1 + lag2 + lag3, start = c(2, 0.1, 0.1,
+ 0.1), link = identity, init.theta = 4.406504429)
+
+Coefficients:
+(Intercept) lag1 lag2 lag3
+ 2.6298 0.1774 0.1407 0.1346
+
+Degrees of Freedom: 41 Total (i.e. Null); 38 Residual
+Null Deviance: 55.07
+Residual Deviance: 50.09 AIC: 215.9
+> glm.nb(y ~ lag1+lag2+lag3, link=identity, start=coef(fit))
+
+Call: glm.nb(formula = y ~ lag1 + lag2 + lag3, start = coef(fit), link = identity,
+ init.theta = 4.406504429)
+
+Coefficients:
+(Intercept) lag1 lag2 lag3
+ 2.6298 0.1774 0.1407 0.1346
+
+Degrees of Freedom: 41 Total (i.e. Null); 38 Residual
+Null Deviance: 55.07
+Residual Deviance: 50.09 AIC: 215.9
+> glm.nb(y ~ lag1+lag2+lag3, link=identity, etastart=rep(5, 42))
+
+Call: glm.nb(formula = y ~ lag1 + lag2 + lag3, etastart = rep(5, 42),
+ link = identity, init.theta = 4.406504429)
+
+Coefficients:
+(Intercept) lag1 lag2 lag3
+ 2.6298 0.1774 0.1407 0.1346
+
+Degrees of Freedom: 41 Total (i.e. Null); 38 Residual
+Null Deviance: 55.07
+Residual Deviance: 50.09 AIC: 215.9
+> ## End Don't show
+>
+>
+> cleanEx()
+> nameEx("glmmPQL")
+> ### * glmmPQL
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: glmmPQL
+> ### Title: Fit Generalized Linear Mixed Models via PQL
+> ### Aliases: glmmPQL
+> ### Keywords: models
+>
+> ### ** Examples
+>
+> library(nlme) # will be loaded automatically if omitted
+> summary(glmmPQL(y ~ trt + I(week > 2), random = ~ 1 | ID,
++ family = binomial, data = bacteria))
+iteration 1
+iteration 2
+iteration 3
+iteration 4
+iteration 5
+iteration 6
+Linear mixed-effects model fit by maximum likelihood
+ Data: bacteria
+ AIC BIC logLik
+ NA NA NA
+
+Random effects:
+ Formula: ~1 | ID
+ (Intercept) Residual
+StdDev: 1.410637 0.7800511
+
+Variance function:
+ Structure: fixed weights
+ Formula: ~invwt
+Fixed effects: y ~ trt + I(week > 2)
+ Value Std.Error DF t-value p-value
+(Intercept) 3.412014 0.5185033 169 6.580506 0.0000
+trtdrug -1.247355 0.6440635 47 -1.936696 0.0588
+trtdrug+ -0.754327 0.6453978 47 -1.168779 0.2484
+I(week > 2)TRUE -1.607257 0.3583379 169 -4.485311 0.0000
+ Correlation:
+ (Intr) trtdrg trtdr+
+trtdrug -0.598
+trtdrug+ -0.571 0.460
+I(week > 2)TRUE -0.537 0.047 -0.001
+
+Standardized Within-Group Residuals:
+ Min Q1 Med Q3 Max
+-5.1985361 0.1572336 0.3513075 0.4949482 1.7448845
+
+Number of Observations: 220
+Number of Groups: 50
+> ## Don't show:
+> # an example of offset
+> summary(glmmPQL(y ~ trt + week, random = ~ 1 | ID,
++ family = binomial, data = bacteria))
+iteration 1
+iteration 2
+iteration 3
+iteration 4
+iteration 5
+iteration 6
+Linear mixed-effects model fit by maximum likelihood
+ Data: bacteria
+ AIC BIC logLik
+ NA NA NA
+
+Random effects:
+ Formula: ~1 | ID
+ (Intercept) Residual
+StdDev: 1.325243 0.7903088
+
+Variance function:
+ Structure: fixed weights
+ Formula: ~invwt
+Fixed effects: y ~ trt + week
+ Value Std.Error DF t-value p-value
+(Intercept) 3.0302276 0.4791396 169 6.324310 0.0000
+trtdrug -1.2176812 0.6160113 47 -1.976719 0.0540
+trtdrug+ -0.7886376 0.6193895 47 -1.273250 0.2092
+week -0.1446463 0.0392343 169 -3.686730 0.0003
+ Correlation:
+ (Intr) trtdrg trtdr+
+trtdrug -0.622
+trtdrug+ -0.609 0.464
+week -0.481 0.050 0.030
+
+Standardized Within-Group Residuals:
+ Min Q1 Med Q3 Max
+-4.2868074 0.2039043 0.3140333 0.5440835 1.9754065
+
+Number of Observations: 220
+Number of Groups: 50
+> summary(glmmPQL(y ~ trt + week + offset(week), random = ~ 1 | ID,
++ family = binomial, data = bacteria))
+iteration 1
+iteration 2
+iteration 3
+iteration 4
+iteration 5
+iteration 6
+Linear mixed-effects model fit by maximum likelihood
+ Data: bacteria
+ AIC BIC logLik
+ NA NA NA
+
+Random effects:
+ Formula: ~1 | ID
+ (Intercept) Residual
+StdDev: 1.325243 0.7903088
+
+Variance function:
+ Structure: fixed weights
+ Formula: ~invwt
+Fixed effects: y ~ trt + week + offset(week)
+ Value Std.Error DF t-value p-value
+(Intercept) 3.0302276 0.4791396 169 6.324310 0.0000
+trtdrug -1.2176812 0.6160113 47 -1.976719 0.0540
+trtdrug+ -0.7886376 0.6193895 47 -1.273250 0.2092
+week -1.1446463 0.0392343 169 -29.174622 0.0000
+ Correlation:
+ (Intr) trtdrg trtdr+
+trtdrug -0.622
+trtdrug+ -0.609 0.464
+week -0.481 0.050 0.030
+
+Standardized Within-Group Residuals:
+ Min Q1 Med Q3 Max
+-4.2868074 0.2039043 0.3140333 0.5440835 1.9754065
+
+Number of Observations: 220
+Number of Groups: 50
+> ## End Don't show
+>
+>
+> cleanEx()
+
+detaching âpackage:nlmeâ
+
+> nameEx("housing")
+> ### * housing
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: housing
+> ### Title: Frequency Table from a Copenhagen Housing Conditions Survey
+> ### Aliases: housing
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> options(contrasts = c("contr.treatment", "contr.poly"))
+>
+> # Surrogate Poisson models
+> house.glm0 <- glm(Freq ~ Infl*Type*Cont + Sat, family = poisson,
++ data = housing)
+> summary(house.glm0, cor = FALSE)
+
+Call:
+glm(formula = Freq ~ Infl * Type * Cont + Sat, family = poisson,
+ data = housing)
+
+Deviance Residuals:
+ Min 1Q Median 3Q Max
+-4.5551 -1.0612 -0.0593 0.6483 4.1478
+
+Coefficients:
+ Estimate Std. Error z value Pr(>|z|)
+(Intercept) 3.136e+00 1.196e-01 26.225 < 2e-16 ***
+InflMedium 2.733e-01 1.586e-01 1.723 0.084868 .
+InflHigh -2.054e-01 1.784e-01 -1.152 0.249511
+TypeApartment 3.666e-01 1.555e-01 2.357 0.018403 *
+TypeAtrium -7.828e-01 2.134e-01 -3.668 0.000244 ***
+TypeTerrace -8.145e-01 2.157e-01 -3.775 0.000160 ***
+ContHigh -1.490e-15 1.690e-01 0.000 1.000000
+Sat.L 1.159e-01 4.038e-02 2.871 0.004094 **
+Sat.Q 2.629e-01 4.515e-02 5.824 5.76e-09 ***
+InflMedium:TypeApartment -1.177e-01 2.086e-01 -0.564 0.572571
+InflHigh:TypeApartment 1.753e-01 2.279e-01 0.769 0.441783
+InflMedium:TypeAtrium -4.068e-01 3.035e-01 -1.340 0.180118
+InflHigh:TypeAtrium -1.692e-01 3.294e-01 -0.514 0.607433
+InflMedium:TypeTerrace 6.292e-03 2.860e-01 0.022 0.982450
+InflHigh:TypeTerrace -9.305e-02 3.280e-01 -0.284 0.776633
+InflMedium:ContHigh -1.398e-01 2.279e-01 -0.613 0.539715
+InflHigh:ContHigh -6.091e-01 2.800e-01 -2.176 0.029585 *
+TypeApartment:ContHigh 5.029e-01 2.109e-01 2.385 0.017083 *
+TypeAtrium:ContHigh 6.774e-01 2.751e-01 2.462 0.013811 *
+TypeTerrace:ContHigh 1.099e+00 2.675e-01 4.106 4.02e-05 ***
+InflMedium:TypeApartment:ContHigh 5.359e-02 2.862e-01 0.187 0.851450
+InflHigh:TypeApartment:ContHigh 1.462e-01 3.380e-01 0.432 0.665390
+InflMedium:TypeAtrium:ContHigh 1.555e-01 3.907e-01 0.398 0.690597
+InflHigh:TypeAtrium:ContHigh 4.782e-01 4.441e-01 1.077 0.281619
+InflMedium:TypeTerrace:ContHigh -4.980e-01 3.671e-01 -1.357 0.174827
+InflHigh:TypeTerrace:ContHigh -4.470e-01 4.545e-01 -0.984 0.325326
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+(Dispersion parameter for poisson family taken to be 1)
+
+ Null deviance: 833.66 on 71 degrees of freedom
+Residual deviance: 217.46 on 46 degrees of freedom
+AIC: 610.43
+
+Number of Fisher Scoring iterations: 5
+
+>
+> addterm(house.glm0, ~. + Sat:(Infl+Type+Cont), test = "Chisq")
+Single term additions
+
+Model:
+Freq ~ Infl * Type * Cont + Sat
+ Df Deviance AIC LRT Pr(Chi)
+<none> 217.46 610.43
+Infl:Sat 4 111.08 512.05 106.371 < 2.2e-16 ***
+Type:Sat 6 156.79 561.76 60.669 3.292e-11 ***
+Cont:Sat 2 212.33 609.30 5.126 0.07708 .
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+>
+> house.glm1 <- update(house.glm0, . ~ . + Sat*(Infl+Type+Cont))
+> summary(house.glm1, cor = FALSE)
+
+Call:
+glm(formula = Freq ~ Infl + Type + Cont + Sat + Infl:Type + Infl:Cont +
+ Type:Cont + Infl:Sat + Type:Sat + Cont:Sat + Infl:Type:Cont,
+ family = poisson, data = housing)
+
+Deviance Residuals:
+ Min 1Q Median 3Q Max
+-1.6022 -0.5282 -0.0641 0.5757 1.9322
+
+Coefficients:
+ Estimate Std. Error z value Pr(>|z|)
+(Intercept) 3.135074 0.120112 26.101 < 2e-16 ***
+InflMedium 0.248327 0.159979 1.552 0.120602
+InflHigh -0.412645 0.184947 -2.231 0.025671 *
+TypeApartment 0.292524 0.157477 1.858 0.063231 .
+TypeAtrium -0.792847 0.214413 -3.698 0.000218 ***
+TypeTerrace -1.018074 0.221263 -4.601 4.20e-06 ***
+ContHigh -0.001407 0.169711 -0.008 0.993385
+Sat.L -0.098106 0.112592 -0.871 0.383570
+Sat.Q 0.285657 0.122283 2.336 0.019489 *
+InflMedium:TypeApartment -0.017882 0.210496 -0.085 0.932302
+InflHigh:TypeApartment 0.386869 0.233297 1.658 0.097263 .
+InflMedium:TypeAtrium -0.360311 0.304979 -1.181 0.237432
+InflHigh:TypeAtrium -0.036788 0.334793 -0.110 0.912503
+InflMedium:TypeTerrace 0.185154 0.288892 0.641 0.521580
+InflHigh:TypeTerrace 0.310749 0.334815 0.928 0.353345
+InflMedium:ContHigh -0.200060 0.228748 -0.875 0.381799
+InflHigh:ContHigh -0.725790 0.282352 -2.571 0.010155 *
+TypeApartment:ContHigh 0.569691 0.212152 2.685 0.007247 **
+TypeAtrium:ContHigh 0.702115 0.276056 2.543 0.010979 *
+TypeTerrace:ContHigh 1.215930 0.269968 4.504 6.67e-06 ***
+InflMedium:Sat.L 0.519627 0.096830 5.366 8.03e-08 ***
+InflHigh:Sat.L 1.140302 0.118180 9.649 < 2e-16 ***
+InflMedium:Sat.Q -0.064474 0.102666 -0.628 0.530004
+InflHigh:Sat.Q 0.115436 0.127798 0.903 0.366380
+TypeApartment:Sat.L -0.520170 0.109793 -4.738 2.16e-06 ***
+TypeAtrium:Sat.L -0.288484 0.149551 -1.929 0.053730 .
+TypeTerrace:Sat.L -0.998666 0.141527 -7.056 1.71e-12 ***
+TypeApartment:Sat.Q 0.055418 0.118515 0.468 0.640068
+TypeAtrium:Sat.Q -0.273820 0.149713 -1.829 0.067405 .
+TypeTerrace:Sat.Q -0.032328 0.149251 -0.217 0.828520
+ContHigh:Sat.L 0.340703 0.087778 3.881 0.000104 ***
+ContHigh:Sat.Q -0.097929 0.094068 -1.041 0.297851
+InflMedium:TypeApartment:ContHigh 0.046900 0.286212 0.164 0.869837
+InflHigh:TypeApartment:ContHigh 0.126229 0.338208 0.373 0.708979
+InflMedium:TypeAtrium:ContHigh 0.157239 0.390719 0.402 0.687364
+InflHigh:TypeAtrium:ContHigh 0.478611 0.444244 1.077 0.281320
+InflMedium:TypeTerrace:ContHigh -0.500162 0.367135 -1.362 0.173091
+InflHigh:TypeTerrace:ContHigh -0.463099 0.454713 -1.018 0.308467
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+(Dispersion parameter for poisson family taken to be 1)
+
+ Null deviance: 833.657 on 71 degrees of freedom
+Residual deviance: 38.662 on 34 degrees of freedom
+AIC: 455.63
+
+Number of Fisher Scoring iterations: 4
+
+>
+> 1 - pchisq(deviance(house.glm1), house.glm1$df.residual)
+[1] 0.2671363
+>
+> dropterm(house.glm1, test = "Chisq")
+Single term deletions
+
+Model:
+Freq ~ Infl + Type + Cont + Sat + Infl:Type + Infl:Cont + Type:Cont +
+ Infl:Sat + Type:Sat + Cont:Sat + Infl:Type:Cont
+ Df Deviance AIC LRT Pr(Chi)
+<none> 38.662 455.63
+Infl:Sat 4 147.780 556.75 109.117 < 2.2e-16 ***
+Type:Sat 6 100.889 505.86 62.227 1.586e-11 ***
+Cont:Sat 2 54.722 467.69 16.060 0.0003256 ***
+Infl:Type:Cont 6 43.952 448.92 5.290 0.5072454
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+>
+> addterm(house.glm1, ~. + Sat:(Infl+Type+Cont)^2, test = "Chisq")
+Single term additions
+
+Model:
+Freq ~ Infl + Type + Cont + Sat + Infl:Type + Infl:Cont + Type:Cont +
+ Infl:Sat + Type:Sat + Cont:Sat + Infl:Type:Cont
+ Df Deviance AIC LRT Pr(Chi)
+<none> 38.662 455.63
+Infl:Type:Sat 12 16.107 457.08 22.5550 0.03175 *
+Infl:Cont:Sat 4 37.472 462.44 1.1901 0.87973
+Type:Cont:Sat 6 28.256 457.23 10.4064 0.10855
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+>
+> hnames <- lapply(housing[, -5], levels) # omit Freq
+> newData <- expand.grid(hnames)
+> newData$Sat <- ordered(newData$Sat)
+> house.pm <- predict(house.glm1, newData,
++ type = "response") # poisson means
+> house.pm <- matrix(house.pm, ncol = 3, byrow = TRUE,
++ dimnames = list(NULL, hnames[[1]]))
+> house.pr <- house.pm/drop(house.pm %*% rep(1, 3))
+> cbind(expand.grid(hnames[-1]), round(house.pr, 2))
+ Infl Type Cont Low Medium High
+1 Low Tower Low 0.40 0.26 0.34
+2 Medium Tower Low 0.26 0.27 0.47
+3 High Tower Low 0.15 0.19 0.66
+4 Low Apartment Low 0.54 0.23 0.23
+5 Medium Apartment Low 0.39 0.26 0.34
+6 High Apartment Low 0.26 0.21 0.53
+7 Low Atrium Low 0.43 0.32 0.25
+8 Medium Atrium Low 0.30 0.35 0.36
+9 High Atrium Low 0.19 0.27 0.54
+10 Low Terrace Low 0.65 0.22 0.14
+11 Medium Terrace Low 0.51 0.27 0.22
+12 High Terrace Low 0.37 0.24 0.39
+13 Low Tower High 0.30 0.28 0.42
+14 Medium Tower High 0.18 0.27 0.54
+15 High Tower High 0.10 0.19 0.71
+16 Low Apartment High 0.44 0.27 0.30
+17 Medium Apartment High 0.30 0.28 0.42
+18 High Apartment High 0.18 0.21 0.61
+19 Low Atrium High 0.33 0.36 0.31
+20 Medium Atrium High 0.22 0.36 0.42
+21 High Atrium High 0.13 0.27 0.60
+22 Low Terrace High 0.55 0.27 0.19
+23 Medium Terrace High 0.40 0.31 0.29
+24 High Terrace High 0.27 0.26 0.47
+>
+> # Iterative proportional scaling
+> loglm(Freq ~ Infl*Type*Cont + Sat*(Infl+Type+Cont), data = housing)
+Call:
+loglm(formula = Freq ~ Infl * Type * Cont + Sat * (Infl + Type +
+ Cont), data = housing)
+
+Statistics:
+ X^2 df P(> X^2)
+Likelihood Ratio 38.66222 34 0.2671359
+Pearson 38.90831 34 0.2582333
+>
+>
+> # multinomial model
+> library(nnet)
+> (house.mult<- multinom(Sat ~ Infl + Type + Cont, weights = Freq,
++ data = housing))
+# weights: 24 (14 variable)
+initial value 1846.767257
+iter 10 value 1747.045232
+final value 1735.041933
+converged
+Call:
+multinom(formula = Sat ~ Infl + Type + Cont, data = housing,
+ weights = Freq)
+
+Coefficients:
+ (Intercept) InflMedium InflHigh TypeApartment TypeAtrium TypeTerrace
+Medium -0.4192316 0.4464003 0.6649367 -0.4356851 0.1313663 -0.6665728
+High -0.1387453 0.7348626 1.6126294 -0.7356261 -0.4079808 -1.4123333
+ ContHigh
+Medium 0.3608513
+High 0.4818236
+
+Residual Deviance: 3470.084
+AIC: 3498.084
+> house.mult2 <- multinom(Sat ~ Infl*Type*Cont, weights = Freq,
++ data = housing)
+# weights: 75 (48 variable)
+initial value 1846.767257
+iter 10 value 1734.465581
+iter 20 value 1717.220153
+iter 30 value 1715.760679
+iter 40 value 1715.713306
+final value 1715.710836
+converged
+> anova(house.mult, house.mult2)
+Likelihood ratio tests of Multinomial Models
+
+Response: Sat
+ Model Resid. df Resid. Dev Test Df LR stat. Pr(Chi)
+1 Infl + Type + Cont 130 3470.084
+2 Infl * Type * Cont 96 3431.422 1 vs 2 34 38.66219 0.2671367
+>
+> house.pm <- predict(house.mult, expand.grid(hnames[-1]), type = "probs")
+> cbind(expand.grid(hnames[-1]), round(house.pm, 2))
+ Infl Type Cont Low Medium High
+1 Low Tower Low 0.40 0.26 0.34
+2 Medium Tower Low 0.26 0.27 0.47
+3 High Tower Low 0.15 0.19 0.66
+4 Low Apartment Low 0.54 0.23 0.23
+5 Medium Apartment Low 0.39 0.26 0.34
+6 High Apartment Low 0.26 0.21 0.53
+7 Low Atrium Low 0.43 0.32 0.25
+8 Medium Atrium Low 0.30 0.35 0.36
+9 High Atrium Low 0.19 0.27 0.54
+10 Low Terrace Low 0.65 0.22 0.14
+11 Medium Terrace Low 0.51 0.27 0.22
+12 High Terrace Low 0.37 0.24 0.39
+13 Low Tower High 0.30 0.28 0.42
+14 Medium Tower High 0.18 0.27 0.54
+15 High Tower High 0.10 0.19 0.71
+16 Low Apartment High 0.44 0.27 0.30
+17 Medium Apartment High 0.30 0.28 0.42
+18 High Apartment High 0.18 0.21 0.61
+19 Low Atrium High 0.33 0.36 0.31
+20 Medium Atrium High 0.22 0.36 0.42
+21 High Atrium High 0.13 0.27 0.60
+22 Low Terrace High 0.55 0.27 0.19
+23 Medium Terrace High 0.40 0.31 0.29
+24 High Terrace High 0.27 0.26 0.47
+>
+> # proportional odds model
+> house.cpr <- apply(house.pr, 1, cumsum)
+> logit <- function(x) log(x/(1-x))
+> house.ld <- logit(house.cpr[2, ]) - logit(house.cpr[1, ])
+> (ratio <- sort(drop(house.ld)))
+ [1] 0.9357341 0.9854433 1.0573182 1.0680491 1.0772649 1.0803574 1.0824895
+ [8] 1.0998759 1.1199975 1.1554228 1.1768138 1.1866427 1.2091541 1.2435026
+[15] 1.2724096 1.2750171 1.2849903 1.3062598 1.3123988 1.3904715 1.4540087
+[22] 1.4947753 1.4967585 1.6068789
+> mean(ratio)
+[1] 1.223835
+>
+> (house.plr <- polr(Sat ~ Infl + Type + Cont,
++ data = housing, weights = Freq))
+Call:
+polr(formula = Sat ~ Infl + Type + Cont, data = housing, weights = Freq)
+
+Coefficients:
+ InflMedium InflHigh TypeApartment TypeAtrium TypeTerrace
+ 0.5663937 1.2888191 -0.5723501 -0.3661866 -1.0910149
+ ContHigh
+ 0.3602841
+
+Intercepts:
+ Low|Medium Medium|High
+ -0.4961353 0.6907083
+
+Residual Deviance: 3479.149
+AIC: 3495.149
+>
+> house.pr1 <- predict(house.plr, expand.grid(hnames[-1]), type = "probs")
+> cbind(expand.grid(hnames[-1]), round(house.pr1, 2))
+ Infl Type Cont Low Medium High
+1 Low Tower Low 0.38 0.29 0.33
+2 Medium Tower Low 0.26 0.27 0.47
+3 High Tower Low 0.14 0.21 0.65
+4 Low Apartment Low 0.52 0.26 0.22
+5 Medium Apartment Low 0.38 0.29 0.33
+6 High Apartment Low 0.23 0.26 0.51
+7 Low Atrium Low 0.47 0.27 0.26
+8 Medium Atrium Low 0.33 0.29 0.38
+9 High Atrium Low 0.19 0.25 0.56
+10 Low Terrace Low 0.64 0.21 0.14
+11 Medium Terrace Low 0.51 0.26 0.23
+12 High Terrace Low 0.33 0.29 0.38
+13 Low Tower High 0.30 0.28 0.42
+14 Medium Tower High 0.19 0.25 0.56
+15 High Tower High 0.10 0.17 0.72
+16 Low Apartment High 0.43 0.28 0.29
+17 Medium Apartment High 0.30 0.28 0.42
+18 High Apartment High 0.17 0.23 0.60
+19 Low Atrium High 0.38 0.29 0.33
+20 Medium Atrium High 0.26 0.27 0.47
+21 High Atrium High 0.14 0.21 0.64
+22 Low Terrace High 0.56 0.25 0.19
+23 Medium Terrace High 0.42 0.28 0.30
+24 High Terrace High 0.26 0.27 0.47
+>
+> Fr <- matrix(housing$Freq, ncol = 3, byrow = TRUE)
+> 2*sum(Fr*log(house.pr/house.pr1))
+[1] 9.065433
+>
+> house.plr2 <- stepAIC(house.plr, ~.^2)
+Start: AIC=3495.15
+Sat ~ Infl + Type + Cont
+
+ Df AIC
++ Infl:Type 6 3484.6
++ Type:Cont 3 3492.5
+<none> 3495.1
++ Infl:Cont 2 3498.9
+- Cont 1 3507.5
+- Type 3 3545.1
+- Infl 2 3599.4
+
+Step: AIC=3484.64
+Sat ~ Infl + Type + Cont + Infl:Type
+
+ Df AIC
++ Type:Cont 3 3482.7
+<none> 3484.6
++ Infl:Cont 2 3488.5
+- Infl:Type 6 3495.1
+- Cont 1 3497.8
+
+Step: AIC=3482.69
+Sat ~ Infl + Type + Cont + Infl:Type + Type:Cont
+
+ Df AIC
+<none> 3482.7
+- Type:Cont 3 3484.6
++ Infl:Cont 2 3486.6
+- Infl:Type 6 3492.5
+> house.plr2$anova
+Stepwise Model Path
+Analysis of Deviance Table
+
+Initial Model:
+Sat ~ Infl + Type + Cont
+
+Final Model:
+Sat ~ Infl + Type + Cont + Infl:Type + Type:Cont
+
+
+ Step Df Deviance Resid. Df Resid. Dev AIC
+1 1673 3479.149 3495.149
+2 + Infl:Type 6 22.509347 1667 3456.640 3484.640
+3 + Type:Cont 3 7.945029 1664 3448.695 3482.695
+>
+>
+>
+> options(contrasts = c(unordered = "contr.treatment",ordered = "contr.poly"))
+> cleanEx()
+
+detaching âpackage:nnetâ
+
+> nameEx("huber")
+> ### * huber
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: huber
+> ### Title: Huber M-estimator of Location with MAD Scale
+> ### Aliases: huber
+> ### Keywords: robust
+>
+> ### ** Examples
+>
+> huber(chem)
+$mu
+[1] 3.206724
+
+$s
+[1] 0.526323
+
+>
+>
+>
+> cleanEx()
+> nameEx("hubers")
+> ### * hubers
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: hubers
+> ### Title: Huber Proposal 2 Robust Estimator of Location and/or Scale
+> ### Aliases: hubers
+> ### Keywords: robust
+>
+> ### ** Examples
+>
+> hubers(chem)
+$mu
+[1] 3.205498
+
+$s
+[1] 0.673652
+
+> hubers(chem, mu=3.68)
+$mu
+[1] 3.68
+
+$s
+[1] 0.9409628
+
+>
+>
+>
+> cleanEx()
+> nameEx("immer")
+> ### * immer
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: immer
+> ### Title: Yields from a Barley Field Trial
+> ### Aliases: immer
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> immer.aov <- aov(cbind(Y1,Y2) ~ Loc + Var, data = immer)
+> summary(immer.aov)
+ Response Y1 :
+ Df Sum Sq Mean Sq F value Pr(>F)
+Loc 5 17829.8 3566.0 21.8923 1.751e-07 ***
+Var 4 2756.6 689.2 4.2309 0.01214 *
+Residuals 20 3257.7 162.9
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+ Response Y2 :
+ Df Sum Sq Mean Sq F value Pr(>F)
+Loc 5 10285.0 2056.99 10.3901 5.049e-05 ***
+Var 4 2845.2 711.29 3.5928 0.02306 *
+Residuals 20 3959.5 197.98
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+>
+> immer.aov <- aov((Y1+Y2)/2 ~ Var + Loc, data = immer)
+> summary(immer.aov)
+ Df Sum Sq Mean Sq F value Pr(>F)
+Var 4 2655 663.7 5.989 0.00245 **
+Loc 5 10610 2122.1 19.148 5.21e-07 ***
+Residuals 20 2217 110.8
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+> model.tables(immer.aov, type = "means", se = TRUE, cterms = "Var")
+Tables of means
+Grand mean
+
+101.09
+
+ Var
+Var
+ M P S T V
+ 94.39 102.54 91.13 118.20 99.18
+
+Standard errors for differences of means
+ Var
+ 6.078
+replic. 6
+>
+>
+>
+> cleanEx()
+> nameEx("isoMDS")
+> ### * isoMDS
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: isoMDS
+> ### Title: Kruskal's Non-metric Multidimensional Scaling
+> ### Aliases: isoMDS Shepard
+> ### Keywords: multivariate
+>
+> ### ** Examples
+>
+> swiss.x <- as.matrix(swiss[, -1])
+> swiss.dist <- dist(swiss.x)
+> swiss.mds <- isoMDS(swiss.dist)
+initial value 2.979731
+iter 5 value 2.431486
+iter 10 value 2.343353
+final value 2.338839
+converged
+> plot(swiss.mds$points, type = "n")
+> text(swiss.mds$points, labels = as.character(1:nrow(swiss.x)))
+> swiss.sh <- Shepard(swiss.dist, swiss.mds$points)
+> plot(swiss.sh, pch = ".")
+> lines(swiss.sh$x, swiss.sh$yf, type = "S")
+>
+>
+>
+> cleanEx()
+> nameEx("kde2d")
+> ### * kde2d
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: kde2d
+> ### Title: Two-Dimensional Kernel Density Estimation
+> ### Aliases: kde2d
+> ### Keywords: dplot
+>
+> ### ** Examples
+>
+> attach(geyser)
+> plot(duration, waiting, xlim = c(0.5,6), ylim = c(40,100))
+> f1 <- kde2d(duration, waiting, n = 50, lims = c(0.5, 6, 40, 100))
+> image(f1, zlim = c(0, 0.05))
+> f2 <- kde2d(duration, waiting, n = 50, lims = c(0.5, 6, 40, 100),
++ h = c(width.SJ(duration), width.SJ(waiting)) )
+> image(f2, zlim = c(0, 0.05))
+> persp(f2, phi = 30, theta = 20, d = 5)
+>
+> plot(duration[-272], duration[-1], xlim = c(0.5, 6),
++ ylim = c(1, 6),xlab = "previous duration", ylab = "duration")
+> f1 <- kde2d(duration[-272], duration[-1],
++ h = rep(1.5, 2), n = 50, lims = c(0.5, 6, 0.5, 6))
+> contour(f1, xlab = "previous duration",
++ ylab = "duration", levels = c(0.05, 0.1, 0.2, 0.4) )
+> f1 <- kde2d(duration[-272], duration[-1],
++ h = rep(0.6, 2), n = 50, lims = c(0.5, 6, 0.5, 6))
+> contour(f1, xlab = "previous duration",
++ ylab = "duration", levels = c(0.05, 0.1, 0.2, 0.4) )
+> f1 <- kde2d(duration[-272], duration[-1],
++ h = rep(0.4, 2), n = 50, lims = c(0.5, 6, 0.5, 6))
+> contour(f1, xlab = "previous duration",
++ ylab = "duration", levels = c(0.05, 0.1, 0.2, 0.4) )
+> detach("geyser")
+>
+>
+>
+> cleanEx()
+> nameEx("lda")
+> ### * lda
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: lda
+> ### Title: Linear Discriminant Analysis
+> ### Aliases: lda lda.default lda.data.frame lda.formula lda.matrix
+> ### model.frame.lda print.lda coef.lda
+> ### Keywords: multivariate
+>
+> ### ** Examples
+>
+> Iris <- data.frame(rbind(iris3[,,1], iris3[,,2], iris3[,,3]),
++ Sp = rep(c("s","c","v"), rep(50,3)))
+> train <- sample(1:150, 75)
+> table(Iris$Sp[train])
+
+ c s v
+28 26 21
+> ## your answer may differ
+> ## c s v
+> ## 22 23 30
+> z <- lda(Sp ~ ., Iris, prior = c(1,1,1)/3, subset = train)
+> predict(z, Iris[-train, ])$class
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c c c c c c c
+[39] c c c c c c c c v v v v v v v v v v v v v v v v v v v v v v v v v v v v v
+Levels: c s v
+> ## [1] s s s s s s s s s s s s s s s s s s s s s s s s s s s c c c
+> ## [31] c c c c c c c v c c c c v c c c c c c c c c c c c v v v v v
+> ## [61] v v v v v v v v v v v v v v v
+> (z1 <- update(z, . ~ . - Petal.W.))
+Call:
+lda(Sp ~ Sepal.L. + Sepal.W. + Petal.L., data = Iris, prior = c(1,
+ 1, 1)/3, subset = train)
+
+Prior probabilities of groups:
+ c s v
+0.3333333 0.3333333 0.3333333
+
+Group means:
+ Sepal.L. Sepal.W. Petal.L.
+c 5.878571 2.785714 4.278571
+s 4.950000 3.338462 1.457692
+v 6.504762 2.957143 5.500000
+
+Coefficients of linear discriminants:
+ LD1 LD2
+Sepal.L. 1.2555097 -0.2975141
+Sepal.W. 0.9085695 2.8401071
+Petal.L. -3.5502485 0.4380715
+
+Proportion of trace:
+ LD1 LD2
+0.9957 0.0043
+>
+>
+>
+> cleanEx()
+> nameEx("leuk")
+> ### * leuk
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: leuk
+> ### Title: Survival Times and White Blood Counts for Leukaemia Patients
+> ### Aliases: leuk
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> library(survival)
+Loading required package: splines
+> plot(survfit(Surv(time) ~ ag, data = leuk), lty = 2:3, col = 2:3)
+>
+> # now Cox models
+> leuk.cox <- coxph(Surv(time) ~ ag + log(wbc), leuk)
+> summary(leuk.cox)
+Call:
+coxph(formula = Surv(time) ~ ag + log(wbc), data = leuk)
+
+ n= 33, number of events= 33
+
+ coef exp(coef) se(coef) z Pr(>|z|)
+agpresent -1.0691 0.3433 0.4293 -2.490 0.01276 *
+log(wbc) 0.3677 1.4444 0.1360 2.703 0.00687 **
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+ exp(coef) exp(-coef) lower .95 upper .95
+agpresent 0.3433 2.9126 0.148 0.7964
+log(wbc) 1.4444 0.6923 1.106 1.8857
+
+Concordance= 0.726 (se = 0.065 )
+Rsquare= 0.377 (max possible= 0.994 )
+Likelihood ratio test= 15.64 on 2 df, p=0.0004014
+Wald test = 15.06 on 2 df, p=0.0005365
+Score (logrank) test = 16.49 on 2 df, p=0.0002629
+
+>
+>
+>
+> cleanEx()
+
+detaching âpackage:survivalâ, âpackage:splinesâ
+
+> nameEx("lm.ridge")
+> ### * lm.ridge
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: lm.ridge
+> ### Title: Ridge Regression
+> ### Aliases: lm.ridge plot.ridgelm print.ridgelm select select.ridgelm
+> ### Keywords: models
+>
+> ### ** Examples
+>
+> longley # not the same as the S-PLUS dataset
+ GNP.deflator GNP Unemployed Armed.Forces Population Year Employed
+1947 83.0 234.289 235.6 159.0 107.608 1947 60.323
+1948 88.5 259.426 232.5 145.6 108.632 1948 61.122
+1949 88.2 258.054 368.2 161.6 109.773 1949 60.171
+1950 89.5 284.599 335.1 165.0 110.929 1950 61.187
+1951 96.2 328.975 209.9 309.9 112.075 1951 63.221
+1952 98.1 346.999 193.2 359.4 113.270 1952 63.639
+1953 99.0 365.385 187.0 354.7 115.094 1953 64.989
+1954 100.0 363.112 357.8 335.0 116.219 1954 63.761
+1955 101.2 397.469 290.4 304.8 117.388 1955 66.019
+1956 104.6 419.180 282.2 285.7 118.734 1956 67.857
+1957 108.4 442.769 293.6 279.8 120.445 1957 68.169
+1958 110.8 444.546 468.1 263.7 121.950 1958 66.513
+1959 112.6 482.704 381.3 255.2 123.366 1959 68.655
+1960 114.2 502.601 393.1 251.4 125.368 1960 69.564
+1961 115.7 518.173 480.6 257.2 127.852 1961 69.331
+1962 116.9 554.894 400.7 282.7 130.081 1962 70.551
+> names(longley)[1] <- "y"
+> lm.ridge(y ~ ., longley)
+ GNP Unemployed Armed.Forces Population
+2946.85636017 0.26352725 0.03648291 0.01116105 -1.73702984
+ Year Employed
+ -1.41879853 0.23128785
+> plot(lm.ridge(y ~ ., longley,
++ lambda = seq(0,0.1,0.001)))
+> select(lm.ridge(y ~ ., longley,
++ lambda = seq(0,0.1,0.0001)))
+modified HKB estimator is 0.006836982
+modified L-W estimator is 0.05267247
+smallest value of GCV at 0.0057
+>
+>
+>
+> cleanEx()
+> nameEx("loglm")
+> ### * loglm
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: loglm
+> ### Title: Fit Log-Linear Models by Iterative Proportional Scaling
+> ### Aliases: loglm
+> ### Keywords: category models
+>
+> ### ** Examples
+>
+> # The data frames Cars93, minn38 and quine are available
+> # in the MASS package.
+>
+> # Case 1: frequencies specified as an array.
+> sapply(minn38, function(x) length(levels(x)))
+ hs phs fol sex f
+ 3 4 7 2 0
+> ## hs phs fol sex f
+> ## 3 4 7 2 0
+> minn38a <- array(0, c(3,4,7,2), lapply(minn38[, -5], levels))
+> minn38a[data.matrix(minn38[,-5])] <- minn38$fol
+> fm <- loglm(~1 + 2 + 3 + 4, minn38a) # numerals as names.
+> deviance(fm)
+[1] 0
+> ##[1] 3711.9
+> fm1 <- update(fm, .~.^2)
+> fm2 <- update(fm, .~.^3, print = TRUE)
+2 iterations: deviation 0
+> ## 5 iterations: deviation 0.0750732
+> anova(fm, fm1, fm2)
+LR tests for hierarchical log-linear models
+
+Model 1:
+ ~`1` + `2` + `3` + `4`
+Model 2:
+ . ~ .v2 + .v1 + .v3
+Model 3:
+ . ~ .v2 + .v1 + .v3
+
+ Deviance df Delta(Dev) Delta(df) P(> Delta(Dev)
+Model 1 0 155
+Model 2 0 108 0 47 1
+Model 3 0 36 0 72 1
+Saturated 0 0 0 36 1
+> ## Not run:
+> ##D LR tests for hierarchical log-linear models
+> ##D
+> ##D Model 1:
+> ##D ~ 1 + 2 + 3 + 4
+> ##D Model 2:
+> ##D . ~ 1 + 2 + 3 + 4 + 1:2 + 1:3 + 1:4 + 2:3 + 2:4 + 3:4
+> ##D Model 3:
+> ##D . ~ 1 + 2 + 3 + 4 + 1:2 + 1:3 + 1:4 + 2:3 + 2:4 + 3:4 +
+> ##D 1:2:3 + 1:2:4 + 1:3:4 + 2:3:4
+> ##D
+> ##D
+> ##D Deviance df Delta(Dev) Delta(df) P(> Delta(Dev)
+> ##D Model 1 3711.915 155
+> ##D Model 2 220.043 108 3491.873 47 0.00000
+> ##D Model 3 47.745 36 172.298 72 0.00000
+> ##D Saturated 0.000 0 47.745 36 0.09114
+> ##D
+> ## End(Not run)
+> # Case 1. An array generated with xtabs.
+>
+> loglm(~ Type + Origin, xtabs(~ Type + Origin, Cars93))
+Call:
+loglm(formula = ~Type + Origin, data = xtabs(~Type + Origin,
+ Cars93))
+
+Statistics:
+ X^2 df P(> X^2)
+Likelihood Ratio 18.36179 5 0.00252554
+Pearson 14.07985 5 0.01511005
+> ## Not run:
+> ##D Call:
+> ##D loglm(formula = ~Type + Origin, data = xtabs(~Type + Origin,
+> ##D Cars93))
+> ##D
+> ##D Statistics:
+> ##D X^2 df P(> X^2)
+> ##D Likelihood Ratio 18.362 5 0.0025255
+> ##D Pearson 14.080 5 0.0151101
+> ##D
+> ## End(Not run)
+> # Case 2. Frequencies given as a vector in a data frame
+> names(quine)
+[1] "Eth" "Sex" "Age" "Lrn" "Days"
+> ## [1] "Eth" "Sex" "Age" "Lrn" "Days"
+> fm <- loglm(Days ~ .^2, quine)
+> gm <- glm(Days ~ .^2, poisson, quine) # check glm.
+> c(deviance(fm), deviance(gm)) # deviances agree
+[1] 1368.669 1368.669
+> ## [1] 1368.7 1368.7
+> c(fm$df, gm$df) # resid df do not!
+[1] 127
+> c(fm$df, gm$df.residual) # resid df do not!
+[1] 127 128
+> ## [1] 127 128
+> # The loglm residual degrees of freedom is wrong because of
+> # a non-detectable redundancy in the model matrix.
+>
+>
+>
+> cleanEx()
+> nameEx("logtrans")
+> ### * logtrans
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: logtrans
+> ### Title: Estimate log Transformation Parameter
+> ### Aliases: logtrans logtrans.formula logtrans.lm logtrans.default
+> ### Keywords: regression models hplot
+>
+> ### ** Examples
+>
+> logtrans(Days ~ Age*Sex*Eth*Lrn, data = quine,
++ alpha = seq(0.75, 6.5, len=20))
+>
+>
+>
+> cleanEx()
+> nameEx("lqs")
+> ### * lqs
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: lqs
+> ### Title: Resistant Regression
+> ### Aliases: lqs lqs.formula lqs.default lmsreg ltsreg
+> ### Keywords: models robust
+>
+> ### ** Examples
+>
+> set.seed(123) # make reproducible
+> lqs(stack.loss ~ ., data = stackloss)
+Call:
+lqs.formula(formula = stack.loss ~ ., data = stackloss)
+
+Coefficients:
+(Intercept) Air.Flow Water.Temp Acid.Conc.
+ -3.631e+01 7.292e-01 4.167e-01 -8.131e-17
+
+Scale estimates 0.9149 1.0148
+
+> lqs(stack.loss ~ ., data = stackloss, method = "S", nsamp = "exact")
+Call:
+lqs.formula(formula = stack.loss ~ ., data = stackloss, nsamp = "exact",
+ method = "S")
+
+Coefficients:
+(Intercept) Air.Flow Water.Temp Acid.Conc.
+ -35.37611 0.82522 0.44248 -0.07965
+
+Scale estimates 1.912
+
+>
+>
+>
+> cleanEx()
+> nameEx("mca")
+> ### * mca
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: mca
+> ### Title: Multiple Correspondence Analysis
+> ### Aliases: mca print.mca
+> ### Keywords: category multivariate
+>
+> ### ** Examples
+>
+> farms.mca <- mca(farms, abbrev=TRUE)
+> farms.mca
+Call:
+mca(df = farms, abbrev = TRUE)
+
+Multiple correspondence analysis of 20 cases of 4 factors
+
+Correlations 0.806 0.745 cumulative % explained 26.87 51.71
+> plot(farms.mca)
+>
+>
+>
+> cleanEx()
+> nameEx("menarche")
+> ### * menarche
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: menarche
+> ### Title: Age of Menarche in Warsaw
+> ### Aliases: menarche
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> mprob <- glm(cbind(Menarche, Total - Menarche) ~ Age,
++ binomial(link = probit), data = menarche)
+>
+>
+>
+> cleanEx()
+> nameEx("motors")
+> ### * motors
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: motors
+> ### Title: Accelerated Life Testing of Motorettes
+> ### Aliases: motors
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> library(survival)
+Loading required package: splines
+> plot(survfit(Surv(time, cens) ~ factor(temp), motors), conf.int = FALSE)
+> # fit Weibull model
+> motor.wei <- survreg(Surv(time, cens) ~ temp, motors)
+> summary(motor.wei)
+
+Call:
+survreg(formula = Surv(time, cens) ~ temp, data = motors)
+ Value Std. Error z p
+(Intercept) 16.3185 0.62296 26.2 3.03e-151
+temp -0.0453 0.00319 -14.2 6.74e-46
+Log(scale) -1.0956 0.21480 -5.1 3.38e-07
+
+Scale= 0.334
+
+Weibull distribution
+Loglik(model)= -147.4 Loglik(intercept only)= -169.5
+ Chisq= 44.32 on 1 degrees of freedom, p= 2.8e-11
+Number of Newton-Raphson Iterations: 7
+n= 40
+
+> # and predict at 130C
+> unlist(predict(motor.wei, data.frame(temp=130), se.fit = TRUE))
+ fit.1 se.fit.1
+33813.06 7506.36
+>
+> motor.cox <- coxph(Surv(time, cens) ~ temp, motors)
+> summary(motor.cox)
+Call:
+coxph(formula = Surv(time, cens) ~ temp, data = motors)
+
+ n= 40, number of events= 17
+
+ coef exp(coef) se(coef) z Pr(>|z|)
+temp 0.09185 1.09620 0.02736 3.358 0.000786 ***
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+ exp(coef) exp(-coef) lower .95 upper .95
+temp 1.096 0.9122 1.039 1.157
+
+Concordance= 0.84 (se = 0.076 )
+Rsquare= 0.472 (max possible= 0.936 )
+Likelihood ratio test= 25.56 on 1 df, p=4.299e-07
+Wald test = 11.27 on 1 df, p=0.0007863
+Score (logrank) test = 22.73 on 1 df, p=1.862e-06
+
+> # predict at temperature 200
+> plot(survfit(motor.cox, newdata = data.frame(temp=200),
++ conf.type = "log-log"))
+> summary( survfit(motor.cox, newdata = data.frame(temp=130)) )
+Call: survfit(formula = motor.cox, newdata = data.frame(temp = 130))
+
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 408 40 4 1.000 0.000254 0.999 1
+ 504 36 3 1.000 0.000498 0.999 1
+ 1344 28 2 0.999 0.001910 0.995 1
+ 1440 26 1 0.998 0.002697 0.993 1
+ 1764 20 1 0.996 0.005325 0.986 1
+ 2772 19 1 0.994 0.007920 0.978 1
+ 3444 18 1 0.991 0.010673 0.971 1
+ 3542 17 1 0.988 0.013667 0.962 1
+ 3780 16 1 0.985 0.016976 0.952 1
+ 4860 15 1 0.981 0.020692 0.941 1
+ 5196 14 1 0.977 0.024941 0.929 1
+>
+>
+>
+> cleanEx()
+
+detaching âpackage:survivalâ, âpackage:splinesâ
+
+> nameEx("muscle")
+> ### * muscle
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: muscle
+> ### Title: Effect of Calcium Chloride on Muscle Contraction in Rat Hearts
+> ### Aliases: muscle
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> A <- model.matrix(~ Strip - 1, data=muscle)
+> rats.nls1 <- nls(log(Length) ~ cbind(A, rho^Conc),
++ data = muscle, start = c(rho=0.1), algorithm="plinear")
+> B <- coef(rats.nls1)
+> B
+ rho .lin.StripS01 .lin.StripS02 .lin.StripS03 .lin.StripS04
+ 0.07776401 3.08304824 3.30137838 3.44562531 2.80464434
+.lin.StripS05 .lin.StripS06 .lin.StripS07 .lin.StripS08 .lin.StripS09
+ 2.60835015 3.03357725 3.52301734 3.38711844 3.46709396
+.lin.StripS10 .lin.StripS11 .lin.StripS12 .lin.StripS13 .lin.StripS14
+ 3.81438456 3.73878664 3.51332581 3.39741115 3.47088608
+.lin.StripS15 .lin.StripS16 .lin.StripS17 .lin.StripS18 .lin.StripS19
+ 3.72895847 3.31863862 3.37938673 2.96452195 3.58468686
+.lin.StripS20 .lin.StripS21 .lin22
+ 3.39628029 3.36998872 -2.96015460
+>
+> st <- list(alpha = B[2:22], beta = B[23], rho = B[1])
+> (rats.nls2 <- nls(log(Length) ~ alpha[Strip] + beta*rho^Conc,
++ data = muscle, start = st))
+Nonlinear regression model
+ model: log(Length) ~ alpha[Strip] + beta * rho^Conc
+ data: muscle
+alpha..lin.StripS01 alpha..lin.StripS02 alpha..lin.StripS03 alpha..lin.StripS04
+ 3.08305 3.30138 3.44563 2.80464
+alpha..lin.StripS05 alpha..lin.StripS06 alpha..lin.StripS07 alpha..lin.StripS08
+ 2.60835 3.03358 3.52302 3.38712
+alpha..lin.StripS09 alpha..lin.StripS10 alpha..lin.StripS11 alpha..lin.StripS12
+ 3.46709 3.81438 3.73879 3.51333
+alpha..lin.StripS13 alpha..lin.StripS14 alpha..lin.StripS15 alpha..lin.StripS16
+ 3.39741 3.47089 3.72896 3.31864
+alpha..lin.StripS17 alpha..lin.StripS18 alpha..lin.StripS19 alpha..lin.StripS20
+ 3.37939 2.96452 3.58469 3.39628
+alpha..lin.StripS21 beta..lin22 rho.rho
+ 3.36999 -2.96015 0.07776
+ residual sum-of-squares: 1.045
+
+Number of iterations to convergence: 0
+Achieved convergence tolerance: 4.923e-06
+>
+> attach(muscle)
+> Muscle <- expand.grid(Conc = sort(unique(Conc)), Strip = levels(Strip))
+> Muscle$Yhat <- predict(rats.nls2, Muscle)
+> Muscle <- cbind(Muscle, logLength = rep(as.numeric(NA), 126))
+> ind <- match(paste(Strip, Conc),
++ paste(Muscle$Strip, Muscle$Conc))
+> Muscle$logLength[ind] <- log(Length)
+> detach()
+>
+> require(lattice)
+Loading required package: lattice
+> xyplot(Yhat ~ Conc | Strip, Muscle, as.table = TRUE,
++ ylim = range(c(Muscle$Yhat, Muscle$logLength), na.rm = TRUE),
++ subscripts = TRUE, xlab = "Calcium Chloride concentration (mM)",
++ ylab = "log(Length in mm)", panel =
++ function(x, y, subscripts, ...) {
++ lines(spline(x, y))
++ panel.xyplot(x, Muscle$logLength[subscripts], ...)
++ })
+>
+>
+>
+> cleanEx()
+
+detaching âpackage:latticeâ
+
+> nameEx("mvrnorm")
+> ### * mvrnorm
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: mvrnorm
+> ### Title: Simulate from a Multivariate Normal Distribution
+> ### Aliases: mvrnorm
+> ### Keywords: distribution multivariate
+>
+> ### ** Examples
+>
+> Sigma <- matrix(c(10,3,3,2),2,2)
+> Sigma
+ [,1] [,2]
+[1,] 10 3
+[2,] 3 2
+> var(mvrnorm(n=1000, rep(0, 2), Sigma))
+ [,1] [,2]
+[1,] 10.697849 3.228279
+[2,] 3.228279 2.165271
+> var(mvrnorm(n=1000, rep(0, 2), Sigma, empirical = TRUE))
+ [,1] [,2]
+[1,] 10 3
+[2,] 3 2
+>
+>
+>
+> cleanEx()
+> nameEx("negative.binomial")
+> ### * negative.binomial
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: negative.binomial
+> ### Title: Family function for Negative Binomial GLMs
+> ### Aliases: negative.binomial
+> ### Keywords: regression models
+>
+> ### ** Examples
+>
+> # Fitting a Negative Binomial model to the quine data
+> # with theta = 2 assumed known.
+> #
+> glm(Days ~ .^4, family = negative.binomial(2), data = quine)
+
+Call: glm(formula = Days ~ .^4, family = negative.binomial(2), data = quine)
+
+Coefficients:
+ (Intercept) EthN SexM
+ 3.0564 -0.1386 -0.4914
+ AgeF1 AgeF2 AgeF3
+ -0.6227 -2.3632 -0.3784
+ LrnSL EthN:SexM EthN:AgeF1
+ -1.9577 -0.7524 0.1029
+ EthN:AgeF2 EthN:AgeF3 EthN:LrnSL
+ -0.5546 0.0633 2.2588
+ SexM:AgeF1 SexM:AgeF2 SexM:AgeF3
+ 0.4092 3.1098 1.1145
+ SexM:LrnSL AgeF1:LrnSL AgeF2:LrnSL
+ 1.5900 2.6421 4.8585
+ AgeF3:LrnSL EthN:SexM:AgeF1 EthN:SexM:AgeF2
+ NA -0.3105 0.3469
+ EthN:SexM:AgeF3 EthN:SexM:LrnSL EthN:AgeF1:LrnSL
+ 0.8329 -0.1639 -3.5493
+ EthN:AgeF2:LrnSL EthN:AgeF3:LrnSL SexM:AgeF1:LrnSL
+ -3.3315 NA -2.4285
+ SexM:AgeF2:LrnSL SexM:AgeF3:LrnSL EthN:SexM:AgeF1:LrnSL
+ -4.1914 NA 2.1711
+EthN:SexM:AgeF2:LrnSL EthN:SexM:AgeF3:LrnSL
+ 2.1029 NA
+
+Degrees of Freedom: 145 Total (i.e. Null); 118 Residual
+Null Deviance: 280.2
+Residual Deviance: 172 AIC: 1095
+>
+>
+>
+> cleanEx()
+> nameEx("nlschools")
+> ### * nlschools
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: nlschools
+> ### Title: Eighth-Grade Pupils in the Netherlands
+> ### Aliases: nlschools
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> library(nlme)
+> nl1 <- nlschools
+> attach(nl1)
+> classMeans <- tapply(IQ, class, mean)
+> nl1$IQave <- classMeans[as.character(class)]
+> nl1$IQ <- nl1$IQ - nl1$IQave
+> detach()
+> cen <- c("IQ", "IQave", "SES")
+> nl1[cen] <- scale(nl1[cen], center = TRUE, scale = FALSE)
+>
+> nl.lme <- lme(lang ~ IQ*COMB + IQave + SES,
++ random = ~ IQ | class, data = nl1)
+> summary(nl.lme)
+Linear mixed-effects model fit by REML
+ Data: nl1
+ AIC BIC logLik
+ 15120.45 15177.78 -7550.226
+
+Random effects:
+ Formula: ~IQ | class
+ Structure: General positive-definite, Log-Cholesky parametrization
+ StdDev Corr
+(Intercept) 2.7870651 (Intr)
+IQ 0.4842392 -0.516
+Residual 6.2483879
+
+Fixed effects: lang ~ IQ * COMB + IQave + SES
+ Value Std.Error DF t-value p-value
+(Intercept) 41.37017 0.3536372 2151 116.98478 0.0000
+IQ 2.12355 0.1007018 2151 21.08752 0.0000
+COMB1 -1.67177 0.5871924 130 -2.84706 0.0051
+IQave 3.24779 0.3002118 130 10.81833 0.0000
+SES 0.15674 0.0146534 2151 10.69673 0.0000
+IQ:COMB1 0.43074 0.1859429 2151 2.31652 0.0206
+ Correlation:
+ (Intr) IQ COMB1 IQave SES
+IQ -0.257
+COMB1 -0.609 0.155
+IQave -0.049 0.041 0.171
+SES 0.010 -0.190 -0.001 -0.168
+IQ:COMB1 0.139 -0.522 -0.206 -0.016 -0.003
+
+Standardized Within-Group Residuals:
+ Min Q1 Med Q3 Max
+-4.05938661 -0.63108408 0.06551865 0.71786438 2.79454034
+
+Number of Observations: 2287
+Number of Groups: 133
+>
+>
+>
+> cleanEx()
+
+detaching âpackage:nlmeâ
+
+> nameEx("npk")
+> ### * npk
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: npk
+> ### Title: Classical N, P, K Factorial Experiment
+> ### Aliases: npk
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> options(contrasts = c("contr.sum", "contr.poly"))
+> npk.aov <- aov(yield ~ block + N*P*K, npk)
+> npk.aov
+Call:
+ aov(formula = yield ~ block + N * P * K, data = npk)
+
+Terms:
+ block N P K N:P N:K P:K
+Sum of Squares 343.2950 189.2817 8.4017 95.2017 21.2817 33.1350 0.4817
+Deg. of Freedom 5 1 1 1 1 1 1
+ Residuals
+Sum of Squares 185.2867
+Deg. of Freedom 12
+
+Residual standard error: 3.929447
+1 out of 13 effects not estimable
+Estimated effects may be unbalanced
+> summary(npk.aov)
+ Df Sum Sq Mean Sq F value Pr(>F)
+block 5 343.3 68.66 4.447 0.01594 *
+N 1 189.3 189.28 12.259 0.00437 **
+P 1 8.4 8.40 0.544 0.47490
+K 1 95.2 95.20 6.166 0.02880 *
+N:P 1 21.3 21.28 1.378 0.26317
+N:K 1 33.1 33.14 2.146 0.16865
+P:K 1 0.5 0.48 0.031 0.86275
+Residuals 12 185.3 15.44
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+> alias(npk.aov)
+Model :
+yield ~ block + N * P * K
+
+Complete :
+ (Intercept) block1 block2 block3 block4 block5 N1 P1 K1 N1:P1 N1:K1
+N1:P1:K1 0 1 -1 -1 -1 1 0 0 0 0 0
+ P1:K1
+N1:P1:K1 0
+
+> coef(npk.aov)
+(Intercept) block1 block2 block3 block4 block5
+ 54.8750000 -0.8500000 2.5750000 5.9000000 -4.7500000 -4.3500000
+ N1 P1 K1 N1:P1 N1:K1 P1:K1
+ -2.8083333 0.5916667 1.9916667 -0.9416667 -1.1750000 0.1416667
+> options(contrasts = c("contr.treatment", "contr.poly"))
+> npk.aov1 <- aov(yield ~ block + N + K, data = npk)
+> summary.lm(npk.aov1)
+
+Call:
+aov(formula = yield ~ block + N + K, data = npk)
+
+Residuals:
+ Min 1Q Median 3Q Max
+-6.4083 -2.1438 0.2042 2.3292 7.0750
+
+Coefficients:
+ Estimate Std. Error t value Pr(>|t|)
+(Intercept) 53.208 2.276 23.381 8.5e-14 ***
+block2 3.425 2.787 1.229 0.23690
+block3 6.750 2.787 2.422 0.02769 *
+block4 -3.900 2.787 -1.399 0.18082
+block5 -3.500 2.787 -1.256 0.22723
+block6 2.325 2.787 0.834 0.41646
+N1 5.617 1.609 3.490 0.00302 **
+K1 -3.983 1.609 -2.475 0.02487 *
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+Residual standard error: 3.942 on 16 degrees of freedom
+Multiple R-squared: 0.7163, Adjusted R-squared: 0.5922
+F-statistic: 5.772 on 7 and 16 DF, p-value: 0.001805
+
+> se.contrast(npk.aov1, list(N=="0", N=="1"), data = npk)
+[1] 1.609175
+> model.tables(npk.aov1, type = "means", se = TRUE)
+Tables of means
+Grand mean
+
+54.875
+
+ block
+block
+ 1 2 3 4 5 6
+54.03 57.45 60.77 50.12 50.52 56.35
+
+ N
+N
+ 0 1
+52.07 57.68
+
+ K
+K
+ 0 1
+56.87 52.88
+
+Standard errors for differences of means
+ block N K
+ 2.787 1.609 1.609
+replic. 4 12 12
+>
+>
+>
+> options(contrasts = c(unordered = "contr.treatment",ordered = "contr.poly"))
+> cleanEx()
+> nameEx("oats")
+> ### * oats
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: oats
+> ### Title: Data from an Oats Field Trial
+> ### Aliases: oats
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> oats$Nf <- ordered(oats$N, levels = sort(levels(oats$N)))
+> oats.aov <- aov(Y ~ Nf*V + Error(B/V), data = oats, qr = TRUE)
+> summary(oats.aov)
+
+Error: B
+ Df Sum Sq Mean Sq F value Pr(>F)
+Residuals 5 15875 3175
+
+Error: B:V
+ Df Sum Sq Mean Sq F value Pr(>F)
+V 2 1786 893.2 1.485 0.272
+Residuals 10 6013 601.3
+
+Error: Within
+ Df Sum Sq Mean Sq F value Pr(>F)
+Nf 3 20020 6673 37.686 2.46e-12 ***
+Nf:V 6 322 54 0.303 0.932
+Residuals 45 7969 177
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+> summary(oats.aov, split = list(Nf=list(L=1, Dev=2:3)))
+
+Error: B
+ Df Sum Sq Mean Sq F value Pr(>F)
+Residuals 5 15875 3175
+
+Error: B:V
+ Df Sum Sq Mean Sq F value Pr(>F)
+V 2 1786 893.2 1.485 0.272
+Residuals 10 6013 601.3
+
+Error: Within
+ Df Sum Sq Mean Sq F value Pr(>F)
+Nf 3 20020 6673 37.686 2.46e-12 ***
+ Nf: L 1 19536 19536 110.323 1.09e-13 ***
+ Nf: Dev 2 484 242 1.367 0.265
+Nf:V 6 322 54 0.303 0.932
+ Nf:V: L 2 168 84 0.475 0.625
+ Nf:V: Dev 4 153 38 0.217 0.928
+Residuals 45 7969 177
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+> par(mfrow = c(1,2), pty = "s")
+> plot(fitted(oats.aov[[4]]), studres(oats.aov[[4]]))
+> abline(h = 0, lty = 2)
+> oats.pr <- proj(oats.aov)
+> qqnorm(oats.pr[[4]][,"Residuals"], ylab = "Stratum 4 residuals")
+> qqline(oats.pr[[4]][,"Residuals"])
+>
+> par(mfrow = c(1,1), pty = "m")
+> oats.aov2 <- aov(Y ~ N + V + Error(B/V), data = oats, qr = TRUE)
+> model.tables(oats.aov2, type = "means", se = TRUE)
+Warning in model.tables.aovlist(oats.aov2, type = "means", se = TRUE) :
+ SEs for type 'means' are not yet implemented
+Tables of means
+Grand mean
+
+103.9722
+
+ N
+N
+0.0cwt 0.2cwt 0.4cwt 0.6cwt
+ 79.39 98.89 114.22 123.39
+
+ V
+V
+Golden.rain Marvellous Victory
+ 104.50 109.79 97.63
+>
+>
+>
+> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
+> cleanEx()
+> nameEx("parcoord")
+> ### * parcoord
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: parcoord
+> ### Title: Parallel Coordinates Plot
+> ### Aliases: parcoord
+> ### Keywords: hplot
+>
+> ### ** Examples
+>
+> parcoord(state.x77[, c(7, 4, 6, 2, 5, 3)])
+>
+> ir <- rbind(iris3[,,1], iris3[,,2], iris3[,,3])
+> parcoord(log(ir)[, c(3, 4, 2, 1)], col = 1 + (0:149)%/%50)
+>
+>
+>
+> cleanEx()
+> nameEx("petrol")
+> ### * petrol
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: petrol
+> ### Title: N. L. Prater's Petrol Refinery Data
+> ### Aliases: petrol
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> library(nlme)
+> Petrol <- petrol
+> Petrol[, 2:5] <- scale(as.matrix(Petrol[, 2:5]), scale = FALSE)
+> pet3.lme <- lme(Y ~ SG + VP + V10 + EP,
++ random = ~ 1 | No, data = Petrol)
+> pet3.lme <- update(pet3.lme, method = "ML")
+> pet4.lme <- update(pet3.lme, fixed = Y ~ V10 + EP)
+> anova(pet4.lme, pet3.lme)
+ Model df AIC BIC logLik Test L.Ratio p-value
+pet4.lme 1 5 149.6119 156.9406 -69.80594
+pet3.lme 2 7 149.3833 159.6435 -67.69166 1 vs 2 4.22855 0.1207
+>
+>
+>
+> cleanEx()
+
+detaching âpackage:nlmeâ
+
+> nameEx("plot.mca")
+> ### * plot.mca
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: plot.mca
+> ### Title: Plot Method for Objects of Class 'mca'
+> ### Aliases: plot.mca
+> ### Keywords: hplot multivariate
+>
+> ### ** Examples
+>
+> plot(mca(farms, abbrev = TRUE))
+>
+>
+>
+> cleanEx()
+> nameEx("plot.profile")
+> ### * plot.profile
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: plot.profile
+> ### Title: Plotting Functions for 'profile' Objects
+> ### Aliases: plot.profile pairs.profile
+> ### Keywords: models hplot
+>
+> ### ** Examples
+>
+> ## see ?profile.glm for an example using glm fits.
+>
+> ## a version of example(profile.nls) from R >= 2.8.0
+> fm1 <- nls(demand ~ SSasympOrig(Time, A, lrc), data = BOD)
+> pr1 <- profile(fm1, alpha = 0.1)
+> MASS:::plot.profile(pr1)
+> pairs(pr1) # a little odd since the parameters are highly correlated
+>
+> ## an example from ?nls
+> x <- -(1:100)/10
+> y <- 100 + 10 * exp(x / 2) + rnorm(x)/10
+> nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100, A=10, B=1))
+> pairs(profile(nlmod))
+>
+>
+>
+> cleanEx()
+> nameEx("polr")
+> ### * polr
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: polr
+> ### Title: Ordered Logistic or Probit Regression
+> ### Aliases: polr
+> ### Keywords: models
+>
+> ### ** Examples
+>
+> options(contrasts = c("contr.treatment", "contr.poly"))
+> house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, data = housing)
+> house.plr
+Call:
+polr(formula = Sat ~ Infl + Type + Cont, data = housing, weights = Freq)
+
+Coefficients:
+ InflMedium InflHigh TypeApartment TypeAtrium TypeTerrace
+ 0.5663937 1.2888191 -0.5723501 -0.3661866 -1.0910149
+ ContHigh
+ 0.3602841
+
+Intercepts:
+ Low|Medium Medium|High
+ -0.4961353 0.6907083
+
+Residual Deviance: 3479.149
+AIC: 3495.149
+> summary(house.plr, digits = 3)
+
+Re-fitting to get Hessian
+
+Call:
+polr(formula = Sat ~ Infl + Type + Cont, data = housing, weights = Freq)
+
+Coefficients:
+ Value Std. Error t value
+InflMedium 0.566 0.1047 5.41
+InflHigh 1.289 0.1272 10.14
+TypeApartment -0.572 0.1192 -4.80
+TypeAtrium -0.366 0.1552 -2.36
+TypeTerrace -1.091 0.1515 -7.20
+ContHigh 0.360 0.0955 3.77
+
+Intercepts:
+ Value Std. Error t value
+Low|Medium -0.496 0.125 -3.974
+Medium|High 0.691 0.125 5.505
+
+Residual Deviance: 3479.149
+AIC: 3495.149
+> ## slightly worse fit from
+> summary(update(house.plr, method = "probit", Hess = TRUE), digits = 3)
+Call:
+polr(formula = Sat ~ Infl + Type + Cont, data = housing, weights = Freq,
+ Hess = TRUE, method = "probit")
+
+Coefficients:
+ Value Std. Error t value
+InflMedium 0.346 0.0641 5.40
+InflHigh 0.783 0.0764 10.24
+TypeApartment -0.348 0.0723 -4.81
+TypeAtrium -0.218 0.0948 -2.30
+TypeTerrace -0.664 0.0918 -7.24
+ContHigh 0.222 0.0581 3.83
+
+Intercepts:
+ Value Std. Error t value
+Low|Medium -0.300 0.076 -3.937
+Medium|High 0.427 0.076 5.585
+
+Residual Deviance: 3479.689
+AIC: 3495.689
+> ## although it is not really appropriate, can fit
+> summary(update(house.plr, method = "cloglog", Hess = TRUE), digits = 3)
+Call:
+polr(formula = Sat ~ Infl + Type + Cont, data = housing, weights = Freq,
+ Hess = TRUE, method = "cloglog")
+
+Coefficients:
+ Value Std. Error t value
+InflMedium 0.367 0.0727 5.05
+InflHigh 0.790 0.0806 9.81
+TypeApartment -0.349 0.0757 -4.61
+TypeAtrium -0.196 0.0988 -1.98
+TypeTerrace -0.698 0.1043 -6.69
+ContHigh 0.268 0.0636 4.21
+
+Intercepts:
+ Value Std. Error t value
+Low|Medium 0.086 0.083 1.038
+Medium|High 0.892 0.087 10.223
+
+Residual Deviance: 3491.41
+AIC: 3507.41
+>
+> predict(house.plr, housing, type = "p")
+ Low Medium High
+1 0.3784493 0.2876752 0.3338755
+2 0.3784493 0.2876752 0.3338755
+3 0.3784493 0.2876752 0.3338755
+4 0.2568264 0.2742122 0.4689613
+5 0.2568264 0.2742122 0.4689613
+6 0.2568264 0.2742122 0.4689613
+7 0.1436924 0.2110836 0.6452240
+8 0.1436924 0.2110836 0.6452240
+9 0.1436924 0.2110836 0.6452240
+10 0.5190445 0.2605077 0.2204478
+11 0.5190445 0.2605077 0.2204478
+12 0.5190445 0.2605077 0.2204478
+13 0.3798514 0.2875965 0.3325521
+14 0.3798514 0.2875965 0.3325521
+15 0.3798514 0.2875965 0.3325521
+16 0.2292406 0.2643196 0.5064398
+17 0.2292406 0.2643196 0.5064398
+18 0.2292406 0.2643196 0.5064398
+19 0.4675584 0.2745383 0.2579033
+20 0.4675584 0.2745383 0.2579033
+21 0.4675584 0.2745383 0.2579033
+22 0.3326236 0.2876008 0.3797755
+23 0.3326236 0.2876008 0.3797755
+24 0.3326236 0.2876008 0.3797755
+25 0.1948548 0.2474226 0.5577225
+26 0.1948548 0.2474226 0.5577225
+27 0.1948548 0.2474226 0.5577225
+28 0.6444840 0.2114256 0.1440905
+29 0.6444840 0.2114256 0.1440905
+30 0.6444840 0.2114256 0.1440905
+31 0.5071210 0.2641196 0.2287594
+32 0.5071210 0.2641196 0.2287594
+33 0.5071210 0.2641196 0.2287594
+34 0.3331573 0.2876330 0.3792097
+35 0.3331573 0.2876330 0.3792097
+36 0.3331573 0.2876330 0.3792097
+37 0.2980880 0.2837746 0.4181374
+38 0.2980880 0.2837746 0.4181374
+39 0.2980880 0.2837746 0.4181374
+40 0.1942209 0.2470589 0.5587202
+41 0.1942209 0.2470589 0.5587202
+42 0.1942209 0.2470589 0.5587202
+43 0.1047770 0.1724227 0.7228003
+44 0.1047770 0.1724227 0.7228003
+45 0.1047770 0.1724227 0.7228003
+46 0.4294564 0.2820629 0.2884807
+47 0.4294564 0.2820629 0.2884807
+48 0.4294564 0.2820629 0.2884807
+49 0.2993357 0.2839753 0.4166890
+50 0.2993357 0.2839753 0.4166890
+51 0.2993357 0.2839753 0.4166890
+52 0.1718050 0.2328648 0.5953302
+53 0.1718050 0.2328648 0.5953302
+54 0.1718050 0.2328648 0.5953302
+55 0.3798387 0.2875972 0.3325641
+56 0.3798387 0.2875972 0.3325641
+57 0.3798387 0.2875972 0.3325641
+58 0.2579546 0.2745537 0.4674917
+59 0.2579546 0.2745537 0.4674917
+60 0.2579546 0.2745537 0.4674917
+61 0.1444202 0.2117081 0.6438717
+62 0.1444202 0.2117081 0.6438717
+63 0.1444202 0.2117081 0.6438717
+64 0.5583813 0.2471826 0.1944361
+65 0.5583813 0.2471826 0.1944361
+66 0.5583813 0.2471826 0.1944361
+67 0.4178031 0.2838213 0.2983756
+68 0.4178031 0.2838213 0.2983756
+69 0.4178031 0.2838213 0.2983756
+70 0.2584149 0.2746916 0.4668935
+71 0.2584149 0.2746916 0.4668935
+72 0.2584149 0.2746916 0.4668935
+> addterm(house.plr, ~.^2, test = "Chisq")
+Single term additions
+
+Model:
+Sat ~ Infl + Type + Cont
+ Df AIC LRT Pr(Chi)
+<none> 3495.1
+Infl:Type 6 3484.6 22.5093 0.0009786 ***
+Infl:Cont 2 3498.9 0.2090 0.9007957
+Type:Cont 3 3492.5 8.6662 0.0340752 *
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+> house.plr2 <- stepAIC(house.plr, ~.^2)
+Start: AIC=3495.15
+Sat ~ Infl + Type + Cont
+
+ Df AIC
++ Infl:Type 6 3484.6
++ Type:Cont 3 3492.5
+<none> 3495.1
++ Infl:Cont 2 3498.9
+- Cont 1 3507.5
+- Type 3 3545.1
+- Infl 2 3599.4
+
+Step: AIC=3484.64
+Sat ~ Infl + Type + Cont + Infl:Type
+
+ Df AIC
++ Type:Cont 3 3482.7
+<none> 3484.6
++ Infl:Cont 2 3488.5
+- Infl:Type 6 3495.1
+- Cont 1 3497.8
+
+Step: AIC=3482.69
+Sat ~ Infl + Type + Cont + Infl:Type + Type:Cont
+
+ Df AIC
+<none> 3482.7
+- Type:Cont 3 3484.6
++ Infl:Cont 2 3486.6
+- Infl:Type 6 3492.5
+> house.plr2$anova
+Stepwise Model Path
+Analysis of Deviance Table
+
+Initial Model:
+Sat ~ Infl + Type + Cont
+
+Final Model:
+Sat ~ Infl + Type + Cont + Infl:Type + Type:Cont
+
+
+ Step Df Deviance Resid. Df Resid. Dev AIC
+1 1673 3479.149 3495.149
+2 + Infl:Type 6 22.509347 1667 3456.640 3484.640
+3 + Type:Cont 3 7.945029 1664 3448.695 3482.695
+> anova(house.plr, house.plr2)
+Likelihood ratio tests of ordinal regression models
+
+Response: Sat
+ Model Resid. df Resid. Dev Test Df
+1 Infl + Type + Cont 1673 3479.149
+2 Infl + Type + Cont + Infl:Type + Type:Cont 1664 3448.695 1 vs 2 9
+ LR stat. Pr(Chi)
+1
+2 30.45438 0.0003670555
+>
+> house.plr <- update(house.plr, Hess=TRUE)
+> pr <- profile(house.plr)
+> confint(pr)
+ 2.5 % 97.5 %
+InflMedium 0.3616415 0.77195375
+InflHigh 1.0409701 1.53958138
+TypeApartment -0.8069590 -0.33940432
+TypeAtrium -0.6705862 -0.06204495
+TypeTerrace -1.3893863 -0.79533958
+ContHigh 0.1733589 0.54792854
+> plot(pr)
+> pairs(pr)
+>
+>
+>
+> options(contrasts = c(unordered = "contr.treatment",ordered = "contr.poly"))
+> cleanEx()
+> nameEx("predict.glmmPQL")
+> ### * predict.glmmPQL
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: predict.glmmPQL
+> ### Title: Predict Method for glmmPQL Fits
+> ### Aliases: predict.glmmPQL
+> ### Keywords: models
+>
+> ### ** Examples
+>
+> fit <- glmmPQL(y ~ trt + I(week > 2), random = ~1 | ID,
++ family = binomial, data = bacteria)
+Loading required package: nlme
+iteration 1
+iteration 2
+iteration 3
+iteration 4
+iteration 5
+iteration 6
+> predict(fit, bacteria, level = 0, type="response")
+ [1] 0.9680779 0.9680779 0.8587270 0.8587270 0.9344832 0.9344832 0.7408574
+ [8] 0.7408574 0.8970307 0.8970307 0.6358511 0.6358511 0.6358511 0.9680779
+ [15] 0.9680779 0.8587270 0.8587270 0.8587270 0.9680779 0.9680779 0.8587270
+ [22] 0.8587270 0.8587270 0.8970307 0.8970307 0.6358511 0.6358511 0.9344832
+ [29] 0.9344832 0.7408574 0.7408574 0.7408574 0.9680779 0.9680779 0.8587270
+ [36] 0.8587270 0.8587270 0.9680779 0.9680779 0.8587270 0.8587270 0.8587270
+ [43] 0.9344832 0.7408574 0.9680779 0.9680779 0.8587270 0.8587270 0.8587270
+ [50] 0.8970307 0.8970307 0.6358511 0.6358511 0.6358511 0.9680779 0.9680779
+ [57] 0.8587270 0.8587270 0.8587270 0.9680779 0.9680779 0.8587270 0.8970307
+ [64] 0.8970307 0.6358511 0.6358511 0.6358511 0.9344832 0.9344832 0.7408574
+ [71] 0.7408574 0.7408574 0.9680779 0.9680779 0.8587270 0.8587270 0.8587270
+ [78] 0.8970307 0.8970307 0.6358511 0.6358511 0.6358511 0.9680779 0.9680779
+ [85] 0.8587270 0.8587270 0.8587270 0.9344832 0.9344832 0.7408574 0.7408574
+ [92] 0.9680779 0.9680779 0.8587270 0.8587270 0.8587270 0.9680779 0.9680779
+ [99] 0.8587270 0.8587270 0.8587270 0.9680779 0.9680779 0.8587270 0.8587270
+[106] 0.8587270 0.9344832 0.9344832 0.7408574 0.7408574 0.7408574 0.8970307
+[113] 0.8970307 0.6358511 0.6358511 0.9680779 0.9680779 0.8587270 0.9680779
+[120] 0.9680779 0.8587270 0.8587270 0.8970307 0.8970307 0.6358511 0.6358511
+[127] 0.6358511 0.9344832 0.7408574 0.7408574 0.7408574 0.9680779 0.8587270
+[134] 0.8587270 0.8587270 0.8970307 0.8970307 0.6358511 0.6358511 0.6358511
+[141] 0.9680779 0.9680779 0.8587270 0.8587270 0.8587270 0.9344832 0.7408574
+[148] 0.8970307 0.8970307 0.6358511 0.6358511 0.9680779 0.9680779 0.8587270
+[155] 0.8970307 0.8970307 0.6358511 0.9680779 0.9680779 0.8587270 0.8587270
+[162] 0.8587270 0.9344832 0.9344832 0.7408574 0.7408574 0.7408574 0.9680779
+[169] 0.9680779 0.8587270 0.8587270 0.8587270 0.9344832 0.7408574 0.8970307
+[176] 0.8970307 0.6358511 0.6358511 0.6358511 0.9344832 0.9344832 0.7408574
+[183] 0.7408574 0.9680779 0.9680779 0.8587270 0.8587270 0.8587270 0.8970307
+[190] 0.8970307 0.6358511 0.6358511 0.6358511 0.9344832 0.9344832 0.7408574
+[197] 0.7408574 0.7408574 0.8970307 0.6358511 0.6358511 0.9344832 0.9344832
+[204] 0.7408574 0.7408574 0.7408574 0.8970307 0.8970307 0.6358511 0.6358511
+[211] 0.9344832 0.9344832 0.7408574 0.7408574 0.7408574 0.9344832 0.9344832
+[218] 0.7408574 0.7408574 0.7408574
+attr(,"label")
+[1] "Predicted values"
+> predict(fit, bacteria, level = 1, type="response")
+ X01 X01 X01 X01 X02 X02 X02 X02
+0.9828449 0.9828449 0.9198935 0.9198935 0.9050782 0.9050782 0.6564944 0.6564944
+ X03 X03 X03 X03 X03 X04 X04 X04
+0.9724022 0.9724022 0.8759665 0.8759665 0.8759665 0.9851548 0.9851548 0.9300763
+ X04 X04 X05 X05 X05 X05 X05 X06
+0.9300763 0.9300763 0.9851548 0.9851548 0.9300763 0.9300763 0.9300763 0.9662755
+ X06 X06 X06 X07 X07 X07 X07 X07
+0.9662755 0.8516962 0.8516962 0.7291679 0.7291679 0.3504978 0.3504978 0.3504978
+ X08 X08 X08 X08 X08 X09 X09 X09
+0.9426815 0.9426815 0.7672499 0.7672499 0.7672499 0.9851548 0.9851548 0.9300763
+ X09 X09 X10 X10 X11 X11 X11 X11
+0.9300763 0.9300763 0.9640326 0.8430706 0.9851548 0.9851548 0.9300763 0.9300763
+ X11 X12 X12 X12 X12 X12 X13 X13
+0.9300763 0.8334870 0.8334870 0.5008219 0.5008219 0.5008219 0.9851548 0.9851548
+ X13 X13 X13 X14 X14 X14 X15 X15
+0.9300763 0.9300763 0.9300763 0.8907227 0.8907227 0.6203155 0.9724022 0.9724022
+ X15 X15 X15 X16 X16 X16 X16 X16
+0.8759665 0.8759665 0.8759665 0.9287777 0.9287777 0.7232833 0.7232833 0.7232833
+ X17 X17 X17 X17 X17 X18 X18 X18
+0.9426815 0.9426815 0.7672499 0.7672499 0.7672499 0.7070916 0.7070916 0.3260827
+ X18 X18 X19 X19 X19 X19 X19 X20
+0.3260827 0.3260827 0.8702991 0.8702991 0.5735499 0.5735499 0.5735499 0.9736293
+ X20 X20 X20 X21 X21 X21 X21 X21
+0.9736293 0.8809564 0.8809564 0.9851548 0.9851548 0.9300763 0.9300763 0.9300763
+ Y01 Y01 Y01 Y01 Y01 Y02 Y02 Y02
+0.9851548 0.9851548 0.9300763 0.9300763 0.9300763 0.7607971 0.7607971 0.3893126
+ Y02 Y02 Y03 Y03 Y03 Y03 Y03 Y04
+0.3893126 0.3893126 0.8487181 0.8487181 0.5292976 0.5292976 0.5292976 0.5734482
+ Y04 Y04 Y04 Y05 Y05 Y05 Y06 Y06
+0.5734482 0.2122655 0.2122655 0.7144523 0.7144523 0.3339997 0.9828449 0.9828449
+ Y06 Y06 Y07 Y07 Y07 Y07 Y07 Y08
+0.9198935 0.9198935 0.8334870 0.8334870 0.5008219 0.5008219 0.5008219 0.9238389
+ Y08 Y08 Y08 Y09 Y09 Y09 Y09 Y10
+0.7085660 0.7085660 0.7085660 0.9847299 0.9281899 0.9281899 0.9281899 0.9188296
+ Y10 Y10 Y10 Y10 Y11 Y11 Y11 Y11
+0.9188296 0.6940862 0.6940862 0.6940862 0.9851548 0.9851548 0.9300763 0.9300763
+ Y11 Y12 Y12 Y13 Y13 Y13 Y13 Y14
+0.9300763 0.9640326 0.8430706 0.5734482 0.5734482 0.2122655 0.2122655 0.9793383
+ Y14 Y14 Z01 Z01 Z01 Z02 Z02 Z02
+0.9793383 0.9047659 0.9556329 0.9556329 0.8119328 0.9851548 0.9851548 0.9300763
+ Z02 Z02 Z03 Z03 Z03 Z03 Z03 Z05
+0.9300763 0.9300763 0.9779690 0.9779690 0.8989642 0.8989642 0.8989642 0.8702991
+ Z05 Z05 Z05 Z05 Z06 Z06 Z07 Z07
+0.8702991 0.5735499 0.5735499 0.5735499 0.8306525 0.4957505 0.8334870 0.8334870
+ Z07 Z07 Z07 Z09 Z09 Z09 Z09 Z10
+0.5008219 0.5008219 0.5008219 0.9736293 0.9736293 0.8809564 0.8809564 0.9851548
+ Z10 Z10 Z10 Z10 Z11 Z11 Z11 Z11
+0.9851548 0.9300763 0.9300763 0.9300763 0.9724022 0.9724022 0.8759665 0.8759665
+ Z11 Z14 Z14 Z14 Z14 Z14 Z15 Z15
+0.8759665 0.9287777 0.9287777 0.7232833 0.7232833 0.7232833 0.9643851 0.8444172
+ Z15 Z19 Z19 Z19 Z19 Z19 Z20 Z20
+0.8444172 0.9779690 0.9779690 0.8989642 0.8989642 0.8989642 0.7620490 0.7620490
+ Z20 Z20 Z24 Z24 Z24 Z24 Z24 Z26
+0.3909523 0.3909523 0.8487181 0.8487181 0.5292976 0.5292976 0.5292976 0.9287777
+ Z26 Z26 Z26 Z26
+0.9287777 0.7232833 0.7232833 0.7232833
+attr(,"label")
+[1] "Predicted values"
+>
+>
+>
+> cleanEx()
+
+detaching âpackage:nlmeâ
+
+> nameEx("predict.lda")
+> ### * predict.lda
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: predict.lda
+> ### Title: Classify Multivariate Observations by Linear Discrimination
+> ### Aliases: predict.lda
+> ### Keywords: multivariate
+>
+> ### ** Examples
+>
+> tr <- sample(1:50, 25)
+> train <- rbind(iris3[tr,,1], iris3[tr,,2], iris3[tr,,3])
+> test <- rbind(iris3[-tr,,1], iris3[-tr,,2], iris3[-tr,,3])
+> cl <- factor(c(rep("s",25), rep("c",25), rep("v",25)))
+> z <- lda(train, cl)
+> predict(z, test)$class
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c c c v c c
+[39] c c c c c c c c c c c c v v v v v v v v v c v v v v v v v v v v v v v v v
+Levels: c s v
+>
+>
+>
+> cleanEx()
+> nameEx("predict.lqs")
+> ### * predict.lqs
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: predict.lqs
+> ### Title: Predict from an lqs Fit
+> ### Aliases: predict.lqs
+> ### Keywords: models
+>
+> ### ** Examples
+>
+> set.seed(123)
+> fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsamp = "exact")
+> predict(fm, stackloss)
+ 1 2 3 4 5 6 7 8
+35.500000 35.579646 30.409292 19.477876 18.592920 19.035398 19.000000 19.000000
+ 9 10 11 12 13 14 15 16
+15.734513 14.079646 13.362832 13.000000 13.920354 13.486726 6.761062 7.000000
+ 17 18 19 20 21
+ 8.557522 8.000000 8.362832 13.154867 23.991150
+>
+>
+>
+> cleanEx()
+> nameEx("predict.qda")
+> ### * predict.qda
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: predict.qda
+> ### Title: Classify from Quadratic Discriminant Analysis
+> ### Aliases: predict.qda
+> ### Keywords: multivariate
+>
+> ### ** Examples
+>
+> tr <- sample(1:50, 25)
+> train <- rbind(iris3[tr,,1], iris3[tr,,2], iris3[tr,,3])
+> test <- rbind(iris3[-tr,,1], iris3[-tr,,2], iris3[-tr,,3])
+> cl <- factor(c(rep("s",25), rep("c",25), rep("v",25)))
+> zq <- qda(train, cl)
+> predict(zq, test)$class
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c c c v c c
+[39] c c c c c c c c c c c c v v v v v v v v v v v v v v v v v v v v v v v v v
+Levels: c s v
+>
+>
+>
+> cleanEx()
+> nameEx("profile.glm")
+> ### * profile.glm
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: profile.glm
+> ### Title: Method for Profiling glm Objects
+> ### Aliases: profile.glm
+> ### Keywords: regression models
+>
+> ### ** Examples
+>
+> options(contrasts = c("contr.treatment", "contr.poly"))
+> ldose <- rep(0:5, 2)
+> numdead <- c(1, 4, 9, 13, 18, 20, 0, 2, 6, 10, 12, 16)
+> sex <- factor(rep(c("M", "F"), c(6, 6)))
+> SF <- cbind(numdead, numalive = 20 - numdead)
+> budworm.lg <- glm(SF ~ sex*ldose, family = binomial)
+> pr1 <- profile(budworm.lg)
+> plot(pr1)
+> pairs(pr1)
+>
+>
+>
+> options(contrasts = c(unordered = "contr.treatment",ordered = "contr.poly"))
+> cleanEx()
+> nameEx("qda")
+> ### * qda
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: qda
+> ### Title: Quadratic Discriminant Analysis
+> ### Aliases: qda qda.data.frame qda.default qda.formula qda.matrix
+> ### model.frame.qda print.qda
+> ### Keywords: multivariate
+>
+> ### ** Examples
+>
+> tr <- sample(1:50, 25)
+> train <- rbind(iris3[tr,,1], iris3[tr,,2], iris3[tr,,3])
+> test <- rbind(iris3[-tr,,1], iris3[-tr,,2], iris3[-tr,,3])
+> cl <- factor(c(rep("s",25), rep("c",25), rep("v",25)))
+> z <- qda(train, cl)
+> predict(z,test)$class
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c c c v c c
+[39] c c c c c c c c c c c c v v v v v v v v v v v v v v v v v v v v v v v v v
+Levels: c s v
+>
+>
+>
+> cleanEx()
+> nameEx("rational")
+> ### * rational
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: rational
+> ### Title: Rational Approximation
+> ### Aliases: rational .rat
+> ### Keywords: math
+>
+> ### ** Examples
+>
+> X <- matrix(runif(25), 5, 5)
+> zapsmall(solve(X, X/5)) # print near-zeroes as zero
+ [,1] [,2] [,3] [,4] [,5]
+[1,] 0.2 0.0 0.0 0.0 0.0
+[2,] 0.0 0.2 0.0 0.0 0.0
+[3,] 0.0 0.0 0.2 0.0 0.0
+[4,] 0.0 0.0 0.0 0.2 0.0
+[5,] 0.0 0.0 0.0 0.0 0.2
+> rational(solve(X, X/5))
+ [,1] [,2] [,3] [,4] [,5]
+[1,] 0.2 0.0 0.0 0.0 0.0
+[2,] 0.0 0.2 0.0 0.0 0.0
+[3,] 0.0 0.0 0.2 0.0 0.0
+[4,] 0.0 0.0 0.0 0.2 0.0
+[5,] 0.0 0.0 0.0 0.0 0.2
+>
+>
+>
+> cleanEx()
+> nameEx("renumerate")
+> ### * renumerate
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: renumerate
+> ### Title: Convert a Formula Transformed by 'denumerate'
+> ### Aliases: renumerate renumerate.formula
+> ### Keywords: models
+>
+> ### ** Examples
+>
+> denumerate(~(1+2+3)^3 + a/b)
+~(.v1 + .v2 + .v3)^3 + a/b
+> ## ~ (.v1 + .v2 + .v3)^3 + a/b
+> renumerate(.Last.value)
+~(`1` + `2` + `3`)^3 + a/b
+> ## ~ (1 + 2 + 3)^3 + a/b
+>
+>
+>
+> cleanEx()
+> nameEx("rlm")
+> ### * rlm
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: rlm
+> ### Title: Robust Fitting of Linear Models
+> ### Aliases: rlm rlm.default rlm.formula print.rlm predict.rlm psi.bisquare
+> ### psi.hampel psi.huber
+> ### Keywords: models robust
+>
+> ### ** Examples
+>
+> summary(rlm(stack.loss ~ ., stackloss))
+
+Call: rlm(formula = stack.loss ~ ., data = stackloss)
+Residuals:
+ Min 1Q Median 3Q Max
+-8.91753 -1.73127 0.06187 1.54306 6.50163
+
+Coefficients:
+ Value Std. Error t value
+(Intercept) -41.0265 9.8073 -4.1832
+Air.Flow 0.8294 0.1112 7.4597
+Water.Temp 0.9261 0.3034 3.0524
+Acid.Conc. -0.1278 0.1289 -0.9922
+
+Residual standard error: 2.441 on 17 degrees of freedom
+> rlm(stack.loss ~ ., stackloss, psi = psi.hampel, init = "lts")
+Call:
+rlm(formula = stack.loss ~ ., data = stackloss, psi = psi.hampel,
+ init = "lts")
+Converged in 9 iterations
+
+Coefficients:
+(Intercept) Air.Flow Water.Temp Acid.Conc.
+-40.4747826 0.7410853 1.2250730 -0.1455245
+
+Degrees of freedom: 21 total; 17 residual
+Scale estimate: 3.09
+> rlm(stack.loss ~ ., stackloss, psi = psi.bisquare)
+Call:
+rlm(formula = stack.loss ~ ., data = stackloss, psi = psi.bisquare)
+Converged in 11 iterations
+
+Coefficients:
+(Intercept) Air.Flow Water.Temp Acid.Conc.
+-42.2852537 0.9275471 0.6507322 -0.1123310
+
+Degrees of freedom: 21 total; 17 residual
+Scale estimate: 2.28
+>
+>
+>
+> cleanEx()
+> nameEx("rms.curv")
+> ### * rms.curv
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: rms.curv
+> ### Title: Relative Curvature Measures for Non-Linear Regression
+> ### Aliases: rms.curv print.rms.curv
+> ### Keywords: nonlinear
+>
+> ### ** Examples
+>
+> # The treated sample from the Puromycin data
+> mmcurve <- deriv3(~ Vm * conc/(K + conc), c("Vm", "K"),
++ function(Vm, K, conc) NULL)
+> Treated <- Puromycin[Puromycin$state == "treated", ]
+> (Purfit1 <- nls(rate ~ mmcurve(Vm, K, conc), data = Treated,
++ start = list(Vm=200, K=0.1)))
+Nonlinear regression model
+ model: rate ~ mmcurve(Vm, K, conc)
+ data: Treated
+ Vm K
+212.68363 0.06412
+ residual sum-of-squares: 1195
+
+Number of iterations to convergence: 6
+Achieved convergence tolerance: 6.096e-06
+> rms.curv(Purfit1)
+Parameter effects: c^theta x sqrt(F) = 0.2121
+ Intrinsic: c^iota x sqrt(F) = 0.092
+> ##Parameter effects: c^theta x sqrt(F) = 0.2121
+> ## Intrinsic: c^iota x sqrt(F) = 0.092
+>
+>
+>
+> cleanEx()
+> nameEx("rnegbin")
+> ### * rnegbin
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: rnegbin
+> ### Title: Simulate Negative Binomial Variates
+> ### Aliases: rnegbin
+> ### Keywords: distribution
+>
+> ### ** Examples
+>
+> # Negative Binomials with means fitted(fm) and theta = 4.5
+> fm <- glm.nb(Days ~ ., data = quine)
+> dummy <- rnegbin(fitted(fm), theta = 4.5)
+>
+>
+>
+> cleanEx()
+> nameEx("sammon")
+> ### * sammon
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: sammon
+> ### Title: Sammon's Non-Linear Mapping
+> ### Aliases: sammon
+> ### Keywords: multivariate
+>
+> ### ** Examples
+>
+> swiss.x <- as.matrix(swiss[, -1])
+> swiss.sam <- sammon(dist(swiss.x))
+Initial stress : 0.00824
+stress after 10 iters: 0.00439, magic = 0.338
+stress after 20 iters: 0.00383, magic = 0.500
+stress after 30 iters: 0.00383, magic = 0.500
+> plot(swiss.sam$points, type = "n")
+> text(swiss.sam$points, labels = as.character(1:nrow(swiss.x)))
+>
+>
+>
+> cleanEx()
+> nameEx("stepAIC")
+> ### * stepAIC
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: stepAIC
+> ### Title: Choose a model by AIC in a Stepwise Algorithm
+> ### Aliases: stepAIC extractAIC.gls terms.gls extractAIC.lme terms.lme
+> ### Keywords: models
+>
+> ### ** Examples
+>
+> quine.hi <- aov(log(Days + 2.5) ~ .^4, quine)
+> quine.nxt <- update(quine.hi, . ~ . - Eth:Sex:Age:Lrn)
+> quine.stp <- stepAIC(quine.nxt,
++ scope = list(upper = ~Eth*Sex*Age*Lrn, lower = ~1),
++ trace = FALSE)
+> quine.stp$anova
+Stepwise Model Path
+Analysis of Deviance Table
+
+Initial Model:
+log(Days + 2.5) ~ Eth + Sex + Age + Lrn + Eth:Sex + Eth:Age +
+ Eth:Lrn + Sex:Age + Sex:Lrn + Age:Lrn + Eth:Sex:Age + Eth:Sex:Lrn +
+ Eth:Age:Lrn + Sex:Age:Lrn
+
+Final Model:
+log(Days + 2.5) ~ Eth + Sex + Age + Lrn + Eth:Sex + Eth:Age +
+ Eth:Lrn + Sex:Age + Sex:Lrn + Age:Lrn + Eth:Sex:Lrn + Eth:Age:Lrn
+
+
+ Step Df Deviance Resid. Df Resid. Dev AIC
+1 120 64.09900 -68.18396
+2 - Eth:Sex:Age 3 0.973869 123 65.07287 -71.98244
+3 - Sex:Age:Lrn 2 1.526754 125 66.59962 -72.59652
+>
+> cpus1 <- cpus
+> attach(cpus)
+> for(v in names(cpus)[2:7])
++ cpus1[[v]] <- cut(cpus[[v]], unique(quantile(cpus[[v]])),
++ include.lowest = TRUE)
+> detach()
+> cpus0 <- cpus1[, 2:8] # excludes names, authors' predictions
+> cpus.samp <- sample(1:209, 100)
+> cpus.lm <- lm(log10(perf) ~ ., data = cpus1[cpus.samp,2:8])
+> cpus.lm2 <- stepAIC(cpus.lm, trace = FALSE)
+> cpus.lm2$anova
+Stepwise Model Path
+Analysis of Deviance Table
+
+Initial Model:
+log10(perf) ~ syct + mmin + mmax + cach + chmin + chmax
+
+Final Model:
+log10(perf) ~ mmax + cach + chmax
+
+
+ Step Df Deviance Resid. Df Resid. Dev AIC
+1 82 3.362324 -303.2538
+2 - syct 3 0.0445369 85 3.406861 -307.9379
+3 - mmin 3 0.1947053 88 3.601566 -308.3801
+4 - chmin 3 0.1924133 91 3.793980 -309.1755
+>
+> example(birthwt)
+
+brthwt> attach(birthwt)
+
+brthwt> race <- factor(race, labels = c("white", "black", "other"))
+
+brthwt> ptd <- factor(ptl > 0)
+
+brthwt> ftv <- factor(ftv)
+
+brthwt> levels(ftv)[-(1:2)] <- "2+"
+
+brthwt> bwt <- data.frame(low = factor(low), age, lwt, race,
+brthwt+ smoke = (smoke > 0), ptd, ht = (ht > 0), ui = (ui > 0), ftv)
+
+brthwt> detach("birthwt")
+
+brthwt> options(contrasts = c("contr.treatment", "contr.poly"))
+
+brthwt> glm(low ~ ., binomial, bwt)
+
+Call: glm(formula = low ~ ., family = binomial, data = bwt)
+
+Coefficients:
+(Intercept) age lwt raceblack raceother smokeTRUE
+ 0.82302 -0.03723 -0.01565 1.19241 0.74068 0.75553
+ ptdTRUE htTRUE uiTRUE ftv1 ftv2+
+ 1.34376 1.91317 0.68020 -0.43638 0.17901
+
+Degrees of Freedom: 188 Total (i.e. Null); 178 Residual
+Null Deviance: 234.7
+Residual Deviance: 195.5 AIC: 217.5
+> birthwt.glm <- glm(low ~ ., family = binomial, data = bwt)
+> birthwt.step <- stepAIC(birthwt.glm, trace = FALSE)
+> birthwt.step$anova
+Stepwise Model Path
+Analysis of Deviance Table
+
+Initial Model:
+low ~ age + lwt + race + smoke + ptd + ht + ui + ftv
+
+Final Model:
+low ~ lwt + race + smoke + ptd + ht + ui
+
+
+ Step Df Deviance Resid. Df Resid. Dev AIC
+1 178 195.4755 217.4755
+2 - ftv 2 1.358185 180 196.8337 214.8337
+3 - age 1 1.017866 181 197.8516 213.8516
+> birthwt.step2 <- stepAIC(birthwt.glm, ~ .^2 + I(scale(age)^2)
++ + I(scale(lwt)^2), trace = FALSE)
+> birthwt.step2$anova
+Stepwise Model Path
+Analysis of Deviance Table
+
+Initial Model:
+low ~ age + lwt + race + smoke + ptd + ht + ui + ftv
+
+Final Model:
+low ~ age + lwt + smoke + ptd + ht + ui + ftv + age:ftv + smoke:ui
+
+
+ Step Df Deviance Resid. Df Resid. Dev AIC
+1 178 195.4755 217.4755
+2 + age:ftv 2 12.474896 176 183.0006 209.0006
+3 + smoke:ui 1 3.056805 175 179.9438 207.9438
+4 - race 2 3.129586 177 183.0734 207.0734
+>
+> quine.nb <- glm.nb(Days ~ .^4, data = quine)
+> quine.nb2 <- stepAIC(quine.nb)
+Start: AIC=1095.32
+Days ~ (Eth + Sex + Age + Lrn)^4
+
+ Df AIC
+- Eth:Sex:Age:Lrn 2 1092.7
+<none> 1095.3
+
+Step: AIC=1092.73
+Days ~ Eth + Sex + Age + Lrn + Eth:Sex + Eth:Age + Eth:Lrn +
+ Sex:Age + Sex:Lrn + Age:Lrn + Eth:Sex:Age + Eth:Sex:Lrn +
+ Eth:Age:Lrn + Sex:Age:Lrn
+
+ Df AIC
+- Eth:Sex:Age 3 1089.4
+<none> 1092.7
+- Eth:Sex:Lrn 1 1093.3
+- Eth:Age:Lrn 2 1094.7
+- Sex:Age:Lrn 2 1095.0
+
+Step: AIC=1089.41
+Days ~ Eth + Sex + Age + Lrn + Eth:Sex + Eth:Age + Eth:Lrn +
+ Sex:Age + Sex:Lrn + Age:Lrn + Eth:Sex:Lrn + Eth:Age:Lrn +
+ Sex:Age:Lrn
+
+ Df AIC
+<none> 1089.4
+- Sex:Age:Lrn 2 1091.1
+- Eth:Age:Lrn 2 1091.2
+- Eth:Sex:Lrn 1 1092.5
+> quine.nb2$anova
+Stepwise Model Path
+Analysis of Deviance Table
+
+Initial Model:
+Days ~ (Eth + Sex + Age + Lrn)^4
+
+Final Model:
+Days ~ Eth + Sex + Age + Lrn + Eth:Sex + Eth:Age + Eth:Lrn +
+ Sex:Age + Sex:Lrn + Age:Lrn + Eth:Sex:Lrn + Eth:Age:Lrn +
+ Sex:Age:Lrn
+
+
+ Step Df Deviance Resid. Df Resid. Dev AIC
+1 118 167.4535 1095.324
+2 - Eth:Sex:Age:Lrn 2 0.09746244 120 167.5509 1092.728
+3 - Eth:Sex:Age 3 0.11060087 123 167.4403 1089.409
+>
+>
+>
+> cleanEx()
+> nameEx("summary.negbin")
+> ### * summary.negbin
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: summary.negbin
+> ### Title: Summary Method Function for Objects of Class 'negbin'
+> ### Aliases: summary.negbin print.summary.negbin
+> ### Keywords: models
+>
+> ### ** Examples
+>
+> summary(glm.nb(Days ~ Eth*Age*Lrn*Sex, quine, link = log))
+
+Call:
+glm.nb(formula = Days ~ Eth * Age * Lrn * Sex, data = quine,
+ link = log, init.theta = 1.928360145)
+
+Deviance Residuals:
+ Min 1Q Median 3Q Max
+-3.2377 -0.9079 -0.2019 0.5173 1.7043
+
+Coefficients: (4 not defined because of singularities)
+ Estimate Std. Error z value Pr(>|z|)
+(Intercept) 3.0564 0.3760 8.128 4.38e-16 ***
+EthN -0.1386 0.5334 -0.260 0.795023
+AgeF1 -0.6227 0.5125 -1.215 0.224334
+AgeF2 -2.3632 1.0770 -2.194 0.028221 *
+AgeF3 -0.3784 0.4546 -0.832 0.405215
+LrnSL -1.9577 0.9967 -1.964 0.049493 *
+SexM -0.4914 0.5104 -0.963 0.335653
+EthN:AgeF1 0.1029 0.7123 0.144 0.885175
+EthN:AgeF2 -0.5546 1.6798 -0.330 0.741297
+EthN:AgeF3 0.0633 0.6396 0.099 0.921159
+EthN:LrnSL 2.2588 1.3019 1.735 0.082743 .
+AgeF1:LrnSL 2.6421 1.0821 2.442 0.014618 *
+AgeF2:LrnSL 4.8585 1.4423 3.369 0.000755 ***
+AgeF3:LrnSL NA NA NA NA
+EthN:SexM -0.7524 0.7220 -1.042 0.297400
+AgeF1:SexM 0.4092 0.8299 0.493 0.621973
+AgeF2:SexM 3.1098 1.1655 2.668 0.007624 **
+AgeF3:SexM 1.1145 0.6365 1.751 0.079926 .
+LrnSL:SexM 1.5900 1.1499 1.383 0.166750
+EthN:AgeF1:LrnSL -3.5493 1.4270 -2.487 0.012876 *
+EthN:AgeF2:LrnSL -3.3315 2.0919 -1.593 0.111256
+EthN:AgeF3:LrnSL NA NA NA NA
+EthN:AgeF1:SexM -0.3105 1.2055 -0.258 0.796735
+EthN:AgeF2:SexM 0.3469 1.7965 0.193 0.846875
+EthN:AgeF3:SexM 0.8329 0.8970 0.929 0.353092
+EthN:LrnSL:SexM -0.1639 1.5250 -0.107 0.914411
+AgeF1:LrnSL:SexM -2.4285 1.4201 -1.710 0.087246 .
+AgeF2:LrnSL:SexM -4.1914 1.6201 -2.587 0.009679 **
+AgeF3:LrnSL:SexM NA NA NA NA
+EthN:AgeF1:LrnSL:SexM 2.1711 1.9192 1.131 0.257963
+EthN:AgeF2:LrnSL:SexM 2.1029 2.3444 0.897 0.369718
+EthN:AgeF3:LrnSL:SexM NA NA NA NA
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+(Dispersion parameter for Negative Binomial(1.9284) family taken to be 1)
+
+ Null deviance: 272.29 on 145 degrees of freedom
+Residual deviance: 167.45 on 118 degrees of freedom
+AIC: 1097.3
+
+Number of Fisher Scoring iterations: 1
+
+
+ Theta: 1.928
+ Std. Err.: 0.269
+
+ 2 x log-likelihood: -1039.324
+>
+>
+>
+> cleanEx()
+> nameEx("summary.rlm")
+> ### * summary.rlm
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: summary.rlm
+> ### Title: Summary Method for Robust Linear Models
+> ### Aliases: summary.rlm print.summary.rlm
+> ### Keywords: robust
+>
+> ### ** Examples
+>
+> summary(rlm(calls ~ year, data = phones, maxit = 50))
+
+Call: rlm(formula = calls ~ year, data = phones, maxit = 50)
+Residuals:
+ Min 1Q Median 3Q Max
+-18.314 -5.953 -1.681 26.460 173.769
+
+Coefficients:
+ Value Std. Error t value
+(Intercept) -102.6222 26.6082 -3.8568
+year 2.0414 0.4299 4.7480
+
+Residual standard error: 9.032 on 22 degrees of freedom
+> ## Not run:
+> ##D Call:
+> ##D rlm(formula = calls ~ year, data = phones, maxit = 50)
+> ##D
+> ##D Residuals:
+> ##D Min 1Q Median 3Q Max
+> ##D -18.31 -5.95 -1.68 26.46 173.77
+> ##D
+> ##D Coefficients:
+> ##D Value Std. Error t value
+> ##D (Intercept) -102.622 26.553 -3.86
+> ##D year 2.041 0.429 4.76
+> ##D
+> ##D Residual standard error: 9.03 on 22 degrees of freedom
+> ##D
+> ##D Correlation of Coefficients:
+> ##D [1] -0.994
+> ##D
+> ## End(Not run)
+>
+>
+> cleanEx()
+> nameEx("theta.md")
+> ### * theta.md
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: theta.md
+> ### Title: Estimate theta of the Negative Binomial
+> ### Aliases: theta.md theta.ml theta.mm
+> ### Keywords: models
+>
+> ### ** Examples
+>
+> quine.nb <- glm.nb(Days ~ .^2, data = quine)
+> theta.md(quine$Days, fitted(quine.nb), dfr = df.residual(quine.nb))
+[1] 1.135441
+> theta.ml(quine$Days, fitted(quine.nb))
+[1] 1.603641
+attr(,"SE")
+[1] 0.2138379
+> theta.mm(quine$Days, fitted(quine.nb), dfr = df.residual(quine.nb))
+[1] 1.562879
+>
+> ## weighted example
+> yeast <- data.frame(cbind(numbers = 0:5, fr = c(213, 128, 37, 18, 3, 1)))
+> fit <- glm.nb(numbers ~ 1, weights = fr, data = yeast)
+> summary(fit)
+
+Call:
+glm.nb(formula = numbers ~ 1, data = yeast, weights = fr, init.theta = 3.586087428,
+ link = log)
+
+Deviance Residuals:
+ 1 2 3 4 5 6
+-16.314 3.682 6.923 7.555 4.033 2.813
+
+Coefficients:
+ Estimate Std. Error z value Pr(>|z|)
+(Intercept) -0.38199 0.06603 -5.785 7.25e-09 ***
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+(Dispersion parameter for Negative Binomial(3.5861) family taken to be 1)
+
+ Null deviance: 408.9 on 5 degrees of freedom
+Residual deviance: 408.9 on 5 degrees of freedom
+AIC: 897.06
+
+Number of Fisher Scoring iterations: 1
+
+
+ Theta: 3.59
+ Std. Err.: 1.75
+
+ 2 x log-likelihood: -893.063
+> attach(yeast)
+> mu <- fitted(fit)
+> theta.md(numbers, mu, dfr = 399, weights = fr)
+[1] 3.027079
+> theta.ml(numbers, mu, weights = fr)
+Warning in theta.ml(numbers, mu, weights = fr) :
+ iteration limit reached
+[1] 3.586071
+attr(,"warn")
+[1] "iteration limit reached"
+attr(,"SE")
+[1] 1.743658
+> theta.mm(numbers, mu, dfr = 399, weights = fr)
+[1] 3.549593
+> detach()
+>
+>
+>
+> cleanEx()
+> nameEx("ucv")
+> ### * ucv
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: ucv
+> ### Title: Unbiased Cross-Validation for Bandwidth Selection
+> ### Aliases: ucv
+> ### Keywords: dplot
+>
+> ### ** Examples
+>
+> ucv(geyser$duration)
+Warning in ucv(geyser$duration) :
+ minimum occurred at one end of the range
+[1] 0.1746726
+>
+>
+>
+> cleanEx()
+> nameEx("waders")
+> ### * waders
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: waders
+> ### Title: Counts of Waders at 15 Sites in South Africa
+> ### Aliases: waders
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> plot(corresp(waders, nf=2))
+>
+>
+>
+> cleanEx()
+> nameEx("whiteside")
+> ### * whiteside
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: whiteside
+> ### Title: House Insulation: Whiteside's Data
+> ### Aliases: whiteside
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> require(lattice)
+Loading required package: lattice
+> xyplot(Gas ~ Temp | Insul, whiteside, panel =
++ function(x, y, ...) {
++ panel.xyplot(x, y, ...)
++ panel.lmline(x, y, ...)
++ }, xlab = "Average external temperature (deg. C)",
++ ylab = "Gas consumption (1000 cubic feet)", aspect = "xy",
++ strip = function(...) strip.default(..., style = 1))
+>
+> gasB <- lm(Gas ~ Temp, whiteside, subset = Insul=="Before")
+> gasA <- update(gasB, subset = Insul=="After")
+> summary(gasB)
+
+Call:
+lm(formula = Gas ~ Temp, data = whiteside, subset = Insul ==
+ "Before")
+
+Residuals:
+ Min 1Q Median 3Q Max
+-0.62020 -0.19947 0.06068 0.16770 0.59778
+
+Coefficients:
+ Estimate Std. Error t value Pr(>|t|)
+(Intercept) 6.85383 0.11842 57.88 <2e-16 ***
+Temp -0.39324 0.01959 -20.08 <2e-16 ***
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+Residual standard error: 0.2813 on 24 degrees of freedom
+Multiple R-squared: 0.9438, Adjusted R-squared: 0.9415
+F-statistic: 403.1 on 1 and 24 DF, p-value: < 2.2e-16
+
+> summary(gasA)
+
+Call:
+lm(formula = Gas ~ Temp, data = whiteside, subset = Insul ==
+ "After")
+
+Residuals:
+ Min 1Q Median 3Q Max
+-0.97802 -0.11082 0.02672 0.25294 0.63803
+
+Coefficients:
+ Estimate Std. Error t value Pr(>|t|)
+(Intercept) 4.72385 0.12974 36.41 < 2e-16 ***
+Temp -0.27793 0.02518 -11.04 1.05e-11 ***
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+Residual standard error: 0.3548 on 28 degrees of freedom
+Multiple R-squared: 0.8131, Adjusted R-squared: 0.8064
+F-statistic: 121.8 on 1 and 28 DF, p-value: 1.046e-11
+
+> gasBA <- lm(Gas ~ Insul/Temp - 1, whiteside)
+> summary(gasBA)
+
+Call:
+lm(formula = Gas ~ Insul/Temp - 1, data = whiteside)
+
+Residuals:
+ Min 1Q Median 3Q Max
+-0.97802 -0.18011 0.03757 0.20930 0.63803
+
+Coefficients:
+ Estimate Std. Error t value Pr(>|t|)
+InsulBefore 6.85383 0.13596 50.41 <2e-16 ***
+InsulAfter 4.72385 0.11810 40.00 <2e-16 ***
+InsulBefore:Temp -0.39324 0.02249 -17.49 <2e-16 ***
+InsulAfter:Temp -0.27793 0.02292 -12.12 <2e-16 ***
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+
+Residual standard error: 0.323 on 52 degrees of freedom
+Multiple R-squared: 0.9946, Adjusted R-squared: 0.9942
+F-statistic: 2391 on 4 and 52 DF, p-value: < 2.2e-16
+
+>
+> gasQ <- lm(Gas ~ Insul/(Temp + I(Temp^2)) - 1, whiteside)
+> coef(summary(gasQ))
+ Estimate Std. Error t value Pr(>|t|)
+InsulBefore 6.759215179 0.150786777 44.826312 4.854615e-42
+InsulAfter 4.496373920 0.160667904 27.985514 3.302572e-32
+InsulBefore:Temp -0.317658735 0.062965170 -5.044991 6.362323e-06
+InsulAfter:Temp -0.137901603 0.073058019 -1.887563 6.489554e-02
+InsulBefore:I(Temp^2) -0.008472572 0.006624737 -1.278930 2.068259e-01
+InsulAfter:I(Temp^2) -0.014979455 0.007447107 -2.011446 4.968398e-02
+>
+> gasPR <- lm(Gas ~ Insul + Temp, whiteside)
+> anova(gasPR, gasBA)
+Analysis of Variance Table
+
+Model 1: Gas ~ Insul + Temp
+Model 2: Gas ~ Insul/Temp - 1
+ Res.Df RSS Df Sum of Sq F Pr(>F)
+1 53 6.7704
+2 52 5.4252 1 1.3451 12.893 0.0007307 ***
+---
+Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1
+> options(contrasts = c("contr.treatment", "contr.poly"))
+> gasBA1 <- lm(Gas ~ Insul*Temp, whiteside)
+> coef(summary(gasBA1))
+ Estimate Std. Error t value Pr(>|t|)
+(Intercept) 6.8538277 0.13596397 50.409146 7.997414e-46
+InsulAfter -2.1299780 0.18009172 -11.827185 2.315921e-16
+Temp -0.3932388 0.02248703 -17.487358 1.976009e-23
+InsulAfter:Temp 0.1153039 0.03211212 3.590665 7.306852e-04
+>
+>
+>
+> options(contrasts = c(unordered = "contr.treatment",ordered = "contr.poly"))
+> cleanEx()
+
+detaching âpackage:latticeâ
+
+> nameEx("width.SJ")
+> ### * width.SJ
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: width.SJ
+> ### Title: Bandwidth Selection by Pilot Estimation of Derivatives
+> ### Aliases: width.SJ
+> ### Keywords: dplot
+>
+> ### ** Examples
+>
+> attach(geyser)
+> width.SJ(duration, method = "dpi")
+[1] 0.5747852
+> width.SJ(duration)
+[1] 0.360518
+> detach()
+>
+> width.SJ(galaxies, method = "dpi")
+[1] 3256.151
+> width.SJ(galaxies)
+[1] 2566.423
+>
+>
+>
+> cleanEx()
+> nameEx("wtloss")
+> ### * wtloss
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: wtloss
+> ### Title: Weight Loss Data from an Obese Patient
+> ### Aliases: wtloss
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> wtloss.fm <- nls(Weight ~ b0 + b1*2^(-Days/th),
++ data = wtloss, start = list(b0=90, b1=95, th=120))
+> wtloss.fm
+Nonlinear regression model
+ model: Weight ~ b0 + b1 * 2^(-Days/th)
+ data: wtloss
+ b0 b1 th
+ 81.37 102.68 141.91
+ residual sum-of-squares: 39.24
+
+Number of iterations to convergence: 3
+Achieved convergence tolerance: 4.324e-06
+> plot(wtloss)
+> with(wtloss, lines(Days, fitted(wtloss.fm)))
+>
+>
+>
+> ### * <FOOTER>
+> ###
+> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
+Time elapsed: 14.809 0.117 20.658 0 0
+> grDevices::dev.off()
+null device
+ 1
+> ###
+> ### Local variables: ***
+> ### mode: outline-minor ***
+> ### outline-regexp: "\\(> \\)?### [*]+" ***
+> ### End: ***
+> quit('no')
diff --git a/win32/deps/library/MASS/tests/confint.R b/win32/deps/library/MASS/tests/confint.R
new file mode 100644
index 0000000..2ae0326
--- /dev/null
+++ b/win32/deps/library/MASS/tests/confint.R
@@ -0,0 +1,26 @@
+library(MASS)
+
+PropCI <- function(x, n, conf = 0.95)
+{
+ DF <- data.frame(y = x / n, weights = n)
+ mod <- glm(y ~ 1, weights = weights, family = binomial(), data = DF)
+ plogis(confint(mod, level = conf))
+}
+
+PropCI(14, 35)
+## had scope error prior to 7.2-31
+
+## single variable cases:
+n.tot <- c(60,17,8,2,187,85,51,23)
+n.hyp <- c(5,2,1,0,35,13,15,8)
+hyp.tbl <- cbind(n.hyp, n.tot-n.hyp)
+glm.hyp <- glm(hyp.tbl ~ 1, binomial)
+plot(profile(glm.hyp))
+x <- cbind(2,20)
+plot(profile(glm(x~1,binomial)))
+# failed in 7.2-39
+
+dat <- data.frame(event = c(2,4,5), nonev = c(4,2,7))
+m <- glm(cbind(event, nonev) ~ 1, data=dat, family=binomial)
+confint(m)
+# failed in 7.2-40
diff --git a/win32/deps/library/MASS/tests/fitdistr.R b/win32/deps/library/MASS/tests/fitdistr.R
new file mode 100644
index 0000000..4860bef
--- /dev/null
+++ b/win32/deps/library/MASS/tests/fitdistr.R
@@ -0,0 +1,30 @@
+## a quick check on vcov for fitdistr (from 7.3-6/7)
+
+library(MASS)
+
+options(digits=4)
+set.seed(1)
+x <- rnorm(100)
+fit <- fitdistr(x, "normal")
+fit
+vcov(fit)
+
+x <- rlnorm(100)
+fit <- fitdistr(x, "lognormal")
+fit
+vcov(fit)
+
+x <- rpois(100, 4.5)
+fit <- fitdistr(x, "poisson")
+fit
+vcov(fit)
+
+x <- rexp(100, 13)
+fit <- fitdistr(x, "exponential")
+fit
+vcov(fit)
+
+x <- rgeom(100, 0.25)
+fit <- fitdistr(x, "geometric")
+fit
+vcov(fit)
diff --git a/win32/deps/library/MASS/tests/fitdistr.Rout.save b/win32/deps/library/MASS/tests/fitdistr.Rout.save
new file mode 100644
index 0000000..bba7e6b
--- /dev/null
+++ b/win32/deps/library/MASS/tests/fitdistr.Rout.save
@@ -0,0 +1,76 @@
+
+R version 2.12.0 Under development (unstable) (2010-05-21 r52065)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> ## a quick check on vcov for fitdistr (from 7.3-6/7)
+>
+> library(MASS)
+>
+> options(digits=4)
+> set.seed(1)
+> x <- rnorm(100)
+> fit <- fitdistr(x, "normal")
+> fit
+ mean sd
+ 0.10889 0.89370
+ (0.08937) (0.06319)
+> vcov(fit)
+ mean sd
+mean 0.007987 0.000000
+sd 0.000000 0.003993
+>
+> x <- rlnorm(100)
+> fit <- fitdistr(x, "lognormal")
+> fit
+ meanlog sdlog
+ -0.03781 0.95308
+ ( 0.09531) ( 0.06739)
+> vcov(fit)
+ meanlog sdlog
+meanlog 0.009084 0.000000
+sdlog 0.000000 0.004542
+>
+> x <- rpois(100, 4.5)
+> fit <- fitdistr(x, "poisson")
+> fit
+ lambda
+ 4.5400
+ (0.2131)
+> vcov(fit)
+ lambda
+lambda 0.0454
+>
+> x <- rexp(100, 13)
+> fit <- fitdistr(x, "exponential")
+> fit
+ rate
+ 15.224
+ ( 1.522)
+> vcov(fit)
+ rate
+rate 2.318
+>
+> x <- rgeom(100, 0.25)
+> fit <- fitdistr(x, "geometric")
+> fit
+ prob
+ 0.22831
+ (0.02006)
+> vcov(fit)
+ prob
+prob 0.0004022
+>
diff --git a/win32/deps/library/MASS/tests/glm.nb.R b/win32/deps/library/MASS/tests/glm.nb.R
new file mode 100644
index 0000000..c9a36e1
--- /dev/null
+++ b/win32/deps/library/MASS/tests/glm.nb.R
@@ -0,0 +1,49 @@
+## glm.nb with weights
+library(MASS)
+yeast <- data.frame(cbind(numbers = 0:5, fr = c(213, 128, 37, 18, 3, 1)))
+
+attach(yeast)
+n <- rep(numbers, fr)
+
+## fitting using glm.nb with weights - wrong results in 7.2-18
+yeast2.fit <- glm.nb(numbers~1, link = log, weights=fr)
+summary(yeast2.fit)
+
+## fitting extending the vector and using glm.nb - correct result ##
+yeast3.fit<-glm.nb(n~1, link = log)
+summary(yeast3.fit)
+
+stopifnot(all.equal(deviance(yeast2.fit), deviance(yeast3.fit)))
+stopifnot(all.equal(yeast2.fit$theta, yeast3.fit$theta))
+
+detach(yeast)
+
+# another one, corrected in 7.2-43
+set.seed(13245)
+x <- c(-5:5)
+mu <- exp(1 + 0.1*x)
+y <- rnegbin(length(mu), mu = mu, theta = 1.5)
+dat <- data.frame(x, y)
+dat2 <- dat[rep(1:11, each=2), ]
+w <- round(runif(11),2)
+dat2$w <- as.vector(rbind(w, 1-w))
+fm2 <- glm.nb(y ~ x, dat)
+gm2 <- glm.nb(y ~ x, dat2, weights = w)
+summary(fm2)
+summary(gm2) # failed before
+stopifnot(all.equal(fm2$theta, gm2$theta)) # differed
+stopifnot(all.equal(deviance(fm2), deviance(gm2)))
+fm3 <- glm(y ~ x, negative.binomial(theta = fm2$theta), dat)
+gm3 <- glm(y ~ x, negative.binomial(theta = fm2$theta), dat2, weights =w)
+summary(fm3)
+summary(gm3)
+stopifnot(all.equal(deviance(fm3), deviance(gm3)))
+
+fit <- glm.nb(Days ~ Sex/(Age + Eth*Lrn), data = quine)
+set.seed(1)
+simulate(fit, nsim=5)[1:10, ]
+if(getRversion() >= "2.9.0") {
+ fit2 <- glm.convert(fit)
+ set.seed(1)
+ print(simulate(fit2, nsim=5)[1:10, ])
+}
diff --git a/win32/deps/library/MASS/tests/hubers.R b/win32/deps/library/MASS/tests/hubers.R
new file mode 100644
index 0000000..cfbad5d
--- /dev/null
+++ b/win32/deps/library/MASS/tests/hubers.R
@@ -0,0 +1,5 @@
+library(MASS)
+x <- c(rep(1.407,3), rep(1.422,4), 1.597, 1.597, rep(1.64,19), 1.649,
+ 1.664, 1.664, 1.67, 1.672, 1.672, 1.787, 4.42, 4.44, rep(6.55,3),
+ rep(6.79,14), rep(7.19,,73), 9.00, 9.38, rep(9.41,10))
+hubers(x) # failed to converge in MASS 7.3-9.
diff --git a/win32/deps/library/MASS/tests/lme.R b/win32/deps/library/MASS/tests/lme.R
new file mode 100644
index 0000000..0b09006
--- /dev/null
+++ b/win32/deps/library/MASS/tests/lme.R
@@ -0,0 +1,16 @@
+## stepAIC on an lme object: an example from Robert Cuffe
+library(nlme)
+library(MASS)
+set.seed(321) # to be sure
+a <- data.frame( resp=rnorm(250), cov1=rnorm(250),
+ cov2=rnorm(250), group=rep(letters[1:10],25) )
+mod1 <- lme(resp~cov1, a, ~cov1|group, method="ML")
+mod2 <- stepAIC(mod1, scope=list(upper=~(cov1+cov2)^2, lower=~1) )
+
+beav <- beav2
+set.seed(123)
+beav$dummy <- rnorm(nrow(beav))
+beav.gls <- gls(temp ~ activ + dummy, data = beav,
+ corr = corAR1(0.8), method = "ML")
+stepAIC(beav.gls)
+
diff --git a/win32/deps/library/MASS/tests/polr.R b/win32/deps/library/MASS/tests/polr.R
new file mode 100644
index 0000000..b47d143
--- /dev/null
+++ b/win32/deps/library/MASS/tests/polr.R
@@ -0,0 +1,48 @@
+## tests from David Firth 2004-Oct-13
+
+library(MASS)
+y <- structure(as.integer(c(1, 2, 3, 1, 2, 3)), .Label = c("1", "2", "3"),
+ class = c("ordered", "factor"))
+Freq <- c(10, 0, 10, 10, 0, 10)
+group <- structure(as.integer(c(1, 1, 1, 2, 2, 2)), .Label = c("1", "2"),
+ class = "factor")
+
+temp <- polr(y ~ group, weights = Freq)
+temp$convergence
+temp
+
+stopifnot(all(abs(coef(temp)) < 1e-4))
+
+Freq <- c(1000000, 1, 1000000, 1000000, 1, 1000000)
+temp2 <- polr(y ~ group, weights = Freq)
+temp2
+
+stopifnot(all(abs(coef(temp2)) < 1e-4))
+
+## tests of rank-deficient model matrix
+
+group <- factor(c(1, 1, 1, 2, 2, 2), levels=1:3)
+polr(y ~ group, weights = Freq)
+group <- factor(c(1, 1, 1, 3, 3, 3), levels=1:3)
+polr(y ~ group, weights = Freq)
+
+## profile on a single-coef model
+## data from McCullagh JRSSB 1980
+tonsils <- data.frame(carrier = factor(rep(c('yes', 'no'), each=3)),
+ size = ordered(rep(c(1,2,3),2)),
+ count = c(19,29,24,497,560,269))
+m <- polr(size ~ carrier, data = tonsils, weights = count)
+confint(m)
+
+
+## refitting needs transformed starting values (Achim Zeileis Mar 2010)
+load("BankWages.rda") # from AER
+bw <- polr(job ~ education, data = BankWages)
+summary(bw)
+## failed due to incorrect restarting values
+
+## missing drop = FALSE in profiling (Joris Meys, Sep 2012)
+house.plr <- polr(Sat ~ Cont, weights = Freq, data = housing)
+pr <- profile(house.plr)
+plot(pr)
+
diff --git a/win32/deps/library/MASS/tests/profile.R b/win32/deps/library/MASS/tests/profile.R
new file mode 100644
index 0000000..7745dea
--- /dev/null
+++ b/win32/deps/library/MASS/tests/profile.R
@@ -0,0 +1,10 @@
+### Example from Merete KjÃr Hansen 2011-07-06
+library(MASS)
+dat <- data.frame(y = c(35, 21, 9, 6, 1),
+ dose = c(0.0028, 0.0056, 0.0112, 0.0225, 0.045),
+ n = c(40, 40, 40, 40, 40), w = 1:5)
+### fit model with two-column response and weights
+fm <- glm(cbind(y, n-y) ~ dose, weights=w, family=binomial, data=dat)
+### Investigating the profile likelihoods of the parameters with profile.glm
+profile(fm)
+## failed in MASS 7.3-13
diff --git a/win32/deps/library/MASS/tests/regression.R b/win32/deps/library/MASS/tests/regression.R
new file mode 100644
index 0000000..42d5034
--- /dev/null
+++ b/win32/deps/library/MASS/tests/regression.R
@@ -0,0 +1,9 @@
+### regression tests
+
+library(MASS)
+
+## uses Matrix
+contr.sdif(6)
+contr.sdif(6, sparse=TRUE)
+stopifnot(all(contr.sdif(6) == contr.sdif(6, sparse=TRUE)))
+
diff --git a/win32/deps/library/MASS/tests/regression.Rout.save b/win32/deps/library/MASS/tests/regression.Rout.save
new file mode 100644
index 0000000..ae01784
--- /dev/null
+++ b/win32/deps/library/MASS/tests/regression.Rout.save
@@ -0,0 +1,47 @@
+
+R version 2.10.0 Under development (unstable) (2009-07-31 r49037)
+Copyright (C) 2009 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+ Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> ### regression tests
+>
+> library(MASS)
+>
+> ## uses Matrix
+> contr.sdif(6)
+ 2-1 3-2 4-3 5-4 6-5
+1 -0.8333333 -0.6666667 -0.5 -0.3333333 -0.1666667
+2 0.1666667 -0.6666667 -0.5 -0.3333333 -0.1666667
+3 0.1666667 0.3333333 -0.5 -0.3333333 -0.1666667
+4 0.1666667 0.3333333 0.5 -0.3333333 -0.1666667
+5 0.1666667 0.3333333 0.5 0.6666667 -0.1666667
+6 0.1666667 0.3333333 0.5 0.6666667 0.8333333
+> contr.sdif(6, sparse=TRUE)
+6 x 5 sparse Matrix of class "dgCMatrix"
+ 2-1 3-2 4-3 5-4 6-5
+1 -0.8333333 -0.6666667 -0.5 -0.3333333 -0.1666667
+2 0.1666667 -0.6666667 -0.5 -0.3333333 -0.1666667
+3 0.1666667 0.3333333 -0.5 -0.3333333 -0.1666667
+4 0.1666667 0.3333333 0.5 -0.3333333 -0.1666667
+5 0.1666667 0.3333333 0.5 0.6666667 -0.1666667
+6 0.1666667 0.3333333 0.5 0.6666667 0.8333333
+> stopifnot(all(contr.sdif(6) == contr.sdif(6, sparse=TRUE)))
+>
+>
+> proc.time()
+ user system elapsed
+ 2.298 0.078 2.377
diff --git a/win32/deps/library/MASS/tests/rlm.R b/win32/deps/library/MASS/tests/rlm.R
new file mode 100644
index 0000000..25805dd
--- /dev/null
+++ b/win32/deps/library/MASS/tests/rlm.R
@@ -0,0 +1,91 @@
+library(MASS)
+
+## Based on incorrect 'bug' report
+
+hills$ispeed <- hills$time/hills$dist
+hills$grad <- hills$climb/hills$dist
+
+## weighted fit
+fit0 <- rlm(time ~ dist + climb - 1, data = hills,
+ weights = 1/dist^2, method="MM")
+summary(fit0, cor=FALSE)
+## equivalent to
+fit1 <- rlm(ispeed ~ grad, data = hills, method="MM")
+summary(fit1, cor=FALSE)
+
+cf0 <- coef(summary(fit0))
+cf1 <- coef(summary(fit1))
+rownames(cf1) <- rownames(cf0)
+stopifnot(all.equal(cf0, cf1))
+stopifnot(all.equal(weighted.residuals(fit0), residuals(fit1)))
+
+# test other cases
+fit0 <- rlm(time ~ dist + climb - 1, data = hills, weights = 1/dist^2)
+summary(fit0, cor=FALSE)
+## equivalent to
+fit1 <- rlm(ispeed ~ grad, data = hills)
+summary(fit1, cor=FALSE)
+
+cf0 <- coef(summary(fit0))
+cf1 <- coef(summary(fit1))
+rownames(cf1) <- rownames(cf0)
+stopifnot(all.equal(cf0, cf1))
+stopifnot(all.equal(weighted.residuals(fit0), residuals(fit1)))
+
+fit0 <- rlm(time ~ dist + climb - 1, data = hills, weights = 1/dist^2,
+ scale.est = "Huber")
+summary(fit0, cor=FALSE)
+## equivalent to
+fit1 <- rlm(ispeed ~ grad, data = hills, scale.est = "Huber")
+summary(fit1, cor=FALSE)
+
+cf0 <- coef(summary(fit0))
+cf1 <- coef(summary(fit1))
+rownames(cf1) <- rownames(cf0)
+stopifnot(all.equal(cf0, cf1))
+stopifnot(all.equal(weighted.residuals(fit0), residuals(fit1)))
+
+
+## cf lm fits
+
+fit2 <- lm(time ~ dist + climb - 1, data = hills, weights = 1/dist^2)
+fit3 <- lm(ispeed ~ grad, data = hills)
+stopifnot(all.equal(weighted.residuals(fit2), residuals(fit3)))
+
+
+## case weights: can't do MM as no weighted lqs.
+wts <- rep(1, 35)
+wts[c(1,11,21)] <- 10
+h2 <- hills[rep(1:35, times=wts), ]
+fit4 <- lm(ispeed ~ grad, data = hills, weights = wts)
+fit5 <- lm(ispeed ~ grad, data = h2)
+## same coefs, different se's.
+fit6 <- rlm(ispeed ~ grad, data = h2, acc=1e-10)
+fit7 <- rlm(ispeed ~ grad, data = hills,
+ weights = wts, wt.method="case", acc=1e-10)
+summary(fit6)
+summary(fit7)
+stopifnot(all.equal(coef(summary(fit6)), coef(summary(fit7))))
+summary(fit6, "XtWX")
+summary(fit7, "XtWX")
+stopifnot(all.equal(coef(summary(fit6, "XtWX")), coef(summary(fit7, "XtWX"))))
+
+fit8 <- rlm(ispeed ~ grad, data = h2, scale.est = "Huber", acc=1e-10)
+fit9 <- rlm(ispeed ~ grad, data = hills, scale.est = "Huber",
+ weights = wts, wt.method="case", acc=1e-10)
+summary(fit8)
+summary(fit9)
+stopifnot(all.equal(coef(summary(fit8)), coef(summary(fit9))))
+summary(fit8, "XtWX")
+summary(fit9, "XtWX")
+stopifnot(all.equal(coef(summary(fit8, "XtWX")), coef(summary(fit9, "XtWX"))))
+
+
+## w was a matrix under some initializations
+x <- matrix(1:200, 100,2)
+B <- c(2.5, -1.3)
+y <- x %*% B + rnorm(100)
+r1 <- rlm(x, y, init=B, psi=psi.huber)
+r2 <- rlm(x, y, init=B, psi=psi.bisquare)
+r3 <- rlm(x, y, init=B, psi=psi.hampel) # failed
+r4 <- rlm(x, y, psi=psi.hampel)
diff --git a/win32/deps/library/MASS/tests/scripts.R b/win32/deps/library/MASS/tests/scripts.R
new file mode 100644
index 0000000..76fd5bc
--- /dev/null
+++ b/win32/deps/library/MASS/tests/scripts.R
@@ -0,0 +1,36 @@
+if(!nzchar(Sys.getenv("MASS_TESTING"))) q("no")
+unlink("scripts", recursive = TRUE)
+dir.create("scripts")
+Sys.unsetenv("R_TESTS") # avoid startup using startup.Rs (which is in the dir above)
+setwd("scripts")
+writeLines(c(".Random.seed <- c(0L,1:3)",
+ "options(width = 65, show.signif.stars=FALSE)"),
+ ".Rprofile")
+
+runone <- function(f)
+{
+ message(" Running ", sQuote(basename(f)))
+ outfile <- paste(basename(f), "out", sep = "")
+ failfile <- paste(outfile, "fail", sep=".")
+ unlink(c(outfile, failfile))
+ res <- system2(file.path(R.home("bin"), "R"),
+ c("CMD BATCH --vanilla", shQuote(f), shQuote(outfile)),
+ env = paste("R_LIBS", Sys.getenv("R_LIBS"), sep = "="))
+ if (res) {
+ cat(tail(readLines(outfile), 20), sep="\n")
+ file.rename(outfile, failfile)
+ return(1L)
+ }
+ 0L
+}
+
+
+library(MASS)
+dd <- system.file("scripts", package="MASS")
+files <- list.files(dd, pattern="\\.R$", full.names=TRUE)
+res <- 0L
+for(f in files) res <- res + runone(f)
+
+proc.time()
+
+if(res) stop(gettextf("%d scripts failed", res))
diff --git a/win32/deps/library/Matrix/DESCRIPTION b/win32/deps/library/Matrix/DESCRIPTION
index 1f03f73..63af964 100644
--- a/win32/deps/library/Matrix/DESCRIPTION
+++ b/win32/deps/library/Matrix/DESCRIPTION
@@ -1,27 +1,28 @@
-Package: Matrix
-Version: 0.999375-30
-Date: 2009-07-28
-Priority: recommended
-Title: Sparse and Dense Matrix Classes and Methods
-Author: Douglas Bates <bates stat wisc edu> and Martin Maechler
- <maechler stat math ethz ch>
-Maintainer: Doug and Martin <Matrix-authors R-project org>
-Description: Classes and methods for dense and sparse matrices and
- operations on them using Lapack and SuiteSparse.
-Depends: R (>= 2.9.0), stats, methods, utils, lattice
-Imports: graphics, lattice, grid, stats
-Enhances: graph, SparseM
-SystemRequirements: GNU make
-LazyLoad: yes
-LazyData: no
-LazyDataNote: no longer available, since we use data/*.R *and* our
- classes
-License: GPL (>= 2)
-LicenseDetails: The Matrix package includes libraries AMD, CHOLMOD,
- COLAMD, CSparse and SPQR from the SuiteSparse collection of Tim
- Davis. All sections of that code are covered by the GPL or
- LGPL licenses. See the directory doc/UFsparse for details.
-Packaged: 2009-07-28 19:09:38 UTC; maechler
-Repository: CRAN
-Date/Publication: 2009-07-30 12:51:23
-Built: R 2.9.2; i386-pc-mingw32; 2009-08-24 13:12:29 UTC; windows
+Package: Matrix
+Version: 1.0-9
+Date: 2012-09-03
+Priority: recommended
+Title: Sparse and Dense Matrix Classes and Methods
+Author: Douglas Bates <bates stat wisc edu> and Martin Maechler <maechler stat math ethz ch>
+Maintainer: Martin Maechler <mmaechler+Matrix gmail com>
+Contact: Doug and Martin <Matrix-authors R-project org>
+Description: Classes and methods for dense and sparse matrices and
+ operations on them using Lapack and SuiteSparse.
+Depends: R (>= 2.15.0), stats, methods, utils, lattice
+Imports: graphics, grid
+Suggests: expm, MASS
+Enhances: MatrixModels, graph, SparseM, sfsmisc
+Encoding: UTF-8
+LazyData: no
+LazyDataNote: no longer available, since we use data/*.R *and* our
+ classes
+BuildResaveData: no
+License: GPL (>= 2)
+LicenseDetails: The Matrix package includes libraries AMD, CHOLMOD,
+ COLAMD, CSparse and SPQR from the SuiteSparse collection of Tim
+ Davis. All sections of that code are covered by the GPL or
+ LGPL licenses. See the directory doc/UFsparse for details.
+URL: http://Matrix.R-forge.R-project.org/
+Packaged: 2012-09-05 08:59:42 UTC; maechler
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:10:56 UTC; windows
+Archs: i386, x64
diff --git a/win32/deps/library/Matrix/Doxyfile b/win32/deps/library/Matrix/Doxyfile
index e140df6..9a658ad 100644
--- a/win32/deps/library/Matrix/Doxyfile
+++ b/win32/deps/library/Matrix/Doxyfile
@@ -1,25 +1,24 @@
-# Dear Emacs, treat me as -*- sh -*-
-# Doxyfile 1.5.3
+# Doxyfile 1.7.4
# This file describes the settings to be used by the documentation system
-# doxygen (www.doxygen.org) for a project
+# doxygen (www.doxygen.org) for a project.
#
-# All text after a hash (#) is considered a comment and will be ignored
+# All text after a hash (#) is considered a comment and will be ignored.
# The format is:
# TAG = value [value, ...]
# For lists items can also be appended using:
# TAG += value [value, ...]
-# Values that contain spaces should be placed between quotes (" ")
+# Values that contain spaces should be placed between quotes (" ").
#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
-# This tag specifies the encoding used for all characters in the config file that
-# follow. The default is UTF-8 which is also the encoding used for all text before
-# the first occurrence of this tag. Doxygen uses libiconv (or the iconv built into
-# libc) for the transcoding. See http://www.gnu.org/software/libiconv for the list of
-# possible encodings.
+# This tag specifies the encoding used for all characters in the config file
+# that follow. The default is UTF-8 which is also the encoding used for all
+# text before the first occurrence of this tag. Doxygen uses libiconv (or the
+# iconv built into libc) for the transcoding. See
+# http://www.gnu.org/software/libiconv for the list of possible encodings.
DOXYFILE_ENCODING = UTF-8
@@ -32,14 +31,27 @@ PROJECT_NAME = Matrix
# This could be handy for archiving the generated documentation or
# if some version control system is used.
-PROJECT_NUMBER = 0.999375
+PROJECT_NUMBER = "$Rev: 2721 $ at $LastChangedDate: 2011-10-06 14:59:16 +0200 (Thu, 06 Oct 2011) $"
+
+# Using the PROJECT_BRIEF tag one can provide an optional one line description
+# for a project that appears at the top of each page and should give viewer
+# a quick idea about the purpose of the project. Keep the description short.
+
+PROJECT_BRIEF =
+
+# With the PROJECT_LOGO tag one can specify an logo or icon that is
+# included in the documentation. The maximum height of the logo should not
+# exceed 55 pixels and the maximum width should not exceed 200 pixels.
+# Doxygen will copy the logo to the output directory.
+
+PROJECT_LOGO =
# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
# base path where the generated documentation will be put.
# If a relative path is entered, it will be relative to the location
# where doxygen was started. If left blank the current directory will be used.
-OUTPUT_DIRECTORY = ../../www/doxygen
+OUTPUT_DIRECTORY = ../../../www/doxygen
# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
# 4096 sub-directories (in 2 levels) under the output directory of each output
@@ -55,10 +67,11 @@ CREATE_SUBDIRS = NO
# information to generate all constant output in the proper language.
# The default language is English, other supported languages are:
# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
-# Croatian, Czech, Danish, Dutch, Finnish, French, German, Greek, Hungarian,
-# Italian, Japanese, Japanese-en (Japanese with English messages), Korean,
-# Korean-en, Lithuanian, Norwegian, Polish, Portuguese, Romanian, Russian,
-# Serbian, Slovak, Slovene, Spanish, Swedish, and Ukrainian.
+# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German,
+# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English
+# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian,
+# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak,
+# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
OUTPUT_LANGUAGE = English
@@ -126,7 +139,7 @@ STRIP_FROM_PATH =
STRIP_FROM_INC_PATH =
# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
-# (but less readable) file names. This can be useful is your file systems
+# (but less readable) file names. This can be useful if your file system
# doesn't support long names like on DOS, Mac, or CD-ROM.
SHORT_NAMES = NO
@@ -155,13 +168,6 @@ QT_AUTOBRIEF = NO
MULTILINE_CPP_IS_BRIEF = NO
-# If the DETAILS_AT_TOP tag is set to YES then Doxygen
-# will output the detailed description near the top, like JavaDoc.
-# If set to NO, the detailed description appears after the member
-# documentation.
-
-DETAILS_AT_TOP = YES
-
# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
# member inherits the documentation from any documented member that it
# re-implements.
@@ -196,17 +202,41 @@ ALIASES =
OPTIMIZE_OUTPUT_FOR_C = YES
# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
-# sources only. Doxygen will then generate output that is more tailored for Java.
-# For instance, namespaces will be presented as packages, qualified scopes
-# will look different, etc.
+# sources only. Doxygen will then generate output that is more tailored for
+# Java. For instance, namespaces will be presented as packages, qualified
+# scopes will look different, etc.
OPTIMIZE_OUTPUT_JAVA = NO
-# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want to
-# include (a tag file for) the STL sources as input, then you should
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+# sources only. Doxygen will then generate output that is more tailored for
+# Fortran.
+
+OPTIMIZE_FOR_FORTRAN = NO
+
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
+# sources. Doxygen will then generate output that is tailored for
+# VHDL.
+
+OPTIMIZE_OUTPUT_VHDL = NO
+
+# Doxygen selects the parser to use depending on the extension of the files it
+# parses. With this tag you can assign which parser to use for a given extension.
+# Doxygen has a built-in mapping, but you can override or extend it using this
+# tag. The format is ext=language, where ext is a file extension, and language
+# is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C,
+# C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make
+# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C
+# (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions
+# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen.
+
+EXTENSION_MAPPING =
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should
# set this tag to YES in order to let doxygen match functions declarations and
# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
-# func(std::string) {}). This also make the inheritance and collaboration
+# func(std::string) {}). This also makes the inheritance and collaboration
# diagrams that involve STL classes more complete and accurate.
BUILTIN_STL_SUPPORT = NO
@@ -216,6 +246,21 @@ BUILTIN_STL_SUPPORT = NO
CPP_CLI_SUPPORT = NO
+# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
+# Doxygen will parse them like normal C++ but will assume all classes use public
+# instead of private inheritance when no explicit protection keyword is present.
+
+SIP_SUPPORT = NO
+
+# For Microsoft's IDL there are propget and propput attributes to indicate getter
+# and setter methods for a property. Setting this option to YES (the default)
+# will make doxygen replace the get and set methods by a property in the
+# documentation. This will only work if the methods are indeed getting or
+# setting a simple type. If this is not the case, or you want to show the
+# methods anyway, you should set this option to NO.
+
+IDL_PROPERTY_SUPPORT = YES
+
# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
# tag is set to YES, then doxygen will reuse the documentation of the first
# member in the group (if any) for the other members of the group. By default
@@ -231,6 +276,39 @@ DISTRIBUTE_GROUP_DOC = NO
SUBGROUPING = YES
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and
+# unions are shown inside the group in which they are included (e.g. using
+# @ingroup) instead of on a separate page (for HTML and Man pages) or
+# section (for LaTeX and RTF).
+
+INLINE_GROUPED_CLASSES = NO
+
+# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
+# is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically
+# be useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+
+TYPEDEF_HIDES_STRUCT = NO
+
+# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
+# determine which symbols to keep in memory and which to flush to disk.
+# When the cache is full, less often used symbols will be written to disk.
+# For small to medium size projects (<1000 input files) the default value is
+# probably good enough. For larger projects a too small cache size can cause
+# doxygen to be busy swapping symbols to and from disk most of the time
+# causing a significant performance penalty.
+# If the system has enough physical memory increasing the cache will improve the
+# performance by keeping more symbols in memory. Note that the value works on
+# a logarithmic scale so increasing the size by one will roughly double the
+# memory usage. The cache size is given by this formula:
+# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
+# corresponding to a cache size of 2^16 = 65536 symbols
+
+SYMBOL_CACHE_SIZE = 0
+
#---------------------------------------------------------------------------
# Build related configuration options
#---------------------------------------------------------------------------
@@ -265,10 +343,11 @@ EXTRACT_LOCAL_CLASSES = YES
EXTRACT_LOCAL_METHODS = NO
-# If this flag is set to YES, the members of anonymous namespaces will be extracted
-# and appear in the documentation as a namespace called 'anonymous_namespace{file}',
-# where file will be replaced with the base name of the file that contains the anonymous
-# namespace. By default anonymous namespace are hidden.
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base
+# name of the file that contains the anonymous namespace. By default
+# anonymous namespaces are hidden.
EXTRACT_ANON_NSPACES = NO
@@ -328,6 +407,12 @@ HIDE_SCOPE_NAMES = NO
SHOW_INCLUDE_FILES = YES
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen
+# will list include files with double quotes in the documentation
+# rather than with sharp brackets.
+
+FORCE_LOCAL_INCLUDES = NO
+
# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
# is inserted in the documentation for inline members.
@@ -347,6 +432,22 @@ SORT_MEMBER_DOCS = YES
SORT_BRIEF_DOCS = YES
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen
+# will sort the (brief and detailed) documentation of class members so that
+# constructors and destructors are listed first. If set to NO (the default)
+# the constructors will appear in the respective orders defined by
+# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS.
+# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO
+# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
+# hierarchy of group names into alphabetical order. If set to NO (the default)
+# the group names will appear in their defined order.
+
+SORT_GROUP_NAMES = NO
+
# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
# sorted by fully-qualified names, including namespaces. If set to
# NO (the default), the class list will be sorted only by class name,
@@ -357,6 +458,15 @@ SORT_BRIEF_DOCS = YES
SORT_BY_SCOPE_NAME = NO
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to
+# do proper type resolution of all parameters of a function it will reject a
+# match between the prototype and the implementation of a member function even
+# if there is only one candidate or it is obvious which candidate to choose
+# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen
+# will still accept a match between prototype and implementation in such cases.
+
+STRICT_PROTO_MATCHING = NO
+
# The GENERATE_TODOLIST tag can be used to enable (YES) or
# disable (NO) the todo list. This list is created by putting \todo
# commands in the documentation.
@@ -387,10 +497,10 @@ GENERATE_DEPRECATEDLIST= YES
ENABLED_SECTIONS =
# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
-# the initial value of a variable or define consists of for it to appear in
+# the initial value of a variable or macro consists of for it to appear in
# the documentation. If the initializer consists of more lines than specified
# here it will be hidden. Use a value of 0 to hide initializers completely.
-# The appearance of the initializer of individual variables and defines in the
+# The appearance of the initializer of individual variables and macros in the
# documentation can be controlled using \showinitializer or \hideinitializer
# command in the documentation regardless of this setting.
@@ -408,9 +518,22 @@ SHOW_USED_FILES = YES
SHOW_DIRECTORIES = NO
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
+# This will remove the Files entry from the Quick Index and from the
+# Folder Tree View (if specified). The default is YES.
+
+SHOW_FILES = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
+# Namespaces page.
+# This will remove the Namespaces entry from the Quick Index
+# and from the Folder Tree View (if specified). The default is YES.
+
+SHOW_NAMESPACES = YES
+
# The FILE_VERSION_FILTER tag can be used to specify a program or script that
-# doxygen should invoke to get the current version for each file (typically from the
-# version control system). Doxygen will invoke the program by executing (via
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
# popen()) the command <command> <input-file>, where <command> is the value of
# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
# provided by doxygen. Whatever the program writes to standard output
@@ -418,6 +541,15 @@ SHOW_DIRECTORIES = NO
FILE_VERSION_FILTER =
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. The create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option.
+# You can optionally specify a file name after the option, if omitted
+# DoxygenLayout.xml will be used as the name of the layout file.
+
+LAYOUT_FILE =
+
#---------------------------------------------------------------------------
# configuration options related to warning and progress messages
#---------------------------------------------------------------------------
@@ -446,7 +578,7 @@ WARN_IF_UNDOCUMENTED = YES
WARN_IF_DOC_ERROR = YES
-# This WARN_NO_PARAMDOC option can be abled to get warnings for
+# The WARN_NO_PARAMDOC option can be enabled to get warnings for
# functions that are documented, but have no documentation for their parameters
# or return value. If set to NO (the default) doxygen will only warn about
# wrong or incomplete parameter documentation, but not about the absence of
@@ -480,10 +612,11 @@ WARN_LOGFILE =
INPUT = ../src
-# This tag can be used to specify the character encoding of the source files that
-# doxygen parses. Internally doxygen uses the UTF-8 encoding, which is also the default
-# input encoding. Doxygen uses libiconv (or the iconv built into libc) for the transcoding.
-# See http://www.gnu.org/software/libiconv for the list of possible encodings.
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
+# also the default input encoding. Doxygen uses libiconv (or the iconv built
+# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
+# the list of possible encodings.
INPUT_ENCODING = UTF-8
@@ -491,8 +624,9 @@ INPUT_ENCODING = UTF-8
# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
# and *.h) to filter out the source-files in the directories. If left
# blank the following patterns are tested:
-# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx
-# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py
+# *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh
+# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py
+# *.f90 *.f *.for *.vhd *.vhdl
FILE_PATTERNS =
@@ -509,7 +643,7 @@ RECURSIVE = NO
EXCLUDE =
# The EXCLUDE_SYMLINKS tag can be used select whether or not files or
-# directories that are symbolic links (a Unix filesystem feature) are excluded
+# directories that are symbolic links (a Unix file system feature) are excluded
# from the input.
EXCLUDE_SYMLINKS = NO
@@ -523,9 +657,10 @@ EXCLUDE_SYMLINKS = NO
EXCLUDE_PATTERNS =
# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
-# (namespaces, classes, functions, etc.) that should be excluded from the output.
-# The symbol name can be a fully qualified name, a word, or if the wildcard * is used,
-# a substring. Examples: ANamespace, AClass, AClass::ANamespace, ANamespace::*Test
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
EXCLUDE_SYMBOLS =
@@ -560,17 +695,20 @@ IMAGE_PATH =
# by executing (via popen()) the command <filter> <input-file>, where <filter>
# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
# input file. Doxygen will then use the output that the filter program writes
-# to standard output. If FILTER_PATTERNS is specified, this tag will be
+# to standard output.
+# If FILTER_PATTERNS is specified, this tag will be
# ignored.
INPUT_FILTER =
# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
-# basis. Doxygen will compare the file name with each pattern and apply the
-# filter if there is a match. The filters are a list of the form:
+# basis.
+# Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match.
+# The filters are a list of the form:
# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
-# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER
-# is applied to all files.
+# info on how filters are used. If FILTER_PATTERNS is empty or if
+# non of the patterns match the file name, INPUT_FILTER is applied.
FILTER_PATTERNS =
@@ -580,6 +718,14 @@ FILTER_PATTERNS =
FILTER_SOURCE_FILES = NO
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any)
+# and it is also possible to disable source filtering for a specific pattern
+# using *.ext= (so without naming a filter). This option only has effect when
+# FILTER_SOURCE_FILES is enabled.
+
+FILTER_SOURCE_PATTERNS =
+
#---------------------------------------------------------------------------
# configuration options related to source browsing
#---------------------------------------------------------------------------
@@ -587,9 +733,7 @@ FILTER_SOURCE_FILES = NO
# If the SOURCE_BROWSER tag is set to YES then a list of source files will
# be generated. Documented entities will be cross-referenced with these sources.
# Note: To get rid of all source code in the generated output, make sure also
-# VERBATIM_HEADERS is set to NO. If you have enabled CALL_GRAPH or CALLER_GRAPH
-# then you must also enable this option. If you don't then doxygen will produce
-# a warning and turn it on anyway
+# VERBATIM_HEADERS is set to NO.
SOURCE_BROWSER = YES
@@ -604,13 +748,13 @@ INLINE_SOURCES = NO
STRIP_CODE_COMMENTS = YES
-# If the REFERENCED_BY_RELATION tag is set to YES (the default)
+# If the REFERENCED_BY_RELATION tag is set to YES
# then for each documented function all documented
# functions referencing it will be listed.
REFERENCED_BY_RELATION = YES
-# If the REFERENCES_RELATION tag is set to YES (the default)
+# If the REFERENCES_RELATION tag is set to YES
# then for each documented function all documented entities
# called/used by that function will be listed.
@@ -619,7 +763,8 @@ REFERENCES_RELATION = YES
# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
-# link to the source code. Otherwise they will link to the documentstion.
+# link to the source code.
+# Otherwise they will link to the documentation.
REFERENCES_LINK_SOURCE = YES
@@ -683,7 +828,13 @@ HTML_FILE_EXTENSION = .html
# The HTML_HEADER tag can be used to specify a personal HTML header for
# each generated HTML page. If it is left blank doxygen will generate a
-# standard header.
+# standard header. Note that when using a custom header you are responsible
+# for the proper inclusion of any scripts and style sheets that doxygen
+# needs, which is dependent on the configuration options used.
+# It is adviced to generate a default header using "doxygen -w html
+# header.html footer.html stylesheet.css YourConfigFile" and then modify
+# that header. Note that the header is subject to change so you typically
+# have to redo this when upgrading to a newer version of doxygen or when changing the value of configuration settings such as GENERATE_TREEVIEW!
HTML_HEADER =
@@ -693,6 +844,10 @@ HTML_HEADER =
HTML_FOOTER =
+# If the HTML_TIMESTAMP tag is set to YES then the generated HTML documentation will contain the timesstamp.
+
+HTML_TIMESTAMP = NO
+
# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
# style sheet that is used by each HTML page. It can be used to
# fine-tune the look of the HTML output. If the tag is left blank doxygen
@@ -702,19 +857,52 @@ HTML_FOOTER =
HTML_STYLESHEET =
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that
+# the files will be copied as-is; there are no commands or markers available.
+
+HTML_EXTRA_FILES =
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output.
+# Doxygen will adjust the colors in the stylesheet and background images
+# according to this color. Hue is specified as an angle on a colorwheel,
+# see http://en.wikipedia.org/wiki/Hue for more information.
+# For instance the value 0 represents red, 60 is yellow, 120 is green,
+# 180 is cyan, 240 is blue, 300 purple, and 360 is red again.
+# The allowed range is 0 to 359.
+
+HTML_COLORSTYLE_HUE = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of
+# the colors in the HTML output. For a value of 0 the output will use
+# grayscales only. A value of 255 will produce the most vivid colors.
+
+HTML_COLORSTYLE_SAT = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to
+# the luminance component of the colors in the HTML output. Values below
+# 100 gradually make the output lighter, whereas values above 100 make
+# the output darker. The value divided by 100 is the actual gamma applied,
+# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2,
+# and 100 does not change the gamma.
+
+HTML_COLORSTYLE_GAMMA = 80
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting
+# this to NO can help when comparing the output of multiple runs.
+
+HTML_TIMESTAMP = YES
+
# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
# files or namespaces will be aligned in HTML using tables. If set to
# NO a bullet list will be used.
HTML_ALIGN_MEMBERS = YES
-# If the GENERATE_HTMLHELP tag is set to YES, additional index files
-# will be generated that can be used as input for tools like the
-# Microsoft HTML help workshop to generate a compressed HTML help file (.chm)
-# of the generated HTML documentation.
-
-GENERATE_HTMLHELP = NO
-
# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
# documentation will contain sections that can be hidden and shown after the
# page has loaded. For this to work a browser that supports
@@ -723,6 +911,50 @@ GENERATE_HTMLHELP = NO
HTML_DYNAMIC_SECTIONS = NO
+# If the GENERATE_DOCSET tag is set to YES, additional index files
+# will be generated that can be used as input for Apple's Xcode 3
+# integrated development environment, introduced with OSX 10.5 (Leopard).
+# To create a documentation set, doxygen will generate a Makefile in the
+# HTML output directory. Running make will produce the docset in that
+# directory and running "make install" will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
+# it at startup.
+# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
+# for more information.
+
+GENERATE_DOCSET = NO
+
+# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
+# feed. A documentation feed provides an umbrella under which multiple
+# documentation sets from a single provider (such as a company or product suite)
+# can be grouped.
+
+DOCSET_FEEDNAME = "Doxygen generated docs"
+
+# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
+# should uniquely identify the documentation set bundle. This should be a
+# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
+# will append .docset to the name.
+
+DOCSET_BUNDLE_ID = org.doxygen.Project
+
+# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
+# string, e.g. com.mycompany.MyDocSet.documentation.
+
+DOCSET_PUBLISHER_ID = org.doxygen.Publisher
+
+# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
+
+DOCSET_PUBLISHER_NAME = Publisher
+
+# If the GENERATE_HTMLHELP tag is set to YES, additional index files
+# will be generated that can be used as input for tools like the
+# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
+# of the generated HTML documentation.
+
+GENERATE_HTMLHELP = NO
+
# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
# be used to specify the file name of the resulting .chm file. You
# can add a path in front of the file if the result should not be
@@ -743,6 +975,12 @@ HHC_LOCATION =
GENERATE_CHI = NO
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
+# is used to encode HtmlHelp index (hhk), content (hhc) and project file
+# content.
+
+CHM_INDEX_ENCODING =
+
# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
# controls whether a binary table of contents is generated (YES) or a
# normal table of contents (NO) in the .chm file.
@@ -754,32 +992,171 @@ BINARY_TOC = NO
TOC_EXPAND = NO
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated
+# that can be used as input for Qt's qhelpgenerator to generate a
+# Qt Compressed Help (.qch) of the generated HTML documentation.
+
+GENERATE_QHP = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
+# be used to specify the file name of the resulting .qch file.
+# The path specified is relative to the HTML output folder.
+
+QCH_FILE =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#namespace
+
+QHP_NAMESPACE =
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#virtual-folders
+
+QHP_VIRTUAL_FOLDER = doc
+
+# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to
+# add. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#custom-filters
+
+QHP_CUST_FILTER_NAME =
+
+# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see
+# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters";>
+# Qt Help Project / Custom Filters</a>.
+
+QHP_CUST_FILTER_ATTRS =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's
+# filter section matches.
+# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes";>
+# Qt Help Project / Filter Attributes</a>.
+
+QHP_SECT_FILTER_ATTRS =
+
+# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
+# be used to specify the location of Qt's qhelpgenerator.
+# If non-empty doxygen will try to run qhelpgenerator on the generated
+# .qhp file.
+
+QHG_LOCATION =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files
+# will be generated, which together with the HTML files, form an Eclipse help
+# plugin. To install this plugin and make it available under the help contents
+# menu in Eclipse, the contents of the directory containing the HTML and XML
+# files needs to be copied into the plugins directory of eclipse. The name of
+# the directory within the plugins directory should be the same as
+# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before
+# the help appears.
+
+GENERATE_ECLIPSEHELP = NO
+
+# A unique identifier for the eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have
+# this name.
+
+ECLIPSE_DOC_ID = org.doxygen.Project
+
# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
# top of each HTML page. The value NO (the default) enables the index and
# the value YES disables it.
DISABLE_INDEX = NO
-# This tag can be used to set the number of enum values (range [1..20])
-# that doxygen will group on one line in the generated HTML documentation.
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values
+# (range [0,1..20]) that doxygen will group on one line in the generated HTML
+# documentation. Note that a value of 0 will completely suppress the enum
+# values from appearing in the overview section.
ENUM_VALUES_PER_LINE = 8
-# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be
-# generated containing a tree-like index structure (just like the one that
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information.
+# If the tag value is set to YES, a side panel will be generated
+# containing a tree-like index structure (just like the one that
# is generated for HTML Help). For this to work a browser that supports
-# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+,
-# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are
-# probably better off using the HTML help feature.
+# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser).
+# Windows users are probably better off using the HTML help feature.
GENERATE_TREEVIEW = YES
+# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
+# and Class Hierarchy pages using a tree view instead of an ordered list.
+
+USE_INLINE_TREES = NO
+
# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
# used to set the initial width (in pixels) of the frame in which the tree
# is shown.
TREEVIEW_WIDTH = 250
+# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open
+# links to external symbols imported via tag files in a separate window.
+
+EXT_LINKS_IN_WINDOW = NO
+
+# Use this tag to change the font size of Latex formulas included
+# as images in the HTML documentation. The default is 10. Note that
+# when you change the font size after a successful doxygen run you need
+# to manually remove any form_*.png images from the HTML output directory
+# to force them to be regenerated.
+
+FORMULA_FONTSIZE = 10
+
+# Use the FORMULA_TRANPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are
+# not supported properly for IE 6.0, but are supported on all modern browsers.
+# Note that when changing this option you need to delete any form_*.png files
+# in the HTML output before the changes have effect.
+
+FORMULA_TRANSPARENT = YES
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax
+# (see http://www.mathjax.org) which uses client side Javascript for the
+# rendering instead of using prerendered bitmaps. Use this if you do not
+# have LaTeX installed or if you want to formulas look prettier in the HTML
+# output. When enabled you also need to install MathJax separately and
+# configure the path to it using the MATHJAX_RELPATH option.
+
+USE_MATHJAX = NO
+
+# When MathJax is enabled you need to specify the location relative to the
+# HTML output directory using the MATHJAX_RELPATH option. The destination
+# directory should contain the MathJax.js script. For instance, if the mathjax
+# directory is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the
+# mathjax.org site, so you can quickly see the result without installing
+# MathJax, but it is strongly recommended to install a local copy of MathJax
+# before deployment.
+
+MATHJAX_RELPATH = http://www.mathjax.org/mathjax
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box
+# for the HTML output. The underlying search engine uses javascript
+# and DHTML and should work on any modern browser. Note that when using
+# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets
+# (GENERATE_DOCSET) there is already a search function so this one should
+# typically be disabled. For large projects the javascript based search engine
+# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
+
+SEARCHENGINE = NO
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a PHP enabled web server instead of at the web client
+# using Javascript. Doxygen will generate the search PHP script and index
+# file to put on the web server. The advantage of the server
+# based approach is that it scales better to large projects and allows
+# full text search. The disadvantages are that it is more difficult to setup
+# and does not have live searching capabilities.
+
+SERVER_BASED_SEARCH = NO
+
#---------------------------------------------------------------------------
# configuration options related to the LaTeX output
#---------------------------------------------------------------------------
@@ -797,6 +1174,9 @@ LATEX_OUTPUT = latex
# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
# invoked. If left blank `latex' will be used as the default command name.
+# Note that when enabling USE_PDFLATEX this option is only used for
+# generating bitmaps for formulas in the HTML output, but not in the
+# Makefile that is written to the output directory.
LATEX_CMD_NAME = latex
@@ -813,7 +1193,7 @@ MAKEINDEX_CMD_NAME = makeindex
COMPACT_LATEX = NO
# The PAPER_TYPE tag can be used to set the paper type that is used
-# by the printer. Possible values are: a4, a4wide, letter, legal and
+# by the printer. Possible values are: a4, letter, legal and
# executive. If left blank a4wide will be used.
PAPER_TYPE = letter
@@ -830,6 +1210,13 @@ EXTRA_PACKAGES =
LATEX_HEADER =
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for
+# the generated latex document. The footer should contain everything after
+# the last chapter. If it is left blank doxygen will generate a
+# standard footer. Notice: only use this tag if you know what you are doing!
+
+LATEX_FOOTER =
+
# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
# is prepared for conversion to pdf (using ps2pdf). The pdf file will
# contain links (just like the HTML output) instead of page references
@@ -856,6 +1243,13 @@ LATEX_BATCHMODE = YES
LATEX_HIDE_INDICES = NO
+# If LATEX_SOURCE_CODE is set to YES then doxygen will include
+# source code with syntax highlighting in the LaTeX output.
+# Note that which sources are shown also depends on other settings
+# such as SOURCE_BROWSER.
+
+LATEX_SOURCE_CODE = NO
+
#---------------------------------------------------------------------------
# configuration options related to the RTF output
#---------------------------------------------------------------------------
@@ -992,8 +1386,10 @@ GENERATE_PERLMOD = NO
PERLMOD_LATEX = NO
# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
-# nicely formatted so it can be parsed by a human reader. This is useful
-# if you want to understand what is going on. On the other hand, if this
+# nicely formatted so it can be parsed by a human reader.
+# This is useful
+# if you want to understand what is going on.
+# On the other hand, if this
# tag is set to NO the size of the Perl module output will be much smaller
# and Perl will parse it just the same.
@@ -1030,7 +1426,7 @@ MACRO_EXPANSION = NO
EXPAND_ONLY_PREDEF = NO
# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
-# in the INCLUDE_PATH (see below) will be search if a #include is found.
+# pointed to by INCLUDE_PATH will be searched when a #include is found.
SEARCH_INCLUDES = YES
@@ -1060,15 +1456,15 @@ PREDEFINED =
# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
# this tag can be used to specify a list of macro names that should be expanded.
# The macro definition that is found in the sources will be used.
-# Use the PREDEFINED tag if you want to use a different macro definition.
+# Use the PREDEFINED tag if you want to use a different macro definition that
+# overrules the definition found in the source code.
EXPAND_AS_DEFINED =
# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
-# doxygen's preprocessor will remove all function-like macros that are alone
-# on a line, have an all uppercase name, and do not end with a semicolon. Such
-# function macros are typically used for boiler-plate code, and will confuse
-# the parser if not removed.
+# doxygen's preprocessor will remove all references to function-like macros
+# that are alone on a line, have an all uppercase name, and do not end with a
+# semicolon, because these will confuse the parser if not removed.
SKIP_FUNCTION_MACROS = YES
@@ -1080,9 +1476,11 @@ SKIP_FUNCTION_MACROS = YES
# Optionally an initial location of the external documentation
# can be added for each tagfile. The format of a tag file without
# this location is as follows:
-# TAGFILES = file1 file2 ...
+#
+# TAGFILES = file1 file2 ...
# Adding location for the tag files is done as follows:
-# TAGFILES = file1=loc1 "file2 = loc2" ...
+#
+# TAGFILES = file1=loc1 "file2 = loc2" ...
# where "loc1" and "loc2" can be relative or absolute paths or
# URLs. If a location is present for each tag, the installdox tool
# does not have to be run to correct the links.
@@ -1122,17 +1520,17 @@ PERL_PATH = /usr/bin/perl
# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
# or super classes. Setting the tag to NO turns the diagrams off. Note that
-# this option is superseded by the HAVE_DOT option below. This is only a
-# fallback. It is recommended to install and use dot, since it yields more
-# powerful graphs.
+# this option also works with HAVE_DOT disabled, but it is recommended to
+# install and use dot, since it yields more powerful graphs.
CLASS_DIAGRAMS = NO
# You can define message sequence charts within doxygen comments using the \msc
-# command. Doxygen will then run the mscgen tool (see http://www.mcternan.me.uk/mscgen/) to
-# produce the chart and insert it in the documentation. The MSCGEN_PATH tag allows you to
-# specify the directory where the mscgen tool resides. If left empty the tool is assumed to
-# be found in the default search path.
+# command. Doxygen will then run the mscgen tool (see
+# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where
+# the mscgen tool resides. If left empty the tool is assumed to be found in the
+# default search path.
MSCGEN_PATH =
@@ -1149,6 +1547,36 @@ HIDE_UNDOC_RELATIONS = YES
HAVE_DOT = YES
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is
+# allowed to run in parallel. When set to 0 (the default) doxygen will
+# base this on the number of processors available in the system. You can set it
+# explicitly to a value larger than 0 to get control over the balance
+# between CPU load and processing speed.
+
+DOT_NUM_THREADS = 0
+
+# By default doxygen will write a font called Helvetica to the output
+# directory and reference it in all dot files that doxygen generates.
+# When you want a differently looking font you can specify the font name
+# using DOT_FONTNAME. You need to make sure dot is able to find the font,
+# which can be done by putting it in a standard location or by setting the
+# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory
+# containing the font.
+
+DOT_FONTNAME = FreeSans
+
+# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
+# The default size is 10pt.
+
+DOT_FONTSIZE = 10
+
+# By default doxygen will tell dot to use the output directory to look for the
+# FreeSans.ttf font (which doxygen will put there itself). If you specify a
+# different font using DOT_FONTNAME you can set the path where dot
+# can find it using this tag.
+
+DOT_FONTPATH =
+
# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
# will generate a graph for each documented class showing the direct and
# indirect inheritance relations. Setting this tag to YES will force the
@@ -1193,24 +1621,24 @@ INCLUDE_GRAPH = YES
INCLUDED_BY_GRAPH = YES
-# If the CALL_GRAPH, SOURCE_BROWSER and HAVE_DOT tags are set to YES then doxygen will
-# generate a call dependency graph for every global function or class method.
-# Note that enabling this option will significantly increase the time of a run.
-# So in most cases it will be better to enable call graphs for selected
-# functions only using the \callgraph command.
+# If the CALL_GRAPH and HAVE_DOT options are set to YES then
+# doxygen will generate a call dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable call graphs
+# for selected functions only using the \callgraph command.
CALL_GRAPH = YES
-# If the CALLER_GRAPH, SOURCE_BROWSER and HAVE_DOT tags are set to YES then doxygen will
-# generate a caller dependency graph for every global function or class method.
-# Note that enabling this option will significantly increase the time of a run.
-# So in most cases it will be better to enable caller graphs for selected
-# functions only using the \callergraph command.
+# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
+# doxygen will generate a caller dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable caller
+# graphs for selected functions only using the \callergraph command.
CALLER_GRAPH = YES
# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
-# will graphical hierarchy of all classes instead of a textual one.
+# will generate a graphical hierarchy of all classes instead of a textual one.
GRAPHICAL_HIERARCHY = YES
@@ -1222,7 +1650,7 @@ GRAPHICAL_HIERARCHY = YES
DIRECTORY_GRAPH = YES
# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
-# generated by dot. Possible values are png, jpg, or gif
+# generated by dot. Possible values are svg, png, jpg, or gif.
# If left blank png will be used.
DOT_IMAGE_FORMAT = png
@@ -1238,12 +1666,18 @@ DOT_PATH =
DOTFILE_DIRS =
-# The MAX_DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
+# The MSCFILE_DIRS tag can be used to specify one or more directories that
+# contain msc files that are included in the documentation (see the
+# \mscfile command).
+
+MSCFILE_DIRS =
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
# nodes that will be shown in the graph. If the number of nodes in a graph
# becomes larger than this value, doxygen will truncate the graph, which is
-# visualized by representing a node as a red box. Note that doxygen if the number
-# of direct children of the root node in a graph is already larger than
-# MAX_DOT_GRAPH_NOTES then the graph will not be shown at all. Also note
+# visualized by representing a node as a red box. Note that doxygen if the
+# number of direct children of the root node in a graph is already larger than
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note
# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
DOT_GRAPH_MAX_NODES = 50
@@ -1259,10 +1693,10 @@ DOT_GRAPH_MAX_NODES = 50
MAX_DOT_GRAPH_DEPTH = 0
# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
-# background. This is disabled by default, which results in a white background.
-# Warning: Depending on the platform used, enabling this option may lead to
-# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
-# read).
+# background. This is disabled by default, because dot on Windows does not
+# seem to support this out of the box. Warning: Depending on the platform used,
+# enabling this option may lead to badly anti-aliased labels on the edges of
+# a graph (i.e. they become hard to read).
DOT_TRANSPARENT = NO
@@ -1284,12 +1718,3 @@ GENERATE_LEGEND = YES
# the various graphs.
DOT_CLEANUP = YES
-
-#---------------------------------------------------------------------------
-# Configuration::additions related to the search engine
-#---------------------------------------------------------------------------
-
-# The SEARCHENGINE tag specifies whether or not a search engine should be
-# used. If set to NO the values of all tags below this one will be ignored.
-
-SEARCHENGINE = NO
diff --git a/win32/deps/library/Matrix/INDEX b/win32/deps/library/Matrix/INDEX
index 2ab8b11..a17d042 100644
--- a/win32/deps/library/Matrix/INDEX
+++ b/win32/deps/library/Matrix/INDEX
@@ -30,8 +30,11 @@ USCounties USCounties Contiguity Matrix
Package 'Matrix'
[<--methods Methods for "[<-" - Assigning to Subsets for
'Matrix'
+abIndex-class Class "abIndex" of Abstract Index Vectors
+abIseq Sequence Generation of "abIndex", Abstract
+ Index Vectors
all-methods "Matrix" Methods for Functions all() and any()
-all.equal-methods Matrix Methods for Function all.equal()
+all.equal-methods Matrix Package Methods for Function all.equal()
atomicVector-class Virtual Class "atomicVector" of Atomic Vectors
band Extract bands of a matrix
bandSparse Construct Sparse Banded Matrix from
@@ -40,10 +43,13 @@ bdiag Construct a Block Diagonal Matrix
cBind Versions of 'cbind' and 'rbind' recursively
built on cbind2/rbind2
chol Choleski Decomposition - 'Matrix' S4 Generic
+chol2inv-methods Inverse from Choleski or QR Decomposition -
+ Matrix Methods
colSums Form Row and Column Sums and Means
compMatrix-class Class "compMatrix" of Composite (Factorizable)
Matrices
-contr.helmert Contrast Matrices, Optionally Sparse
+condest Compute Approximate CONDition number and 1-Norm
+ of (Large) Matrices
dMatrix-class (Virtual) Class "dMatrix" of "double" Matrices
ddenseMatrix-class Virtual Class "ddenseMatrix" of Numeric Dense
Matrices
@@ -57,6 +63,8 @@ dgRMatrix-class Sparse Compressed, Row-oriented Numeric
dgTMatrix-class Sparse matrices in triplet form
dgeMatrix-class Class "dgeMatrix" of Dense Numeric (S4 Class)
Matrices
+diagU2N Transform Triangular Matrices from Unit
+ Triangular to General and back
diagonalMatrix-class Class "diagonalMatrix" of Diagonal Matrices
dpoMatrix-class Positive Semi-definite Dense Numeric Matrices
drop0 Drop "Explicit Zeroes" from a Sparse Matrix
@@ -75,13 +83,15 @@ expm Matrix Exponential
facmul Multiplication by Decomposition Factors
forceSymmetric Force a Matrix to 'symmetricMatrix' Without
Symmetry Checks
+formatSparseM Formatting Sparse Numeric Matrices Utilities
generalMatrix-class Class "generalMatrix" of General Matrices
iMatrix-class Virtual Classes Not Yet Really Implemented and
Used
image-methods Methods for image() in Package 'Matrix'
index-class Virtual Class "index" - Simple Class for Matrix
Indices
-is.na-methods is.na() Methods for 'Matrix' Objects
+is.na-methods is.na(), is.infinite() Methods for 'Matrix'
+ Objects
isSymmetric-methods Methods for Function isSymmetric in Package
'Matrix'
kronecker-methods Methods for Function 'kronecker()' in Package
@@ -94,11 +104,12 @@ lgeMatrix-class Class "lgeMatrix" of General Dense Logical
lsparseMatrix-class Sparse logical matrices
lsyMatrix-class Symmetric Dense Logical Matrices
ltrMatrix-class Triangular Dense Logical Matrices
-lu Triangular Decomposition of a Square Matrix
+lu (Generalized) Triangular Decomposition of a
+ Matrix
nMatrix-class Class "nMatrix" of Non-zero Pattern Matrices
ndenseMatrix-class Virtual Class "ndenseMatrix" of Dense Logical
Matrices
-nearPD Nearest Matrix to a Positive Definite Matrix
+nearPD Nearest Positive Definite Matrix
ngeMatrix-class Class "ngeMatrix" of General Dense
Nonzero-pattern Matrices
nnzero The Number of Non-Zero Values of a Matrix
@@ -108,22 +119,25 @@ nsyMatrix-class Symmetric Dense Nonzero-Pattern Matrices
ntrMatrix-class Triangular Dense Logical Matrices
number-class Class "number" of Possibly Complex Numbers
pMatrix-class Permutation matrices
-printSpMatrix Print Sparse Matrices Flexibly
-qr-methods QR Decomposition -- S4 Methods and Generic
+printSpMatrix Format and Print Sparse Matrices Flexibly
+qr-methods QR Decomposition - S4 Methods and Generic
rankMatrix Rank of a Matrix
rcond Estimate the Reciprocal Condition Number
readHB Read and write external matrix formats
+rep2abI Replicate Vectors into 'abIndex' Result
replValue-class Virtual Class "replValue" - Simple Class for
subassignment Values
+rleDiff-class Class "rleDiff" of rle(diff(.)) Stored Vectors
spMatrix Sparse Matrix Constructor From Triplet
sparse.model.matrix Construct Sparse Design / Model Matrices
sparseLU-class Sparse LU decomposition of a square sparse
matrix
sparseMatrix General Sparse Matrix Construction from Nonzero
Entries
-sparseMatrix-class Virtual Class "sparseMatrix" -- Mother of
- Sparse Matrices
+sparseMatrix-class Virtual Class "sparseMatrix" - Mother of Sparse
+ Matrices
sparseQR-class Sparse QR decomposition of a sparse matrix
+sparseVector Sparse Vector Construction from Nonzero Entries
sparseVector-class Sparse Vector Classes
symmetricMatrix-class Virtual Class of Symmetric Matrices in
package:Matrix
@@ -133,5 +147,6 @@ tcrossprod Cross-product of transpose
triangularMatrix-class
Virtual Class of Triangular Matrices in
package:Matrix
-unpack Full Storage Representation of Packed Matrices
-xtabs Cross Tabulation, Optionally Sparse
+unpack Representation of Packed and Unpacked (Dense)
+ Matrices
+updown Up- and Down-Dating a Cholesky Decomposition
diff --git a/win32/deps/library/Matrix/Meta/Rd.rds b/win32/deps/library/Matrix/Meta/Rd.rds
index 9eb3222..0344360 100644
Binary files a/win32/deps/library/Matrix/Meta/Rd.rds and b/win32/deps/library/Matrix/Meta/Rd.rds differ
diff --git a/win32/deps/library/Matrix/Meta/data.rds b/win32/deps/library/Matrix/Meta/data.rds
index fd821ec..456f073 100644
Binary files a/win32/deps/library/Matrix/Meta/data.rds and b/win32/deps/library/Matrix/Meta/data.rds differ
diff --git a/win32/deps/library/Matrix/Meta/hsearch.rds b/win32/deps/library/Matrix/Meta/hsearch.rds
index 9a8fc45..540d8b4 100644
Binary files a/win32/deps/library/Matrix/Meta/hsearch.rds and b/win32/deps/library/Matrix/Meta/hsearch.rds differ
diff --git a/win32/deps/library/Matrix/Meta/links.rds b/win32/deps/library/Matrix/Meta/links.rds
new file mode 100644
index 0000000..d4f3d2c
Binary files /dev/null and b/win32/deps/library/Matrix/Meta/links.rds differ
diff --git a/win32/deps/library/Matrix/Meta/nsInfo.rds b/win32/deps/library/Matrix/Meta/nsInfo.rds
index 9df72fd..7d3745a 100644
Binary files a/win32/deps/library/Matrix/Meta/nsInfo.rds and b/win32/deps/library/Matrix/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/Matrix/Meta/package.rds b/win32/deps/library/Matrix/Meta/package.rds
index 3c59973..2c3ef27 100644
Binary files a/win32/deps/library/Matrix/Meta/package.rds and b/win32/deps/library/Matrix/Meta/package.rds differ
diff --git a/win32/deps/library/Matrix/Meta/vignette.rds b/win32/deps/library/Matrix/Meta/vignette.rds
index 8254b73..90d7b12 100644
Binary files a/win32/deps/library/Matrix/Meta/vignette.rds and b/win32/deps/library/Matrix/Meta/vignette.rds differ
diff --git a/win32/deps/library/Matrix/NAMESPACE b/win32/deps/library/Matrix/NAMESPACE
index 1672fb7..5d49024 100644
--- a/win32/deps/library/Matrix/NAMESPACE
+++ b/win32/deps/library/Matrix/NAMESPACE
@@ -4,27 +4,43 @@ useDynLib(Matrix, .registration=TRUE)
## notably for which we define methods:
importFrom("lattice", levelplot)
importFrom("graphics", image)
-importFrom("utils", head, tail)
-importFrom("stats", cov2cor, update)
+importFrom("utils", head, tail, assignInNamespace)
+importFrom("stats", cov2cor, update#, vcov
+ )
+
importFrom("grid", grid.rect, gpar, grob)# others via 'grid::'
-## Currently, group generics need to be explicitly imported (Bug?):
-importFrom("methods", Ops, Arith, Compare, Logic, Math, Math2, Summary, Complex)
+importFrom("methods",
+ ## still needed {group generics needed to be explicitly imported} ?
+ Ops, Arith, Compare, Logic, Math, Math2, Summary, Complex,
+ ## generics for which we export new methods:
+ cbind2, rbind2, coerce, show
+ , kronecker
+ ## things we call,.. necessary when Matrix is loaded, but not attached, as in
+ ## Rscript --vanilla -e 'require(methods);(M <- Matrix::Matrix(0:1,3,3));as(M,"sparseMatrix")'
+ , is, as, new
+ )
+
## Generics and functions defined in this package
export("Cholesky",
- "Diagonal", ".symDiagonal",
+ "Diagonal", ".symDiagonal", ".sparseDiagonal",
"Hilbert",
"Matrix",
"spMatrix",
"sparseMatrix",
"Schur",
+ "abIseq", "abIseq1", "rep2abI",
"band",
"bandSparse",
- "bdiag",
- "colMeans", "colSums", ## these needed a "..." added
- "rowMeans", "rowSums",
-##NOT_YET "det", # = a copy of base::det() but with Matrix namespace
+ "bdiag", ".bdiag",
+## no longer; implicit generics now
+ ## "colMeans", "colSums", ## these needed a "..." added
+ ## "rowMeans", "rowSums",
+ "condest", "onenormest",
+ "det",# << "identical" as base - but with correct determinant()
+ ".diag.dsC",# -> R/dsCMatrix.R --has FIXME
+ "diagN2U", "diagU2N", ".diagU2N",
"drop0",
"expand",
"expm",
@@ -34,26 +50,30 @@ export("Cholesky",
# "isDiagonal",
"isLDL",
"lu",
- "norm",
"nearPD",
"nnzero",
+ "formatSpMatrix", "formatSparseM", ".formatSparseSimple",
"printSpMatrix",
"printSpMatrix2",
"rankMatrix",
"readHB",
"readMM",
"sparse.model.matrix",
+ "sparseVector",
"symmpart",
"skewpart",
"tcrossprod",
"tril",
"triu",
- "unpack"
+ "updown",
+ "pack", "unpack"
+ , ".updateCHMfactor"
, ".validateCsparse"
# "writeHB",
, "writeMM"
- , ".M.classEnv"
)
+if(getRversion() < "2.15.0" || R.version$`svn rev` < 57849)
+ export(".M.classEnv")
## substitute for using cbind() / rbind()
export("cBind",
@@ -67,6 +87,7 @@ exportClasses(
"atomicVector",
"number",
## LOGIC "logic",
+ "abIndex", "rleDiff",
## --- 'Matrix' mother and all its daughters : ---------------
"Matrix",
@@ -161,6 +182,7 @@ exportClasses(
## --- 'MatrixFactorization' mother and all its daughters : ---
"MatrixFactorization",
+ "CholeskyFactorization",
"LU",
"denseLU",
@@ -189,6 +211,7 @@ exportClasses(
)
+
exportMethods(## for both own and "other" generics:
## Group Methods
@@ -200,6 +223,10 @@ exportMethods(## for both own and "other" generics:
"Ops",
"Summary",
+ ## re-export S4 methods, for "stats"-S3-generics:
+ "cov2cor",
+ "update",
+
"!",
"+",# for dgT(Matrix) only
"%*%",
@@ -215,16 +242,17 @@ exportMethods(## for both own and "other" generics:
"as.matrix",
"as.vector",
"as.numeric",
+ "as.integer",
"as.logical",
"band",
"chol",
+ "chol2inv",
"colMeans",
"colSums",
- "cov2cor",
"coerce",
"crossprod",
"determinant",
- "diag",
+ "diag", "diag<-",
"diff",
"dim",
"dim<-",
@@ -233,17 +261,20 @@ exportMethods(## for both own and "other" generics:
"drop",
"expand",
"expm",
+ "format",
"head",
"image",
"forceSymmetric",
"isSymmetric",
## "isDiagonal",
## "isTriangular",
- "is.na",
+ "is.na",
+ "is.finite", "is.infinite",
"kronecker",
"length",
"mean",
"norm",
+ "nnzero",
"print",# print(x, ...) when show(x) is not sufficient
"qr",
"qr.R",
@@ -267,19 +298,20 @@ exportMethods(## for both own and "other" generics:
"tcrossprod",
"tril",
"triu",
+ "updown",
"unname",
- "update",
+ "which",
"zapsmall"
)
-if(getRversion() < "2.10.0")# The version of R -- at *install* time (!)
- exportPattern("^contr\\..*")
-
-if(getRversion() < "2.10.0")
- export("xtabs")
-
-
exportMethods("rbind2")
exportMethods("cbind2")
S3method(print, sparseSummary)
+S3method(print, diagSummary)
+S3method(c, abIndex)# < for now -- S4 method on c() seems "difficult"
+
+## So that such dispatch also works inside base functions:
+S3method(as.array, Matrix)
+S3method(as.matrix, Matrix)
+S3method(as.vector, Matrix)
diff --git a/win32/deps/library/Matrix/R/Matrix b/win32/deps/library/Matrix/R/Matrix
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/Matrix/R/Matrix
+++ b/win32/deps/library/Matrix/R/Matrix
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/Matrix/R/Matrix.rdb b/win32/deps/library/Matrix/R/Matrix.rdb
index 3048b95..b4855c9 100644
Binary files a/win32/deps/library/Matrix/R/Matrix.rdb and b/win32/deps/library/Matrix/R/Matrix.rdb differ
diff --git a/win32/deps/library/Matrix/R/Matrix.rdx b/win32/deps/library/Matrix/R/Matrix.rdx
index a778594..1483674 100644
Binary files a/win32/deps/library/Matrix/R/Matrix.rdx and b/win32/deps/library/Matrix/R/Matrix.rdx differ
diff --git a/win32/deps/library/Matrix/doc/Announce.txt b/win32/deps/library/Matrix/doc/Announce.txt
index 2962b62..f5ed97d 100644
--- a/win32/deps/library/Matrix/doc/Announce.txt
+++ b/win32/deps/library/Matrix/doc/Announce.txt
@@ -1,3 +1,7 @@
+Basically the text of the R-packages posting on Mar 28, 2008 :
+ https://stat.ethz.ch/pipermail/r-packages/2008/000911.html
+------------------------------------------------------------------------
+
This weekend, a new version of "the Matrix" (well, actually the R
package named "Matrix") will become available on the CRAN mirrors.
diff --git a/win32/deps/library/Matrix/doc/Comparisons.R b/win32/deps/library/Matrix/doc/Comparisons.R
index 35187a0..6f452b0 100644
--- a/win32/deps/library/Matrix/doc/Comparisons.R
+++ b/win32/deps/library/Matrix/doc/Comparisons.R
@@ -1,11 +1,13 @@
+### R code from vignette source 'Comparisons.Rnw'
+
###################################################
-### chunk number 1: preliminaries
+### code chunk number 1: preliminaries
###################################################
options(width=75)
###################################################
-### chunk number 2: modelMatrix
+### code chunk number 2: modelMatrix
###################################################
data(Formaldehyde)
str(Formaldehyde)
@@ -14,26 +16,26 @@ str(Formaldehyde)
###################################################
-### chunk number 3: naiveCalc
+### code chunk number 3: naiveCalc
###################################################
solve(t(m) %*% m) %*% t(m) %*% yo
###################################################
-### chunk number 4: timedNaive
+### code chunk number 4: timedNaive
###################################################
system.time(solve(t(m) %*% m) %*% t(m) %*% yo)
###################################################
-### chunk number 5: catNaive
+### code chunk number 5: catNaive
###################################################
dput(c(solve(t(m) %*% m) %*% t(m) %*% yo))
dput(unname(lm.fit(m, yo)$coefficients))
###################################################
-### chunk number 6: KoenNg
+### code chunk number 6: KoenNg
###################################################
library(Matrix)
data(KNex, package = "Matrix")
@@ -44,20 +46,20 @@ system.time(naive.sol <- solve(t(mm) %*% mm) %*% t(mm) %*% y)
###################################################
-### chunk number 7: crossKoenNg
+### code chunk number 7: crossKoenNg
###################################################
system.time(cpod.sol <- solve(crossprod(mm), crossprod(mm,y)))
all.equal(naive.sol, cpod.sol)
###################################################
-### chunk number 8: xpxKoenNg
+### code chunk number 8: xpxKoenNg
###################################################
system.time(t(mm) %*% mm)
###################################################
-### chunk number 9: fullMatrix_crossprod
+### code chunk number 9: fullMatrix_crossprod
###################################################
fm <- mm
set.seed(11)
@@ -68,7 +70,7 @@ stopifnot(all.equal(c1, c2, tol = 1e-12))
###################################################
-### chunk number 10: naiveChol
+### code chunk number 10: naiveChol
###################################################
system.time(ch <- chol(crossprod(mm)))
system.time(chol.sol <-
@@ -78,7 +80,7 @@ stopifnot(all.equal(chol.sol, naive.sol))
###################################################
-### chunk number 11: MatrixKoenNg
+### code chunk number 11: MatrixKoenNg
###################################################
mm <- as(KNex$mm, "dgeMatrix")
class(crossprod(mm))
@@ -87,7 +89,7 @@ stopifnot(all.equal(naive.sol, unname(as(Mat.sol,"matrix"))))
###################################################
-### chunk number 12: saveFactor
+### code chunk number 12: saveFactor
###################################################
xpx <- crossprod(mm)
xpy <- crossprod(mm, y)
@@ -96,7 +98,7 @@ system.time(solve(xpx, xpy)) # reusing factorization
###################################################
-### chunk number 13: SparseKoenNg
+### code chunk number 13: SparseKoenNg
###################################################
mm <- KNex$mm
class(mm)
@@ -105,7 +107,7 @@ stopifnot(all.equal(naive.sol, unname(as(sparse.sol, "matrix"))))
###################################################
-### chunk number 14: SparseSaveFactor
+### code chunk number 14: SparseSaveFactor
###################################################
xpx <- crossprod(mm)
xpy <- crossprod(mm, y)
@@ -114,13 +116,13 @@ system.time(solve(xpx, xpy))
###################################################
-### chunk number 15: sessionInfo
+### code chunk number 15: sessionInfo
###################################################
toLatex(sessionInfo())
###################################################
-### chunk number 16: from_pkg_sfsmisc
+### code chunk number 16: from_pkg_sfsmisc
###################################################
if(identical(1L, grep("linux", R.version[["os"]]))) { ##----- Linux - only ----
@@ -141,7 +143,7 @@ Smem <- Sys.procinfo("/proc/meminfo")
###################################################
-### chunk number 17: Sys_proc_fake eval=FALSE
+### code chunk number 17: Sys_proc_fake (eval = FALSE)
###################################################
## if(identical(1L, grep("linux", R.version[["os"]]))) { ## Linux - only ---
## Scpu <- sfsmisc::Sys.procinfo("/proc/cpuinfo")
@@ -152,7 +154,7 @@ Smem <- Sys.procinfo("/proc/meminfo")
###################################################
-### chunk number 18: Sys_proc_out
+### code chunk number 18: Sys_proc_out
###################################################
if(identical(1L, grep("linux", R.version[["os"]]))) { ## Linux - only ---
print(Scpu[c("model name", "cpu MHz", "cache size", "bogomips")])
diff --git a/win32/deps/library/Matrix/doc/Comparisons.Rnw b/win32/deps/library/Matrix/doc/Comparisons.Rnw
index fb2876e..c7060fb 100644
--- a/win32/deps/library/Matrix/doc/Comparisons.Rnw
+++ b/win32/deps/library/Matrix/doc/Comparisons.Rnw
@@ -5,7 +5,7 @@
%%\VignetteIndexEntry{Comparisons of Least Squares calculation speeds}
%%\VignetteDepends{Matrix}
\begin{document}
-\SweaveOpts{engine=R,eps=FALSE,pdf=TRUE,width=5,height=3,strip.white=TRUE,keep.source=TRUE}
+\SweaveOpts{engine=R,eps=FALSE,pdf=TRUE,width=5,height=3,strip.white=true,keep.source=TRUE}
\setkeys{Gin}{width=\textwidth}
\title{Comparing Least Squares Calculations}
\author{Douglas Bates\\R Development Core Team\\\email{Douglas Bates R-project org}}
diff --git a/win32/deps/library/Matrix/doc/Comparisons.pdf b/win32/deps/library/Matrix/doc/Comparisons.pdf
index e7ea55a..564c49c 100644
Binary files a/win32/deps/library/Matrix/doc/Comparisons.pdf and b/win32/deps/library/Matrix/doc/Comparisons.pdf differ
diff --git a/win32/deps/library/Matrix/doc/Design-issues.R b/win32/deps/library/Matrix/doc/Design-issues.R
index b4bf98a..1ece87e 100644
--- a/win32/deps/library/Matrix/doc/Design-issues.R
+++ b/win32/deps/library/Matrix/doc/Design-issues.R
@@ -1,11 +1,13 @@
+### R code from vignette source 'Design-issues.Rnw'
+
###################################################
-### chunk number 1: preliminaries
+### code chunk number 1: preliminaries
###################################################
options(width=75)
###################################################
-### chunk number 2: diag-class
+### code chunk number 2: diag-class
###################################################
library(Matrix)
(D4 <- Diagonal(4, 10*(1:4)))
@@ -14,14 +16,14 @@ diag(D4)
###################################################
-### chunk number 3: diag-2
+### code chunk number 3: diag-2
###################################################
diag(D4) <- diag(D4) + 1:4
D4
###################################################
-### chunk number 4: unit-diag
+### code chunk number 4: unit-diag
###################################################
str(I3 <- Diagonal(3)) ## empty 'x' slot
@@ -29,7 +31,7 @@ getClass("diagonalMatrix") ## extending "denseMatrix"
###################################################
-### chunk number 5: Matrix-ex
+### code chunk number 5: Matrix-ex
###################################################
(M <- spMatrix(4,4, i=1:4, j=c(3:1,4), x=c(4,1,4,8))) # dgTMatrix
m <- as(M, "matrix")
@@ -37,7 +39,7 @@ m <- as(M, "matrix")
###################################################
-### chunk number 6: sessionInfo
+### code chunk number 6: sessionInfo
###################################################
toLatex(sessionInfo())
diff --git a/win32/deps/library/Matrix/doc/Design-issues.Rnw b/win32/deps/library/Matrix/doc/Design-issues.Rnw
index 76c0f99..90adb23 100644
--- a/win32/deps/library/Matrix/doc/Design-issues.Rnw
+++ b/win32/deps/library/Matrix/doc/Design-issues.Rnw
@@ -8,7 +8,7 @@
%% vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
%%\VignetteIndexEntry{Design Issues in Matrix package Development}
%%\VignetteDepends{Matrix}
-\SweaveOpts{engine=R,eps=FALSE,pdf=TRUE,width=5,height=3,strip.white=TRUE,keep.source=TRUE}
+\SweaveOpts{engine=R,eps=FALSE,pdf=TRUE,width=5,height=3,strip.white=true,keep.source=TRUE}
% ^^^^^^^^^^^^^^^^
\title{Design Issues in Matrix package Development}
\author{Martin Maechler and Douglas Bates\\R Core Development Team
diff --git a/win32/deps/library/Matrix/doc/Design-issues.pdf b/win32/deps/library/Matrix/doc/Design-issues.pdf
index 83a7fd1..7fd09f6 100644
Binary files a/win32/deps/library/Matrix/doc/Design-issues.pdf and b/win32/deps/library/Matrix/doc/Design-issues.pdf differ
diff --git a/win32/deps/library/Matrix/doc/Intro2Matrix.R b/win32/deps/library/Matrix/doc/Intro2Matrix.R
index 35adbee..8cea1c1 100644
--- a/win32/deps/library/Matrix/doc/Intro2Matrix.R
+++ b/win32/deps/library/Matrix/doc/Intro2Matrix.R
@@ -1,11 +1,13 @@
+### R code from vignette source 'Intro2Matrix.Rnw'
+
###################################################
-### chunk number 1: preliminaries
+### code chunk number 1: preliminaries
###################################################
options(width=75)
###################################################
-### chunk number 2: ex1
+### code chunk number 2: ex1
###################################################
library(Matrix)
@@ -15,7 +17,7 @@ tM <- t(M)
###################################################
-### chunk number 3: ex2
+### code chunk number 3: ex2
###################################################
(M2 <- cBind(-1, M))
M[2, 1]
@@ -23,7 +25,7 @@ M[4, ]
###################################################
-### chunk number 4: set0
+### code chunk number 4: set0
###################################################
M2[, c(2,4:6)] <- 0
M2[2, ] <- 0
@@ -32,7 +34,7 @@ M2[1:2,2] <- M2[3,4:5] <- NA
###################################################
-### chunk number 5: asSparse
+### code chunk number 5: asSparse
###################################################
sM <- as(M2, "sparseMatrix")
10 * sM
@@ -41,41 +43,41 @@ is(sM / 10 + M2 %/% 2, "sparseMatrix")
###################################################
-### chunk number 6: add1
+### code chunk number 6: add1
###################################################
sM + 10
###################################################
-### chunk number 7: Comp1
+### code chunk number 7: Comp1
###################################################
Mg2 <- (sM > 2)
Mg2
###################################################
-### chunk number 8: str_mat
+### code chunk number 8: str_mat
###################################################
str(Mg2)
summary(Mg2)
###################################################
-### chunk number 9: drop0
+### code chunk number 9: drop0
###################################################
Mg2 <- drop0(Mg2)
str(Mg2 x) # length 13, was 16
###################################################
-### chunk number 10: image
+### code chunk number 10: image
###################################################
data(CAex)
print(image(CAex, main = "image(CAex)")) # print(.) needed for Sweave
###################################################
-### chunk number 11: sub_logi
+### code chunk number 11: sub_logi
###################################################
sM[sM > 2]
sml <- sM[sM <= 2]
@@ -83,14 +85,14 @@ sml
###################################################
-### chunk number 12: Tsparse-class
+### code chunk number 12: Tsparse-class
###################################################
getClass("TsparseMatrix") # (i,j, Dim, Dimnames) slots are common to all
getClass("dgTMatrix")
###################################################
-### chunk number 13: sessionInfo
+### code chunk number 13: sessionInfo
###################################################
toLatex(sessionInfo())
diff --git a/win32/deps/library/Matrix/doc/Intro2Matrix.Rnw b/win32/deps/library/Matrix/doc/Intro2Matrix.Rnw
index 414184f..c8bb084 100644
--- a/win32/deps/library/Matrix/doc/Intro2Matrix.Rnw
+++ b/win32/deps/library/Matrix/doc/Intro2Matrix.Rnw
@@ -9,7 +9,7 @@
%
%%\VignetteIndexEntry{2nd Introduction to the Matrix Package}
%%\VignetteDepends{Matrix}
-\SweaveOpts{engine=R,eps=FALSE,pdf=TRUE,width=7,height=4,strip.white=TRUE,keep.source=TRUE}
+\SweaveOpts{engine=R,eps=FALSE,pdf=TRUE,width=7,height=4,strip.white=true,keep.source=TRUE}
% ^^^^^^^^^^^^^^^^
\title{2nd Introduction to the Matrix package}
\author{Martin Maechler and Douglas Bates\\ R Core Development Team
diff --git a/win32/deps/library/Matrix/doc/Intro2Matrix.pdf b/win32/deps/library/Matrix/doc/Intro2Matrix.pdf
index ebe8228..b1f2b88 100644
Binary files a/win32/deps/library/Matrix/doc/Intro2Matrix.pdf and b/win32/deps/library/Matrix/doc/Intro2Matrix.pdf differ
diff --git a/win32/deps/library/Matrix/doc/Introduction.R b/win32/deps/library/Matrix/doc/Introduction.R
index 6359a4e..7e4d62d 100644
--- a/win32/deps/library/Matrix/doc/Introduction.R
+++ b/win32/deps/library/Matrix/doc/Introduction.R
@@ -1,5 +1,7 @@
+### R code from vignette source 'Introduction.Rnw'
+
###################################################
-### chunk number 1: preliminaries
+### code chunk number 1: preliminaries
###################################################
options(width=75)
diff --git a/win32/deps/library/Matrix/doc/Introduction.Rnw b/win32/deps/library/Matrix/doc/Introduction.Rnw
index 3d5b2d8..18edc2e 100644
--- a/win32/deps/library/Matrix/doc/Introduction.Rnw
+++ b/win32/deps/library/Matrix/doc/Introduction.Rnw
@@ -4,7 +4,7 @@
\bibliographystyle{plainnat}
%%\VignetteIndexEntry{Introduction to the Matrix Package}
%%\VignetteDepends{Matrix}
-\SweaveOpts{engine=R,eps=FALSE,pdf=TRUE,width=5,height=3,strip.white=TRUE,keep.source=TRUE}
+\SweaveOpts{engine=R,eps=FALSE,pdf=TRUE,width=5,height=3,strip.white=true,keep.source=TRUE}
\title{Introduction to the Matrix package --- as of Feb.~2005\footnote{
There's an unfinished ``2nd Introduction to the Matrix package''
which contains partly newer information, but is not at all self-contained.
diff --git a/win32/deps/library/Matrix/doc/Introduction.pdf b/win32/deps/library/Matrix/doc/Introduction.pdf
index 10148b4..de97a32 100644
Binary files a/win32/deps/library/Matrix/doc/Introduction.pdf and b/win32/deps/library/Matrix/doc/Introduction.pdf differ
diff --git a/win32/deps/library/Matrix/doc/SuiteSparse/AMD.txt b/win32/deps/library/Matrix/doc/SuiteSparse/AMD.txt
new file mode 100644
index 0000000..2f0a4ff
--- /dev/null
+++ b/win32/deps/library/Matrix/doc/SuiteSparse/AMD.txt
@@ -0,0 +1,213 @@
+AMD, Copyright (c) 2009-2012 by Timothy A. Davis (http://www.suitesparse.com),
+Patrick R. Amestoy, and Iain S. Duff. All Rights Reserved. AMD is available
+under alternate licences; contact T. Davis for details.
+
+AMD: a set of routines for permuting sparse matrices prior to
+ factorization. Includes a version in C, a version in Fortran, and a MATLAB
+ mexFunction.
+
+Requires SuiteSparse_config, in the ../SuiteSparse_config directory relative to
+this directory.
+
+Quick start (Unix, or Windows with Cygwin):
+
+ To compile, test, and install AMD, you may wish to first configure the
+ installation by editting the ../SuiteSparse_config/SuiteSparse_config.mk
+ file. Next, cd to this directory (AMD) and type "make" (or "make lib" if
+ you do not have MATLAB). To compile and run a demo program for the Fortran
+ version, type "make fortran". When done, type "make clean" to remove
+ unused *.o files (keeps the compiled libraries and demo programs). See the
+ User Guide (Doc/AMD_UserGuide.pdf), or
+ ../SuiteSparse_config/SuiteSparse_config.mk for more details.
+
+Quick start (for MATLAB users);
+
+ To compile, test, and install the AMD mexFunction, cd to the
+ AMD/MATLAB directory and type amd_make at the MATLAB prompt.
+
+-------------------------------------------------------------------------------
+
+AMD License:
+
+ Your use or distribution of AMD or any modified version of
+ AMD implies that you agree to this License.
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301
+ USA
+
+ Permission is hereby granted to use or copy this program under the
+ terms of the GNU LGPL, provided that the Copyright, this License,
+ and the Availability of the original version is retained on all copies.
+ User documentation of any code that uses this code or any modified
+ version of this code must cite the Copyright, this License, the
+ Availability note, and "Used by permission." Permission to modify
+ the code and to distribute modified code is granted, provided the
+ Copyright, this License, and the Availability note are retained,
+ and a notice that the code was modified is included.
+
+Availability:
+
+ http://www.suitesparse.com
+
+-------------------------------------------------------------------------------
+
+This is the AMD README file. It is a terse overview of AMD.
+Refer to the User Guide (Doc/AMD_UserGuide.pdf) for how to install
+and use AMD.
+
+Description:
+
+ AMD is a set of routines for pre-ordering sparse matrices prior to Cholesky
+ or LU factorization, using the approximate minimum degree ordering
+ algorithm. Written in ANSI/ISO C with a MATLAB interface, and in
+ Fortran 77.
+
+Authors:
+
+ Timothy A. Davis (DrTimothyAldenDavis gmail com)
+ Patrick R. Amestory, ENSEEIHT, Toulouse, France.
+ Iain S. Duff, Rutherford Appleton Laboratory, UK.
+
+Acknowledgements:
+
+ This work was supported by the National Science Foundation, under
+ grants DMS-9504974, DMS-9803599, and CCR-0203270.
+
+ Portions of this work were done while on sabbatical at Stanford University
+ and Lawrence Berkeley National Laboratory (with funding from the SciDAC
+ program). I would like to thank Gene Golub, Esmond Ng, and Horst Simon
+ for making this sabbatical possible.
+
+-------------------------------------------------------------------------------
+Files and directories in the AMD distribution:
+-------------------------------------------------------------------------------
+
+ ---------------------------------------------------------------------------
+ Subdirectories of the AMD directory:
+ ---------------------------------------------------------------------------
+
+ Doc documentation
+ Source primary source code
+ Include include file for use in your code that calls AMD
+ Demo demo programs. also serves as test of the AMD installation.
+ MATLAB AMD mexFunction for MATLAB, and supporting m-files
+ Lib where the compiled C-callable and Fortran-callable
+ AMD libraries placed.
+
+ ---------------------------------------------------------------------------
+ Files in the AMD directory:
+ ---------------------------------------------------------------------------
+
+ Makefile top-level Makefile for GNU make or original make.
+ Windows users would require Cygwin to use "make"
+
+ README.txt this file
+
+ ---------------------------------------------------------------------------
+ Doc directory: documentation
+ ---------------------------------------------------------------------------
+
+ ChangeLog change log
+ License the AMD License
+ Makefile for creating the documentation
+ AMD_UserGuide.bib AMD User Guide (references)
+ AMD_UserGuide.tex AMD User Guide (LaTeX)
+ AMD_UserGuide.pdf AMD User Guide (PDF)
+ lesser.txt the GNU LGPL license
+
+ ---------------------------------------------------------------------------
+ Source directory:
+ ---------------------------------------------------------------------------
+
+ amd_order.c user-callable, primary AMD ordering routine
+ amd_control.c user-callable, prints the control parameters
+ amd_defaults.c user-callable, sets default control parameters
+ amd_info.c user-callable, prints the statistics from AMD
+
+ amd_1.c non-user-callable, construct A+A'
+ amd_2.c user-callable, primary ordering kernel
+ (a C version of amd.f and amdbar.f, with
+ post-ordering added)
+ amd_aat.c non-user-callable, computes nnz (A+A')
+ amd_dump.c non-user-callable, debugging routines
+ amd_postorder.c non-user-callable, postorder
+ amd_post_tree.c non-user-callable, postorder just one tree
+ amd_valid.c non-user-callable, verifies a matrix
+ amd_preprocess.c non-user-callable, computes A', removes duplic
+
+ amd.f user-callable Fortran 77 version
+ amdbar.f user-callable Fortran 77 version
+
+ ---------------------------------------------------------------------------
+ Include directory:
+ ---------------------------------------------------------------------------
+
+ amd.h include file for C programs that use AMD
+ amd_internal.h non-user-callable, include file for AMD
+
+ ---------------------------------------------------------------------------
+ Demo directory:
+ ---------------------------------------------------------------------------
+
+ Makefile for GNU make or original make
+
+ amd_demo.c C demo program for AMD
+ amd_demo.out output of amd_demo.c
+
+ amd_demo2.c C demo program for AMD, jumbled matrix
+ amd_demo2.out output of amd_demo2.c
+
+ amd_l_demo.c C demo program for AMD (long integer version)
+ amd_l_demo.out output of amd_l_demo.c
+
+ amd_simple.c simple C demo program for AMD
+ amd_simple.out output of amd_simple.c
+
+ amd_f77demo.f Fortran 77 demo program for AMD
+ amd_f77demo.out output of amd_f77demo.f
+
+ amd_f77simple.c simple Fortran 77 demo program for AMD
+ amd_f77simple.out output of amd_f77simple.f
+
+ amd_f77cross.f Fortran 77 demo, calls the C version of AMD
+ amd_f77cross.out output of amd_f77cross.f
+ amd_f77wrapper.c Fortran-callable wrapper for C version of AMD
+
+ ---------------------------------------------------------------------------
+ MATLAB directory:
+ ---------------------------------------------------------------------------
+
+ GNUmakefile a nice Makefile, for GNU make
+ Makefile an ugly Unix Makefile (for older make's)
+
+ Contents.m for "help amd2" listing of toolbox contents
+
+ amd2.m MATLAB help file for AMD
+ amd_make.m MATLAB m-file for compiling AMD mexFunction
+ amd_install.m compile and install the AMD mexFunction
+
+ amd_mex.c AMD mexFunction for MATLAB
+
+ amd_demo.m MATLAB demo for AMD
+ amd_demo.m.out diary output of amd_demo.m
+ can_24.mat input file for AMD demo
+
+ ---------------------------------------------------------------------------
+ Lib directory: libamd.a and libamdf77.a libraries placed here
+ ---------------------------------------------------------------------------
+
+ GNUmakefile a nice Makefile, for GNU make
+ Makefile an ugly Unix Makefile (for older make's)
+ libamd.def AMD definitions for Windows
diff --git a/win32/deps/library/Matrix/doc/SuiteSparse/CHOLMOD.txt b/win32/deps/library/Matrix/doc/SuiteSparse/CHOLMOD.txt
new file mode 100644
index 0000000..08eb0a2
--- /dev/null
+++ b/win32/deps/library/Matrix/doc/SuiteSparse/CHOLMOD.txt
@@ -0,0 +1,81 @@
+CHOLMOD: a sparse CHOLesky MODification package, Copyright (c) 2005-2012.
+http://www.suitesparse.com
+-----------------------------------------------
+
+ CHOLMOD is a set of routines for factorizing sparse symmetric positive
+ definite matrices of the form A or AA', updating/downdating a sparse
+ Cholesky factorization, solving linear systems, updating/downdating
+ the solution to the triangular system Lx=b, and many other sparse matrix
+ functions for both symmetric and unsymmetric matrices. Its supernodal
+ Cholesky factorization relies on LAPACK and the Level-3 BLAS, and obtains
+ a substantial fraction of the peak performance of the BLAS. Both real and
+ complex matrices are supported. CHOLMOD is written in ANSI/ISO C, with both
+ C and MATLAB interfaces. This code works on Microsoft Windows and many
+ versions of Unix and Linux.
+
+
+Some Modules of CHOLMOD are copyrighted by the University of Florida (the
+Core and Partition Modules). The rest are copyrighted by the authors:
+Timothy A. Davis (all of them), and William W. Hager (the Modify Module).
+
+CHOLMOD relies on several other packages: AMD, CAMD, COLAMD, CCOLAMD,
+SuiteSparse_config, METIS, the BLAS, and LAPACK. All but METIS, the BLAS, and
+LAPACK are part of SuiteSparse.
+
+AMD is authored by T. Davis, Iain Duff, and Patrick Amestoy.
+COLAMD is authored by T. Davis and Stefan Larimore, with algorithmic design
+in collaboration with John Gilbert and Esmond Ng.
+CCOLAMD is authored by T. Davis and Siva Rajamanickam.
+CAMD is authored by T. Davis and Y. Chen.
+
+LAPACK and the BLAS are authored by Jack Dongarra and many others.
+LAPACK is available at http://www.netlib.org/lapack
+
+METIS is authored by George Karypis, Univ. of Minnesota. Its use in CHOLMOD
+is optional. See http://www-users.cs.umn.edu/~karypis/metis.
+Place a copy of the metis-4.0 directory in the same directory that
+contains the CHOLMOD, AMD, COLAMD, and CCOLAMD directories prior to compiling
+with "make".
+
+If you do not wish to use METIS, you must edit SuiteSparse_config and change
+the line:
+
+ CHOLMOD_CONFIG =
+
+to
+
+ CHOLMOD_CONFIG = -DNPARTITION
+
+The CHOLMOD, AMD, COLAMD, CCOLAMD, and SuiteSparse)config directories must all
+reside in a common parent directory. To compile all these libraries, edit
+SuiteSparse)config/SuiteSparse)config.mk to reflect your environment (C
+compiler, location of the BLAS, and so on) and then type "make" in either the
+CHOLMOD directory or in the parent directory of CHOLMOD. See each package for
+more details on how to compile them.
+
+For use in MATLAB (on any system, including Windows): start MATLAB,
+cd to the CHOLMOD/MATLAB directory, and type cholmod_make in the MATLAB
+Command Window. This is the best way to compile CHOLMOD for MATLAB; it
+provides a workaround for a METIS design feature, in which METIS terminates
+your program (and thus MATLAB) if it runs out of memory. Using cholmod_make
+also ensures your mexFunctions are compiled with -fexceptions, so that
+exceptions are handled properly (when hitting control-C in the MATLAB command
+window, for example).
+
+On the Pentium, do NOT use the Intel MKL BLAS prior to MKL Version 8.0 with
+CHOLMOD. Older versions (prior to 8.0) have a bug in dgemm when computing
+A*B'. The bug generates a NaN result, when the inputs are well-defined. Use
+the Goto BLAS or the MKL v8.0 BLAS instead. The Goto BLAS is faster and more
+reliable. See http://www.tacc.utexas.edu/~kgoto/ or
+http://www.cs.utexas.edu/users/flame/goto/.
+Sadly, the Intel MKL BLAS 7.x is the default for MATLAB 7.0.4. See
+http://www.mathworks.com/support/bugreports/details.html?rp=252103 for more
+details. To workaround this problem on Linux, set environment variable
+BLAS_VERSION to libmkl_p3.so:libguide.so. On Windows, set environment variable
+BLAS_VERSION to mkl_p3.dll. Better yet, get MATLAB 7sp3 (MATLAB 7.1) or later.
+
+Acknowledgements: this work was supported in part by the National Science
+Foundation (NFS CCR-0203270 and DMS-9803599), and a grant from Sandia National
+Laboratories (Dept. of Energy) which supported the development of CHOLMOD's
+Partition Module.
+
diff --git a/win32/deps/library/Matrix/doc/SuiteSparse/COLAMD.txt b/win32/deps/library/Matrix/doc/SuiteSparse/COLAMD.txt
new file mode 100644
index 0000000..6c5edf0
--- /dev/null
+++ b/win32/deps/library/Matrix/doc/SuiteSparse/COLAMD.txt
@@ -0,0 +1,118 @@
+COLAMD, Copyright 1998-2012, Timothy A. Davis. http://www.suitesparse.com
+-------------------------------------------------------------------------------
+
+The COLAMD column approximate minimum degree ordering algorithm computes
+a permutation vector P such that the LU factorization of A (:,P)
+tends to be sparser than that of A. The Cholesky factorization of
+(A (:,P))'*(A (:,P)) will also tend to be sparser than that of A'*A.
+SYMAMD is a symmetric minimum degree ordering method based on COLAMD,
+available as a MATLAB-callable function. It constructs a matrix M such
+that M'*M has the same pattern as A, and then uses COLAMD to compute a column
+ordering of M. Colamd and symamd tend to be faster and generate better
+orderings than their MATLAB counterparts, colmmd and symmmd.
+
+To compile and test the colamd m-files and mexFunctions, just unpack the
+COLAMD/ directory from the COLAMD.tar.gz file, and run MATLAB from
+within that directory. Next, type colamd_test to compile and test colamd
+and symamd. This will work on any computer with MATLAB (Unix, PC, or Mac).
+Alternatively, type "make" (in Unix) to compile and run a simple example C
+code, without using MATLAB.
+
+To compile and install the colamd m-files and mexFunctions, just cd to
+COLAMD/MATLAB and type colamd_install in the MATLAB command window.
+A short demo will run. Optionally, type colamd_test to run an extensive tests.
+Type "make" in Unix in the COLAMD directory to compile the C-callable
+library and to run a short demo.
+
+Colamd is a built-in routine in MATLAB, available from The
+Mathworks, Inc. Under most cases, the compiled COLAMD from Versions 2.0 to the
+current version do not differ. Colamd Versions 2.2 and 2.3 differ only in their
+mexFunction interaces to MATLAB. v2.4 fixes a bug in the symamd routine in
+v2.3. The bug (in v2.3 and earlier) has no effect on the MATLAB symamd
+mexFunction. v2.5 adds additional checks for integer overflow, so that
+the "int" version can be safely used with 64-bit pointers. Refer to the
+ChangeLog for more details.
+
+To use colamd and symamd within an application written in C, all you need are
+colamd.c, colamd_global.c, and colamd.h, which are the C-callable
+colamd/symamd codes. See colamd.c for more information on how to call
+colamd from a C program.
+
+Requires SuiteSparse_config, in the ../SuiteSparse_config directory relative to
+this directory.
+
+See the colamd.c file or http://www.suitesparse.com for the license to COLAMD.
+
+Related papers:
+
+ T. A. Davis, J. R. Gilbert, S. Larimore, E. Ng, An approximate column
+ minimum degree ordering algorithm, ACM Transactions on Mathematical
+ Software, vol. 30, no. 3., pp. 353-376, 2004.
+
+ T. A. Davis, J. R. Gilbert, S. Larimore, E. Ng, Algorithm 836: COLAMD,
+ an approximate column minimum degree ordering algorithm, ACM
+ Transactions on Mathematical Software, vol. 30, no. 3., pp. 377-380,
+ 2004.
+
+ "An approximate minimum degree column ordering algorithm",
+ S. I. Larimore, MS Thesis, Dept. of Computer and Information
+ Science and Engineering, University of Florida, Gainesville, FL,
+ 1998. CISE Tech Report TR-98-016.
+
+ Approximate Deficiency for Ordering the Columns of a Matrix,
+ J. L. Kern, Senior Thesis, Dept. of Computer and Information
+ Science and Engineering, University of Florida, Gainesville, FL,
+ 1999.
+
+
+Authors: Stefan I. Larimore and Timothy A. Davis,
+in collaboration with John Gilbert, Xerox PARC (now at UC Santa Barbara),
+and Esmong Ng, Lawrence Berkeley National Laboratory (much of this work
+he did while at Oak Ridge National Laboratory).
+
+COLAMD files:
+
+ Demo simple demo
+ Doc additional documentation (see colamd.c for more)
+ Include include file
+ Lib compiled C-callable library
+ Makefile primary Unix Makefile
+ MATLAB MATLAB functions
+ README.txt this file
+ Source C source code
+
+ ./Demo:
+ colamd_example.c simple example
+ colamd_example.out output of colamd_example.c
+ colamd_l_example.c simple example, long integers
+ colamd_l_example.out output of colamd_l_example.c
+ Makefile Makefile for C demos
+
+ ./Doc:
+ ChangeLog change log
+ lesser.txt license
+
+ ./Include:
+ colamd.h include file
+
+ ./Lib:
+ Makefile Makefile for C-callable library
+
+ ./MATLAB:
+ colamd2.m MATLAB interface for colamd2
+ colamd_demo.m simple demo
+ colamd_install.m compile and install colamd2 and symamd2
+ colamd_make.m compile colamd2 and symamd2
+ colamdmex.ca MATLAB mexFunction for colamd2
+ colamd_test.m extensive test
+ colamdtestmex.c test function for colamd
+ Contents.m contents of the MATLAB directory
+ luflops.m test code
+ Makefile Makefile for MATLAB functions
+ symamd2.m MATLAB interface for symamd2
+ symamdmex.c MATLAB mexFunction for symamd2
+ symamdtestmex.c test function for symamd
+
+ ./Source:
+ colamd.c primary source code
+ colamd_global.c globally defined function pointers (malloc, free, ...)
diff --git a/win32/deps/library/Matrix/doc/UFsparse/SPQR.txt b/win32/deps/library/Matrix/doc/SuiteSparse/SPQR.txt
similarity index 100%
rename from win32/deps/library/Matrix/doc/UFsparse/SPQR.txt
rename to win32/deps/library/Matrix/doc/SuiteSparse/SPQR.txt
diff --git a/win32/deps/library/Matrix/doc/SuiteSparse/SuiteSparse_config.txt b/win32/deps/library/Matrix/doc/SuiteSparse/SuiteSparse_config.txt
new file mode 100644
index 0000000..2dbaacd
--- /dev/null
+++ b/win32/deps/library/Matrix/doc/SuiteSparse/SuiteSparse_config.txt
@@ -0,0 +1,44 @@
+SuiteSparse_config, 2012, Timothy A. Davis, http://www.suitesparse.com
+(formerly the UFconfig package)
+
+SuiteSparse_config contains configuration settings for all many of the software
+packages that I develop or co-author. Note that older versions of some of
+these packages do not require SuiteSparse_config.
+
+ Package Description
+ ------- -----------
+ AMD approximate minimum degree ordering
+ CAMD constrained AMD
+ COLAMD column approximate minimum degree ordering
+ CCOLAMD constrained approximate minimum degree ordering
+ UMFPACK sparse LU factorization, with the BLAS
+ CXSparse int/long/real/complex version of CSparse
+ CHOLMOD sparse Cholesky factorization, update/downdate
+ KLU sparse LU factorization, BLAS-free
+ BTF permutation to block triangular form
+ LDL concise sparse LDL'
+ LPDASA LP Dual Active Set Algorithm
+ RBio read/write files in Rutherford/Boeing format
+ SPQR sparse QR factorization (full name: SuiteSparseQR)
+
+SuiteSparse_config is not required by these packages:
+
+ CSparse a Concise Sparse matrix package
+ MATLAB_Tools toolboxes for use in MATLAB
+
+In addition, the xerbla/ directory contains Fortan and C versions of the
+BLAS/LAPACK xerbla routine, which is called when an invalid input is passed to
+the BLAS or LAPACK. The xerbla provided here does not print any message, so
+the entire Fortran I/O library does not need to be linked into a C application.
+Most versions of the BLAS contain xerbla, but those from K. Goto do not. Use
+this if you need too.
+
+--------------------------------------------------------------------------------
+A note on the update to SuiteSparse Version 4.0.0: The SuiteSparse_long macro
+defines an integer that is 64-bits in size on 64-bit platforms, and 32-bits on
+32-bit platforms. It was formerly called UF_long, but UF_long has been removed
+because of potential name conflicts. UF_long is still available to user codes,
+but it can now be safely #undef'd in case of name conflicts in user code.
+Future codes should use SuiteSparse_long in place of UF_long.
+--------------------------------------------------------------------------------
+
diff --git a/win32/deps/library/Matrix/doc/UFsparse/UserGuides.txt b/win32/deps/library/Matrix/doc/SuiteSparse/UserGuides.txt
similarity index 100%
rename from win32/deps/library/Matrix/doc/UFsparse/UserGuides.txt
rename to win32/deps/library/Matrix/doc/SuiteSparse/UserGuides.txt
diff --git a/win32/deps/library/Matrix/doc/index.html b/win32/deps/library/Matrix/doc/index.html
index dd737cf..acbbc4f 100644
--- a/win32/deps/library/Matrix/doc/index.html
+++ b/win32/deps/library/Matrix/doc/index.html
@@ -1,18 +1,47 @@
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head><title>R: Matrix vignettes</title>
-<link rel="stylesheet" type="text/css" href="../../R.css">
+<html><head><title>R: Vignettes</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="/doc/html/R.css">
</head><body>
-<h2>Vignettes of package Matrix </h2>
-<dl>
-<dt><a href="Comparisons.pdf">Comparisons.pdf</a>:
-<dd> Comparisons of Least Squares calculation speeds
-<dt><a href="Design-issues.pdf">Design-issues.pdf</a>:
-<dd> Design Issues in Matrix package Development
-<dt><a href="Intro2Matrix.pdf">Intro2Matrix.pdf</a>:
-<dd> 2nd Introduction to the Matrix Package
-<dt><a href="Introduction.pdf">Introduction.pdf</a>:
-<dd> Introduction to the Matrix Package
-<dt><a href="sparseModels.pdf">sparseModels.pdf</a>:
-<dd> Sparse Model Matrices
-</dl>
+<h1> Vignettes
+<img class="toplogo" src="/doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="/doc/html/index.html"><img src="/doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div>
+<h2>Vignettes from package 'Matrix'</h2>
+<table width="100%">
+<col width="22%">
+<col width="2%">
+<col width="50%">
+<col width="8%">
+<col width="8%">
+<col width="8%">
+<tr><td align="right" valign="top"><a href="../../../library/Matrix/doc/Comparisons.pdf">Matrix::Comparisons</a></td>
+<td></td><td valign="top">Comparisons of Least Squares calculation speeds</td>
+<td valign="top"><a href="../../../library/Matrix/doc/Comparisons.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/Matrix/doc/Comparisons.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/Matrix/doc/Comparisons.R">R code</a></td></tr>
+<tr><td align="right" valign="top"><a href="../../../library/Matrix/doc/Design-issues.pdf">Matrix::Design-issues</a></td>
+<td></td><td valign="top">Design Issues in Matrix package Development</td>
+<td valign="top"><a href="../../../library/Matrix/doc/Design-issues.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/Matrix/doc/Design-issues.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/Matrix/doc/Design-issues.R">R code</a></td></tr>
+<tr><td align="right" valign="top"><a href="../../../library/Matrix/doc/Intro2Matrix.pdf">Matrix::Intro2Matrix</a></td>
+<td></td><td valign="top">2nd Introduction to the Matrix Package</td>
+<td valign="top"><a href="../../../library/Matrix/doc/Intro2Matrix.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/Matrix/doc/Intro2Matrix.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/Matrix/doc/Intro2Matrix.R">R code</a></td></tr>
+<tr><td align="right" valign="top"><a href="../../../library/Matrix/doc/Introduction.pdf">Matrix::Introduction</a></td>
+<td></td><td valign="top">Introduction to the Matrix Package</td>
+<td valign="top"><a href="../../../library/Matrix/doc/Introduction.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/Matrix/doc/Introduction.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/Matrix/doc/Introduction.R">R code</a></td></tr>
+<tr><td align="right" valign="top"><a href="../../../library/Matrix/doc/sparseModels.pdf">Matrix::sparseModels</a></td>
+<td></td><td valign="top">Sparse Model Matrices</td>
+<td valign="top"><a href="../../../library/Matrix/doc/sparseModels.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/Matrix/doc/sparseModels.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/Matrix/doc/sparseModels.R">R code</a></td></tr>
+</table>
</body></html>
diff --git a/win32/deps/library/Matrix/doc/sparseModels.R b/win32/deps/library/Matrix/doc/sparseModels.R
index dd4c3fe..3d3ff37 100644
--- a/win32/deps/library/Matrix/doc/sparseModels.R
+++ b/win32/deps/library/Matrix/doc/sparseModels.R
@@ -1,11 +1,13 @@
+### R code from vignette source 'sparseModels.Rnw'
+
###################################################
-### chunk number 1: preliminaries
+### code chunk number 1: preliminaries
###################################################
options(width=75)
###################################################
-### chunk number 2: ex1
+### code chunk number 2: ex1
###################################################
(ff <- factor(strsplit("statistics_is_a_task", "")[[1]], levels=c("_",letters)))
factor(ff) # drops the levels that do not occur
@@ -13,7 +15,7 @@ options(width=75)
###################################################
-### chunk number 3: ex1.2
+### code chunk number 3: ex1.2
###################################################
levels(f1)[match(c("c","k"), levels(f1))] <- "ck"
library(Matrix)
@@ -25,37 +27,35 @@ options(width=75)
###################################################
-### chunk number 4: as_factor_sparse
+### code chunk number 4: as_factor_sparse
###################################################
as(f1, "sparseMatrix")
###################################################
-### chunk number 5: contrasts_sub
+### code chunk number 5: contrasts_sub
###################################################
printSpMatrix( t( Matrix(contrasts(f1))[as.character(f1) ,] ),
col.names=TRUE)
###################################################
-### chunk number 6: ex1-model.matrix
+### code chunk number 6: ex1-model.matrix
###################################################
t( Matrix(model.matrix(~ 0+ f1))) # model with*OUT* intercept
###################################################
-### chunk number 7: chickwts-ex
+### code chunk number 7: chickwts-ex
###################################################
str(chickwts)# a standard R data set, 71 x 2
x.feed <- as(chickwts$feed, "sparseMatrix")
x.feed[ , (1:72)[c(TRUE,FALSE,FALSE)]] ## every 3rd column:
-## Provisional (hence unexported) sparse lm.fit():
-Matrix:::lm.fit.sparse(x = t(x.feed), y = chickwts[,1])
###################################################
-### chunk number 8: warpbreaks-data
+### code chunk number 8: warpbreaks-data
###################################################
data(warpbreaks)# a standard R data set
str(warpbreaks) # 2 x 3 (x 9) balanced two-way with 9 replicates:
@@ -63,7 +63,7 @@ xtabs(~ wool + tension, data = warpbreaks)
###################################################
-### chunk number 9: modMat-warpbreaks
+### code chunk number 9: modMat-warpbreaks
###################################################
tmm <- with(warpbreaks,
rBind(as(tension, "sparseMatrix"),
@@ -72,7 +72,7 @@ print( image(tmm) ) # print(.) the lattice object
###################################################
-### chunk number 10: morley-data
+### code chunk number 10: morley-data
###################################################
data(morley) # a standard R data set
morley$Expt <- factor(morley$Expt)
@@ -85,7 +85,7 @@ print( image(t.mm) ) # print(.) the lattice object
###################################################
-### chunk number 11: npk_ex
+### code chunk number 11: npk_ex
###################################################
data(npk, package="MASS")
@@ -99,7 +99,7 @@ t(M.npk) # easier to display, column names readably displayed as row.names(t(.))
###################################################
-### chunk number 12: aov-large-ex
+### code chunk number 12: aov-large-ex
###################################################
id <- factor(1:20)
a <- factor(1:2)
@@ -111,7 +111,7 @@ dim(aDat) # 120'000 x 5 (120'000 = 2*2*1500 * 20 = 6000 * 20)
###################################################
-### chunk number 13: aov-ex-X-sparse
+### code chunk number 13: aov-ex-X-sparse
###################################################
d2 <- factor(1:150) # 10 times smaller
tmp2 <- expand.grid(id=id, a=a, b=b, d=d2)
@@ -124,13 +124,24 @@ round(object.size(mm) / object.size(smm), 1)
###################################################
-### chunk number 14: X-sparse-image
+### code chunk number 14: X-sparse-image (eval = FALSE)
+###################################################
+## image(t(smm), aspect = 1/3, lwd=0, col.regions = "red")
+
+
+###################################################
+### code chunk number 15: X-sparse-image-fake
###################################################
-print( image(t(smm), aspect=1/3, col.regions= "red") ) # print(<lattice>)
+png("sparseModels-X-sparse-image.png", width=6, height=3,
+ units='in', res=150)
+print(
+image(t(smm), aspect = 1/3, lwd=0, col.regions = "red")
+ )
+dev.off()
###################################################
-### chunk number 15: X-sparse-mult
+### code chunk number 16: X-sparse-mult
###################################################
x <- 1:600
system.time(y <- smm %*% x) ## sparse is much faster
@@ -139,7 +150,7 @@ identical(as.matrix(y), y.) ## TRUE
###################################################
-### chunk number 16: sessionInfo
+### code chunk number 17: sessionInfo
###################################################
toLatex(sessionInfo())
diff --git a/win32/deps/library/Matrix/doc/sparseModels.Rnw b/win32/deps/library/Matrix/doc/sparseModels.Rnw
index c381186..4724843 100644
--- a/win32/deps/library/Matrix/doc/sparseModels.Rnw
+++ b/win32/deps/library/Matrix/doc/sparseModels.Rnw
@@ -7,10 +7,7 @@
\newcommand{\noFootnote}[1]{{\small (\textit{#1})}}
\newcommand{\myOp}[1]{{$\left\langle\ensuremath{#1}\right\rangle$}}
%%\VignetteIndexEntry{Sparse Model Matrices}
-%%\VignetteDepends{Matrix}
-\SweaveOpts{engine=R, keep.source=TRUE}
-% ^^^^^^^^^^^^^^^^
-\SweaveOpts{eps=FALSE, pdf=TRUE, width=5, height=3, strip.white=TRUE}
+%%\VignetteDepends{Matrix,MASS}
\title{Sparse Model Matrices}
\author{Martin Maechler\\ R Core Development Team
\\\email{maechler R-project org}}
@@ -18,6 +15,9 @@
%
\begin{document}
\maketitle
+\SweaveOpts{engine=R, keep.source=TRUE}
+\SweaveOpts{eps=FALSE, pdf=TRUE, width=8, height=5.5, strip.white=true}
+\setkeys{Gin}{width=\textwidth}
% \begin{abstract}
% ............................ FIXME
@@ -94,9 +94,11 @@ str(chickwts)# a standard R data set, 71 x 2
x.feed <- as(chickwts$feed, "sparseMatrix")
x.feed[ , (1:72)[c(TRUE,FALSE,FALSE)]] ## every 3rd column:
-## Provisional (hence unexported) sparse lm.fit():
-Matrix:::lm.fit.sparse(x = t(x.feed), y = chickwts[,1])
@
+% FIXME: Move this to ../../../MatrixModels/inst/doc/ ???
+% ## Provisional (hence unexported) sparse lm.fit():
+% Matrix:::lm.fit.sparse(x = t(x.feed), y = chickwts[,1])
+
%- for emacs: $
@@ -104,22 +106,22 @@ Matrix:::lm.fit.sparse(x = t(x.feed), y = chickwts[,1])
To create the model matrix for the case of one factor and one continuous
predictor---called ``analysis of covariance'' in the historical literature---
-we can adopt the following simple scheme:
+we can adopt the following simple scheme.
%% Possible examples:
%% - Puromycin
%% - ToothGrowth
---- FIXME ---
+%--- FIXME ---
-The final model matrix is the catenation of
+The final model matrix is the concatenation of:
-1) create the sparse 0-1 matrix \code{m1} from the factor -- == f1 main-effect
+1) create the sparse 0-1 matrix \code{m1} from the f1 main-effect
2) the single row/column 'x' == 'x' main-effect
3) replacing the values 1 in \code{m1 x} (the x-slot of the factor model matrix),
- by the values of \code{x} (our continuous predictor)
+ by the values of \code{x} (our continuous predictor).
\section{Two (or more) factors, main effects only: \texttt{y $\sim$ f1 + f2}}
@@ -132,9 +134,10 @@ str(warpbreaks) # 2 x 3 (x 9) balanced two-way with 9 replicates:
xtabs(~ wool + tension, data = warpbreaks)
@
-It is \emph{not} statistically sensible to assume that \code{Run} is a
-fixed effect, however the example is handy to depict how a model matrix
-would be built for the model \code{Speed ~ Expt + Run}.
+%It is \emph{not} statistically sensible to assume that \code{Run} is a
+%fixed effect, however the example is handy to depict how a model matrix
+This example depicts how a model matrix
+would be built for the model \code{breaks ~ wool + tension}.
Since this is a main effects model (no interactions), the desired model
matrix is simply the concatenation of the model matrices of the main
effects. There are two here, but the principle applies to general main
@@ -194,17 +197,16 @@ t(M.npk) # easier to display, column names readably displayed as row.names(t(.))
@
%% printSpMatrix(M.npk, col.names = "abb1")
-An other example is the it seems realistic situation of a user who
-enquired on R-help (July 15, 2008,
+Another example was reported by a user on R-help (July 15, 2008,
{\small \url{https://stat.ethz.ch/pipermail/r-help/2008-July/167772.html}})
-about an ``aov error with large data set'':
+about an ``aov error with large data set''.
-\begin{citation}
- I'm looking to analyze a large data set: a within-Ss 2*2*1500 design
- with 20 Ss. However, aov() gives me an error, reproducible as follows:
+\begin{citation} % RAS: in my PDF, I don't see the first character I
+I'm looking to analyze a large data set: a within-Ss 2*2*1500 design
+with 20 Ss. However, aov() gives me an error. %, reproducible as follows:
\end{citation}
-and gave the following code example (slightly edited):
+And gave the following code example (slightly edited):
<<aov-large-ex>>=
id <- factor(1:20)
a <- factor(1:2)
@@ -219,14 +221,12 @@ and then continued with
\begin{Sinput}
m.aov <- aov(y ~ a*b*d + Error(id/(a*b*d)), data=aDat)
\end{Sinput}
-which
+
\begin{citation}\sffamily
- yields the following error:\\
- "\\ \ttfamily
+ which yields the following error:\\
+ \ttfamily
Error in model.matrix.default(mt, mf, contrasts) :\\
allocMatrix: too many elements specified\\
- "
- Any suggestions?
\end{citation}
to which he got the explanation by Peter Dalgaard that the formal model matrix involved
was much too large in this case, and that PD assumed, \pkg{lme4} would be
@@ -261,19 +261,24 @@ round(object.size(mm) / object.size(smm), 1)
shows that even for the small \code{d} here, the memory reduction would be
more than an order of magnitude.
\\
-<<X-sparse-image, fig=TRUE>>=
-print( image(t(smm), aspect=1/3, col.regions= "red") ) # print(<lattice>)
+%% Reasons to fake here:
+%% 1) print() is needed for lattice -- but looks ugly,
+%% 2) the resulting pdf file is too large -- use png instead:
+<<X-sparse-image, eval=FALSE>>=
+image(t(smm), aspect = 1/3, lwd=0, col.regions = "red")
+<<X-sparse-image-fake, fig=TRUE, include=FALSE, echo=FALSE, results=hide, keep.source=FALSE>>=
+png("sparseModels-X-sparse-image.png", width=6, height=3,
+ units='in', res=150)
+print(
+<<X-sparse-image>>
+ )
+dev.off()
@
-% % print() is needed for lattice -- but looks ugly, hence
-% <<X-sparse-image-fake, fig=TRUE, include=FALSE, echo=FALSE, results=hide>>=
-% print( image(t(smm), aspect=1/3, lwd=0, col.regions = "red") )
-% @
-% <<X-sparse-image, eval=FALSE>>=
-% image(t(smm), aspect=3, lwd=0, col.r = "red")
-% @
-% \includegraphics{sparseModels-X-sparse-image-fake}
-%
-\\
+%%--NB: 'keep.source=FALSE' above is workaround-a-bug-in-R-devel-(2.13.x)---
+\par\vspace*{-1ex}
+\centerline{%
+ \includegraphics[width=1.1\textwidth]{sparseModels-X-sparse-image.png}}
+
and working with the sparse instead of the dense model matrix is
considerably faster as well,
<<X-sparse-mult>>=
diff --git a/win32/deps/library/Matrix/doc/sparseModels.pdf b/win32/deps/library/Matrix/doc/sparseModels.pdf
index 94be0c0..c6bb76d 100644
Binary files a/win32/deps/library/Matrix/doc/sparseModels.pdf and b/win32/deps/library/Matrix/doc/sparseModels.pdf differ
diff --git a/win32/deps/library/Matrix/help/AnIndex b/win32/deps/library/Matrix/help/AnIndex
index d8630af..78d550a 100644
--- a/win32/deps/library/Matrix/help/AnIndex
+++ b/win32/deps/library/Matrix/help/AnIndex
@@ -10,6 +10,7 @@
!,nsparseMatrix-method nsparseMatrix-classes
!,ntpMatrix-method ntrMatrix-class
!,ntrMatrix-method ntrMatrix-class
+!,sparseVector-method sparseVector-class
%%,ddiMatrix,ddenseMatrix-method diagonalMatrix-class
%%,ddiMatrix,ldenseMatrix-method diagonalMatrix-class
%%,ddiMatrix,Matrix-method diagonalMatrix-class
@@ -49,11 +50,14 @@
%*%,diagonalMatrix,matrix-method diagonalMatrix-class
%*%,diagonalMatrix,sparseMatrix-method diagonalMatrix-class
%*%,dMatrix,integer-method dMatrix-class
+%*%,dMatrix,lMatrix-method dMatrix-class
+%*%,dMatrix,nMatrix-method dMatrix-class
%*%,dsparseMatrix,ddenseMatrix-method dsparseMatrix-class
%*%,dsparseMatrix,dgeMatrix-method dsparseMatrix-class
%*%,dspMatrix,ddenseMatrix-method dsyMatrix-class
%*%,dspMatrix,matrix-method dsyMatrix-class
%*%,dsyMatrix,ddenseMatrix-method dsyMatrix-class
+%*%,dsyMatrix,dsyMatrix-method dsyMatrix-class
%*%,dsyMatrix,matrix-method dsyMatrix-class
%*%,dtpMatrix,ddenseMatrix-method dtpMatrix-class
%*%,dtpMatrix,matrix-method dtpMatrix-class
@@ -64,6 +68,9 @@
%*%,ldenseMatrix,lsparseMatrix-method lsparseMatrix-classes
%*%,lgCMatrix,lgCMatrix-method lsparseMatrix-classes
%*%,lgeMatrix,diagonalMatrix-method diagonalMatrix-class
+%*%,lMatrix,dMatrix-method dMatrix-class
+%*%,lMatrix,lMatrix-method dMatrix-class
+%*%,lMatrix,nMatrix-method dMatrix-class
%*%,lsparseMatrix,ldenseMatrix-method lsparseMatrix-classes
%*%,lsparseMatrix,lsparseMatrix-method lsparseMatrix-classes
%*%,Matrix,ANY-method Matrix-class
@@ -83,6 +90,9 @@
%*%,Matrix,TsparseMatrix-method TsparseMatrix-class
%*%,ndenseMatrix,nsparseMatrix-method nsparseMatrix-classes
%*%,ngCMatrix,ngCMatrix-method nsparseMatrix-classes
+%*%,nMatrix,dMatrix-method dMatrix-class
+%*%,nMatrix,lMatrix-method dMatrix-class
+%*%,nMatrix,nMatrix-method dMatrix-class
%*%,nsparseMatrix,ndenseMatrix-method nsparseMatrix-classes
%*%,nsparseMatrix,nsparseMatrix-method nsparseMatrix-classes
%*%,numeric,CsparseMatrix-method CsparseMatrix-class
@@ -96,6 +106,7 @@
%*%,sparseVector,Matrix-method sparseVector-class
%*%,TsparseMatrix,ANY-method TsparseMatrix-class
%*%,TsparseMatrix,Matrix-method TsparseMatrix-class
+%*%,TsparseMatrix,TsparseMatrix-method TsparseMatrix-class
%/%,ddiMatrix,ddenseMatrix-method diagonalMatrix-class
%/%,ddiMatrix,ldenseMatrix-method diagonalMatrix-class
%/%,ddiMatrix,Matrix-method diagonalMatrix-class
@@ -138,13 +149,21 @@
*,ndenseMatrix,ldiMatrix-method diagonalMatrix-class
+,dgTMatrix,dgTMatrix-method dgTMatrix-class
+,Matrix,missing-method Matrix-class
+-,ddiMatrix,missing-method diagonalMatrix-class
+-,denseMatrix,missing-method denseMatrix-class
-,dsparseVector,missing-method sparseVector-class
+-,ldiMatrix,missing-method diagonalMatrix-class
-,lsparseMatrix,missing-method lsparseMatrix-classes
-,Matrix,missing-method Matrix-class
-,nsparseMatrix,missing-method nsparseMatrix-classes
-,pMatrix,missing-method pMatrix-class
-,sparseMatrix,missing-method sparseMatrix-class
+.bdiag bdiag
+.diagU2N diagU2N
+.formatSparseSimple formatSparseM
+.sparseDiagonal Diagonal
.symDiagonal Diagonal
+.updateCHMfactor CHMfactor-class
.validateCsparse CsparseMatrix-class
/,ddiMatrix,ddenseMatrix-method diagonalMatrix-class
/,ddiMatrix,ldenseMatrix-method diagonalMatrix-class
@@ -154,6 +173,9 @@
/,ldiMatrix,ldenseMatrix-method diagonalMatrix-class
/,ldiMatrix,Matrix-method diagonalMatrix-class
/,ldiMatrix,ndenseMatrix-method diagonalMatrix-class
+abIndex-class abIndex-class
+abIseq abIseq
+abIseq1 abIseq
all,ddiMatrix-method diagonalMatrix-class
all,ldenseMatrix-method all-methods
all,ldiMatrix-method diagonalMatrix-class
@@ -162,11 +184,14 @@ all,lsyMatrix-method all-methods
all,Matrix-method all-methods
all,nsparseMatrix-method nsparseMatrix-classes
all-methods all-methods
+all.equal,abIndex,abIndex-method all.equal-methods
+all.equal,abIndex,numLike-method all.equal-methods
all.equal,ANY,Matrix-method all.equal-methods
all.equal,ANY,sparseMatrix-method all.equal-methods
all.equal,ANY,sparseVector-method all.equal-methods
all.equal,Matrix,ANY-method all.equal-methods
all.equal,Matrix,Matrix-method all.equal-methods
+all.equal,numLike,abIndex-method all.equal-methods
all.equal,sparseMatrix,ANY-method all.equal-methods
all.equal,sparseMatrix,sparseMatrix-method all.equal-methods
all.equal,sparseMatrix,sparseVector-method all.equal-methods
@@ -179,29 +204,56 @@ any,ldiMatrix-method diagonalMatrix-class
any,lMatrix-method all-methods
any,Matrix-method all-methods
any,nsparseMatrix-method nsparseMatrix-classes
+Arith,abIndex,abIndex-method abIndex-class
+Arith,abIndex,numLike-method abIndex-class
Arith,CsparseMatrix,CsparseMatrix-method CsparseMatrix-class
Arith,CsparseMatrix,numeric-method CsparseMatrix-class
Arith,ddenseMatrix,ddenseMatrix-method ddenseMatrix-class
+Arith,ddenseMatrix,logical-method ddenseMatrix-class
Arith,ddenseMatrix,numeric-method ddenseMatrix-class
+Arith,ddenseMatrix,sparseVector-method sparseVector-class
+Arith,ddiMatrix,logical-method diagonalMatrix-class
Arith,ddiMatrix,numeric-method diagonalMatrix-class
Arith,dgCMatrix,dgCMatrix-method dgCMatrix-class
+Arith,dgCMatrix,logical-method dgCMatrix-class
Arith,dgCMatrix,numeric-method dgCMatrix-class
Arith,dgeMatrix,dgeMatrix-method dgeMatrix-class
+Arith,dgeMatrix,logical-method dgeMatrix-class
Arith,dgeMatrix,numeric-method dgeMatrix-class
+Arith,dgeMatrix,sparseVector-method sparseVector-class
Arith,dMatrix,dMatrix-method dMatrix-class
+Arith,dpoMatrix,logical-method dpoMatrix-class
+Arith,dpoMatrix,numeric-method dpoMatrix-class
+Arith,dppMatrix,logical-method dpoMatrix-class
+Arith,dppMatrix,numeric-method dpoMatrix-class
Arith,dsCMatrix,dsCMatrix-method dsCMatrix-class
+Arith,dsparseMatrix,logical-method dsparseMatrix-class
+Arith,dsparseMatrix,numeric-method dsparseMatrix-class
Arith,dsparseVector,dsparseVector-method sparseVector-class
Arith,dtCMatrix,dtCMatrix-method dtCMatrix-class
+Arith,ldiMatrix,logical-method diagonalMatrix-class
Arith,ldiMatrix,numeric-method diagonalMatrix-class
Arith,lgCMatrix,lgCMatrix-method lsparseMatrix-classes
Arith,lgeMatrix,lgeMatrix-method lgeMatrix-class
Arith,lgTMatrix,lgTMatrix-method lsparseMatrix-classes
+Arith,lMatrix,logical-method dMatrix-class
Arith,lMatrix,numeric-method dMatrix-class
+Arith,logical,ddenseMatrix-method ddenseMatrix-class
+Arith,logical,ddiMatrix-method diagonalMatrix-class
+Arith,logical,dgCMatrix-method dgCMatrix-class
+Arith,logical,dgeMatrix-method dgeMatrix-class
+Arith,logical,dpoMatrix-method dpoMatrix-class
+Arith,logical,dppMatrix-method dpoMatrix-class
+Arith,logical,dsparseMatrix-method dsparseMatrix-class
+Arith,logical,ldiMatrix-method diagonalMatrix-class
+Arith,logical,lMatrix-method dMatrix-class
+Arith,logical,nMatrix-method nMatrix-class
Arith,lsparseMatrix,Matrix-method lsparseMatrix-classes
Arith,Matrix,lsparseMatrix-method lsparseMatrix-classes
Arith,Matrix,Matrix-method Matrix-class
Arith,Matrix,nsparseMatrix-method nsparseMatrix-classes
Arith,ngeMatrix,ngeMatrix-method ngeMatrix-class
+Arith,nMatrix,logical-method nMatrix-class
Arith,nMatrix,numeric-method nMatrix-class
Arith,nsparseMatrix,Matrix-method nsparseMatrix-classes
Arith,numeric,CsparseMatrix-method CsparseMatrix-class
@@ -209,18 +261,30 @@ Arith,numeric,ddenseMatrix-method ddenseMatrix-class
Arith,numeric,ddiMatrix-method diagonalMatrix-class
Arith,numeric,dgCMatrix-method dgCMatrix-class
Arith,numeric,dgeMatrix-method dgeMatrix-class
+Arith,numeric,dpoMatrix-method dpoMatrix-class
+Arith,numeric,dppMatrix-method dpoMatrix-class
+Arith,numeric,dsparseMatrix-method dsparseMatrix-class
Arith,numeric,ldiMatrix-method diagonalMatrix-class
Arith,numeric,lMatrix-method dMatrix-class
Arith,numeric,nMatrix-method nMatrix-class
+Arith,numLike,abIndex-method abIndex-class
+Arith,sparseVector,ddenseMatrix-method sparseVector-class
+Arith,sparseVector,dgeMatrix-method sparseVector-class
Arith,sparseVector,sparseVector-method sparseVector-class
+Arith,triangularMatrix,diagonalMatrix-method diagonalMatrix-class
as.array,Matrix-method Matrix-class
+as.integer,abIndex-method abIndex-class
as.logical,ldenseMatrix-method ldenseMatrix-class
as.logical,Matrix-method Matrix-class
as.logical,ndenseMatrix-method ndenseMatrix-class
+as.logical,sparseVector-method sparseVector-class
as.matrix,Matrix-method Matrix-class
+as.numeric,abIndex-method abIndex-class
as.numeric,ddenseMatrix-method ddenseMatrix-class
as.numeric,Matrix-method Matrix-class
as.numeric,sparseVector-method sparseVector-class
+as.vector,abIndex,ANY-method abIndex-class
+as.vector,abIndex,character-method abIndex-class
as.vector,dgeMatrix,missing-method dgeMatrix-class
as.vector,diagonalMatrix,missing-method diagonalMatrix-class
as.vector,ldenseMatrix,missing-method ldenseMatrix-class
@@ -246,6 +310,7 @@ BunchKaufman,dspMatrix-method BunchKaufman-methods
BunchKaufman,dsyMatrix-method BunchKaufman-methods
BunchKaufman-class Cholesky-class
BunchKaufman-methods BunchKaufman-methods
+c.abIndex abIseq
CAex CAex
cBind cBind
cbind2,ANY,Matrix-method Matrix-class
@@ -257,6 +322,7 @@ cbind2,ddiMatrix,matrix-method diagonalMatrix-class
cbind2,denseMatrix,denseMatrix-method denseMatrix-class
cbind2,denseMatrix,matrix-method denseMatrix-class
cbind2,denseMatrix,numeric-method denseMatrix-class
+cbind2,denseMatrix,sparseMatrix-method sparseMatrix-class
cbind2,diagonalMatrix,sparseMatrix-method diagonalMatrix-class
cbind2,ldiMatrix,atomicVector-method diagonalMatrix-class
cbind2,ldiMatrix,matrix-method diagonalMatrix-class
@@ -272,6 +338,7 @@ cbind2,matrix,sparseMatrix-method sparseMatrix-class
cbind2,NULL,Matrix-method Matrix-class
cbind2,numeric,denseMatrix-method denseMatrix-class
cbind2,numeric,sparseMatrix-method sparseMatrix-class
+cbind2,sparseMatrix,denseMatrix-method sparseMatrix-class
cbind2,sparseMatrix,diagonalMatrix-method diagonalMatrix-class
cbind2,sparseMatrix,matrix-method sparseMatrix-class
cbind2,sparseMatrix,numeric-method sparseMatrix-class
@@ -286,15 +353,19 @@ chol,dgeMatrix-method chol
chol,dpoMatrix-method chol
chol,dppMatrix-method chol
chol,dsCMatrix-method chol
-chol,dsCMatrix-method chol
chol,dsparseMatrix-method chol
chol,ldiMatrix-method chol
chol,lsCMatrix-method chol
-chol,lsCMatrix-method chol
chol,Matrix-method chol
chol,nsCMatrix-method chol
-chol,nsCMatrix-method chol
chol-methods chol
+chol2inv,ANY-method chol2inv-methods
+chol2inv,CHMfactor-method chol2inv-methods
+chol2inv,denseMatrix-method chol2inv-methods
+chol2inv,diagonalMatrix-method diagonalMatrix-class
+chol2inv,dtrMatrix-method chol2inv-methods
+chol2inv,sparseMatrix-method chol2inv-methods
+chol2inv-methods chol2inv-methods
Cholesky Cholesky
Cholesky,CsparseMatrix-method Cholesky
Cholesky,dsCMatrix-method Cholesky
@@ -302,7 +373,13 @@ Cholesky,Matrix-method Cholesky
Cholesky,nsparseMatrix-method Cholesky
Cholesky,sparseMatrix-method Cholesky
Cholesky-class Cholesky-class
+CholeskyFactorization-class MatrixFactorization-class
+coerce,abIndex,integer-method abIndex-class
+coerce,abIndex,numeric-method abIndex-class
+coerce,abIndex,seqMat-method abIndex-class
+coerce,abIndex,vector-method abIndex-class
coerce,ANY,denseMatrix-method denseMatrix-class
+coerce,ANY,nsparseVector-method sparseVector-class
coerce,ANY,sparseMatrix-method sparseMatrix-class
coerce,ANY,sparseVector-method sparseVector-class
coerce,atomicVector,dsparseVector-method sparseVector-class
@@ -321,14 +398,15 @@ coerce,CsparseMatrix,matrix.csc-method SparseM-conv
coerce,CsparseMatrix,matrix.csr-method SparseM-conv
coerce,CsparseMatrix,nMatrix-method CsparseMatrix-class
coerce,CsparseMatrix,nsparseMatrix-method CsparseMatrix-class
+coerce,CsparseMatrix,sparseVector-method sparseVector-class
coerce,CsparseMatrix,symmetricMatrix-method symmetricMatrix-class
coerce,CsparseMatrix,TsparseMatrix-method CsparseMatrix-class
-coerce,ddenseMatrix,CsparseMatrix-method ddenseMatrix-class
coerce,ddenseMatrix,dgeMatrix-method ddenseMatrix-class
coerce,ddenseMatrix,matrix-method ddenseMatrix-class
coerce,ddiMatrix,CsparseMatrix-method diagonalMatrix-class
coerce,ddiMatrix,ddenseMatrix-method diagonalMatrix-class
coerce,ddiMatrix,dgeMatrix-method diagonalMatrix-class
+coerce,ddiMatrix,dsparseMatrix-method diagonalMatrix-class
coerce,ddiMatrix,symmetricMatrix-method diagonalMatrix-class
coerce,ddiMatrix,triangularMatrix-method diagonalMatrix-class
coerce,ddiMatrix,TsparseMatrix-method diagonalMatrix-class
@@ -378,9 +456,11 @@ coerce,dpoMatrix,corMatrix-method dpoMatrix-class
coerce,dpoMatrix,dppMatrix-method dpoMatrix-class
coerce,dpoMatrix,lMatrix-method dpoMatrix-class
coerce,dpoMatrix,nMatrix-method dpoMatrix-class
+coerce,dppMatrix,CsparseMatrix-method dpoMatrix-class
coerce,dppMatrix,dpoMatrix-method dpoMatrix-class
coerce,dppMatrix,lMatrix-method dpoMatrix-class
coerce,dppMatrix,nMatrix-method dpoMatrix-class
+coerce,dppMatrix,sparseMatrix-method dpoMatrix-class
coerce,dsCMatrix,dgCMatrix-method dsCMatrix-class
coerce,dsCMatrix,dgeMatrix-method dsCMatrix-class
coerce,dsCMatrix,dgTMatrix-method dsCMatrix-class
@@ -392,11 +472,13 @@ coerce,dsCMatrix,lsCMatrix-method dsCMatrix-class
coerce,dsCMatrix,matrix-method dsCMatrix-class
coerce,dsCMatrix,nsCMatrix-method dsCMatrix-class
coerce,dsparseMatrix,matrix.csr-method SparseM-conv
+coerce,dspMatrix,CsparseMatrix-method dsyMatrix-class
coerce,dspMatrix,dpoMatrix-method dpoMatrix-class
coerce,dspMatrix,dppMatrix-method dpoMatrix-class
coerce,dspMatrix,dsyMatrix-method dsyMatrix-class
coerce,dspMatrix,lspMatrix-method dsyMatrix-class
coerce,dspMatrix,matrix-method dsyMatrix-class
+coerce,dspMatrix,sparseMatrix-method dsyMatrix-class
coerce,dsTMatrix,dgeMatrix-method dsCMatrix-class
coerce,dsTMatrix,dgTMatrix-method dsCMatrix-class
coerce,dsTMatrix,dsCMatrix-method dsCMatrix-class
@@ -438,6 +520,7 @@ coerce,dtTMatrix,matrix-method dtCMatrix-class
coerce,factor,dgCMatrix-method dgCMatrix-class
coerce,factor,sparseMatrix-method sparseMatrix-class
coerce,graph,CsparseMatrix-method sparseMatrix-class
+coerce,graph,Matrix-method sparseMatrix-class
coerce,graph,sparseMatrix-method sparseMatrix-class
coerce,graphAM,sparseMatrix-method sparseMatrix-class
coerce,graphNEL,CsparseMatrix-method sparseMatrix-class
@@ -449,6 +532,7 @@ coerce,ldiMatrix,CsparseMatrix-method diagonalMatrix-class
coerce,ldiMatrix,ldenseMatrix-method diagonalMatrix-class
coerce,ldiMatrix,lgCMatrix-method ldiMatrix-class
coerce,ldiMatrix,lgTMatrix-method ldiMatrix-class
+coerce,ldiMatrix,lsparseMatrix-method diagonalMatrix-class
coerce,ldiMatrix,symmetricMatrix-method diagonalMatrix-class
coerce,ldiMatrix,triangularMatrix-method diagonalMatrix-class
coerce,ldiMatrix,TsparseMatrix-method diagonalMatrix-class
@@ -476,6 +560,7 @@ coerce,lgTMatrix,matrix-method lsparseMatrix-classes
coerce,lMatrix,dgCMatrix-method dMatrix-class
coerce,lMatrix,dMatrix-method dMatrix-class
coerce,lMatrix,nMatrix-method nMatrix-class
+coerce,logical,abIndex-method abIndex-class
coerce,lsCMatrix,dgTMatrix-method lsparseMatrix-classes
coerce,lsCMatrix,dsCMatrix-method lsparseMatrix-classes
coerce,lsCMatrix,generalMatrix-method lsparseMatrix-classes
@@ -641,6 +726,10 @@ coerce,nsCMatrix,matrix-method nsparseMatrix-classes
coerce,nsCMatrix,ngCMatrix-method nsparseMatrix-classes
coerce,nsCMatrix,nsTMatrix-method nsparseMatrix-classes
coerce,nsparseMatrix,dsparseMatrix-method nsparseMatrix-classes
+coerce,nsparseVector,dsparseVector-method sparseVector-class
+coerce,nsparseVector,isparseVector-method sparseVector-class
+coerce,nsparseVector,lsparseVector-method sparseVector-class
+coerce,nsparseVector,zsparseVector-method sparseVector-class
coerce,nspMatrix,dspMatrix-method nsyMatrix-class
coerce,nspMatrix,lspMatrix-method ndenseMatrix-class
coerce,nspMatrix,ngeMatrix-method nsyMatrix-class
@@ -679,8 +768,10 @@ coerce,ntTMatrix,ngCMatrix-method nsparseMatrix-classes
coerce,ntTMatrix,ngTMatrix-method nsparseMatrix-classes
coerce,ntTMatrix,ntCMatrix-method nsparseMatrix-classes
coerce,ntTMatrix,ntrMatrix-method nsparseMatrix-classes
+coerce,numeric,abIndex-method abIndex-class
coerce,numeric,CsparseMatrix-method CsparseMatrix-class
coerce,numeric,pMatrix-method pMatrix-class
+coerce,numeric,seqMat-method abIndex-class
coerce,numeric,TsparseMatrix-method TsparseMatrix-class
coerce,pBunchKaufman,lMatrix-method Cholesky-class
coerce,pCholesky,lMatrix-method Cholesky-class
@@ -706,16 +797,26 @@ coerce,RsparseMatrix,matrix-method RsparseMatrix-class
coerce,RsparseMatrix,nMatrix-method RsparseMatrix-class
coerce,RsparseMatrix,nsparseMatrix-method RsparseMatrix-class
coerce,RsparseMatrix,TsparseMatrix-method RsparseMatrix-class
+coerce,seqMat,abIndex-method abIndex-class
+coerce,seqMat,numeric-method abIndex-class
coerce,sparseMatrix,generalMatrix-method sparseMatrix-class
coerce,sparseMatrix,graph-method sparseMatrix-class
coerce,sparseMatrix,graphNEL-method sparseMatrix-class
+coerce,sparseMatrix,pMatrix-method pMatrix-class
coerce,sparseMatrix,RsparseMatrix-method RsparseMatrix-class
coerce,sparseMatrix,sparseVector-method sparseVector-class
coerce,sparseMatrix,symmetricMatrix-method sparseMatrix-class
coerce,sparseMatrix,triangularMatrix-method sparseMatrix-class
+coerce,sparseVector,CsparseMatrix-method sparseVector-class
+coerce,sparseVector,integer-method sparseVector-class
+coerce,sparseVector,logical-method sparseVector-class
+coerce,sparseVector,Matrix-method sparseVector-class
+coerce,sparseVector,numeric-method sparseVector-class
+coerce,sparseVector,sparseMatrix-method sparseVector-class
+coerce,sparseVector,TsparseMatrix-method sparseVector-class
coerce,sparseVector,vector-method sparseVector-class
+coerce,table,sparseMatrix-method sparseMatrix-class
coerce,triangularMatrix,symmetricMatrix-method triangularMatrix-class
-coerce,triangularVector,sparseVector-method sparseVector-class
coerce,TsparseMatrix,CsparseMatrix-method TsparseMatrix-class
coerce,TsparseMatrix,graphNEL-method sparseMatrix-class
coerce,TsparseMatrix,lMatrix-method TsparseMatrix-class
@@ -735,6 +836,7 @@ colMeans,ddenseMatrix-method colSums
colMeans,denseMatrix-method colSums
colMeans,dgCMatrix-method colSums
colMeans,dgeMatrix-method dgeMatrix-class
+colMeans,diagonalMatrix-method colSums
colMeans,igCMatrix-method colSums
colMeans,lgCMatrix-method colSums
colMeans,ngCMatrix-method colSums
@@ -746,24 +848,32 @@ colSums,ddenseMatrix-method colSums
colSums,denseMatrix-method colSums
colSums,dgCMatrix-method colSums
colSums,dgeMatrix-method dgeMatrix-class
+colSums,diagonalMatrix-method colSums
colSums,igCMatrix-method colSums
colSums,lgCMatrix-method colSums
colSums,ngCMatrix-method colSums
colSums,RsparseMatrix-method colSums
colSums,TsparseMatrix-method colSums
Compare,CsparseMatrix,CsparseMatrix-method CsparseMatrix-class
+Compare,dMatrix,logical-method dMatrix-class
Compare,dMatrix,numeric-method dMatrix-class
Compare,lgeMatrix,lgeMatrix-method lgeMatrix-class
+Compare,lMatrix,logical-method dMatrix-class
+Compare,lMatrix,numeric-method dMatrix-class
+Compare,logical,dMatrix-method dMatrix-class
+Compare,logical,lMatrix-method dMatrix-class
+Compare,logical,nMatrix-method nMatrix-class
Compare,lsparseMatrix,lsparseMatrix-method lsparseMatrix-classes
Compare,ngeMatrix,ngeMatrix-method ngeMatrix-class
+Compare,nMatrix,logical-method nMatrix-class
Compare,nMatrix,nMatrix-method nMatrix-class
+Compare,nMatrix,numeric-method nMatrix-class
Compare,numeric,dMatrix-method dMatrix-class
+Compare,numeric,lMatrix-method dMatrix-class
+Compare,numeric,nMatrix-method nMatrix-class
+Compare,triangularMatrix,diagonalMatrix-method diagonalMatrix-class
compMatrix-class compMatrix-class
-contr.helmert contrast
-contr.poly contrast
-contr.SAS contrast
-contr.sum contrast
-contr.treatment contrast
+condest condest
corMatrix-class dpoMatrix-class
cov2cor,Matrix-method Matrix-class
cov2cor,sparseMatrix-method sparseMatrix-class
@@ -776,6 +886,7 @@ crossprod,CsparseMatrix,matrix-method CsparseMatrix-class
crossprod,CsparseMatrix,missing-method CsparseMatrix-class
crossprod,CsparseMatrix,numeric-method CsparseMatrix-class
crossprod,ddenseMatrix,CsparseMatrix-method CsparseMatrix-class
+crossprod,ddenseMatrix,dgCMatrix-method ddenseMatrix-class
crossprod,ddenseMatrix,dsparseMatrix-method dsparseMatrix-class
crossprod,ddenseMatrix,missing-method ddenseMatrix-class
crossprod,dgCMatrix,dgeMatrix-method dgCMatrix-class
@@ -799,6 +910,9 @@ crossprod,diagonalMatrix,sparseMatrix-method diagonalMatrix-class
crossprod,dMatrix,integer-method dMatrix-class
crossprod,dsparseMatrix,ddenseMatrix-method dsparseMatrix-class
crossprod,dsparseMatrix,dgeMatrix-method dsparseMatrix-class
+crossprod,dtrMatrix,ddenseMatrix-method dtrMatrix-class
+crossprod,dtrMatrix,dtrMatrix-method dtrMatrix-class
+crossprod,dtrMatrix,matrix-method dtrMatrix-class
crossprod,dtrMatrix,missing-method dtrMatrix-class
crossprod,integer,dMatrix-method dMatrix-class
crossprod,ldenseMatrix,lsparseMatrix-method lsparseMatrix-classes
@@ -814,6 +928,7 @@ crossprod,matrix,dgeMatrix-method dgeMatrix-class
crossprod,Matrix,Matrix-method Matrix-class
crossprod,Matrix,matrix-method Matrix-class
crossprod,matrix,Matrix-method Matrix-class
+crossprod,Matrix,missing-method Matrix-class
crossprod,Matrix,numeric-method Matrix-class
crossprod,Matrix,sparseVector-method sparseVector-class
crossprod,Matrix,TsparseMatrix-method TsparseMatrix-class
@@ -826,12 +941,16 @@ crossprod,nsparseMatrix,nsparseMatrix-method nsparseMatrix-classes
crossprod,nsparseMatrix-method nsparseMatrix-classes
crossprod,numeric,dgeMatrix-method dgeMatrix-class
crossprod,numeric,Matrix-method Matrix-class
+crossprod,pMatrix,Matrix-method pMatrix-class
+crossprod,pMatrix,matrix-method pMatrix-class
crossprod,pMatrix,missing-method pMatrix-class
+crossprod,pMatrix,pMatrix-method pMatrix-class
crossprod,sparseMatrix,diagonalMatrix-method diagonalMatrix-class
crossprod,sparseVector,Matrix-method sparseVector-class
crossprod,TsparseMatrix,ANY-method TsparseMatrix-class
crossprod,TsparseMatrix,Matrix-method TsparseMatrix-class
crossprod,TsparseMatrix,missing-method TsparseMatrix-class
+crossprod,TsparseMatrix,TsparseMatrix-method TsparseMatrix-class
CsparseMatrix-class CsparseMatrix-class
dCHMsimpl-class CHMfactor-class
dCHMsuper-class CHMfactor-class
@@ -839,6 +958,7 @@ ddenseMatrix-class ddenseMatrix-class
ddiMatrix-class ddiMatrix-class
denseLU-class LU-class
denseMatrix-class denseMatrix-class
+det Matrix-class
determinant,CHMfactor,logical-method CHMfactor-class
determinant,CHMfactor,missing-method CHMfactor-class
determinant,ddenseMatrix,logical-method ddenseMatrix-class
@@ -872,17 +992,38 @@ diag,dgCMatrix-method dgCMatrix-class
diag,dgeMatrix-method dgeMatrix-class
diag,dgRMatrix-method dgRMatrix-class
diag,diagonalMatrix-method diagonalMatrix-class
+diag,dspMatrix-method dsyMatrix-class
+diag,dsyMatrix-method dsyMatrix-class
diag,dtpMatrix-method dtpMatrix-class
diag,dtrMatrix-method dtrMatrix-class
diag,ldenseMatrix-method ldenseMatrix-class
diag,lgeMatrix-method lgeMatrix-class
+diag,lspMatrix-method lsyMatrix-class
+diag,lsyMatrix-method lsyMatrix-class
diag,ltpMatrix-method ltrMatrix-class
diag,ltrMatrix-method ltrMatrix-class
diag,Matrix-method Matrix-class
diag,ndenseMatrix-method ndenseMatrix-class
diag,sparseMatrix-method sparseMatrix-class
+diag<-,dgeMatrix-method dgeMatrix-class
+diag<-,dspMatrix-method dsyMatrix-class
+diag<-,dsyMatrix-method dsyMatrix-class
+diag<-,dtpMatrix-method dtpMatrix-class
+diag<-,dtrMatrix-method dtrMatrix-class
+diag<-,lgeMatrix-method lgeMatrix-class
+diag<-,lspMatrix-method lsyMatrix-class
+diag<-,lsyMatrix-method lsyMatrix-class
+diag<-,ltpMatrix-method ltrMatrix-class
+diag<-,ltrMatrix-method ltrMatrix-class
+diag<-,ngeMatrix-method ngeMatrix-class
+diag<-,nspMatrix-method nsyMatrix-class
+diag<-,nsyMatrix-method nsyMatrix-class
+diag<-,ntpMatrix-method ntrMatrix-class
+diag<-,ntrMatrix-method ntrMatrix-class
+diagN2U diagU2N
Diagonal Diagonal
diagonalMatrix-class diagonalMatrix-class
+diagU2N diagU2N
diff,Matrix-method Matrix-class
dim,dgCMatrix-method dgCMatrix-class
dim,dgeMatrix-method dgeMatrix-class
@@ -900,6 +1041,7 @@ dimnames<-,Matrix,NULL-method Matrix-class
dMatrix-class dMatrix-class
dpoMatrix-class dpoMatrix-class
dppMatrix-class dpoMatrix-class
+drop,abIndex-method abIndex-class
drop,Matrix-method Matrix-class
drop0 drop0
dsCMatrix-class dsCMatrix-class
@@ -974,10 +1116,14 @@ forceSymmetric,nsTMatrix,missing-method forceSymmetric
forceSymmetric,nsyMatrix,character-method forceSymmetric
forceSymmetric,nsyMatrix,missing-method forceSymmetric
forceSymmetric,sparseMatrix,ANY-method forceSymmetric
+format,sparseMatrix-method sparseMatrix-class
+formatSparseM formatSparseM
+formatSpMatrix printSpMatrix
gamma,dgCMatrix-method dgCMatrix-class
gamma,dMatrix-method dMatrix-class
generalMatrix-class generalMatrix-class
head,Matrix-method Matrix-class
+head,sparseVector-method sparseVector-class
Hilbert Hilbert
image,ANY-method image-methods
image,CHMfactor-method image-methods
@@ -991,10 +1137,32 @@ image,nsparseMatrix-method image-methods
image-methods image-methods
iMatrix-class unused-classes
index-class index-class
+is.finite,abIndex-method abIndex-class
+is.finite,ddenseMatrix-method is.na-methods
+is.finite,dgeMatrix-method is.na-methods
+is.finite,diagonalMatrix-method is.na-methods
+is.finite,dsparseMatrix-method is.na-methods
+is.finite,lMatrix-method is.na-methods
+is.finite,nMatrix-method is.na-methods
+is.finite,nsparseVector-method sparseVector-class
+is.finite,pMatrix-method is.na-methods
+is.finite,sparseVector-method sparseVector-class
+is.infinite,abIndex-method abIndex-class
+is.infinite,ddenseMatrix-method is.na-methods
+is.infinite,diagonalMatrix-method is.na-methods
+is.infinite,dsparseMatrix-method is.na-methods
+is.infinite,lMatrix-method is.na-methods
+is.infinite,nMatrix-method is.na-methods
+is.infinite,nsparseVector-method sparseVector-class
+is.infinite,pMatrix-method is.na-methods
+is.infinite,sparseVector-method sparseVector-class
+is.na,abIndex-method abIndex-class
is.na,denseMatrix-method is.na-methods
is.na,nsparseMatrix-method nsparseMatrix-classes
-is.na,pMatrix-method pMatrix-class
+is.na,nsparseVector-method sparseVector-class
+is.na,pMatrix-method is.na-methods
is.na,sparseMatrix-method is.na-methods
+is.na,sparseVector-method sparseVector-class
is.na-methods is.na-methods
isLDL CHMfactor-class
isparseVector-class sparseVector-class
@@ -1011,10 +1179,12 @@ kronecker,ANY,sparseMatrix-method kronecker-methods
kronecker,dgTMatrix,dgTMatrix-method kronecker-methods
kronecker,dgTMatrix,dtTMatrix-method kronecker-methods
kronecker,diagonalMatrix,ANY-method kronecker-methods
+kronecker,diagonalMatrix,Matrix-method kronecker-methods
kronecker,dsparseMatrix,dsparseMatrix-method kronecker-methods
kronecker,dtTMatrix,dgTMatrix-method kronecker-methods
kronecker,dtTMatrix,dtTMatrix-method kronecker-methods
kronecker,Matrix,ANY-method kronecker-methods
+kronecker,Matrix,diagonalMatrix-method kronecker-methods
kronecker,sparseMatrix,ANY-method kronecker-methods
kronecker,sparseMatrix,TsparseMatrix-method kronecker-methods
kronecker,TsparseMatrix,sparseMatrix-method kronecker-methods
@@ -1022,6 +1192,7 @@ kronecker,TsparseMatrix,TsparseMatrix-method kronecker-methods
kronecker-methods kronecker-methods
ldenseMatrix-class ldenseMatrix-class
ldiMatrix-class ldiMatrix-class
+length,abIndex-method abIndex-class
length,Matrix-method Matrix-class
length,sparseVector-method sparseVector-class
lgamma,dgCMatrix-method dgCMatrix-class
@@ -1035,13 +1206,20 @@ log,dgCMatrix-method dgCMatrix-class
log,dMatrix-method dMatrix-class
Logic,ANY,Matrix-method Matrix-class
Logic,CsparseMatrix,CsparseMatrix-method CsparseMatrix-class
+Logic,dMatrix,logical-method dMatrix-class
+Logic,dMatrix,numeric-method dMatrix-class
+Logic,dMatrix,sparseVector-method sparseVector-class
Logic,ldenseMatrix,lsparseMatrix-method ldenseMatrix-class
Logic,lgCMatrix,lgCMatrix-method lsparseMatrix-classes
Logic,lgeMatrix,lgeMatrix-method lgeMatrix-class
Logic,lgTMatrix,lgTMatrix-method lsparseMatrix-classes
Logic,lMatrix,logical-method dMatrix-class
+Logic,lMatrix,numeric-method dMatrix-class
+Logic,lMatrix,sparseVector-method sparseVector-class
+Logic,logical,dMatrix-method dMatrix-class
Logic,logical,lMatrix-method dMatrix-class
Logic,logical,Matrix-method Matrix-class
+Logic,logical,nMatrix-method nMatrix-class
Logic,lsCMatrix,lsCMatrix-method lsparseMatrix-classes
Logic,lsparseMatrix,ldenseMatrix-method ldenseMatrix-class
Logic,lsparseMatrix,lsparseMatrix-method lsparseMatrix-classes
@@ -1051,8 +1229,20 @@ Logic,Matrix,ANY-method Matrix-class
Logic,Matrix,logical-method Matrix-class
Logic,Matrix,nMatrix-method nMatrix-class
Logic,ngeMatrix,ngeMatrix-method ngeMatrix-class
+Logic,nMatrix,logical-method nMatrix-class
Logic,nMatrix,Matrix-method nMatrix-class
+Logic,nMatrix,nMatrix-method nMatrix-class
+Logic,nMatrix,numeric-method nMatrix-class
+Logic,nMatrix,sparseVector-method sparseVector-class
+Logic,nsparseVector,nsparseVector-method sparseVector-class
+Logic,numeric,dMatrix-method dMatrix-class
+Logic,numeric,lMatrix-method dMatrix-class
+Logic,numeric,nMatrix-method nMatrix-class
+Logic,sparseVector,dMatrix-method sparseVector-class
+Logic,sparseVector,lMatrix-method sparseVector-class
+Logic,sparseVector,nMatrix-method sparseVector-class
Logic,sparseVector,sparseVector-method sparseVector-class
+Logic,triangularMatrix,diagonalMatrix-method diagonalMatrix-class
lsCMatrix-class lsparseMatrix-classes
lsparseMatrix-class lsparseMatrix-classes
lsparseVector-class sparseVector-class
@@ -1067,9 +1257,10 @@ ltrMatrix-class ltrMatrix-class
ltTMatrix-class lsparseMatrix-classes
lu lu
lu,ddenseMatrix-method ddenseMatrix-class
-lu,dgCMatrix-method dgCMatrix-class
+lu,dgCMatrix-method lu
lu,dgeMatrix-method lu
lu,dsparseMatrix-method dsparseMatrix-class
+lu,matrix-method lu
lu,sparseMatrix-method sparseMatrix-class
LU-class LU-class
Math,CsparseMatrix-method CsparseMatrix-class
@@ -1083,6 +1274,8 @@ Matrix Matrix
Matrix-class Matrix-class
MatrixFactorization-class MatrixFactorization-class
mean,Matrix-method Matrix-class
+mean,sparseMatrix-method sparseMatrix-class
+mean,sparseVector-method sparseVector-class
nCHMsimpl-class CHMfactor-class
nCHMsuper-class CHMfactor-class
ndenseMatrix-class ndenseMatrix-class
@@ -1093,6 +1286,12 @@ ngRMatrix-class nsparseMatrix-classes
ngTMatrix-class nsparseMatrix-classes
nMatrix-class nMatrix-class
nnzero nnzero
+nnzero,ANY-method nnzero
+nnzero,CHMfactor-method nnzero
+nnzero,denseMatrix-method nnzero
+nnzero,diagonalMatrix-method nnzero
+nnzero,pMatrix-method nnzero
+nnzero,sparseMatrix-method nnzero
norm norm
norm,ANY,missing-method norm
norm,ddenseMatrix,character-method ddenseMatrix-class
@@ -1126,6 +1325,11 @@ ntRMatrix-class nsparseMatrix-classes
ntrMatrix-class ntrMatrix-class
ntTMatrix-class nsparseMatrix-classes
number-class number-class
+onenormest condest
+Ops,abIndex,abIndex-method abIndex-class
+Ops,abIndex,ANY-method abIndex-class
+Ops,abIndex,numeric-method abIndex-class
+Ops,ANY,abIndex-method abIndex-class
Ops,ANY,ddiMatrix-method diagonalMatrix-class
Ops,ANY,ldiMatrix-method diagonalMatrix-class
Ops,ANY,Matrix-method Matrix-class
@@ -1136,23 +1340,30 @@ Ops,ddiMatrix,ddiMatrix-method diagonalMatrix-class
Ops,ddiMatrix,diagonalMatrix-method diagonalMatrix-class
Ops,ddiMatrix,dMatrix-method diagonalMatrix-class
Ops,ddiMatrix,ldiMatrix-method diagonalMatrix-class
+Ops,ddiMatrix,logical-method diagonalMatrix-class
Ops,ddiMatrix,Matrix-method diagonalMatrix-class
Ops,ddiMatrix,numeric-method diagonalMatrix-class
Ops,ddiMatrix,sparseMatrix-method diagonalMatrix-class
Ops,diagonalMatrix,ddiMatrix-method diagonalMatrix-class
Ops,diagonalMatrix,diagonalMatrix-method diagonalMatrix-class
Ops,diagonalMatrix,sparseMatrix-method sparseMatrix-class
+Ops,diagonalMatrix,triangularMatrix-method diagonalMatrix-class
Ops,dMatrix,ddiMatrix-method diagonalMatrix-class
Ops,dMatrix,dMatrix-method dMatrix-class
Ops,dMatrix,ldiMatrix-method diagonalMatrix-class
Ops,dMatrix,lMatrix-method dMatrix-class
Ops,dMatrix,nMatrix-method dMatrix-class
+Ops,dpoMatrix,logical-method dpoMatrix-class
+Ops,dpoMatrix,numeric-method dpoMatrix-class
+Ops,dppMatrix,logical-method dpoMatrix-class
+Ops,dppMatrix,numeric-method dpoMatrix-class
Ops,dsparseMatrix,nsparseMatrix-method nsparseMatrix-classes
Ops,ldenseMatrix,ldenseMatrix-method ldenseMatrix-class
Ops,ldiMatrix,ANY-method diagonalMatrix-class
Ops,ldiMatrix,ddiMatrix-method diagonalMatrix-class
Ops,ldiMatrix,dMatrix-method diagonalMatrix-class
Ops,ldiMatrix,ldiMatrix-method diagonalMatrix-class
+Ops,ldiMatrix,logical-method diagonalMatrix-class
Ops,ldiMatrix,Matrix-method diagonalMatrix-class
Ops,ldiMatrix,numeric-method diagonalMatrix-class
Ops,ldiMatrix,sparseMatrix-method diagonalMatrix-class
@@ -1160,6 +1371,10 @@ Ops,lMatrix,dMatrix-method dMatrix-class
Ops,lMatrix,lMatrix-method dMatrix-class
Ops,lMatrix,nMatrix-method nMatrix-class
Ops,lMatrix,numeric-method dMatrix-class
+Ops,logical,ddiMatrix-method diagonalMatrix-class
+Ops,logical,dpoMatrix-method dpoMatrix-class
+Ops,logical,dppMatrix-method dpoMatrix-class
+Ops,logical,ldiMatrix-method diagonalMatrix-class
Ops,logical,Matrix-method Matrix-class
Ops,lsparseMatrix,lsparseMatrix-method lsparseMatrix-classes
Ops,lsparseMatrix,nsparseMatrix-method nsparseMatrix-classes
@@ -1170,6 +1385,7 @@ Ops,Matrix,logical-method Matrix-class
Ops,Matrix,Matrix-method Matrix-class
Ops,Matrix,matrix-method Matrix-class
Ops,matrix,Matrix-method Matrix-class
+Ops,Matrix,sparseVector-method sparseVector-class
Ops,ndenseMatrix,ndenseMatrix-method ndenseMatrix-class
Ops,nMatrix,dMatrix-method dMatrix-class
Ops,nMatrix,lMatrix-method nMatrix-class
@@ -1177,7 +1393,10 @@ Ops,nMatrix,numeric-method nMatrix-class
Ops,nsparseMatrix,dsparseMatrix-method nsparseMatrix-classes
Ops,nsparseMatrix,lsparseMatrix-method nsparseMatrix-classes
Ops,nsparseMatrix,sparseMatrix-method nsparseMatrix-classes
+Ops,numeric,abIndex-method abIndex-class
Ops,numeric,ddiMatrix-method diagonalMatrix-class
+Ops,numeric,dpoMatrix-method dpoMatrix-class
+Ops,numeric,dppMatrix-method dpoMatrix-class
Ops,numeric,ldiMatrix-method diagonalMatrix-class
Ops,numeric,lMatrix-method dMatrix-class
Ops,numeric,nMatrix-method nMatrix-class
@@ -1190,6 +1409,13 @@ Ops,sparseMatrix,numeric-method sparseMatrix-class
Ops,sparseMatrix,sparseMatrix-method sparseMatrix-class
Ops,sparseVector,ANY-method sparseVector-class
Ops,sparseVector,atomicVector-method sparseVector-class
+Ops,sparseVector,Matrix-method sparseVector-class
+Ops,sparseVector,sparseVector-method sparseVector-class
+pack unpack
+pack,matrix-method unpack
+pack,sparseMatrix-method unpack
+pack,symmetricMatrix-method unpack
+pack,triangularMatrix-method unpack
pBunchKaufman-class Cholesky-class
pCholesky-class Cholesky-class
pMatrix-class pMatrix-class
@@ -1210,9 +1436,11 @@ qr.fitted,sparseQR,dgeMatrix-method sparseQR-class
qr.fitted,sparseQR,matrix-method sparseQR-class
qr.fitted,sparseQR,numeric-method sparseQR-class
qr.qty,sparseQR,dgeMatrix-method sparseQR-class
+qr.qty,sparseQR,Matrix-method sparseQR-class
qr.qty,sparseQR,matrix-method sparseQR-class
qr.qty,sparseQR,numeric-method sparseQR-class
qr.qy,sparseQR,dgeMatrix-method sparseQR-class
+qr.qy,sparseQR,Matrix-method sparseQR-class
qr.qy,sparseQR,matrix-method sparseQR-class
qr.qy,sparseQR,numeric-method sparseQR-class
qr.R,sparseQR-method sparseQR-class
@@ -1230,6 +1458,7 @@ rbind2,ddiMatrix,matrix-method diagonalMatrix-class
rbind2,denseMatrix,denseMatrix-method denseMatrix-class
rbind2,denseMatrix,matrix-method denseMatrix-class
rbind2,denseMatrix,numeric-method denseMatrix-class
+rbind2,denseMatrix,sparseMatrix-method sparseMatrix-class
rbind2,diagonalMatrix,sparseMatrix-method diagonalMatrix-class
rbind2,ldiMatrix,atomicVector-method diagonalMatrix-class
rbind2,ldiMatrix,matrix-method diagonalMatrix-class
@@ -1245,6 +1474,7 @@ rbind2,matrix,sparseMatrix-method sparseMatrix-class
rbind2,NULL,Matrix-method Matrix-class
rbind2,numeric,denseMatrix-method denseMatrix-class
rbind2,numeric,sparseMatrix-method sparseMatrix-class
+rbind2,sparseMatrix,denseMatrix-method sparseMatrix-class
rbind2,sparseMatrix,diagonalMatrix-method diagonalMatrix-class
rbind2,sparseMatrix,matrix-method sparseMatrix-class
rbind2,sparseMatrix,numeric-method sparseMatrix-class
@@ -1272,11 +1502,13 @@ rcond,ldenseMatrix,character-method rcond
rcond,Matrix,character-method rcond
rcond,matrix,character-method rcond
rcond,ndenseMatrix,character-method rcond
-rcond,sparseMatrix,character-method sparseMatrix-class
+rcond,sparseMatrix,character-method rcond
readHB externalFormats
readMM externalFormats
rep,sparseVector-method sparseVector-class
+rep2abI rep2abI
replValue-class replValue-class
+rleDiff-class rleDiff-class
round,dgCMatrix,numeric-method dgCMatrix-class
rowMeans colSums
rowMeans,CsparseMatrix-method colSums
@@ -1284,6 +1516,7 @@ rowMeans,ddenseMatrix-method colSums
rowMeans,denseMatrix-method colSums
rowMeans,dgCMatrix-method colSums
rowMeans,dgeMatrix-method dgeMatrix-class
+rowMeans,diagonalMatrix-method colSums
rowMeans,igCMatrix-method colSums
rowMeans,lgCMatrix-method colSums
rowMeans,ngCMatrix-method colSums
@@ -1295,6 +1528,7 @@ rowSums,ddenseMatrix-method colSums
rowSums,denseMatrix-method colSums
rowSums,dgCMatrix-method colSums
rowSums,dgeMatrix-method dgeMatrix-class
+rowSums,diagonalMatrix-method colSums
rowSums,igCMatrix-method colSums
rowSums,lgCMatrix-method colSums
rowSums,ngCMatrix-method colSums
@@ -1307,11 +1541,15 @@ Schur,dgeMatrix,missing-method Schur
Schur,diagonalMatrix,logical-method Schur
Schur,diagonalMatrix,missing-method Schur
Schur,dsyMatrix,ANY-method Schur
-Schur,generalMatrix,ANY-method Schur
-Schur,symmetricMatrix,ANY-method Schur
+Schur,generalMatrix,logical-method Schur
+Schur,generalMatrix,missing-method Schur
+Schur,symmetricMatrix,logical-method Schur
+Schur,symmetricMatrix,missing-method Schur
Schur,triangularMatrix,logical-method Schur
Schur,triangularMatrix,missing-method Schur
Schur-class Schur-class
+seqMat-class abIndex-class
+show,abIndex-method abIndex-class
show,BunchKaufman-method Cholesky-class
show,ddenseMatrix-method ddenseMatrix-class
show,denseMatrix-method denseMatrix-class
@@ -1323,6 +1561,7 @@ show,Matrix-method Matrix-class
show,MatrixFactorization-method MatrixFactorization-class
show,nMatrix-method nMatrix-class
show,pBunchKaufman-method Cholesky-class
+show,rleDiff-method rleDiff-class
show,sparseMatrix-method sparseMatrix-class
show,sparseVector-method sparseVector-class
signif,dgCMatrix,numeric-method dgCMatrix-class
@@ -1337,11 +1576,16 @@ skewpart-methods symmpart
solve,ANY,Matrix-method Matrix-class
solve,CHMfactor,ANY-method CHMfactor-class
solve,CHMfactor,ddenseMatrix-method CHMfactor-class
+solve,CHMfactor,diagonalMatrix-method CHMfactor-class
solve,CHMfactor,dsparseMatrix-method CHMfactor-class
solve,CHMfactor,matrix-method CHMfactor-class
+solve,CHMfactor,missing-method CHMfactor-class
solve,CHMfactor,numeric-method CHMfactor-class
solve,ddenseMatrix,ANY-method ddenseMatrix-class
+solve,ddenseMatrix,Matrix-method ddenseMatrix-class
+solve,ddenseMatrix,matrix-method ddenseMatrix-class
solve,ddenseMatrix,missing-method ddenseMatrix-class
+solve,ddenseMatrix,numeric-method ddenseMatrix-class
solve,denseLU,missing-method LU-class
solve,dgCMatrix,ddenseMatrix-method dgCMatrix-class
solve,dgCMatrix,dsparseMatrix-method dgCMatrix-class
@@ -1385,6 +1629,8 @@ solve,dtpMatrix,ddenseMatrix-method dtpMatrix-class
solve,dtpMatrix,matrix-method dtpMatrix-class
solve,dtpMatrix,missing-method dtpMatrix-class
solve,dtrMatrix,ddenseMatrix-method dtrMatrix-class
+solve,dtrMatrix,dMatrix-method dtrMatrix-class
+solve,dtrMatrix,Matrix-method dtrMatrix-class
solve,dtrMatrix,matrix-method dtrMatrix-class
solve,dtrMatrix,missing-method dtrMatrix-class
solve,Matrix,ANY-method Matrix-class
@@ -1398,6 +1644,8 @@ solve,Matrix,sparseVector-method sparseVector-class
solve,MatrixFactorization,ANY-method MatrixFactorization-class
solve,MatrixFactorization,missing-method MatrixFactorization-class
solve,MatrixFactorization,numeric-method MatrixFactorization-class
+solve,pMatrix,Matrix-method pMatrix-class
+solve,pMatrix,matrix-method pMatrix-class
solve,pMatrix,missing-method pMatrix-class
solve,sparseQR,ANY-method sparseQR-class
solve,TsparseMatrix,ANY-method TsparseMatrix-class
@@ -1408,20 +1656,25 @@ SparseM-coerce-methods SparseM-conv
sparseMatrix sparseMatrix
sparseMatrix-class sparseMatrix-class
sparseQR-class sparseQR-class
+sparseVector sparseVector
sparseVector-class sparseVector-class
spMatrix spMatrix
Subassign-methods Subassign-methods
sum,ddiMatrix-method diagonalMatrix-class
sum,ldiMatrix-method diagonalMatrix-class
+Summary,abIndex-method abIndex-class
Summary,ddenseMatrix-method ddenseMatrix-class
Summary,ddiMatrix-method diagonalMatrix-class
+summary,diagonalMatrix-method diagonalMatrix-class
Summary,dsparseMatrix-method dsparseMatrix-class
Summary,ldiMatrix-method diagonalMatrix-class
Summary,lMatrix-method dMatrix-class
Summary,Matrix-method Matrix-class
Summary,nMatrix-method nMatrix-class
+Summary,nsparseVector-method sparseVector-class
Summary,pMatrix-method pMatrix-class
summary,sparseMatrix-method sparseMatrix-class
+Summary,sparseVector-method sparseVector-class
symmetricMatrix-class symmetricMatrix-class
symmpart symmpart
symmpart,ddenseMatrix-method symmpart
@@ -1473,12 +1726,14 @@ t,pMatrix-method pMatrix-class
t,RsparseMatrix-method RsparseMatrix-class
t,TsparseMatrix-method TsparseMatrix-class
tail,Matrix-method Matrix-class
+tail,sparseVector-method sparseVector-class
tcrossprod tcrossprod
tcrossprod,ANY,Matrix-method Matrix-class
tcrossprod,ANY,TsparseMatrix-method TsparseMatrix-class
tcrossprod,CsparseMatrix,CsparseMatrix-method CsparseMatrix-class
tcrossprod,CsparseMatrix,diagonalMatrix-method diagonalMatrix-class
tcrossprod,CsparseMatrix,missing-method CsparseMatrix-class
+tcrossprod,ddenseMatrix,dtrMatrix-method dtrMatrix-class
tcrossprod,ddenseMatrix,missing-method ddenseMatrix-class
tcrossprod,dgCMatrix,missing-method tcrossprod
tcrossprod,dgeMatrix,dgeMatrix-method dgeMatrix-class
@@ -1492,6 +1747,7 @@ tcrossprod,diagonalMatrix,diagonalMatrix-method diagonalMatrix-class
tcrossprod,diagonalMatrix,matrix-method diagonalMatrix-class
tcrossprod,diagonalMatrix,missing-method diagonalMatrix-class
tcrossprod,diagonalMatrix,sparseMatrix-method diagonalMatrix-class
+tcrossprod,dtrMatrix,dtrMatrix-method dtrMatrix-class
tcrossprod,lgCMatrix,missing-method lsparseMatrix-classes
tcrossprod,lgeMatrix,diagonalMatrix-method diagonalMatrix-class
tcrossprod,lgTMatrix,missing-method lsparseMatrix-classes
@@ -1499,10 +1755,14 @@ tcrossprod,lsparseMatrix,missing-method lsparseMatrix-classes
tcrossprod,Matrix,ANY-method Matrix-class
tcrossprod,matrix,dgeMatrix-method dgeMatrix-class
tcrossprod,matrix,diagonalMatrix-method diagonalMatrix-class
+tcrossprod,matrix,dtrMatrix-method dtrMatrix-class
tcrossprod,Matrix,Matrix-method Matrix-class
tcrossprod,Matrix,matrix-method Matrix-class
tcrossprod,matrix,Matrix-method Matrix-class
+tcrossprod,Matrix,missing-method Matrix-class
tcrossprod,Matrix,numeric-method Matrix-class
+tcrossprod,Matrix,pMatrix-method pMatrix-class
+tcrossprod,matrix,pMatrix-method pMatrix-class
tcrossprod,Matrix,sparseVector-method sparseVector-class
tcrossprod,Matrix,TsparseMatrix-method TsparseMatrix-class
tcrossprod,ngCMatrix,missing-method nsparseMatrix-classes
@@ -1511,11 +1771,13 @@ tcrossprod,nsparseMatrix,missing-method nsparseMatrix-classes
tcrossprod,numeric,dgeMatrix-method dgeMatrix-class
tcrossprod,numeric,Matrix-method Matrix-class
tcrossprod,pMatrix,missing-method pMatrix-class
+tcrossprod,pMatrix,pMatrix-method pMatrix-class
tcrossprod,sparseMatrix,diagonalMatrix-method diagonalMatrix-class
tcrossprod,sparseVector,Matrix-method sparseVector-class
tcrossprod,TsparseMatrix,ANY-method TsparseMatrix-class
tcrossprod,TsparseMatrix,Matrix-method TsparseMatrix-class
tcrossprod,TsparseMatrix,missing-method TsparseMatrix-class
+tcrossprod,TsparseMatrix,TsparseMatrix-method TsparseMatrix-class
tcrossprod-methods tcrossprod
triangularMatrix-class triangularMatrix-class
tril band
@@ -1580,21 +1842,46 @@ TsparseMatrix-class TsparseMatrix-class
unname,Matrix,missing-method Matrix-class
unname,Matrix-method Matrix-class
unpack unpack
-unpack,dspMatrix-method dsyMatrix-class
-unpack,dtpMatrix-method dtpMatrix-class
+unpack,dspMatrix-method unpack
+unpack,dtpMatrix-method unpack
+unpack,sparseMatrix-method unpack
+unpack,symmetricMatrix-method unpack
+unpack,triangularMatrix-method unpack
update,CHMfactor-method CHMfactor-class
+updown updown
+updown,ANY,ANY,ANY-method updown
+updown,character,mMatrix,CHMfactor-method updown
+updown,logical,mMatrix,CHMfactor-method updown
+updown-methods updown
USCounties USCounties
+which,ldenseMatrix-method ldenseMatrix-class
+which,ldiMatrix-method diagonalMatrix-class
+which,lgTMatrix-method lsparseMatrix-classes
+which,lsparseMatrix-method lsparseMatrix-classes
+which,lsparseVector-method lsparseMatrix-classes
+which,lsTMatrix-method lsparseMatrix-classes
+which,ltTMatrix-method lsparseMatrix-classes
+which,ndenseMatrix-method ndenseMatrix-class
+which,ngTMatrix-method nsparseMatrix-classes
+which,nsparseMatrix-method nsparseMatrix-classes
+which,nsparseVector-method nsparseMatrix-classes
+which,nsTMatrix-method nsparseMatrix-classes
+which,ntTMatrix-method nsparseMatrix-classes
writeMM externalFormats
writeMM,CsparseMatrix-method externalFormats
-writeMM,TsparseMatrix-method externalFormats
+writeMM,sparseMatrix-method externalFormats
xsparseVector-class sparseVector-class
-xtabs xtabs
zapsmall,dMatrix-method dMatrix-class
zMatrix-class unused-classes
zsparseVector-class sparseVector-class
+[,abIndex,index,ANY,ANY-method abIndex-class
+[,CsparseMatrix,index,index,logical-method Xtrct-methods
+[,CsparseMatrix,index,missing,logical-method Xtrct-methods
+[,CsparseMatrix,missing,index,logical-method Xtrct-methods
[,denseMatrix,index,index,logical-method Xtrct-methods
[,denseMatrix,index,missing,logical-method Xtrct-methods
[,denseMatrix,matrix,missing,ANY-method Xtrct-methods
+[,denseMatrix,matrix,missing,missing-method Xtrct-methods
[,denseMatrix,missing,index,logical-method Xtrct-methods
[,diagonalMatrix,index,index,logical-method Xtrct-methods
[,diagonalMatrix,index,missing,logical-method Xtrct-methods
@@ -1605,14 +1892,19 @@ zsparseVector-class sparseVector-class
[,Matrix,index,index,missing-method Xtrct-methods
[,Matrix,index,missing,missing-method Xtrct-methods
[,Matrix,lMatrix,missing,ANY-method Xtrct-methods
+[,Matrix,lMatrix,missing,missing-method Xtrct-methods
[,Matrix,logical,missing,ANY-method Xtrct-methods
+[,Matrix,logical,missing,missing-method Xtrct-methods
[,Matrix,matrix,missing,ANY-method Xtrct-methods
+[,Matrix,matrix,missing,missing-method Xtrct-methods
[,Matrix,missing,index,missing-method Xtrct-methods
[,Matrix,missing,missing,ANY-method Xtrct-methods
[,sparseMatrix,index,index,logical-method Xtrct-methods
[,sparseMatrix,index,missing,logical-method Xtrct-methods
[,sparseMatrix,missing,index,logical-method Xtrct-methods
[,sparseVector,index,ANY,ANY-method sparseVector-class
+[,sparseVector,lsparseVector,ANY,ANY-method sparseVector-class
+[,sparseVector,nsparseVector,ANY,ANY-method sparseVector-class
[,TsparseMatrix,index,index,logical-method Xtrct-methods
[,TsparseMatrix,index,missing,logical-method Xtrct-methods
[,TsparseMatrix,missing,index,logical-method Xtrct-methods
@@ -1621,13 +1913,18 @@ zsparseVector-class sparseVector-class
[<-,CsparseMatrix,index,index,sparseVector-method Subassign-methods
[<-,CsparseMatrix,index,missing,replValue-method Subassign-methods
[<-,CsparseMatrix,index,missing,sparseVector-method Subassign-methods
+[<-,CsparseMatrix,ldenseMatrix,missing,replValue-method Subassign-methods
+[<-,CsparseMatrix,lsparseMatrix,missing,replValue-method Subassign-methods
[<-,CsparseMatrix,matrix,missing,replValue-method Subassign-methods
[<-,CsparseMatrix,missing,index,replValue-method Subassign-methods
[<-,CsparseMatrix,missing,index,sparseVector-method Subassign-methods
+[<-,CsparseMatrix,ndenseMatrix,missing,replValue-method Subassign-methods
+[<-,CsparseMatrix,nsparseMatrix,missing,replValue-method Subassign-methods
[<-,denseMatrix,index,index,replValue-method Subassign-methods
[<-,denseMatrix,index,missing,replValue-method Subassign-methods
[<-,denseMatrix,matrix,missing,replValue-method Subassign-methods
[<-,denseMatrix,missing,index,replValue-method Subassign-methods
+[<-,denseMatrix,missing,missing,ANY-method Subassign-methods
[<-,diagonalMatrix,index,index,replValue-method Subassign-methods
[<-,diagonalMatrix,index,index,sparseMatrix-method Subassign-methods
[<-,diagonalMatrix,index,index,sparseVector-method Subassign-methods
@@ -1643,12 +1940,16 @@ zsparseVector-class sparseVector-class
[<-,Matrix,ANY,ANY,matrix-method Subassign-methods
[<-,Matrix,ANY,missing,Matrix-method Subassign-methods
[<-,Matrix,ANY,missing,matrix-method Subassign-methods
+[<-,Matrix,ldenseMatrix,missing,replValue-method Subassign-methods
+[<-,Matrix,lsparseMatrix,missing,replValue-method Subassign-methods
[<-,Matrix,matrix,missing,replValue-method Subassign-methods
[<-,Matrix,missing,ANY,Matrix-method Subassign-methods
[<-,Matrix,missing,ANY,matrix-method Subassign-methods
-[<-,Matrix,missing,missing,ANY-method Subassign-methods
-[<-,pMatrix,index,ANY,ANY-method pMatrix-class
-[<-,pMatrix,missing,index,ANY-method pMatrix-class
+[<-,Matrix,ndenseMatrix,missing,replValue-method Subassign-methods
+[<-,Matrix,nsparseMatrix,missing,replValue-method Subassign-methods
+[<-,pMatrix,index,ANY,ANY-method Subassign-methods
+[<-,pMatrix,missing,index,ANY-method Subassign-methods
+[<-,pMatrix,missing,missing,ANY-method Subassign-methods
[<-,RsparseMatrix,index,index,replValue-method Subassign-methods
[<-,RsparseMatrix,index,index,sparseVector-method Subassign-methods
[<-,RsparseMatrix,index,missing,replValue-method Subassign-methods
@@ -1659,14 +1960,18 @@ zsparseVector-class sparseVector-class
[<-,sparseMatrix,ANY,ANY,sparseMatrix-method Subassign-methods
[<-,sparseMatrix,ANY,missing,sparseMatrix-method Subassign-methods
[<-,sparseMatrix,missing,ANY,sparseMatrix-method Subassign-methods
+[<-,sparseMatrix,missing,missing,ANY-method Subassign-methods
[<-,sparseVector,index,missing,replValue-method sparseVector-class
+[<-,sparseVector,sparseVector,missing,replValue-method sparseVector-class
[<-,TsparseMatrix,index,index,replValue-method Subassign-methods
[<-,TsparseMatrix,index,index,sparseVector-method Subassign-methods
[<-,TsparseMatrix,index,missing,replValue-method Subassign-methods
[<-,TsparseMatrix,index,missing,sparseVector-method Subassign-methods
+[<-,TsparseMatrix,lMatrix,missing,replValue-method Subassign-methods
[<-,TsparseMatrix,matrix,missing,replValue-method Subassign-methods
[<-,TsparseMatrix,missing,index,replValue-method Subassign-methods
[<-,TsparseMatrix,missing,index,sparseVector-method Subassign-methods
+[<-,TsparseMatrix,nMatrix,missing,replValue-method Subassign-methods
[<--methods Subassign-methods
^,ddenseMatrix,ddiMatrix-method diagonalMatrix-class
^,ddenseMatrix,ldiMatrix-method diagonalMatrix-class
diff --git a/win32/deps/library/Matrix/help/Matrix.rdb b/win32/deps/library/Matrix/help/Matrix.rdb
new file mode 100644
index 0000000..3ddc172
Binary files /dev/null and b/win32/deps/library/Matrix/help/Matrix.rdb differ
diff --git a/win32/deps/library/Matrix/help/Matrix.rdx b/win32/deps/library/Matrix/help/Matrix.rdx
new file mode 100644
index 0000000..8267559
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diff --git a/win32/deps/library/Matrix/help/aliases.rds b/win32/deps/library/Matrix/help/aliases.rds
new file mode 100644
index 0000000..03d1e59
Binary files /dev/null and b/win32/deps/library/Matrix/help/aliases.rds differ
diff --git a/win32/deps/library/Matrix/help/paths.rds b/win32/deps/library/Matrix/help/paths.rds
new file mode 100644
index 0000000..fda6656
Binary files /dev/null and b/win32/deps/library/Matrix/help/paths.rds differ
diff --git a/win32/deps/library/Matrix/html/00Index.html b/win32/deps/library/Matrix/html/00Index.html
new file mode 100644
index 0000000..bd0935f
--- /dev/null
+++ b/win32/deps/library/Matrix/html/00Index.html
@@ -0,0 +1,1411 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Sparse and Dense Matrix Classes and Methods</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Sparse and Dense Matrix Classes and Methods
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘Matrix’ version 1.0-9</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+<li><a href="../doc/index.html">Overview of user guides and package vignettes</a>; browse <a href="../doc">directory</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<p align="center">
+<a href="#A">A</a>
+<a href="#B">B</a>
+<a href="#C">C</a>
+<a href="#D">D</a>
+<a href="#E">E</a>
+<a href="#F">F</a>
+<a href="#G">G</a>
+<a href="#H">H</a>
+<a href="#I">I</a>
+<a href="#K">K</a>
+<a href="#L">L</a>
+<a href="#M">M</a>
+<a href="#N">N</a>
+<a href="#O">O</a>
+<a href="#P">P</a>
+<a href="#Q">Q</a>
+<a href="#R">R</a>
+<a href="#S">S</a>
+<a href="#T">T</a>
+<a href="#U">U</a>
+<a href="#W">W</a>
+<a href="#X">X</a>
+<a href="#Z">Z</a>
+<a href="#misc">misc</a>
+</p>
+
+
+<h2><a name="A">-- A --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="abIndex-class.html">abIndex-class</a></td>
+<td>Class "abIndex" of Abstract Index Vectors</td></tr>
+<tr><td width="25%"><a href="abIseq.html">abIseq</a></td>
+<td>Sequence Generation of "abIndex", Abstract Index Vectors</td></tr>
+<tr><td width="25%"><a href="abIseq.html">abIseq1</a></td>
+<td>Sequence Generation of "abIndex", Abstract Index Vectors</td></tr>
+<tr><td width="25%"><a href="all-methods.html">all-method</a></td>
+<td>"Matrix" Methods for Functions all() and any()</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">all-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">all-method</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="all-methods.html">all-methods</a></td>
+<td>"Matrix" Methods for Functions all() and any()</td></tr>
+<tr><td width="25%"><a href="all.equal-methods.html">all.equal-method</a></td>
+<td>Matrix Package Methods for Function all.equal()</td></tr>
+<tr><td width="25%"><a href="all.equal-methods.html">all.equal-methods</a></td>
+<td>Matrix Package Methods for Function all.equal()</td></tr>
+<tr><td width="25%"><a href="all-methods.html">any-method</a></td>
+<td>"Matrix" Methods for Functions all() and any()</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">any-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">any-method</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="CsparseMatrix-class.html">Arith-method</a></td>
+<td>Class "CsparseMatrix" of Sparse Matrices in Column-compressed Form</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">Arith-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="abIndex-class.html">Arith-method</a></td>
+<td>Class "abIndex" of Abstract Index Vectors</td></tr>
+<tr><td width="25%"><a href="dMatrix-class.html">Arith-method</a></td>
+<td>(Virtual) Class "dMatrix" of "double" Matrices</td></tr>
+<tr><td width="25%"><a href="ddenseMatrix-class.html">Arith-method</a></td>
+<td>Virtual Class "ddenseMatrix" of Numeric Dense Matrices</td></tr>
+<tr><td width="25%"><a href="dgCMatrix-class.html">Arith-method</a></td>
+<td>Compressed, sparse, column-oriented numeric matrices</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">Arith-method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">Arith-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="dpoMatrix-class.html">Arith-method</a></td>
+<td>Positive Semi-definite Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dsCMatrix-class.html">Arith-method</a></td>
+<td>Numeric Symmetric Sparse (column compressed) Matrices</td></tr>
+<tr><td width="25%"><a href="dsparseMatrix-class.html">Arith-method</a></td>
+<td>Virtual Class "dsparseMatrix" of Numeric Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="dtCMatrix-class.html">Arith-method</a></td>
+<td>Triangular, (compressed) sparse column matrices</td></tr>
+<tr><td width="25%"><a href="lgeMatrix-class.html">Arith-method</a></td>
+<td>Class "lgeMatrix" of General Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">Arith-method</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="nMatrix-class.html">Arith-method</a></td>
+<td>Class "nMatrix" of Non-zero Pattern Matrices</td></tr>
+<tr><td width="25%"><a href="ngeMatrix-class.html">Arith-method</a></td>
+<td>Class "ngeMatrix" of General Dense Nonzero-pattern Matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">Arith-method</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">Arith-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">as.array-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="abIndex-class.html">as.integer-method</a></td>
+<td>Class "abIndex" of Abstract Index Vectors</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">as.logical-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="ldenseMatrix-class.html">as.logical-method</a></td>
+<td>Virtual Class "ldenseMatrix" of Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="ndenseMatrix-class.html">as.logical-method</a></td>
+<td>Virtual Class "ndenseMatrix" of Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">as.logical-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">as.matrix-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">as.numeric-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="abIndex-class.html">as.numeric-method</a></td>
+<td>Class "abIndex" of Abstract Index Vectors</td></tr>
+<tr><td width="25%"><a href="ddenseMatrix-class.html">as.numeric-method</a></td>
+<td>Virtual Class "ddenseMatrix" of Numeric Dense Matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">as.numeric-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">as.vector-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="abIndex-class.html">as.vector-method</a></td>
+<td>Class "abIndex" of Abstract Index Vectors</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">as.vector-method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">as.vector-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="ldenseMatrix-class.html">as.vector-method</a></td>
+<td>Virtual Class "ldenseMatrix" of Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="lgeMatrix-class.html">as.vector-method</a></td>
+<td>Class "lgeMatrix" of General Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="ndenseMatrix-class.html">as.vector-method</a></td>
+<td>Virtual Class "ndenseMatrix" of Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="ngeMatrix-class.html">as.vector-method</a></td>
+<td>Class "ngeMatrix" of General Dense Nonzero-pattern Matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">as.vector-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="atomicVector-class.html">atomicVector-class</a></td>
+<td>Virtual Class "atomicVector" of Atomic Vectors</td></tr>
+</table>
+
+<h2><a name="B">-- B --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="band.html">band</a></td>
+<td>Extract bands of a matrix</td></tr>
+<tr><td width="25%"><a href="band.html">band-method</a></td>
+<td>Extract bands of a matrix</td></tr>
+<tr><td width="25%"><a href="band.html">band-methods</a></td>
+<td>Extract bands of a matrix</td></tr>
+<tr><td width="25%"><a href="bandSparse.html">bandSparse</a></td>
+<td>Construct Sparse Banded Matrix from (Sup-/Super-) Diagonals</td></tr>
+<tr><td width="25%"><a href="bdiag.html">bdiag</a></td>
+<td>Construct a Block Diagonal Matrix</td></tr>
+<tr><td width="25%"><a href="BunchKaufman-methods.html">BunchKaufman</a></td>
+<td>Bunch-Kaufman Decomposition Methods</td></tr>
+<tr><td width="25%"><a href="Cholesky-class.html">BunchKaufman-class</a></td>
+<td>Cholesky and Bunch-Kaufman Decompositions</td></tr>
+<tr><td width="25%"><a href="BunchKaufman-methods.html">BunchKaufman-method</a></td>
+<td>Bunch-Kaufman Decomposition Methods</td></tr>
+<tr><td width="25%"><a href="BunchKaufman-methods.html">BunchKaufman-methods</a></td>
+<td>Bunch-Kaufman Decomposition Methods</td></tr>
+</table>
+
+<h2><a name="C">-- C --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="abIseq.html">c.abIndex</a></td>
+<td>Sequence Generation of "abIndex", Abstract Index Vectors</td></tr>
+<tr><td width="25%"><a href="CAex.html">CAex</a></td>
+<td>Albers' example Matrix with "Difficult" Eigen Factorization</td></tr>
+<tr><td width="25%"><a href="cBind.html">cBind</a></td>
+<td>Versions of 'cbind' and 'rbind' recursively built on cbind2/rbind2</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">cbind2-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="denseMatrix-class.html">cbind2-method</a></td>
+<td>Virtual Class "denseMatrix" of All Dense Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">cbind2-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="sparseMatrix-class.html">cbind2-method</a></td>
+<td>Virtual Class "sparseMatrix" - Mother of Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="CHMfactor-class.html">CHMfactor-class</a></td>
+<td>CHOLMOD-based Cholesky Factorizations</td></tr>
+<tr><td width="25%"><a href="CHMfactor-class.html">CHMsimpl-class</a></td>
+<td>CHOLMOD-based Cholesky Factorizations</td></tr>
+<tr><td width="25%"><a href="CHMfactor-class.html">CHMsuper-class</a></td>
+<td>CHOLMOD-based Cholesky Factorizations</td></tr>
+<tr><td width="25%"><a href="chol.html">chol</a></td>
+<td>Choleski Decomposition - 'Matrix' S4 Generic</td></tr>
+<tr><td width="25%"><a href="chol.html">chol-method</a></td>
+<td>Choleski Decomposition - 'Matrix' S4 Generic</td></tr>
+<tr><td width="25%"><a href="chol.html">chol-methods</a></td>
+<td>Choleski Decomposition - 'Matrix' S4 Generic</td></tr>
+<tr><td width="25%"><a href="chol2inv-methods.html">chol2inv-method</a></td>
+<td>Inverse from Choleski or QR Decomposition - Matrix Methods</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">chol2inv-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="chol2inv-methods.html">chol2inv-methods</a></td>
+<td>Inverse from Choleski or QR Decomposition - Matrix Methods</td></tr>
+<tr><td width="25%"><a href="Cholesky.html">Cholesky</a></td>
+<td>Cholesky Decomposition of a Sparse Matrix</td></tr>
+<tr><td width="25%"><a href="Cholesky-class.html">Cholesky-class</a></td>
+<td>Cholesky and Bunch-Kaufman Decompositions</td></tr>
+<tr><td width="25%"><a href="Cholesky.html">Cholesky-method</a></td>
+<td>Cholesky Decomposition of a Sparse Matrix</td></tr>
+<tr><td width="25%"><a href="MatrixFactorization-class.html">CholeskyFactorization-class</a></td>
+<td>Class "MatrixFactorization" of Matrix Factorizations</td></tr>
+<tr><td width="25%"><a href="CHMfactor-class.html">coerce-method</a></td>
+<td>CHOLMOD-based Cholesky Factorizations</td></tr>
+<tr><td width="25%"><a href="Cholesky-class.html">coerce-method</a></td>
+<td>Cholesky and Bunch-Kaufman Decompositions</td></tr>
+<tr><td width="25%"><a href="CsparseMatrix-class.html">coerce-method</a></td>
+<td>Class "CsparseMatrix" of Sparse Matrices in Column-compressed Form</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">coerce-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="RsparseMatrix-class.html">coerce-method</a></td>
+<td>Class "RsparseMatrix" of Sparse Matrices in Column-compressed Form</td></tr>
+<tr><td width="25%"><a href="SparseM-conv.html">coerce-method</a></td>
+<td>Sparse Matrix Coercion from and to those from package "SparseM"</td></tr>
+<tr><td width="25%"><a href="TsparseMatrix-class.html">coerce-method</a></td>
+<td>Class "TsparseMatrix" of Sparse Matrices in Triplet Form</td></tr>
+<tr><td width="25%"><a href="abIndex-class.html">coerce-method</a></td>
+<td>Class "abIndex" of Abstract Index Vectors</td></tr>
+<tr><td width="25%"><a href="dMatrix-class.html">coerce-method</a></td>
+<td>(Virtual) Class "dMatrix" of "double" Matrices</td></tr>
+<tr><td width="25%"><a href="ddenseMatrix-class.html">coerce-method</a></td>
+<td>Virtual Class "ddenseMatrix" of Numeric Dense Matrices</td></tr>
+<tr><td width="25%"><a href="denseMatrix-class.html">coerce-method</a></td>
+<td>Virtual Class "denseMatrix" of All Dense Matrices</td></tr>
+<tr><td width="25%"><a href="dgCMatrix-class.html">coerce-method</a></td>
+<td>Compressed, sparse, column-oriented numeric matrices</td></tr>
+<tr><td width="25%"><a href="dgTMatrix-class.html">coerce-method</a></td>
+<td>Sparse matrices in triplet form</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">coerce-method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">coerce-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="dpoMatrix-class.html">coerce-method</a></td>
+<td>Positive Semi-definite Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dsCMatrix-class.html">coerce-method</a></td>
+<td>Numeric Symmetric Sparse (column compressed) Matrices</td></tr>
+<tr><td width="25%"><a href="dsyMatrix-class.html">coerce-method</a></td>
+<td>Symmetric Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dtCMatrix-class.html">coerce-method</a></td>
+<td>Triangular, (compressed) sparse column matrices</td></tr>
+<tr><td width="25%"><a href="dtpMatrix-class.html">coerce-method</a></td>
+<td>Packed triangular dense matrices</td></tr>
+<tr><td width="25%"><a href="dtrMatrix-class.html">coerce-method</a></td>
+<td>Triangular, dense, numeric matrices</td></tr>
+<tr><td width="25%"><a href="ldenseMatrix-class.html">coerce-method</a></td>
+<td>Virtual Class "ldenseMatrix" of Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="ldiMatrix-class.html">coerce-method</a></td>
+<td>Class "ldiMatrix" of Diagonal Logical Matrices</td></tr>
+<tr><td width="25%"><a href="lgeMatrix-class.html">coerce-method</a></td>
+<td>Class "lgeMatrix" of General Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">coerce-method</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="lsyMatrix-class.html">coerce-method</a></td>
+<td>Symmetric Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="ltrMatrix-class.html">coerce-method</a></td>
+<td>Triangular Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="nMatrix-class.html">coerce-method</a></td>
+<td>Class "nMatrix" of Non-zero Pattern Matrices</td></tr>
+<tr><td width="25%"><a href="ndenseMatrix-class.html">coerce-method</a></td>
+<td>Virtual Class "ndenseMatrix" of Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="ngeMatrix-class.html">coerce-method</a></td>
+<td>Class "ngeMatrix" of General Dense Nonzero-pattern Matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">coerce-method</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="nsyMatrix-class.html">coerce-method</a></td>
+<td>Symmetric Dense Nonzero-Pattern Matrices</td></tr>
+<tr><td width="25%"><a href="ntrMatrix-class.html">coerce-method</a></td>
+<td>Triangular Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="pMatrix-class.html">coerce-method</a></td>
+<td>Permutation matrices</td></tr>
+<tr><td width="25%"><a href="sparseMatrix-class.html">coerce-method</a></td>
+<td>Virtual Class "sparseMatrix" - Mother of Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">coerce-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="symmetricMatrix-class.html">coerce-method</a></td>
+<td>Virtual Class of Symmetric Matrices in package:Matrix</td></tr>
+<tr><td width="25%"><a href="triangularMatrix-class.html">coerce-method</a></td>
+<td>Virtual Class of Triangular Matrices in package:Matrix</td></tr>
+<tr><td width="25%"><a href="colSums.html">colMeans</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="colSums.html">colMeans-method</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">colMeans-method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="colSums.html">colSums</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="colSums.html">colSums-method</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">colSums-method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="CsparseMatrix-class.html">Compare-method</a></td>
+<td>Class "CsparseMatrix" of Sparse Matrices in Column-compressed Form</td></tr>
+<tr><td width="25%"><a href="dMatrix-class.html">Compare-method</a></td>
+<td>(Virtual) Class "dMatrix" of "double" Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">Compare-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="lgeMatrix-class.html">Compare-method</a></td>
+<td>Class "lgeMatrix" of General Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">Compare-method</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="nMatrix-class.html">Compare-method</a></td>
+<td>Class "nMatrix" of Non-zero Pattern Matrices</td></tr>
+<tr><td width="25%"><a href="ngeMatrix-class.html">Compare-method</a></td>
+<td>Class "ngeMatrix" of General Dense Nonzero-pattern Matrices</td></tr>
+<tr><td width="25%"><a href="compMatrix-class.html">compMatrix-class</a></td>
+<td>Class "compMatrix" of Composite (Factorizable) Matrices</td></tr>
+<tr><td width="25%"><a href="condest.html">condest</a></td>
+<td>Compute Approximate CONDition number and 1-Norm of (Large) Matrices</td></tr>
+<tr><td width="25%"><a href="dpoMatrix-class.html">corMatrix-class</a></td>
+<td>Positive Semi-definite Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">cov2cor-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="sparseMatrix-class.html">cov2cor-method</a></td>
+<td>Virtual Class "sparseMatrix" - Mother of Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="CsparseMatrix-class.html">crossprod-method</a></td>
+<td>Class "CsparseMatrix" of Sparse Matrices in Column-compressed Form</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">crossprod-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="TsparseMatrix-class.html">crossprod-method</a></td>
+<td>Class "TsparseMatrix" of Sparse Matrices in Triplet Form</td></tr>
+<tr><td width="25%"><a href="dMatrix-class.html">crossprod-method</a></td>
+<td>(Virtual) Class "dMatrix" of "double" Matrices</td></tr>
+<tr><td width="25%"><a href="ddenseMatrix-class.html">crossprod-method</a></td>
+<td>Virtual Class "ddenseMatrix" of Numeric Dense Matrices</td></tr>
+<tr><td width="25%"><a href="dgCMatrix-class.html">crossprod-method</a></td>
+<td>Compressed, sparse, column-oriented numeric matrices</td></tr>
+<tr><td width="25%"><a href="dgTMatrix-class.html">crossprod-method</a></td>
+<td>Sparse matrices in triplet form</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">crossprod-method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">crossprod-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="dsparseMatrix-class.html">crossprod-method</a></td>
+<td>Virtual Class "dsparseMatrix" of Numeric Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="dtrMatrix-class.html">crossprod-method</a></td>
+<td>Triangular, dense, numeric matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">crossprod-method</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">crossprod-method</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="pMatrix-class.html">crossprod-method</a></td>
+<td>Permutation matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">crossprod-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="CsparseMatrix-class.html">CsparseMatrix-class</a></td>
+<td>Class "CsparseMatrix" of Sparse Matrices in Column-compressed Form</td></tr>
+</table>
+
+<h2><a name="D">-- D --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="CHMfactor-class.html">dCHMsimpl-class</a></td>
+<td>CHOLMOD-based Cholesky Factorizations</td></tr>
+<tr><td width="25%"><a href="CHMfactor-class.html">dCHMsuper-class</a></td>
+<td>CHOLMOD-based Cholesky Factorizations</td></tr>
+<tr><td width="25%"><a href="ddenseMatrix-class.html">ddenseMatrix-class</a></td>
+<td>Virtual Class "ddenseMatrix" of Numeric Dense Matrices</td></tr>
+<tr><td width="25%"><a href="ddiMatrix-class.html">ddiMatrix-class</a></td>
+<td>Class "ddiMatrix" of Diagonal Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="LU-class.html">denseLU-class</a></td>
+<td>LU (dense) Matrix Decompositions</td></tr>
+<tr><td width="25%"><a href="denseMatrix-class.html">denseMatrix-class</a></td>
+<td>Virtual Class "denseMatrix" of All Dense Matrices</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">det</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="CHMfactor-class.html">determinant-method</a></td>
+<td>CHOLMOD-based Cholesky Factorizations</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">determinant-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="ddenseMatrix-class.html">determinant-method</a></td>
+<td>Virtual Class "ddenseMatrix" of Numeric Dense Matrices</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">determinant-method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">determinant-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="dpoMatrix-class.html">determinant-method</a></td>
+<td>Positive Semi-definite Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dsCMatrix-class.html">determinant-method</a></td>
+<td>Numeric Symmetric Sparse (column compressed) Matrices</td></tr>
+<tr><td width="25%"><a href="dtpMatrix-class.html">determinant-method</a></td>
+<td>Packed triangular dense matrices</td></tr>
+<tr><td width="25%"><a href="dtrMatrix-class.html">determinant-method</a></td>
+<td>Triangular, dense, numeric matrices</td></tr>
+<tr><td width="25%"><a href="pMatrix-class.html">determinant-method</a></td>
+<td>Permutation matrices</td></tr>
+<tr><td width="25%"><a href="sparseMatrix-class.html">determinant-method</a></td>
+<td>Virtual Class "sparseMatrix" - Mother of Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="dgCMatrix-class.html">dgCMatrix-class</a></td>
+<td>Compressed, sparse, column-oriented numeric matrices</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">dgeMatrix-class</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="dgRMatrix-class.html">dgRMatrix-class</a></td>
+<td>Sparse Compressed, Row-oriented Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dgTMatrix-class.html">dgTMatrix-class</a></td>
+<td>Sparse matrices in triplet form</td></tr>
+<tr><td width="25%"><a href="CsparseMatrix-class.html">diag-method</a></td>
+<td>Class "CsparseMatrix" of Sparse Matrices in Column-compressed Form</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">diag-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="ddenseMatrix-class.html">diag-method</a></td>
+<td>Virtual Class "ddenseMatrix" of Numeric Dense Matrices</td></tr>
+<tr><td width="25%"><a href="dgCMatrix-class.html">diag-method</a></td>
+<td>Compressed, sparse, column-oriented numeric matrices</td></tr>
+<tr><td width="25%"><a href="dgRMatrix-class.html">diag-method</a></td>
+<td>Sparse Compressed, Row-oriented Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">diag-method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">diag-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="dsyMatrix-class.html">diag-method</a></td>
+<td>Symmetric Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dtpMatrix-class.html">diag-method</a></td>
+<td>Packed triangular dense matrices</td></tr>
+<tr><td width="25%"><a href="dtrMatrix-class.html">diag-method</a></td>
+<td>Triangular, dense, numeric matrices</td></tr>
+<tr><td width="25%"><a href="ldenseMatrix-class.html">diag-method</a></td>
+<td>Virtual Class "ldenseMatrix" of Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="lgeMatrix-class.html">diag-method</a></td>
+<td>Class "lgeMatrix" of General Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="lsyMatrix-class.html">diag-method</a></td>
+<td>Symmetric Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="ltrMatrix-class.html">diag-method</a></td>
+<td>Triangular Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="ndenseMatrix-class.html">diag-method</a></td>
+<td>Virtual Class "ndenseMatrix" of Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="sparseMatrix-class.html">diag-method</a></td>
+<td>Virtual Class "sparseMatrix" - Mother of Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">diag<--method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="dsyMatrix-class.html">diag<--method</a></td>
+<td>Symmetric Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dtpMatrix-class.html">diag<--method</a></td>
+<td>Packed triangular dense matrices</td></tr>
+<tr><td width="25%"><a href="dtrMatrix-class.html">diag<--method</a></td>
+<td>Triangular, dense, numeric matrices</td></tr>
+<tr><td width="25%"><a href="lgeMatrix-class.html">diag<--method</a></td>
+<td>Class "lgeMatrix" of General Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="lsyMatrix-class.html">diag<--method</a></td>
+<td>Symmetric Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="ltrMatrix-class.html">diag<--method</a></td>
+<td>Triangular Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="ngeMatrix-class.html">diag<--method</a></td>
+<td>Class "ngeMatrix" of General Dense Nonzero-pattern Matrices</td></tr>
+<tr><td width="25%"><a href="nsyMatrix-class.html">diag<--method</a></td>
+<td>Symmetric Dense Nonzero-Pattern Matrices</td></tr>
+<tr><td width="25%"><a href="ntrMatrix-class.html">diag<--method</a></td>
+<td>Triangular Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="diagU2N.html">diagN2U</a></td>
+<td>Transform Triangular Matrices from Unit Triangular to General and back</td></tr>
+<tr><td width="25%"><a href="Diagonal.html">Diagonal</a></td>
+<td>Create Diagonal Matrix Object</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">diagonalMatrix-class</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="diagU2N.html">diagU2N</a></td>
+<td>Transform Triangular Matrices from Unit Triangular to General and back</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">diff-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">dim-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="MatrixFactorization-class.html">dim-method</a></td>
+<td>Class "MatrixFactorization" of Matrix Factorizations</td></tr>
+<tr><td width="25%"><a href="dgCMatrix-class.html">dim-method</a></td>
+<td>Compressed, sparse, column-oriented numeric matrices</td></tr>
+<tr><td width="25%"><a href="dgRMatrix-class.html">dim-method</a></td>
+<td>Sparse Compressed, Row-oriented Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">dim-method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">dim<--method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="denseMatrix-class.html">dim<--method</a></td>
+<td>Virtual Class "denseMatrix" of All Dense Matrices</td></tr>
+<tr><td width="25%"><a href="sparseMatrix-class.html">dim<--method</a></td>
+<td>Virtual Class "sparseMatrix" - Mother of Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">dim<--method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">dimnames-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">dimnames-method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">dimnames<--method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="dMatrix-class.html">dMatrix-class</a></td>
+<td>(Virtual) Class "dMatrix" of "double" Matrices</td></tr>
+<tr><td width="25%"><a href="dpoMatrix-class.html">dpoMatrix-class</a></td>
+<td>Positive Semi-definite Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dpoMatrix-class.html">dppMatrix-class</a></td>
+<td>Positive Semi-definite Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">drop-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="abIndex-class.html">drop-method</a></td>
+<td>Class "abIndex" of Abstract Index Vectors</td></tr>
+<tr><td width="25%"><a href="drop0.html">drop0</a></td>
+<td>Drop "Explicit Zeroes" from a Sparse Matrix</td></tr>
+<tr><td width="25%"><a href="dsCMatrix-class.html">dsCMatrix-class</a></td>
+<td>Numeric Symmetric Sparse (column compressed) Matrices</td></tr>
+<tr><td width="25%"><a href="dsparseMatrix-class.html">dsparseMatrix-class</a></td>
+<td>Virtual Class "dsparseMatrix" of Numeric Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">dsparseVector-class</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="dsyMatrix-class.html">dspMatrix-class</a></td>
+<td>Symmetric Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dsRMatrix-class.html">dsRMatrix-class</a></td>
+<td>Symmetric Sparse Compressed Row Matrices</td></tr>
+<tr><td width="25%"><a href="dsCMatrix-class.html">dsTMatrix-class</a></td>
+<td>Numeric Symmetric Sparse (column compressed) Matrices</td></tr>
+<tr><td width="25%"><a href="dsyMatrix-class.html">dsyMatrix-class</a></td>
+<td>Symmetric Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dtCMatrix-class.html">dtCMatrix-class</a></td>
+<td>Triangular, (compressed) sparse column matrices</td></tr>
+<tr><td width="25%"><a href="dtpMatrix-class.html">dtpMatrix-class</a></td>
+<td>Packed triangular dense matrices</td></tr>
+<tr><td width="25%"><a href="dtRMatrix-class-def.html">dtRMatrix-class</a></td>
+<td>Triangular Sparse Compressed Row Matrices</td></tr>
+<tr><td width="25%"><a href="dtrMatrix-class.html">dtrMatrix-class</a></td>
+<td>Triangular, dense, numeric matrices</td></tr>
+<tr><td width="25%"><a href="dtCMatrix-class.html">dtTMatrix-class</a></td>
+<td>Triangular, (compressed) sparse column matrices</td></tr>
+</table>
+
+<h2><a name="E">-- E --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="dgeMatrix-class.html">eigen-method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="expand.html">expand</a></td>
+<td>Expand a Decomposition into Factors</td></tr>
+<tr><td width="25%"><a href="CHMfactor-class.html">expand-method</a></td>
+<td>CHOLMOD-based Cholesky Factorizations</td></tr>
+<tr><td width="25%"><a href="LU-class.html">expand-method</a></td>
+<td>LU (dense) Matrix Decompositions</td></tr>
+<tr><td width="25%"><a href="MatrixFactorization-class.html">expand-method</a></td>
+<td>Class "MatrixFactorization" of Matrix Factorizations</td></tr>
+<tr><td width="25%"><a href="sparseLU-class.html">expand-method</a></td>
+<td>Sparse LU decomposition of a square sparse matrix</td></tr>
+<tr><td width="25%"><a href="expm.html">expm</a></td>
+<td>Matrix Exponential</td></tr>
+<tr><td width="25%"><a href="expm.html">expm-method</a></td>
+<td>Matrix Exponential</td></tr>
+</table>
+
+<h2><a name="F">-- F --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="facmul.html">facmul</a></td>
+<td>Multiplication by Decomposition Factors</td></tr>
+<tr><td width="25%"><a href="facmul.html">facmul.default</a></td>
+<td>Multiplication by Decomposition Factors</td></tr>
+<tr><td width="25%"><a href="forceSymmetric.html">forceSymmetric</a></td>
+<td>Force a Matrix to 'symmetricMatrix' Without Symmetry Checks</td></tr>
+<tr><td width="25%"><a href="forceSymmetric.html">forceSymmetric-method</a></td>
+<td>Force a Matrix to 'symmetricMatrix' Without Symmetry Checks</td></tr>
+<tr><td width="25%"><a href="sparseMatrix-class.html">format-method</a></td>
+<td>Virtual Class "sparseMatrix" - Mother of Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="formatSparseM.html">formatSparseM</a></td>
+<td>Formatting Sparse Numeric Matrices Utilities</td></tr>
+<tr><td width="25%"><a href="printSpMatrix.html">formatSpMatrix</a></td>
+<td>Format and Print Sparse Matrices Flexibly</td></tr>
+</table>
+
+<h2><a name="G">-- G --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="dMatrix-class.html">gamma-method</a></td>
+<td>(Virtual) Class "dMatrix" of "double" Matrices</td></tr>
+<tr><td width="25%"><a href="dgCMatrix-class.html">gamma-method</a></td>
+<td>Compressed, sparse, column-oriented numeric matrices</td></tr>
+<tr><td width="25%"><a href="generalMatrix-class.html">generalMatrix-class</a></td>
+<td>Class "generalMatrix" of General Matrices</td></tr>
+</table>
+
+<h2><a name="H">-- H --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Matrix-class.html">head-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">head-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="Hilbert.html">Hilbert</a></td>
+<td>Generate a Hilbert matrix</td></tr>
+</table>
+
+<h2><a name="I">-- I --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="image-methods.html">image-method</a></td>
+<td>Methods for image() in Package 'Matrix'</td></tr>
+<tr><td width="25%"><a href="image-methods.html">image-methods</a></td>
+<td>Methods for image() in Package 'Matrix'</td></tr>
+<tr><td width="25%"><a href="unused-classes.html">iMatrix-class</a></td>
+<td>Virtual Classes Not Yet Really Implemented and Used</td></tr>
+<tr><td width="25%"><a href="index-class.html">index-class</a></td>
+<td>Virtual Class "index" - Simple Class for Matrix Indices</td></tr>
+<tr><td width="25%"><a href="abIndex-class.html">is.finite-method</a></td>
+<td>Class "abIndex" of Abstract Index Vectors</td></tr>
+<tr><td width="25%"><a href="is.na-methods.html">is.finite-method</a></td>
+<td>is.na(), is.infinite() Methods for 'Matrix' Objects</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">is.finite-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="abIndex-class.html">is.infinite-method</a></td>
+<td>Class "abIndex" of Abstract Index Vectors</td></tr>
+<tr><td width="25%"><a href="is.na-methods.html">is.infinite-method</a></td>
+<td>is.na(), is.infinite() Methods for 'Matrix' Objects</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">is.infinite-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="abIndex-class.html">is.na-method</a></td>
+<td>Class "abIndex" of Abstract Index Vectors</td></tr>
+<tr><td width="25%"><a href="is.na-methods.html">is.na-method</a></td>
+<td>is.na(), is.infinite() Methods for 'Matrix' Objects</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">is.na-method</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">is.na-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="is.na-methods.html">is.na-methods</a></td>
+<td>is.na(), is.infinite() Methods for 'Matrix' Objects</td></tr>
+<tr><td width="25%"><a href="CHMfactor-class.html">isLDL</a></td>
+<td>CHOLMOD-based Cholesky Factorizations</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">isparseVector-class</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="isSymmetric-methods.html">isSymmetric-method</a></td>
+<td>Methods for Function isSymmetric in Package 'Matrix'</td></tr>
+<tr><td width="25%"><a href="isSymmetric-methods.html">isSymmetric-methods</a></td>
+<td>Methods for Function isSymmetric in Package 'Matrix'</td></tr>
+</table>
+
+<h2><a name="K">-- K --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="KNex.html">KNex</a></td>
+<td>Koenker-Ng Example Sparse Model Matrix and Response Vector</td></tr>
+<tr><td width="25%"><a href="kronecker-methods.html">kronecker-method</a></td>
+<td>Methods for Function 'kronecker()' in Package 'Matrix'</td></tr>
+<tr><td width="25%"><a href="kronecker-methods.html">kronecker-methods</a></td>
+<td>Methods for Function 'kronecker()' in Package 'Matrix'</td></tr>
+</table>
+
+<h2><a name="L">-- L --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="ldenseMatrix-class.html">ldenseMatrix-class</a></td>
+<td>Virtual Class "ldenseMatrix" of Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="ldiMatrix-class.html">ldiMatrix-class</a></td>
+<td>Class "ldiMatrix" of Diagonal Logical Matrices</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">length-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="abIndex-class.html">length-method</a></td>
+<td>Class "abIndex" of Abstract Index Vectors</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">length-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="dMatrix-class.html">lgamma-method</a></td>
+<td>(Virtual) Class "dMatrix" of "double" Matrices</td></tr>
+<tr><td width="25%"><a href="dgCMatrix-class.html">lgamma-method</a></td>
+<td>Compressed, sparse, column-oriented numeric matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">lgCMatrix-class</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="lgeMatrix-class.html">lgeMatrix-class</a></td>
+<td>Class "lgeMatrix" of General Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">lgRMatrix-class</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">lgTMatrix-class</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="dMatrix-class.html">lMatrix-class</a></td>
+<td>(Virtual) Class "dMatrix" of "double" Matrices</td></tr>
+<tr><td width="25%"><a href="dMatrix-class.html">log-method</a></td>
+<td>(Virtual) Class "dMatrix" of "double" Matrices</td></tr>
+<tr><td width="25%"><a href="dgCMatrix-class.html">log-method</a></td>
+<td>Compressed, sparse, column-oriented numeric matrices</td></tr>
+<tr><td width="25%"><a href="CsparseMatrix-class.html">Logic-method</a></td>
+<td>Class "CsparseMatrix" of Sparse Matrices in Column-compressed Form</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">Logic-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="dMatrix-class.html">Logic-method</a></td>
+<td>(Virtual) Class "dMatrix" of "double" Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">Logic-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="ldenseMatrix-class.html">Logic-method</a></td>
+<td>Virtual Class "ldenseMatrix" of Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="lgeMatrix-class.html">Logic-method</a></td>
+<td>Class "lgeMatrix" of General Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">Logic-method</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="nMatrix-class.html">Logic-method</a></td>
+<td>Class "nMatrix" of Non-zero Pattern Matrices</td></tr>
+<tr><td width="25%"><a href="ngeMatrix-class.html">Logic-method</a></td>
+<td>Class "ngeMatrix" of General Dense Nonzero-pattern Matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">Logic-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">lsCMatrix-class</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">lsparseMatrix-class</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">lsparseVector-class</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="lsyMatrix-class.html">lspMatrix-class</a></td>
+<td>Symmetric Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">lsRMatrix-class</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">lsTMatrix-class</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="lsyMatrix-class.html">lsyMatrix-class</a></td>
+<td>Symmetric Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">ltCMatrix-class</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="ltrMatrix-class.html">ltpMatrix-class</a></td>
+<td>Triangular Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">ltRMatrix-class</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="ltrMatrix-class.html">ltrMatrix-class</a></td>
+<td>Triangular Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">ltTMatrix-class</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="lu.html">lu</a></td>
+<td>(Generalized) Triangular Decomposition of a Matrix</td></tr>
+<tr><td width="25%"><a href="LU-class.html">LU-class</a></td>
+<td>LU (dense) Matrix Decompositions</td></tr>
+<tr><td width="25%"><a href="ddenseMatrix-class.html">lu-method</a></td>
+<td>Virtual Class "ddenseMatrix" of Numeric Dense Matrices</td></tr>
+<tr><td width="25%"><a href="dsparseMatrix-class.html">lu-method</a></td>
+<td>Virtual Class "dsparseMatrix" of Numeric Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="lu.html">lu-method</a></td>
+<td>(Generalized) Triangular Decomposition of a Matrix</td></tr>
+<tr><td width="25%"><a href="sparseMatrix-class.html">lu-method</a></td>
+<td>Virtual Class "sparseMatrix" - Mother of Sparse Matrices</td></tr>
+</table>
+
+<h2><a name="M">-- M --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="CsparseMatrix-class.html">Math-method</a></td>
+<td>Class "CsparseMatrix" of Sparse Matrices in Column-compressed Form</td></tr>
+<tr><td width="25%"><a href="ddenseMatrix-class.html">Math-method</a></td>
+<td>Virtual Class "ddenseMatrix" of Numeric Dense Matrices</td></tr>
+<tr><td width="25%"><a href="denseMatrix-class.html">Math-method</a></td>
+<td>Virtual Class "denseMatrix" of All Dense Matrices</td></tr>
+<tr><td width="25%"><a href="dgCMatrix-class.html">Math-method</a></td>
+<td>Compressed, sparse, column-oriented numeric matrices</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">Math-method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="sparseMatrix-class.html">Math-method</a></td>
+<td>Virtual Class "sparseMatrix" - Mother of Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="dMatrix-class.html">Math2-method</a></td>
+<td>(Virtual) Class "dMatrix" of "double" Matrices</td></tr>
+<tr><td width="25%"><a href="Matrix.html">Matrix</a></td>
+<td>Construct a Classed Matrix</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">Matrix-class</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="MatrixFactorization-class.html">MatrixFactorization-class</a></td>
+<td>Class "MatrixFactorization" of Matrix Factorizations</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">mean-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="sparseMatrix-class.html">mean-method</a></td>
+<td>Virtual Class "sparseMatrix" - Mother of Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">mean-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+</table>
+
+<h2><a name="N">-- N --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="CHMfactor-class.html">nCHMsimpl-class</a></td>
+<td>CHOLMOD-based Cholesky Factorizations</td></tr>
+<tr><td width="25%"><a href="CHMfactor-class.html">nCHMsuper-class</a></td>
+<td>CHOLMOD-based Cholesky Factorizations</td></tr>
+<tr><td width="25%"><a href="ndenseMatrix-class.html">ndenseMatrix-class</a></td>
+<td>Virtual Class "ndenseMatrix" of Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="nearPD.html">nearPD</a></td>
+<td>Nearest Positive Definite Matrix</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">ngCMatrix-class</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="ngeMatrix-class.html">ngeMatrix-class</a></td>
+<td>Class "ngeMatrix" of General Dense Nonzero-pattern Matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">ngRMatrix-class</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">ngTMatrix-class</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="nMatrix-class.html">nMatrix-class</a></td>
+<td>Class "nMatrix" of Non-zero Pattern Matrices</td></tr>
+<tr><td width="25%"><a href="nnzero.html">nnzero</a></td>
+<td>The Number of Non-Zero Values of a Matrix</td></tr>
+<tr><td width="25%"><a href="nnzero.html">nnzero-method</a></td>
+<td>The Number of Non-Zero Values of a Matrix</td></tr>
+<tr><td width="25%"><a href="norm.html">norm</a></td>
+<td>Matrix Norms</td></tr>
+<tr><td width="25%"><a href="ddenseMatrix-class.html">norm-method</a></td>
+<td>Virtual Class "ddenseMatrix" of Numeric Dense Matrices</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">norm-method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">norm-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="dsyMatrix-class.html">norm-method</a></td>
+<td>Symmetric Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dtpMatrix-class.html">norm-method</a></td>
+<td>Packed triangular dense matrices</td></tr>
+<tr><td width="25%"><a href="dtrMatrix-class.html">norm-method</a></td>
+<td>Triangular, dense, numeric matrices</td></tr>
+<tr><td width="25%"><a href="ldenseMatrix-class.html">norm-method</a></td>
+<td>Virtual Class "ldenseMatrix" of Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="ndenseMatrix-class.html">norm-method</a></td>
+<td>Virtual Class "ndenseMatrix" of Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="norm.html">norm-method</a></td>
+<td>Matrix Norms</td></tr>
+<tr><td width="25%"><a href="sparseMatrix-class.html">norm-method</a></td>
+<td>Virtual Class "sparseMatrix" - Mother of Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">nsCMatrix-class</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">nsparseMatrix-class</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">nsparseVector-class</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="nsyMatrix-class.html">nspMatrix-class</a></td>
+<td>Symmetric Dense Nonzero-Pattern Matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">nsRMatrix-class</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">nsTMatrix-class</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="nsyMatrix-class.html">nsyMatrix-class</a></td>
+<td>Symmetric Dense Nonzero-Pattern Matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">ntCMatrix-class</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="ntrMatrix-class.html">ntpMatrix-class</a></td>
+<td>Triangular Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">ntRMatrix-class</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="ntrMatrix-class.html">ntrMatrix-class</a></td>
+<td>Triangular Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">ntTMatrix-class</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="number-class.html">number-class</a></td>
+<td>Class "number" of Possibly Complex Numbers</td></tr>
+</table>
+
+<h2><a name="O">-- O --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="condest.html">onenormest</a></td>
+<td>Compute Approximate CONDition number and 1-Norm of (Large) Matrices</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">Ops-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="abIndex-class.html">Ops-method</a></td>
+<td>Class "abIndex" of Abstract Index Vectors</td></tr>
+<tr><td width="25%"><a href="dMatrix-class.html">Ops-method</a></td>
+<td>(Virtual) Class "dMatrix" of "double" Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">Ops-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="dpoMatrix-class.html">Ops-method</a></td>
+<td>Positive Semi-definite Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="ldenseMatrix-class.html">Ops-method</a></td>
+<td>Virtual Class "ldenseMatrix" of Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">Ops-method</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="nMatrix-class.html">Ops-method</a></td>
+<td>Class "nMatrix" of Non-zero Pattern Matrices</td></tr>
+<tr><td width="25%"><a href="ndenseMatrix-class.html">Ops-method</a></td>
+<td>Virtual Class "ndenseMatrix" of Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">Ops-method</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="sparseMatrix-class.html">Ops-method</a></td>
+<td>Virtual Class "sparseMatrix" - Mother of Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">Ops-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+</table>
+
+<h2><a name="P">-- P --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="unpack.html">pack</a></td>
+<td>Representation of Packed and Unpacked (Dense) Matrices</td></tr>
+<tr><td width="25%"><a href="unpack.html">pack-method</a></td>
+<td>Representation of Packed and Unpacked (Dense) Matrices</td></tr>
+<tr><td width="25%"><a href="Cholesky-class.html">pBunchKaufman-class</a></td>
+<td>Cholesky and Bunch-Kaufman Decompositions</td></tr>
+<tr><td width="25%"><a href="Cholesky-class.html">pCholesky-class</a></td>
+<td>Cholesky and Bunch-Kaufman Decompositions</td></tr>
+<tr><td width="25%"><a href="pMatrix-class.html">pMatrix-class</a></td>
+<td>Permutation matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">print-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="sparseMatrix-class.html">print-method</a></td>
+<td>Virtual Class "sparseMatrix" - Mother of Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="printSpMatrix.html">printSpMatrix</a></td>
+<td>Format and Print Sparse Matrices Flexibly</td></tr>
+<tr><td width="25%"><a href="printSpMatrix.html">printSpMatrix2</a></td>
+<td>Format and Print Sparse Matrices Flexibly</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">prod-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+</table>
+
+<h2><a name="Q">-- Q --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="qr-methods.html">qr</a></td>
+<td>QR Decomposition - S4 Methods and Generic</td></tr>
+<tr><td width="25%"><a href="qr-methods.html">qr-method</a></td>
+<td>QR Decomposition - S4 Methods and Generic</td></tr>
+<tr><td width="25%"><a href="qr-methods.html">qr-methods</a></td>
+<td>QR Decomposition - S4 Methods and Generic</td></tr>
+<tr><td width="25%"><a href="sparseQR-class.html">qr.coef-method</a></td>
+<td>Sparse QR decomposition of a sparse matrix</td></tr>
+<tr><td width="25%"><a href="sparseQR-class.html">qr.fitted-method</a></td>
+<td>Sparse QR decomposition of a sparse matrix</td></tr>
+<tr><td width="25%"><a href="sparseQR-class.html">qr.qty-method</a></td>
+<td>Sparse QR decomposition of a sparse matrix</td></tr>
+<tr><td width="25%"><a href="sparseQR-class.html">qr.qy-method</a></td>
+<td>Sparse QR decomposition of a sparse matrix</td></tr>
+<tr><td width="25%"><a href="sparseQR-class.html">qr.R-method</a></td>
+<td>Sparse QR decomposition of a sparse matrix</td></tr>
+<tr><td width="25%"><a href="sparseQR-class.html">qr.resid-method</a></td>
+<td>Sparse QR decomposition of a sparse matrix</td></tr>
+</table>
+
+<h2><a name="R">-- R --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="rankMatrix.html">rankMatrix</a></td>
+<td>Rank of a Matrix</td></tr>
+<tr><td width="25%"><a href="cBind.html">rBind</a></td>
+<td>Versions of 'cbind' and 'rbind' recursively built on cbind2/rbind2</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">rbind2-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="denseMatrix-class.html">rbind2-method</a></td>
+<td>Virtual Class "denseMatrix" of All Dense Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">rbind2-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="sparseMatrix-class.html">rbind2-method</a></td>
+<td>Virtual Class "sparseMatrix" - Mother of Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="rcond.html">rcond</a></td>
+<td>Estimate the Reciprocal Condition Number</td></tr>
+<tr><td width="25%"><a href="ddenseMatrix-class.html">rcond-method</a></td>
+<td>Virtual Class "ddenseMatrix" of Numeric Dense Matrices</td></tr>
+<tr><td width="25%"><a href="denseMatrix-class.html">rcond-method</a></td>
+<td>Virtual Class "denseMatrix" of All Dense Matrices</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">rcond-method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="dpoMatrix-class.html">rcond-method</a></td>
+<td>Positive Semi-definite Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dsyMatrix-class.html">rcond-method</a></td>
+<td>Symmetric Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dtpMatrix-class.html">rcond-method</a></td>
+<td>Packed triangular dense matrices</td></tr>
+<tr><td width="25%"><a href="dtrMatrix-class.html">rcond-method</a></td>
+<td>Triangular, dense, numeric matrices</td></tr>
+<tr><td width="25%"><a href="rcond.html">rcond-method</a></td>
+<td>Estimate the Reciprocal Condition Number</td></tr>
+<tr><td width="25%"><a href="externalFormats.html">readHB</a></td>
+<td>Read and write external matrix formats</td></tr>
+<tr><td width="25%"><a href="externalFormats.html">readMM</a></td>
+<td>Read and write external matrix formats</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">rep-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="rep2abI.html">rep2abI</a></td>
+<td>Replicate Vectors into 'abIndex' Result</td></tr>
+<tr><td width="25%"><a href="replValue-class.html">replValue-class</a></td>
+<td>Virtual Class "replValue" - Simple Class for subassignment Values</td></tr>
+<tr><td width="25%"><a href="rleDiff-class.html">rleDiff-class</a></td>
+<td>Class "rleDiff" of rle(diff(.)) Stored Vectors</td></tr>
+<tr><td width="25%"><a href="dgCMatrix-class.html">round-method</a></td>
+<td>Compressed, sparse, column-oriented numeric matrices</td></tr>
+<tr><td width="25%"><a href="colSums.html">rowMeans</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="colSums.html">rowMeans-method</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">rowMeans-method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="colSums.html">rowSums</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="colSums.html">rowSums-method</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">rowSums-method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="RsparseMatrix-class.html">RsparseMatrix-class</a></td>
+<td>Class "RsparseMatrix" of Sparse Matrices in Column-compressed Form</td></tr>
+</table>
+
+<h2><a name="S">-- S --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Schur.html">Schur</a></td>
+<td>Schur Decomposition of a Matrix</td></tr>
+<tr><td width="25%"><a href="Schur-class.html">Schur-class</a></td>
+<td>Class "Schur" of Schur Matrix Factorizations</td></tr>
+<tr><td width="25%"><a href="Schur.html">Schur-method</a></td>
+<td>Schur Decomposition of a Matrix</td></tr>
+<tr><td width="25%"><a href="abIndex-class.html">seqMat-class</a></td>
+<td>Class "abIndex" of Abstract Index Vectors</td></tr>
+<tr><td width="25%"><a href="Cholesky-class.html">show-method</a></td>
+<td>Cholesky and Bunch-Kaufman Decompositions</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">show-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="MatrixFactorization-class.html">show-method</a></td>
+<td>Class "MatrixFactorization" of Matrix Factorizations</td></tr>
+<tr><td width="25%"><a href="abIndex-class.html">show-method</a></td>
+<td>Class "abIndex" of Abstract Index Vectors</td></tr>
+<tr><td width="25%"><a href="dMatrix-class.html">show-method</a></td>
+<td>(Virtual) Class "dMatrix" of "double" Matrices</td></tr>
+<tr><td width="25%"><a href="ddenseMatrix-class.html">show-method</a></td>
+<td>Virtual Class "ddenseMatrix" of Numeric Dense Matrices</td></tr>
+<tr><td width="25%"><a href="denseMatrix-class.html">show-method</a></td>
+<td>Virtual Class "denseMatrix" of All Dense Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">show-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="dsyMatrix-class.html">show-method</a></td>
+<td>Symmetric Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dtrMatrix-class.html">show-method</a></td>
+<td>Triangular, dense, numeric matrices</td></tr>
+<tr><td width="25%"><a href="nMatrix-class.html">show-method</a></td>
+<td>Class "nMatrix" of Non-zero Pattern Matrices</td></tr>
+<tr><td width="25%"><a href="rleDiff-class.html">show-method</a></td>
+<td>Class "rleDiff" of rle(diff(.)) Stored Vectors</td></tr>
+<tr><td width="25%"><a href="sparseMatrix-class.html">show-method</a></td>
+<td>Virtual Class "sparseMatrix" - Mother of Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">show-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="dgCMatrix-class.html">signif-method</a></td>
+<td>Compressed, sparse, column-oriented numeric matrices</td></tr>
+<tr><td width="25%"><a href="symmpart.html">skewpart</a></td>
+<td>Symmetric Part and Skew(symmetric) Part of a Matrix</td></tr>
+<tr><td width="25%"><a href="symmpart.html">skewpart-method</a></td>
+<td>Symmetric Part and Skew(symmetric) Part of a Matrix</td></tr>
+<tr><td width="25%"><a href="symmpart.html">skewpart-methods</a></td>
+<td>Symmetric Part and Skew(symmetric) Part of a Matrix</td></tr>
+<tr><td width="25%"><a href="CHMfactor-class.html">solve-method</a></td>
+<td>CHOLMOD-based Cholesky Factorizations</td></tr>
+<tr><td width="25%"><a href="LU-class.html">solve-method</a></td>
+<td>LU (dense) Matrix Decompositions</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">solve-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="MatrixFactorization-class.html">solve-method</a></td>
+<td>Class "MatrixFactorization" of Matrix Factorizations</td></tr>
+<tr><td width="25%"><a href="TsparseMatrix-class.html">solve-method</a></td>
+<td>Class "TsparseMatrix" of Sparse Matrices in Triplet Form</td></tr>
+<tr><td width="25%"><a href="dMatrix-class.html">solve-method</a></td>
+<td>(Virtual) Class "dMatrix" of "double" Matrices</td></tr>
+<tr><td width="25%"><a href="ddenseMatrix-class.html">solve-method</a></td>
+<td>Virtual Class "ddenseMatrix" of Numeric Dense Matrices</td></tr>
+<tr><td width="25%"><a href="dgCMatrix-class.html">solve-method</a></td>
+<td>Compressed, sparse, column-oriented numeric matrices</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">solve-method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">solve-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="dpoMatrix-class.html">solve-method</a></td>
+<td>Positive Semi-definite Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dsCMatrix-class.html">solve-method</a></td>
+<td>Numeric Symmetric Sparse (column compressed) Matrices</td></tr>
+<tr><td width="25%"><a href="dsyMatrix-class.html">solve-method</a></td>
+<td>Symmetric Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dtCMatrix-class.html">solve-method</a></td>
+<td>Triangular, (compressed) sparse column matrices</td></tr>
+<tr><td width="25%"><a href="dtpMatrix-class.html">solve-method</a></td>
+<td>Packed triangular dense matrices</td></tr>
+<tr><td width="25%"><a href="dtrMatrix-class.html">solve-method</a></td>
+<td>Triangular, dense, numeric matrices</td></tr>
+<tr><td width="25%"><a href="pMatrix-class.html">solve-method</a></td>
+<td>Permutation matrices</td></tr>
+<tr><td width="25%"><a href="sparseQR-class.html">solve-method</a></td>
+<td>Sparse QR decomposition of a sparse matrix</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">solve-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="sparse.model.matrix.html">sparse.model.matrix</a></td>
+<td>Construct Sparse Design / Model Matrices</td></tr>
+<tr><td width="25%"><a href="sparseLU-class.html">sparseLU-class</a></td>
+<td>Sparse LU decomposition of a square sparse matrix</td></tr>
+<tr><td width="25%"><a href="SparseM-conv.html">SparseM-coerce-methods</a></td>
+<td>Sparse Matrix Coercion from and to those from package "SparseM"</td></tr>
+<tr><td width="25%"><a href="sparseMatrix.html">sparseMatrix</a></td>
+<td>General Sparse Matrix Construction from Nonzero Entries</td></tr>
+<tr><td width="25%"><a href="sparseMatrix-class.html">sparseMatrix-class</a></td>
+<td>Virtual Class "sparseMatrix" - Mother of Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="sparseQR-class.html">sparseQR-class</a></td>
+<td>Sparse QR decomposition of a sparse matrix</td></tr>
+<tr><td width="25%"><a href="sparseVector.html">sparseVector</a></td>
+<td>Sparse Vector Construction from Nonzero Entries</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">sparseVector-class</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="spMatrix.html">spMatrix</a></td>
+<td>Sparse Matrix Constructor From Triplet</td></tr>
+<tr><td width="25%"><a href="Subassign-methods.html">Subassign-methods</a></td>
+<td>Methods for "[<-" - Assigning to Subsets for 'Matrix'</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">sum-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">Summary-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="abIndex-class.html">Summary-method</a></td>
+<td>Class "abIndex" of Abstract Index Vectors</td></tr>
+<tr><td width="25%"><a href="dMatrix-class.html">Summary-method</a></td>
+<td>(Virtual) Class "dMatrix" of "double" Matrices</td></tr>
+<tr><td width="25%"><a href="ddenseMatrix-class.html">Summary-method</a></td>
+<td>Virtual Class "ddenseMatrix" of Numeric Dense Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">Summary-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="dsparseMatrix-class.html">Summary-method</a></td>
+<td>Virtual Class "dsparseMatrix" of Numeric Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="nMatrix-class.html">Summary-method</a></td>
+<td>Class "nMatrix" of Non-zero Pattern Matrices</td></tr>
+<tr><td width="25%"><a href="pMatrix-class.html">Summary-method</a></td>
+<td>Permutation matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">Summary-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">summary-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="sparseMatrix-class.html">summary-method</a></td>
+<td>Virtual Class "sparseMatrix" - Mother of Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="symmetricMatrix-class.html">symmetricMatrix-class</a></td>
+<td>Virtual Class of Symmetric Matrices in package:Matrix</td></tr>
+<tr><td width="25%"><a href="symmpart.html">symmpart</a></td>
+<td>Symmetric Part and Skew(symmetric) Part of a Matrix</td></tr>
+<tr><td width="25%"><a href="symmpart.html">symmpart-method</a></td>
+<td>Symmetric Part and Skew(symmetric) Part of a Matrix</td></tr>
+<tr><td width="25%"><a href="symmpart.html">symmpart-methods</a></td>
+<td>Symmetric Part and Skew(symmetric) Part of a Matrix</td></tr>
+</table>
+
+<h2><a name="T">-- T --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="CsparseMatrix-class.html">t-method</a></td>
+<td>Class "CsparseMatrix" of Sparse Matrices in Column-compressed Form</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">t-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="RsparseMatrix-class.html">t-method</a></td>
+<td>Class "RsparseMatrix" of Sparse Matrices in Column-compressed Form</td></tr>
+<tr><td width="25%"><a href="TsparseMatrix-class.html">t-method</a></td>
+<td>Class "TsparseMatrix" of Sparse Matrices in Triplet Form</td></tr>
+<tr><td width="25%"><a href="ddenseMatrix-class.html">t-method</a></td>
+<td>Virtual Class "ddenseMatrix" of Numeric Dense Matrices</td></tr>
+<tr><td width="25%"><a href="dgCMatrix-class.html">t-method</a></td>
+<td>Compressed, sparse, column-oriented numeric matrices</td></tr>
+<tr><td width="25%"><a href="dgRMatrix-class.html">t-method</a></td>
+<td>Sparse Compressed, Row-oriented Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">t-method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">t-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="dpoMatrix-class.html">t-method</a></td>
+<td>Positive Semi-definite Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dsCMatrix-class.html">t-method</a></td>
+<td>Numeric Symmetric Sparse (column compressed) Matrices</td></tr>
+<tr><td width="25%"><a href="dsyMatrix-class.html">t-method</a></td>
+<td>Symmetric Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dtCMatrix-class.html">t-method</a></td>
+<td>Triangular, (compressed) sparse column matrices</td></tr>
+<tr><td width="25%"><a href="dtpMatrix-class.html">t-method</a></td>
+<td>Packed triangular dense matrices</td></tr>
+<tr><td width="25%"><a href="dtrMatrix-class.html">t-method</a></td>
+<td>Triangular, dense, numeric matrices</td></tr>
+<tr><td width="25%"><a href="lgeMatrix-class.html">t-method</a></td>
+<td>Class "lgeMatrix" of General Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">t-method</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="lsyMatrix-class.html">t-method</a></td>
+<td>Symmetric Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="ltrMatrix-class.html">t-method</a></td>
+<td>Triangular Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="ngeMatrix-class.html">t-method</a></td>
+<td>Class "ngeMatrix" of General Dense Nonzero-pattern Matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">t-method</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="nsyMatrix-class.html">t-method</a></td>
+<td>Symmetric Dense Nonzero-Pattern Matrices</td></tr>
+<tr><td width="25%"><a href="ntrMatrix-class.html">t-method</a></td>
+<td>Triangular Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="pMatrix-class.html">t-method</a></td>
+<td>Permutation matrices</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">tail-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">tail-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="tcrossprod.html">tcrossprod</a></td>
+<td>Cross-product of transpose</td></tr>
+<tr><td width="25%"><a href="CsparseMatrix-class.html">tcrossprod-method</a></td>
+<td>Class "CsparseMatrix" of Sparse Matrices in Column-compressed Form</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">tcrossprod-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="TsparseMatrix-class.html">tcrossprod-method</a></td>
+<td>Class "TsparseMatrix" of Sparse Matrices in Triplet Form</td></tr>
+<tr><td width="25%"><a href="ddenseMatrix-class.html">tcrossprod-method</a></td>
+<td>Virtual Class "ddenseMatrix" of Numeric Dense Matrices</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">tcrossprod-method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">tcrossprod-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="dtrMatrix-class.html">tcrossprod-method</a></td>
+<td>Triangular, dense, numeric matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">tcrossprod-method</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">tcrossprod-method</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="pMatrix-class.html">tcrossprod-method</a></td>
+<td>Permutation matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">tcrossprod-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="tcrossprod.html">tcrossprod-method</a></td>
+<td>Cross-product of transpose</td></tr>
+<tr><td width="25%"><a href="tcrossprod.html">tcrossprod-methods</a></td>
+<td>Cross-product of transpose</td></tr>
+<tr><td width="25%"><a href="triangularMatrix-class.html">triangularMatrix-class</a></td>
+<td>Virtual Class of Triangular Matrices in package:Matrix</td></tr>
+<tr><td width="25%"><a href="band.html">tril</a></td>
+<td>Extract bands of a matrix</td></tr>
+<tr><td width="25%"><a href="band.html">tril-method</a></td>
+<td>Extract bands of a matrix</td></tr>
+<tr><td width="25%"><a href="band.html">tril-methods</a></td>
+<td>Extract bands of a matrix</td></tr>
+<tr><td width="25%"><a href="band.html">triu</a></td>
+<td>Extract bands of a matrix</td></tr>
+<tr><td width="25%"><a href="band.html">triu-method</a></td>
+<td>Extract bands of a matrix</td></tr>
+<tr><td width="25%"><a href="band.html">triu-methods</a></td>
+<td>Extract bands of a matrix</td></tr>
+<tr><td width="25%"><a href="TsparseMatrix-class.html">TsparseMatrix-class</a></td>
+<td>Class "TsparseMatrix" of Sparse Matrices in Triplet Form</td></tr>
+</table>
+
+<h2><a name="U">-- U --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Matrix-class.html">unname-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="unpack.html">unpack</a></td>
+<td>Representation of Packed and Unpacked (Dense) Matrices</td></tr>
+<tr><td width="25%"><a href="unpack.html">unpack-method</a></td>
+<td>Representation of Packed and Unpacked (Dense) Matrices</td></tr>
+<tr><td width="25%"><a href="CHMfactor-class.html">update-method</a></td>
+<td>CHOLMOD-based Cholesky Factorizations</td></tr>
+<tr><td width="25%"><a href="updown.html">updown</a></td>
+<td>Up- and Down-Dating a Cholesky Decomposition</td></tr>
+<tr><td width="25%"><a href="updown.html">updown-method</a></td>
+<td>Up- and Down-Dating a Cholesky Decomposition</td></tr>
+<tr><td width="25%"><a href="updown.html">updown-methods</a></td>
+<td>Up- and Down-Dating a Cholesky Decomposition</td></tr>
+<tr><td width="25%"><a href="USCounties.html">USCounties</a></td>
+<td>USCounties Contiguity Matrix</td></tr>
+</table>
+
+<h2><a name="W">-- W --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="diagonalMatrix-class.html">which-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="ldenseMatrix-class.html">which-method</a></td>
+<td>Virtual Class "ldenseMatrix" of Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">which-method</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="ndenseMatrix-class.html">which-method</a></td>
+<td>Virtual Class "ndenseMatrix" of Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">which-method</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="externalFormats.html">writeMM</a></td>
+<td>Read and write external matrix formats</td></tr>
+<tr><td width="25%"><a href="externalFormats.html">writeMM-method</a></td>
+<td>Read and write external matrix formats</td></tr>
+</table>
+
+<h2><a name="X">-- X --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="sparseVector-class.html">xsparseVector-class</a></td>
+<td>Sparse Vector Classes</td></tr>
+</table>
+
+<h2><a name="Z">-- Z --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="dMatrix-class.html">zapsmall-method</a></td>
+<td>(Virtual) Class "dMatrix" of "double" Matrices</td></tr>
+<tr><td width="25%"><a href="unused-classes.html">zMatrix-class</a></td>
+<td>Virtual Classes Not Yet Really Implemented and Used</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">zsparseVector-class</a></td>
+<td>Sparse Vector Classes</td></tr>
+</table>
+
+<h2><a name="misc">-- misc --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Matrix-class.html">!-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="ldenseMatrix-class.html">!-method</a></td>
+<td>Virtual Class "ldenseMatrix" of Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="ldiMatrix-class.html">!-method</a></td>
+<td>Class "ldiMatrix" of Diagonal Logical Matrices</td></tr>
+<tr><td width="25%"><a href="lgeMatrix-class.html">!-method</a></td>
+<td>Class "lgeMatrix" of General Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">!-method</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="ltrMatrix-class.html">!-method</a></td>
+<td>Triangular Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="ndenseMatrix-class.html">!-method</a></td>
+<td>Virtual Class "ndenseMatrix" of Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="ngeMatrix-class.html">!-method</a></td>
+<td>Class "ngeMatrix" of General Dense Nonzero-pattern Matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">!-method</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="ntrMatrix-class.html">!-method</a></td>
+<td>Triangular Dense Logical Matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">!-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">%%-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="CsparseMatrix-class.html">%*%-method</a></td>
+<td>Class "CsparseMatrix" of Sparse Matrices in Column-compressed Form</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">%*%-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="TsparseMatrix-class.html">%*%-method</a></td>
+<td>Class "TsparseMatrix" of Sparse Matrices in Triplet Form</td></tr>
+<tr><td width="25%"><a href="dMatrix-class.html">%*%-method</a></td>
+<td>(Virtual) Class "dMatrix" of "double" Matrices</td></tr>
+<tr><td width="25%"><a href="ddenseMatrix-class.html">%*%-method</a></td>
+<td>Virtual Class "ddenseMatrix" of Numeric Dense Matrices</td></tr>
+<tr><td width="25%"><a href="dgCMatrix-class.html">%*%-method</a></td>
+<td>Compressed, sparse, column-oriented numeric matrices</td></tr>
+<tr><td width="25%"><a href="dgeMatrix-class.html">%*%-method</a></td>
+<td>Class "dgeMatrix" of Dense Numeric (S4 Class) Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">%*%-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="dsparseMatrix-class.html">%*%-method</a></td>
+<td>Virtual Class "dsparseMatrix" of Numeric Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="dsyMatrix-class.html">%*%-method</a></td>
+<td>Symmetric Dense Numeric Matrices</td></tr>
+<tr><td width="25%"><a href="dtpMatrix-class.html">%*%-method</a></td>
+<td>Packed triangular dense matrices</td></tr>
+<tr><td width="25%"><a href="dtrMatrix-class.html">%*%-method</a></td>
+<td>Triangular, dense, numeric matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">%*%-method</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">%*%-method</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="pMatrix-class.html">%*%-method</a></td>
+<td>Permutation matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">%*%-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">%/%-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">&-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">*-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">+-method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="dgTMatrix-class.html">+-method</a></td>
+<td>Sparse matrices in triplet form</td></tr>
+<tr><td width="25%"><a href="Matrix-class.html">--method</a></td>
+<td>Virtual Class "Matrix" Class of Matrices</td></tr>
+<tr><td width="25%"><a href="denseMatrix-class.html">--method</a></td>
+<td>Virtual Class "denseMatrix" of All Dense Matrices</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">--method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="lsparseMatrix-classes.html">--method</a></td>
+<td>Sparse logical matrices</td></tr>
+<tr><td width="25%"><a href="nsparseMatrix-classes.html">--method</a></td>
+<td>Sparse "pattern" Matrices</td></tr>
+<tr><td width="25%"><a href="pMatrix-class.html">--method</a></td>
+<td>Permutation matrices</td></tr>
+<tr><td width="25%"><a href="sparseMatrix-class.html">--method</a></td>
+<td>Virtual Class "sparseMatrix" - Mother of Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">--method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="bdiag.html">.bdiag</a></td>
+<td>Construct a Block Diagonal Matrix</td></tr>
+<tr><td width="25%"><a href="diagU2N.html">.diagU2N</a></td>
+<td>Transform Triangular Matrices from Unit Triangular to General and back</td></tr>
+<tr><td width="25%"><a href="formatSparseM.html">.formatSparseSimple</a></td>
+<td>Formatting Sparse Numeric Matrices Utilities</td></tr>
+<tr><td width="25%"><a href="Diagonal.html">.sparseDiagonal</a></td>
+<td>Create Diagonal Matrix Object</td></tr>
+<tr><td width="25%"><a href="Diagonal.html">.symDiagonal</a></td>
+<td>Create Diagonal Matrix Object</td></tr>
+<tr><td width="25%"><a href="CHMfactor-class.html">.updateCHMfactor</a></td>
+<td>CHOLMOD-based Cholesky Factorizations</td></tr>
+<tr><td width="25%"><a href="CsparseMatrix-class.html">.validateCsparse</a></td>
+<td>Class "CsparseMatrix" of Sparse Matrices in Column-compressed Form</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">/-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+<tr><td width="25%"><a href="Xtrct-methods.html">[-method</a></td>
+<td>Methods for "[": Extraction or Subsetting in Package 'Matrix'</td></tr>
+<tr><td width="25%"><a href="abIndex-class.html">[-method</a></td>
+<td>Class "abIndex" of Abstract Index Vectors</td></tr>
+<tr><td width="25%"><a href="dMatrix-class.html">[-method</a></td>
+<td>(Virtual) Class "dMatrix" of "double" Matrices</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">[-method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="Xtrct-methods.html">[-methods</a></td>
+<td>Methods for "[": Extraction or Subsetting in Package 'Matrix'</td></tr>
+<tr><td width="25%"><a href="Subassign-methods.html">[<--method</a></td>
+<td>Methods for "[<-" - Assigning to Subsets for 'Matrix'</td></tr>
+<tr><td width="25%"><a href="sparseVector-class.html">[<--method</a></td>
+<td>Sparse Vector Classes</td></tr>
+<tr><td width="25%"><a href="Subassign-methods.html">[<--methods</a></td>
+<td>Methods for "[<-" - Assigning to Subsets for 'Matrix'</td></tr>
+<tr><td width="25%"><a href="diagonalMatrix-class.html">^-method</a></td>
+<td>Class "diagonalMatrix" of Diagonal Matrices</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/Matrix/html/R.css b/win32/deps/library/Matrix/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/Matrix/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/Matrix/include/Matrix.h b/win32/deps/library/Matrix/include/Matrix.h
index 590a94c..2ba4a9c 100644
--- a/win32/deps/library/Matrix/include/Matrix.h
+++ b/win32/deps/library/Matrix/include/Matrix.h
@@ -2,10 +2,13 @@
#define MATRIX_H
#include <Rdefines.h>
#include <Rconfig.h>
-#include "cholmod.h"
+#include "cholmod.h" //---> M_cholmod_*() declarations
#ifdef __cplusplus
extern "C" {
+// and bool is defined
+#else
+# define bool Rboolean
#endif
#ifdef HAVE_VISIBILITY_ATTRIBUTE
@@ -14,13 +17,40 @@ extern "C" {
# define attribute_hidden
#endif
+// Copied from ../../src/Mutils.h ----------------------------------------
+#define MATRIX_VALID_dense \
+ "dmatrix", "dgeMatrix", \
+ "lmatrix", "lgeMatrix", \
+ "nmatrix", "ngeMatrix", \
+ "zmatrix", "zgeMatrix"
+
+#define MATRIX_VALID_Csparse \
+ "dgCMatrix", "dsCMatrix", "dtCMatrix", \
+ "lgCMatrix", "lsCMatrix", "ltCMatrix", \
+ "ngCMatrix", "nsCMatrix", "ntCMatrix", \
+ "zgCMatrix", "zsCMatrix", "ztCMatrix"
+
+#define MATRIX_VALID_Tsparse \
+ "dgTMatrix", "dsTMatrix", "dtTMatrix", \
+ "lgTMatrix", "lsTMatrix", "ltTMatrix", \
+ "ngTMatrix", "nsTMatrix", "ntTMatrix", \
+ "zgTMatrix", "zsTMatrix", "ztTMatrix"
+
+#define MATRIX_VALID_Rsparse \
+ "dgRMatrix", "dsRMatrix", "dtRMatrix", \
+ "lgRMatrix", "lsRMatrix", "ltRMatrix", \
+ "ngRMatrix", "nsRMatrix", "ntRMatrix", \
+ "zgRMatrix", "zsRMatrix", "ztRMatrix"
+
+#define MATRIX_VALID_CHMfactor "dCHMsuper", "dCHMsimpl", "nCHMsuper", "nCHMsimpl"
+
CHM_SP M_as_cholmod_sparse (CHM_SP ans, SEXP x, Rboolean check_Udiag, Rboolean sort_in_place);
CHM_TR M_as_cholmod_triplet(CHM_TR ans, SEXP x, Rboolean check_Udiag);
CHM_DN M_as_cholmod_dense(CHM_DN ans, SEXP x);
CHM_DN M_numeric_as_chm_dense(CHM_DN ans, double *v, int nr, int nc);
CHM_FR M_as_cholmod_factor(CHM_FR ans, SEXP x);
-double M_chm_factor_ldetL2(CHM_FR f);
-CHM_FR M_chm_factor_update(CHM_FR f, CHM_SP A, double mult);
+double M_chm_factor_ldetL2(const_CHM_FR f);
+CHM_FR M_chm_factor_update(CHM_FR f, const_CHM_SP A, double mult);
#define AS_CHM_DN(x) M_as_cholmod_dense((CHM_DN)alloca(sizeof(cholmod_dense)), x )
#define AS_CHM_FR(x) M_as_cholmod_factor((CHM_FR)alloca(sizeof(cholmod_factor)), x )
@@ -34,14 +64,25 @@ CHM_FR M_chm_factor_update(CHM_FR f, CHM_SP A, double mult);
#define N_AS_CHM_DN(x,nr,nc) M_numeric_as_chm_dense((CHM_DN)alloca(sizeof(cholmod_dense)), x , nr, nc )
SEXP M_Csparse_diagU2N(SEXP x);
-SEXP M_chm_factor_to_SEXP(CHM_FR f, int dofree);
-SEXP M_chm_sparse_to_SEXP(CHM_SP a, int dofree, int uploT, int Rkind,
- char *diag, SEXP dn);
-SEXP M_chm_triplet_to_SEXP(CHM_TR a, int dofree, int uploT, int Rkind,
+SEXP M_chm_factor_to_SEXP(const_CHM_FR f, int dofree);
+SEXP M_chm_sparse_to_SEXP(const_CHM_SP a, int dofree, int uploT, int Rkind,
+ const char *diag, SEXP dn);
+SEXP M_chm_triplet_to_SEXP(const CHM_TR a, int dofree, int uploT, int Rkind,
const char* diag, SEXP dn);
SEXP M_dpoMatrix_chol(SEXP x);
+int M_Matrix_check_class_etc(SEXP x, const char **valid);
+
+// ./Matrix_stubs.c "illustrative example code" (of the above):
+bool Matrix_isclass_Csparse(SEXP x);
+bool Matrix_isclass_triplet(SEXP x);
+bool Matrix_isclass_dense(SEXP x);
+bool Matrix_isclass_CHMfactor(SEXP x);
+
+
+/* TODO: Utilities for C level of model_matrix(*, sparse) */
+
#ifdef __cplusplus
}
#endif
diff --git a/win32/deps/library/Matrix/include/Matrix_stubs.c b/win32/deps/library/Matrix/include/Matrix_stubs.c
index 679ec78..210d115 100644
--- a/win32/deps/library/Matrix/include/Matrix_stubs.c
+++ b/win32/deps/library/Matrix/include/Matrix_stubs.c
@@ -1,10 +1,15 @@
#include <Rconfig.h>
#include <Rinternals.h>
#include <R_ext/Rdynload.h>
+#include <Rversion.h>
#include "cholmod.h"
+#include "Matrix.h"
#ifdef __cplusplus
extern "C" {
+// and bool is defined
+#else
+# define bool Rboolean
#endif
#ifdef HAVE_VISIBILITY_ATTRIBUTE
@@ -43,12 +48,12 @@ M_as_cholmod_sparse(CHM_SP ans, SEXP x, Rboolean check_Udiag, Rboolean sort_in_p
return fun(ans, x, check_Udiag, sort_in_place);
}
-CHM_SP attribute_hidden
-M_as_cholmod_triplet(CHM_SP ans, SEXP x, Rboolean check_Udiag)
+CHM_TR attribute_hidden
+M_as_cholmod_triplet(CHM_TR ans, SEXP x, Rboolean check_Udiag)
{
- static CHM_SP(*fun)(CHM_SP,SEXP,Rboolean)= NULL;
+ static CHM_TR(*fun)(CHM_TR,SEXP,Rboolean)= NULL;
if(fun == NULL)
- fun = (CHM_SP(*)(CHM_SP,SEXP,Rboolean))
+ fun = (CHM_TR(*)(CHM_TR,SEXP,Rboolean))
R_GetCCallable("Matrix", "as_cholmod_triplet");
return fun(ans, x, check_Udiag);
}
@@ -64,83 +69,94 @@ M_Csparse_diagU2N(SEXP x)
}
SEXP attribute_hidden
-M_chm_factor_to_SEXP(CHM_FR f, int dofree)
+M_chm_factor_to_SEXP(const_CHM_FR f, int dofree)
{
- static SEXP(*fun)(CHM_FR,int) = NULL;
+ static SEXP(*fun)(const_CHM_FR,int) = NULL;
if(fun == NULL)
- fun = (SEXP(*)(CHM_FR,int))
+ fun = (SEXP(*)(const_CHM_FR,int))
R_GetCCallable("Matrix", "chm_factor_to_SEXP");
return fun(f, dofree);
}
double attribute_hidden
-M_chm_factor_ldetL2(CHM_FR f)
+M_chm_factor_ldetL2(const_CHM_FR f)
{
- static double(*fun)(CHM_FR) = NULL;
+ static double(*fun)(const_CHM_FR) = NULL;
if(fun == NULL)
- fun = (double(*)(CHM_FR))
+ fun = (double(*)(const_CHM_FR))
R_GetCCallable("Matrix", "chm_factor_ldetL2");
return fun(f);
}
CHM_FR attribute_hidden
-M_chm_factor_update(CHM_FR f, CHM_SP A, double mult)
+M_chm_factor_update(CHM_FR f, const_CHM_SP A, double mult)
{
- static CHM_FR(*fun)(CHM_FR,CHM_SP,double) = NULL;
+ static CHM_FR(*fun)(CHM_FR,const_CHM_SP,double) = NULL;
if(fun == NULL)
- fun = (CHM_FR(*)(CHM_FR,CHM_SP,double))
+ fun = (CHM_FR(*)(CHM_FR,const_CHM_SP,double))
R_GetCCallable("Matrix", "chm_factor_update");
return fun(f, A, mult);
}
SEXP attribute_hidden
-M_chm_sparse_to_SEXP(CHM_SP a, int dofree,
- int uploT, int Rkind, char *diag, SEXP dn)
+M_chm_sparse_to_SEXP(const_CHM_SP a, int dofree,
+ int uploT, int Rkind, const char *diag, SEXP dn)
{
- static SEXP(*fun)(CHM_SP,int,int,int,char*,SEXP) = NULL;
+ static SEXP(*fun)(const_CHM_SP,int,int,int,const char*,SEXP) = NULL;
if(fun == NULL)
- fun = (SEXP(*)(CHM_SP,int,int,int,char*,SEXP))
+ fun = (SEXP(*)(const_CHM_SP,int,int,int,const char*,SEXP))
R_GetCCallable("Matrix", "chm_sparse_to_SEXP");
return fun(a, dofree, uploT, Rkind, diag, dn);
}
SEXP attribute_hidden
-M_chm_triplet_to_SEXP(CHM_TR a, int dofree,
+M_chm_triplet_to_SEXP(const CHM_TR a, int dofree,
int uploT, int Rkind, const char *diag, SEXP dn)
{
- static SEXP(*fun)(CHM_TR,int,int,int,const char*,SEXP) = NULL;
+ static SEXP(*fun)(const CHM_TR,int,int,int,const char*,SEXP) = NULL;
if(fun == NULL)
- fun = (SEXP(*)(CHM_TR,int,int,int,const char*,SEXP))
+ fun = (SEXP(*)(const CHM_TR,int,int,int,const char*,SEXP))
R_GetCCallable("Matrix", "chm_triplet_to_SEXP");
return fun(a, dofree, uploT, Rkind, diag, dn);
}
CHM_SP attribute_hidden
-M_cholmod_aat(CHM_SP A, int *fset, size_t fsize,
+M_cholmod_aat(const_CHM_SP A, int *fset, size_t fsize,
int mode, CHM_CM Common)
{
- static CHM_SP(*fun)(CHM_SP,int*,size_t,
+ static CHM_SP(*fun)(const_CHM_SP,int*,size_t,
int,CHM_CM) = NULL;
if(fun == NULL)
- fun = (CHM_SP(*)(CHM_SP,int*,size_t,
+ fun = (CHM_SP(*)(const_CHM_SP,int*,size_t,
int,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_aat");
+ R_GetCCallable("Matrix", "cholmod_aat");
return fun(A, fset, fsize, mode, Common);
}
+int attribute_hidden
+M_cholmod_band_inplace(CHM_SP A, int k1, int k2, int mode,
+ CHM_CM Common)
+{
+ static int(*fun)(CHM_SP,int,int,int,CHM_CM) = NULL;
+ if (fun == NULL)
+ fun = (int(*)(CHM_SP,int,int,int,CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_band_inplace");
+ return fun(A, k1, k2, mode, Common);
+}
+
CHM_SP attribute_hidden
-M_cholmod_add(CHM_SP A, CHM_SP B,
+M_cholmod_add(const_CHM_SP A, const_CHM_SP B,
double alpha[2], double beta[2], int values,
int sorted, CHM_CM Common)
{
- static CHM_SP(*fun)(CHM_SP,CHM_SP,
+ static CHM_SP(*fun)(const_CHM_SP,const_CHM_SP,
double*,double*,int,int,
CHM_CM) = NULL;
if (fun == NULL)
- fun = (CHM_SP(*)(CHM_SP,CHM_SP,
+ fun = (CHM_SP(*)(const_CHM_SP,const_CHM_SP,
double*,double*,int,int,
CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_add");
+ R_GetCCallable("Matrix", "cholmod_add");
return fun(A, B, alpha, beta, values, sorted, Common);
}
@@ -153,7 +169,7 @@ M_cholmod_allocate_dense(size_t nrow, size_t ncol, size_t d,
if (fun == NULL)
fun = (CHM_DN(*)(size_t,size_t,size_t,
int,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_allocate_dense");
+ R_GetCCallable("Matrix", "cholmod_allocate_dense");
return fun(nrow, ncol, d, xtype, Common);
}
@@ -167,7 +183,7 @@ M_cholmod_allocate_sparse(size_t nrow, size_t ncol, size_t nzmax,
if (fun == NULL)
fun = (CHM_SP(*)
(size_t,size_t,size_t,int,int,int,int,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_allocate_sparse");
+ R_GetCCallable("Matrix", "cholmod_allocate_sparse");
return fun(nrow,ncol,nzmax,sorted,packed,stype,xtype,Common);
}
@@ -175,101 +191,95 @@ CHM_TR attribute_hidden
M_cholmod_allocate_triplet(size_t nrow, size_t ncol, size_t nzmax,
int stype, int xtype, CHM_CM Common)
{
- static cholmod_triplet*(*fun)(size_t,size_t,size_t,
- int,int,CHM_CM) = NULL;
+ static CHM_TR(*fun)(size_t,size_t,size_t, int,int,CHM_CM) = NULL;
if (fun == NULL)
- fun = (cholmod_triplet*(*)
- (size_t,size_t,size_t,int,int,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_allocate_triplet");
+ fun = (CHM_TR(*)(size_t,size_t,size_t,int,int,CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_allocate_triplet");
return fun(nrow,ncol,nzmax,stype,xtype,Common);
}
CHM_SP attribute_hidden
-M_cholmod_triplet_to_sparse(cholmod_triplet *T, int nzmax,
+M_cholmod_triplet_to_sparse(const cholmod_triplet* T, int nzmax,
CHM_CM Common)
{
- static CHM_SP(*fun)
- (cholmod_triplet*,int,CHM_CM) = NULL;
+ static CHM_SP(*fun)(const cholmod_triplet*,int,CHM_CM) = NULL;
if (fun == NULL)
- fun = (CHM_SP(*)(cholmod_triplet*,int,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_triplet_to_sparse");
+ fun = (CHM_SP(*)(const cholmod_triplet*,int,CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_triplet_to_sparse");
return fun(T, nzmax, Common);
}
CHM_TR attribute_hidden
-M_cholmod_sparse_to_triplet(CHM_SP A, CHM_CM Common)
+M_cholmod_sparse_to_triplet(const_CHM_SP A, CHM_CM Common)
{
- static cholmod_triplet*(*fun)
- (CHM_SP,CHM_CM) = NULL;
+ static CHM_TR(*fun)(const_CHM_SP,CHM_CM) = NULL;
if (fun == NULL)
- fun = (cholmod_triplet*(*)(CHM_SP,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_sparse_to_triplet");
+ fun = (CHM_TR(*)(const_CHM_SP,CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_sparse_to_triplet");
return fun(A, Common);
}
CHM_DN attribute_hidden
-M_cholmod_sparse_to_dense(CHM_SP A, CHM_CM Common)
+M_cholmod_sparse_to_dense(const_CHM_SP A, CHM_CM Common)
{
- static CHM_DN(*fun)
- (CHM_SP,CHM_CM) = NULL;
+ static CHM_DN(*fun)(const_CHM_SP,CHM_CM) = NULL;
if (fun == NULL)
- fun = (CHM_DN(*)(CHM_SP,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_sparse_to_dense");
+ fun = (CHM_DN(*)(const_CHM_SP,CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_sparse_to_dense");
return fun(A, Common);
}
CHM_FR attribute_hidden
-M_cholmod_analyze(CHM_SP A, CHM_CM Common)
+M_cholmod_analyze(const_CHM_SP A, CHM_CM Common)
{
- static CHM_FR(*fun)(CHM_SP,CHM_CM) = NULL;
+ static CHM_FR(*fun)(const_CHM_SP,CHM_CM) = NULL;
if (fun == NULL)
- fun = (CHM_FR(*)(CHM_SP,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_analyze");
+ fun = (CHM_FR(*)(const_CHM_SP,CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_analyze");
return fun(A, Common);
}
CHM_FR attribute_hidden
-M_cholmod_analyze_p(CHM_SP A, int *Perm, int *fset,
+M_cholmod_analyze_p(const_CHM_SP A, int *Perm, int *fset,
size_t fsize, CHM_CM Common)
{
- static CHM_FR(*fun)(CHM_SP,int*,int*,size_t,
+ static CHM_FR(*fun)(const_CHM_SP,int*,int*,size_t,
CHM_CM) = NULL;
if (fun == NULL)
- fun = (CHM_FR(*)(CHM_SP,int*,int*,
+ fun = (CHM_FR(*)(const_CHM_SP,int*,int*,
size_t,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_analyze_p");
+ R_GetCCallable("Matrix", "cholmod_analyze_p");
return fun(A, Perm, fset, fsize, Common);
}
CHM_SP attribute_hidden
-M_cholmod_copy(CHM_SP A, int stype,
+M_cholmod_copy(const_CHM_SP A, int stype,
int mode, CHM_CM Common)
{
- static CHM_SP(*fun)
- (CHM_SP,int,int,CHM_CM) = NULL;
+ static CHM_SP(*fun)(const_CHM_SP,int,int,CHM_CM) = NULL;
if (fun == NULL)
- fun = (CHM_SP(*)(CHM_SP,int,int,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_copy");
+ fun = (CHM_SP(*)(const_CHM_SP,int,int,CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_copy");
return fun(A, stype, mode, Common);
}
CHM_DN attribute_hidden
-M_cholmod_copy_dense(CHM_DN A, CHM_CM Common)
+M_cholmod_copy_dense(const_CHM_DN A, CHM_CM Common)
{
- static CHM_DN(*fun)(CHM_DN,CHM_CM) = NULL;
+ static CHM_DN(*fun)(const_CHM_DN,CHM_CM) = NULL;
if (fun == NULL)
- fun = (CHM_DN(*)(CHM_DN,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_copy_dense");
+ fun = (CHM_DN(*)(const_CHM_DN,CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_copy_dense");
return fun(A, Common);
}
CHM_FR attribute_hidden
-M_cholmod_copy_factor(CHM_FR L, CHM_CM Common)
+M_cholmod_copy_factor(const_CHM_FR L, CHM_CM Common)
{
- static CHM_FR(*fun)(CHM_FR,CHM_CM) = NULL;
+ static CHM_FR(*fun)(const_CHM_FR,CHM_CM) = NULL;
if (fun == NULL)
- fun = (CHM_FR(*)(CHM_FR,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_copy_factor");
+ fun = (CHM_FR(*)(const_CHM_FR,CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_copy_factor");
return fun(L, Common);
}
@@ -280,75 +290,74 @@ M_cholmod_change_factor(int to_xtype, int to_ll, int to_super, int to_packed,
static int(*fun)(int,int,int,int,int,CHM_FR,CHM_CM) = NULL;
if (fun == NULL)
fun = (int(*)(int,int,int,int,int,CHM_FR,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_change_factor");
+ R_GetCCallable("Matrix", "cholmod_change_factor");
return fun(to_xtype, to_ll, to_super, to_packed, to_monotonic, L, Common);
}
CHM_SP attribute_hidden
-M_cholmod_copy_sparse(CHM_SP A, CHM_CM Common)
+M_cholmod_copy_sparse(const_CHM_SP A, CHM_CM Common)
{
- static CHM_SP(*fun)(CHM_SP,CHM_CM) = NULL;
+ static CHM_SP(*fun)(const_CHM_SP,CHM_CM) = NULL;
if (fun == NULL)
- fun = (CHM_SP(*)(CHM_SP,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_copy_sparse");
+ fun = (CHM_SP(*)(const_CHM_SP,CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_copy_sparse");
return fun(A, Common);
}
CHM_SP attribute_hidden
-M_cholmod_factor_to_sparse(CHM_FR L, CHM_CM Common)
+M_cholmod_factor_to_sparse(const_CHM_FR L, CHM_CM Common)
{
- static CHM_SP(*fun)(CHM_FR,CHM_CM) = NULL;
+ static CHM_SP(*fun)(const_CHM_FR,CHM_CM) = NULL;
if (fun == NULL)
- fun = (CHM_SP(*)(CHM_FR,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_factor_to_sparse");
+ fun = (CHM_SP(*)(const_CHM_FR,CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_factor_to_sparse");
return fun(L, Common);
}
CHM_SP attribute_hidden
-M_cholmod_submatrix(CHM_SP A, int *rset, int rsize, int *cset,
+M_cholmod_submatrix(const_CHM_SP A, int *rset, int rsize, int *cset,
int csize, int values, int sorted, CHM_CM Common)
{
- static CHM_SP(*fun)(CHM_SP,int*,int,int*,int,
+ static CHM_SP(*fun)(const_CHM_SP,int*,int,int*,int,
int,int,CHM_CM) = NULL;
if (fun == NULL)
- fun = (CHM_SP(*)(CHM_SP,int*,int,int*,
+ fun = (CHM_SP(*)(const_CHM_SP,int*,int,int*,
int,int,int,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_submatrix");
+ R_GetCCallable("Matrix", "cholmod_submatrix");
return fun(A, rset, rsize, cset, csize, values, sorted, Common);
}
CHM_SP attribute_hidden
-M_cholmod_dense_to_sparse(CHM_DN X, int values, CHM_CM Common)
+M_cholmod_dense_to_sparse(const_CHM_DN X, int values, CHM_CM Common)
{
- static CHM_SP(*fun)(CHM_DN,int,CHM_CM) = NULL;
+ static CHM_SP(*fun)(const_CHM_DN,int,CHM_CM) = NULL;
if (fun == NULL)
- fun = (CHM_SP(*)(CHM_DN,int,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_dense_to_sparse");
+ fun = (CHM_SP(*)(const_CHM_DN,int,CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_dense_to_sparse");
return fun(X, values, Common);
}
int attribute_hidden
-M_cholmod_factorize(CHM_SP A, CHM_FR L,
- CHM_CM Common)
+M_cholmod_factorize(const_CHM_SP A, CHM_FR L, CHM_CM Common)
{
- static int(*fun)(CHM_SP,CHM_FR,CHM_CM) = NULL;
+ static int(*fun)(const_CHM_SP,CHM_FR,CHM_CM) = NULL;
if (fun == NULL)
- fun = (int(*)(CHM_SP,CHM_FR,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_factorize");
+ fun = (int(*)(const_CHM_SP,CHM_FR,CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_factorize");
return fun(A, L, Common);
}
int attribute_hidden
-M_cholmod_factorize_p(CHM_SP A, double *beta, int *fset,
+M_cholmod_factorize_p(const_CHM_SP A, double *beta, int *fset,
size_t fsize, CHM_FR L,
CHM_CM Common)
{
- static int(*fun)(CHM_SP,double*,int*,size_t,
+ static int(*fun)(const_CHM_SP,double*,int*,size_t,
CHM_FR,CHM_CM) = NULL;
if (fun == NULL)
- fun = (int(*)(CHM_SP,double*,int*,size_t,
+ fun = (int(*)(const_CHM_SP,double*,int*,size_t,
CHM_FR,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_factorize_p");
+ R_GetCCallable("Matrix", "cholmod_factorize_p");
return fun(A, beta, fset, fsize, L, Common);
}
@@ -359,7 +368,7 @@ M_cholmod_finish(CHM_CM Common)
static int(*fun)(CHM_CM) = NULL;
if (fun == NULL)
fun = (int(*)(CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_finish");
+ R_GetCCallable("Matrix", "cholmod_finish");
return fun(Common);
}
@@ -369,7 +378,7 @@ M_cholmod_sort(CHM_SP A, CHM_CM Common)
static int(*fun)(CHM_SP,CHM_CM) = NULL;
if (fun == NULL)
fun = (int(*)(CHM_SP,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_sort");
+ R_GetCCallable("Matrix", "cholmod_sort");
return fun(A, Common);
}
@@ -379,7 +388,7 @@ M_cholmod_free_dense(CHM_DN *A, CHM_CM Common)
static int(*fun)(CHM_DN*,CHM_CM) = NULL;
if (fun == NULL)
fun = (int(*)(CHM_DN*,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_free_dense");
+ R_GetCCallable("Matrix", "cholmod_free_dense");
return fun(A, Common);
}
@@ -389,7 +398,7 @@ M_cholmod_free_factor(CHM_FR *L, CHM_CM Common)
static int(*fun)(CHM_FR*,CHM_CM) = NULL;
if (fun == NULL)
fun = (int(*)(CHM_FR*,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_free_factor");
+ R_GetCCallable("Matrix", "cholmod_free_factor");
return fun(L, Common);
}
@@ -399,7 +408,7 @@ M_cholmod_free_sparse(CHM_SP *A, CHM_CM Common)
static int(*fun)(CHM_SP*,CHM_CM) = NULL;
if (fun == NULL)
fun = (int(*)(CHM_SP*,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_free_sparse");
+ R_GetCCallable("Matrix", "cholmod_free_sparse");
return fun(A, Common);
}
@@ -409,59 +418,61 @@ M_cholmod_free_triplet(cholmod_triplet **T, CHM_CM Common)
static int(*fun)(cholmod_triplet**,CHM_CM) = NULL;
if (fun == NULL)
fun = (int(*)(cholmod_triplet**,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_free_triplet");
+ R_GetCCallable("Matrix", "cholmod_free_triplet");
return fun(T, Common);
}
long attribute_hidden
-M_cholmod_nnz(CHM_SP A, CHM_CM Common)
+M_cholmod_nnz(const_CHM_SP A, CHM_CM Common)
{
- static long(*fun)(CHM_SP,CHM_CM) = NULL;
+ static long(*fun)(const_CHM_SP,CHM_CM) = NULL;
if (fun == NULL)
- fun = (long(*)(CHM_SP,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_nnz");
+ fun = (long(*)(const_CHM_SP,CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_nnz");
return fun(A, Common);
}
int attribute_hidden
-M_cholmod_sdmult(CHM_SP A, int transpose,
- double alpha [2], double beta [2],
- CHM_DN X, CHM_DN Y,
+M_cholmod_sdmult(const_CHM_SP A, int transpose,
+ const double *alpha, const double *beta,
+ const_CHM_DN X, CHM_DN Y,
CHM_CM Common)
{
- static int(*fun)(CHM_SP,int,double*,double*,
- CHM_DN,CHM_DN,CHM_CM) = NULL;
+ static int(*fun)(const_CHM_SP,int,const double*,
+ const double*,const_CHM_DN,
+ CHM_DN,CHM_CM) = NULL;
if (fun == NULL)
- fun = (int(*)(CHM_SP,int,double*,double*,
- CHM_DN,CHM_DN,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_sdmult");
+ fun = (int(*)(const_CHM_SP,int,const double*,
+ const double*, const_CHM_DN,
+ CHM_DN,CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_sdmult");
return fun(A, transpose, alpha, beta, X, Y, Common);
}
CHM_SP attribute_hidden
-M_cholmod_ssmult(CHM_SP A, CHM_SP B,
+M_cholmod_ssmult(const_CHM_SP A, const_CHM_SP B,
int stype, int values, int sorted,
CHM_CM Common)
{
- static CHM_SP(*fun)(CHM_SP,CHM_SP,
+ static CHM_SP(*fun)(const_CHM_SP,const_CHM_SP,
int,int,int,CHM_CM) = NULL;
if (fun == NULL)
- fun = (CHM_SP(*)(CHM_SP,CHM_SP,
+ fun = (CHM_SP(*)(const_CHM_SP,const_CHM_SP,
int,int,int,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_ssmult");
+ R_GetCCallable("Matrix", "cholmod_ssmult");
return fun(A, B, stype, values, sorted, Common);
}
CHM_DN attribute_hidden
-M_cholmod_solve(int sys, CHM_FR L,
- CHM_DN B, CHM_CM Common)
+M_cholmod_solve(int sys, const_CHM_FR L,
+ const_CHM_DN B, CHM_CM Common)
{
- static CHM_DN(*fun)(int,CHM_FR,CHM_DN,
+ static CHM_DN(*fun)(int,const_CHM_FR,const_CHM_DN,
CHM_CM) = NULL;
if (fun == NULL)
- fun = (CHM_DN(*)(int,CHM_FR,CHM_DN,
+ fun = (CHM_DN(*)(int,const_CHM_FR,const_CHM_DN,
CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_solve");
+ R_GetCCallable("Matrix", "cholmod_solve");
return fun(sys, L, B, Common);
}
@@ -472,29 +483,67 @@ M_cholmod_speye(size_t nrow, size_t ncol,
static CHM_SP(*fun)(size_t,size_t,int,CHM_CM) = NULL;
if (fun == NULL)
fun = (CHM_SP(*)(size_t,size_t,int,CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_speye");
+ R_GetCCallable("Matrix", "cholmod_speye");
return fun(nrow, ncol, xtype, Common);
}
CHM_SP attribute_hidden
-M_cholmod_spsolve(int sys, CHM_FR L,
- CHM_SP B, CHM_CM Common)
+M_cholmod_spsolve(int sys, const_CHM_FR L,
+ const_CHM_SP B, CHM_CM Common)
{
- static CHM_SP(*fun)(int,CHM_FR,
- CHM_SP, CHM_CM) = NULL;
+ static CHM_SP(*fun)(int,const_CHM_FR,
+ const_CHM_SP, CHM_CM) = NULL;
if (fun == NULL)
- fun = (CHM_SP(*)(int,CHM_FR,
- CHM_SP, CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_spsolve");
+ fun = (CHM_SP(*)(int,const_CHM_FR,
+ const_CHM_SP, CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_spsolve");
return fun(sys, L, B, Common);
}
+int attribute_hidden
+M_cholmod_defaults (CHM_CM Common)
+{
+ static int(*fun)(CHM_CM) = NULL;
+ if (fun == NULL)
+ fun = (int(*)(CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_defaults");
+ return fun(Common);
+}
+
+int attribute_hidden
+M_cholmod_updown(int update, const_CHM_SP C,
+ const_CHM_FR L, CHM_CM Common)
+{
+ static int(*fun)(int,const_CHM_SP,const_CHM_FR,
+ CHM_CM) = NULL;
+ if (fun == NULL)
+ fun = (int(*)(int,const_CHM_SP,const_CHM_FR,
+ CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_updown");
+ return fun(update, C, L, Common);
+}
+
+/* extern cholmod_common c; */
+
void attribute_hidden
M_R_cholmod_error(int status, const char *file, int line, const char *message)
{
- error("Cholmod error `%s' at file:%s, line %d", message, file, line);
+/* NB: keep in sync with R_cholmod_error(), ../../src/chm_common.c */
+
+ if(status < 0) {
+/* Note: Matrix itself uses CHM_set_common_env, CHM_store_common
+ * and CHM_restore_common to preserve settings through error calls.
+ * Consider defining your own error handler, *and* possibly restoring
+ * *your* version of the cholmod_common that *you* use.
+ */
+ error("Cholmod error '%s' at file '%s', line %d", message, file, line);
+ }
+ else
+ warning("Cholmod warning '%s' at file '%s', line %d",
+ message, file, line);
}
+#if 0 /* no longer used */
/* just to get 'int' instead of 'void' as required by CHOLMOD's print_function */
static int
R_cholmod_printf(const char* fmt, ...)
@@ -506,6 +555,7 @@ R_cholmod_printf(const char* fmt, ...)
va_end(ap);
return 0;
}
+#endif
int attribute_hidden
M_R_cholmod_start(CHM_CM Common)
@@ -514,34 +564,33 @@ M_R_cholmod_start(CHM_CM Common)
static int(*fun)(CHM_CM) = NULL;
if (fun == NULL)
fun = (int(*)(CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_start");
+ R_GetCCallable("Matrix", "cholmod_start");
val = fun(Common);
- Common->print_function = R_cholmod_printf; /* Rprintf gives warning */
+/*-- NB: keep in sync with R_cholmod_start() --> ../../src/chm_common.c */
+ /* do not allow CHOLMOD printing - currently */
+ Common->print_function = NULL;/* was R_cholmod_printf; /.* Rprintf gives warning */
+/* Consider using your own error handler: */
Common->error_handler = M_R_cholmod_error;
return val;
}
CHM_SP attribute_hidden
-M_cholmod_transpose(CHM_SP A, int values, CHM_CM Common)
+M_cholmod_transpose(const_CHM_SP A, int values, CHM_CM Common)
{
- static CHM_SP(*fun)(CHM_SP,int,
- CHM_CM) = NULL;
+ static CHM_SP(*fun)(const_CHM_SP,int,CHM_CM) = NULL;
if (fun == NULL)
- fun = (CHM_SP(*)(CHM_SP,int,
- CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_transpose");
+ fun = (CHM_SP(*)(const_CHM_SP,int,CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_transpose");
return fun(A, values, Common);
}
CHM_SP attribute_hidden
-M_cholmod_vertcat(CHM_SP A, CHM_SP B,
- int values, CHM_CM Common)
+M_cholmod_vertcat(const_CHM_SP A, const_CHM_SP B, int values, CHM_CM Common)
{
- static CHM_SP(*fun)(CHM_SP, CHM_SP,
- int, CHM_CM) = NULL;
+ static CHM_SP(*fun)(const_CHM_SP,const_CHM_SP,int,CHM_CM) = NULL;
if (fun == NULL)
- fun = (CHM_SP(*)(CHM_SP,CHM_SP, int, CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_vertcat");
+ fun = (CHM_SP(*)(const_CHM_SP,const_CHM_SP, int, CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_vertcat");
return fun(A, B, values, Common);
}
@@ -566,16 +615,53 @@ M_numeric_as_chm_dense(CHM_DN ans, double *v, int nr, int nc)
}
int attribute_hidden
-M_cholmod_scale(CHM_DN S, int scale, CHM_SP A,
+M_cholmod_scale(const_CHM_DN S, int scale, CHM_SP A,
CHM_CM Common)
{
- static int(*fun)(CHM_DN,int,CHM_SP, CHM_CM) = NULL;
+ static int(*fun)(const_CHM_DN,int,CHM_SP, CHM_CM) = NULL;
if (fun == NULL)
- fun = (int(*)(CHM_DN,int,CHM_SP, CHM_CM))
- R_GetCCallable("Matrix", "cholmod_l_scale");
+ fun = (int(*)(const_CHM_DN,int,CHM_SP, CHM_CM))
+ R_GetCCallable("Matrix", "cholmod_scale");
return fun(S, scale, A, Common);
}
+
+// for now still *export* M_Matrix_check_class_etc() -- deprecate it later__FIXME__
+int M_Matrix_check_class_etc(SEXP x, const char **valid)
+{
+#if R_VERSION < R_Version(2, 15, 0) // || R_SVN_REVISION < 57849
+ static int(*fun)(SEXP, const char**) = NULL;
+ if (fun == NULL)
+ fun = (int(*)(SEXP, const char**))
+ R_GetCCallable("Matrix", "Matrix_check_class_etc");
+ return fun(x, valid);
+#else
+ return R_check_class_etc(x, valid);
+#endif
+}
+
+const char *Matrix_valid_Csparse[] = { MATRIX_VALID_Csparse, ""};
+const char *Matrix_valid_dense[] = { MATRIX_VALID_dense, ""};
+const char *Matrix_valid_triplet[] = { MATRIX_VALID_Tsparse, ""};
+const char *Matrix_valid_CHMfactor[]={ MATRIX_VALID_CHMfactor, ""};
+
+bool Matrix_isclass_Csparse(SEXP x) {
+ return M_Matrix_check_class_etc(x, Matrix_valid_Csparse) >= 0;
+}
+
+bool Matrix_isclass_triplet(SEXP x) {
+ return M_Matrix_check_class_etc(x, Matrix_valid_triplet) >= 0;
+}
+
+bool Matrix_isclass_dense(SEXP x) {
+ return M_Matrix_check_class_etc(x, Matrix_valid_dense) >= 0;
+}
+
+bool Matrix_isclass_CHMfactor(SEXP x) {
+ return M_Matrix_check_class_etc(x, Matrix_valid_CHMfactor) >= 0;
+}
+
#ifdef __cplusplus
}
#endif
+
diff --git a/win32/deps/library/Matrix/include/cholmod.h b/win32/deps/library/Matrix/include/cholmod.h
index b8ee3e1..f592889 100644
--- a/win32/deps/library/Matrix/include/cholmod.h
+++ b/win32/deps/library/Matrix/include/cholmod.h
@@ -8,48 +8,92 @@
extern "C" {
#endif
+// from ../../src/UFconfig/UFconfig.h - line 51 :
+#ifndef UF_long
+
+#ifdef _WIN64
+
+#define UF_long __int64
+#define UF_long_max _I64_MAX
+#define UF_long_idd "I64d"
+
+#else
+
#define UF_long long
#define UF_long_max LONG_MAX
-#define UF_long_id "%ld"
-#define UFSPARSE_DATE "Aug 31, 2006"
-#define UFSPARSE_VER_CODE(main,sub) ((main) * 1000 + (sub))
-#define UFSPARSE_MAIN_VERSION 2
-#define UFSPARSE_SUB_VERSION 1
-#define UFSPARSE_SUBSUB_VERSION 0
-#define UFSPARSE_VERSION \
- UFSPARSE_VER_CODE(UFSPARSE_MAIN_VERSION,UFSPARSE_SUB_VERSION)
+#define UF_long_idd "ld"
+
+#endif
+#define UF_long_id "%" UF_long_idd
+#endif
+
+#define CHOLMOD_DATE "Jan 25, 2011"
+// from ../../src/CHOLMOD/Include/cholmod_core.h - line 275 :
+/* Each CHOLMOD object has its own type code. */
+
+#define CHOLMOD_COMMON 0
+#define CHOLMOD_SPARSE 1
+#define CHOLMOD_FACTOR 2
+#define CHOLMOD_DENSE 3
+#define CHOLMOD_TRIPLET 4
+/* ========================================================================== */
+/* === CHOLMOD Common ======================================================= */
+/* ========================================================================== */
+
+/* itype defines the types of integer used: */
#define CHOLMOD_INT 0 /* all integer arrays are int */
-#define CHOLMOD_INTLONG 1 /* most are int, some are long */
-#define CHOLMOD_LONG 2 /* all integer arrays are long */
+#define CHOLMOD_INTLONG 1 /* most are int, some are UF_long */
+#define CHOLMOD_LONG 2 /* all integer arrays are UF_long */
+
+/* dtype defines what the numerical type is (double or float): */
+#define CHOLMOD_DOUBLE 0 /* all numerical values are double */
+#define CHOLMOD_SINGLE 1 /* all numerical values are float */
+/* The dtype of all parameters for all CHOLMOD routines must match.
+ *
+ * Scalar floating-point values are always passed as double arrays of size 2
+ * (for the real and imaginary parts). They are typecast to float as needed.
+ * FUTURE WORK: the float case is not supported yet.
+ */
+
+/* xtype defines the kind of numerical values used: */
#define CHOLMOD_PATTERN 0 /* pattern only, no numerical values */
#define CHOLMOD_REAL 1 /* a real matrix */
#define CHOLMOD_COMPLEX 2 /* a complex matrix (ANSI C99 compatible) */
#define CHOLMOD_ZOMPLEX 3 /* a complex matrix (MATLAB compatible) */
-#define CHOLMOD_MAXMETHODS 9 /* maximum number of different methods that
- * cholmod_analyze can try. Must be >= 9. */
+/* Definitions for cholmod_common: */
+#define CHOLMOD_MAXMETHODS 9 /* maximum number of different methods that */
+ /* cholmod_analyze can try. Must be >= 9. */
+
+/* Common->status values. zero means success, negative means a fatal error,
+ * positive is a warning. */
#define CHOLMOD_OK 0 /* success */
#define CHOLMOD_NOT_INSTALLED (-1) /* failure: method not installed */
#define CHOLMOD_OUT_OF_MEMORY (-2) /* failure: out of memory */
#define CHOLMOD_TOO_LARGE (-3) /* failure: integer overflow occured */
#define CHOLMOD_INVALID (-4) /* failure: invalid input */
#define CHOLMOD_NOT_POSDEF (1) /* warning: matrix not pos. def. */
-#define CHOLMOD_DSMALL (2) /* warning: D for LDL' or diag(L) or
- * LL' has tiny absolute value */
+#define CHOLMOD_DSMALL (2) /* warning: D for LDL' or diag(L) or */
+ /* LL' has tiny absolute value */
+/* ordering method (also used for L->ordering) */
#define CHOLMOD_NATURAL 0 /* use natural ordering */
#define CHOLMOD_GIVEN 1 /* use given permutation */
#define CHOLMOD_AMD 2 /* use minimum degree (AMD) */
#define CHOLMOD_METIS 3 /* use METIS' nested dissection */
-#define CHOLMOD_NESDIS 4 /* use CHOLMOD's version of nested dissection:
- * node bisector applied recursively, followed
+#define CHOLMOD_NESDIS 4 /* use CHOLMOD's version of nested dissection:*/
+ /* node bisector applied recursively, followed
* by constrained minimum degree (CSYMAMD or
* CCOLAMD) */
#define CHOLMOD_COLAMD 5 /* use AMD for A, COLAMD for A*A' */
+
+/* POSTORDERED is not a method, but a result of natural ordering followed by a
+ * weighted postorder. It is used for L->ordering, not method [ ].ordering. */
#define CHOLMOD_POSTORDERED 6 /* natural ordering, postordered. */
+/* supernodal strategy (for Common->supernodal) */
#define CHOLMOD_SIMPLICIAL 0 /* always do simplicial */
#define CHOLMOD_AUTO 1 /* select simpl/super depending on matrix */
#define CHOLMOD_SUPERNODAL 2 /* always do supernodal */
@@ -195,7 +239,8 @@ typedef struct cholmod_common_struct
* of a try/catch block. No error message is printed
* and the Common->error_handler function is not called. */
- void (*error_handler) (int status, const char *file, int line, const char *message) ;
+ void (*error_handler) (int status, const char *file,
+ int line, const char *message) ;
/* Common->error_handler is the user's error handling routine. If not
* NULL, this routine is called if an error occurs in CHOLMOD. status
@@ -562,12 +607,33 @@ typedef struct cholmod_common_struct
* and workspace. Note: additional entries were added in v1.1 to the
* method array, above, and thus v1.0 and v1.1 are not binary compatible.
*
- * v1.1 and v1.2 are binary compatible.
+ * v1.1 to the current version are binary compatible.
*/
- double other1 [16] ;
- UF_long other2 [16] ;
- int other3 [14] ; /* reduced from size 16 in v1.1. */
+ /* ---------------------------------------------------------------------- */
+ double other1 [10] ;
+
+ double SPQR_xstat [4] ; /* for SuiteSparseQR statistics */
+
+ /* SuiteSparseQR control parameters: */
+ double SPQR_grain ; /* task size is >= max (total flops / grain) */
+ double SPQR_small ; /* task size is >= small */
+
+ /* ---------------------------------------------------------------------- */
+ UF_long SPQR_istat [10] ; /* for SuiteSparseQR statistics */
+ UF_long other2 [6] ; /* reduced from size 16 in v1.6 */
+
+ /* ---------------------------------------------------------------------- */
+ int other3 [10] ; /* reduced from size 16 in v1.1. */
+
+ int prefer_binary ; /* cholmod_read_triplet converts a symmetric
+ * pattern-only matrix into a real matrix. If
+ * prefer_binary is FALSE, the diagonal entries are set to 1 + the degree
+ * of the row/column, and off-diagonal entries are set to -1 (resulting
+ * in a positive definite matrix if the diagonal is zero-free). Most
+ * symmetric patterns are the pattern a positive definite matrix. If
+ * this parameter is TRUE, then the matrix is returned with a 1 in each
+ * entry, instead. Default: FALSE. Added in v1.3. */
/* control parameter (added for v1.2): */
int default_nesdis ; /* Default: FALSE. If FALSE, then the default
@@ -580,11 +646,23 @@ typedef struct cholmod_common_struct
int called_nd ; /* TRUE if the last call to
* cholmod_analyze called NESDIS or METIS. */
+ int blas_ok ; /* FALSE if BLAS int overflow; TRUE otherwise */
+
+ /* SuiteSparseQR control parameters: */
+ int SPQR_shrink ; /* controls stack realloc method */
+ int SPQR_nthreads ; /* number of TBB threads, 0 = auto */
+
+ /* ---------------------------------------------------------------------- */
size_t other4 [16] ;
+
+ /* ---------------------------------------------------------------------- */
void *other5 [16] ;
} cholmod_common ;
+// in ../../src/CHOLMOD/Include/cholmod_core.h skip forward to - line 1114 :
+/* A sparse matrix stored in compressed-column form. */
+
typedef struct cholmod_sparse_struct
{
size_t nrow ; /* the matrix is nrow-by-ncol */
@@ -635,6 +713,10 @@ typedef struct cholmod_sparse_struct
} cholmod_sparse ;
+// in ../../src/CHOLMOD/Include/cholmod_core.h skip forward to - line 1495 :
+/* A symbolic and numeric factorization, either simplicial or supernodal.
+ * In all cases, the row indices in the columns of L are kept sorted. */
+
typedef struct cholmod_factor_struct
{
/* ---------------------------------------------------------------------- */
@@ -756,6 +838,11 @@ typedef struct cholmod_factor_struct
} cholmod_factor ;
+// in ../../src/CHOLMOD/Include/cholmod_core.h skip forward to - line 1773 :
+/* A dense matrix in column-oriented form. It has no itype since it contains
+ * no integers. Entry in row i and column j is located in x [i+j*d].
+ */
+
typedef struct cholmod_dense_struct
{
size_t nrow ; /* the matrix is nrow-by-ncol */
@@ -769,6 +856,9 @@ typedef struct cholmod_dense_struct
} cholmod_dense ;
+// in ../../src/CHOLMOD/Include/cholmod_core.h skip forward to - line 1952 :
+/* A sparse matrix stored in triplet form. */
+
typedef struct cholmod_triplet_struct
{
size_t nrow ; /* the matrix is nrow-by-ncol */
@@ -782,40 +872,50 @@ typedef struct cholmod_triplet_struct
void *z ; /* size nzmax, if present */
int stype ; /* symmetry type */
+ // [................................]
int itype ; /* CHOLMOD_LONG: i and j are UF_long. Otherwise int. */
int xtype ; /* pattern, real, complex, or zomplex */
int dtype ; /* x and z are double or float */
} cholmod_triplet ;
-typedef struct cholmod_common_struct *CHM_CM ;
-typedef struct cholmod_dense_struct *CHM_DN ;
-typedef struct cholmod_factor_struct *CHM_FR ;
-typedef struct cholmod_sparse_struct *CHM_SP ;
-typedef struct cholmod_triplet_struct *CHM_TR ;
+// -------- our (Matrix) short and const_ forms of of the pointers :
+typedef cholmod_common* CHM_CM;
+typedef cholmod_dense* CHM_DN;
+typedef const cholmod_dense* const_CHM_DN;
+typedef cholmod_factor* CHM_FR;
+typedef const cholmod_factor* const_CHM_FR;
+typedef cholmod_sparse* CHM_SP;
+typedef const cholmod_sparse* const_CHM_SP;
+typedef cholmod_triplet* CHM_TR;
+typedef const cholmod_triplet* const_CHM_TR;
+
-int M_R_cholmod_start(CHM_CM Common);
+// --------- Matrix ("M_") R ("R_") pkg routines "re-exported": ---------------
+
+int M_R_cholmod_start(CHM_CM);
void M_R_cholmod_error(int status, const char *file, int line, const char *message);
-int M_cholmod_finish(CHM_CM Common);
+int M_cholmod_finish(CHM_CM);
CHM_SP M_cholmod_allocate_sparse(size_t nrow, size_t ncol,
size_t nzmax, int sorted,
int packed, int stype, int xtype,
- CHM_CM Common);
-int M_cholmod_free_factor(CHM_FR *L, CHM_CM Common);
-int M_cholmod_free_dense(CHM_DN *A, CHM_CM Common);
-int M_cholmod_free_sparse(CHM_SP *A, CHM_CM Common);
-int M_cholmod_free_triplet(CHM_TR *T, CHM_CM Common);
-
-long M_cholmod_nnz(CHM_SP A, CHM_CM Common);
-CHM_SP M_cholmod_speye(size_t nrow, size_t ncol, int xtype, CHM_CM Common);
-CHM_SP M_cholmod_transpose(CHM_SP A, int values, CHM_CM Common);
-int M_cholmod_sort(CHM_SP A, CHM_CM Common);
-CHM_SP M_cholmod_vertcat(CHM_SP A, CHM_SP B, int values, CHM_CM Common);
-CHM_SP M_cholmod_copy(CHM_SP A, int stype, int mode, CHM_CM Common);
-CHM_SP M_cholmod_add(CHM_SP A, CHM_SP B, double alpha [2], double beta [2],
- int values, int sorted, CHM_CM Common);
-
+ CHM_CM);
+int M_cholmod_free_factor(CHM_FR *L, CHM_CM);
+int M_cholmod_free_dense(CHM_DN *A, CHM_CM);
+int M_cholmod_free_sparse(CHM_SP *A, CHM_CM);
+int M_cholmod_free_triplet(CHM_TR *T, CHM_CM);
+
+long M_cholmod_nnz(const_CHM_SP, CHM_CM);
+CHM_SP M_cholmod_speye(size_t nrow, size_t ncol, int xtype, CHM_CM);
+CHM_SP M_cholmod_transpose(const_CHM_SP, int values, CHM_CM);
+int M_cholmod_sort(CHM_SP A, CHM_CM);
+CHM_SP M_cholmod_vertcat(const_CHM_SP, const_CHM_SP, int values, CHM_CM);
+CHM_SP M_cholmod_copy(const_CHM_SP, int stype, int mode, CHM_CM);
+CHM_SP M_cholmod_add(const_CHM_SP, const_CHM_SP, double alpha [2], double beta [2],
+ int values, int sorted, CHM_CM);
+
+// from ../../src/CHOLMOD/Include/cholmod_cholesky.h - line 178 :
#define CHOLMOD_A 0 /* solve Ax=b */
#define CHOLMOD_LDLt 1 /* solve LDL'x=b */
#define CHOLMOD_LD 2 /* solve LDx=b */
@@ -826,48 +926,51 @@ CHM_SP M_cholmod_add(CHM_SP A, CHM_SP B, double alpha [2], double beta [2],
#define CHOLMOD_P 7 /* permute x=Px */
#define CHOLMOD_Pt 8 /* permute x=P'x */
-CHM_DN M_cholmod_solve(int sys, CHM_FR L, CHM_DN B, CHM_CM Common);
-CHM_SP M_cholmod_spsolve(int sys, CHM_FR L, CHM_SP B, CHM_CM Common);
-int M_cholmod_sdmult(CHM_SP A, int transpose, double alpha [2],
- double beta [2], CHM_DN X, CHM_DN Y, CHM_CM Common);
-CHM_SP M_cholmod_ssmult(CHM_SP A, CHM_SP B, int stype, int values,
- int sorted, CHM_CM Common);
-int M_cholmod_factorize(CHM_SP A, CHM_FR L, CHM_CM Common);
-int M_cholmod_factorize_p(CHM_SP A, double *beta, int *fset,
- size_t fsize, CHM_FR L, CHM_CM Common);
-CHM_SP M_cholmod_copy_sparse(CHM_SP A, CHM_CM Common);
-CHM_DN M_cholmod_copy_dense(CHM_DN A, CHM_CM Common);
-CHM_SP M_cholmod_aat(CHM_SP A, int *fset, size_t fsize, int mode,
- CHM_CM Common);
-CHM_SP M_cholmod_add(CHM_SP A, CHM_SP B, double alpha[2], double beta[2],
- int values, int sorted, CHM_CM Common);
+CHM_DN M_cholmod_solve(int, const_CHM_FR, const_CHM_DN, CHM_CM);
+CHM_SP M_cholmod_spsolve(int, const_CHM_FR, const_CHM_SP, CHM_CM);
+int M_cholmod_sdmult(const_CHM_SP, int, const double*, const double*,
+ const_CHM_DN, CHM_DN Y, CHM_CM);
+CHM_SP M_cholmod_ssmult(const_CHM_SP, const_CHM_SP, int, int, int,
+ CHM_CM);
+int M_cholmod_factorize(const_CHM_SP, CHM_FR L, CHM_CM);
+int M_cholmod_factorize_p(const_CHM_SP, double *beta, int *fset,
+ size_t fsize, CHM_FR L, CHM_CM);
+CHM_SP M_cholmod_copy_sparse(const_CHM_SP, CHM_CM);
+CHM_DN M_cholmod_copy_dense(const_CHM_DN, CHM_CM);
+CHM_SP M_cholmod_aat(const_CHM_SP, int *fset, size_t fsize, int mode,
+ CHM_CM);
+int M_cholmod_band_inplace(CHM_SP A, int k1, int k2, int mode, CHM_CM);
+CHM_SP M_cholmod_add(const_CHM_SP, const_CHM_SP, double alpha[2], double beta[2],
+ int values, int sorted, CHM_CM);
CHM_DN M_cholmod_allocate_dense(size_t nrow, size_t ncol, size_t d,
- int xtype, CHM_CM Common);
-CHM_FR M_cholmod_analyze(CHM_SP A, CHM_CM Common);
-CHM_FR M_cholmod_analyze_p(CHM_SP A, int *Perm, int *fset,
- size_t fsize, CHM_CM Common);
+ int xtype, CHM_CM);
+CHM_FR M_cholmod_analyze(const_CHM_SP, CHM_CM);
+CHM_FR M_cholmod_analyze_p(const_CHM_SP, int *Perm, int *fset,
+ size_t fsize, CHM_CM);
int M_cholmod_change_factor(int to_xtype, int to_ll, int to_super,
int to_packed, int to_monotonic,
- CHM_FR L, CHM_CM Common);
-CHM_FR M_cholmod_copy_factor(CHM_FR L, CHM_CM Common);
-CHM_SP M_cholmod_factor_to_sparse(CHM_FR L, CHM_CM Common);
-CHM_SP M_cholmod_dense_to_sparse(CHM_DN X, int values, CHM_CM Common);
-CHM_SP M_cholmod_triplet_to_sparse(CHM_TR T, int nzmax, CHM_CM Common);
-CHM_SP M_cholmod_submatrix(CHM_SP A, int *rset, int rsize, int *cset,
+ CHM_FR L, CHM_CM);
+CHM_FR M_cholmod_copy_factor(const_CHM_FR, CHM_CM);
+CHM_SP M_cholmod_factor_to_sparse(const_CHM_FR, CHM_CM);
+CHM_SP M_cholmod_dense_to_sparse(const_CHM_DN, int values, CHM_CM);
+int M_cholmod_defaults (CHM_CM);
+CHM_SP M_cholmod_triplet_to_sparse(const cholmod_triplet*, int nzmax, CHM_CM);
+CHM_SP M_cholmod_submatrix(const_CHM_SP, int *rset, int rsize, int *cset,
int csize, int values, int sorted,
- CHM_CM Common);
-CHM_TR M_cholmod_sparse_to_triplet(CHM_SP A, CHM_CM Common);
-CHM_DN M_cholmod_sparse_to_dense(CHM_SP A, CHM_CM Common);
+ CHM_CM);
+CHM_TR M_cholmod_sparse_to_triplet(const_CHM_SP, CHM_CM);
+CHM_DN M_cholmod_sparse_to_dense(const_CHM_SP, CHM_CM);
CHM_TR M_cholmod_allocate_triplet (size_t nrow, size_t ncol, size_t nzmax,
- int stype, int xtype, CHM_CM Common);
+ int stype, int xtype, CHM_CM);
+// from ../../src/CHOLMOD/Include/cholmod_matrixops.h - line 107 :
/* scaling modes, selected by the scale input parameter: */
#define CHOLMOD_SCALAR 0 /* A = s*A */
#define CHOLMOD_ROW 1 /* A = diag(s)*A */
#define CHOLMOD_COL 2 /* A = A*diag(s) */
#define CHOLMOD_SYM 3 /* A = diag(s)*A*diag(s) */
-int M_cholmod_scale(CHM_DN S, int scale, CHM_SP A, CHM_CM Common);
+int M_cholmod_scale(const_CHM_DN, int scale, CHM_SP, CHM_CM);
#ifdef __cplusplus
}
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diff --git a/win32/deps/library/Matrix/test-tools-1.R b/win32/deps/library/Matrix/test-tools-1.R
new file mode 100644
index 0000000..661053c
--- /dev/null
+++ b/win32/deps/library/Matrix/test-tools-1.R
@@ -0,0 +1,200 @@
+#### Tools for Package Testing --- in Matrix, sourced by ./test-tools.R
+#### -------------------------
+## to be used as, e.g.,
+## source(system.file("test-tools-1.R", package="Matrix"), keep.source=FALSE)
+
+### ------- Part I -- unrelated to "Matrix" classes ---------------
+
+if(!exists("paste0", .BaseNamespaceEnv)) # have in R >= 2.15.0
+ paste0 <- function(...) paste(..., sep = '')
+
+identical3 <- function(x,y,z) identical(x,y) && identical (y,z)
+identical4 <- function(a,b,c,d) identical(a,b) && identical3(b,c,d)
+identical5 <- function(a,b,c,d,e) identical(a,b) && identical4(b,c,d,e)
+
+## Make sure errors are signaled
+assertError <- function(expr) {
+ d.expr <- deparse(substitute(expr))
+ t.res <- tryCatch(expr, error = function(e) e)
+ if(!inherits(t.res, "error"))
+ stop(d.expr, "\n\t did not give an error", call. = FALSE)
+ invisible(t.res)
+}
+assertWarningAtLeast <- function(expr) {
+ d.expr <- deparse(substitute(expr))
+ t.res <- tryCatch(expr, error = function(e)e, warning = function(w)w)
+ if(!inherits(t.res, "error") && !inherits(t.res, "warning"))
+ stop(d.expr, "\n\t did not give an error or warning", call. = FALSE)
+ invisible(t.res)
+}
+assertWarning <- function(expr) {
+ d.expr <- deparse(substitute(expr))
+ t.res <- tryCatch(expr, warning = function(w)w)
+ if(!inherits(t.res, "warning"))
+ stop(d.expr, "\n\t did not give a warning", call. = FALSE)
+ invisible(t.res)
+}
+
+##' [ from R's demo(error.catching) ]
+##' We want to catch *and* save both errors and warnings, and in the case of
+##' a warning, also keep the computed result.
+##'
+##' @title tryCatch both warnings and errors
+##' @param expr
+##' @return a list with 'value' and 'warning', where
+##' 'value' may be an error caught.
+##' @author Martin Maechler
+tryCatch.W.E <- function(expr)
+{
+ W <- NULL
+ w.handler <- function(w){ # warning handler
+ W <<- w
+ invokeRestart("muffleWarning")
+ }
+ list(value = withCallingHandlers(tryCatch(expr, error = function(e) e),
+ warning = w.handler),
+ warning = W)
+}
+
+
+isValid <- function(x, class) validObject(x, test=TRUE) && is(x, class)
+
+is.all.equal3 <- function(x,y,z, tol = .Machine$double.eps^0.5)
+ isTRUE(all.equal(x,y, tol=tol)) && isTRUE(all.equal(y,z, tol=tol))
+
+is.all.equal4 <- function(x,y,z,u, tol = .Machine$double.eps^0.5)
+ is.all.equal3(x,y,z, tol=tol) && isTRUE(all.equal(z,u, tol=tol))
+
+## A version of all.equal() for the slots
+all.slot.equal <- function(x,y, ...) {
+ slts <- slotNames(x)
+ for(sl in slts) {
+ aeq <- all.equal(slot(x,sl), slot(y,sl), ...)
+ if(!identical(TRUE, aeq))
+ return(paste("slot '",sl,"': ", aeq, sep=''))
+ }
+ TRUE
+}
+
+## all.equal() for list-coercible objects -- apart from *some* components
+all.equal.X <- function(x,y, except, ...)
+{
+ .trunc <- function(x) {
+ ll <- as.list(x)
+ ll[ - match(except, names(ll), nomatch = 0L)]
+ }
+ all.equal(.trunc(x), .trunc(y), ...)
+}
+## e.g. in lme4:
+## all.equal.X(env(m1), env(m2), except = c("call", "frame"))
+
+## The relative error typically returned by all.equal:
+relErr <- function(target, current) { ## make this work for 'Matrix'
+ ## ==> no mean() ..
+ n <- length(current)
+ if(length(target) < n)
+ target <- rep(target, length.out = n)
+ sum(abs(target - current)) / sum(abs(target))
+}
+
+##' Compute the signed relative error between target and current vector -- vectorized
+##' @title Relative Error (:= 0 when absolute error == 0)
+##' @param target
+##' @param current {maybe scalar; need length(current) a multiple of length(target)}
+##' @return *vector* of the same length as target and current
+##' @author Martin Maechler
+relErrV <- function(target, current) {
+ n <- length(target <- as.vector(target))
+ ## assert( <length current> is multiple of <length target>) :
+ if(length(current) %% n)
+ stop("length(current) must be a multiple of length(target)")
+ RE <- current
+ RE[] <- 0
+ fr <- current/target
+ neq <- is.na(current) | (current != target)
+ RE[neq] <- 1 - fr[neq]
+ RE
+}
+
+## is.R22 <- (paste(R.version$major, R.version$minor, sep=".") >= "2.2")
+
+pkgRversion <- function(pkgname)
+ sub("^R ([0-9.]+).*", "\\1", packageDescription(pkgname)[["Built"]])
+
+showSys.time <- function(expr) {
+ ## prepend 'Time' for R CMD Rdiff
+ st <- system.time(expr)
+ writeLines(paste("Time", capture.output(print(st))))
+ invisible(st)
+}
+showProc.time <- local({ ## function + 'pct' variable
+ pct <- proc.time()
+ function(final="\n") { ## CPU elapsed __since last called__
+ ot <- pct ; pct <<- proc.time()
+ ## 'Time ..' *not* to be translated: tools::Rdiff() skips its lines!
+ cat('Time elapsed: ', (pct - ot)[1:3], final)
+ }
+})
+
+##' @title turn an S4 object (with slots) into a list with corresponding components
+##' @param obj an R object with a formal class (aka "S4")
+##' @return a list with named components where \code{obj} had slots
+##' @author Martin Maechler
+S4_2list <- function(obj) {
+ sn <- slotNames(obj)
+ structure(lapply(sn, slot, object = obj), .Names = sn)
+}
+
+
+### ------- Part II -- related to matrices, but *not* "Matrix" -----------
+
+add.simpleDimnames <- function(m) {
+ stopifnot(length(d <- dim(m)) == 2)
+ dimnames(m) <- list(if(d[1]) paste0("r", seq_len(d[1])),
+ if(d[2]) paste0("c", seq_len(d[2])))
+ m
+}
+
+as.mat <- function(m) {
+ ## as(., "matrix") but with no extraneous empty dimnames
+ m <- as(m, "matrix")
+ if(identical(dimnames(m), list(NULL,NULL)))
+ dimnames(m) <- NULL
+ m
+}
+
+assert.EQ.mat <- function(M, m, tol = if(show) 0 else 1e-15, show=FALSE) {
+ ## Purpose: check equality of 'Matrix' M with 'matrix' m
+ ## ----------------------------------------------------------------------
+ ## Arguments: M: is(., "Matrix") typically {but just needs working as(., "matrix")}
+ ## m: is(., "matrix")
+ ## show: if TRUE, return (and hence typically print) all.equal(...)
+ validObject(M)
+ MM <- as.mat(M) # as(M, "matrix")
+ if(is.logical(MM) && is.numeric(m))
+ storage.mode(MM) <- "integer"
+ attr(MM, "dimnames") <- attr(m, "dimnames") <- NULL
+ if(show) all.equal(MM, m, tol = tol)
+ else if(!isTRUE(r <- all.equal(MM, m, tol = tol)))
+ stop("all.equal() |-> ", r)
+}
+## a short cut
+assert.EQ.Mat <- function(M, M2, tol = if(show) 0 else 1e-15, show=FALSE)
+ assert.EQ.mat(M, as.mat(M2), tol=tol, show=show)
+
+
+chk.matrix <- function(M) {
+ ## check object; including coercion to "matrix" :
+ cl <- class(M)
+ cat("class ", dQuote(cl), " [",nrow(M)," x ",ncol(M),"]; slots (",
+ paste(slotNames(M), collapse=","), ")\n", sep='')
+ stopifnot(validObject(M),
+ dim(M) == c(nrow(M), ncol(M)),
+ identical(dim(m <- as(M, "matrix")), dim(M))
+ )
+}
+
+isOrthogonal <- function(x, tol = 1e-15) {
+ all.equal(diag(as(zapsmall(crossprod(x)), "diagonalMatrix")),
+ rep(1, ncol(x)), tol = tol)
+}
diff --git a/win32/deps/library/Matrix/test-tools-Matrix.R b/win32/deps/library/Matrix/test-tools-Matrix.R
new file mode 100644
index 0000000..9bd5cd3
--- /dev/null
+++ b/win32/deps/library/Matrix/test-tools-Matrix.R
@@ -0,0 +1,633 @@
+#### Tools for Package Testing --- in Matrix, sourced by ./test-tools.R
+#### -------------------------
+
+### ------- Part III -- "Matrix" (classes) specific ----------------------
+
+lsM <- function(...) {
+ for(n in ls(..., envir=parent.frame()))
+ if(is((. <- get(n)),"Matrix"))
+ cat(sprintf("%5s: '%s' [%d x %d]\n",n,class(.), nrow(.),ncol(.)))
+}
+
+asD <- function(m) { ## as "Dense"
+ if(canCoerce(m, "denseMatrix")) as(m, "denseMatrix")
+ else if(canCoerce(m, (cl <- paste(.M.kind(m), "denseMatrix", sep=''))))
+ as(m, cl)
+ else if(canCoerce(m, "dgeMatrix")) as(m, "dgeMatrix")
+ else stop("cannot coerce to a typical dense Matrix")
+}
+
+## "normal" sparse Matrix: Csparse, no diag="U"
+asCsp <- function(x) Matrix:::diagU2N(as(x, "CsparseMatrix"))
+
+isNull.dimnames <- function(dn) {
+ is.null(dn) || {
+ dn <- unname(dn)
+ ch0 <- character(0)
+ identical(dn, list(NULL,NULL)) ||
+ identical(dn, list(ch0, NULL)) ||
+ identical(dn, list(NULL, ch0)) ||
+ identical(dn, list(ch0, ch0))
+ }
+}
+
+Qidentical.DN <- function(dx, dy) {
+ ## quasi-identical dimnames
+ stopifnot(is.list(dx) || is.null(dx),
+ is.list(dy) || is.null(dy))
+ ## "empty"
+ (isNull.dimnames(dx) && isNull.dimnames(dy)) || identical(dx, dy)
+}
+
+Qidentical <- function(x,y, strictClass = TRUE) {
+ ## quasi-identical - for 'Matrix' matrices
+ if(class(x) != class(y)) {
+ if(strictClass || !is(x, class(y)))
+ return(FALSE)
+ ## else try further
+ }
+ slts <- slotNames(x)
+ if("Dimnames" %in% slts) { ## always (or we have no 'Matrix')
+ slts <- slts[slts != "Dimnames"]
+ if(!(Qidentical.DN(x Dimnames, y Dimnames)))
+ return(FALSE)
+ }
+ if("factors" %in% slts) { ## allow one empty and one non-empty 'factors'
+ slts <- slts[slts != "factors"]
+ ## if both are not empty, they must be the same:
+ if(length(xf <- x factors) && length(yf <- y factors))
+ if(!identical(xf, yf)) return(FALSE)
+ }
+ for(sl in slts)
+ if(!identical(slot(x,sl), slot(y,sl)))
+ return(FALSE)
+ TRUE
+}
+
+Q.C.identical <- function(x,y, sparse = is(x,"sparseMatrix"),
+ checkClass = TRUE, strictClass = TRUE) {
+ if(checkClass && class(x) != class(y)) {
+ if(strictClass || !is(x, class(y)))
+ return(FALSE) ## else try further
+ }
+ if(sparse)
+ Qidentical(as(x,"CsparseMatrix"), as(y,"CsparseMatrix"),
+ strictClass=strictClass)
+ else Qidentical(x,y, strictClass=strictClass)
+}
+
+##' <description>
+##'
+##' <details>
+##' @title Quasi-equal for 'Matrix' matrices
+##' @param x Matrix
+##' @param y Matrix
+##' @param superclasses x and y must coincide in (not) extending these
+##' @param dimnames.check logical indicating if dimnames(.) much match
+##' @param tol NA (--> use "==") or numerical tolerance for all.equal()
+##' @return logical: Are x and y (quasi) equal ?
+Q.eq <- function(x, y,
+ superclasses =
+ c("sparseMatrix", "denseMatrix",
+ "dMatrix", "lMatrix", "nMatrix"),
+ dimnames.check = TRUE, tol = NA) {
+ ## quasi-equal - for 'Matrix' matrices
+ if(any(dim(x) != dim(y)))
+ return(FALSE)
+ if(dimnames.check &&
+ !identical(dimnames(x),
+ dimnames(y))) return(FALSE)
+ xcl <- getClassDef(class(x))
+ ycl <- getClassDef(class(y))
+ for(SC in superclasses) {
+ if( extends(xcl, SC) &&
+ !extends(ycl, SC)) return(FALSE)
+ }
+ asC <- ## asCommon
+ if((isDense <- extends(xcl,"denseMatrix")))
+ function(m) as(m, "matrix")
+ else function(m)
+ as(as(as(m,"CsparseMatrix"), "dMatrix"), "dgCMatrix")
+ if(is.na(tol)) {
+ if(isDense)
+ all(x == y | (is.na(x) & is.na(y)))
+ else ## 'x == y' blows up for large sparse matrices:
+ isTRUE(all.equal(asC(x), asC(y), tol = 0.,
+ check.attributes = dimnames.check))
+ }
+ else if(is.numeric(tol) && tol >= 0) {
+ isTRUE(all.equal(asC(x), asC(y), tol = tol,
+ check.attributes = dimnames.check))
+ }
+ else stop("'tol' must be NA or non-negative number")
+}
+
+Q.eq2 <- function(x, y,
+ superclasses = c("sparseMatrix", "denseMatrix"),
+ dimnames.check = FALSE, tol = NA)
+ Q.eq(x,y, superclasses=superclasses,
+ dimnames.check=dimnames.check, tol=tol)
+
+##' <description>
+##'
+##' <details>
+##' @title Quasi-equality of symmpart(m) + skewpart(m) with m
+##' @param m Matrix
+##' @param tol numerical tolerance for all.equal()
+##' @return logical
+##' @author Martin Maechler
+Q.eq.symmpart <- function(m, tol = 8 * .Machine$double.eps)
+{
+ ss <- symmpart(m) + skewpart(m)
+ if(hasNA <- any(iNA <- is.na(ss))) {
+ ## ss has the NA's symmetrically, but typically m has *not*
+ iiNA <- which(iNA) # <- useful! -- this tests which() methods!
+ ## assign NA's too -- using correct kind of NA:
+ m[iiNA] <- as(NA, Matrix:::.type.kind[Matrix:::.M.kind(m)])
+ }
+ Q.eq2(m, ss, tol = tol)
+}
+
+##' sample.int(n, size, replace=FALSE) for large n:
+sampleL <- function(n, size) {
+ if(n < .Machine$integer.max)
+ sample(n, size, replace=FALSE)
+ else {
+ i <- unique(round(n * runif(1.8 * size)))
+ while(length(i) < size) {
+ i <- unique(c(i, round(n * runif(size))))
+ }
+ i[seq_len(size)]
+ }
+}
+
+
+## Useful Matrix constructors for testing:
+
+##' @title Random Sparse Matrix
+##' @param n
+##' @param m number of columns; default (=n) ==> square matrix
+##' @param density the desired sparseness density:
+##' @param nnz number of non-zero entries; default from \code{density}
+##' @param giveCsparse logical specifying if result should be CsparseMatrix
+##' @return a [TC]sparseMatrix, n x m
+##' @author Martin Maechler, Mar 2008
+rspMat <- function(n, m = n, density = 1/4, nnz = round(density * n*m),
+ giveCsparse = TRUE)
+{
+ stopifnot(length(n) == 1, n == as.integer(n),
+ length(m) == 1, m == as.integer(m),
+ 0 <= density, density <= 1,
+ 0 <= nnz,
+ nnz <= (N <- n*m))
+ in0 <- sampleL(N, nnz)
+ x <- sparseVector(i = in0, x = as.numeric(1L + seq_along(in0)), length = N)
+ dim(x) <- c(n,m)#-> sparseMatrix
+ if (giveCsparse) as(x, "CsparseMatrix") else x
+}
+
+
+## From \examples{..} in ../man/sparseMatrix.Rd :
+rSparseMatrix <- function(nrow, ncol, nnz,
+ rand.x = function(n) round(rnorm(nnz), 2), ...)
+{
+ stopifnot((nnz <- as.integer(nnz)) >= 0,
+ nrow >= 0, ncol >= 0, nnz <= nrow * ncol)
+ sparseMatrix(i = sample(nrow, nnz, replace = TRUE),
+ j = sample(ncol, nnz, replace = TRUE),
+ x = rand.x(nnz), dims = c(nrow, ncol), ...)
+}
+
+
+rUnitTri <- function(n, upper = TRUE, ...)
+{
+ ## Purpose: random unit-triangular sparse Matrix .. built from rspMat()
+ ## ----------------------------------------------------------------------
+ ## Arguments: n: matrix dimension
+ ## upper: logical indicating if upper or lower triangular
+ ## ... : further arguments passed to rspMat(), eg. 'density'
+ ## ----------------------------------------------------------------------
+ ## Author: Martin Maechler, Date: 5 Mar 2008, 11:35
+
+ r <- (if(upper) triu else tril)(rspMat(n, ...))
+ ## make sure the diagonal is empty
+ diag(r) <- 0
+ r <- drop0(r)
+ r diag <- "U"
+ r
+}
+
+mkLDL <- function(n, density = 1/3) {
+ ## Purpose: make nice artificial A = L D L' (with exact numbers) decomp
+ ## ----------------------------------------------------------------------
+ ## Author: Martin Maechler, Date: 15 Mar 2008
+ stopifnot(n == round(n))
+ n <- as.integer(n)
+ L <- Matrix(0, n,n)
+
+ nnz <- round(n*n * density)
+ L[sample(n*n, nnz)] <- seq_len(nnz)
+ L <- tril(L,-1)
+ diag(L) <- 1
+ d.half <- sample(10*(n:1))# random permutation ; use '10*' to be "different" from L entries
+ D <- Diagonal(x = d.half * d.half)
+ A <- tcrossprod(L * rep(d.half, each=n))
+ ## = as(L %*% D %*% t(L), "symmetricMatrix")
+ list(A = A, L = L, d.half = d.half, D = D)
+}
+
+eqDeterminant <- function(m1, m2, NA.Inf.ok=FALSE, ...) {
+ d1 <- determinant(m1) ## logarithm = TRUE
+ d2 <- determinant(m2)
+ d1m <- as.vector(d1$modulus)# dropping attribute
+ d2m <- as.vector(d2$modulus)
+ if((identical(d1m, -Inf) && identical(d2m, -Inf)) ||
+ ## <==> det(m1) == det(m2) == 0, then 'sign' may even differ !
+ (is.na(d1m) && is.na(d2m)))
+ ## if both are NaN or NA, we "declare" that's fine here
+ return(TRUE)
+ else if(NA.Inf.ok && ## first can be NA, second infinite:
+ ## wanted: base::determinant.matrix() sometimes gives -Inf instead
+ ## of NA,e.g. for matrix(c(0,NA,0,0,NA,NA,0,NA,0,0,1,0,0,NA,0,1), 4,4))
+ is.na(d1m) && is.infinite(d2m)) return(TRUE)
+ ## else
+ if(is.infinite(d1m)) d1$modulus <- sign(d1m)* .Machine$double.xmax
+ if(is.infinite(d2m)) d2$modulus <- sign(d2m)* .Machine$double.xmax
+ ## now they are finite or *one* of them is NA/NaN, and all.equal() will tell so:
+ all.equal(d1, d2, ...)
+}
+
+##' @param A a non-negative definite sparseMatrix, typically "dsCMatrix"
+##'
+##' @return a list with components resulting from calling
+##' Cholesky(., perm = .P., LDL = .L., super = .S.)
+##'
+##' for all 2*2*3 combinations of (.P., .L., .S.)
+allCholesky <- function(A, verbose = FALSE, silentTry = FALSE)
+{
+ ## Author: Martin Maechler, Date: 16 Jul 2009
+
+ ##' @param r list of CHMfactor objects, typically with names() as '. | .'
+ ##'
+ ##' @return an is(perm,LDL,super) matrix with interesting and *named* rownames
+ CHM_to_pLs <- function(r) {
+ is.perm <- function(.)
+ if(inherits(., "try-error")) NA else !all( perm == 0:( Dim[1]-1))
+ is.LDL <- function(.)if(inherits(., "try-error")) NA else isLDL(.)
+ r.st <-
+ cbind(perm = sapply(r, is.perm),
+ LDL = sapply(r, is.LDL),
+ super = sapply(r, class) == "dCHMsuper")
+ names(dimnames(r.st)) <- list(" p L s", "")
+ r.st
+ }
+
+ my.Cholesky <- {
+ if(verbose)
+ function (A, perm = TRUE, LDL = !super, super = FALSE, Imult = 0, ...) {
+ cat(sprintf("Chol..(*, perm= %1d, LDL= %1d, super=%1d):",
+ perm, LDL, super))
+ r <- Cholesky(A, perm=perm, LDL=LDL, super=super, Imult=Imult, ...)
+ cat(" [Ok]\n")
+ r
+ }
+ else Cholesky
+ }
+ logi <- c(FALSE, TRUE)
+ d12 <- expand.grid(perm = logi, LDL = logi, super = c(logi,NA),
+ KEEP.OUT.ATTRS = FALSE)
+ r1 <- lapply(seq_len(nrow(d12)),
+ function(i) try(do.call(my.Cholesky,
+ c(list(A = A), as.list(d12[i,]))),
+ silent=silentTry))
+ names(r1) <- apply(d12, 1,
+ function(.) paste(symnum(.), collapse=" "))
+ dup.r1 <- duplicated(r1)
+ r.all <- CHM_to_pLs(r1)
+ if(!identical(dup.r1, duplicated(r.all)))
+ warning("duplicated( <pLs-matrix> ) differs from duplicated( <CHM-list> )",
+ immediate. = TRUE)
+ list(Chol.A = r1,
+ dup.r.all = dup.r1,
+ r.all = r.all,
+ r.uniq = CHM_to_pLs(r1[ ! dup.r1]))
+}
+
+
+###----- Checking a "Matrix" -----------------------------------------
+
+##' <description>
+##'
+##' <details>
+##' @title Compatibility tests "Matrix" <-> "traditional matrix"
+##' and many more consistency checks
+##'
+##' @param m a "Matrix"
+##' @param m.m as(m, "matrix") {if 'do.matrix' }
+##' @param do.matrix logical indicating if as(m, "matrix") should be applied;
+##' typically false for large sparse matrices
+##' @param do.t logical: is t(m) "feasible" ?
+##' @param doNorm
+##' @param doOps
+##' @param doSummary
+##' @param doCoerce
+##' @param doCoerce2
+##' @param do.prod
+##' @param verbose logical indicating if "progress output" is produced.
+##' @param catFUN (when 'verbose' is TRUE): function to be used as generalized cat()
+##' @return TRUE (invisibly), unless an error is signalled
+##' @author Martin Maechler, since 11 Apr 2008
+checkMatrix <- function(m, m.m = if(do.matrix) as(m, "matrix"),
+ do.matrix = !isSparse || prod(dim(m)) < 1e6,
+ do.t = TRUE, doNorm = TRUE, doOps = TRUE,
+ doSummary = TRUE, doCoerce = TRUE,
+ doCoerce2 = doCoerce && !extends(cld, "RsparseMatrix"),
+ do.prod = do.t && do.matrix && !extends(cld, "RsparseMatrix"),
+ verbose = TRUE, catFUN = cat)
+{
+ ## is also called from dotestMat() in ../tests/Class+Meth.R
+
+ stopifnot(is(m, "Matrix"))
+ validObject(m) # or error(....)
+
+ clNam <- class(m)
+ cld <- getClassDef(clNam) ## extends(cld, FOO) is faster than is(m, FOO)
+ isCor <- extends(cld, "corMatrix")
+ isSparse <- extends(cld, "sparseMatrix") # also true for diagonalMatrix !
+ isSym <- extends(cld, "symmetricMatrix")
+ isDiag <- extends(cld, "diagonalMatrix")
+ isPerm <- extends(cld, "pMatrix")
+ isTri <- !isSym && !isDiag && !isPerm && extends(cld, "triangularMatrix")
+ is.n <- extends(cld, "nMatrix")
+ nonMatr <- clNam != Matrix:::MatrixClass(clNam, cld)
+
+ Cat <- function(...) if(verbose) cat(...)
+ CatF <- function(...) if(verbose) catFUN(...)
+ ## warnNow <- function(...) warning(..., call. = FALSE, immediate. = TRUE)
+
+ DO.m <- function(expr) if(do.matrix) eval(expr) else TRUE
+
+ vec <- function(x) {
+ dim(x) <- c(length(x), 1L)
+ dimnames(x) <- list(NULL,NULL)
+ x
+ }
+ eps16 <- 16 * .Machine$double.eps
+
+ ina <- is.na(m)
+ if(do.matrix) {
+ stopifnot(all(ina == is.na(m.m)),
+ all(is.finite(m) == is.finite(m.m)),
+ all(is.infinite(m) == is.infinite(m.m)),
+ all(m == m | ina), ## check all() , "==" [Compare], "|" [Logic]
+ if(ncol(m) > 0) identical3(unname(m[,1]), unname(m.m[,1]),
+ as(m[,1,drop=FALSE], "vector"))
+ else identical(as(m, "vector"), as.vector(m.m)))
+ if(any(m != m & !ina)) stop(" any (m != m) should not be true")
+ } else {
+ if(any(m != m)) stop(" any (m != m) should not be true")
+ if(ncol(m) > 0)
+ stopifnot(identical(unname(m[,1]), as(m[,1,drop=FALSE], "vector")))
+ else stopifnot(identical(as(m, "vector"), as.vector(as(m, "matrix"))))
+ }
+ if(do.t) {
+ tm <- t(m)
+ if(isSym) ## check that t() swaps 'uplo' L <--> U :
+ stopifnot(c("L","U") == sort(c(m uplo, tm uplo)))
+ ttm <- t(tm)
+ if(extends(cld, "CsparseMatrix") ||
+ extends(cld, "generalMatrix") || isDiag)
+ stopifnot(Qidentical(m, ttm, strictClass = !nonMatr))
+ else if(do.matrix)
+ stopifnot(nonMatr || class(ttm) == clNam,
+ all(m == ttm | ina))
+ ## else : not testing
+
+ ## crossprod() %*% etc
+ if(do.prod) {
+ c.m <- crossprod(m)
+ tcm <- tcrossprod(m)
+ tolQ <- if(isSparse) NA else eps16
+ stopifnot(dim(c.m) == rep.int(ncol(m), 2),
+ dim(tcm) == rep.int(nrow(m), 2),
+ ## FIXME: %*% drops dimnames
+ Q.eq2(c.m, tm %*% m, tol = tolQ),
+ Q.eq2(tcm, m %*% tm, tol = tolQ))
+ }
+ }
+ if(!do.matrix) {
+ CatF(" will *not* coerce to 'matrix' since do.matrix is FALSE\n")
+ } else if(doNorm) {
+ CatF(sprintf(" norm(m [%d x %d]) :", nrow(m), ncol(m)))
+ for(typ in c("1","I","F","M")) {
+ Cat('', typ, '')
+ stopifnot(all.equal(norm(m,typ), norm(m.m,typ)))
+ }
+ Cat(" ok\n")
+ }
+ if(do.matrix && doSummary) {
+ summList <- lapply(getGroupMembers("Summary"), get,
+ envir = asNamespace("Matrix"))
+ CatF(" Summary: ")
+ for(f in summList) {
+ ## suppressWarnings(): e.g. any(<double>) would warn here:
+ r <- suppressWarnings(if(isCor) all.equal(f(m), f(m.m)) else
+ identical(f(m), f(m.m)))
+ if(!isTRUE(r)) {
+ f.nam <- sub("..$", '', sub("^\\.Primitive..", '', format(f)))
+ ## prod() is delicate: NA or NaN can both happen
+ (if(f.nam == "prod") message else stop)(
+ sprintf("%s(m) [= %g] differs from %s(m.m) [= %g]",
+ f.nam, f(m), f.nam, f(m.m)))
+ }
+ }
+ if(verbose) cat(" ok\n")
+ }
+
+ ## and test 'dim()' as well:
+ d <- dim(m)
+ isSqr <- d[1] == d[2]
+ if(do.t) stopifnot(identical(diag(m), diag(t(m))))
+ ## TODO: also === diag(band(m,0,0))
+
+ if(prod(d) < .Machine$integer.max && !extends(cld, "modelMatrix")) {
+ vm <- vec(m)
+ stopifnot(is(vm, "Matrix"), validObject(vm), dim(vm) == c(d[1]*d[2], 1))
+ }
+
+ if(!isPerm)
+ m.d <- local({ m. <- m; diag(m.) <- diag(m); m. })
+ if(do.matrix)
+ stopifnot(identical(dim(m.m), dim(m)),
+ ## base::diag() keeps names [Matrix FIXME]
+## now that "pMatrix" subsetting gives *LOGICAL*
+## if(isPerm) {
+## identical(as.integer(unname(diag(m))), unname(diag(m.m)))
+## } else
+ identical(unname(diag(m)),
+ unname(diag(m.m))),## not for NA: diag(m) == diag(m.m),
+ identical(nnzero(m), sum(m.m != 0)),
+ identical(nnzero(m, na.= FALSE), sum(m.m != 0, na.rm = TRUE)),
+ identical(nnzero(m, na.= TRUE), sum(m.m != 0 | is.na(m.m)))
+ )
+
+ if(isSparse) {
+ n0m <- drop0(m) #==> n0m is Csparse
+ has0 <- !Qidentical(n0m, as(m,"CsparseMatrix"))
+ if(!isPerm && !extends(cld, "RsparseMatrix") &&
+ !(extends(cld, "TsparseMatrix") && Matrix:::is_duplicatedT(m, di = d)))
+ # 'diag<-' is does not change attrib:
+ stopifnot(identical(m, m.d))
+ }
+ else if(!identical(m, m.d)) { # dense : 'diag<-' is does not change attrib
+ if(isTri && m diag == "U" && m d diag == "N" &&
+ all(m == m.d))
+ message("unitriangular m: diag(m) <- diag(m) lost \"U\" .. is ok")
+ else stop("diag(m) <- diag(m) has changed 'm' too much")
+ }
+ ## use non-square matrix when "allowed":
+
+ ## m12: sparse and may have 0s even if this is not: if(isSparse && has0)
+ m12 <- as(as( m, "lMatrix"),"CsparseMatrix")
+ m12 <- drop0(m12)
+ if(do.matrix) {
+ ## "!" should work (via as(*, "l...")) :
+ m11 <- as(as(!!m,"CsparseMatrix"), "lMatrix")
+ if(!Qidentical(m11, m12))
+ stopifnot(Qidentical(as(m11, "generalMatrix"),
+ as(m12, "generalMatrix")))
+ }
+ if(isSparse && !is.n) {
+ ## ensure that as(., "nMatrix") gives nz-pattern
+ CatF("as(., \"nMatrix\") giving full nonzero-pattern: ")
+ n1 <- as(m, "nMatrix")
+ ns <- as(m, "nsparseMatrix")
+ stopifnot(identical(n1,ns),
+ isDiag || ((if(isSym) Matrix:::nnzSparse else sum)(n1) ==
+ length(if(isPerm) m perm else Matrix:::diagU2N(m)@x)))
+ Cat("ok\n")
+ }
+
+ if(doOps) {
+ ## makes sense with non-trivial m (!)
+ CatF("2*m =?= m+m: ")
+ if(identical(2*m, m+m)) Cat("identical\n")
+ else if(do.matrix) {
+ eq <- as(2*m,"matrix") == as(m+m, "matrix") # but work for NA's:
+ stopifnot(all(eq | (is.na(m) & is.na(eq))))
+ Cat("ok\n")
+ } else {# !do.matrix
+ stopifnot(identical(as(2*m, "CsparseMatrix"),
+ as(m+m, "CsparseMatrix")))
+ Cat("ok\n")
+ }
+ if(do.matrix) {
+ ## m == m etc, now for all, see above
+ CatF("m >= m for all: "); stopifnot(all(m >= m | ina)); Cat("ok\n")
+ }
+ if(prod(d) > 0) {
+ CatF("m < m for none: ")
+ mlm <- m < m
+ if(!any(ina)) stopifnot(!any(mlm))
+ else if(do.matrix) stopifnot(!any(mlm & !ina))
+ else { ## !do.matrix & any(ina) : !ina can *not* be used
+ mlm[ina] <- FALSE
+ stopifnot(!any(mlm))
+ }
+ Cat("ok\n")
+ }
+
+ if(isSqr) {
+ if(do.matrix) {
+ ## determinant(<dense>) "fails" for triangular with NA such as
+ ## (m <- matrix(c(1:0,NA,1), 2))
+ CatF("symmpart(m) + skewpart(m) == m: ")
+ Q.eq.symmpart(m)
+ CatF("ok; determinant(): ")
+ if(any(is.na(m.m)) && extends(cld, "triangularMatrix"))
+ Cat(" skipped: is triang. and has NA")
+ else
+ stopifnot(eqDeterminant(m, m.m, NA.Inf.ok=TRUE))
+ Cat("ok\n")
+ }
+ } else assertError(determinant(m))
+ }# end{doOps}
+
+ if(doCoerce && do.matrix && canCoerce("matrix", clNam)) {
+ CatF("as(<matrix>, ",clNam,"): ", sep='')
+ m3 <- as(m.m, clNam)
+ Cat("valid:", validObject(m3), "\n")
+ ## m3 should ``ideally'' be identical to 'm'
+ }
+
+ if(doCoerce2 && do.matrix) { ## not for large m: !m will be dense
+
+ if(is.n) {
+ stopifnot(identical(m, as(as(m, "dMatrix"),"nMatrix")),
+ identical(m, as(as(m, "lMatrix"),"nMatrix")),
+ identical(which(m), which(m.m)))
+ }
+ else if(extends(cld, "lMatrix")) { ## should fulfill even with NA:
+ stopifnot(all(m | !m | ina), !any(!m & m & !ina))
+ if(extends(cld, "TsparseMatrix")) # allow modify, since at end here
+ m <- Matrix:::uniqTsparse(m, clNam)
+ stopifnot(identical(m, m & TRUE),
+ identical(m, FALSE | m))
+ ## also check the coercions to [dln]Matrix
+ m. <- if(isSparse && has0) n0m else m
+ m1. <- m. # replace NA by 1 in m1. , carefully not changing class:
+ if(any(ina)) m1 x[is na(m1 x)] <- TRUE
+ stopifnot(identical(m. , as(as(m. , "dMatrix"),"lMatrix")),
+ clNam == "ldiMatrix" || # <- there's no "ndiMatrix"
+ ## coercion to n* and back: only identical when no extra 0s:
+ identical(m1., as(as(m1., "nMatrix"),"lMatrix")),
+ identical(which(m), which(m.m)))
+ }
+ else if(extends(cld, "dMatrix")) {
+ m. <- if(isSparse && has0) n0m else m
+ m1 <- (m. != 0)*1
+ if(!isSparse && substr(clNam,1,3) == "dpp")
+ ## no "nppMatrix" possible
+ m1 <- unpack(m1)
+
+ m1. <- m1 # replace NA by 1 in m1. , carefully not changing class:
+ if(any(ina)) m1 x[is na(m1 x)] <- 1
+ ## coercion to n* (nz-pattern!) and back: only identical when no extra 0s and no NAs:
+ stopifnot(Q.C.identical(m1., as(as(m., "nMatrix"),"dMatrix"),
+ isSparse, checkClass = FALSE),
+ Q.C.identical(m1 , as(as(m., "lMatrix"),"dMatrix"),
+ isSparse, checkClass = FALSE))
+ }
+
+ if(extends(cld, "triangularMatrix")) {
+ mm. <- m
+ i0 <- if(m uplo == "L")
+ upper.tri(mm.) else lower.tri(mm.)
+ n.catchWarn <- if(is.n) suppressWarnings else identity
+ n.catchWarn( mm.[i0] <- 0 ) # ideally, mm. remained triangular, but can be dge*
+ CatF("as(<triangular (ge)matrix>, ",clNam,"): ", sep='')
+ tm <- as(as(mm., "triangularMatrix"), clNam)
+ Cat("valid:", validObject(tm), "\n")
+ if(m uplo == tm uplo) ## otherwise, the matrix effectively was *diagonal*
+ ## note that diagU2N(<dtr>) |-> dtC :
+ stopifnot(Qidentical(tm, as(Matrix:::diagU2N(m), clNam)))
+ }
+ else if(isDiag) {
+
+ ## TODO
+
+ } else {
+
+ ## TODO
+ }
+ }# end {doCoerce2 && ..}
+
+ if(doCoerce && isSparse) { ## coerce to sparseVector and back :
+ v <- as(m, "sparseVector")
+ stopifnot(length(v) == prod(d))
+ dim(v) <- d
+ stopifnot(Q.eq2(m, v))
+ }
+
+ invisible(TRUE)
+}
diff --git a/win32/deps/library/Matrix/test-tools.R b/win32/deps/library/Matrix/test-tools.R
index 918b662..9ae66f9 100644
--- a/win32/deps/library/Matrix/test-tools.R
+++ b/win32/deps/library/Matrix/test-tools.R
@@ -1,535 +1,10 @@
#### Will be sourced by several R scripts in ../tests/
-### ------- Part I -- unrelated to "Matrix" classes ---------------
-
-paste0 <- function(...) paste(..., sep = '')
-
-identical3 <- function(x,y,z) identical(x,y) && identical (y,z)
-identical4 <- function(a,b,c,d) identical(a,b) && identical3(b,c,d)
-identical5 <- function(a,b,c,d,e) identical(a,b) && identical4(b,c,d,e)
-
-## Make sure errors are signaled
-assertError <- function(expr) {
- d.expr <- deparse(substitute(expr))
- t.res <- try(expr, silent = TRUE)
- if(!inherits(t.res, "try-error"))
- stop(d.expr, "\n\t did not give an error", call. = FALSE)
- invisible(t.res)
-}
-
-isValid <- function(x, class) validObject(x, test=TRUE) && is(x, class)
-
-is.all.equal3 <- function(x,y,z, tol = .Machine$double.eps^0.5)
- isTRUE(all.equal(x,y, tol=tol)) && isTRUE(all.equal(y,z, tol=tol))
-
-is.all.equal4 <- function(x,y,z,u, tol = .Machine$double.eps^0.5)
- is.all.equal3(x,y,z, tol=tol) && isTRUE(all.equal(z,u, tol=tol))
-
-## A version of all.equal() for the slots
-all.slot.equal <- function(x,y, ...) {
- slts <- slotNames(x)
- for(sl in slts) {
- aeq <- all.equal(slot(x,sl), slot(y,sl), ...)
- if(!identical(TRUE, aeq))
- return(paste("slot '",sl,"': ", aeq, sep=''))
- }
- TRUE
-}
-
-## The relative error typically returned by all.equal:
-relErr <- function(target, current) { ## make this work for 'Matrix'
- ## ==> no mean() ..
- n <- length(current)
- if(length(target) < n)
- target <- rep(target, length.out = n)
- sum(abs(target - current)) / sum(abs(target))
-}
-
-## is.R22 <- (paste(R.version$major, R.version$minor, sep=".") >= "2.2")
-
-pkgRversion <- function(pkgname)
- substring(packageDescription(pkgname)[["Built"]], 3,5)
-
-
+### ------- Part I & -- unrelated to "Matrix" classes ---------------
### ------- Part II -- related to matrices, but *not* "Matrix" -----------
-
-add.simpleDimnames <- function(m) {
- stopifnot(length(d <- dim(m)) == 2)
- dimnames(m) <- list(paste0("r", seq_len(d[1])),
- paste0("c", seq_len(d[2])))
- m
-}
-
-as.mat <- function(m) {
- ## as(., "matrix") but with no extraneous empty dimnames
- m <- as(m, "matrix")
- if(identical(dimnames(m), list(NULL,NULL)))
- dimnames(m) <- NULL
- m
-}
-
-assert.EQ.mat <- function(M, m, tol = if(show) 0 else 1e-15, show=FALSE) {
- ## Purpose: check equality of 'Matrix' M with 'matrix' m
- ## ----------------------------------------------------------------------
- ## Arguments: M: is(., "Matrix") typically {but just needs working as(., "matrix")}
- ## m: is(., "matrix")
- ## show: if TRUE, return (and hence typically print) all.equal(...)
- validObject(M)
- MM <- as.mat(M) # as(M, "matrix")
- if(is.logical(MM) && is.numeric(m))
- storage.mode(MM) <- "integer"
- attr(MM, "dimnames") <- attr(m, "dimnames") <- NULL
- if(show) all.equal(MM, m, tol = tol)
- else if(!isTRUE(r <- all.equal(MM, m, tol = tol)))
- stop("all.equal() |-> ", r)
-}
-
-chk.matrix <- function(M) {
- ## check object; including coercion to "matrix" :
- cl <- class(M)
- cat("class ", dQuote(cl), " [",nrow(M)," x ",ncol(M),"]; slots (",
- paste(slotNames(M), collapse=","), ")\n", sep='')
- stopifnot(validObject(M),
- dim(M) == c(nrow(M), ncol(M)),
- identical(dim(m <- as(M, "matrix")), dim(M))
- )
-}
-
-isOrthogonal <- function(x, tol = 1e-15) {
- all.equal(diag(as(zapsmall(crossprod(x)), "diagonalMatrix")),
- rep(1, ncol(x)), tol = tol)
-}
-
-
+source(system.file("test-tools-1.R", package = "Matrix"), keep.source = FALSE)
### ------- Part III -- "Matrix" (classes) specific ----------------------
+source(system.file("test-tools-Matrix.R", package = "Matrix"), keep.source = FALSE)
-lsM <- function(...) {
- for(n in ls(..., envir=parent.frame()))
- if(is((. <- get(n)),"Matrix"))
- cat(sprintf("%5s: '%s' [%d x %d]\n",n,class(.), nrow(.),ncol(.)))
-}
-
-asD <- function(m) { ## as "Dense"
- if(canCoerce(m, "denseMatrix")) as(m, "denseMatrix")
- else if(canCoerce(m, (cl <- paste(.M.kind(m), "denseMatrix", sep=''))))
- as(m, cl)
- else if(canCoerce(m, "dgeMatrix")) as(m, "dgeMatrix")
- else stop("cannot coerce to a typical dense Matrix")
-}
-
-## "normal" sparse Matrix: Csparse, no diag="U"
-asCsp <- function(x) Matrix:::diagU2N(as(x, "CsparseMatrix"))
-
-Qidentical <- function(x,y, strictClass = TRUE) {
- ## quasi-identical - for 'Matrix' matrices
- if(class(x) != class(y)) {
- if(strictClass || !is(x, class(y)))
- return(FALSE)
- ## else try further
- }
- slts <- slotNames(x)
- if("factors" %in% slts) { ## allow one empty and one non-empty 'factors'
- slts <- slts[slts != "factors"]
- ## if both are not empty, they must be the same:
- if(length(xf <- x factors) && length(yf <- y factors))
- if(!identical(xf, yf)) return(FALSE)
- }
- for(sl in slts)
- if(!identical(slot(x,sl), slot(y,sl)))
- return(FALSE)
- TRUE
-}
-
-Q.C.identical <- function(x,y, sparse = is(x,"sparseMatrix")) {
- if(sparse) Qidentical(as(x,"CsparseMatrix"), as(y,"CsparseMatrix"))
- else Qidentical(x,y)
-}
-
-## Useful Matrix constructors for testing:
-
-rspMat <- function(n, m = n, density = 1/4, nnz = round(density * n*m))
-{
- ## Purpose: random sparse Matrix
- ## ----------------------------------------------------------------------
- ## Arguments: (n,m) : dimension [default m=n ==> *square* matrix}
- ## density: the desired sparseness density:
- ## ----------------------------------------------------------------------
- ## Author: Martin Maechler, Date: 5 Mar 2008, 11:07
- stopifnot(length(n) == 1, n == as.integer(n),
- length(m) == 1, m == as.integer(m),
- 0 <= density, density <= 1,
- 0 <= nnz, nnz <= n*m)
- x <- numeric(n*m)
- ## entries 2 : (nnz+1) {so we can have '1' as 'special'}
- x[sample(n*m, nnz, replace=FALSE)] <- as.numeric(1L + seq_len(nnz))
- Matrix(x, n,m, sparse=TRUE)
-}
-
-
-
-rUnitTri <- function(n, upper = TRUE, ...)
-{
- ## Purpose: random unit-triangular sparse Matrix .. built from rspMat()
- ## ----------------------------------------------------------------------
- ## Arguments: n: matrix dimension
- ## upper: logical indicating if upper or lower triangular
- ## ... : further arguments passed to rspMat(), eg. 'density'
- ## ----------------------------------------------------------------------
- ## Author: Martin Maechler, Date: 5 Mar 2008, 11:35
-
- r <- (if(upper) triu else tril)(rspMat(n, ...))
- ## make sure the diagonal is empty
- diag(r) <- 0
- r <- drop0(r)
- r diag <- "U"
- r
-}
-
-## This is related to rUnitTri(), ver
-mkLDL <- function(n, density = 1/3) {
- ## Purpose: make nice artifical A = L D L' (with exact numbers) decomp
- ## ----------------------------------------------------------------------
- ## Author: Martin Maechler, Date: 15 Mar 2008
- stopifnot(n == round(n))
- n <- as.integer(n)
- L <- Matrix(0, n,n)
-
- nnz <- round(n*n * density)
- L[sample(n*n, nnz)] <- seq_len(nnz)
- L <- tril(L,-1)
- diag(L) <- 1
- d.half <- sample(10*(n:1))# random permutation ; use '10*' to be "different" from L entries
- D <- Diagonal(x = d.half * d.half)
- A <- tcrossprod(L * rep(d.half, each=n))
- ## = as(L %*% D %*% t(L), "symmetricMatrix")
- list(A = A, L = L, d.half = d.half, D = D)
-}
-
-eqDeterminant <- function(m1, m2, ...) {
- d1 <- determinant(m1) ## logarithm = TRUE
- d2 <- determinant(m2)
- d1m <- as.vector(d1$modulus)# dropping attribute
- d2m <- as.vector(d2$modulus)
- if((identical(d1m, -Inf) && identical(d2m, -Inf)) ||
- ## <==> det(m1) == det(m2) == 0, then 'sign' may even differ !
- (is.na(d1m) && is.na(d2m)))
- ## if both are NaN or NA, we "declare" that's fine here
- return(TRUE)
- ## else
- if(is.infinite(d1m)) d1$modulus <- sign(d1m)* .Machine$double.xmax
- if(is.infinite(d2m)) d2$modulus <- sign(d2m)* .Machine$double.xmax
- ## now they are finite or *one* of them is NA/NaN, and all.equal() will tell so:
- all.equal(d1, d2, ...)
-}
-
-##' @param A a non-negative definite sparseMatrix, typically "dsCMatrix"
-##'
-##' @return a list with components resulting from calling
-##' Cholesky(., perm = .P., LDL = .L., super = .S.)
-##'
-##' for all 2*2*3 combinations of (.P., .L., .S.)
-allCholesky <- function(A, verbose = FALSE, silentTry = FALSE)
-{
- ## Author: Martin Maechler, Date: 16 Jul 2009
-
- ##' @param r list of CHMfactor objects, typically with names() as '. | .'
- ##'
- ##' @return an is(perm,LDL,super) matrix with interesting and *named* rownames
- CHM_to_pLs <- function(r) {
- is.perm <- function(.)
- if(inherits(., "try-error")) NA else !all( perm == 0:( Dim[1]-1))
- is.LDL <- function(.)if(inherits(., "try-error")) NA else isLDL(.)
- r.st <-
- cbind(perm = sapply(r, is.perm),
- LDL = sapply(r, is.LDL),
- super = sapply(r, class) == "dCHMsuper")
- names(dimnames(r.st)) <- list(" p L s", "")
- r.st
- }
-
- my.Cholesky <- {
- if(verbose)
- function (A, perm = TRUE, LDL = !super, super = FALSE, Imult = 0, ...) {
- cat(sprintf("Chol..(*, perm= %1d, LDL= %1d, super=%1d):",
- perm, LDL, super))
- r <- Cholesky(A, perm=perm, LDL=LDL, super=super, Imult=Imult, ...)
- cat(" [Ok]\n")
- r
- }
- else Cholesky
- }
- logi <- c(FALSE, TRUE)
- d12 <- expand.grid(perm = logi, LDL = logi, super = c(logi,NA),
- KEEP.OUT.ATTRS = FALSE)
- r1 <- lapply(seq_len(nrow(d12)),
- function(i) try(do.call(my.Cholesky,
- c(list(A = A), as.list(d12[i,]))),
- silent=silentTry))
- names(r1) <- apply(d12, 1,
- function(.) paste(symnum(.), collapse=" "))
- dup.r1 <- duplicated(r1)
- r.all <- CHM_to_pLs(r1)
- if(!identical(dup.r1, duplicated(r.all)))
- warning("duplicated( <pLs-matrix> ) differs from duplicated( <CHM-list> )",
- immediate. = TRUE)
- list(dup.r.all = dup.r1,
- r.all = r.all,
- r.uniq = CHM_to_pLs(r1[ ! dup.r1]))
-}
-
-
-##--- Compatibility tests "Matrix" =!= "traditional Matrix" ---
-checkMatrix <- function(m, m.m = if(do.matrix) as(m, "matrix"),
- do.matrix = !(isSparse || isDiag) || prod(dim(m)) < 1e6,
- do.t = TRUE, doNorm = TRUE, doOps = TRUE,
- doSummary = TRUE, doCoerce = TRUE,
- doCoerce2 = doCoerce && !extends(cld, "RsparseMatrix"),
- verbose = TRUE, catFUN = cat)
-{
- ## Purpose: Compatibility tests "Matrix" <-> "traditional matrix"
- ## ----------------------------------------------------------------------
- ## Arguments: m: is(., "Matrix")
- ## ----------------------------------------------------------------------
- ## Author: Martin Maechler, Date: 11 Apr 2008; building on tests originally
- ## in dotestMat() ../tests/Class+Meth.R
- stopifnot(is(m, "Matrix"))
- validObject(m)
-
- clNam <- class(m)
- cld <- getClassDef(clNam) ## extends(cld, FOO) is faster than is(m, FOO)
- isCor <- extends(cld, "corMatrix")
- isSparse <- extends(cld, "sparseMatrix")
- isSym <- extends(cld, "symmetricMatrix")
- isDiag <- extends(cld, "diagonalMatrix")
- nonMatr <- clNam != Matrix:::MatrixClass(clNam, cld)
-
- Cat <- function(...) if(verbose) cat(...)
- CatF <- function(...) if(verbose) catFUN(...)
- ## warnNow <- function(...) warning(..., call. = FALSE, immediate. = TRUE)
-
- DO.m <- function(expr) if(do.matrix) eval(expr) else TRUE
-
- vec <- function(x) {
- dim(x) <- c(length(x), 1L)
- dimnames(x) <- list(NULL,NULL)
- x
- }
-
- ina <- is.na(m)
- if(do.matrix) {
- stopifnot(all(ina == is.na(m.m)),
- all(m == m | ina), ## check all() , "==" [Compare], "|" [Logic]
- if(ncol(m) > 0) identical3(unname(m[,1]), unname(m.m[,1]),
- as(m[,1,drop=FALSE], "vector"))
- else identical(as(m, "vector"), as.vector(m.m)))
- if(any(m != m & !ina)) stop(" any (m != m) should not be true")
- } else {
- if(any(m != m)) stop(" any (m != m) should not be true")
- if(ncol(m) > 0)
- stopifnot(identical(unname(m[,1]), as(m[,1,drop=FALSE], "vector")))
- else stopifnot(identical(as(m, "vector"), as.vector(as(m, "matrix"))))
- }
- if(do.t) {
- tm <- t(m)
- if(isSym) ## check that t() swaps 'uplo' L <--> U :
- stopifnot(c("L","U") == sort(c(m uplo, tm uplo)))
- ttm <- t(tm)
- if(extends(cld, "CsparseMatrix") ||
- extends(cld, "generalMatrix") || isDiag)
- stopifnot(Qidentical(m, ttm, strictClass = !nonMatr))
- else if(do.matrix)
- stopifnot(nonMatr || class(ttm) == clNam,
- all(m == ttm | ina))
- ## else : not testing
- }
- if(!do.matrix) {
- CatF(" will *not* coerce to 'matrix' since do.matrix is FALSE\n")
- } else if(doNorm) {
- CatF(sprintf(" norm(m [%d x %d]) :", nrow(m), ncol(m)))
- for(typ in c("1","I","F","M")) {
- Cat('', typ, '')
- stopifnot(all.equal(norm(m,typ), norm(m.m,typ)))
- }
- Cat(" ok\n")
- }
- if(do.matrix && doSummary) {
- summList <- lapply(getGroupMembers("Summary"), get,
- envir = asNamespace("Matrix"))
- CatF(" Summary: ")
- for(f in summList) {
- ## suppressWarnings(): e.g. any(<double>) would warn here:
- r <- suppressWarnings(if(isCor) all.equal(f(m), f(m.m)) else
- identical(f(m), f(m.m)))
- if(!isTRUE(r)) {
- f.nam <- sub("..$", '', sub("^\\.Primitive..", '', format(f)))
- ## prod() is delicate: NA or NaN can both happen
- (if(f.nam == "prod") message else stop)(
- sprintf("%s(m) [= %g] differs from %s(m.m) [= %g]",
- f.nam, f(m), f.nam, f(m.m)))
- }
- }
- if(verbose) cat(" ok\n")
- }
-
- ## and test 'dim()' as well:
- d <- dim(m)
- isSqr <- d[1] == d[2]
- isPerm <- extends(cld, "pMatrix")
- if(do.t) stopifnot(identical(diag(m), diag(t(m))))
- ## TODO: also === diag(band(m,0,0))
-
- if(prod(d) < .Machine$integer.max) {
- vm <- vec(m)
- stopifnot(is(vm, "Matrix"), validObject(vm), dim(vm) == c(d[1]*d[2], 1))
- }
-
- if(do.matrix)
- stopifnot(identical(dim(m.m), dim(m)),
- ## base::diag() keeps names [Matrix FIXME]
-## now that "pMatrix" subsetting gives *LOGICAL*
-## if(isPerm) {
-## identical(as.integer(unname(diag(m))), unname(diag(m.m)))
-## } else
- identical(unname(diag(m)),
- unname(diag(m.m))),## not for NA: diag(m) == diag(m.m),
- identical(nnzero(m), sum(m.m != 0)),
- identical(nnzero(m, na.= FALSE), sum(m.m != 0, na.rm = TRUE)),
- identical(nnzero(m, na.= TRUE), sum(m.m != 0 | is.na(m.m)))
- )
-
- if(isSparse) {
- n0m <- drop0(m) #==> n0m is Csparse
- has0 <- !Qidentical(n0m, as(m,"CsparseMatrix"))
- }
- ## use non-square matrix when "allowed":
-
- ## m12: sparse and may have 0s even if this is not: if(isSparse && has0)
- m12 <- as(as( m, "lMatrix"),"CsparseMatrix")
- m12 <- drop0(m12)
- if(do.matrix) {
- ## "!" should work (via as(*, "l...")) :
- m11 <- as(as(!!m,"CsparseMatrix"), "lMatrix")
- if(!Qidentical(m11, m12))
- stopifnot(Qidentical(as(m11, "generalMatrix"),
- as(m12, "generalMatrix")))
- }
- if(isSparse && !extends(cld,"nMatrix")) {
- ## ensure that as(., "nMatrix") gives nz-pattern
- CatF("as(., \"nMatrix\") giving full nonzero-pattern: ")
- n1 <- as(m, "nMatrix")
- ns <- as(m, "nsparseMatrix")
- stopifnot(identical(n1,ns),
- isDiag || ((if(isSym) Matrix:::nnzSparse else sum)(n1) ==
- length(if(isPerm) m perm else Matrix:::diagU2N(m)@x)))
- Cat("ok\n")
- }
-
- if(doOps) {
- ## makes sense with non-trivial m (!)
- CatF("2*m =?= m+m: ")
- if(identical(2*m, m+m)) Cat("identical\n")
- else if(do.matrix) {
- eq <- as(2*m,"matrix") == as(m+m, "matrix") # but work for NA's:
- stopifnot(all(eq | (is.na(m) & is.na(eq))))
- Cat("ok\n")
- } else {# !do.matrix
- stopifnot(identical(as(2*m, "CsparseMatrix"),
- as(m+m, "CsparseMatrix")))
- Cat("ok\n")
- }
- if(do.matrix) {
- ## m == m etc, now for all, see above
- CatF("m >= m for all: "); stopifnot(all(m >= m | ina)); Cat("ok\n")
- }
- if(prod(d) > 0) {
- CatF("m < m for none: ")
- mlm <- m < m
- if(!any(ina)) stopifnot(!any(mlm))
- else if(do.matrix) stopifnot(!any(mlm & !ina))
- else { ## !do.matrix & any(ina) : !ina can *not* be used
- mlm[ina] <- FALSE
- stopifnot(!any(mlm))
- }
- Cat("ok\n")
- }
-
- if(isSqr) {
- if(do.matrix) {
- ## determinant(<dense>) "fails" for triangular with NA such as
- ## (m <- matrix(c(1:0,NA,1), 2))
- CatF("det...(): ")
- if(any(is.na(m.m)) && extends(cld, "triangularMatrix"))
- Cat(" skipped: is triang. and has NA")
- else
- stopifnot(eqDeterminant(m, m.m))
- Cat("ok\n")
- }
- } else assertError(determinant(m))
- }# end{doOps}
-
- if(doCoerce && do.matrix && canCoerce("matrix", clNam)) {
- CatF("as(<matrix>, ",clNam,"): ", sep='')
- m3 <- as(m.m, clNam)
- Cat("valid:", validObject(m3), "\n")
- ## m3 should ``ideally'' be identical to 'm'
- }
-
- if(doCoerce2 && do.matrix) { ## not for large m: !m will be dense
-
- if(extends(cld, "nMatrix")) {
- stopifnot(identical(m, as(as(m, "dMatrix"),"nMatrix")),
- identical(m, as(as(m, "lMatrix"),"nMatrix")))
- }
- else if(extends(cld, "lMatrix")) { ## should fulfill even with NA:
- stopifnot(all(m | !m | ina), !any(!m & m & !ina))
- if(extends(cld, "TsparseMatrix")) # allow modify, since at end here
- m <- Matrix:::uniqTsparse(m, clNam)
- stopifnot(identical(m, m & TRUE),
- identical(m, FALSE | m))
- ## also check the coercions to [dln]Matrix
- m. <- if(isSparse && has0) n0m else m
- m1. <- m. # replace NA by 1 in m1. , carefully not changing class:
- if(any(ina)) m1 x[is na(m1 x)] <- TRUE
- stopifnot(identical(m. , as(as(m. , "dMatrix"),"lMatrix")),
- clNam == "ldiMatrix" || # <- there's no "ndiMatrix"
- ## coercion to n* and back: only identical when no extra 0s:
- identical(m1., as(as(m1., "nMatrix"),"lMatrix")))
- }
- else if(extends(cld, "dMatrix")) {
- m. <- if(isSparse && has0) n0m else m
- m1 <- (m. != 0)*1
- if(!isSparse && substr(clNam,1,3) == "dpp")
- ## no "nppMatrix" possible
- m1 <- unpack(m1)
-
- m1. <- m1 # replace NA by 1 in m1. , carefully not changing class:
- if(any(ina)) m1 x[is na(m1 x)] <- 1
- ## coercion to n* (nz-pattern!) and back: only identical when no extra 0s and no NAs:
- stopifnot(Q.C.identical(m1., as(as(m., "nMatrix"),"dMatrix"), isSparse),
- Q.C.identical(m1 , as(as(m., "lMatrix"),"dMatrix"), isSparse))
- }
-
- if(extends(cld, "triangularMatrix")) {
- mm. <- m
- i0 <- if(m uplo == "L")
- upper.tri(mm.) else lower.tri(mm.)
- mm.[i0] <- 0 # ideally, mm. remained triangular, but can be dge*
- CatF("as(<triangular (ge)matrix>, ",clNam,"): ", sep='')
- tm <- as(as(mm., "triangularMatrix"), clNam)
- Cat("valid:", validObject(tm), "\n")
- if(m uplo == tm uplo) ## otherwise, the matrix effectively was *diagonal*
- ## note that diagU2N(<dtr>) |-> dtC :
- stopifnot(Qidentical(tm, as(Matrix:::diagU2N(m), clNam)))
- }
- else if(extends(cld, "diagonalMatrix")) {
-
- ## TODO
-
- } else {
-
- ## TODO
- }
- }
- invisible(TRUE)
-}
-
+doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK_EXTRA")) ||
+ identical("true", unname(Sys.getenv("R_PKG_CHECKING_doExtras")))
diff --git a/win32/deps/library/Matrix/tests/Class+Meth.R b/win32/deps/library/Matrix/tests/Class+Meth.R
new file mode 100644
index 0000000..8a2de69
--- /dev/null
+++ b/win32/deps/library/Matrix/tests/Class+Meth.R
@@ -0,0 +1,348 @@
+library(Matrix)
+source(system.file("test-tools.R", package = "Matrix"))# identical3(),
+ # further checkMatrix(), etc
+if(interactive()) options(error = recover)
+cat("doExtras:",doExtras,"\n")
+
+setClass("myDGC", contains = "dgCMatrix")
+M <- new("myDGC", as(Matrix(c(-2:4, rep(0,9)), 4), "CsparseMatrix"))
+M
+stopifnot(M[-4,2] == 2:4,
+ Matrix:::MatrixClass("myDGC") == "dgCMatrix",
+ Matrix:::MatrixClass("Cholesky") == "dtrMatrix",
+ Matrix:::MatrixClass("pCholesky") == "dtpMatrix")
+
+setClass("posDef", contains = "dspMatrix")
+N <- as(as(crossprod(M) + Diagonal(4), "denseMatrix"),"dspMatrix")
+(N <- new("posDef", N))
+stopifnot(is(N[1:2, 1:2], "symmetricMatrix"))
+
+#### Automatically display the class inheritance structure
+#### possibly augmented with methods
+
+allCl <- getClasses("package:Matrix")
+cat("actual and virtual classes:\n")
+tt <- table( isVirt <- sapply(allCl, isVirtualClass) )
+names(tt) <- c('"actual"', "virtual")
+tt
+## The "actual" Matrix classes:
+aCl <- allCl[!isVirt]
+(aMcl <- aCl[grep("Matrix$", aCl)]) # length 48
+aMc2 <- aCl[sapply(aCl, extends, class2 = "Matrix")]
+stopifnot(all( aMcl %in% aMc2 ))
+aMc2[!(aMc2 %in% aMcl)] ## only 4 : p?Cholesky & p?BunchKaufman
+
+## Really nice would be to construct an inheritance graph and display
+## it. Following things are computational variations on the theme..
+
+## We use a version of canCoerce() that works with two *classes* instead of
+## canCoerce <- function (object, Class)
+classCanCoerce <- function (class1, class2)
+{
+ extends(class1, class2) ||
+ !is.null(selectMethod("coerce", optional = TRUE,
+ signature = c(from = class1, to = class2),
+ useInherited = c(from = TRUE, to = FALSE)))
+}
+.dq <- function(ch) paste0('"', ch, '"')
+.subclasses <- function(cnam) {
+ cd <- getClass(cnam)
+ unique(c(cd className, unlist(lapply(names(cd subclasses), .subclasses))))
+}
+for(n in allCl) {
+ if(isVirtualClass(n))
+ cat("Virtual class", .dq(n),"\n")
+ else {
+ cat("\"Actual\" class", .dq(n),":\n")
+ x <- new(n)
+ if(doExtras) for(m in allCl)
+ if(classCanCoerce(n,m)) {
+ ext <- extends(n, m)
+ if(ext) {
+ cat(sprintf(" extends %20s %20s \n", "", .dq(m)))
+ } else {
+ cat(sprintf(" can coerce: %20s -> %20s: ", .dq(n), .dq(m)))
+ tt <- try(as(x, m), silent = TRUE)
+ if(inherits(tt, "try-error")) {
+ cat("\t *ERROR* !!\n")
+ } else {
+ cat("as() ok; validObject: ")
+ vo <- validObject(tt, test = TRUE)
+ cat(if(isTRUE(vo)) "ok" else paste("OOOOOOPS:", vo), "\n")
+ }
+ }
+ }
+ cat("---\n")
+ }
+}
+
+cat('Time elapsed: ', proc.time(),'\n') # for the above "part I"
+
+
+if(!interactive()) { # don't want to see on source()
+
+cat("All classes in the 'Matrix' package:\n")
+for(cln in allCl) {
+ cat("\n-----\n\nClass", dQuote(cln),":\n ",
+ paste(rep("~",nchar(cln)),collapse=''),"\n")
+ ## A smarter version would use getClass() instead of showClass(),
+ ## build the "graph" and only then display.
+ ##
+ showClass(cln)
+}
+
+cat("\n \n")
+
+## One could extend the `display' by using (something smarter than)
+## are the "coerce" methods showing more than the 'Extends' output above?
+cat("All (S4) methods in the 'Matrix' package:\n")
+showMethods(where="package:Matrix")
+
+} # end{non-interactive}
+
+## 1-indexing instead of 0-indexing for direct "dgT" should give error:
+ii <- as.integer(c(1,2,2))
+jj <- as.integer(c(1,1,3))
+assertError(new("dgTMatrix", i=ii, j=jj, x= 10*(1:3), Dim=2:3))
+assertError(new("dgTMatrix", i=ii, j=jj - 1:1, x= 10*(1:3), Dim=2:3))
+assertError(new("dgTMatrix", i=ii - 1:1, j=jj, x= 10*(1:3), Dim=2:3))
+(mm <- new("dgTMatrix", i=ii - 1:1, j=jj - 1:1, x= 10*(1:3), Dim=2:3))
+validObject(mm)
+
+### Sparse Logical:
+m <- Matrix(c(0,0,2:0), 3,5)
+mT <- as(mC <- as(m, "CsparseMatrix"), "TsparseMatrix")
+stopifnot(identical(as(mT,"CsparseMatrix"), mC))
+(mC. <- as(mT[1:2, 2:3], "CsparseMatrix"))
+(mlC <- as(mC. , "lMatrix"))
+as(mlC,"ltCMatrix")
+
+
+
+### Test all classes: validObject(new( * )) should be fulfilled -----------
+
+## need stoplist for now:
+Rcl.struc <- c("gR", "sR", "tR")
+(dR.classes <- paste0(paste0("d", Rcl.struc[Rcl.struc != "gR"]), "Matrix"))
+(.R.classes <- paste0(sort(outer(c("l", "n"), Rcl.struc, paste0)), "Matrix"))
+ # have only stub implementation
+
+Mat.MatFact <- c("Cholesky", "pCholesky",
+ "BunchKaufman", "pBunchKaufman")##, "LDL"
+##FIXME maybe move to ../../MatrixModels/tests/ :
+## (modmat.classes <- .subclasses("modelMatrix"))
+no.t.etc <- c(.R.classes, dR.classes, Mat.MatFact)#, modmat.classes)
+no.t.classes <- c(no.t.etc) # no t() available
+no.norm.classes <- no.t.classes
+not.Ops <- NULL # "Ops", e.g. "+" fails
+not.coerce1 <- no.t.etc # not coercable from "dgeMatrix"
+not.coerce2 <- no.t.etc # not coercable from "matrix"
+
+tstMatrixClass <-
+ function(cl, mM = Matrix(c(2,1,1,2) + 0, 2,2,
+ dimnames=rep( list(c("A","B")), 2)), # dimnames: *symmetric*
+ mm = as(mM, "matrix"), recursive = TRUE, offset = 0)
+{
+ ## Purpose: Test 'Matrix' class {and do this for all of them}
+ ## ----------------------------------------------------------------------
+ ## Arguments: cl: class object of a class that extends "Matrix"
+ ## mM: a "Matrix"-matrix which will be coerced to class 'cl'
+ ## mm: a S3-matrix which will be coerced to class 'cl'
+ ## ----------------------------------------------------------------------
+ ## Author: Martin Maechler
+
+ ## from pkg sfsmisc :
+ bl.string <- function(no) sprintf("%*s", no, "")
+
+ ## Compute a few things only once :
+ mM <- as(mM, "dgeMatrix")
+ trm <- mm; trm[lower.tri(mm)] <- 0
+ summList <- lapply(getGroupMembers("Summary"), get,
+ envir = asNamespace("Matrix"))
+ if(recursive)
+ cList <- character(0)
+
+ extraValid <- function(m, cl = class(m)) {
+ sN <- slotNames(cl)
+ sN <- sN[sN != "factors"]
+ for(nm in sN)
+ if(!is.null(a <- attributes(slot(m, nm))))
+ stop(sprintf("slot '%s' with %d attributes, named: ",
+ nm, length(a)), paste(names(a), collapse=", "))
+ invisible(TRUE)
+ }
+
+
+ ## This is the recursive function
+ dotestMat <- function(cl, offset)
+ {
+ cat. <- function(...) cat(bl.string(offset), ...)
+
+ clNam <- cl subClass
+ cat("\n")
+ cat.(clNam)
+ ##---------
+ clD <- getClassDef(clNam)
+ if(isVirtualClass(clD)) {
+ cat(" - is virtual\n")
+ if(recursive) {
+ cat.("----- begin{class :", clNam, "}----new subclasses----\n")
+ for(ccl in clD subclasses) {
+ cclN <- ccl subClass
+ if(cclN %in% cList)
+ cat.(cclN,": see above\n")
+ else {
+ cList <<- c(cList, cclN)
+ dotestMat(ccl, offset = offset + 3)
+ }
+ }
+ cat.("----- end{class :", clNam, "}---------------------\n")
+ }
+ } else { ## --- actual class ---
+ genC <- extends(clD, "generalMatrix")
+ symC <- extends(clD, "symmetricMatrix")
+ triC <- extends(clD, "triangularMatrix")
+ diaC <- extends(clD, "diagonalMatrix")
+ if(!(genC || symC || triC || diaC))
+ stop("does not extend one of 'general', 'symmetric', 'triangular', or 'diagonal'")
+ sparseC <- extends(clD, "sparseMatrix")
+ denseC <- extends(clD, "denseMatrix")
+ if(!(sparseC || denseC))
+ stop("does not extend either 'sparse' or 'dense'")
+ cat("; new(..): ")
+ m <- new(clNam) ; cat("ok; ")
+ m0 <- matrix(,0,0)
+ if(canCoerce(m0, clNam)) {
+ cat("; as(matrix(,0,0), <.>): ")
+ stopifnot(Qidentical(m, as(m0, clNam))); cat("ok; ")
+ }
+ is_p <- extends(clD, "pMatrix")
+ is_cor <- extends(clD, "corMatrix") # has diagonal divided out
+ if(canCoerce(mm, clNam)) { ## replace 'm' by `non-empty' version
+ cat("canCoerce() ")
+ m0 <- {
+ if(triC) trm
+ else if(is_p)
+ mm == 1 # logical *and* "true" permutation
+ else mm
+ }
+ if(extends(clD, "lMatrix") ||
+ extends(clD, "nMatrix"))
+ storage.mode(m0) <- "logical"
+ else if(extends(clD, "zMatrix"))
+ storage.mode(m0) <- "complex"
+ validObject(m) ## validity of trivial 'm' before replacing
+ m <- as(m0, clNam)
+ if(is_cor)
+ m0 <- cov2cor(m0)
+ } else {
+ m0 <- vector(Matrix:::.type.kind[Matrix:::.M.kindC(clNam)])
+ dim(m0) <- c(0L,0L)
+ }
+ ## m0 is the 'matrix' version of our 'Matrix' m
+ m. <- m0 ##m. <- if(is_p) as.integer(m0) else m0
+ EQ <- if(is_cor) all.equal else identical
+ stopifnot(EQ(m0[FALSE], m[FALSE])
+ , EQ(m.[TRUE], m[TRUE])
+ , if(length(m) >= 2) EQ(m.[2:1], m[2:1]) else TRUE)
+
+ if(all(dim(m) > 0)) { ## matrix(0,0,0)[FALSE,] is invalid too
+ m00 <- m[FALSE,FALSE]
+ m.. <- m[TRUE , TRUE]
+ stopifnot(dim(m00) == c(0L,0L),
+ dim(m..) == dim(m))
+ ## not yet , class(m00) == clNam , identical(m.. , m)
+ }
+
+ cat("valid: ", validObject(m), extraValid(m, clNam),"\n")
+
+ ## This can only work as long as 'm' has no NAs :
+ ## not yet -- have version in not.Ops below
+ ## once we have is.na():
+ ## stopifnot(all(m == m | is.na(m))) ## check all() and "==" [Compare]
+ ## if(any(m != m && !is.na(m)))
+
+ show(m)
+ ## coerce to 'matrix'
+ m.m <- as(m, "matrix")
+ ##=========##
+ checkMatrix(m, m.m,
+ ##=========##
+ do.t= !(clNam %in% no.t.classes),
+ doNorm= !(clNam %in% no.norm.classes),
+ doOps = all(clNam != not.Ops),
+ doCoerce = all(clNam != not.coerce1),
+ catFUN = cat.)
+
+### FIXME: organize differently :
+### 1) produce 'mM' and 'mm' for the other cases,
+### 2) use identical code for all cases
+
+ if(is(m, "dMatrix") && is(m, "compMatrix")) {
+ if(any(clNam == not.coerce1))
+ cat.("not coercable_1\n")
+ else if(canCoerce(mM, clNam)) {
+ m2 <- as(mM, clNam)
+ cat("valid:", validObject(m2), "\n")
+ if(!is_cor) ## as.vector()
+ stopifnot(as.vector(m2) == as.vector(mM))
+ cat.("[cr]bind2():"); mm2 <- cbind2(m2,m2)
+ stopifnot(dim(rbind2(m2,m2)) == 2:1 * dim(mM)); cat(" ok")
+ if(genC && class(mm2) == clNam) ## non-square matrix when "allowed"
+ m2 <- mm2
+ dd <- diag(m2)
+ cat("; `diag<-` ")
+ diag(m2) <- 10*dd
+ stopifnot(is_cor || identical(dd, diag(mM)),
+ identical(10*dd, diag(m2))); cat("ok ")
+ }
+## if(all(clNam != not.coerce2)) {
+ if(canCoerce("matrix", clNam)) {
+ cat.("as(matrix, <class>): ")
+ m3 <- as(mm, clNam)
+ cat("valid:", validObject(m3), "\n")
+ } else cat.(" not coerceable from \"matrix\"\n")
+## }
+ }
+
+ ## else { ... no happens in tstMatrix() above .. }
+
+ ## if(is(m, "denseMatrix")) {
+ ## ## .........
+ ## cat.("as dsparse* ")
+ ## msp <- as(m, "dsparseMatrix")
+ ## cat.("; valid coercion: ", validObject(msp), "\n")
+ ## } else if(is(m, "sparseMatrix")) {
+
+ ## } else cat.("-- not dense nor sparse -- should not happen(!?)\n")
+
+ if(is(m, "dsparseMatrix")) {
+ if(any(clNam == not.coerce1))
+ cat.("not coercable_1\n")
+ else {
+ ## make sure we can coerce to dgT* -- needed, e.g. for "image"
+ ## change: use Tsparse instead of dgT, unless it *is* Tsparse:
+ isT <- is(m, "TsparseMatrix")
+ prefix <- if(isT) "dgT" else "Tsparse"
+ Tcl <- paste(prefix, "Matrix", sep='')
+ cat.(sprintf("as %s* ", prefix))
+ mgT <- as(m, Tcl)
+ cat(sprintf("; valid %s* coercion: %s\n",
+ prefix, validObject(mgT)))
+ }
+ }
+ }
+ } # end{dotestMat}
+
+ for(scl in getClass(cl)@subclasses)
+ dotestMat(scl, offset + 1)
+}
+
+tstMatrixClass("Matrix")
+if(FALSE)## or just a sub class
+tstMatrixClass("triangularMatrix")
+
+
+cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''
+
+if(!interactive()) warnings()
diff --git a/win32/deps/library/Matrix/tests/Simple.R b/win32/deps/library/Matrix/tests/Simple.R
new file mode 100644
index 0000000..4536ec2
--- /dev/null
+++ b/win32/deps/library/Matrix/tests/Simple.R
@@ -0,0 +1,837 @@
+#### Currently a collection of simple tests
+## (since 'Matrix' takes long to load, rather have fewer source files!)
+
+##-------- *BEFORE* attaching Matrix: --------------------------------
+str(Matrix::Matrix)# -> load the namespace
+T <- new("ngTMatrix", i=0L, j=2L, Dim = c(2L,6L))
+T
+as(T, "CsparseMatrix")
+## gave Error in asMethod(object) : could not find function ".M.classEnv"
+## from 0.999375-23 to *-25
+
+## another even shorter version of this:
+n <- new("dgCMatrix")
+n
+## this:
+m <- Matrix::Matrix(cbind(1,0,diag(x=2:4)))
+m
+##--------------------------------------------------------------------
+
+library(Matrix)
+
+source(system.file("test-tools.R", package = "Matrix"))# identical3() etc
+
+if(interactive()) {
+ options(error = recover)
+} else options(Matrix.verbose = TRUE)# to show Matrix.msg()s
+
+### Matrix() ''smartness''
+(d4 <- Matrix(diag(4)))
+(z4 <- Matrix(0*diag(4)))
+(o4 <- Matrix(1+diag(4)))
+(tr <- Matrix(cbind(1,0:1)))
+(M4 <- Matrix(m4 <- cbind(0,rbind(6*diag(3),0))))
+dM4 <- Matrix(M4, sparse = FALSE)
+class(mN <- Matrix(NA, 3,4)) # NA *is* logical
+validObject(Matrix(NA))
+bd4 <- bdiag(M4,dM4,M4)
+stopifnot(isValid(o4, "dsyMatrix"),
+ isValid(M4, "dtCMatrix"),
+ validObject(dM4), validObject(mN),
+ identical(bdiag(M4), bdiag(dM4)),
+ identical(bd4 p, c(0L,0:3,3:6,6:9)),
+ identical(bd4 i, c(0:2, 4:6, 8:10)), bd4 x == 6
+ )
+assert.EQ.mat(dM4, m4)
+assert.EQ.mat(M4^M4, m4^m4)
+assert.EQ.mat(mN, matrix(NA, 3,4))
+assert.EQ.mat(bdiag(diag(4)), diag(4))
+sL <- Matrix(, 3,4, sparse=TRUE)# -> "lgC"
+trS <- Matrix(tr, sparse=TRUE)# failed in 0.9975-11
+stopifnot(isValid(d4, "diagonalMatrix"), isValid(z4, "diagonalMatrix"),
+ isValid(tr, "triangularMatrix"), isValid(trS, "triangularMatrix"),
+ all(is.na(sL x)), ## not yet: all(is.na(sL)),
+ !any(sL, na.rm=TRUE), all(!sL, na.rm=TRUE),
+ validObject(Matrix(c(NA,0), 4, 3, byrow = TRUE)),
+ validObject(Matrix(c(NA,0), 4, 4)),
+ isValid(Matrix(c(NA,0,0,0), 4, 4), "sparseMatrix"))
+I <- i1 <- I1 <- Diagonal(1)
+I1[1,1] <- i1[1, ] <- I [ ,1] <- NA
+stopifnot(identical3(I,i1,I1))
+image(d4) # gave infinite recursion
+
+assertError( Matrix(factor(letters)) )
+mlp <- matrix(.leap.seconds)## 24 x 1 numeric matrix
+Mlp <- Matrix(.leap.seconds)
+assert.EQ.mat(Mlp, mlp)
+if(FALSE) { ## TODO -- once R itself does better ...
+ .Leap.seconds <- as.POSIXlt(.leap.seconds)
+ mLp <- matrix(.Leap.seconds)## 24 x 1 list each of length 24 -- yuck!!!
+ MLp <- Matrix(.Leap.seconds)## --> error (for now)
+}
+
+I <- Diagonal(3)
+stopifnot(identical(I != 0, Diagonal(3, TRUE)), I diag == "U")
+I[,1] <- NA; I[2,2] <- NA ; I[3,] <- NaN
+stopifnot(isValid(I, "sparseMatrix"))
+I # gave error in printSpMatrix() - because of R bug in format.info()
+
+L <- spMatrix(9, 30, i = rep(1:9, 3), 1:27, (1:27) %% 4 != 1)
+M <- drop0(crossprod(L))
+diag(M) <- diag(M) + 5 # to make it pos.def.
+M. <- M[1:12,1:12] # small ex
+N3 <- as(Matrix(upper.tri(diag(3))), "nMatrix")
+isValid(bdN <- bdiag(N3, N3),"nsparseMatrix")
+
+stopifnot(identical(L, L == TRUE), ## used to give infinite recursion
+ all(drop0((0 - L) != 0) == drop0(L)))
+L[sample(length(L), 10)] <- NA
+ll <- as(L,"logical")
+stopifnot(all.equal(mean(L, na.rm=TRUE),
+ mean(ll, na.rm=TRUE), tol= 1e-14),
+ all.equal(mean(L, na.rm=TRUE, trim=1/4),# <- with a warning
+ mean(ll, na.rm=TRUE, trim=1/4), tol= 1e-14))
+
+
+## Examples where is.na(.) was wrong:
+validObject(sc <- new("dsCMatrix", i=as.integer(c(0,0:1,1:2,0:1,3)), Dim=c(4L,4L),
+ p = c(0L,1L,3L,5L,8L), x = c(0,NA,NA,0:1,0,NA,1)))
+validObject(gc <- as(sc, "generalMatrix"))
+
+stopifnot(isSymmetric(M), isSymmetric(M.),
+ is(bdiag(M., M.),"symmetricMatrix"),
+ is(bdN, "triangularMatrix"),
+ all(sc == gc | (is.na(sc) & is.na(gc))),
+ all.equal(N3,N3),
+ tail(all.equal(N3, t(N3)), 1) == all.equal(1,-1),# ~= "Mean relative difference: 2"
+ all((bdN != t(bdN)) == (bdN + t(bdN))), # <nsparse> != <nsparse> failed to work...
+ !any((0+bdN) > bdN), # <dsparse> o <nsparse>
+ !any(bdN != (0+bdN)), # <nsparse> o <dsparse>
+ length(grep("Length", all.equal(M., (vM <- as.vector(M.))))) > 0,
+ identical(M., (M2 <- Matrix(vM, 12,12))),
+ all.equal(M., M2, tol=0)
+ )
+
+## large sparse ones: these now directly "go sparse":
+str(m0 <- Matrix(0, nrow=100, ncol = 1000))
+str(l0 <- Matrix(FALSE, nrow=100, ncol = 200))
+stopifnot(all(!l0),
+ identical(FALSE, any(l0)))
+
+if(!interactive()) warnings()
+## really large {length(<dense equivalent>) is beyond R's limits}:
+op <- options(warn = 2) # warnings (e.g. integer overflow!) become errors:
+n <- 50000L
+stopifnot(n^2 > .Machine$integer.max)
+## had integer overflow in index constructions:
+x <- 1:n
+D <- Diagonal(n, x=x[n:1])
+summary(D)# special method
+summary(D != 0)
+stopifnot(identical(x*D, (Dx <- D*x)),
+ identical(D != 0, as(D, "lMatrix")),
+ identical(Dx, local({d <- D; d x <- d x * x; d})))
+
+Lrg <- new("dgTMatrix", Dim = c(n,n))
+diag(Lrg[2:9,1:8]) <- 1:8
+## ==: Lrg[2:9,1:8] <- `diag<-`(Lrg[2:9,1:8], 1:8)
+e1 <- try(Lrg == Lrg) # error message almost ok
+e2 <- try(!Lrg) # error message was "bad", now perfect
+ina <- is.na(Lrg)# "all FALSE"
+stopifnot(grep("too large", e1) == 1,
+ grep("too large", e2) == 1,
+ !any(ina))# <- gave warning previously
+stopifnot(suppressWarnings(any(Lrg)))# (double -> logical warning)
+
+## with dimnames:
+m. <- matrix(c(0, 0, 2:0), 3, 5)
+dimnames(m.) <- list(LETTERS[1:3], letters[1:5])
+(m0 <- m <- Matrix(m.))
+m Dimnames[[2]] <- m Dimnames[[1]]
+## not valid anymore:
+(val <- validObject(m, test=TRUE)); stopifnot(is.character(val))
+dm <- as(m0, "denseMatrix")
+stopifnot(all.equal(rcond(dm), rcond(m.), tol = 1e-14),
+ ##^^^^^^^ dm and m. are both dense, interestingly small differences
+ ## show in at least one case of optimized BLAS
+ all.equal(rcond(dm), 0.4899474520656),
+ ## show(<dgRMatrix>) had revealed a bug in C:
+ identical(capture.output(show(as(m0, "RsparseMatrix")))[-(1:2)],
+ gsub("0", ".", capture.output(show(m.))[-1])))
+rm(m)
+
+###-- Sparse Triangular :
+
+g5 <- new("dgCMatrix", Dim = c(5L, 5L),
+ x = c(10, 1, 3, 10, 1, 10, 1, 10, 10),
+ i = c(0L,2L,4L, 1L, 3L,2L,4L, 3L, 4L),
+ p = c(0L, 3L, 5L, 7:9))
+t5 <- as(g5, "triangularMatrix") # fine
+stopifnot(class(t5) == "dtCMatrix",
+ identical(t5, tril(g5)))
+## This is really a regression test for 'methods::selectMethod()'
+## Maybe move to R once 'Matrix' is recommended
+sm <- selectMethod(coerce, c("dgCMatrix", "triangularMatrix"), verbose=TRUE)
+stopifnot(identical(sm(g5), t5))
+
+
+(t1 <- new("dtTMatrix", x= c(3,7), i= 0:1, j=3:2,
+ Dim= as.integer(c(4,4))))
+## Diagonal o Sparse
+I4 <- Diagonal(4)
+D4 <- Diagonal(4, x=1:4)
+validObject(t2 <- t1 + I4)
+validObject(tt2 <- t(t1) + I4)
+validObject(t1c <- as(t1, "CsparseMatrix"))
+validObject(t2c <- as(t2, "CsparseMatrix"))
+stopifnot(validObject(t1),
+ isValid(2 * I4, "diagonalMatrix"),
+ isValid(D4 * 3, "diagonalMatrix"),
+ isValid(I4 / 5, "diagonalMatrix"),
+ isValid(D4 / 2, "diagonalMatrix"),
+ identical(t1, t(t(t1))),
+ identical(t1c, t(t(t1c))),
+ isValid(t1c + I4,"triangularMatrix"), isValid(t2c + I4,"triangularMatrix"),
+ c(class(t2), class(t1c), class(t2c), class(tt2)) == "dtCMatrix",
+ identical(t(tt2), t2))
+assert.EQ.mat(t1, as(t1c, "matrix"))
+D4. <- D4 * (A4 <- Matrix(1:4, 4,4))
+D4p <- A4 + D4
+Lg1 <- D4 > 0 & D4 > 1
+nLg <- !Lg1
+nnLg <- !nLg
+D4m <- D4 * 4:1
+assert.EQ.mat(D4., diag(x= (1:4)^2))
+assert.EQ.mat(D4p, diag(x= (1:4)) + (1:4))
+assert.EQ.mat(D4m, diag(x=c(4,6,6,4)))
+assert.EQ.mat(Lg1, diag(x= c(FALSE, rep(TRUE,3))))
+stopifnot(is(Lg1, "diagonalMatrix"), is(D4m, "diagonalMatrix"),
+ is(D4., "diagonalMatrix"),
+ is(nLg, "symmetricMatrix"), is(nnLg, "symmetricMatrix"),
+ identical3(Lg1, Matrix(nnLg), as(nnLg, "diagonalMatrix")),
+ all(Lg1 != (!Lg1)))
+
+
+## as(<diag>, <anything>) :
+str(cls <- names(getClass("Matrix")@subclasses))# all Matrix classes
+for(cl in cls)
+ if(canCoerce(I4, cl)) {
+ cat(cl,":")
+ M <- as(I4, cl)
+ M. <- as(D4, cl)
+ stopifnot(diag(4) == as(M,"matrix"),
+ if(is(cl,"dMatrix")) diag(x=1:4) == as(M.,"matrix") else TRUE)
+ cat(" [Ok]\n")
+ }
+s4 <- as(D4,"sparseMatrix")
+v <- c(11,2,2,12); s4[2:3,2:3] <- v; validObject(s4)
+s4. <- D4; s4.[2:3,2:3] <- v; validObject(s4.)
+stopifnot(all(s4 == s4.))
+## now assign symmetrically to symmetricMatrix
+s4 <- as(as(D4,"sparseMatrix"),"symmetricMatrix")
+s4[2:3,2:3] <- v
+validObject(s4)
+stopifnot(is(s4,"symmetricMatrix"))
+assert.EQ.mat(s4, as(s4.,"matrix"),tol=0)
+
+## lower-triangular unit-diagonal
+L <- new("dtCMatrix", i = 1L, p = c(0:1, 1L), Dim = c(2L, 2L),
+ x = 0.5, uplo = "L", diag = "U")
+stopifnot(range(L) == 0:1, all.equal(mean(L), 5/8))
+
+## from 0-diagonal to unit-diagonal triangular {low-level step}:
+tu <- t1 ; tu diag <- "U"
+tu
+validObject(cu <- as(tu, "dtCMatrix"))
+validObject(cnu <- Matrix:::diagU2N(cu))# <- testing diagU2N
+validObject(tu. <- as(cu, "dtTMatrix"))
+validObject(tt <- as(cu, "TsparseMatrix"))
+stopifnot(## NOT: identical(tu, tu.), # since T* is not unique!
+ identical(cu, as(tu., "dtCMatrix")),
+ length(cnu i) == length(cu i) + nrow(cu),
+ identical(cu, Matrix:::diagN2U(cnu)),# <- testing diagN2U
+ all(cu >= 0, na.rm = TRUE), all(cu >= 0),
+ any(cu >= 7))
+validObject(tcu <- t(cu))
+validObject(ttu <- t(tu))
+validObject(ltu <- as(ttu, "lMatrix"))
+validObject(ldtu <- as(ltu, "denseMatrix"))
+validObject(Cltu <- as(ltu, "CsparseMatrix"))
+stopifnot(identical(asCsp(ttu > 0), asCsp(ltu)),
+ all(ltu == as(ttu > 0,"denseMatrix")))
+ltu - (ttu > 0) # failed
+assert.EQ.mat(cu, as(tu,"matrix"), tol=0)
+assert.EQ.mat(cnu, as(tu,"matrix"), tol=0)
+
+C <- suppressWarnings(Matrix(c(0,1,0,0), 5,5)) + Diagonal(5)
+(tU <- Matrix:::diagN2U(tril(C))) # dtC Unitriangular
+ntU <- as(tU, "nMatrix")
+nT <- as(ntU, "TsparseMatrix")
+R <- as(tU, "RsparseMatrix")
+Tt <- Matrix:::diagU2N(R) # used to accidentally drop the diag.
+stopifnot(R x == c(1,1,1), diag(Tt) == 1)
+
+lcu <- new("ltCMatrix", Dim = c(4L, 4L), i = c(0:1, 0L), p = c(0L, 0:3),
+ x = c(TRUE, FALSE, FALSE), uplo = "U", diag = "U")
+(lTu <- as(lcu,"TsparseMatrix"))# prints wrongly (in Matrix 0.999375-31)
+stopifnot(identical3(rowSums(lcu), rowSums(lTu), rowSums(drop0(lcu))))
+(ncu <- as(lcu, "nMatrix"))# -- gives the "pattern" of lcu, i.e. FALSE are *there*
+ncn <- Matrix:::diagU2N(ncu)
+(cncn <- crossprod(ncn))# works -> "nsCMatrix"
+stopifnot(identical(ncu, as(lcu,"nsparseMatrix")),
+ identical(rowSums(ncu), c(3:1, 1L)),
+ Q.eq(ncn, ncu),
+ Q.eq(crossprod(drop0(lcu)), crossprod(lcu)),# crossprod works -> "dsCMatrix"
+ identical(crossprod(ncu), cncn),
+ Q.eq(cncn, t(ncu) %*% ncu)) #used to seg.fault
+
+U <- new("dtCMatrix", Dim = c(6L, 6L),
+ i = c(0:1, 0L, 2:3, 1L, 4L),
+ p = c(0L,0L,0L, 2:3, 5L, 7L),
+ x = rep.int(-0.5, 7), diag = "U")
+validObject(U)
+U. <- solve(iU <- solve(U))#-> gave segmentation fault
+stopifnot(validObject(U), ## had a case where solve(U) modified U !
+ validObject(iU),
+ validObject(U.),
+ ## no rounding error, since have iU x * 8 is integer :
+ identical(U, Matrix:::diagN2U(drop0(U.))))
+
+## <sparse> o <numeric> (of length > 1):
+stopifnot(isValid(tm <- tu * 1:8, "sparseMatrix"),
+ identical4(tm, cu * 1:8, 1:8 * cu, 1:8 * tu))
+
+cu[1,2] <- tu[1,2] <- NA
+mu <- as(tu,"matrix")
+stopifnot(isValid(cu, "CsparseMatrix"), isValid(cu, "triangularMatrix"),
+ isValid(tu, "TsparseMatrix"), isValid(tu, "triangularMatrix"),
+ identical(cu * 1:8, tu * 1:8), # but are no longer triangular
+ all(cu >= 0, na.rm=TRUE), !all(cu >= 1), is.na(all(tu >= 0)),
+ ## Csparse_drop: preserves triangularity incl diag="U"
+ identical(cu, .Call(Matrix:::Csparse_drop, cu, 0.))
+ )
+assert.EQ.mat(cu * 1:8, mu * 1:8)
+
+ina <- is.na(as(cu,"matrix"))
+## These 3 were each different (2008-03) !!
+stopifnot(all(ina == is.na(cu)),
+ all(ina == is.na(as(cu,"generalMatrix"))),
+ all(ina == as(is.na(as(cu,"matrix")),"nMatrix")))
+
+
+set.seed(7)
+xx <- rpois(10, 50)
+Samp <- function(n,size) sample(n, size, replace=TRUE)
+Tn <- sparseMatrix(i=Samp(8, 50), j=Samp(9,50), x=xx, giveCsparse=FALSE)
+Tn
+stopifnot(xx == Tn x,
+ max(xx) < max(Tn), 0 == min(Tn),
+ (sT <- sum(Tn)) == sum(colSums(Tn)), sT == sum(Tn x),
+ range(Tn) == range(as(Tn, "CsparseMatrix")))
+
+## tu. is diag "U", but tu2 not:
+tu2 <- as(as(tu., "generalMatrix"), "triangularMatrix")
+assert.EQ.mat(cu, mu, tol=0)
+stopifnot(identical3(cu[cu > 1], tu [tu > 1], mu [mu > 1]),
+ identical3(cu <= 1, tu <= 1, as(mu <= 1, "lMatrix")),# all lgeMatrix
+ identical3(cu[cu <= 1], tu[tu <= 1], mu[mu <= 1]),
+ identical3(cu , triu(cu ), t(t(cu))),
+ identical3(tu , triu(tu ), t(t(tu))),
+ identical3(tu., triu(tu.), t(t(tu.))),
+ identical(tu2, triu(tu2)),
+ identical(tcu , tril(tcu)),
+ identical(ttu , tril(ttu)),
+ identical(t(tu), tril(t(tu)))
+ )
+assert.EQ.mat(triu(cu), as.matrix(triu(as.matrix(cu))))
+for(k in -1:1)
+ assert.EQ.mat(tril(cu,k), as.matrix(tril(as.matrix(cu),k)))
+
+(dtr <- Matrix(local({m <- diag(2); m[1,2] <- 3;m})))
+identical(dtr, triu(dtr))
+assert.EQ.mat(tril(dtr), diag(2))
+
+
+(t4 <- new("dgTMatrix", i = 3:0, j = 0:3, x = rep(1,4), Dim = as.integer(c(4,4))))
+c4 <- as(t4, "CsparseMatrix")
+## the same but "dsT" (symmetric)
+suppressWarnings(M <- Matrix(c(0, rep(c(0,0:1),4)), 4,4))# warning:.. length [13] is not ..multiple
+tt <- as(M, "TsparseMatrix")
+stopifnot(all.equal(triu(t4) + tril(t4), c4),
+ all.equal(triu(tt) + tril(tt), c4))
+
+
+###-- Numeric Dense: Crossprod & Solve
+
+set.seed(123)
+mm. <- mm <- Matrix(rnorm(500 * 150), nc = 150)
+stopifnot(validObject(mm))
+xpx <- crossprod(mm)
+stopifnot(identical(mm, mm.),# once upon a time, mm was altered by crossprod()
+ isValid(xpx, "dpoMatrix"))
+str(mm) # 'dge*"
+str(xpx)# 'dpo*"
+xpy <- crossprod(mm, rnorm(500))
+res <- solve(xpx, xpy)
+str(xpx)# now with Cholesky factor
+stopifnot(validObject(xpx),
+ validObject(xpy),
+ validObject(res))
+stopifnot(all.equal(xpx %*% res, xpy, tol= 1e-12))
+lp <- xpx >= 1
+slp <- as(lp, "sparseMatrix")
+
+ltlp <- lp[ lower.tri(lp) ]
+sltlp <- slp[ lower.tri(slp) ]
+dim(ij <- which(lower.tri(lp), arr.ind = TRUE))
+ss <- slp[ij] # now fast (!)
+stopifnot(identical4(lp[ij], ltlp, sltlp, as(lp, "matrix")[ij]),
+ identical(ss, sltlp),
+ isValid(lp, "lsyMatrix"), lp uplo == "U")
+
+###-- more solve() methods {was ./solve.R }
+
+## first for "dgeMatrix" and all kinds of RHS :
+(m6 <- 1 + as(diag(0:5), "dgeMatrix"))
+rcond(m6)
+I6 <- as(diag(6), "dgeMatrix")
+stopifnot(all.equal(I6, m6 %*% solve(m6)),
+ all.equal(I6, solve(m6) %*% m6) )
+
+(i6 <- solve(m6, Matrix(1:6)))
+stopifnot(identical(i6, as(cbind(c(-4, rep(1,5))), "dgeMatrix")),
+ identical(i6, solve(m6, 1:6)),
+ identical(i6, solve(m6, matrix(1:6))),
+ identical(i6, solve(m6, matrix(c(1,2,3,4,5,6))))
+ )
+
+## solve(<sparse>)
+(m <- t1+ t(t1) + Diagonal(4))
+i.m <- solve(as.mat(m))
+I1 <- m %*% i.m
+o4 <- diag(I1)
+im <- solve(m)
+(I2 <- m %*% im)
+(ms <- as(m, "symmetricMatrix"))
+## solve(<sparse>, <sparse>):
+s.mm <- solve(m,m)
+s.mms <- solve(m, ms)
+## these now work "fully-sparse"
+s.ms2 <- solve(ms, ms)
+s.msm <- solve(ms, m)
+I4c <- as(Matrix(diag(4),sparse=TRUE), "generalMatrix")
+stopifnot(isValid(im, "Matrix"), isValid(I2, "Matrix"), class(I4c) == "dgCMatrix",
+ all.equal(I1, I2, tol = 1e-14),
+ all.equal(diag(4), as.mat(I2), tol = 1e-12),
+ all.equal(s.mm, I2, tol = 1e-14),
+ all.equal(s.mms, I2, tol = 1e-14),
+ all.equal(s.ms2, s.msm, tol = 4e-15),
+ all.equal(s.ms2, I4c , tol = 4e-15),
+ abs(o4 - 1) < 1e-14)
+
+image(T125 <- kronecker(kronecker(t5,t5),t5),
+ main = paste("T125:",class(T125)))
+dim(T3k <- kronecker(t5,kronecker(T125, t5)))
+system.time(IT3 <- solve(T3k))# incredibly fast
+I. <- drop0(zapsmall(IT3 %*% T3k))
+I.. <- Matrix:::diagN2U(I.)
+I <- Diagonal(5^5)
+stopifnot(isValid(IT3, "dtCMatrix"),
+ ## something like the equivalent of all(I. == Diagonal(3125)) :
+ identical(as(I., "diagonalMatrix"), I),
+ identical(as(I..,"diagonalMatrix"), I)
+ )
+
+###-- row- and column operations {was ./rowcolOps.R }
+
+set.seed(321)
+(m1 <- round(Matrix(rnorm(25), 5), 2))
+m1k <- Matrix(round(rnorm(1000), 2), 50, 20)
+m.m <- as(m1k, "matrix")
+stopifnot(all.equal(colMeans(m1k), colMeans(m.m)),
+ all.equal(colSums (m1k), colSums (m.m)),
+ all.equal(rowMeans(m1k), rowMeans(m.m)),
+ all.equal(rowSums (m1k), rowSums (m.m)))
+
+###-- kronecker for nonsparse uses Matrix(.):
+stopifnot(isValid(kr <- kronecker(m1, m6), "Matrix"))
+assert.EQ.mat(kr,
+ kronecker(as(m1, "matrix"),
+ as(m6, "matrix")), tol = 0)
+
+## sparse:
+(kt1 <- kronecker(t1, tu))
+kt2 <- kronecker(t1c, cu)
+stopifnot(identical(Matrix:::uniq(kt1), Matrix:::uniq(kt2)))
+## but kt1 and kt2, both "dgT" are different since entries are not ordered!
+ktf <- kronecker(as.matrix(t1), as.matrix(tu))
+if(FALSE) # FIXME? our kronecker treats "0 * NA" as "0" for structural-0
+assert.EQ.mat(kt2, ktf, tol= 0)
+(cs1 <- colSums(kt1))
+NA.or.True <- function(x) is.na(x) | x
+eq <- (cs1 == colSums(as(kt1, "matrix")))
+stopifnot(NA.or.True(eq), identical(is.na(eq), is.na(cs1)))
+nt1 <- as(kt1, "nMatrix") # no NA's anymore
+(ng1 <- as(as(nt1, "generalMatrix"),"CsparseMatrix")) # ngC
+dg1 <- as(ng1, "dMatrix")# dgC
+lt1 <- kt1 > 5
+nt1 <- as(lt1, "nMatrix")
+(colSums(nt1, sparseResult = TRUE))
+(colSums(kt1, sparseResult = TRUE)) # dsparse, with NA
+(colSums(lt1, sparseResult = TRUE)) # isparse, with NA
+(colSums(lt1, sparseResult = TRUE, na.rm = TRUE))
+(colSums(nt1, sparseResult = TRUE)) # isparse, no NA
+## check correct sparseness of both:
+for(M in list(kt1, nt1, ng1, dg1, lt1, nt1)) {
+ m <- as(M, "matrix")
+ for(na.rm in c(FALSE,TRUE)) {
+ cs <- colSums(M, na.rm = na.rm)
+ cs. <- colSums(M, na.rm = na.rm, sparseResult = TRUE)
+ rs <- rowSums(M, na.rm = na.rm)
+ rs. <- rowSums(M, na.rm = na.rm, sparseResult = TRUE)
+ stopifnot(isValid(cs., "sparseVector"), identical(cs, as(cs., "vector")),
+ isValid(rs., "sparseVector"), identical(rs, as(rs., "vector")),
+ {eq <- cs == colSums(m, na.rm = na.rm) ; ineq <- is.na(eq)
+ all(ineq | eq) && identical(ineq, is.na(cs)) },
+ {eq <- rs == rowSums(m, na.rm = na.rm) ; ineq <- is.na(eq)
+ all(ineq | eq) && identical(ineq, is.na(rs)) } )
+ }
+}
+
+i1 <- cs. == 1
+cs2 <- cs.
+cs2[i1] <- 0 # failed in *-31 !!
+## now *index* with a NA-sparseVector :
+i2 <- i1 ; i2[3] <- NA ; li2 <- as.logical(i2)
+cs3 <- cs. ; cs3 [i2] <- 0
+v3 <- as(cs.,"vector"); v3[li2] <- 0
+cs4 <- cs. ; cs4[li2] <- 0
+stopifnot(length(i1 x) == 2, identical(li2, as(i2,"vector")),
+ identical(cs3, cs4),
+ cs3 == v3, all(as(v3, "sparseVector") == cs3)
+ ## indexing simple "numeric" with sparseVector:
+ ## see 'R_FIXME' in ../R/sparseVector.R
+ ## , identical(v3[i2], v3[li2])
+ ## TODO:
+ ## sub-assigning into simple "numeric" with sparseVector index:
+ )
+
+
+
+M <- Matrix(c(2:0,1),2); M. <- as(M, "sparseMatrix")
+(N <- as(crossprod(kronecker(diag(2), M)) > 0,
+ "nMatrix"))
+(L. <- as(N,"lMatrix"))
+stopifnot(identical(N, as(L.,"nMatrix")),
+ identical(kronecker( c(1,0), M),
+ kronecker(cbind(1:0), M)))
+assert.EQ.mat(kronecker(M, c(1,0,0)),
+ kronecker(as.matrix(M), c(1,0,0)))
+
+## coercion from "dpo" or "dsy"
+xx <- as(xpx, "dsyMatrix")
+stopifnot(isSymmetric(xxS <- as(xx, "sparseMatrix")),
+ isSymmetric(xpxS <- as(xpx, "sparseMatrix")))
+
+tm <- matrix(0, 8,8)
+tm[cbind(c(1,1,2,7,8),
+ c(3,6,4,8,8))] <- c(2,-30,15,20,80)
+(tM <- Matrix(tm)) ## dtC
+(mM <- Matrix(m <- (tm + t(tm)))) ## dsC
+mT <- as(mM, "dsTMatrix")
+gC <- as(as(mT, "dgTMatrix"), "dgCMatrix")
+lT <- as(Matrix(TRUE, 2,2),"TsparseMatrix")
+## Check that mT, lT, and gC print properly :
+pr.mT <- capture.output(mT)
+pr.lT <- capture.output(lT)[-(1:2)]
+nn <- unlist(strsplit(gsub(" +\\.", "", sub("^....", "", pr.mT[-(1:2)])), " "))
+stopifnot(as.numeric(nn[nn != ""]) == m[m != 0],
+ identical(1:2, grep("|", pr.lT, fixed=TRUE)),
+ identical(pr.lT, capture.output(as(lT, "nMatrix"))[-(1:2)]),
+ capture.output(gC)[-1] == pr.mT[-1])
+assert.EQ.mat(tM, tm, tol=0)
+assert.EQ.mat(gC, m, tol=0)
+assert.EQ.mat(mT, m, tol=0)
+stopifnot(isValid(mM, "dsCMatrix"), isValid(tM, "dtCMatrix")
+ , identical(mT, as(mM, "TsparseMatrix"))
+ , identical(gC, as(mM, "generalMatrix"))
+ ## coercions general <-> symmetric
+ , identical(as(as(mM, "generalMatrix"), "symmetricMatrix"), mM)
+ , identical(as(as(mM, "dgTMatrix"), "symmetricMatrix"), mT)
+ , identical(as(as(tM, "generalMatrix"),"triangularMatrix"), tM)
+ , identical(tM + Diagonal(8), tMD <- Diagonal(8) + tM)
+ , isValid(tMD, "dtCMatrix")
+ )
+eM <- eigen(mM) # works thanks to base::as.matrix hack in ../R/zzz.R
+stopifnot(all.equal(eM$values,
+ { v <- c(162.462112512353, 30.0665927567458)
+ c(v, 15, 0, 0, 160-v[1], -15, -v[2])}, tol=1e-14))
+
+##--- symmetric -> pos.def. needs valid test:
+m5 <- Matrix(diag(5) - 1)
+assertError(as(m5, "dpoMatrix"))# not pos.definite!
+pm5 <- as(m5, "dspMatrix") # packed
+assertError(as(pm5, "dppMatrix"))# not pos.definite!
+sm <- as(Matrix(diag(5) + 1),"dspMatrix")
+pm <- as(sm,"dpoMatrix")## gave infinite recursion (for a day or so)
+pp <- as(pm,"dppMatrix")
+
+x <- round(100 * crossprod(Matrix(runif(25),5)))
+D <- Diagonal(5, round(1000*runif(5)))
+px <- pack(x)
+stopifnot(is(x, "dpoMatrix"), is(px,"dppMatrix"), is(D, "ddiMatrix"))
+
+class(x+D)#--> now "dsyMatrix"
+stopifnot(is(x+D, "symmetricMatrix"),
+ is(D+px, "dspMatrix"),
+ identical(x+D, D+x), identical(px+D, D+px), identical(pack(x-D), px-D))
+
+
+tx <- tril(x)
+ptx <- pack(tx)
+stopifnot(is(tx, "dtrMatrix"), is(ptx, "dtpMatrix"),
+ is(t(tx), "dtrMatrix"), is(t(ptx), "dtpMatrix"),
+ is(D + tx, "dtrMatrix"), is(tx + D, "dtrMatrix"),
+ is(ptx + D, "dtpMatrix"), is(D + ptx, "dtpMatrix"))
+
+
+###-- dense nonzero pattern:
+class(m <- Matrix(TRUE,2,2)) # lsy
+isValid(n <- as(m, "nMatrix"), "nsyMatrix")
+
+## 1)
+as(n,"CsparseMatrix") # used to give CHOLMOD error: invalid xtype...
+ls2 <- as(m, "CsparseMatrix") # works fine
+## and really 'm' and 'n' are interally slot identical (!!!)
+
+as(n,"sparseMatrix")
+as(m,"sparseMatrix")
+
+### -- now when starting with nsparse :
+nT <- new("ngTMatrix",
+ i = as.integer(c(0, 1, 0)),
+ j = as.integer(c(0, 0, 1)), Dim = as.integer(c(2,2)))
+(nC <- as(nT, "ngCMatrix"))
+str(nC)# of course, no 'x' slot
+
+tt <- as(nT,"denseMatrix") # nge (was lge "wrongly")
+stopifnot(is(tt,"ngeMatrix"),
+ identical(as(tt, "lMatrix"),
+ as(as(nT, "lMatrix"), "denseMatrix")))
+tt
+as(nC,"denseMatrix")
+
+
+###-- sparse nonzero pattern : ----------
+
+(nkt <- as(as(as(kt1, "generalMatrix"), "CsparseMatrix"), "ngCMatrix"))# ok
+dkt <- as(nkt, "denseMatrix")
+(clt <- crossprod(nkt))
+stopifnot(isValid(nkt, "ngCMatrix"),
+ isValid(clt, "nsCMatrix"))
+suppressWarnings(crossprod(clt)) ## warning "crossprod() of symmetric ..."
+
+## a Csparse with *repeated* entry is not valid!
+assertError(new("ngCMatrix", p = c(0L,2L), i = c(0L,0L), Dim = 2:1))
+
+
+### "d" <-> "l" for (symmetric) sparse : ---------------------------------------
+suppressWarnings( data(KNex) ) ## may warn, as 'Matrix' is recommended
+ ## and exist more than once at check-time
+mm <- KNex$mm
+xpx <- crossprod(mm)
+## extract nonzero pattern
+nxpx <- as(xpx, "nsCMatrix")
+show(nxpx) ## now ok, since subsetting works
+r <- nxpx[1:2,]
+lmm <- as(mm, "lgCMatrix")
+nmm <- as(lmm, "nMatrix")
+xlx <- crossprod(lmm)
+x.x <- crossprod(nmm)
+## now A = lxpx and B = xlx should be close, but not quite the same
+## since <x,y> = 0 is well possible when x!=0 and y!=0 .
+## However, A[i,j] != 0 ==> B[i,j] != 0:
+A <- as(as(nxpx, "lMatrix"), "TsparseMatrix")
+B <- as(as(xlx, "lMatrix"), "TsparseMatrix")
+ij <- function(a) a i + ncol(a) * a j
+stopifnot(all(ij(A) %in% ij(B)))
+
+l3 <- upper.tri(matrix(,3,3))
+stopifnot(isValid(c3 <- as(l3, "CsparseMatrix"), "CsparseMatrix"),# lgC
+ is(c3, "lMatrix"))
+(M <- Matrix(l3))
+stopifnot(isValid(M, "ltCMatrix"),
+ isValid(M2 <- M %x% M, "triangularMatrix"), # is "dtT" (why not "dtC" ?)
+ dim(M2) == c(9,9), identical(M2, kronecker(M,M)))
+M3 <- M %x% M2 #ok
+(cM3 <- colSums(M3, sparse=TRUE))
+identical(as.vector(cM3),
+ as(rev(rowSums(M3, sparse=TRUE)), "vector"))
+M. <- M2 %x% M # gave infinite recursion
+
+## diagonal, sparse & interactions
+stopifnot(isValid(as(Diagonal(3), "TsparseMatrix"), "TsparseMatrix"),
+ isValid(X <- Diagonal(7) + 1.5 * tM[1:7,1:7], "sparseMatrix"),
+ isValid(X, "triangularMatrix"),
+ isValid(XX <- X - chol(crossprod(X)), "triangularMatrix"))
+X
+XX
+XX <- as(drop0(XX), "dsCMatrix")
+stopifnot(identical(XX, Matrix(0, nrow(X), ncol(X))))
+
+M <- Matrix(m., sparse = FALSE)
+(sM <- Matrix(m.))
+class(dlM <- M >= 1)
+stopifnot(identical(dlM, !(M < 1)),
+ isValid(sM, "sparseMatrix"),
+ isValid(dlM, "denseMatrix"))
+(lM <- as(dlM, "sparseMatrix"))
+lM2 <- as(dlM, "CsparseMatrix") #-> now ok
+lM0 <- Matrix:::as_Csparse(dlM)
+stopifnot(identical3(lM, lM2, lM0))
+
+selectMethod("coerce", c("lgeMatrix", "CsparseMatrix"),
+ useInherited = c(from = TRUE, to = FALSE))
+
+ms0 <- Matrix(c(0,1,1,0), 2,2)
+ms <- as(ms0, "TsparseMatrix")
+cs <- as(ms, "CsparseMatrix")
+ll <- as(ms, "lMatrix")
+lt <- as(ll, "lgTMatrix")
+nn <- as(cs, "nsparseMatrix")
+l2 <- as(cs, "lsparseMatrix")
+nt <- triu(nn)
+n3 <- as(nt, "lsparseMatrix")
+da <- nt + t(nt)
+dm <- nt * t(nt) + da
+##
+mnt <- as(nt, "matrix")
+m <- rbind(v <- 2:3)
+assert.EQ.mat(nt %*% v, mnt %*% v)
+assert.EQ.mat(v %*% nt, v %*% mnt)
+assert.EQ.mat( crossprod(nt, v), crossprod(mnt,v))
+assert.EQ.mat( crossprod(v, nt), crossprod(v,mnt))
+assert.EQ.mat(tcrossprod(v, nt), tcrossprod(v,mnt))
+assert.EQ.mat(tcrossprod(nt, m), tcrossprod(mnt, m))
+##
+stopifnot(isValid(ms, "dsTMatrix"),
+ as(ms0,"matrix") == as(ll, "matrix"), # coercing num |-> log
+ as(lt, "matrix") == as(ll, "matrix"),
+ identical(ms, as(ll, "dMatrix")),
+ identical4(as(ll, "CsparseMatrix"), as(cs, "lMatrix"),# lsC*
+ as(nn, "lsparseMatrix"), l2),
+ identical3(da, dm, as(cs, "generalMatrix")), # dgC*
+ identical(as(da, "lMatrix"), as(lt, "CsparseMatrix")) # lgC*
+ )
+## Dense *packed* ones:
+s4 <- as(D4, "symmetricMatrix")
+sp <- as(as(as(D4, "symmetricMatrix"),"denseMatrix"),"dspMatrix")
+tp <- as(triu(sp),"dtpMatrix")
+tpL <- as(tril(sp),"dtpMatrix")
+(spL <- t(sp))
+stopifnot(sp @uplo=="U", tp @uplo=="U",
+ spL uplo=="L", tpL uplo=="L")
+
+## band():
+n <- 4 ; m <- 6
+r1 <- Matrix(1:24, n,m)
+validObject(M1 <- band(r1, 0,0))
+(M1 <- as(M1, "sparseMatrix"))
+r2 <- Matrix(1:18, 3, 6)
+stopifnot(identical(M1, bandSparse(n,m, k=0, diag = list(diag(r1)))),
+ identical(band(r2, 0,4),
+ band(r2, 0,3) + band(r2, 4,4)))
+s1 <- as(r1, "sparseMatrix") # such that band(s1) is sparse, too
+for(k1 in (-n):m)
+ for(k2 in k1:m) {
+ isValid(br1 <- band(r1, k1,k2), "ddenseMatrix")
+ isValid(bs1 <- band(s1, k1,k2), "CsparseMatrix")
+ stopifnot(all(r1 == s1))
+ }
+
+D. <- Diagonal(x= c(-2,3:4)); D.[lower.tri(D.)] <- 1:3 ; D.
+D0 <- Diagonal(x= 0:3); D0[upper.tri(D0)] <- 1:6 ; D0
+stopifnot(all.equal(list(modulus = structure(24, logarithm = FALSE), sign = -1L),
+ unclass(determinant(D.,FALSE)), tol=1e-15),
+ det(Matrix(0,1)) == 0,
+ all.equal(list(modulus = structure(0, logarithm = FALSE), sign = 1L),
+ unclass(determinant(D0,FALSE)), tol=0)
+ )
+
+### More sparseVector checks: -------------------------------
+validObject(new("isparseVector"))
+R <- sv <- as(D4, "sparseVector")
+## dim(<sparseVector>) <- (n1,n2) --> sparse Matrix :
+dim(R) <- dim(D4)
+stopifnot(isValid(sv,"sparseVector"),
+ isValid(R, "sparseMatrix"),
+ identical(D4, as(R, "diagonalMatrix")))
+iv <- c(rep(0, 5), 3, 0,0,7,0,0,0)
+sv <- as(iv, "sparseVector")
+sv. <- as(as.integer(iv), "sparseVector")
+## Note: Method with signature "numeric#sparseVector" chosen ...
+(sv2 <- as(sv, "isparseVector")) ## gave error
+as(sv, "zsparseVector")
+stopifnot(identical(sv., sv2),
+ identical( Matrix(sv, 3,4, byrow=TRUE),
+ t(Matrix(sv, 4,3))))
+options(warn = 0)# no longer error
+
+
+## "Large" sparse:
+n <- 100000
+m <- 50000 ; nnz <- 47
+M <- spMatrix(n, m,
+ i = sample(n, nnz, replace = TRUE),
+ j = sample(m, nnz, replace = TRUE),
+ x = round(rnorm(nnz),1))
+validObject(Mv <- as(M, "sparseVector"))
+validObject(Dv <- as(Diagonal(60000), "sparseVector"))
+validObject(LD <- Diagonal(60000, TRUE))
+validObject(Lv <- as(LD, "sparseVector"))
+Dm <- Dv; dim(Dm) <- c(180000L, 20000L)
+stopifnot(!doExtras || isValid(Md <- M * rowSums(M, sparseResult=TRUE), "sparseMatrix"),
+ LD diag == "U",
+ isValid(Dm, "sparseMatrix"),
+ identical(Dv, as(Dm, "sparseVector")))
+
+p. <- new("dtCMatrix", i = c(2:3, 2L), p = c(0L, 2:3, 3L, 3L),
+ Dim = c(4L, 4L), x = rep(-0.5, 3), uplo = "L", diag = "U")
+assert.EQ.mat(solve(solve(p.)), as(p., "matrix"))
+dimnames(p.)[[1]] <- paste(1:4)
+ii <- is.na(p.)
+stopifnot(all(!ii), !any(as(ii, "denseMatrix")))# used to fail
+
+lst <- ls()
+table(istri <- sapply(lst, function(.) is(get(.),"triangularMatrix")))
+table(triC <- sapply(lst[istri], function(.) class(get(.))))
+table(uniC <- sapply(lst[istri], function(.) get(.)@diag == "U"))
+lsUtr <- lst[istri][uniC]
+(di <- sapply(lsUtr, function(.) dim(get(.))))
+## TODO: use %*%, crossprod(), .. on all those 4 x 4 -- and check "triangular rules"
+cat('Time elapsed: ', (.pt <- proc.time()),'\n') # "stats"
+##
+
+cat("doExtras:",doExtras,"\n")
+if(doExtras) {
+ cat("checkMatrix() of all: \n---------\n")
+ Sys.setlocale("LC_COLLATE", "C") # to keep ls() reproducible
+ for(nm in ls()) if(is(.m <- get(nm), "Matrix")) {
+ cat("\n", rep("-",nchar(nm)),"\n",nm, ":\n", sep='')
+ checkMatrix(.m)
+ }
+ cat('Time elapsed: ', proc.time() - .pt,'\n') # "stats"
+}
+
+if(!interactive()) warnings()
+
+## Platform - and other such info -- so we find it in old saved outputs
+SysI <- Sys.info()
+structure(Sys.info()[c(4,5,1:3)], class="simple.list")
+sessionInfo()
+c(Matrix = packageDescription("Matrix")$Built)
+if(SysI[["sysname"]] == "Linux" && require("sfsmisc")) local({
+ nn <- names(.Sc <- sfsmisc::Sys.cpuinfo())
+ nn <- names(.Sc <- .Sc[nn != "flags"])
+ print(.Sc[grep("\\.[0-9]$", nn, invert=TRUE)])
+})
diff --git a/win32/deps/library/Matrix/tests/abIndex-tsts.R b/win32/deps/library/Matrix/tests/abIndex-tsts.R
new file mode 100644
index 0000000..d770f94
--- /dev/null
+++ b/win32/deps/library/Matrix/tests/abIndex-tsts.R
@@ -0,0 +1,121 @@
+#### Testing consistency of "abIndex" == "abstract-indexing vectors" class :
+library(Matrix)
+
+source(system.file("test-tools.R", package = "Matrix"))# identical3() etc
+
+validObject(ab <- new("abIndex"))
+str(ab)
+
+set.seed(1)
+ex. <- list(2:1000, 0:10, sample(100), c(-3:40, 20:70),
+ c(1:100,77L, 50:40, 10L), c(17L, 3L*(12:3)))
+## we know which kinds will come out: "compressed" for all but random:
+rD <- "rleDiff"; kinds <- c(rD,rD,"int32", rD, rD, rD)
+isCmpr <- kinds == rD
+ab. <- lapply(ex., as, Class = "abIndex")
+nu. <- lapply(ab., as, Class = "numeric")
+in. <- lapply(ab., as, Class = "integer")
+rles <- lapply(ab.[isCmpr], function(u) u rleD@rle)
+r.x <- lapply(ex.[isCmpr], function(.) rle(diff(.)))
+
+stopifnot(sapply(ab., validObject),
+ identical(ex., nu.),
+ identical(ex., in.),
+ ## Check that the relevant cases really *are* "compressed":
+ sapply(ab., slot, "kind") == kinds,
+ ## Using rle(diff(.)) is equivalent to using our C code:
+ identical(rles, r.x),
+ ## Checking Group Methods - "Summary" :
+ sapply(ab., range) == sapply(ex., range),
+ sapply(ab., any) == sapply(ex., any),
+ TRUE)
+
+## testing c() method, i.e. currently c.abIndex():
+tst.c.abI <- function(lii) {
+ stopifnot(is.list(lii),
+ all(unlist(lapply(lii, mode)) == "numeric"))
+ aii <- lapply(lii, as, "abIndex")
+ v.i <- do.call(c, lii)
+ a.i <- do.call(c, aii)
+ avi <- as(v.i, "abIndex")
+ ## identical() is too hard, as values & lengths can be double/integer
+ stopifnot(all.equal(a.i, avi, tol = 0))
+}
+tst.c.abI(list(2:6, 70:50, 5:-2))
+## now an example where *all* are uncompressed:
+tst.c.abI(list(c(5, 3, 2, 4, 7, 1, 6), 3:4, 1:-1))
+## and one with parts that are already non-trivial:
+exc <- ex.[isCmpr]
+tst.c.abI(exc)
+set.seed(101)
+N <- length(exc) # 5
+for(i in 1:10) {
+ tst.c.abI(exc[sample(N, replace=TRUE)])
+ tst.c.abI(exc[sample(N, N-1)])
+ tst.c.abI(exc[sample(N, N-2)])
+}
+
+for(n in 1:120) {
+ cat(".")
+ k <- 1 + 4*rpois(1, 5) # >= 1
+ ## "random" rle -- NB: consecutive values *must* differ (for uniqueness)
+ v <- as.integer(1+ 10*rnorm(k))
+ while(any(dv <- duplicated(v)))
+ v[dv] <- v[dv] + 1L
+ rl <- structure(list(lengths = as.integer(1 + rpois(k, 10)), values = v),
+ class = "rle")
+ ai <- new("abIndex", kind = "rleDiff",
+ rleD = new("rleDiff", first = rpois(1, 20), rle = rl))
+ validObject(ai)
+ ii <- as(ai, "numeric")
+ iN <- ii; iN[180] <- NA; aiN <- as(iN,"abIndex")
+ iN <- as(aiN, "numeric") ## NA from 180 on
+ stopifnot(is.numeric(ii), ii == round(ii),
+ identical(ai, as(ii, "abIndex")),
+ identical(is.na(ai), is.na(ii)),
+ identical(is.na(aiN), is.na(iN)),
+ identical(is.finite (aiN), is.finite(iN)),
+ identical(is.infinite(aiN), is.infinite(iN))
+ )
+ if(n %% 40 == 0) cat(n,"\n")
+}
+
+## we have : identical(lapply(ex., as, "abIndex"), ab.)
+
+mkStr <- function(ch, n) paste(rep.int(ch, n), collapse="")
+
+##O for(grMeth in getGroupMembers("Ops")) {
+##O cat(sprintf("\n%s :\n%s\n", grMeth, mkStr("=", nchar(grMeth))))
+grMeth <- "Arith"
+ for(ng in getGroupMembers(grMeth)) {
+ cat(ng, ": ")
+ G <- get(ng)
+ t.tol <- if(ng == "/") 8e-16 else 0
+ ## now using special all.equal() method!
+ AEq <- function(a,b, ...) all.equal(a, b, tol=t.tol)
+ for(v in ex.) {
+ va <- as(v, "abIndex")
+ for(s in list(-1, 17L, TRUE, FALSE)) {# numeric *and* logical
+ if(!(identical(s, FALSE) && ng == "/")) ## division by 0 often "fails"
+ stopifnot(AEq(as(G(v, s), "abIndex"), G(va, s)),
+ AEq(as(G(s, v), "abIndex"), G(s, va)))
+ }
+ cat(".")
+ }
+ cat(" [Ok]\n")
+ }
+##O }
+
+## check the abIndex versions of indDiag() and indTri() :
+for(n in 1:7)
+ stopifnot(isValid(ii <- Matrix:::abIindDiag(n), "abIndex"),
+ ii kind == "rleDiff",
+ Matrix:::indDiag(n) == as(ii, "numeric"))
+
+for(n in 0:7)
+ for(diag in c(TRUE,FALSE))
+ for(upper in c(TRUE,FALSE))
+ stopifnot(isValid(ii <- Matrix:::abIindTri(n, diag=diag,upper=upper), "abIndex"),
+ Matrix:::indTri(n, diag=diag,upper=upper) == as(ii, "numeric"))
+
+cat('Time elapsed: ', (.pt <- proc.time()),'\n') # "stats"
diff --git a/win32/deps/library/Matrix/tests/base-matrix-fun.R b/win32/deps/library/Matrix/tests/base-matrix-fun.R
new file mode 100644
index 0000000..4f6862e
--- /dev/null
+++ b/win32/deps/library/Matrix/tests/base-matrix-fun.R
@@ -0,0 +1,45 @@
+#### Thanks to the manipulation in base namespace, see ../R/zzz.R ,
+#### all the functions (in 'base' or namespaces that import it)
+#### starting with something like
+#### " x <- as.matrix(x) " or " X <- as.array(X) "
+#### will work for 'Matrix'-matrices
+
+library(Matrix)
+
+data(KNex); mm <- KNex$mm
+str(m1 <- mm[1:500, 1:200])
+m11 <- m1[1:100, 1:20]
+## These now work thanks to using our as.matrix():
+str(D1 <- dist(m11))
+str(rs <- apply(m1, 1, sum))
+
+stopifnot(identical(kappa(Matrix(2:5, 2)),
+ kappa(matrix(2:5, 2))))
+## used to seg.fault, PR#7984,
+## because qr() was calling the wrong as.matrix()
+
+## also matplot() or pairs().
+
+## a regression test for as.matrix.dist(.) still working
+stopifnot(c(43, 43) == dim(as.matrix(d <- dist(USJudgeRatings))))
+
+m <- Matrix(0:5, 3, 2)
+(m2 <- Matrix(diag(c(3,1))))
+(m3 <- crossprod(t(m))) # <- that's an S4 method; nothing "base"
+
+str( svd(m) )
+str( lapply(eigen(m3), zapsmall))
+
+### outer() used to work thanks to as.array() -- up to R 2.2.1
+## no longer, because the definition of outer has changed -- FIXME?
+## Whould work by providing an as.vector(.) method
+## *and* is.array(.) \-> TRUE which may be too strong
+##--> For %o%: "need" to make outer(.,.) an S3 generic
+## *and* provide Matrix S3 methods
+## stopifnot(identical(outer(m, m2),
+## outer(as(m,"matrix"), as(m2,"matrix"))),
+## identical(outer(m3, m2),
+## outer(as(m3,"matrix"), as(m2,"matrix"))))
+
+
+cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''
diff --git a/win32/deps/library/Matrix/tests/bind.R b/win32/deps/library/Matrix/tests/bind.R
new file mode 100644
index 0000000..4f25e34
--- /dev/null
+++ b/win32/deps/library/Matrix/tests/bind.R
@@ -0,0 +1,131 @@
+#### Testing cBind() & rBind()
+
+library(Matrix)
+
+source(system.file("test-tools.R", package = "Matrix"))# identical3() etc
+
+### --- Dense Matrices ---
+
+m1 <- m2 <- m <- Matrix(1:12, 3,4)
+dimnames(m2) <- list(LETTERS[1:3],
+ letters[1:4])
+dimnames(m1) <- list(NULL,letters[1:4])
+
+stopifnot(identical(cBind ( m, 10*m) -> R,
+ cbind2( m, 10*m))); R
+stopifnot(identical(cBind (m1,100+m1) -> R,
+ cbind2(m1,100+m1))); R
+stopifnot(identical(cBind (m1, 10*m2) -> R,
+ cbind2(m1, 10*m2))); R
+stopifnot(identical(cBind (m2, m1+m2) -> R,
+ cbind2(m2, m1+m2))); R
+
+cBind(m1, MM = -1)
+rBind(R1 = 10:11, m1)
+cBind(0, Matrix(0+0:1, 1,2), 3:2)# FIXME? should warn - as with matrix()
+
+as(rBind(0, Matrix(0+0:1, 1,2), 3:2),
+ "sparseMatrix")
+cBind(m2, 10*m2[nrow(m2):1 ,])# keeps the rownames from the first
+
+(im <- cBind(I = 100, m))
+str(im)
+(mi <- cBind(m2, I = 1000))
+str(mi)
+(m1m <- cBind(m,I=100,m2))
+showProc.time()
+
+### --- Diagonal / Sparse - had bugs
+
+D4 <- Diagonal(4)
+(D4T <- as(D4, "TsparseMatrix"))
+D4C <- as(D4T, "CsparseMatrix")
+c1 <- Matrix(0+0:3, 4, sparse=TRUE) ; r1 <- t(c1); r1
+
+d4 <- rBind(Diagonal(4), 0:3)
+m4 <- cBind(Diagonal(x=-1:2), 0:3)
+c4. <- cBind(Diagonal(4), c1)
+c.4 <- cBind(c1, Diagonal(4))
+r4. <- rBind(Diagonal(4), r1)
+r.4 <- rBind(r1, Diagonal(4))
+assert.EQ.mat(d4, rBind(diag(4), 0:3))
+assert.EQ.mat(m4, cBind(diag(-1:2), 0:3))
+stopifnot(identical(Matrix(cbind(diag(3),0)), cbind2(Diagonal(3),0)),
+ is(d4, "sparseMatrix"), is(m4, "sparseMatrix"),
+ identical(t(d4), cBind(Diagonal(4), 0:3)),
+ identical(t(m4), rBind(Diagonal(x=-1:2), 0:3)))
+showProc.time()
+
+### --- Sparse Matrices ---
+
+identical4(cBind(diag(4), diag(4)),
+ cBind(D4C, D4C),
+ cBind(D4T, D4C),
+ cBind(D4C, D4T))
+nr <- 4
+m. <- matrix(c(0, 2:-1), nr ,6)
+M <- Matrix(m.)
+(mC <- as(M, "dgCMatrix"))
+(mT <- as(M, "dgTMatrix"))
+stopifnot(identical(mT, as(mC, "dgTMatrix")),
+ identical(mC, as(mT, "dgCMatrix")))
+
+for(v in list(0, 2, 1:0))
+ for(fnam in c("cBind", "rBind")) {
+ cat(fnam,"(m, v=", deparse(v),"), class(m) :")
+ FUN <- get(fnam)
+ for(m in list(M, mC, mT)) {
+ cat("", class(m),"")
+ assert.EQ.mat(FUN(v, m), FUN(v, m.)) ; cat(",")
+ assert.EQ.mat(FUN(m, v), FUN(m., v)) ; cat(".")
+ }
+ cat("\n")
+ }
+showProc.time()
+
+cBind(0, mC); cBind(mC, 0)
+cBind(0, mT); cBind(mT, 2)
+cBind(diag(nr), mT)
+stopifnot(identical(t(cBind(diag(nr), mT)),
+ rBind(diag(nr), t(mT))))
+(cc <- cBind(mC, 0,7,0, diag(nr), 0))
+stopifnot(identical3(cc, cBind(mT, 0,7,0, diag(nr), 0),
+ as( cBind( M, 0,7,0, diag(nr), 0), "dgCMatrix")))
+
+cBind(mC, 1, 100*mC, 0, 0:2)
+cBind(mT, 1, 0, mT+10*mT, 0, 0:2)
+
+## logical (sparse) - should remain logical :
+L5 <- Diagonal(n = 5, x = TRUE); v5 <- rep(x = c(FALSE,TRUE), length = ncol(L5))
+stopifnot(is(show(rBind(L5,v5)), "lsparseMatrix"),
+ is(show(cBind(v5,L5)), "lsparseMatrix"),
+ is(rBind(L5, 2* v5), "dsparseMatrix"),
+ is(cBind(2* v5, L5), "dsparseMatrix"))
+
+## print() / show() of non-structural zeros:
+(m <- Matrix(c(0, 0, 2:0), 3, 5))
+(m2 <- cBind(m,m))
+(m4 <- rBind(m2,m2))
+diag(m4)
+for(i in 1:6) {
+ m4[i, i ] <- i
+ m4[i,i+1] <- 0
+}
+m4 ## now show some non-structural zeros:
+
+## Mixture of dense and sparse/diagonal -- used to fail, even in 1.0-0
+D5 <- Diagonal(x = 10*(1:5))
+(D5.1 <- cbind2(D5, 1))
+## "FIXME" in newer versions of R, do not need Matrix() here:
+s42 <- Matrix(z42 <- cbind2(rep(0:1,4), rep(1:0,4)),
+ sparse=TRUE)
+(C86 <- rBind(1, 0, D5.1, 0))
+stopifnot(TRUE
+ ,isValid(D5.1, "dgCMatrix")
+ ,isValid(print(rbind2(Matrix(1:10, 2,5), D5)), "dgCMatrix")
+ ,isValid(print(cbind2(Matrix(10:1, 5,2), D5.1)), "dgeMatrix")
+ ,isValid(zz <- cbind2(z42, C86), "dgCMatrix")
+ ,identical(zz, cbind2(s42, C86))
+ )
+
+showProc.time()
diff --git a/win32/deps/library/Matrix/tests/bind.Rout.save b/win32/deps/library/Matrix/tests/bind.Rout.save
new file mode 100644
index 0000000..68197df
--- /dev/null
+++ b/win32/deps/library/Matrix/tests/bind.Rout.save
@@ -0,0 +1,385 @@
+
+R Under development (unstable) (2012-02-27 r58508)
+Copyright (C) 2012 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> #### Testing cBind() & rBind()
+>
+> library(Matrix)
+Loading required package: lattice
+>
+> source(system.file("test-tools.R", package = "Matrix"))# identical3() etc
+>
+> ### --- Dense Matrices ---
+>
+> m1 <- m2 <- m <- Matrix(1:12, 3,4)
+> dimnames(m2) <- list(LETTERS[1:3],
++ letters[1:4])
+> dimnames(m1) <- list(NULL,letters[1:4])
+>
+> stopifnot(identical(cBind ( m, 10*m) -> R,
++ cbind2( m, 10*m))); R
+3 x 8 Matrix of class "dgeMatrix"
+ [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
+[1,] 1 4 7 10 10 40 70 100
+[2,] 2 5 8 11 20 50 80 110
+[3,] 3 6 9 12 30 60 90 120
+> stopifnot(identical(cBind (m1,100+m1) -> R,
++ cbind2(m1,100+m1))); R
+3 x 8 Matrix of class "dgeMatrix"
+ a b c d a b c d
+[1,] 1 4 7 10 101 104 107 110
+[2,] 2 5 8 11 102 105 108 111
+[3,] 3 6 9 12 103 106 109 112
+> stopifnot(identical(cBind (m1, 10*m2) -> R,
++ cbind2(m1, 10*m2))); R
+3 x 8 Matrix of class "dgeMatrix"
+ a b c d a b c d
+A 1 4 7 10 10 40 70 100
+B 2 5 8 11 20 50 80 110
+C 3 6 9 12 30 60 90 120
+> stopifnot(identical(cBind (m2, m1+m2) -> R,
++ cbind2(m2, m1+m2))); R
+3 x 8 Matrix of class "dgeMatrix"
+ a b c d a b c d
+A 1 4 7 10 2 8 14 20
+B 2 5 8 11 4 10 16 22
+C 3 6 9 12 6 12 18 24
+>
+> cBind(m1, MM = -1)
+3 x 5 Matrix of class "dgeMatrix"
+ a b c d MM
+[1,] 1 4 7 10 -1
+[2,] 2 5 8 11 -1
+[3,] 3 6 9 12 -1
+> rBind(R1 = 10:11, m1)
+4 x 4 Matrix of class "dgeMatrix"
+ a b c d
+R1 10 11 10 11
+ 1 4 7 10
+ 2 5 8 11
+ 3 6 9 12
+> cBind(0, Matrix(0+0:1, 1,2), 3:2)# FIXME? should warn - as with matrix()
+1 x 4 Matrix of class "dgeMatrix"
+ [,1] [,2] [,3] [,4]
+[1,] 0 0 1 3
+>
+> as(rBind(0, Matrix(0+0:1, 1,2), 3:2),
++ "sparseMatrix")
+3 x 2 sparse Matrix of class "dgCMatrix"
+
+[1,] . .
+[2,] . 1
+[3,] 3 2
+> cBind(m2, 10*m2[nrow(m2):1 ,])# keeps the rownames from the first
+3 x 8 Matrix of class "dgeMatrix"
+ a b c d a b c d
+A 1 4 7 10 30 60 90 120
+B 2 5 8 11 20 50 80 110
+C 3 6 9 12 10 40 70 100
+>
+> (im <- cBind(I = 100, m))
+3 x 5 Matrix of class "dgeMatrix"
+ I
+[1,] 100 1 4 7 10
+[2,] 100 2 5 8 11
+[3,] 100 3 6 9 12
+> str(im)
+Formal class 'dgeMatrix' [package "Matrix"] with 4 slots
+ ..@ x : num [1:15] 100 100 100 1 2 3 4 5 6 7 ...
+ ..@ Dim : int [1:2] 3 5
+ ..@ Dimnames:List of 2
+ .. ..$ : NULL
+ .. ..$ : chr [1:5] "I" "" "" "" ...
+ ..@ factors : list()
+> (mi <- cBind(m2, I = 1000))
+3 x 5 Matrix of class "dgeMatrix"
+ a b c d I
+A 1 4 7 10 1000
+B 2 5 8 11 1000
+C 3 6 9 12 1000
+> str(mi)
+Formal class 'dgeMatrix' [package "Matrix"] with 4 slots
+ ..@ x : num [1:15] 1 2 3 4 5 6 7 8 9 10 ...
+ ..@ Dim : int [1:2] 3 5
+ ..@ Dimnames:List of 2
+ .. ..$ : chr [1:3] "A" "B" "C"
+ .. ..$ : chr [1:5] "a" "b" "c" "d" ...
+ ..@ factors : list()
+> (m1m <- cBind(m,I=100,m2))
+3 x 9 Matrix of class "dgeMatrix"
+ I a b c d
+A 1 4 7 10 100 1 4 7 10
+B 2 5 8 11 100 2 5 8 11
+C 3 6 9 12 100 3 6 9 12
+> showProc.time()
+Time elapsed: 0.176 0.012 0.189
+>
+> ### --- Diagonal / Sparse - had bugs
+>
+> D4 <- Diagonal(4)
+> (D4T <- as(D4, "TsparseMatrix"))
+4 x 4 sparse Matrix of class "dtTMatrix" (unitriangular)
+
+[1,] 1 . . .
+[2,] . 1 . .
+[3,] . . 1 .
+[4,] . . . 1
+> D4C <- as(D4T, "CsparseMatrix")
+> c1 <- Matrix(0+0:3, 4, sparse=TRUE) ; r1 <- t(c1); r1
+1 x 4 sparse Matrix of class "dgCMatrix"
+
+[1,] . 1 2 3
+>
+> d4 <- rBind(Diagonal(4), 0:3)
+> m4 <- cBind(Diagonal(x=-1:2), 0:3)
+> c4. <- cBind(Diagonal(4), c1)
+> c.4 <- cBind(c1, Diagonal(4))
+> r4. <- rBind(Diagonal(4), r1)
+> r.4 <- rBind(r1, Diagonal(4))
+> assert.EQ.mat(d4, rBind(diag(4), 0:3))
+> assert.EQ.mat(m4, cBind(diag(-1:2), 0:3))
+> stopifnot(identical(Matrix(cbind(diag(3),0)), cbind2(Diagonal(3),0)),
++ is(d4, "sparseMatrix"), is(m4, "sparseMatrix"),
++ identical(t(d4), cBind(Diagonal(4), 0:3)),
++ identical(t(m4), rBind(Diagonal(x=-1:2), 0:3)))
+> showProc.time()
+Time elapsed: 0.076 0 0.076
+>
+> ### --- Sparse Matrices ---
+>
+> identical4(cBind(diag(4), diag(4)),
++ cBind(D4C, D4C),
++ cBind(D4T, D4C),
++ cBind(D4C, D4T))
+[1] FALSE
+> nr <- 4
+> m. <- matrix(c(0, 2:-1), nr ,6)
+Warning message:
+In matrix(c(0, 2:-1), nr, 6) :
+ data length [5] is not a sub-multiple or multiple of the number of rows [4]
+> M <- Matrix(m.)
+> (mC <- as(M, "dgCMatrix"))
+4 x 6 sparse Matrix of class "dgCMatrix"
+
+[1,] . -1 . 1 2 .
+[2,] 2 . -1 . 1 2
+[3,] 1 2 . -1 . 1
+[4,] . 1 2 . -1 .
+> (mT <- as(M, "dgTMatrix"))
+4 x 6 sparse Matrix of class "dgTMatrix"
+
+[1,] . -1 . 1 2 .
+[2,] 2 . -1 . 1 2
+[3,] 1 2 . -1 . 1
+[4,] . 1 2 . -1 .
+> stopifnot(identical(mT, as(mC, "dgTMatrix")),
++ identical(mC, as(mT, "dgCMatrix")))
+>
+> for(v in list(0, 2, 1:0))
++ for(fnam in c("cBind", "rBind")) {
++ cat(fnam,"(m, v=", deparse(v),"), class(m) :")
++ FUN <- get(fnam)
++ for(m in list(M, mC, mT)) {
++ cat("", class(m),"")
++ assert.EQ.mat(FUN(v, m), FUN(v, m.)) ; cat(",")
++ assert.EQ.mat(FUN(m, v), FUN(m., v)) ; cat(".")
++ }
++ cat("\n")
++ }
+cBind (m, v= 0 ), class(m) : dgeMatrix ,. dgCMatrix ,. dgTMatrix ,.
+rBind (m, v= 0 ), class(m) : dgeMatrix ,. dgCMatrix ,. dgTMatrix ,.
+cBind (m, v= 2 ), class(m) : dgeMatrix ,. dgCMatrix ,. dgTMatrix ,.
+rBind (m, v= 2 ), class(m) : dgeMatrix ,. dgCMatrix ,. dgTMatrix ,.
+cBind (m, v= c(1L, 0L) ), class(m) : dgeMatrix ,. dgCMatrix ,. dgTMatrix ,.
+rBind (m, v= c(1L, 0L) ), class(m) : dgeMatrix ,. dgCMatrix ,. dgTMatrix ,.
+> showProc.time()
+Time elapsed: 0.248 0 0.249
+>
+> cBind(0, mC); cBind(mC, 0)
+4 x 7 sparse Matrix of class "dgCMatrix"
+
+[1,] . . -1 . 1 2 .
+[2,] . 2 . -1 . 1 2
+[3,] . 1 2 . -1 . 1
+[4,] . . 1 2 . -1 .
+4 x 7 sparse Matrix of class "dgCMatrix"
+
+[1,] . -1 . 1 2 . .
+[2,] 2 . -1 . 1 2 .
+[3,] 1 2 . -1 . 1 .
+[4,] . 1 2 . -1 . .
+> cBind(0, mT); cBind(mT, 2)
+4 x 7 sparse Matrix of class "dgCMatrix"
+
+[1,] . . -1 . 1 2 .
+[2,] . 2 . -1 . 1 2
+[3,] . 1 2 . -1 . 1
+[4,] . . 1 2 . -1 .
+4 x 7 sparse Matrix of class "dgCMatrix"
+
+[1,] . -1 . 1 2 . 2
+[2,] 2 . -1 . 1 2 2
+[3,] 1 2 . -1 . 1 2
+[4,] . 1 2 . -1 . 2
+> cBind(diag(nr), mT)
+4 x 10 sparse Matrix of class "dgCMatrix"
+
+[1,] 1 . . . . -1 . 1 2 .
+[2,] . 1 . . 2 . -1 . 1 2
+[3,] . . 1 . 1 2 . -1 . 1
+[4,] . . . 1 . 1 2 . -1 .
+> stopifnot(identical(t(cBind(diag(nr), mT)),
++ rBind(diag(nr), t(mT))))
+> (cc <- cBind(mC, 0,7,0, diag(nr), 0))
+4 x 14 sparse Matrix of class "dgCMatrix"
+
+[1,] . -1 . 1 2 . . 7 . 1 . . . .
+[2,] 2 . -1 . 1 2 . 7 . . 1 . . .
+[3,] 1 2 . -1 . 1 . 7 . . . 1 . .
+[4,] . 1 2 . -1 . . 7 . . . . 1 .
+> stopifnot(identical3(cc, cBind(mT, 0,7,0, diag(nr), 0),
++ as( cBind( M, 0,7,0, diag(nr), 0), "dgCMatrix")))
+>
+> cBind(mC, 1, 100*mC, 0, 0:2)
+4 x 15 sparse Matrix of class "dgCMatrix"
+
+[1,] . -1 . 1 2 . 1 . -100 . 100 200 . . .
+[2,] 2 . -1 . 1 2 1 200 . -100 . 100 200 . 1
+[3,] 1 2 . -1 . 1 1 100 200 . -100 . 100 . 2
+[4,] . 1 2 . -1 . 1 . 100 200 . -100 . . .
+> cBind(mT, 1, 0, mT+10*mT, 0, 0:2)
+4 x 16 sparse Matrix of class "dgCMatrix"
+
+[1,] . -1 . 1 2 . 1 . . -11 . 11 22 . . .
+[2,] 2 . -1 . 1 2 1 . 22 . -11 . 11 22 . 1
+[3,] 1 2 . -1 . 1 1 . 11 22 . -11 . 11 . 2
+[4,] . 1 2 . -1 . 1 . . 11 22 . -11 . . .
+>
+> ## logical (sparse) - should remain logical :
+> L5 <- Diagonal(n = 5, x = TRUE); v5 <- rep(x = c(FALSE,TRUE), length = ncol(L5))
+> stopifnot(is(show(rBind(L5,v5)), "lsparseMatrix"),
++ is(show(cBind(v5,L5)), "lsparseMatrix"),
++ is(rBind(L5, 2* v5), "dsparseMatrix"),
++ is(cBind(2* v5, L5), "dsparseMatrix"))
+6 x 5 sparse Matrix of class "lgCMatrix"
+
+ | . . . .
+ . | . . .
+ . . | . .
+ . . . | .
+ . . . . |
+v5 . | . | .
+5 x 6 sparse Matrix of class "lgCMatrix"
+ v5
+[1,] . | . . . .
+[2,] | . | . . .
+[3,] . . . | . .
+[4,] | . . . | .
+[5,] . . . . . |
+>
+> ## print() / show() of non-structural zeros:
+> (m <- Matrix(c(0, 0, 2:0), 3, 5))
+3 x 5 sparse Matrix of class "dgCMatrix"
+
+[1,] . 1 . . 2
+[2,] . . 2 . 1
+[3,] 2 . 1 . .
+> (m2 <- cBind(m,m))
+3 x 10 sparse Matrix of class "dgCMatrix"
+
+[1,] . 1 . . 2 . 1 . . 2
+[2,] . . 2 . 1 . . 2 . 1
+[3,] 2 . 1 . . 2 . 1 . .
+> (m4 <- rBind(m2,m2))
+6 x 10 sparse Matrix of class "dgCMatrix"
+
+[1,] . 1 . . 2 . 1 . . 2
+[2,] . . 2 . 1 . . 2 . 1
+[3,] 2 . 1 . . 2 . 1 . .
+[4,] . 1 . . 2 . 1 . . 2
+[5,] . . 2 . 1 . . 2 . 1
+[6,] 2 . 1 . . 2 . 1 . .
+> diag(m4)
+[1] 0 0 1 0 1 2
+> for(i in 1:6) {
++ m4[i, i ] <- i
++ m4[i,i+1] <- 0
++ }
+> m4 ## now show some non-structural zeros:
+6 x 10 sparse Matrix of class "dgCMatrix"
+
+[1,] 1 . . . 2 . 1 . . 2
+[2,] . 2 . . 1 . . 2 . 1
+[3,] 2 . 3 . . 2 . 1 . .
+[4,] . 1 . 4 . . 1 . . 2
+[5,] . . 2 . 5 . . 2 . 1
+[6,] 2 . 1 . . 6 . 1 . .
+>
+> ## Mixture of dense and sparse/diagonal -- used to fail, even in 1.0-0
+> D5 <- Diagonal(x = 10*(1:5))
+> (D5.1 <- cbind2(D5, 1))
+5 x 6 sparse Matrix of class "dgCMatrix"
+
+[1,] 10 . . . . 1
+[2,] . 20 . . . 1
+[3,] . . 30 . . 1
+[4,] . . . 40 . 1
+[5,] . . . . 50 1
+> ## "FIXME" in newer versions of R, do not need Matrix() here:
+> s42 <- Matrix(z42 <- cbind2(rep(0:1,4), rep(1:0,4)),
++ sparse=TRUE)
+> (C86 <- rBind(1, 0, D5.1, 0))
+8 x 6 sparse Matrix of class "dgCMatrix"
+
+[1,] 1 1 1 1 1 1
+[2,] . . . . . .
+[3,] 10 . . . . 1
+[4,] . 20 . . . 1
+[5,] . . 30 . . 1
+[6,] . . . 40 . 1
+[7,] . . . . 50 1
+[8,] . . . . . .
+> stopifnot(TRUE
++ ,isValid(D5.1, "dgCMatrix")
++ ,isValid(print(rbind2(Matrix(1:10, 2,5), D5)), "dgCMatrix")
++ ,isValid(print(cbind2(Matrix(10:1, 5,2), D5.1)), "dgeMatrix")
++ ,isValid(zz <- cbind2(z42, C86), "dgCMatrix")
++ ,identical(zz, cbind2(s42, C86))
++ )
+7 x 5 sparse Matrix of class "dgCMatrix"
+
+[1,] 1 3 5 7 9
+[2,] 2 4 6 8 10
+[3,] 10 . . . .
+[4,] . 20 . . .
+[5,] . . 30 . .
+[6,] . . . 40 .
+[7,] . . . . 50
+5 x 8 Matrix of class "dgeMatrix"
+ [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
+[1,] 10 5 10 0 0 0 0 1
+[2,] 9 4 0 20 0 0 0 1
+[3,] 8 3 0 0 30 0 0 1
+[4,] 7 2 0 0 0 40 0 1
+[5,] 6 1 0 0 0 0 50 1
+>
+> showProc.time()
+Time elapsed: 0.208 0.004 0.213
+>
+> proc.time()
+ user system elapsed
+ 2.716 0.060 2.779
diff --git a/win32/deps/library/Matrix/tests/dg_Matrix.R b/win32/deps/library/Matrix/tests/dg_Matrix.R
new file mode 100644
index 0000000..32c678c
--- /dev/null
+++ b/win32/deps/library/Matrix/tests/dg_Matrix.R
@@ -0,0 +1,95 @@
+library(Matrix)
+
+source(system.file("test-tools.R", package = "Matrix"))
+
+data(KNex) ; mm <- KNex$mm
+stopifnot(##is(mm) == c("dgCMatrix", "dMatrix", "Matrix"),
+ dim(mm) == (dm <- c(1850, 712)),
+ identical(dimnames(mm), list(NULL,NULL)))
+str(mm)
+tmm <- t(mm)
+str(tmm)
+
+str(mTm <- crossprod(mm))
+mmT <- crossprod(tmm)
+mmT. <- tcrossprod(mm)
+stopifnot(all.equal(mmT, mmT.))
+## Previously these were not the same
+## Should be the same but not quite: even length( * @ x ) differs!
+##str(mmT, max=2)# much larger than mTm (i.e less sparse)
+##str(mmT., max=2)# x slot is currently slightly larger --> improve tcrossprod()?
+##system.time(ae <- all.equal(as(mmT.,"matrix"), as(mmT,"matrix"), tol = 1e-14))
+## 4-5 seconds on a 850 MHz, P III
+##stopifnot(ae)
+
+stopifnot(validObject(tmm), dim(tmm) == dm[2:1],
+ validObject(mTm), dim(mTm) == dm[c(2,2)],
+ validObject(mmT), dim(mmT) == dm[c(1,1)],
+ identical(as(tmm, "matrix"), t(as(mm, "matrix"))))
+
+## from a bug report by Guissepe Ragusa <gragusa ucsd edu>
+set.seed(101)
+for(i in 1:10) {
+ A <- matrix(rnorm(400), nrow = 100, ncol = 4)
+ A[A < +1] <- 0 ; Am <- A
+ Acsc <- as(Am, "dgCMatrix")
+ A <- as(Am, "dgeMatrix")
+ b <- matrix(rnorm(400), nrow = 4, ncol = 100)
+ B <- as(b, "dgeMatrix")
+ assert.EQ.mat(A %*% B, Am %*% b, tol=0)
+ assert.EQ.mat(B %*% A, b %*% Am, tol=0)
+ stopifnot(identical(A, as(Acsc, "dgeMatrix")),
+ identical(Acsc, as(A, "dgCMatrix")),
+ is.all.equal4(A %*% B, Acsc %*% B,
+ A %*% b, Acsc %*% b),
+ is.all.equal4(b %*% A, b %*% Acsc,
+ B %*% A, B %*% Acsc))
+}
+
+###--- dgTMatrix {was ./dgTMatrix.R } -------
+
+### Use ``non-unique'' versions of dgTMatrix objects
+
+N <- 200
+set.seed(1)
+i <- as.integer(round(runif (N, 0, 100)))
+j <- as.integer(3* rpois (N, lam=15))
+x <- round(rnorm(N), 2)
+which(duplicated(cbind(i,j))) # 8 index pairs are duplicated
+
+m1 <- new("dgTMatrix", Dim = c(max(i)+1:1, max(j)+1:1), i = i, j = j, x = x)
+mc <- as(m1, "dgCMatrix")
+m2 <- as(mc, "dgTMatrix")## the same as 'm1' but without duplicates
+
+stopifnot(!isTRUE(all.equal.default(m1, m2)),
+ all.equal(as(m1,"matrix"), as(m2,"matrix"), tol=1e-15),
+ all.equal(crossprod(m1), crossprod(m2), tol=1e-15),
+ identical(mc, as(m2, "dgCMatrix")))
+
+### -> uniq* functions now in ../R/Auxiliaries.R
+(t2 <- system.time(um2 <- Matrix:::uniq(m1)))
+stopifnot(identical(m2,um2))
+
+### -> error/warning condition for solve() of a singular matrix (Barry Rowlingson)
+(M <- Matrix(0+ 1:16, nc = 4))
+assertError(solve(M))## -> an error + a warning about singularity -- and caches the LU decomp
+assertError(solve(t(M)))
+options(warn=2) # no more warnings allowed from here
+lum <- lu(M, warnSing=FALSE)
+stopifnot(is(fLU <- M factors $ LU, "MatrixFactorization"),
+ identical(lum, fLU))
+(e.lu <- expand(fLU))
+M2 <- with(e.lu, P %*% L %*% U)
+assert.EQ.mat(M2, as(M, "matrix"))
+## now the sparse LU :
+M. <- as(M,"sparseMatrix")
+tt <- try(solve(M.)) # less nice: factor is *not* cached
+## use a non-singular one:
+M1 <- M. + 0.5*Diagonal(nrow(M.))
+luM1 <- lu(M1)
+d1 <- determinant(as(M1,"denseMatrix"))
+stopifnot(identical(luM1, M1 factors$LU),
+ diag(luM1 L) == 1,# L is *unit*-triangular
+ all.equal(log(-prod(diag(luM1 U))), c(d1$modulus)))
+
+cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''
diff --git a/win32/deps/library/Matrix/tests/dpo-test.R b/win32/deps/library/Matrix/tests/dpo-test.R
new file mode 100644
index 0000000..eee9735
--- /dev/null
+++ b/win32/deps/library/Matrix/tests/dpo-test.R
@@ -0,0 +1,171 @@
+### Testing positive definite matrices
+library(Matrix)
+source(system.file("test-tools.R", package = "Matrix"))# identical3() etc
+
+h9 <- Hilbert(9)
+stopifnot(c(0,0) == dim(Hilbert(0)),
+ c(9,9) == dim(h9))
+str(h9)
+all.equal(c(determinant(h9)$modulus), -96.7369456, tol= 2e-8)
+stopifnot(0 == length(h9 factors))# nothing yet
+round(ch9 <- chol(h9), 3) ## round() preserves 'triangular' !
+str(f9 <- as(ch9, "dtrMatrix"))
+## h9 now has factorization
+stopifnot(names(h9 factors) == "Cholesky",
+ all.equal(rcond(h9), 9.0938e-13),
+ all.equal(rcond(f9), 9.1272e-7, tol = 1e-6))# more precision fails
+str(h9)# has 'factors $ Cholesky'
+options(digits=4)
+(cf9 <- crossprod(f9))# looks the same as h9 :
+assert.EQ.mat(h9, as.matrix(cf9), tol=1e-15)
+
+h9. <- round(h9, 2)# actually loses pos.def. "slightly"
+ # ==> the above may be invalid in the future
+h9p <- as(h9, "dppMatrix")
+h9.p <- as(h9., "dppMatrix")
+ch9p <- chol(h9p)
+stopifnot(identical(ch9p, h9p factors$pCholesky))
+h4 <- h9.[1:4, 1:4] # this and the next
+h9.[1,1] <- 10 # had failed in 0.995-14
+h9p[1,1] <- 10
+stopifnot(isValid(h9., "symmetricMatrix"),
+ isValid(h9p, "symmetricMatrix"),
+ isValid(h4, "symmetricMatrix"))
+
+h9p[1,2] <- 99
+stopifnot(class(h9p) == "dgeMatrix", h9p[1,1:2] == c(10,99))
+
+str(h9p <- as(h9, "dppMatrix"))# {again}
+h6 <- h9[1:6,1:6]
+stopifnot(all(h6 == Hilbert(6)), length(h6 factors) == 0,
+ is(th9p <- t(h9p), "dppMatrix"),
+ is(h9p factors$Cholesky,"Cholesky"))
+H6 <- as(h6, "dspMatrix")
+pp6 <- as(H6, "dppMatrix")
+po6 <- as(pp6,"dpoMatrix")
+hs <- as(h9p, "dspMatrix")
+stopifnot(names(H6 factors) == "pCholesky",
+ names(pp6 factors) == "pCholesky",
+ names(hs factors) == "Cholesky") # for now
+chol(hs) # and that is cached in 'hs' too :
+stopifnot(names(hs factors) %in% c("Cholesky","pCholesky"),
+ all.equal(h9, crossprod(hs factors$pCholesky), tol=1e-13),
+ all.equal(h9, crossprod(hs factors$ Cholesky), tol=1e-13))
+
+hs x <- 1/h9p x # is not pos.def. anymore
+validObject(hs) # "but" this does not check
+stopifnot(diag(hs) == seq(1, by = 2, length = 9))
+
+s9 <- solve(h9p, seq(nrow(h9p)))
+signif(t(s9)/10000, 4)# only rounded numbers are platform-independent
+(I9 <- h9p %*% s9)
+m9 <- matrix(1:9, dimnames = list(NULL,NULL))
+stopifnot(all.equal(m9, as.matrix(I9), tol = 2e-9))
+
+### Testing nearPD() --- this is partly in ../man/nearPD.Rd :
+pr <- Matrix(c(1, 0.477, 0.644, 0.478, 0.651, 0.826,
+ 0.477, 1, 0.516, 0.233, 0.682, 0.75,
+ 0.644, 0.516, 1, 0.599, 0.581, 0.742,
+ 0.478, 0.233, 0.599, 1, 0.741, 0.8,
+ 0.651, 0.682, 0.581, 0.741, 1, 0.798,
+ 0.826, 0.75, 0.742, 0.8, 0.798, 1),
+ nrow = 6, ncol = 6)
+
+nL <-
+ list(r = nearPD(pr, conv.tol = 1e-7), # default
+ r.1 = nearPD(pr, conv.tol = 1e-7, corr = TRUE),
+ rs = nearPD(pr, conv.tol = 1e-7, doDyk=FALSE),
+ rs1 = nearPD(pr, conv.tol = 1e-7, doDyk=FALSE, corr = TRUE),
+ rH = nearPD(pr, conv.tol = 1e-15),
+ rH.1= nearPD(pr, conv.tol = 1e-15, corr = TRUE))
+
+sapply(nL, `[`, c("iterations", "normF"))
+
+allnorms <- function(d) sapply(c("1","I","F","M"), function(typ) norm(d, typ))
+
+## "F" and "M" distances are larger for the (corr=TRUE) constrained:
+100 * sapply(nL, function(rr) allnorms((pr - rr $ mat)))
+
+## But indeed, the 'corr = TRUE' constraint yield a better solution,
+## if you need the constraint : cov2cor() does not just fix it up :
+100 * (nn <- sapply(nL, function(rr) allnorms((pr - cov2cor(rr $ mat)))))
+
+stopifnot(
+all.equal(nn["1",],
+ c(r =0.0999444286984696, r.1= 0.0880468666522317,
+ rs=0.0999444286984702, rs1= 0.0874614179943388,
+ rH=0.0999444286984696, rH.1=0.0880468927726625),
+ tol=1e-9))
+
+nr <- nL $rH.1 $mat
+stopifnot(
+ all.equal(nr[lower.tri(nr)],
+ c(0.4877861230299, 0.6429309061748, 0.4904554299278, 0.6447150779852,
+ 0.8082100656035, 0.514511537243, 0.2503412693503, 0.673249718642,
+ 0.7252316891977, 0.5972811755863, 0.5818673040157, 0.7444549621769,
+ 0.7308954865819, 0.7713984381710, 0.8124321235679),
+ tol = 1e-9))
+showProc.time()
+
+
+set.seed(27)
+m9 <- h9 + rnorm(9^2)/1000 ; m9 <- (m9 + t(m9))/2
+nm9 <- nearPD(m9)
+
+nRep <- if(doExtras) 50 else 4
+CPU <- 0
+for(M in c(5, 12))
+ for(i in 1:nRep) {
+ m <- matrix(round(rnorm(M^2),2), M, M)
+ m <- m + t(m)
+ diag(m) <- pmax(0, diag(m)) + 1
+ m <- cov2cor(m)
+ CPU <- CPU + system.time(n.m <- nearPD(m))[1]
+ X <- as(n.m$mat, "matrix")
+ stopifnot(all.equal(X, (X + t(X))/2, tol = 8*.Machine$double.eps),
+ all.equal(eigen(n.m$mat, only.values=TRUE)$values,
+ n.m$eigenvalues, tol = 4e-8))
+ }
+cat('Time elapsed for ',nRep, 'nearPD(): ', CPU,'\n')
+showProc.time()
+
+## cov2cor()
+m <- diag(6:1) %*% as(pr,"matrix") %*% diag(6:1) # so we can "vector-index"
+m[upper.tri(m)] <- 0
+ltm <- which(lower.tri(m))
+ne <- length(ltm)
+set.seed(17)
+m[ltm[sample(ne, 3/4*ne)]] <- 0
+m <- (m + t(m))/2 # now is a covariance matrix with many 0 entries
+(spr <- Matrix(m))
+cspr <- cov2cor(spr)
+ev <- eigen(cspr, only.v = TRUE)$values
+stopifnot(is(spr, "dsCMatrix"),
+ is(cspr,"dsCMatrix"),
+ all.equal(ev, c(1.5901626099, 1.1902658504, 1, 1,
+ 0.80973414959, 0.40983739006), tol=1e-10))
+
+x <- c(2,1,1,2)
+mM <- Matrix(x, 2,2, dimnames=rep( list(c("A","B")), 2))# dsy
+mM
+stopifnot(length(mM factors)== 0)
+(po <- as(mM, "dpoMatrix")) # still has dimnames
+mm <- as(mM, "matrix")
+msy <- as(mm, "dsyMatrix")
+stopifnot(Qidentical(mM, msy),
+ length(mM @factors)== 1,
+ length(msy factors)== 0)
+
+c1 <- as(mm, "corMatrix")
+c2 <- as(mM, "corMatrix")
+c3 <- as(po, "corMatrix")
+(co.x <- matrix(x/2, 2,2))
+checkMatrix(c1)
+assert.EQ.mat(c1, co.x)
+assert.EQ.mat(c2, co.x) # failed in Matrix 0.999375-9, because of
+## the wrong automatic "dsyMatrix" -> "corMatrix" coerce method
+stopifnot(identical(dimnames(c1), dimnames(mM)),
+ all.equal(c1, c3, tol=1e-15))
+
+showProc.time()
+
diff --git a/win32/deps/library/Matrix/tests/dtpMatrix.R b/win32/deps/library/Matrix/tests/dtpMatrix.R
new file mode 100644
index 0000000..fbe087b
--- /dev/null
+++ b/win32/deps/library/Matrix/tests/dtpMatrix.R
@@ -0,0 +1,63 @@
+### triangular packed
+library(Matrix)
+source(system.file("test-tools.R", package = "Matrix"))# identical3() etc
+
+cp6 <- chol(H6 <- Hilbert(6))
+tp6 <- as(cp6,"dtpMatrix")
+round(tp6, 3)## round() is "Math2" group method
+1/tp6 ## "Arith" group : gives 'dgeMatrix'
+str(tp6)
+## arithmetic with a mix of dimnames / no dimnames
+tp <- tp6; dimnames(tp) <- list(LETTERS[1:6], letters[11:16])
+## as.matrix() --> "logical" matrix
+stopifnot(as.matrix(tp - tp6 == tp6 - tp),
+ as.matrix(0 == tp - tp6),
+ identical(as(tp6,"CsparseMatrix"),
+ as(cp6,"CsparseMatrix")))
+
+stopifnot(validObject(tp6),
+ all.equal(tp6 %*% diag(6), as(tp6, "dgeMatrix")),
+ validObject(tp6. <- diag(6) %*% tp6),
+ class((tt6 <- t(tp6))) == "dtpMatrix",
+ identical(t(tt6), tp6),
+ tp6 uplo == "U" && tt6 uplo == "L")
+
+all.equal(as(tp6.,"matrix"),
+ as(tp6, "matrix"), tol= 1e-15)
+(tr6 <- as(tp6, "dtrMatrix"))
+dH6 <- determinant(H6)
+D. <- determinant(tp6)
+rc <- rcond(tp6)
+stopifnot(all.equal(dH6$modulus, determinant(as.matrix(H6))$modulus),
+ is.all.equal3(c(D.$modulus), c(dH6$modulus) / 2, -19.883103353),
+ all.equal(rc, 1.791511257e-4),
+ all.equal(norm(tp6, "I") , 2.45),
+ all.equal(norm(tp6, "1") , 1),
+ all.equal(norm(tp6, "F") , 1.37047826623)
+ )
+object.size(tp6)
+object.size(as(tp6, "dtrMatrix"))
+object.size(as(tp6, "matrix"))
+D6 <- as(diag(6), "dgeMatrix")
+ge6 <- as(tp6, "dgeMatrix")
+stopifnot(all.equal(D6 %*% tp6, ge6),
+ all.equal(tp6 %*% D6, ge6))
+
+## larger case
+set.seed(123)
+rl <- new("dtpMatrix", uplo="L", diag="N", Dim = rep.int(1000:1000,2),
+ x = rnorm(500*1001))
+validObject(rl)
+str(rl)
+sapply(c("I", "1", "F"), function(type) norm(rl, type=type))
+rcond(rl)# 0 !
+stopifnot(all.equal(as(rl %*% diag(1000),"matrix"),
+ as(rl, "matrix")))
+object.size(rl) ## 4 MB
+object.size(as(rl, "dtrMatrix"))# 8 MB
+object.size(as(rl, "matrix"))# ditto
+print(drl <- determinant(rl), digits = 12)
+stopifnot(all.equal(c(drl$modulus), -638.257312422))
+
+
+cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''
diff --git a/win32/deps/library/Matrix/tests/factorizing.R b/win32/deps/library/Matrix/tests/factorizing.R
new file mode 100644
index 0000000..c0d0b74
--- /dev/null
+++ b/win32/deps/library/Matrix/tests/factorizing.R
@@ -0,0 +1,399 @@
+#### Matrix Factorizations --- of all kinds
+
+library(Matrix)
+
+source(system.file("test-tools.R", package = "Matrix"))# identical3() etc
+
+
+### "sparseQR" : Check consistency of methods
+## --------
+data(KNex); mm <- KNex$mm; y <- KNex$y
+stopifnot(is((Y <- Matrix(y)), "dgeMatrix"))
+md <- as(mm, "matrix") # dense
+
+system.time(mmq <- qr(mm))
+system.time(mdq <- qr(md))# much (~ 150 x) slower
+
+## qr.qy and qr.qty should be inverses
+stopifnot(all.equal(qr.qy (mmq, qr.qty(mmq, y))@x, y),
+ all.equal(qr.qty(mmq, qr.qy (mmq, y))@x, y),
+ all.equal(qr.qty(mmq, y), qr.qty(mmq, Y)) )
+
+## consistency of results dense and sparse
+stopifnot(is.all.equal3(qr.coef (mdq, y), qr.coef (mmq,y)@x, qr.coef (mmq,Y)@x) ,
+ is.all.equal3(qr.resid (mdq, y), qr.resid (mmq,y)@x, qr.resid (mmq,Y)@x) ,
+ is.all.equal3(qr.fitted(mdq, y), qr.fitted(mmq,y)@x, qr.fitted(mmq,Y)@x) )
+
+
+### "denseLU"
+
+## Testing expansions of factorizations {was ./expand.R, then in simple.R }
+## new: [m x n] where m and n may differ
+x. <- c(2^(0:5),9:1,-3:8, round(sqrt(0:16)))
+set.seed(1)
+for(nnn in 1:100) {
+ y <- sample(x., replace=TRUE)
+ m <- sample(2:6, 1)
+ n <- sample(2:7, 1)
+ x <- suppressWarnings(matrix(y, m,n))
+ lux <- lu(x)# occasionally a warning about exact singularity
+ xx <- with(expand(lux), (P %*% L %*% U))
+ print(dim(xx))
+ assert.EQ.mat(xx, x, tol = 16*.Machine$double.eps)
+}
+
+### "sparseLU"
+por1 <- readMM(system.file("external/pores_1.mtx", package = "Matrix"))
+lu1 <- lu(por1)
+pm <- as(por1, "CsparseMatrix")
+(pmLU <- lu(pm)) # -> show(<MatrixFactorization>)
+xp <- expand(pmLU)
+## permute rows and columns of original matrix
+ppm <- pm[pmLU p + 1:1, pmLU q + 1:1]
+Ppm <- pmLU L %*% pmLU U
+## identical only as long as we don't keep the original class info:
+stopifnot(identical3(lu1, pmLU, pm factors$LU),# TODO === por1 factors$LU
+ identical(ppm, with(xp, P %*% pm %*% t(Q))),
+ sapply(xp, is, class="Matrix"))
+## make sure 'factors' are *NOT* kept, when they should not:
+spm <- solve(pm)
+stopifnot(abs(as.vector(solve(Diagonal(30, x=10) %*% pm) / spm) - 1/10) < 1e-7,
+ abs(as.vector(solve(rep.int(4, 30) * pm) / spm) - 1/ 4) < 1e-7)
+
+
+## these two should be the same, and `are' in some ways:
+assert.EQ.mat(ppm, as(Ppm, "matrix"), tol = 1e-14)
+## *however*
+length(ppm x)# 180
+length(Ppm x)# 317 !
+table(Ppm x == 0)# (194, 123) - has 123 "zero" and 14 ``almost zero" entries
+
+##-- determinant() and det() --- working via LU ---
+m <- matrix(c(0, NA, 0, NA, NA, 0, 0, 0, 1), 3,3)
+m0 <- rbind(0,cbind(0,m))
+M <- as(m,"Matrix"); M ## "dsCMatrix" ...
+M0 <- rBind(0, cBind(0, M))
+dM <- as(M, "denseMatrix")
+dM0 <- as(M0,"denseMatrix")
+try( lum <- lu(M) )# Err: "near-singular A"
+(lum <- lu(M, errSing=FALSE))# NA --- *BUT* it is not stored in @factors
+(lum0 <- lu(M0, errSing=FALSE))# NA --- and it is stored in M0 factors[["LU"]]
+## "FIXME" - TODO: Consider
+replNA <- function(x, value) { x[is.na(x)] <- value ; x }
+(EL.1 <- expand(lu.1 <- lu(M.1 <- replNA(M, -10))))
+## so it's quite clear how lu() of the *singular* matrix M should work
+## but it's not supported by the C code in ../src/cs.c which errors out
+stopifnot(all.equal(M.1, with(EL.1, P %*% L %*% U %*% Q)),
+ is.na(det(M)), is.na(det(dM)),
+ is.na(det(M0)), is.na(det(dM0)) )
+
+###________ Cholesky() ________
+
+##-------- LDL' ---- small exact examples
+
+set.seed(1)
+for(n in c(5:12)) {
+ cat("\nn = ",n,"\n-------\n")
+ rr <- mkLDL(n)
+ ## -------- from 'test-tools.R'
+ stopifnot(all(with(rr, A ==
+ as(L %*% D %*% t(L), "symmetricMatrix"))),
+ all(with(rr, A == tcrossprod(L %*% sqrt(D)))))
+ d <- rr$d.half
+ A <- rr$A
+ R <- chol(A)
+ assert.EQ.Mat(R, chol(as(A, "TsparseMatrix"))) # gave infinite recursion
+ print(d. <- diag(R))
+ D. <- Diagonal(x= d.^2)
+ L. <- t(R) %*% Diagonal(x = 1/d.)
+ stopifnot(all.equal(as.matrix(D.), as.matrix(rr$ D)),
+ all.equal(as.matrix(L.), as.matrix(rr$ L)))
+ ##
+ CAp <- Cholesky(A)# perm=TRUE --> Permutation:
+ p <- CAp perm + 1L
+ P <- as(p, "pMatrix")
+ ## the inverse permutation:
+ invP <- solve(P)@perm
+ lDet <- sum(2* log(d))# the "true" value
+ ldet <- Matrix:::.diag.dsC(Chx = CAp, res.kind = "sumLog")
+ ##
+ CA <- Cholesky(A,perm=FALSE)
+ ldet2 <- Matrix:::.diag.dsC(Chx = CA, res.kind = "sumLog")
+ ## not printing CAp : ends up non-integer for n >= 11
+ mCAp <- as(CAp,"sparseMatrix")
+ print(mCA <- drop0(as(CA, "sparseMatrix")))
+ stopifnot(identical(A[p,p], as(P %*% A %*% t(P),
+ "symmetricMatrix")),
+ all.equal(lDet, sum(log(Matrix:::.diag.dsC(Chx= CAp,res.kind="diag")))),
+ relErr(d.^2, Matrix:::.diag.dsC(Chx= CA, res.kind="diag")) < 1e-14,
+ all.equal(lDet, ldet),
+ all.equal(lDet, ldet2),
+ relErr(A[p,p], tcrossprod(mCAp)) < 1e-14)
+}## for()
+
+set.seed(17)
+(rr <- mkLDL(4))
+(CA <- Cholesky(rr$A))
+stopifnot(all.equal(determinant(rr$A) -> detA,
+ determinant(as(rr$A, "matrix"))),
+ is.all.equal3(c(detA$modulus), log(det(rr$D)), sum(log(rr$D x))))
+A12 <- mkLDL(12, 1/10)
+(r12 <- allCholesky(A12$A))[-1]
+aCh.hash <- r12$r.all %*% (2^(2:0))
+if(FALSE)## if(require("sfsmisc"))
+split(rownames(r12$r.all), Duplicated(aCh.hash))
+
+## TODO: find cases for both choices when we leave it to CHOLMOD to chose
+for(n in 1:50) { ## used to seg.fault at n = 10 !
+ mkA <- mkLDL(1+rpois(1, 30), 1/10)
+ cat(sprintf("n = %3d, LDL-dim = %d x %d ", n, nrow(mkA$A), ncol(mkA$A)))
+ r <- allCholesky(mkA$A, silentTry=TRUE)
+ ## Compare .. apart from the NAs that happen from (perm=FALSE, super=TRUE)
+ iNA <- apply(is.na(r$r.all), 1, any)
+ cat(sprintf(" -> %3s NAs\n", if(any(iNA)) format(sum(iNA)) else "no"))
+ stopifnot(aCh.hash[!iNA] == r$r.all[!iNA,] %*% (2^(2:0)))
+## cat("--------\n")
+}
+
+
+## This is a relatively small "critical example" :
+A. <-
+ new("dsCMatrix", Dim = c(25L, 25L), uplo = "U"
+ , i = as.integer(
+ c(0, 1, 2, 3, 4, 2, 5, 6, 0, 8, 8, 9, 3, 4, 10, 11, 6, 12, 13, 4,
+ 10, 14, 15, 1, 2, 5, 16, 17, 0, 7, 8, 18, 9, 19, 10, 11, 16, 20,
+ 0, 6, 7, 16, 17, 18, 20, 21, 6, 9, 12, 14, 19, 21, 22, 9, 11, 19,
+ 20, 22, 23, 1, 16, 24))
+ ##
+ , p = c(0:6, 8:10, 12L, 15:16, 18:19, 22:23, 27:28, 32L, 34L, 38L, 46L, 53L, 59L, 62L)
+ ##
+ , x = c(1, 1, 1, 1, 2, 100, 2, 40, 1, 2, 100, 6700, 100, 100, 13200,
+ 1, 50, 4100, 1, 5, 400, 20, 1, 40, 100, 5600, 9100, 5000, 5,
+ 100, 100, 5900, 100, 6200, 30, 20, 9, 2800, 1, 100, 8, 10, 8000,
+ 100, 600, 23900, 30, 100, 2800, 50, 5000, 3100, 15100, 100, 10,
+ 5600, 800, 4500, 5500, 7, 600, 18200))
+validObject(A.)
+## A1: the same pattern as A. just simply filled with '1's :
+A1 <- A.; A1 x[] <- 1; A1 factors <- list()
+A1.8 <- A1; diag(A1.8) <- 8
+##
+nT. <- as(AT <- as(A., "TsparseMatrix"),"nMatrix")
+stopifnot(all(nT i <= nT j),
+ identical(qr(A1.8), qr(as(A1.8, "dgCMatrix"))))
+CA <- Cholesky(A.)
+stopifnot(isValid(CAinv <- solve(CA), "dsCMatrix"))
+MA <- as(CA, "Matrix") # with a confusing warning -- FIXME!
+isValid(MAinv <- solve(MA), "dtCMatrix")
+## comparing MAinv with some solve(CA, system="...") .. *not* trivial? - TODO
+##
+CAinv2 <- solve(CA, Diagonal(nrow(A.)))
+CAinv2 <- as(CAinv2, "symmetricMatrix")
+stopifnot(identical(CAinv, CAinv2))
+
+## FINALLY fix this "TODO":
+try( tc <- Cholesky(nT.) )
+
+for(p in c(FALSE,TRUE))
+ for(L in c(FALSE,TRUE))
+ for(s in c(FALSE,TRUE, NA)) {
+ cat(sprintf("p,L,S = (%2d,%2d,%2d): ", p,L,s))
+ r <- tryCatch(Cholesky(A., perm=p, LDL=L, super=s),
+ error = function(e)e)
+ cat(if(inherits(r, "error")) " *** E ***" else
+ sprintf("%3d", r type),"\n", sep="")
+ }
+str(A., max=3) ## look at the 'factors'
+
+facs <- A factors
+names(facs) <- sub("Cholesky$", "", names(facs))
+facs <- facs[order(names(facs))]
+
+sapply(facs, class)
+str(lapply(facs, slot, "type"))
+## super = TRUE currently always entails LDL=FALSE :
+## hence isLDL is TRUE for ("D" and not "S"):
+sapply(facs, isLDL)
+
+chkCholesky <- function(chmf, A) {
+ stopifnot(is(chmf, "CHMfactor"),
+ is(A, "Matrix"), isSymmetric(A))
+ if(!is(A, "dsCMatrix"))
+ A <- as(A, "dsCMatrix")
+ L <- drop0(zapsmall(L. <- as(chmf, "Matrix")))
+ cat("no. nonzeros in L {before / after drop0(zapsmall(.))}: ",
+ c(nnzero(L.), nnzero(L)), "\n") ## 112, 95
+ ecc <- expand(chmf)
+ A... <- with(ecc, crossprod(crossprod(L,P)))
+ stopifnot(all.equal(L., ecc$L, tol = 1e-14),
+ all.equal(A, A..., tol = 1e-14, factorsCheck = FALSE))
+ invisible(ecc)
+}
+
+c1.8 <- try(Cholesky(A1.8, super = TRUE))# works "always", interestingly ...
+chkCholesky(c1.8, A1.8)
+
+
+
+## --- now a "large" (712 x 712) real data example ---------------------------
+
+data(KNex)
+mtm <- with(KNex, crossprod(mm))
+ld.3 <- .Call("dsCMatrix_LDL_D", mtm, perm=TRUE, "sumLog")
+stopifnot(names(mtm factors) == "sPDCholesky")
+ld.4 <- .Call("dsCMatrix_LDL_D", mtm, perm=FALSE, "sumLog")# clearly slower
+stopifnot(names(mtm factors) == paste(c("sPD", "spD"),"Cholesky", sep=''))
+c2 <- Cholesky(mtm, super = TRUE)
+stopifnot(names(mtm factors) == paste(c("sPD", "spD", "SPd"),
+ "Cholesky", sep=''))
+
+r <- allCholesky(mtm)
+r[-1]
+
+## is now taken from cache
+c1 <- Cholesky(mtm)
+
+bv <- 1:nrow(mtm) # even integer
+b <- matrix(bv)
+## solve(c2, b) by default solves Ax = b, where A = c2'c2 !
+x <- solve(c2,b)
+stopifnot(identical3(x, solve(c2, bv), solve(c2, b, system = "A")),
+ all.equal(x, solve(mtm, b)))
+for(sys in c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P", "Pt")) {
+ x <- solve(c2, b, system = sys)
+ cat(sys,":\n"); print(head(x))
+ stopifnot(dim(x) == c(712, 1),
+ identical(x, solve(c2, bv, system = sys)))
+}
+
+## log(|LL'|) - check if super = TRUE and simplicial give same determinant
+ld1 <- .Call("CHMfactor_ldetL2", c1)
+ld2 <- .Call("CHMfactor_ldetL2", c2)
+(ld1. <- determinant(mtm))
+## experimental
+ld3 <- .Call("dsCMatrix_LDL_D", mtm, TRUE, "sumLog")
+ld4 <- .Call("dsCMatrix_LDL_D", mtm, FALSE, "sumLog")
+stopifnot(all.equal(ld1, ld2),
+ is.all.equal3(ld2, ld3, ld4),
+ all.equal(ld.3, ld3, tol = 1e-14),
+ all.equal(ld.4, ld4, tol = 1e-14),
+ all.equal(ld1, as.vector(ld1.$modulus), tol = 1e-14))
+
+## Some timing measurements
+mtm <- with(KNex, crossprod(mm))
+I <- .symDiagonal(n=nrow(mtm))
+set.seed(101); r <- runif(100)
+
+system.time(D1 <- sapply(r, function(rho) Matrix:::ldet1.dsC(mtm + (1/rho) * I)))
+## 0.842 on fast cmath-5
+system.time(D2 <- sapply(r, function(rho) Matrix:::ldet2.dsC(mtm + (1/rho) * I)))
+## 0.819
+system.time(D3 <- sapply(r, function(rho) Matrix:::ldet3.dsC(mtm + (1/rho) * I)))
+## 0.810
+stopifnot(is.all.equal3(D1,D2,D3, tol = 1e-13))
+
+## Updating LL' should remain LL' and not become LDL' :
+cholCheck <- function(Ut, tol = 1e-12, super = FALSE, LDL = !super) {
+ L <- Cholesky(UtU <- tcrossprod(Ut), super=super, LDL=LDL, Imult = 1)
+ L1 <- update(L, UtU, mult = 1)
+ L2 <- update(L, Ut, mult = 1)
+ stopifnot(is.all.equal3(L, L1, L2, tol = tol),
+ all.equal(update(L, UtU, mult = pi),
+ update(L, Ut, mult = pi), tol = tol)
+ )
+}
+
+## Inspired by
+## data(Dyestuff, package = "lme4")
+## Zt <- as(Dyestuff$Batch, "sparseMatrix")
+Zt <- new("dgCMatrix", Dim = c(6L, 30L), x = 2*1:30,
+ i = rep(0:5, each=5),
+ p = 0:30, Dimnames = list(LETTERS[1:6], NULL))
+cholCheck(0.78 * Zt, tol=1e-14)
+
+for(i in 1:120) {
+ set.seed(i); cat(sprintf("%3d: ", i))
+ M <- rspMat(n=rpois(1,50), m=rpois(1,20), density = 1/(4*rpois(1, 4)))
+ for(super in c(FALSE,TRUE)) {
+ cat("super=",super," M: ")
+ cholCheck( M , super=super); cat(" M': ")
+ cholCheck(t(M), super=super)
+ }
+ cat(" [Ok]\n")
+}
+
+.updateCHMfactor
+## TODO: (--> ../TODO "Cholesky"):
+## ----
+## allow Cholesky(A,..) when A is not symmetric *AND*
+## we really want to factorize AA' ( + beta * I)
+
+
+## Schur() ----------------------
+checkSchur <- function(A, SchurA = Schur(A), tol = 1e-14) {
+ stopifnot(is(SchurA, "Schur"),
+ isOrthogonal(Q <- SchurA Q),
+ all.equal(as.mat(A),
+ as.mat(Q %*% SchurA T %*% t(Q)), tol = tol))
+}
+
+SH <- Schur(H5 <- Hilbert(5))
+checkSchur(H5, SH)
+checkSchur(Diagonal(x = 9:3))
+
+p <- 4L
+uTp <- new("dtpMatrix", x=c(2, 3, -1, 4:6, -2:1), Dim = c(p,p))
+(uT <- as(uTp, "dtrMatrix"))
+## Schur ( <general> ) <--> Schur( <triangular> )
+Su <- Schur(uT) ; checkSchur(uT, Su)
+gT <- as(uT,"generalMatrix")
+Sg <- Schur(gT) ; checkSchur(gT, Sg)
+Stg <- Schur(t(gT));checkSchur(t(gT), Stg)
+Stu <- Schur(t(uT));checkSchur(t(uT), Stu)
+
+stopifnot(identical3(Sg T, uT, Su T),
+ identical(Sg Q, as(diag(p), "dgeMatrix")),
+ identical(Stg T, as(t(gT[,p:1])[,p:1], "triangularMatrix")),
+ identical(Stg Q, as(diag(p)[,p:1], "dgeMatrix")),
+ identical(Stu T, Stg T))
+assert.EQ.mat(Stu Q, as(Stg Q,"matrix"), tol=0)
+
+## the pedigreemm example where solve(.) failed:
+p <- new("dtCMatrix", i = c(2L, 3L, 2L, 5L, 4L, 4:5), p = c(0L, 2L, 4:7, 7L),
+ Dim = c(6L, 6L), Dimnames = list(as.character(1:6), NULL),
+ x = rep.int(-0.5, 7), uplo = "L", diag = "U")
+Sp <- Schur(p)
+Sp. <- Schur(as(p,"generalMatrix"))
+Sp.p <- Schur(crossprod(p))
+## the last two failed
+ip <- solve(p)
+assert.EQ.mat(solve(ip), as(p,"matrix"))
+
+
+## chol2inv() for a traditional matrix
+assert.EQ.mat( crossprod(chol2inv(chol(Diagonal(x = 5:1)))),
+ C <- crossprod(chol2inv(chol( diag(x = 5:1)))))
+stopifnot(all.equal(C, diag((5:1)^-2)))
+## failed in some versions because of a "wrong" implicit generic
+
+## From [Bug 14834] New: chol2inv *** caught segfault ***
+n <- 1e6 # was 595362
+A <- chol( D <- Diagonal(n) )
+stopifnot(identical(A,D)) # A remains (unit)diagonal
+is(tA <- as(A,"triangularMatrix"))
+isValid(tA, "dsparseMatrix")# currently is dtTMatrix
+CA <- as(tA, "CsparseMatrix")
+
+selectMethod(solve, c("dtCMatrix","missing"))
+##--> .Call(dtCMatrix_sparse_solve, a, .trDiagonal(n)) in ../src/dtCMatrix.c
+sA <- solve(CA)## -- R_CheckStack() segfault in Matrix <= 1.0-4
+nca <- diagU2N(CA)
+stopifnot(identical(sA, nca))
+## same check with non-unit-diagonal D :
+A <- chol(D <- Diagonal(n, x = 0.5))
+ia <- chol2inv(A)
+stopifnot(is(ia, "diagonalMatrix"),
+ all.equal(ia x, rep(2,n), tol = 1e-15))
+
+
+cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''
+if(!interactive()) warnings()
diff --git a/win32/deps/library/Matrix/tests/group-methods.R b/win32/deps/library/Matrix/tests/group-methods.R
new file mode 100644
index 0000000..98ff115
--- /dev/null
+++ b/win32/deps/library/Matrix/tests/group-methods.R
@@ -0,0 +1,272 @@
+### Testing the group methods --- some also happens in ./Class+Meth.R
+
+library(Matrix)
+source(system.file("test-tools.R", package = "Matrix"))# identical3() etc
+cat("doExtras:",doExtras,"\n")
+
+set.seed(2001)
+
+mm <- Matrix(rnorm(50 * 7), nc = 7)
+xpx <- crossprod(mm)# -> "factors" in mm !
+round(xpx, 3) # works via "Math2"
+
+y <- rnorm(nrow(mm))
+xpy <- crossprod(mm, y)
+res <- solve(xpx, xpy)
+signif(res, 4) # 7 x 1 Matrix
+
+stopifnot(all(signif(res) == signif(res, 6)),
+ all(round (xpx) == round (xpx, 0)))
+
+## exp(): component wise
+signif(dd <- (expm(xpx) - exp(xpx)) / 1e34, 3)# 7 x 7
+
+stopifnot(validObject(xpx),
+ validObject(xpy),
+ validObject(dd))
+
+## "Math" also, for log() and [l]gamma() which need special treatment
+stopifnot(identical(exp(res)@x, exp(res x)),
+ identical(log(abs(res))@x, log(abs((res x)))),
+ identical(lgamma(res)@x, lgamma(res x)))
+
+
+###--- sparse matrices ---------
+
+m <- Matrix(c(0,0,2:0), 3,5)
+(mC <- as(m, "dgCMatrix"))
+sm <- sin(mC)
+stopifnot(class(sm) == class(mC), class(mC) == class(mC^2),
+ dim(sm) == dim(mC),
+ class(0 + 100*mC) == class(mC),
+ all.equal(0.1 * ((0 + 100*mC)/10), mC),
+ all.equal(sqrt(mC ^ 2), mC),
+ all.equal(m^m, mC^mC),
+ identical(mC^2, mC * mC),
+ identical(mC*2, mC + mC)
+ )
+
+x <- Matrix(rbind(0,cbind(0, 0:3,0,0,-1:2,0),0))
+x # sparse
+(x2 <- x + 10*t(x))
+stopifnot(is(x2, "sparseMatrix"),
+ identical(x2, t(x*10 + t(x))),
+ identical(x, as((x + 10) - 10, class(x))))
+
+(px <- Matrix(x^x - 1))#-> sparse again
+stopifnot(px i == c(3,4,1,4),
+ px x == c(3,26,-2,3))
+
+## From: "Florent D." .. Thu, 23 Feb 2012 -- bug report
+##---> MM: Make a regression test:
+tst <- function(n, i = 1) {
+ stopifnot(i >= 1, n >= i)
+ D <- .sparseDiagonal(n)
+ ee <- numeric(n) ; ee[i] <- 1
+ stopifnot(all(D - ee == diag(n) - ee),
+ all(D * ee == diag(n) * ee),
+ all(ee - D == ee - diag(n)),
+ {C <- (ee / D == ee / diag(n)); all(is.na(C) | C)},
+ TRUE)
+}
+tmp <- sapply(1:16, tst) # failed in Matrix 1.0-4
+i <- sapply(1:16, function(i) sample(i,1))
+tmp <- mapply(tst, n= 1:16, i= i)# failed too
+
+showProc.time()
+set.seed(111)
+local({
+ for(i in 1:20) {
+ M <- rspMat(n=1000, 200, density = 1/20)
+ v <- rnorm(ncol(M))
+ m <- as(M,"matrix")
+ stopifnot(all(t(M)/v == t(m)/v))
+ cat(".")
+ }});cat("\n")
+
+## Now just once, with a large such matrix:
+local({
+ n <- 100000; m <- 30000
+ AA <- rspMat(n, m, density = 1/20000)
+ v <- rnorm(m)
+ st <- system.time({
+ BB <- t(AA)/v # should happen *fast*
+ stopifnot(dim(BB) == c(m,n), is(BB, "sparseMatrix"))
+ })
+ str(BB)
+ print(st)
+ if(Sys.info()[["sysname"]] == "Linux") {
+ mips <- as.numeric(sub(".*: *", '',
+ grep("bogomips", readLines("/proc/cpuinfo"),
+ value=TRUE)[[1]]))
+ stopifnot(st[1] < 1000/mips)# ensure there was no gross inefficiency
+ }
+})
+
+
+###----- Compare methods ---> logical Matrices ------------
+l3 <- upper.tri(matrix(, 3, 3))
+(ll3 <- Matrix(l3))
+dt3 <- (99* Diagonal(3) + (10 * ll3 + Diagonal(3)))/10
+(dsc <- crossprod(ll3))
+stopifnot(validObject(ll3), validObject(dsc),
+ identical(ll3, t(t(ll3))),
+ identical(dsc, t(t(dsc))),
+ isValid(dsc + 3 * Diagonal(nrow(dsc)), "dsCMatrix"),
+ isValid(dt3, "triangularMatrix"), # remained triangular
+ isValid(dt3 > 0, "triangularMatrix")# ditto
+ )
+
+(lm1 <- dsc >= 1) # now ok
+(lm2 <- dsc == 1) # now ok
+nm1 <- as(lm1, "nMatrix")
+(nm2 <- as(lm2, "nMatrix"))
+
+stopifnot(validObject(lm1), validObject(lm2),
+ validObject(nm1), validObject(nm2),
+ identical(dsc, as(dsc * as(lm1, "dMatrix"), "dsCMatrix")))
+
+crossprod(lm1) # lm1: "lsC*"
+cnm1 <- crossprod(nm1)
+stopifnot(is(cnm1, "symmetricMatrix"), ## whereas the %*% is not:
+ Q.eq(cnm1, nm1 %*% nm1))
+dn1 <- as(nm1, "denseMatrix")
+stopifnot(all(dn1 == nm1))
+
+dsc[2,3] <- NA ## now has an NA (and no longer is symmetric)
+## ----- and "everything" is different
+## also add "non-structural 0":
+dsc x[1] <- 0
+dsc
+dsc/ 5
+dsc + dsc
+dsc - dsc
+dsc + 1 # -> no longer sparse
+Tsc <- as(dsc, "TsparseMatrix")
+dsc. <- drop0(dsc)
+stopifnot(identical(dsc., Matrix((dsc + 1) -1)),
+ identical(as(-Tsc,"CsparseMatrix"), (-1) * Tsc),
+ identical(-dsc., (-1) * dsc.),
+ identical3(-Diagonal(3), Diagonal(3, -1), (-1) * Diagonal(3)),
+ identical(dsc., Matrix((Tsc + 1) -1)), # ok (exact arithmetic)
+ Q.eq(0 != dsc, dsc != Matrix(0, 3, 3)),
+ Q.eq(0 != dsc, dsc != c(0,0)) # with a warning ("not multiple ..")
+ )
+str(lm1 <- dsc >= 1) # now ok (NA in proper place, however:
+lm1 ## NA used to print as ' ' , now 'N'
+(lm2 <- dsc == 1)# ditto
+
+ddsc <- kronecker(Diagonal(7), dsc)
+isValid(ddv <- rowSums(ddsc, sparse=TRUE), "sparseVector")
+sv <- colSums(kC <- kronecker(mC,kronecker(mC,mC)), sparse=TRUE)
+EQ <- ddv == rowSums(ddsc)
+na.ddv <- is.na(ddv)
+sM <- Matrix(pmax(0, round(rnorm(50*15, -1.5), 2)), 50,15)
+stopifnot(sv == colSums(kC), is.na(as.vector(ddv)) == na.ddv,
+ isValid(sM/(-7:7), "CsparseMatrix"),
+ all(EQ | na.ddv))
+
+## Just for print "show":
+z <- round(rnorm(77), 2)
+z[sample(77,10)] <- NA
+(D <- Matrix(z, 7)) # dense
+z[sample(77,15)] <- 0
+(D <- Matrix(z, 7)) # sparse
+abs(D) >= 0.5 # logical sparse
+
+stopifnot(identical(crossprod(lm1),# "lgC": here works!
+ crossprod(as(lm1, "dMatrix"))
+ ))
+
+## For the checks below, remove some and add a few more objects:
+rm(list= ls(pat="^.[mMC]?$"))
+D3 <- Diagonal(x=4:2); L7 <- Diagonal(7) > 0
+T3 <- Diagonal(3) > 0; stopifnot(T3 diag == "U") # "uni-diagonal"
+validObject(xpp <- pack(round(xpx,2)))
+validObject(dtp <- pack(as(dt3, "denseMatrix")))
+lsp <- xpp > 0
+isValid(lsC <- as(lsp, "sparseMatrix"), "lsCMatrix")
+
+showProc.time()
+
+### Systematically look at all "Ops" group generics for "all" Matrix classes
+### -------------- Main issue: Detect infinite recursion problems
+cl <- sapply(ls(), function(.) class(get(.)))
+Mcl <- c(grep("Matrix$", cl, value=TRUE),
+ grep("sparseVector", cl, value=TRUE))
+table(Mcl)
+## choose *one* of each class:
+## M.objs <- names(Mcl[!duplicated(Mcl)])
+## choose all
+M.objs <- names(Mcl)
+Mat.objs <- M.objs[vapply(M.objs, function(nm) is(get(nm), "Matrix"), NA)]
+MatDims <- t(vapply(Mat.objs, function(nm) dim(get(nm)), 0:1))
+noquote(cbind(Mcl[Mat.objs], format(MatDims)))
+mDims <- MatDims %*% (d.sig <- c(1, 1000)) # "dim-signature" to match against
+
+m2num <- function(m) { if(is.integer(m)) storage.mode(m) <- "double" ; m }
+M.knd <- Matrix:::.M.kind
+cat("Checking all group generics for a set of arguments:\n",
+ "---------------------------------------------------\n", sep='')
+options(warn = 2)#, error=recover)
+for(gr in getGroupMembers("Ops")) {
+ cat(gr,"\n",paste(rep.int("=",nchar(gr)),collapse=""),"\n", sep='')
+ for(f in getGroupMembers(gr)) {
+ cat(sprintf("%9s :\n%9s\n", paste0('"',f,'"'), "--"))
+ for(nm in M.objs) {
+ if(doExtras) cat(" '",nm,"' ", sep="")
+ M <- get(nm, inherits=FALSE)
+ n.m <- NROW(M)
+ cat("o")
+ for(x in list(TRUE, -3.2, 0L, seq_len(n.m))) {
+ cat(".")
+ validObject(r1 <- do.call(f, list(M,x)))
+ validObject(r2 <- do.call(f, list(x,M)))
+ stopifnot(dim(r1) == dim(M), dim(r2) == dim(M))
+ }
+ ## M o <sparseVector>
+ x <- numeric(n.m)
+ x[c(1,length(x))] <- 1:2
+ sv <- as(x, "sparseVector")
+ cat("s.")
+ validObject(r3 <- do.call(f, list(M, sv)))
+ stopifnot(dim(r3) == dim(M))
+ if(doExtras && is(M, "Matrix")) { ## M o <Matrix>
+ d <- dim(M)
+ ds <- sum(d * d.sig) # signature .. match with all other sigs
+ match. <- ds == mDims # (matches at least itself)
+ cat("\nM o M:")
+ for(oM in Mat.objs[match.]) {
+ M2 <- get(oM)
+ ## R4 := M f M2
+ validObject(R4 <- do.call(f, list(M, M2)))
+ cat(".")
+ for(M. in list(as.mat(M), M)) { ## two cases ..
+ r4 <- m2num(as.mat(do.call(f, list(M., as.mat(M2)))))
+ cat(",")
+ if(!identical(r4, as.mat(R4))) {
+ cat(sprintf("\n %s %s %s not identical: r4 \\ R4:\n",
+ nm, f, oM))
+ print(r4); print(R4)
+ C1 <- (eq <- R4 == r4) | ((nr4 <- is.na(r4)) & !is.finite(R4))
+ if(isTRUE(all(C1)) && (k1 <- M.knd(M)) != "d" && (k2 <- M.knd(M2)) != "d")
+ cat(" --> ",k1,"",f,"", k2,
+ " (ok): only difference is NA (matrix) and NaN/Inf (Matrix)\n")
+ else if(isTRUE(all(eq | (nr4 & Matrix:::is0(R4)))))
+ cat(" --> 'ok': only difference is 'NA' (matrix) and 0 (Matrix)\n")
+ else stop("differing \"too much\"")
+ }
+ }
+ cat("i")
+ }
+ }
+ }
+ cat("\n")
+ }
+}
+
+stopifnot(identical(lm2, lm1 & lm2),
+ identical(lm1, lm1 | lm2))
+
+
+cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''
diff --git a/win32/deps/library/Matrix/tests/indexing.R b/win32/deps/library/Matrix/tests/indexing.R
new file mode 100644
index 0000000..134e15a
--- /dev/null
+++ b/win32/deps/library/Matrix/tests/indexing.R
@@ -0,0 +1,839 @@
+#### For both 'Extract' ("[") and 'Replace' ("[<-") Method testing
+#### aka subsetting and subassignment
+
+#### suppressPackageStartupMessages(...) as we have an *.Rout.save to Rdiff against
+stopifnot(suppressPackageStartupMessages(require(Matrix)))
+
+source(system.file("test-tools.R", package = "Matrix"), keep.source = FALSE)
+##-> identical3() etc
+cat("doExtras:",doExtras,"\n")
+
+if(interactive()) {
+ options(error = recover, warn = 1)
+} else if(FALSE) { ## MM @ testing
+ options(error = recover, Matrix.verbose = TRUE, warn = 1)
+} else {
+ options(Matrix.verbose = TRUE, warn = 1)
+}
+
+
+### Dense Matrices
+
+m <- Matrix(1:28 +0, nrow = 7)
+validObject(m)
+stopifnot(identical(m, m[]),
+ identical(m[2, 3], 16), # simple number
+ identical(m[2, 3:4], c(16,23)), # simple numeric of length 2
+ identical(m[NA,NA], as(Matrix(NA, 7,4), "dMatrix")))
+
+m[2, 3:4, drop=FALSE] # sub matrix of class 'dgeMatrix'
+m[-(4:7), 3:4] # ditto; the upper right corner of 'm'
+
+## rows or columns only:
+m[1,] # first row, as simple numeric vector
+m[,2] # 2nd column
+m[,1:2] # sub matrix of first two columns
+m[-(1:6),, drop=FALSE] # not the first 6 rows, i.e. only the 7th
+m[integer(0),] #-> 0 x 4 Matrix
+m[2:4, numeric(0)] #-> 3 x 0 Matrix
+
+## logical indexing
+stopifnot(identical(m[2,3], m[(1:nrow(m)) == 2, (1:ncol(m)) == 3]),
+ identical(m[2,], m[(1:nrow(m)) == 2, ]),
+ identical(m[,3:4], m[, (1:4) >= 3]))
+
+## dimnames indexing:
+mn <- m
+dimnames(mn) <- list(paste("r",letters[1:nrow(mn)],sep=""),
+ LETTERS[1:ncol(mn)])
+checkMatrix(mn)
+mn["rd", "D"]
+msr <- ms <- as(mn,"sparseMatrix")
+mnr <- mn
+v <- rev(as(ms, "vector"))
+mnr[] <- v
+msr[] <- v # [<- "sparse" -- not very sensical; did fail w/o a message
+z <- msr; z[] <- 0
+zz <- as(array(0, dim(z)), "sparseMatrix")
+a.m <- as(mnr,"matrix")
+stopifnot(identical(mn["rc", "D"], mn[3,4]), mn[3,4] == 24,
+ identical(mn[, "A"], mn[,1]), mn[,1] == 1:7,
+ identical(mn[c("re", "rb"), "B"], mn[c(5,2), 2]),
+ identical(ms["rc", "D"], ms[3,4]), ms[3,4] == 24,
+ identical(ms[, "A"], ms[,1]), ms[,1] == 1:7,
+ identical(ms[ci <- c("re", "rb"), "B"], ms[c(5,2), 2]),
+ identical(rownames(mn[ci, ]), ci),
+ identical(rownames(ms[ci, ]), ci),
+ identical(colnames(mn[,cj <- c("B","D")]), cj),
+ identical(colnames(ms[,cj]), cj),
+ identical(a.m, as(msr,"matrix")),
+ identical(unname(z), zz),
+ identical(a.m, array(v, dim=dim(mn), dimnames=dimnames(mn)))
+ )
+showProc.time()
+
+## Printing sparse colnames:
+ms[sample(28, 20)] <- 0
+ms <- t(rbind2(ms, 3*ms))
+cnam1 <- capture.output(show(ms))[2] ; op <- options("sparse.colnames" = "abb3")
+cnam2 <- capture.output(show(ms))[2] ; options(op) # revert
+stopifnot(## sparse printing
+ grep("^ +$", cnam1) == 1, # cnam1 is empty
+ identical(cnam2,
+ paste(" ", paste(rep(rownames(mn), 2), collapse=" "))))
+
+mo <- m
+m[2,3] <- 100
+m[1:2, 4] <- 200
+m[, 1] <- -1
+m[1:3,]
+
+m. <- as.matrix(m)
+
+## m[ cbind(i,j) ] indexing:
+iN <- ij <- cbind(1:6, 2:3)
+iN[2:3,] <- iN[5,2] <- NA
+stopifnot(identical(m[ij], m.[ij]),
+ identical(m[iN], m.[iN]))
+
+## testing operations on logical Matrices rather more than indexing:
+g10 <- m [ m > 10 ]
+stopifnot(18 == length(g10))
+stopifnot(10 == length(m[ m <= 10 ]))
+sel <- (20 < m) & (m < 150)
+sel.<- (20 < m.)& (m.< 150)
+nsel <-(20 >= m) | (m >= 150)
+(ssel <- as(sel, "sparseMatrix"))
+stopifnot(is(sel, "lMatrix"), is(ssel, "lsparseMatrix"),
+ identical3(as.mat(sel.), as.mat(sel), as.mat(ssel)),
+ identical3(!sel, !ssel, nsel), # !<sparse> is typically dense
+ identical3(m[ sel], m[ ssel], as.matrix(m)[as.matrix( ssel)]),
+ identical3(m[!sel], m[!ssel], as.matrix(m)[as.matrix(!ssel)])
+ )
+showProc.time()
+
+## more sparse Matrices --------------------------------------
+
+##' @title Check sparseMatrix sub-assignment m[i,j] <- v
+##' @param ms sparse Matrix
+##' @param mm its [traditional matrix]-equivalent
+##' @param k (approximate) length of index vectors (i,j)
+##' @param n.uniq (approximate) number of unique values in i,j
+##' @param show logical; if TRUE, it will not stop on error
+##' @return
+##' @author Martin Maechler
+chkAssign <- function(ms, mm = as(ms, "matrix"),
+ k = min(20,dim(mm)), n.uniq = k %/% 3,
+ vRNG = { if(is.numeric(mm) || is.complex(mm))
+ function(n) rpois(n,lambda= 0.75)# <- about 47% zeros
+ else ## logical
+ function(n) runif(n) > 0.8 }, ## 80% zeros
+ show=FALSE)
+{
+ stopifnot(is(ms,"sparseMatrix"))
+ s1 <- function(n) sample(n, pmin(n, pmax(1, rpois(1, n.uniq))))
+ i <- sample(s1(nrow(ms)), k/2+ rpois(1, k/2), replace = TRUE)
+ j <- sample(s1(ncol(ms)), k/2+ rpois(1, k/2), replace = TRUE)
+ assert.EQ.mat(ms[i,j], mm[i,j])
+ ## now sub*assign* to these repeated indices, and then compare -----
+ v <- vRNG(length(i) * length(j))
+ mm[i,j] <- v
+ ms[i,j] <- v
+ if(!show) { op <- options(error = recover); on.exit(options(op)) }
+ assert.EQ.mat(ms, mm, show=show)
+}
+
+## Get duplicated index {because these are "hard" (and rare)
+getDuplIndex <- function(n, k) {
+ repeat {
+ i <- sample(n, k, replace=TRUE) # 3 4 6 9 2 9 : 9 is twice
+ if(anyDuplicated(i)) break
+ }
+ i
+}
+
+## From package 'sfsmisc':
+repChar <- function (char, no) paste(rep.int(char, no), collapse = "")
+
+m <- 1:800
+set.seed(101) ; m[sample(800, 600)] <- 0
+m0 <- Matrix(m, nrow = 40)
+m1 <- add.simpleDimnames(m0)
+for(kind in c("n", "l", "d")) {
+ for(m in list(m0,m1)) { ## -- with and without dimnames -------------------------
+ kClass <- paste(kind, "Matrix", sep="")
+ Ckind <- paste(kind, "gCMatrix", sep="")
+ Tkind <- paste(kind, "gTMatrix", sep="")
+ str(mC <- as(m, Ckind))
+ str(mT <- as(as(as(m, kClass), "TsparseMatrix"), Tkind))
+ mm <- as(mC, "matrix") # also logical or double
+ IDENT <- if(kind == "n") function(x,y) Q.eq2(x,y, tol=0) else identical
+ stopifnot(identical(mT, as(as(mC, "TsparseMatrix"), Tkind)),
+ identical(mC, as(mT, Ckind)),
+ Qidentical(mC[0,0], new(Ckind)),
+ Qidentical(mT[0,0], new(Tkind)),
+ identical(unname(mT[0,]), new(Tkind, Dim = c(0L,20L))),
+ identical(unname(mT[,0]), new(Tkind, Dim = c(40L,0L))),
+ IDENT(mC[0,], as(mT[FALSE,], Ckind)),
+ IDENT(mC[,0], as(mT[,FALSE], Ckind)),
+ sapply(c(0:2, 5:10),
+ function(k) {i <- seq_len(k); all(mC[i,i] == mT[i,i])}),
+ TRUE)
+ cat("ok\n")
+ show(mC[,1])
+ show(mC[1:2,])
+ show(mC[7, drop = FALSE])
+ assert.EQ.mat(mC[1:2,], mm[1:2,])
+ assert.EQ.mat(mC[0,], mm[0,])
+ assert.EQ.mat(mC[,FALSE], mm[,FALSE])
+ ##
+ ## *repeated* (aka 'duplicated') indices - did not work at all ...
+ i <- rep(8:10,2)
+ j <- c(2:4, 4:3)
+ assert.EQ.mat(mC[i,], mm[i,])
+ assert.EQ.mat(mC[,j], mm[,j])
+ ## FIXME? assert.EQ.mat(mC[,NA], mm[,NA]) -- mC[,NA] is all 0 "instead" of all NA
+ ## MM currently thinks we should NOT allow <sparse>[ <NA> ]
+ assert.EQ.mat(mC[i, 2:1], mm[i, 2:1])
+ assert.EQ.mat(mC[c(4,1,2:1), j], mm[c(4,1,2:1), j])
+ assert.EQ.mat(mC[i,j], mm[i,j])
+ ##
+ ## set.seed(7)
+ cat(" for(): ")
+ for(n in 1:(if(doExtras) 50 else 5)) {
+ chkAssign(mC, mm)
+ chkAssign(mC[-3,-2], mm[-3,-2])
+ cat(".")
+ }
+ cat(sprintf("\n[Ok]%s\n\n", repChar("-", 64)))
+ }
+ cat(sprintf("\nok( %s )\n== ###%s\n\n", kind, repChar("=", 70)))
+}## end{for}---------------------------------------------------------------
+showProc.time()
+
+##---- Symmetric indexing of symmetric Matrix ----------
+m. <- mC
+m.[, c(2, 7:12)] <- 0
+isValid(S <- crossprod(add.simpleDimnames(m.) %% 100), "dsCMatrix")
+ss <- as(S, "matrix")
+ds <- as(S, "denseMatrix")
+## NA-indexing of *dense* Matrices: should work as traditionally
+assert.EQ.mat(ds[NA,NA], ss[NA,NA])
+assert.EQ.mat(ds[NA, ], ss[NA,])
+assert.EQ.mat(ds[ ,NA], ss[,NA])
+T <- as(S, "TsparseMatrix")
+stopifnot(identical(ds[2 ,NA], ss[2,NA]),
+ identical(ds[NA, 1], ss[NA, 1]),
+ identical(S, as(T, "CsparseMatrix")) )
+
+## non-repeated indices:
+i <- c(7:5, 2:4);assert.EQ.mat(T[i,i], ss[i,i])
+## NA in indices -- check that we get a helpful error message:
+i[2] <- NA
+er <- tryCatch(T[i,i], error = function(e)e)
+stopifnot(as.logical(grep("indices.*sparse Matrices", er$message)))
+
+N <- nrow(T)
+set.seed(11)
+for(n in 1:(if(doExtras) 50 else 3)) {
+ i <- sample(N, max(2, sample(N,1)), replace = FALSE)
+ validObject(Tii <- T[i,i]) ; tTi <- t(T)[i,i]
+ stopifnot(is(Tii, "dsTMatrix"), # remained symmetric Tsparse
+ is(tTi, "dsTMatrix"), # may not be identical when *sorted* differently
+ identical(as(t(Tii),"CsparseMatrix"), as(tTi,"CsparseMatrix")))
+ assert.EQ.mat(Tii, ss[i,i])
+}
+
+b <- diag(1:2)[,c(1,1,2,2)]
+cb <- crossprod(b)
+cB <- crossprod(Matrix(b, sparse=TRUE))
+a <- matrix(0, 6, 6)
+a[1:4, 1:4] <- cb
+A1 <- A2 <- Matrix(0, 6, 6)#-> sparse
+A1[1:4, 1:4] <- cb
+A2[1:4, 1:4] <- cB
+assert.EQ.mat(A1, a)# indeed
+stopifnot(identical(A1, A2), is(A1, "dsCMatrix"))
+
+## repeated ones ``the challenge'' (to do smartly):
+j <- c(4, 4, 9, 12, 9, 4, 17, 3, 18, 4, 12, 18, 4, 9)
+assert.EQ.mat(T[j,j], ss[j,j])
+## and another two sets (a, A) & (a., A.) :
+a <- matrix(0, 6,6)
+a[upper.tri(a)] <- (utr <- c(2, 0,-1, 0,0,5, 7,0,0,0, 0,0,-2,0,8))
+ta <- t(a); ta[upper.tri(a)] <- utr; a <- t(ta)
+diag(a) <- c(0,3,0,4,6,0)
+A <- as(Matrix(a), "TsparseMatrix")
+A. <- A
+diag(A.) <- 10 * (1:6)
+a. <- as(A., "matrix")
+## More testing {this was not working for a long time..}
+set.seed(1)
+for(n in 1:(if(doExtras) 100 else 6)) {
+ i <- sample(1:nrow(A), 3+2*rpois(1, lam=3), replace=TRUE)
+ Aii <- A[i,i]
+ A.ii <- A.[i,i]
+ stopifnot(class(Aii) == class(A),
+ class(A.ii) == class(A.))
+ assert.EQ.mat(Aii , a [i,i])
+ assert.EQ.mat(A.ii, a.[i,i])
+ assert.EQ.mat(T[i,i], ss[i,i])
+}
+showProc.time()
+
+stopifnot(all.equal(mC[,3], mm[,3]),
+ identical(mC[ij], mC[ij + 0.4]),
+ identical(mC[ij], mm[ij]),
+ identical(mC[iN], mm[iN]))
+## out of bound indexing must be detected:
+assertError(mC[cbind(ij[,1] - 5, ij[,2])])
+assertError(mC[cbind(ij[,1], ij[,2] + ncol(mC))])
+
+assert.EQ.mat(mC[7, , drop=FALSE], mm[7, , drop=FALSE])
+identical (mC[7, drop=FALSE], mm[7, drop=FALSE]) # *vector* indexing
+
+stopifnot(dim(mC[numeric(0), ]) == c(0,20), # used to give warnings
+ dim(mC[, integer(0)]) == c(40,0),
+ identical(mC[, integer(0)], mC[, FALSE]))
+validObject(print(mT[,c(2,4)]))
+stopifnot(all.equal(mT[2,], mm[2,]),
+ ## row or column indexing in combination with t() :
+ Q.C.identical(mT[2,], t(mT)[,2]),
+ Q.C.identical(mT[-2,], t(t(mT)[,-2])),
+ Q.C.identical(mT[c(2,5),], t(t(mT)[,c(2,5)])) )
+assert.EQ.mat(mT[4,, drop = FALSE], mm[4,, drop = FALSE])
+stopifnot(identical3(mm[,1], mC[,1], mT[,1]),
+ identical3(mm[3,], mC[3,], mT[3,]),
+ identical3(mT[2,3], mC[2,3], 0),
+ identical(mT[], mT),
+ identical4( mm[c(3,7), 2:4], as.mat( m[c(3,7), 2:4]),
+ as.mat(mT[c(3,7), 2:4]), as.mat(mC[c(3,7), 2:4]))
+ )
+
+x.x <- crossprod(mC)
+stopifnot(class(x.x) == "dsCMatrix",
+ class(x.x. <- round(x.x / 10000)) == "dsCMatrix",
+ identical(x.x[cbind(2:6, 2:6)],
+ diag(x.x [2:6, 2:6])))
+head(x.x.) # Note the *non*-structural 0's printed as "0"
+tail(x.x., -3) # all but the first three lines
+
+lx.x <- as(x.x, "lsCMatrix") # FALSE only for "structural" 0
+(l10 <- lx.x[1:10, 1:10])# "lsC"
+(l3 <- lx.x[1:3, ])
+m.x <- as.mat(x.x) # as.mat() *drops* (NULL,NULL) dimnames
+stopifnot(class(l10) == "lsCMatrix", # symmetric indexing -> symmetric !
+ identical(as.mat(lx.x), m.x != 0),
+ identical(as.logical(lx.x), as.logical(m.x)),
+ identical(as.mat(l10), m.x[1:10, 1:10] != 0),
+ identical(as.mat(l3 ), m.x[1:3, ] != 0)
+ )
+
+##-- Sub*assignment* with repeated / duplicated index:
+A <- Matrix(0,4,3) ; A[c(1,2,1), 2] <- 1 ; A
+B <- A; B[c(1,2,1), 2] <- 1:3; B; B. <- B
+B.[3,] <- rbind(4:2)
+## change the diagonal and the upper and lower subdiagonal :
+diag(B.) <- 10 * diag(B.)
+diag(B.[,-1]) <- 5* diag(B.[,-1])
+diag(B.[-1,]) <- 4* diag(B.[-1,]) ; B.
+C <- B.; C[,2] <- C[,2]; C[1,] <- C[1,]; C[2:3,2:1] <- C[2:3,2:1]
+stopifnot(identical(unname(as.matrix(A)),
+ local({a <- matrix(0,4,3); a[c(1,2,1), 2] <- 1 ; a})),
+ identical(unname(as.matrix(B)),
+ local({a <- matrix(0,4,3); a[c(1,2,1), 2] <- 1:3; a})),
+ identical(C, drop0(B.)))
+## <sparse>[<logicalSparse>] <- v failed in the past
+T <- as(C,"TsparseMatrix"); C. <- C
+T[T>0] <- 21
+C[C>0] <- 21
+a. <- local({a <- as.matrix(C.); a[a>0] <- 21; a})
+assert.EQ.mat(C, a.)
+stopifnot(identical(C, as(T, "CsparseMatrix")))
+
+## used to fail
+n <- 5 ## or much larger
+sm <- new("dsTMatrix", i=1L, j=1L, Dim=as.integer(c(n,n)), x = 1)
+(cm <- as(sm, "CsparseMatrix"))
+sm[2,]
+stopifnot(sm[2,] == c(0:1, rep.int(0,ncol(sm)-2)),
+ sm[2,] == cm[2,],
+ sm[,3] == sm[3,],
+ all(sm[,-(1:3)] == t(sm[-(1:3),])), # all(<lge.>)
+ all(sm[,-(1:3)] == 0)
+ )
+showProc.time()
+
+##--- "nsparse*" sub-assignment :----------
+M <- Matrix(c(1, rep(0,7), 1:4), 3,4)
+N0 <- kronecker(M,M)
+Nn <- as(N0, "nMatrix"); nn <- as(Nn,"matrix")
+(Nn00 <- Nn0 <- Nn); nn00 <- nn0 <- nn
+
+set.seed(1)
+Nn0 <- Nn00; nn0 <- nn00
+for(i in 1:(if(doExtras) 200 else 25)) {
+ Nn <- Nn0
+ nn <- nn0
+ i. <- getDuplIndex(nrow(N0), 6)
+ j. <- getDuplIndex(ncol(N0), 4)
+ vv <- sample(c(FALSE,TRUE),
+ length(i.)*length(j.), replace=TRUE)
+ cat(",")
+ Nn[i., j.] <- vv
+ nn[i., j.] <- vv
+ assert.EQ.mat(Nn, nn)
+ if(!all(Nn == nn)) {
+ cat("i=",i,":\n i. <- "); dput(i.)
+ cat("j. <- "); dput(j.)
+ cat("which(vv): "); dput(which(vv))
+ cat("Difference matrix:\n")
+ show(drop0(Nn - nn))
+ }
+ cat("k")
+ ## sub-assign double precision to logical sparseMatrices should error:
+ ## well... warning for now {back compatibility: gave *no* warning, nothing .. !}:
+ assertWarning(Nn[1:2,] <- -pi)
+ assertWarning(Nn[, 5] <- -pi)
+ assertWarning(Nn[2:4, 5:8] <- -pi)
+ ##
+ cat(".")
+ if(i %% 10 == 0) cat("\n")
+ if(i == 100) {
+ Nn0 <- as(Nn0, "CsparseMatrix")
+ cat("Now: class", class(Nn0)," :\n~~~~~~~~~~~~~~~~~\n")
+ }
+}
+showProc.time()
+
+m0 <- Diagonal(5)
+stopifnot(identical(m0[2,], m0[,2]),
+ identical(m0[,1], c(1,0,0,0,0)))
+### Diagonal -- Sparse:
+(m1 <- as(m0, "TsparseMatrix")) # dtTMatrix
+(m2 <- as(m0, "CsparseMatrix")) # dtCMatrix
+m1g <- as(m1, "generalMatrix")
+stopifnot(is(m1g, "dgTMatrix"))
+assert.EQ.mat(m2[1:3,], diag(5)[1:3,])
+assert.EQ.mat(m2[,c(4,1)], diag(5)[,c(4,1)])
+stopifnot(identical(m2[1:3,], as(m1[1:3,], "CsparseMatrix")),
+ identical(Matrix:::uniqTsparse(m1[, c(4,2)]),
+ Matrix:::uniqTsparse(as(m2[, c(4,2)], "TsparseMatrix")))
+ )## failed in 0.9975-11
+
+(uTr <- new("dtTMatrix", Dim = c(3L,3L), diag="U"))
+uTr[1,] <- 0
+assert.EQ.mat(uTr, cbind(0, rbind(0,diag(2))))
+
+M <- m0; M[1,] <- 0
+stopifnot(identical(M, Diagonal(x=c(0, rep(1,4)))))
+M <- m0; M[,3] <- 3 ; M ; stopifnot(is(M, "sparseMatrix"), M[,3] == 3)
+checkMatrix(M)
+M <- m0; M[1:3, 3] <- 0 ;M
+T <- m0; T[1:3, 3] <- 10
+stopifnot(identical(M, Diagonal(x=c(1,1, 0, 1,1))),
+ isValid(T, "triangularMatrix"), identical(T[,3], c(10,10,10,0,0)))
+
+M <- m1; M[1,] <- 0 ; M ; assert.EQ.mat(M, diag(c(0,rep(1,4))), tol=0)
+M <- m1; M[,3] <- 3 ; stopifnot(is(M,"sparseMatrix"), M[,3] == 3)
+checkMatrix(M)
+M <- m1; M[1:3, 3] <- 0 ;M
+assert.EQ.mat(M, diag(c(1,1, 0, 1,1)), tol=0)
+T <- m1; T[1:3, 3] <- 10; checkMatrix(T)
+stopifnot(is(T, "triangularMatrix"), identical(T[,3], c(10,10,10,0,0)))
+
+M <- m2; M[1,] <- 0 ; M ; assert.EQ.mat(M, diag(c(0,rep(1,4))), tol=0)
+M <- m2; M[,3] <- 3 ; stopifnot(is(M,"sparseMatrix"), M[,3] == 3)
+checkMatrix(M)
+M <- m2; M[1:3, 3] <- 0 ;M
+assert.EQ.mat(M, diag(c(1,1, 0, 1,1)), tol=0)
+T <- m2; T[1:3, 3] <- 10; checkMatrix(T)
+stopifnot(is(T, "dtCMatrix"), identical(T[,3], c(10,10,10,0,0)))
+showProc.time()
+
+
+## "Vector indices" -------------------
+.iniDiag.example <- expression({
+ D <- Diagonal(6)
+ M <- as(D,"dgeMatrix")
+ m <- as(D,"matrix")
+ s <- as(D,"TsparseMatrix")
+ S <- as(s,"CsparseMatrix")
+})
+eval(.iniDiag.example)
+i <- c(3,1,6); v <- c(10,15,20)
+## (logical,value) which both are recycled:
+L <- c(TRUE, rep(FALSE,8)) ; z <- c(50,99)
+
+## vector subassignment, both with integer & logical
+## these now work correctly {though not very efficiently; hence warnings}
+m[i] <- v # the role model: only first column is affected
+M[i] <- v; assert.EQ.mat(M,m) # dge
+D[i] <- v; assert.EQ.mat(D,m) # ddi -> dtT -> dgT
+s[i] <- v; assert.EQ.mat(s,m) # dtT -> dgT
+S[i] <- v; assert.EQ.mat(S,m); S # dtC -> dtT -> dgT -> dgC
+stopifnot(Q.C.identical(D,s, checkClass=FALSE))
+## logical
+eval(.iniDiag.example)
+m[L] <- z
+M[L] <- z; assert.EQ.mat(M,m)
+D[L] <- z; assert.EQ.mat(D,m)
+s[L] <- z; assert.EQ.mat(s,m)
+S[L] <- z; assert.EQ.mat(S,m) ; S
+
+## indexing [i] vs [i,] --- now ok
+eval(.iniDiag.example)
+stopifnot(identical5(m[i], M[i], D[i], s[i], S[i]))
+stopifnot(identical5(m[L], M[L], D[L], s[L], S[L]))
+## bordercase ' drop = .' *vector* indexing {failed till 2009-04-..)
+stopifnot(identical5(m[i,drop=FALSE], M[i,drop=FALSE], D[i,drop=FALSE],
+ s[i,drop=FALSE], S[i,drop=FALSE]))
+stopifnot(identical5(m[L,drop=FALSE], M[L,drop=FALSE], D[L,drop=FALSE],
+ s[L,drop=FALSE], S[L,drop=FALSE]))
+## using L for row-indexing should give an error
+assertError(m[L,]); assertError(m[L,, drop=FALSE])
+## these did not signal an error, upto (including) 0.999375-30:
+assertError(s[L,]); assertError(s[L,, drop=FALSE])
+assertError(S[L,]); assertError(S[L,, drop=FALSE])
+
+## row indexing:
+assert.EQ.mat(D[i,], m[i,])
+assert.EQ.mat(M[i,], m[i,])
+assert.EQ.mat(s[i,], m[i,])
+assert.EQ.mat(S[i,], m[i,])
+## column indexing:
+assert.EQ.mat(D[,i], m[,i])
+assert.EQ.mat(M[,i], m[,i])
+assert.EQ.mat(s[,i], m[,i])
+assert.EQ.mat(S[,i], m[,i])
+
+
+## --- negative indices ----------
+mc <- mC[1:5, 1:7]
+mt <- mT[1:5, 1:7]
+## sub matrix
+assert.EQ.mat(mC[1:2, 0:3], mm[1:2, 0:3]) # test 0-index
+stopifnot(identical(mc[-(3:5), 0:2], mC[1:2, 0:2]),
+ identical(mt[-(3:5), 0:2], mT[1:2, 0:2]),
+ identical(mC[2:3, 4], mm[2:3, 4]))
+assert.EQ.mat(mC[1:2,], mm[1:2,])
+## sub vector
+stopifnot(identical4(mc[-(1:4), ], mC[5, 1:7],
+ mt[-(1:4), ], mT[5, 1:7]))
+stopifnot(identical4(mc[-(1:4), -(2:4)], mC[5, c(1,5:7)],
+ mt[-(1:4), -(2:4)], mT[5, c(1,5:7)]))
+
+## mixing of negative and positive must give error
+assertError(mT[-1:1,])
+showProc.time()
+
+## Sub *Assignment* ---- now works (partially):
+mt0 <- mt
+nt <- as(mt, "nMatrix")
+mt[1, 4] <- -99
+mt[2:3, 1:6] <- 0
+mt
+m2 <- mt+mt
+m2[1,4] <- -200
+m2[c(1,3), c(5:6,2)] <- 1:6
+stopifnot(m2[1,4] == -200,
+ as.vector(m2[c(1,3), c(5:6,2)]) == 1:6)
+mt[,3] <- 30
+mt[2:3,] <- 250
+mt[1:5 %% 2 == 1, 3] <- 0
+mt[3:1, 1:7 > 5] <- 0
+mt
+
+tt <- as(mt,"matrix")
+ii <- c(0,2,5)
+jj <- c(2:3,5)
+tt[ii, jj] <- 1:6 # 0 is just "dropped"
+mt[ii, jj] <- 1:6
+assert.EQ.mat(mt, tt)
+
+mt[1:5, 2:6]
+as((mt0 - mt)[1:5,], "dsparseMatrix")# [1,5] and lines 2:3
+
+mt[c(2,4), ] <- 0; stopifnot(as(mt[c(2,4), ],"matrix") == 0)
+mt[2:3, 4:7] <- 33
+checkMatrix(mt)
+mt
+
+mc[1,4] <- -99 ; stopifnot(mc[1,4] == -99)
+mc[1,4] <- 00 ; stopifnot(mc[1,4] == 00)
+mc[1,4] <- -99 ; stopifnot(mc[1,4] == -99)
+mc[1:2,4:3] <- 4:1; stopifnot(as.matrix(mc[1:2,4:3]) == 4:1)
+
+mc[-1, 3] <- -2:1 # 0 should not be entered; 'value' recycled
+mt[-1, 3] <- -2:1
+stopifnot(mc x != 0, mt x != 0,
+ mc[-1,3] == -2:1, mt[-1,3] == -2:1) ## failed earlier
+
+mc0 <- mc
+mt0 <- as(mc0, "TsparseMatrix")
+m0 <- as(mc0, "matrix")
+set.seed(1); options(Matrix.verbose = FALSE)
+for(i in 1:(if(doExtras) 50 else 4)) {
+ mc <- mc0; mt <- mt0 ; m <- m0
+ ev <- 1:5 %% 2 == round(runif(1))# 0 or 1
+ j <- sample(ncol(mc), 1 + round(runif(1)))
+ nv <- rpois(sum(ev) * length(j), lambda = 1)
+ mc[ev, j] <- nv
+ m[ev, j] <- nv
+ mt[ev, j] <- nv
+ if(i %% 10 == 1) print(mc[ev,j, drop = FALSE])
+ stopifnot(as.vector(mc[ev, j]) == nv, ## failed earlier...
+ as.vector(mt[ev, j]) == nv)
+ validObject(mc) ; assert.EQ.mat(mc, m)
+ validObject(mt) ; assert.EQ.mat(mt, m)
+}
+showProc.time()
+options(Matrix.verbose = TRUE)
+
+mc # no longer has non-structural zeros
+mc[ii, jj] <- 1:6
+mc[c(2,5), c(3,5)] <- 3.2
+checkMatrix(mc)
+m. <- mc
+mc[4,] <- 0
+mc
+
+S <- as(Diagonal(5),"TsparseMatrix")
+H <- Hilbert(9)
+Hc <- as(round(H, 3), "dsCMatrix")# a sparse matrix with no 0 ...
+(trH <- tril(Hc[1:5, 1:5]))
+stopifnot(is(trH, "triangularMatrix"), trH uplo == "L",
+ is(S, "triangularMatrix"))
+
+## triangular assignment
+## the slick (but inefficient in case of sparse!) way to assign sub-diagonals:
+## equivalent to tmp <- `diag<-`(S[,-1], -2:1); S[,-1] <- tmp
+## which dispatches to (x="TsparseMatrix", i="missing",j="index", value="replValue")
+diag(S[,-1]) <- -2:1 # used to give a wrong warning
+S <- as(S,"triangularMatrix")
+assert.EQ.mat(S, local({s <- diag(5); diag(s[,-1]) <- -2:1; s}))
+
+trH[c(1:2,4), c(2:3,5)] <- 0 # gave an *error* upto Jan.2008
+trH[ lower.tri(trH) ] <- 0 # ditto, because of callNextMethod()
+
+m <- Matrix(0+1:28, nrow = 4)
+m[-3,c(2,4:5,7)] <- m[ 3, 1:4] <- m[1:3, 6] <- 0
+mT <- as(m, "dgTMatrix")
+stopifnot(identical(mT[lower.tri(mT)],
+ m [lower.tri(m) ]))
+lM <- upper.tri(mT, diag=TRUE)
+mT[lM] <- 0
+ m[lM] <- 0
+assert.EQ.mat(mT, as(m,"matrix"))
+mT[lM] <- -1:0
+ m[lM] <- -1:0
+assert.EQ.mat(mT, as(m,"matrix"))
+(mT <- drop0(mT))
+
+i <- c(1:2, 4, 6:7); j <- c(2:4,6)
+H[i,j] <- 0
+(H. <- round(as(H, "sparseMatrix"), 3)[ , 2:7])
+Hc. <- Hc
+Hc.[i,j] <- 0 ## now "works", but setting "non-structural" 0s
+stopifnot(as.matrix(Hc.[i,j]) == 0)
+Hc.[, 1:6]
+
+## an example that failed for a long time
+sy3 <- new("dsyMatrix", Dim = as.integer(c(2, 2)), x = c(14, -1, 2, -7))
+checkMatrix(dm <- kronecker(Diagonal(2), sy3))# now sparse with new kronecker
+dm <- Matrix(as.matrix(dm))# -> "dsyMatrix"
+(s2 <- as(dm, "sparseMatrix"))
+checkMatrix(st <- as(s2, "TsparseMatrix"))
+stopifnot(is(s2, "symmetricMatrix"),
+ is(st, "symmetricMatrix"))
+checkMatrix(s.32 <- st[1:3,1:2]) ## 3 x 2 - and *not* dsTMatrix
+checkMatrix(s2.32 <- s2[1:3,1:2])
+I <- c(1,4:3)
+stopifnot(is(s2.32, "generalMatrix"),
+ is(s.32, "generalMatrix"),
+ identical(as.mat(s.32), as.mat(s2.32)),
+ identical3(dm[1:3,-1], asD(s2[1:3,-1]), asD(st[1:3,-1])),
+ identical4(2, dm[4,3], s2[4,3], st[4,3]),
+ identical3(diag(dm), diag(s2), diag(st)),
+ is((cI <- s2[I,I]), "dsCMatrix"),
+ is((tI <- st[I,I]), "dsTMatrix"),
+ identical4(as.mat(dm)[I,I], as.mat(dm[I,I]), as.mat(tI), as.mat(cI))
+ )
+
+## now sub-assign and check for consistency
+## symmetric subassign should keep symmetry
+st[I,I] <- 0; checkMatrix(st); stopifnot(is(st,"symmetricMatrix"))
+s2[I,I] <- 0; checkMatrix(s2); stopifnot(is(s2,"symmetricMatrix"))
+##
+m <- as.mat(st)
+ m[2:1,2:1] <- 4:1
+st[2:1,2:1] <- 4:1
+s2[2:1,2:1] <- 4:1
+stopifnot(identical(m, as.mat(st)),
+ 1:4 == as.vector(s2[1:2,1:2]),
+ identical(m, as.mat(s2)))
+
+## now a slightly different situation for 's2' (had bug)
+s2 <- as(dm, "sparseMatrix")
+s2[I,I] <- 0; diag(s2)[2:3] <- -(1:2)
+stopifnot(is(s2,"symmetricMatrix"), diag(s2) == c(0:-2,0))
+t2 <- as(s2, "TsparseMatrix")
+m <- as.mat(s2)
+s2[2:1,2:1] <- 4:1
+t2[2:1,2:1] <- 4:1
+ m[2:1,2:1] <- 4:1
+assert.EQ.mat(t2, m)
+assert.EQ.mat(s2, m)
+## and the same (for a different s2 !)
+s2[2:1,2:1] <- 4:1
+t2[2:1,2:1] <- 4:1
+assert.EQ.mat(t2, m)# ok
+assert.EQ.mat(s2, m)# failed in 0.9975-8
+showProc.time()
+
+
+## m[cbind(i,j)] <- value: (2-column matrix subassignment):
+m.[ cbind(3:5, 1:3) ] <- 1:3
+stopifnot(m.[3,1] == 1, m.[4,2] == 2)
+nt. <- nt ; nt[rbind(2:3, 3:4, c(3,3))] <- FALSE
+s. <- m. ; m.[cbind(3,4:6)] <- 0 ## assigning 0 where there *is* 0 ..
+stopifnot(identical(nt.,nt), ## should not have changed
+ identical(s., m.))
+x.x[ cbind(2:6, 2:6)] <- 12:16
+stopifnot(isValid(x.x, "dsCMatrix"),
+ 12:16 == as.mat(x.x)[cbind(2:6, 2:6)])
+(ne1 <- (mc - m.) != 0)
+stopifnot(identical(ne1, 0 != abs(mc - m.)))
+(ge <- m. >= mc) # contains "=" -> result is dense
+ne. <- mc != m. # was wrong (+ warning)
+stopifnot(identical(!(m. < mc), m. >= mc),
+ identical(m. < mc, as(!ge, "sparseMatrix")),
+ identical(ne., drop0(ne1)))
+
+d6 <- Diagonal(6)
+ii <- c(1:2, 4:5)
+d6[cbind(ii,ii)] <- 7*ii
+stopifnot(is(d6, "ddiMatrix"), identical(d6, Diagonal(x=c(7*1:2,1,7*4:5,1))))
+
+for(j in 3:6) { ## even and odd j used to behave differently
+ M <- Matrix(0, j,j); m <- matrix(0, j,j)
+ T <- as(M, "TsparseMatrix")
+ TG <- as(T, "generalMatrix")
+ G <- as(M, "generalMatrix")
+ id <- cbind(1:j,1:j)
+ i2 <- cbind(1:j,j:1)
+ m[id] <- 1:j
+ M[id] <- 1:j ; stopifnot(is(M,"symmetricMatrix"))
+ T[id] <- 1:j ; stopifnot(is(T,"symmetricMatrix"))
+ G[id] <- 1:j
+ TG[id]<- 1:j
+ m[i2] <- 10
+ M[i2] <- 10 ; stopifnot(is(M,"symmetricMatrix"))
+ T[i2] <- 10 ; stopifnot(is(T,"symmetricMatrix"))
+ G[i2] <- 10
+ TG[i2]<- 10
+ ##
+ assert.EQ.mat(M, m)
+ assert.EQ.mat(T, m)
+ assert.EQ.mat(G, m)
+ assert.EQ.mat(TG,m)
+}
+
+
+## drop, triangular, ...
+(M3 <- Matrix(upper.tri(matrix(, 3, 3)))) # ltC; indexing used to fail
+T3 <- as(M3, "TsparseMatrix")
+stopifnot(identical(drop(M3), M3),
+ identical4(drop(M3[,2, drop = FALSE]), M3[,2, drop = TRUE],
+ drop(T3[,2, drop = FALSE]), T3[,2, drop = TRUE]),
+ is(T3, "triangularMatrix"),
+ !is(T3[,2, drop=FALSE], "triangularMatrix")
+ )
+
+(T6 <- as(as(kronecker(Matrix(c(0,0,1,0),2,2), t(T3)), "lMatrix"),
+ "triangularMatrix"))
+T6[1:4, -(1:3)] # failed (trying to coerce back to ltTMatrix)
+stopifnot(identical(T6[1:4, -(1:3)][2:3, -3],
+ spMatrix(2,2, i=c(1,2,2), j=c(1,1,2), x=rep(TRUE,3))))
+
+M <- Diagonal(4); M[1,2] <- 2
+M. <- as(M, "CsparseMatrix")
+(R <- as(M., "RsparseMatrix"))
+(Ms <- symmpart(M.))
+Rs <- as(Ms, "RsparseMatrix")
+stopifnot(isValid(M, "triangularMatrix"),
+ isValid(M.,"triangularMatrix"),
+ isValid(Ms, "dsCMatrix"),
+ isValid(R, "dtRMatrix"),
+ isValid(Rs, "dsRMatrix") )
+stopifnot(dim(M[2:3, FALSE]) == c(2,0),
+ dim(R[2:3, FALSE]) == c(2,0),
+ identical(M [2:3,TRUE], M [2:3,]),
+ identical(M.[2:3,TRUE], M.[2:3,]),
+ identical(R [2:3,TRUE], R [2:3,]),
+ dim(R[FALSE, FALSE]) == c(0,0))
+
+n <- 50000L
+Lrg <- new("dgTMatrix", Dim = c(n,n))
+diag(Lrg) <- 1:n
+dLrg <- as(Lrg, "diagonalMatrix")
+stopifnot(identical(Diagonal(x = 1:n), dLrg))
+diag(dLrg) <- 1 + diag(dLrg)
+Clrg <- as(Lrg,"CsparseMatrix")
+Ctrg <- as(Clrg, "triangularMatrix")
+diag(Ctrg) <- 1 + diag(Ctrg)
+stopifnot(identical(Diagonal(x = 1+ 1:n), dLrg),
+ identical(Ctrg, as(dLrg,"CsparseMatrix")))
+
+cc <- capture.output(show(dLrg))# show(<diag>) used to error for large n
+showProc.time()
+
+## Large Matrix indexing / subassignment
+## ------------------------------------- (from ex. by Imran Rashid)
+n <- 7000000
+m <- 100000
+nnz <- 20000
+
+set.seed(12)
+f <- sparseMatrix(i = sample(n, size=nnz, replace=TRUE),
+ j = sample(m, size=nnz, replace=TRUE))
+str(f)
+dim(f) # 6999863 x 99992
+prod(dim(f)) # 699930301096 == 699'930'301'096 (~ 700'000 millions)
+str(thisCol <- f[,5000])# logi [~ 7 mio....]
+sv <- as(thisCol, "sparseVector")
+str(sv) ## "empty" !
+validObject(spCol <- f[,5000, drop=FALSE])
+##
+## *not* identical(): as(spCol, "sparseVector")@length is "double"prec:
+stopifnot(all.equal(as(spCol, "sparseVector"),
+ as(sv, "nsparseVector"), tol=0))
+if(doExtras) {#-----------------------------------------------------------------
+f[,5762] <- thisCol # now "fine" <<<<<<<<<< FIXME uses LARGE objects -- slow --
+## is using replCmat() in ../R/Csparse.R, then
+## replTmat() in ../R/Tsparse.R
+
+fx <- sparseMatrix(i = sample(n, size=nnz, replace=TRUE),
+ j = sample(m, size=nnz, replace=TRUE),
+ x = round(10*rnorm(nnz)))
+class(fx)## dgCMatrix
+fx[,6000] <- (tC <- rep(thisCol, length=nrow(fx)))# slow (as above)
+thCol <- fx[,2000]
+fx[,5762] <- thCol# slow
+stopifnot(is(f, "ngCMatrix"), is(fx, "dgCMatrix"),
+ identical(thisCol, f[,5762]),# perfect
+ identical(as.logical(fx[,6000]), tC),
+ identical(thCol, fx[,5762]))
+
+showProc.time()
+##
+cat("checkMatrix() of all: \n---------\n")
+Sys.setlocale("LC_COLLATE", "C")# to keep ls() reproducible
+for(nm in ls()) if(is(.m <- get(nm), "Matrix")) {
+ cat(nm, "\n")
+ checkMatrix(.m, verbose = FALSE)
+}
+showProc.time()
+}#--------------end if(doExtras) -----------------------------------------------
+
+if(!interactive()) warnings()
diff --git a/win32/deps/library/Matrix/tests/indexing.Rout.save b/win32/deps/library/Matrix/tests/indexing.Rout.save
new file mode 100644
index 0000000..7eebb30
--- /dev/null
+++ b/win32/deps/library/Matrix/tests/indexing.Rout.save
@@ -0,0 +1,1634 @@
+
+R version 2.15.1 Patched (2012-07-24 r59961) -- "Roasted Marshmallows"
+Copyright (C) 2012 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> #### For both 'Extract' ("[") and 'Replace' ("[<-") Method testing
+> #### aka subsetting and subassignment
+>
+> #### suppressPackageStartupMessages(...) as we have an *.Rout.save to Rdiff against
+> stopifnot(suppressPackageStartupMessages(require(Matrix)))
+>
+> source(system.file("test-tools.R", package = "Matrix"), keep.source = FALSE)
+> ##-> identical3() etc
+> cat("doExtras:",doExtras,"\n")
+doExtras: FALSE
+>
+> if(interactive()) {
++ options(error = recover, warn = 1)
++ } else if(FALSE) { ## MM @ testing
++ options(error = recover, Matrix.verbose = TRUE, warn = 1)
++ } else {
++ options(Matrix.verbose = TRUE, warn = 1)
++ }
+>
+>
+> ### Dense Matrices
+>
+> m <- Matrix(1:28 +0, nrow = 7)
+> validObject(m)
+[1] TRUE
+> stopifnot(identical(m, m[]),
++ identical(m[2, 3], 16), # simple number
++ identical(m[2, 3:4], c(16,23)), # simple numeric of length 2
++ identical(m[NA,NA], as(Matrix(NA, 7,4), "dMatrix")))
+>
+> m[2, 3:4, drop=FALSE] # sub matrix of class 'dgeMatrix'
+1 x 2 Matrix of class "dgeMatrix"
+ [,1] [,2]
+[1,] 16 23
+> m[-(4:7), 3:4] # ditto; the upper right corner of 'm'
+3 x 2 Matrix of class "dgeMatrix"
+ [,1] [,2]
+[1,] 15 22
+[2,] 16 23
+[3,] 17 24
+>
+> ## rows or columns only:
+> m[1,] # first row, as simple numeric vector
+[1] 1 8 15 22
+> m[,2] # 2nd column
+[1] 8 9 10 11 12 13 14
+> m[,1:2] # sub matrix of first two columns
+7 x 2 Matrix of class "dgeMatrix"
+ [,1] [,2]
+[1,] 1 8
+[2,] 2 9
+[3,] 3 10
+[4,] 4 11
+[5,] 5 12
+[6,] 6 13
+[7,] 7 14
+> m[-(1:6),, drop=FALSE] # not the first 6 rows, i.e. only the 7th
+1 x 4 Matrix of class "dgeMatrix"
+ [,1] [,2] [,3] [,4]
+[1,] 7 14 21 28
+> m[integer(0),] #-> 0 x 4 Matrix
+0 x 4 Matrix of class "dgeMatrix"
+ [,1] [,2] [,3] [,4]
+> m[2:4, numeric(0)] #-> 3 x 0 Matrix
+3 x 0 Matrix of class "dgeMatrix"
+
+[1,]
+[2,]
+[3,]
+>
+> ## logical indexing
+> stopifnot(identical(m[2,3], m[(1:nrow(m)) == 2, (1:ncol(m)) == 3]),
++ identical(m[2,], m[(1:nrow(m)) == 2, ]),
++ identical(m[,3:4], m[, (1:4) >= 3]))
+>
+> ## dimnames indexing:
+> mn <- m
+> dimnames(mn) <- list(paste("r",letters[1:nrow(mn)],sep=""),
++ LETTERS[1:ncol(mn)])
+> checkMatrix(mn)
+ norm(m [7 x 4]) : 1 I F M ok
+ Summary: ok
+2*m =?= m+m: identical
+m >= m for all: ok
+m < m for none: ok
+> mn["rd", "D"]
+[1] 25
+> msr <- ms <- as(mn,"sparseMatrix")
+> mnr <- mn
+> v <- rev(as(ms, "vector"))
+> mnr[] <- v
+> msr[] <- v # [<- "sparse" -- not very sensical; did fail w/o a message
+diagnosing replTmat(x,i,j,v): nargs()= 3; missing (i,j) = (0,1)
+> z <- msr; z[] <- 0
+> zz <- as(array(0, dim(z)), "sparseMatrix")
+> a.m <- as(mnr,"matrix")
+> stopifnot(identical(mn["rc", "D"], mn[3,4]), mn[3,4] == 24,
++ identical(mn[, "A"], mn[,1]), mn[,1] == 1:7,
++ identical(mn[c("re", "rb"), "B"], mn[c(5,2), 2]),
++ identical(ms["rc", "D"], ms[3,4]), ms[3,4] == 24,
++ identical(ms[, "A"], ms[,1]), ms[,1] == 1:7,
++ identical(ms[ci <- c("re", "rb"), "B"], ms[c(5,2), 2]),
++ identical(rownames(mn[ci, ]), ci),
++ identical(rownames(ms[ci, ]), ci),
++ identical(colnames(mn[,cj <- c("B","D")]), cj),
++ identical(colnames(ms[,cj]), cj),
++ identical(a.m, as(msr,"matrix")),
++ identical(unname(z), zz),
++ identical(a.m, array(v, dim=dim(mn), dimnames=dimnames(mn)))
++ )
+> showProc.time()
+Time elapsed: 0.652 0.008 0.661
+>
+> ## Printing sparse colnames:
+> ms[sample(28, 20)] <- 0
+diagnosing replTmat(x,i,j,v): nargs()= 3; missing (i,j) = (0,1)
+> ms <- t(rbind2(ms, 3*ms))
+> cnam1 <- capture.output(show(ms))[2] ; op <- options("sparse.colnames" = "abb3")
+ [[ suppressing 14 column names 'ra', 'rb', 'rc' ... ]]
+> cnam2 <- capture.output(show(ms))[2] ; options(op) # revert
+> stopifnot(## sparse printing
++ grep("^ +$", cnam1) == 1, # cnam1 is empty
++ identical(cnam2,
++ paste(" ", paste(rep(rownames(mn), 2), collapse=" "))))
+>
+> mo <- m
+> m[2,3] <- 100
+> m[1:2, 4] <- 200
+> m[, 1] <- -1
+> m[1:3,]
+3 x 4 Matrix of class "dgeMatrix"
+ [,1] [,2] [,3] [,4]
+[1,] -1 8 15 200
+[2,] -1 9 100 200
+[3,] -1 10 17 24
+>
+> m. <- as.matrix(m)
+>
+> ## m[ cbind(i,j) ] indexing:
+> iN <- ij <- cbind(1:6, 2:3)
+> iN[2:3,] <- iN[5,2] <- NA
+> stopifnot(identical(m[ij], m.[ij]),
++ identical(m[iN], m.[iN]))
+>
+> ## testing operations on logical Matrices rather more than indexing:
+> g10 <- m [ m > 10 ]
+> stopifnot(18 == length(g10))
+> stopifnot(10 == length(m[ m <= 10 ]))
+> sel <- (20 < m) & (m < 150)
+> sel.<- (20 < m.)& (m.< 150)
+> nsel <-(20 >= m) | (m >= 150)
+> (ssel <- as(sel, "sparseMatrix"))
+7 x 4 sparse Matrix of class "lgCMatrix"
+
+[1,] . . . .
+[2,] . . | .
+[3,] . . . |
+[4,] . . . |
+[5,] . . . |
+[6,] . . . |
+[7,] . . | |
+> stopifnot(is(sel, "lMatrix"), is(ssel, "lsparseMatrix"),
++ identical3(as.mat(sel.), as.mat(sel), as.mat(ssel)),
++ identical3(!sel, !ssel, nsel), # !<sparse> is typically dense
++ identical3(m[ sel], m[ ssel], as.matrix(m)[as.matrix( ssel)]),
++ identical3(m[!sel], m[!ssel], as.matrix(m)[as.matrix(!ssel)])
++ )
+> showProc.time()
+Time elapsed: 0.16 0 0.16
+>
+> ## more sparse Matrices --------------------------------------
+>
+> ##' @title Check sparseMatrix sub-assignment m[i,j] <- v
+> ##' @param ms sparse Matrix
+> ##' @param mm its [traditional matrix]-equivalent
+> ##' @param k (approximate) length of index vectors (i,j)
+> ##' @param n.uniq (approximate) number of unique values in i,j
+> ##' @param show logical; if TRUE, it will not stop on error
+> ##' @return
+> ##' @author Martin Maechler
+> chkAssign <- function(ms, mm = as(ms, "matrix"),
++ k = min(20,dim(mm)), n.uniq = k %/% 3,
++ vRNG = { if(is.numeric(mm) || is.complex(mm))
++ function(n) rpois(n,lambda= 0.75)# <- about 47% zeros
++ else ## logical
++ function(n) runif(n) > 0.8 }, ## 80% zeros
++ show=FALSE)
++ {
++ stopifnot(is(ms,"sparseMatrix"))
++ s1 <- function(n) sample(n, pmin(n, pmax(1, rpois(1, n.uniq))))
++ i <- sample(s1(nrow(ms)), k/2+ rpois(1, k/2), replace = TRUE)
++ j <- sample(s1(ncol(ms)), k/2+ rpois(1, k/2), replace = TRUE)
++ assert.EQ.mat(ms[i,j], mm[i,j])
++ ## now sub*assign* to these repeated indices, and then compare -----
++ v <- vRNG(length(i) * length(j))
++ mm[i,j] <- v
++ ms[i,j] <- v
++ if(!show) { op <- options(error = recover); on.exit(options(op)) }
++ assert.EQ.mat(ms, mm, show=show)
++ }
+>
+> ## Get duplicated index {because these are "hard" (and rare)
+> getDuplIndex <- function(n, k) {
++ repeat {
++ i <- sample(n, k, replace=TRUE) # 3 4 6 9 2 9 : 9 is twice
++ if(anyDuplicated(i)) break
++ }
++ i
++ }
+>
+> ## From package 'sfsmisc':
+> repChar <- function (char, no) paste(rep.int(char, no), collapse = "")
+>
+> m <- 1:800
+> set.seed(101) ; m[sample(800, 600)] <- 0
+> m0 <- Matrix(m, nrow = 40)
+> m1 <- add.simpleDimnames(m0)
+> for(kind in c("n", "l", "d")) {
++ for(m in list(m0,m1)) { ## -- with and without dimnames -------------------------
++ kClass <- paste(kind, "Matrix", sep="")
++ Ckind <- paste(kind, "gCMatrix", sep="")
++ Tkind <- paste(kind, "gTMatrix", sep="")
++ str(mC <- as(m, Ckind))
++ str(mT <- as(as(as(m, kClass), "TsparseMatrix"), Tkind))
++ mm <- as(mC, "matrix") # also logical or double
++ IDENT <- if(kind == "n") function(x,y) Q.eq2(x,y, tol=0) else identical
++ stopifnot(identical(mT, as(as(mC, "TsparseMatrix"), Tkind)),
++ identical(mC, as(mT, Ckind)),
++ Qidentical(mC[0,0], new(Ckind)),
++ Qidentical(mT[0,0], new(Tkind)),
++ identical(unname(mT[0,]), new(Tkind, Dim = c(0L,20L))),
++ identical(unname(mT[,0]), new(Tkind, Dim = c(40L,0L))),
++ IDENT(mC[0,], as(mT[FALSE,], Ckind)),
++ IDENT(mC[,0], as(mT[,FALSE], Ckind)),
++ sapply(c(0:2, 5:10),
++ function(k) {i <- seq_len(k); all(mC[i,i] == mT[i,i])}),
++ TRUE)
++ cat("ok\n")
++ show(mC[,1])
++ show(mC[1:2,])
++ show(mC[7, drop = FALSE])
++ assert.EQ.mat(mC[1:2,], mm[1:2,])
++ assert.EQ.mat(mC[0,], mm[0,])
++ assert.EQ.mat(mC[,FALSE], mm[,FALSE])
++ ##
++ ## *repeated* (aka 'duplicated') indices - did not work at all ...
++ i <- rep(8:10,2)
++ j <- c(2:4, 4:3)
++ assert.EQ.mat(mC[i,], mm[i,])
++ assert.EQ.mat(mC[,j], mm[,j])
++ ## FIXME? assert.EQ.mat(mC[,NA], mm[,NA]) -- mC[,NA] is all 0 "instead" of all NA
++ ## MM currently thinks we should NOT allow <sparse>[ <NA> ]
++ assert.EQ.mat(mC[i, 2:1], mm[i, 2:1])
++ assert.EQ.mat(mC[c(4,1,2:1), j], mm[c(4,1,2:1), j])
++ assert.EQ.mat(mC[i,j], mm[i,j])
++ ##
++ ## set.seed(7)
++ cat(" for(): ")
++ for(n in 1:(if(doExtras) 50 else 5)) {
++ chkAssign(mC, mm)
++ chkAssign(mC[-3,-2], mm[-3,-2])
++ cat(".")
++ }
++ cat(sprintf("\n[Ok]%s\n\n", repChar("-", 64)))
++ }
++ cat(sprintf("\nok( %s )\n== ###%s\n\n", kind, repChar("=", 70)))
++ }## end{for}---------------------------------------------------------------
+Formal class 'ngCMatrix' [package "Matrix"] with 5 slots
+ ..@ i : int [1:200] 2 6 11 21 24 29 37 38 1 4 ...
+ ..@ p : int [1:21] 0 8 22 28 37 41 50 63 71 81 ...
+ ..@ Dim : int [1:2] 40 20
+ ..@ Dimnames:List of 2
+ .. ..$ : NULL
+ .. ..$ : NULL
+ ..@ factors : list()
+Formal class 'ngTMatrix' [package "Matrix"] with 5 slots
+ ..@ i : int [1:200] 2 6 11 21 24 29 37 38 1 4 ...
+ ..@ j : int [1:200] 0 0 0 0 0 0 0 0 1 1 ...
+ ..@ Dim : int [1:2] 40 20
+ ..@ Dimnames:List of 2
+ .. ..$ : NULL
+ .. ..$ : NULL
+ ..@ factors : list()
+Note: Method with signature "nsparseMatrix#sparseMatrix" chosen for function "==",
+ target signature "ngCMatrix#ngTMatrix".
+ "nMatrix#nMatrix", "sparseMatrix#nsparseMatrix" would also be valid
+ok
+ [1] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE
+[13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE
+[25] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE
+[37] FALSE TRUE TRUE FALSE
+2 x 20 sparse Matrix of class "ngCMatrix"
+
+[1,] . . . | . . | . . . . | . . | . | . . .
+[2,] . | . . . | . . . . . . | | . . . . | .
+[1] TRUE
+ for(): .....
+[Ok]----------------------------------------------------------------
+
+Formal class 'ngCMatrix' [package "Matrix"] with 5 slots
+ ..@ i : int [1:200] 2 6 11 21 24 29 37 38 1 4 ...
+ ..@ p : int [1:21] 0 8 22 28 37 41 50 63 71 81 ...
+ ..@ Dim : int [1:2] 40 20
+ ..@ Dimnames:List of 2
+ .. ..$ : chr [1:40] "r1" "r2" "r3" "r4" ...
+ .. ..$ : chr [1:20] "c1" "c2" "c3" "c4" ...
+ ..@ factors : list()
+Formal class 'ngTMatrix' [package "Matrix"] with 5 slots
+ ..@ i : int [1:200] 2 6 11 21 24 29 37 38 1 4 ...
+ ..@ j : int [1:200] 0 0 0 0 0 0 0 0 1 1 ...
+ ..@ Dim : int [1:2] 40 20
+ ..@ Dimnames:List of 2
+ .. ..$ : chr [1:40] "r1" "r2" "r3" "r4" ...
+ .. ..$ : chr [1:20] "c1" "c2" "c3" "c4" ...
+ ..@ factors : list()
+ok
+ r1 r2 r3 r4 r5 r6 r7 r8 r9 r10 r11 r12 r13
+FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE
+ r14 r15 r16 r17 r18 r19 r20 r21 r22 r23 r24 r25 r26
+FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE
+ r27 r28 r29 r30 r31 r32 r33 r34 r35 r36 r37 r38 r39
+FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE
+ r40
+FALSE
+2 x 20 sparse Matrix of class "ngCMatrix"
+ [[ suppressing 20 column names 'c1', 'c2', 'c3' ... ]]
+
+r1 . . . | . . | . . . . | . . | . | . . .
+r2 . | . . . | . . . . . . | | . . . . | .
+[1] TRUE
+ for(): .....
+[Ok]----------------------------------------------------------------
+
+
+ok( n )
+== ###======================================================================
+
+Formal class 'lgCMatrix' [package "Matrix"] with 6 slots
+ ..@ i : int [1:200] 2 6 11 21 24 29 37 38 1 4 ...
+ ..@ p : int [1:21] 0 8 22 28 37 41 50 63 71 81 ...
+ ..@ Dim : int [1:2] 40 20
+ ..@ Dimnames:List of 2
+ .. ..$ : NULL
+ .. ..$ : NULL
+ ..@ x : logi [1:200] TRUE TRUE TRUE TRUE TRUE TRUE ...
+ ..@ factors : list()
+Formal class 'lgTMatrix' [package "Matrix"] with 6 slots
+ ..@ i : int [1:200] 2 6 11 21 24 29 37 38 1 4 ...
+ ..@ j : int [1:200] 0 0 0 0 0 0 0 0 1 1 ...
+ ..@ Dim : int [1:2] 40 20
+ ..@ Dimnames:List of 2
+ .. ..$ : NULL
+ .. ..$ : NULL
+ ..@ x : logi [1:200] TRUE TRUE TRUE TRUE TRUE TRUE ...
+ ..@ factors : list()
+ok
+ [1] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE
+[13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE
+[25] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE
+[37] FALSE TRUE TRUE FALSE
+2 x 20 sparse Matrix of class "lgCMatrix"
+
+[1,] . . . | . . | . . . . | . . | . | . . .
+[2,] . | . . . | . . . . . . | | . . . . | .
+[1] TRUE
+ for(): .....
+[Ok]----------------------------------------------------------------
+
+Formal class 'lgCMatrix' [package "Matrix"] with 6 slots
+ ..@ i : int [1:200] 2 6 11 21 24 29 37 38 1 4 ...
+ ..@ p : int [1:21] 0 8 22 28 37 41 50 63 71 81 ...
+ ..@ Dim : int [1:2] 40 20
+ ..@ Dimnames:List of 2
+ .. ..$ : chr [1:40] "r1" "r2" "r3" "r4" ...
+ .. ..$ : chr [1:20] "c1" "c2" "c3" "c4" ...
+ ..@ x : logi [1:200] TRUE TRUE TRUE TRUE TRUE TRUE ...
+ ..@ factors : list()
+Formal class 'lgTMatrix' [package "Matrix"] with 6 slots
+ ..@ i : int [1:200] 2 6 11 21 24 29 37 38 1 4 ...
+ ..@ j : int [1:200] 0 0 0 0 0 0 0 0 1 1 ...
+ ..@ Dim : int [1:2] 40 20
+ ..@ Dimnames:List of 2
+ .. ..$ : chr [1:40] "r1" "r2" "r3" "r4" ...
+ .. ..$ : chr [1:20] "c1" "c2" "c3" "c4" ...
+ ..@ x : logi [1:200] TRUE TRUE TRUE TRUE TRUE TRUE ...
+ ..@ factors : list()
+ok
+ r1 r2 r3 r4 r5 r6 r7 r8 r9 r10 r11 r12 r13
+FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE
+ r14 r15 r16 r17 r18 r19 r20 r21 r22 r23 r24 r25 r26
+FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE
+ r27 r28 r29 r30 r31 r32 r33 r34 r35 r36 r37 r38 r39
+FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE
+ r40
+FALSE
+2 x 20 sparse Matrix of class "lgCMatrix"
+ [[ suppressing 20 column names 'c1', 'c2', 'c3' ... ]]
+
+r1 . . . | . . | . . . . | . . | . | . . .
+r2 . | . . . | . . . . . . | | . . . . | .
+[1] TRUE
+ for(): .....
+[Ok]----------------------------------------------------------------
+
+
+ok( l )
+== ###======================================================================
+
+Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
+ ..@ i : int [1:200] 2 6 11 21 24 29 37 38 1 4 ...
+ ..@ p : int [1:21] 0 8 22 28 37 41 50 63 71 81 ...
+ ..@ Dim : int [1:2] 40 20
+ ..@ Dimnames:List of 2
+ .. ..$ : NULL
+ .. ..$ : NULL
+ ..@ x : num [1:200] 3 7 12 22 25 30 38 39 42 45 ...
+ ..@ factors : list()
+Formal class 'dgTMatrix' [package "Matrix"] with 6 slots
+ ..@ i : int [1:200] 2 6 11 21 24 29 37 38 1 4 ...
+ ..@ j : int [1:200] 0 0 0 0 0 0 0 0 1 1 ...
+ ..@ Dim : int [1:2] 40 20
+ ..@ Dimnames:List of 2
+ .. ..$ : NULL
+ .. ..$ : NULL
+ ..@ x : num [1:200] 3 7 12 22 25 30 38 39 42 45 ...
+ ..@ factors : list()
+ok
+ [1] 0 0 3 0 0 0 7 0 0 0 0 12 0 0 0 0 0 0 0 0 0 22 0 0 25
+[26] 0 0 0 0 30 0 0 0 0 0 0 0 38 39 0
+2 x 20 sparse Matrix of class "dgCMatrix"
+
+[1,] . . . 121 . . 241 . . . . 441 . . 561 . 641 . . .
+[2,] . 42 . . . 202 . . . . . . 482 522 . . . . 722 .
+[1] 7
+ for(): .....
+[Ok]----------------------------------------------------------------
+
+Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
+ ..@ i : int [1:200] 2 6 11 21 24 29 37 38 1 4 ...
+ ..@ p : int [1:21] 0 8 22 28 37 41 50 63 71 81 ...
+ ..@ Dim : int [1:2] 40 20
+ ..@ Dimnames:List of 2
+ .. ..$ : chr [1:40] "r1" "r2" "r3" "r4" ...
+ .. ..$ : chr [1:20] "c1" "c2" "c3" "c4" ...
+ ..@ x : num [1:200] 3 7 12 22 25 30 38 39 42 45 ...
+ ..@ factors : list()
+Formal class 'dgTMatrix' [package "Matrix"] with 6 slots
+ ..@ i : int [1:200] 2 6 11 21 24 29 37 38 1 4 ...
+ ..@ j : int [1:200] 0 0 0 0 0 0 0 0 1 1 ...
+ ..@ Dim : int [1:2] 40 20
+ ..@ Dimnames:List of 2
+ .. ..$ : chr [1:40] "r1" "r2" "r3" "r4" ...
+ .. ..$ : chr [1:20] "c1" "c2" "c3" "c4" ...
+ ..@ x : num [1:200] 3 7 12 22 25 30 38 39 42 45 ...
+ ..@ factors : list()
+ok
+ r1 r2 r3 r4 r5 r6 r7 r8 r9 r10 r11 r12 r13 r14 r15 r16 r17 r18 r19 r20
+ 0 0 3 0 0 0 7 0 0 0 0 12 0 0 0 0 0 0 0 0
+r21 r22 r23 r24 r25 r26 r27 r28 r29 r30 r31 r32 r33 r34 r35 r36 r37 r38 r39 r40
+ 0 22 0 0 25 0 0 0 0 30 0 0 0 0 0 0 0 38 39 0
+2 x 20 sparse Matrix of class "dgCMatrix"
+ [[ suppressing 20 column names 'c1', 'c2', 'c3' ... ]]
+
+r1 . . . 121 . . 241 . . . . 441 . . 561 . 641 . . .
+r2 . 42 . . . 202 . . . . . . 482 522 . . . . 722 .
+[1] 7
+ for(): .....
+[Ok]----------------------------------------------------------------
+
+
+ok( d )
+== ###======================================================================
+
+> showProc.time()
+Time elapsed: 2.344 0.016 2.367
+>
+> ##---- Symmetric indexing of symmetric Matrix ----------
+> m. <- mC
+> m.[, c(2, 7:12)] <- 0
+> isValid(S <- crossprod(add.simpleDimnames(m.) %% 100), "dsCMatrix")
+[1] TRUE
+> ss <- as(S, "matrix")
+> ds <- as(S, "denseMatrix")
+> ## NA-indexing of *dense* Matrices: should work as traditionally
+> assert.EQ.mat(ds[NA,NA], ss[NA,NA])
+> assert.EQ.mat(ds[NA, ], ss[NA,])
+> assert.EQ.mat(ds[ ,NA], ss[,NA])
+> T <- as(S, "TsparseMatrix")
+> stopifnot(identical(ds[2 ,NA], ss[2,NA]),
++ identical(ds[NA, 1], ss[NA, 1]),
++ identical(S, as(T, "CsparseMatrix")) )
+>
+> ## non-repeated indices:
+> i <- c(7:5, 2:4);assert.EQ.mat(T[i,i], ss[i,i])
+> ## NA in indices -- check that we get a helpful error message:
+> i[2] <- NA
+> er <- tryCatch(T[i,i], error = function(e)e)
+> stopifnot(as.logical(grep("indices.*sparse Matrices", er$message)))
+>
+> N <- nrow(T)
+> set.seed(11)
+> for(n in 1:(if(doExtras) 50 else 3)) {
++ i <- sample(N, max(2, sample(N,1)), replace = FALSE)
++ validObject(Tii <- T[i,i]) ; tTi <- t(T)[i,i]
++ stopifnot(is(Tii, "dsTMatrix"), # remained symmetric Tsparse
++ is(tTi, "dsTMatrix"), # may not be identical when *sorted* differently
++ identical(as(t(Tii),"CsparseMatrix"), as(tTi,"CsparseMatrix")))
++ assert.EQ.mat(Tii, ss[i,i])
++ }
+>
+> b <- diag(1:2)[,c(1,1,2,2)]
+> cb <- crossprod(b)
+> cB <- crossprod(Matrix(b, sparse=TRUE))
+> a <- matrix(0, 6, 6)
+> a[1:4, 1:4] <- cb
+> A1 <- A2 <- Matrix(0, 6, 6)#-> sparse
+> A1[1:4, 1:4] <- cb
+> A2[1:4, 1:4] <- cB
+> assert.EQ.mat(A1, a)# indeed
+> stopifnot(identical(A1, A2), is(A1, "dsCMatrix"))
+>
+> ## repeated ones ``the challenge'' (to do smartly):
+> j <- c(4, 4, 9, 12, 9, 4, 17, 3, 18, 4, 12, 18, 4, 9)
+> assert.EQ.mat(T[j,j], ss[j,j])
+> ## and another two sets (a, A) & (a., A.) :
+> a <- matrix(0, 6,6)
+> a[upper.tri(a)] <- (utr <- c(2, 0,-1, 0,0,5, 7,0,0,0, 0,0,-2,0,8))
+> ta <- t(a); ta[upper.tri(a)] <- utr; a <- t(ta)
+> diag(a) <- c(0,3,0,4,6,0)
+> A <- as(Matrix(a), "TsparseMatrix")
+> A. <- A
+> diag(A.) <- 10 * (1:6)
+> a. <- as(A., "matrix")
+> ## More testing {this was not working for a long time..}
+> set.seed(1)
+> for(n in 1:(if(doExtras) 100 else 6)) {
++ i <- sample(1:nrow(A), 3+2*rpois(1, lam=3), replace=TRUE)
++ Aii <- A[i,i]
++ A.ii <- A.[i,i]
++ stopifnot(class(Aii) == class(A),
++ class(A.ii) == class(A.))
++ assert.EQ.mat(Aii , a [i,i])
++ assert.EQ.mat(A.ii, a.[i,i])
++ assert.EQ.mat(T[i,i], ss[i,i])
++ }
+> showProc.time()
+Time elapsed: 0.532 0.004 0.539
+>
+> stopifnot(all.equal(mC[,3], mm[,3]),
++ identical(mC[ij], mC[ij + 0.4]),
++ identical(mC[ij], mm[ij]),
++ identical(mC[iN], mm[iN]))
+> ## out of bound indexing must be detected:
+> assertError(mC[cbind(ij[,1] - 5, ij[,2])])
+> assertError(mC[cbind(ij[,1], ij[,2] + ncol(mC))])
+>
+> assert.EQ.mat(mC[7, , drop=FALSE], mm[7, , drop=FALSE])
+> identical (mC[7, drop=FALSE], mm[7, drop=FALSE]) # *vector* indexing
+[1] TRUE
+>
+> stopifnot(dim(mC[numeric(0), ]) == c(0,20), # used to give warnings
++ dim(mC[, integer(0)]) == c(40,0),
++ identical(mC[, integer(0)], mC[, FALSE]))
+> validObject(print(mT[,c(2,4)]))
+40 x 2 sparse Matrix of class "dgTMatrix"
+ c2 c4
+r1 . 121
+r2 42 .
+r3 . .
+r4 . .
+r5 45 .
+r6 . .
+r7 . .
+r8 . 128
+r9 . 129
+r10 50 .
+r11 . .
+r12 52 132
+r13 . 133
+r14 . .
+r15 55 .
+r16 . .
+r17 . .
+r18 . 138
+r19 . .
+r20 . .
+r21 . 141
+r22 . 142
+r23 63 .
+r24 . .
+r25 65 .
+r26 . .
+r27 67 .
+r28 68 .
+r29 . .
+r30 . .
+r31 71 .
+r32 72 .
+r33 . .
+r34 74 .
+r35 . .
+r36 76 .
+r37 . .
+r38 . .
+r39 . 159
+r40 80 .
+[1] TRUE
+> stopifnot(all.equal(mT[2,], mm[2,]),
++ ## row or column indexing in combination with t() :
++ Q.C.identical(mT[2,], t(mT)[,2]),
++ Q.C.identical(mT[-2,], t(t(mT)[,-2])),
++ Q.C.identical(mT[c(2,5),], t(t(mT)[,c(2,5)])) )
+> assert.EQ.mat(mT[4,, drop = FALSE], mm[4,, drop = FALSE])
+> stopifnot(identical3(mm[,1], mC[,1], mT[,1]),
++ identical3(mm[3,], mC[3,], mT[3,]),
++ identical3(mT[2,3], mC[2,3], 0),
++ identical(mT[], mT),
++ identical4( mm[c(3,7), 2:4], as.mat( m[c(3,7), 2:4]),
++ as.mat(mT[c(3,7), 2:4]), as.mat(mC[c(3,7), 2:4]))
++ )
+>
+> x.x <- crossprod(mC)
+> stopifnot(class(x.x) == "dsCMatrix",
++ class(x.x. <- round(x.x / 10000)) == "dsCMatrix",
++ identical(x.x[cbind(2:6, 2:6)],
++ diag(x.x [2:6, 2:6])))
+> head(x.x.) # Note the *non*-structural 0's printed as "0"
+6 x 20 sparse Matrix of class "dgCMatrix"
+ [[ suppressing 20 column names 'c1', 'c2', 'c3' ... ]]
+
+c1 1 0 . 1 . 1 1 3 . 3 2 1 6 1 . 2 4 6 5 1
+c2 0 6 2 1 3 5 7 5 12 14 14 9 11 16 12 13 17 19 19 10
+c3 . 2 6 . 4 2 5 3 8 12 5 16 9 11 23 . . 6 7 7
+c4 1 1 . 17 . 8 10 13 8 6 18 18 29 35 14 8 25 10 19 21
+c5 . 3 4 . 14 4 10 . . 29 8 9 19 11 11 . . 26 26 16
+c6 1 5 2 8 4 42 5 19 14 9 8 10 42 56 50 27 29 32 64 16
+> tail(x.x., -3) # all but the first three lines
+17 x 20 sparse Matrix of class "dgCMatrix"
+ [[ suppressing 20 column names 'c1', 'c2', 'c3' ... ]]
+
+c4 1 1 . 17 . 8 10 13 8 6 18 18 29 35 14 8 25 10 19 21
+c5 . 3 4 . 14 4 10 . . 29 8 9 19 11 11 . . 26 26 16
+c6 1 5 2 8 4 42 5 19 14 9 8 10 42 56 50 27 29 32 64 16
+c7 1 7 5 10 10 5 87 14 9 31 77 47 79 43 28 17 67 110 36 121
+c8 3 5 3 13 . 19 14 70 10 24 37 13 59 62 34 19 58 21 64 44
+c9 . 12 8 8 . 14 9 10 116 41 58 33 33 72 78 43 69 72 75 25
+c10 3 14 12 6 29 9 31 24 41 167 69 56 99 44 70 24 105 82 85 32
+c11 2 14 5 18 8 8 77 37 58 69 267 80 86 139 49 105 194 119 122 129
+c12 1 9 16 18 9 10 47 13 33 56 80 194 70 77 81 . 90 32 . 106
+c13 6 11 9 29 19 42 79 59 33 99 86 70 324 157 55 . 69 142 144 155
+c14 1 16 11 35 11 56 43 62 72 44 139 77 157 375 123 102 145 39 196 81
+c15 . 12 23 14 11 50 28 34 78 70 49 81 55 123 368 71 112 41 41 86
+c16 2 13 . 8 . 27 17 19 43 24 105 . . 102 71 233 124 44 139 .
+c17 4 17 . 25 . 29 67 58 69 105 194 90 69 145 112 124 523 141 245 100
+c18 6 19 6 10 26 32 110 21 72 82 119 32 142 39 41 44 141 497 104 111
+c19 5 19 7 19 26 64 36 64 75 85 122 . 144 196 41 139 245 104 542 55
+c20 1 10 7 21 16 16 121 44 25 32 129 106 155 81 86 . 100 111 55 541
+>
+> lx.x <- as(x.x, "lsCMatrix") # FALSE only for "structural" 0
+> (l10 <- lx.x[1:10, 1:10])# "lsC"
+10 x 10 sparse Matrix of class "lsCMatrix"
+ [[ suppressing 10 column names 'c1', 'c2', 'c3' ... ]]
+
+c1 | | . | . | | | . |
+c2 | | | | | | | | | |
+c3 . | | . | | | | | |
+c4 | | . | . | | | | |
+c5 . | | . | | | . . |
+c6 | | | | | | | | | |
+c7 | | | | | | | | | |
+c8 | | | | . | | | | |
+c9 . | | | . | | | | |
+c10 | | | | | | | | | |
+> (l3 <- lx.x[1:3, ])
+3 x 20 sparse Matrix of class "lgCMatrix"
+ [[ suppressing 20 column names 'c1', 'c2', 'c3' ... ]]
+
+c1 | | . | . | | | . | | | | | . | | | | |
+c2 | | | | | | | | | | | | | | | | | | | |
+c3 . | | . | | | | | | | | | | | . . | | |
+> m.x <- as.mat(x.x) # as.mat() *drops* (NULL,NULL) dimnames
+> stopifnot(class(l10) == "lsCMatrix", # symmetric indexing -> symmetric !
++ identical(as.mat(lx.x), m.x != 0),
++ identical(as.logical(lx.x), as.logical(m.x)),
++ identical(as.mat(l10), m.x[1:10, 1:10] != 0),
++ identical(as.mat(l3 ), m.x[1:3, ] != 0)
++ )
+>
+> ##-- Sub*assignment* with repeated / duplicated index:
+> A <- Matrix(0,4,3) ; A[c(1,2,1), 2] <- 1 ; A
+4 x 3 sparse Matrix of class "dgCMatrix"
+
+[1,] . 1 .
+[2,] . 1 .
+[3,] . . .
+[4,] . . .
+> B <- A; B[c(1,2,1), 2] <- 1:3; B; B. <- B
+Note: Method with signature "numeric#sparseVector" chosen for function "coerce",
+ target signature "integer#sparseVector".
+ "atomicVector#sparseVector" would also be valid
+4 x 3 sparse Matrix of class "dgCMatrix"
+
+[1,] . 3 .
+[2,] . 2 .
+[3,] . . .
+[4,] . . .
+> B.[3,] <- rbind(4:2)
+> ## change the diagonal and the upper and lower subdiagonal :
+> diag(B.) <- 10 * diag(B.)
+> diag(B.[,-1]) <- 5* diag(B.[,-1])
+> diag(B.[-1,]) <- 4* diag(B.[-1,]) ; B.
+4 x 3 sparse Matrix of class "dgCMatrix"
+
+[1,] . 15 .
+[2,] . 20 .
+[3,] 4 12 20
+[4,] . . .
+> C <- B.; C[,2] <- C[,2]; C[1,] <- C[1,]; C[2:3,2:1] <- C[2:3,2:1]
+> stopifnot(identical(unname(as.matrix(A)),
++ local({a <- matrix(0,4,3); a[c(1,2,1), 2] <- 1 ; a})),
++ identical(unname(as.matrix(B)),
++ local({a <- matrix(0,4,3); a[c(1,2,1), 2] <- 1:3; a})),
++ identical(C, drop0(B.)))
+> ## <sparse>[<logicalSparse>] <- v failed in the past
+> T <- as(C,"TsparseMatrix"); C. <- C
+> T[T>0] <- 21
+diagnosing replTmat(x,i,j,v): nargs()= 3; missing (i,j) = (0,1)
+> C[C>0] <- 21
+diagnosing replTmat(x,i,j,v): nargs()= 3; missing (i,j) = (0,1)
+> a. <- local({a <- as.matrix(C.); a[a>0] <- 21; a})
+> assert.EQ.mat(C, a.)
+> stopifnot(identical(C, as(T, "CsparseMatrix")))
+>
+> ## used to fail
+> n <- 5 ## or much larger
+> sm <- new("dsTMatrix", i=1L, j=1L, Dim=as.integer(c(n,n)), x = 1)
+> (cm <- as(sm, "CsparseMatrix"))
+5 x 5 sparse Matrix of class "dsCMatrix"
+
+[1,] . . . . .
+[2,] . 1 . . .
+[3,] . . . . .
+[4,] . . . . .
+[5,] . . . . .
+> sm[2,]
+[1] 0 1 0 0 0
+> stopifnot(sm[2,] == c(0:1, rep.int(0,ncol(sm)-2)),
++ sm[2,] == cm[2,],
++ sm[,3] == sm[3,],
++ all(sm[,-(1:3)] == t(sm[-(1:3),])), # all(<lge.>)
++ all(sm[,-(1:3)] == 0)
++ )
+> showProc.time()
+Time elapsed: 0.712 0.004 0.719
+>
+> ##--- "nsparse*" sub-assignment :----------
+> M <- Matrix(c(1, rep(0,7), 1:4), 3,4)
+> N0 <- kronecker(M,M)
+> Nn <- as(N0, "nMatrix"); nn <- as(Nn,"matrix")
+> (Nn00 <- Nn0 <- Nn); nn00 <- nn0 <- nn
+9 x 16 sparse Matrix of class "ngTMatrix"
+
+ [1,] | . . | . . . . . . . . | . . |
+ [2,] . . . | . . . . . . . . . . . |
+ [3,] . . | | . . . . . . . . . . | |
+ [4,] . . . . . . . . . . . . | . . |
+ [5,] . . . . . . . . . . . . . . . |
+ [6,] . . . . . . . . . . . . . . | |
+ [7,] . . . . . . . . | . . | | . . |
+ [8,] . . . . . . . . . . . | . . . |
+ [9,] . . . . . . . . . . | | . . | |
+>
+> set.seed(1)
+> Nn0 <- Nn00; nn0 <- nn00
+> for(i in 1:(if(doExtras) 200 else 25)) {
++ Nn <- Nn0
++ nn <- nn0
++ i. <- getDuplIndex(nrow(N0), 6)
++ j. <- getDuplIndex(ncol(N0), 4)
++ vv <- sample(c(FALSE,TRUE),
++ length(i.)*length(j.), replace=TRUE)
++ cat(",")
++ Nn[i., j.] <- vv
++ nn[i., j.] <- vv
++ assert.EQ.mat(Nn, nn)
++ if(!all(Nn == nn)) {
++ cat("i=",i,":\n i. <- "); dput(i.)
++ cat("j. <- "); dput(j.)
++ cat("which(vv): "); dput(which(vv))
++ cat("Difference matrix:\n")
++ show(drop0(Nn - nn))
++ }
++ cat("k")
++ ## sub-assign double precision to logical sparseMatrices should error:
++ ## well... warning for now {back compatibility: gave *no* warning, nothing .. !}:
++ assertWarning(Nn[1:2,] <- -pi)
++ assertWarning(Nn[, 5] <- -pi)
++ assertWarning(Nn[2:4, 5:8] <- -pi)
++ ##
++ cat(".")
++ if(i %% 10 == 0) cat("\n")
++ if(i == 100) {
++ Nn0 <- as(Nn0, "CsparseMatrix")
++ cat("Now: class", class(Nn0)," :\n~~~~~~~~~~~~~~~~~\n")
++ }
++ }
+,k.,k.,k.,k.,k.,k.,k.,k.,k.,k.
+,k.,k.,k.,k.,k.,k.,k.,k.,k.,k.
+,k.,k.,k.,k.,k.> showProc.time()
+Time elapsed: 0.552 0.008 0.562
+>
+> m0 <- Diagonal(5)
+> stopifnot(identical(m0[2,], m0[,2]),
++ identical(m0[,1], c(1,0,0,0,0)))
+> ### Diagonal -- Sparse:
+> (m1 <- as(m0, "TsparseMatrix")) # dtTMatrix
+5 x 5 sparse Matrix of class "dtTMatrix" (unitriangular)
+
+[1,] 1 . . . .
+[2,] . 1 . . .
+[3,] . . 1 . .
+[4,] . . . 1 .
+[5,] . . . . 1
+> (m2 <- as(m0, "CsparseMatrix")) # dtCMatrix
+5 x 5 sparse Matrix of class "dtCMatrix" (unitriangular)
+
+[1,] 1 . . . .
+[2,] . 1 . . .
+[3,] . . 1 . .
+[4,] . . . 1 .
+[5,] . . . . 1
+> m1g <- as(m1, "generalMatrix")
+> stopifnot(is(m1g, "dgTMatrix"))
+> assert.EQ.mat(m2[1:3,], diag(5)[1:3,])
+> assert.EQ.mat(m2[,c(4,1)], diag(5)[,c(4,1)])
+> stopifnot(identical(m2[1:3,], as(m1[1:3,], "CsparseMatrix")),
++ identical(Matrix:::uniqTsparse(m1[, c(4,2)]),
++ Matrix:::uniqTsparse(as(m2[, c(4,2)], "TsparseMatrix")))
++ )## failed in 0.9975-11
+>
+> (uTr <- new("dtTMatrix", Dim = c(3L,3L), diag="U"))
+3 x 3 sparse Matrix of class "dtTMatrix" (unitriangular)
+
+[1,] 1 . .
+[2,] . 1 .
+[3,] . . 1
+> uTr[1,] <- 0
+> assert.EQ.mat(uTr, cbind(0, rbind(0,diag(2))))
+>
+> M <- m0; M[1,] <- 0
+> stopifnot(identical(M, Diagonal(x=c(0, rep(1,4)))))
+> M <- m0; M[,3] <- 3 ; M ; stopifnot(is(M, "sparseMatrix"), M[,3] == 3)
+5 x 5 sparse Matrix of class "dgCMatrix"
+
+[1,] 1 . 3 . .
+[2,] . 1 3 . .
+[3,] . . 3 . .
+[4,] . . 3 1 .
+[5,] . . 3 . 1
+> checkMatrix(M)
+Note: Method with signature "sparseMatrix#ldiMatrix" chosen for function "==",
+ target signature "nsCMatrix#ldiMatrix".
+ "nsparseMatrix#sparseMatrix", "nMatrix#lMatrix" would also be valid
+ norm(m [5 x 5]) : 1 I F M ok
+ Summary: ok
+as(., "nMatrix") giving full nonzero-pattern: ok
+2*m =?= m+m: identical
+m >= m for all: ok
+m < m for none: ok
+symmpart(m) + skewpart(m) == m: ok; determinant(): ok
+> M <- m0; M[1:3, 3] <- 0 ;M
+5 x 5 diagonal matrix of class "ddiMatrix"
+ [,1] [,2] [,3] [,4] [,5]
+[1,] 1 . . . .
+[2,] . 1 . . .
+[3,] . . 0 . .
+[4,] . . . 1 .
+[5,] . . . . 1
+> T <- m0; T[1:3, 3] <- 10
+> stopifnot(identical(M, Diagonal(x=c(1,1, 0, 1,1))),
++ isValid(T, "triangularMatrix"), identical(T[,3], c(10,10,10,0,0)))
+>
+> M <- m1; M[1,] <- 0 ; M ; assert.EQ.mat(M, diag(c(0,rep(1,4))), tol=0)
+5 x 5 sparse Matrix of class "dtTMatrix"
+
+[1,] . . . . .
+[2,] . 1 . . .
+[3,] . . 1 . .
+[4,] . . . 1 .
+[5,] . . . . 1
+> M <- m1; M[,3] <- 3 ; stopifnot(is(M,"sparseMatrix"), M[,3] == 3)
+M[i,j] <- v : coercing symmetric M[] into non-symmetric
+> checkMatrix(M)
+ norm(m [5 x 5]) : 1 I F M ok
+ Summary: ok
+as(., "nMatrix") giving full nonzero-pattern: ok
+2*m =?= m+m: Note: Method with signature "sparseMatrix#ldiMatrix" chosen for function "&",
+ target signature "nsCMatrix#ldiMatrix".
+ "nsparseMatrix#sparseMatrix", "nMatrix#lMatrix" would also be valid
+ok
+m >= m for all: ok
+m < m for none: ok
+symmpart(m) + skewpart(m) == m: ok; determinant(): ok
+> M <- m1; M[1:3, 3] <- 0 ;M
+5 x 5 sparse Matrix of class "dtTMatrix"
+
+[1,] 1 . . . .
+[2,] . 1 . . .
+[3,] . . . . .
+[4,] . . . 1 .
+[5,] . . . . 1
+> assert.EQ.mat(M, diag(c(1,1, 0, 1,1)), tol=0)
+> T <- m1; T[1:3, 3] <- 10; checkMatrix(T)
+ norm(m [5 x 5]) : 1 I F M ok
+ Summary: ok
+as(., "nMatrix") giving full nonzero-pattern: ok
+2*m =?= m+m: identical
+m >= m for all: ok
+m < m for none: ok
+symmpart(m) + skewpart(m) == m: ok; determinant(): ok
+diagnosing replTmat(x,i,j,v): nargs()= 3; missing (i,j) = (0,1)
+'sub-optimal sparse 'x[i] <- v' assignment: Coercing class dtTMatrix to dgTMatrix
+as(<triangular (ge)matrix>, dtTMatrix): valid: TRUE
+> stopifnot(is(T, "triangularMatrix"), identical(T[,3], c(10,10,10,0,0)))
+>
+> M <- m2; M[1,] <- 0 ; M ; assert.EQ.mat(M, diag(c(0,rep(1,4))), tol=0)
+5 x 5 sparse Matrix of class "dtCMatrix"
+
+[1,] . . . . .
+[2,] . 1 . . .
+[3,] . . 1 . .
+[4,] . . . 1 .
+[5,] . . . . 1
+> M <- m2; M[,3] <- 3 ; stopifnot(is(M,"sparseMatrix"), M[,3] == 3)
+> checkMatrix(M)
+ norm(m [5 x 5]) : 1 I F M ok
+ Summary: ok
+as(., "nMatrix") giving full nonzero-pattern: ok
+2*m =?= m+m: identical
+m >= m for all: ok
+m < m for none: ok
+symmpart(m) + skewpart(m) == m: ok; determinant(): ok
+> M <- m2; M[1:3, 3] <- 0 ;M
+5 x 5 sparse Matrix of class "dtCMatrix"
+
+[1,] 1 . . . .
+[2,] . 1 . . .
+[3,] . . . . .
+[4,] . . . 1 .
+[5,] . . . . 1
+> assert.EQ.mat(M, diag(c(1,1, 0, 1,1)), tol=0)
+> T <- m2; T[1:3, 3] <- 10; checkMatrix(T)
+ norm(m [5 x 5]) : 1 I F M ok
+ Summary: ok
+as(., "nMatrix") giving full nonzero-pattern: ok
+2*m =?= m+m: identical
+m >= m for all: ok
+m < m for none: ok
+symmpart(m) + skewpart(m) == m: ok; determinant(): ok
+diagnosing replTmat(x,i,j,v): nargs()= 3; missing (i,j) = (0,1)
+'sub-optimal sparse 'x[i] <- v' assignment: Coercing class dtTMatrix to dgTMatrix
+as(<triangular (ge)matrix>, dtCMatrix): valid: TRUE
+> stopifnot(is(T, "dtCMatrix"), identical(T[,3], c(10,10,10,0,0)))
+> showProc.time()
+Time elapsed: 2.196 0.016 2.219
+>
+>
+> ## "Vector indices" -------------------
+> .iniDiag.example <- expression({
++ D <- Diagonal(6)
++ M <- as(D,"dgeMatrix")
++ m <- as(D,"matrix")
++ s <- as(D,"TsparseMatrix")
++ S <- as(s,"CsparseMatrix")
++ })
+> eval(.iniDiag.example)
+> i <- c(3,1,6); v <- c(10,15,20)
+> ## (logical,value) which both are recycled:
+> L <- c(TRUE, rep(FALSE,8)) ; z <- c(50,99)
+>
+> ## vector subassignment, both with integer & logical
+> ## these now work correctly {though not very efficiently; hence warnings}
+> m[i] <- v # the role model: only first column is affected
+> M[i] <- v; assert.EQ.mat(M,m) # dge
+> D[i] <- v; assert.EQ.mat(D,m) # ddi -> dtT -> dgT
+diagnosing replTmat(x,i,j,v): nargs()= 3; missing (i,j) = (0,1)
+'sub-optimal sparse 'x[i] <- v' assignment: Coercing class dtTMatrix to dgTMatrix
+> s[i] <- v; assert.EQ.mat(s,m) # dtT -> dgT
+diagnosing replTmat(x,i,j,v): nargs()= 3; missing (i,j) = (0,1)
+'sub-optimal sparse 'x[i] <- v' assignment: Coercing class dtTMatrix to dgTMatrix
+> S[i] <- v; assert.EQ.mat(S,m); S # dtC -> dtT -> dgT -> dgC
+diagnosing replTmat(x,i,j,v): nargs()= 3; missing (i,j) = (0,1)
+'sub-optimal sparse 'x[i] <- v' assignment: Coercing class dtTMatrix to dgTMatrix
+6 x 6 sparse Matrix of class "dgCMatrix"
+
+[1,] 15 . . . . .
+[2,] . 1 . . . .
+[3,] 10 . 1 . . .
+[4,] . . . 1 . .
+[5,] . . . . 1 .
+[6,] 20 . . . . 1
+> stopifnot(Q.C.identical(D,s, checkClass=FALSE))
+> ## logical
+> eval(.iniDiag.example)
+> m[L] <- z
+> M[L] <- z; assert.EQ.mat(M,m)
+> D[L] <- z; assert.EQ.mat(D,m)
+diagnosing replTmat(x,i,j,v): nargs()= 3; missing (i,j) = (0,1)
+'sub-optimal sparse 'x[i] <- v' assignment: Coercing class dtTMatrix to dgTMatrix
+> s[L] <- z; assert.EQ.mat(s,m)
+diagnosing replTmat(x,i,j,v): nargs()= 3; missing (i,j) = (0,1)
+'sub-optimal sparse 'x[i] <- v' assignment: Coercing class dtTMatrix to dgTMatrix
+> S[L] <- z; assert.EQ.mat(S,m) ; S
+diagnosing replTmat(x,i,j,v): nargs()= 3; missing (i,j) = (0,1)
+'sub-optimal sparse 'x[i] <- v' assignment: Coercing class dtTMatrix to dgTMatrix
+6 x 6 sparse Matrix of class "dgCMatrix"
+
+[1,] 50 . . 50 . .
+[2,] . 1 . . . .
+[3,] . . 1 . . .
+[4,] . 99 . 1 99 .
+[5,] . . . . 1 .
+[6,] . . . . . 1
+>
+> ## indexing [i] vs [i,] --- now ok
+> eval(.iniDiag.example)
+> stopifnot(identical5(m[i], M[i], D[i], s[i], S[i]))
+> stopifnot(identical5(m[L], M[L], D[L], s[L], S[L]))
+<sparse>[ <logic> ] : .M.sub.i.logical() maybe inefficient
+<sparse>[ <logic> ] : .M.sub.i.logical() maybe inefficient
+<sparse>[ <logic> ] : .M.sub.i.logical() maybe inefficient
+> ## bordercase ' drop = .' *vector* indexing {failed till 2009-04-..)
+> stopifnot(identical5(m[i,drop=FALSE], M[i,drop=FALSE], D[i,drop=FALSE],
++ s[i,drop=FALSE], S[i,drop=FALSE]))
+> stopifnot(identical5(m[L,drop=FALSE], M[L,drop=FALSE], D[L,drop=FALSE],
++ s[L,drop=FALSE], S[L,drop=FALSE]))
+> ## using L for row-indexing should give an error
+> assertError(m[L,]); assertError(m[L,, drop=FALSE])
+> ## these did not signal an error, upto (including) 0.999375-30:
+> assertError(s[L,]); assertError(s[L,, drop=FALSE])
+> assertError(S[L,]); assertError(S[L,, drop=FALSE])
+>
+> ## row indexing:
+> assert.EQ.mat(D[i,], m[i,])
+> assert.EQ.mat(M[i,], m[i,])
+> assert.EQ.mat(s[i,], m[i,])
+> assert.EQ.mat(S[i,], m[i,])
+> ## column indexing:
+> assert.EQ.mat(D[,i], m[,i])
+> assert.EQ.mat(M[,i], m[,i])
+> assert.EQ.mat(s[,i], m[,i])
+> assert.EQ.mat(S[,i], m[,i])
+>
+>
+> ## --- negative indices ----------
+> mc <- mC[1:5, 1:7]
+> mt <- mT[1:5, 1:7]
+> ## sub matrix
+> assert.EQ.mat(mC[1:2, 0:3], mm[1:2, 0:3]) # test 0-index
+> stopifnot(identical(mc[-(3:5), 0:2], mC[1:2, 0:2]),
++ identical(mt[-(3:5), 0:2], mT[1:2, 0:2]),
++ identical(mC[2:3, 4], mm[2:3, 4]))
+> assert.EQ.mat(mC[1:2,], mm[1:2,])
+> ## sub vector
+> stopifnot(identical4(mc[-(1:4), ], mC[5, 1:7],
++ mt[-(1:4), ], mT[5, 1:7]))
+> stopifnot(identical4(mc[-(1:4), -(2:4)], mC[5, c(1,5:7)],
++ mt[-(1:4), -(2:4)], mT[5, c(1,5:7)]))
+>
+> ## mixing of negative and positive must give error
+> assertError(mT[-1:1,])
+> showProc.time()
+Time elapsed: 0.284 0.004 0.288
+>
+> ## Sub *Assignment* ---- now works (partially):
+> mt0 <- mt
+> nt <- as(mt, "nMatrix")
+> mt[1, 4] <- -99
+> mt[2:3, 1:6] <- 0
+> mt
+5 x 7 sparse Matrix of class "dgTMatrix"
+ c1 c2 c3 c4 c5 c6 c7
+r1 . . . -99 . . 241
+r2 . . . . . . .
+r3 . . . . . . 243
+r4 . . . . . . .
+r5 . 45 . . . . .
+> m2 <- mt+mt
+> m2[1,4] <- -200
+> m2[c(1,3), c(5:6,2)] <- 1:6
+> stopifnot(m2[1,4] == -200,
++ as.vector(m2[c(1,3), c(5:6,2)]) == 1:6)
+> mt[,3] <- 30
+> mt[2:3,] <- 250
+> mt[1:5 %% 2 == 1, 3] <- 0
+> mt[3:1, 1:7 > 5] <- 0
+> mt
+5 x 7 sparse Matrix of class "dgTMatrix"
+ c1 c2 c3 c4 c5 c6 c7
+r1 . . . -99 . . .
+r2 250 250 250 250 250 . .
+r3 250 250 . 250 250 . .
+r4 . . 30 . . . .
+r5 . 45 . . . . .
+>
+> tt <- as(mt,"matrix")
+> ii <- c(0,2,5)
+> jj <- c(2:3,5)
+> tt[ii, jj] <- 1:6 # 0 is just "dropped"
+> mt[ii, jj] <- 1:6
+> assert.EQ.mat(mt, tt)
+>
+> mt[1:5, 2:6]
+5 x 5 sparse Matrix of class "dgTMatrix"
+ c2 c3 c4 c5 c6
+r1 . . -99 . .
+r2 1 3 250 5 .
+r3 250 . 250 250 .
+r4 . 30 . . .
+r5 2 4 . 6 .
+> as((mt0 - mt)[1:5,], "dsparseMatrix")# [1,5] and lines 2:3
+5 x 7 sparse Matrix of class "dgCMatrix"
+ c1 c2 c3 c4 c5 c6 c7
+r1 . . . 220 . . 241
+r2 -250 41 -3 -250 -5 202 .
+r3 -247 -250 . -250 -250 . 243
+r4 . . -30 . . . .
+r5 . 43 -4 . -6 . .
+>
+> mt[c(2,4), ] <- 0; stopifnot(as(mt[c(2,4), ],"matrix") == 0)
+> mt[2:3, 4:7] <- 33
+> checkMatrix(mt)
+ norm(m [5 x 7]) : 1 I F M ok
+ Summary: ok
+as(., "nMatrix") giving full nonzero-pattern: ok
+2*m =?= m+m: ok
+m >= m for all: ok
+m < m for none: ok
+> mt
+5 x 7 sparse Matrix of class "dgTMatrix"
+ c1 c2 c3 c4 c5 c6 c7
+r1 . . . -99 . . .
+r2 . . . 33 33 33 33
+r3 250 250 . 33 33 33 33
+r4 . . . . . . .
+r5 . 2 4 . 6 . .
+>
+> mc[1,4] <- -99 ; stopifnot(mc[1,4] == -99)
+> mc[1,4] <- 00 ; stopifnot(mc[1,4] == 00)
+> mc[1,4] <- -99 ; stopifnot(mc[1,4] == -99)
+> mc[1:2,4:3] <- 4:1; stopifnot(as.matrix(mc[1:2,4:3]) == 4:1)
+>
+> mc[-1, 3] <- -2:1 # 0 should not be entered; 'value' recycled
+> mt[-1, 3] <- -2:1
+> stopifnot(mc x != 0, mt x != 0,
++ mc[-1,3] == -2:1, mt[-1,3] == -2:1) ## failed earlier
+>
+> mc0 <- mc
+> mt0 <- as(mc0, "TsparseMatrix")
+> m0 <- as(mc0, "matrix")
+> set.seed(1); options(Matrix.verbose = FALSE)
+> for(i in 1:(if(doExtras) 50 else 4)) {
++ mc <- mc0; mt <- mt0 ; m <- m0
++ ev <- 1:5 %% 2 == round(runif(1))# 0 or 1
++ j <- sample(ncol(mc), 1 + round(runif(1)))
++ nv <- rpois(sum(ev) * length(j), lambda = 1)
++ mc[ev, j] <- nv
++ m[ev, j] <- nv
++ mt[ev, j] <- nv
++ if(i %% 10 == 1) print(mc[ev,j, drop = FALSE])
++ stopifnot(as.vector(mc[ev, j]) == nv, ## failed earlier...
++ as.vector(mt[ev, j]) == nv)
++ validObject(mc) ; assert.EQ.mat(mc, m)
++ validObject(mt) ; assert.EQ.mat(mt, m)
++ }
+2 x 1 sparse Matrix of class "dgCMatrix"
+ c5
+r2 2
+r4 .
+> showProc.time()
+Time elapsed: 0.584 0.004 0.59
+> options(Matrix.verbose = TRUE)
+>
+> mc # no longer has non-structural zeros
+5 x 7 sparse Matrix of class "dgCMatrix"
+ c1 c2 c3 c4 c5 c6 c7
+r1 . . 2 4 . . 241
+r2 . 42 . 3 . 202 .
+r3 3 . -1 . . . 243
+r4 . . 1 . . . .
+r5 . 45 1 . . . .
+> mc[ii, jj] <- 1:6
+> mc[c(2,5), c(3,5)] <- 3.2
+> checkMatrix(mc)
+ norm(m [5 x 7]) : 1 I F M ok
+ Summary: ok
+as(., "nMatrix") giving full nonzero-pattern: ok
+2*m =?= m+m: identical
+m >= m for all: ok
+m < m for none: ok
+> m. <- mc
+> mc[4,] <- 0
+> mc
+5 x 7 sparse Matrix of class "dgCMatrix"
+ c1 c2 c3 c4 c5 c6 c7
+r1 . . 2.0 4 . . 241
+r2 . 1 3.2 3 3.2 202 .
+r3 3 . -1.0 . . . 243
+r4 . . . . . . .
+r5 . 2 3.2 . 3.2 . .
+>
+> S <- as(Diagonal(5),"TsparseMatrix")
+> H <- Hilbert(9)
+> Hc <- as(round(H, 3), "dsCMatrix")# a sparse matrix with no 0 ...
+> (trH <- tril(Hc[1:5, 1:5]))
+5 x 5 sparse Matrix of class "dtCMatrix"
+
+[1,] 1.000 . . . .
+[2,] 0.500 0.333 . . .
+[3,] 0.333 0.250 0.200 . .
+[4,] 0.250 0.200 0.167 0.143 .
+[5,] 0.200 0.167 0.143 0.125 0.111
+> stopifnot(is(trH, "triangularMatrix"), trH uplo == "L",
++ is(S, "triangularMatrix"))
+>
+> ## triangular assignment
+> ## the slick (but inefficient in case of sparse!) way to assign sub-diagonals:
+> ## equivalent to tmp <- `diag<-`(S[,-1], -2:1); S[,-1] <- tmp
+> ## which dispatches to (x="TsparseMatrix", i="missing",j="index", value="replValue")
+> diag(S[,-1]) <- -2:1 # used to give a wrong warning
+M[i,j] <- v : coercing symmetric M[] into non-symmetric
+> S <- as(S,"triangularMatrix")
+> assert.EQ.mat(S, local({s <- diag(5); diag(s[,-1]) <- -2:1; s}))
+>
+> trH[c(1:2,4), c(2:3,5)] <- 0 # gave an *error* upto Jan.2008
+> trH[ lower.tri(trH) ] <- 0 # ditto, because of callNextMethod()
+diagnosing replTmat(x,i,j,v): nargs()= 3; missing (i,j) = (0,1)
+'sub-optimal sparse 'x[i] <- v' assignment: Coercing class dtTMatrix to dgTMatrix
+>
+> m <- Matrix(0+1:28, nrow = 4)
+> m[-3,c(2,4:5,7)] <- m[ 3, 1:4] <- m[1:3, 6] <- 0
+> mT <- as(m, "dgTMatrix")
+> stopifnot(identical(mT[lower.tri(mT)],
++ m [lower.tri(m) ]))
+<sparse>[ <logic> ] : .M.sub.i.logical() maybe inefficient
+> lM <- upper.tri(mT, diag=TRUE)
+> mT[lM] <- 0
+diagnosing replTmat(x,i,j,v): nargs()= 3; missing (i,j) = (0,1)
+> m[lM] <- 0
+> assert.EQ.mat(mT, as(m,"matrix"))
+> mT[lM] <- -1:0
+diagnosing replTmat(x,i,j,v): nargs()= 3; missing (i,j) = (0,1)
+> m[lM] <- -1:0
+> assert.EQ.mat(mT, as(m,"matrix"))
+> (mT <- drop0(mT))
+4 x 7 sparse Matrix of class "dgCMatrix"
+
+[1,] -1 . . -1 -1 -1 -1
+[2,] 2 -1 -1 . . . .
+[3,] . . . -1 -1 -1 -1
+[4,] 4 . 12 . . . .
+>
+> i <- c(1:2, 4, 6:7); j <- c(2:4,6)
+> H[i,j] <- 0
+> (H. <- round(as(H, "sparseMatrix"), 3)[ , 2:7])
+9 x 6 sparse Matrix of class "dgCMatrix"
+
+ [1,] . . . 0.200 . 0.143
+ [2,] . . . 0.167 . 0.125
+ [3,] 0.250 0.200 0.167 0.143 0.125 0.111
+ [4,] . . . 0.125 . 0.100
+ [5,] 0.167 0.143 0.125 0.111 0.100 0.091
+ [6,] . . . 0.100 . 0.083
+ [7,] . . . 0.091 . 0.077
+ [8,] 0.111 0.100 0.091 0.083 0.077 0.071
+ [9,] 0.100 0.091 0.083 0.077 0.071 0.067
+> Hc. <- Hc
+> Hc.[i,j] <- 0 ## now "works", but setting "non-structural" 0s
+> stopifnot(as.matrix(Hc.[i,j]) == 0)
+> Hc.[, 1:6]
+9 x 6 sparse Matrix of class "dgCMatrix"
+
+ [1,] 1.000 . . . 0.200 .
+ [2,] 0.500 . . . 0.167 .
+ [3,] 0.333 0.250 0.200 0.167 0.143 0.125
+ [4,] 0.250 . . . 0.125 .
+ [5,] 0.200 0.167 0.143 0.125 0.111 0.100
+ [6,] 0.167 . . . 0.100 .
+ [7,] 0.143 . . . 0.091 .
+ [8,] 0.125 0.111 0.100 0.091 0.083 0.077
+ [9,] 0.111 0.100 0.091 0.083 0.077 0.071
+>
+> ## an example that failed for a long time
+> sy3 <- new("dsyMatrix", Dim = as.integer(c(2, 2)), x = c(14, -1, 2, -7))
+> checkMatrix(dm <- kronecker(Diagonal(2), sy3))# now sparse with new kronecker
+Note: Method with signature "sparseMatrix#ANY" chosen for function "kronecker",
+ target signature "dtTMatrix#dsyMatrix".
+ "ANY#Matrix" would also be valid
+ norm(m [4 x 4]) : 1 I F M ok
+ Summary: ok
+as(., "nMatrix") giving full nonzero-pattern: ok
+2*m =?= m+m: ok
+m >= m for all: ok
+m < m for none: ok
+symmpart(m) + skewpart(m) == m: ok; determinant(): ok
+> dm <- Matrix(as.matrix(dm))# -> "dsyMatrix"
+> (s2 <- as(dm, "sparseMatrix"))
+4 x 4 sparse Matrix of class "dsCMatrix"
+
+[1,] 14 2 . .
+[2,] 2 -7 . .
+[3,] . . 14 2
+[4,] . . 2 -7
+> checkMatrix(st <- as(s2, "TsparseMatrix"))
+ norm(m [4 x 4]) : 1 I F M ok
+ Summary: ok
+as(., "nMatrix") giving full nonzero-pattern: ok
+2*m =?= m+m: suboptimal 'Arith' implementation of 'dsC* o dsC*'
+identical
+m >= m for all: ok
+m < m for none: ok
+symmpart(m) + skewpart(m) == m: suboptimal 'Arith' implementation of 'dsC* o dsC*'
+ok; determinant(): ok
+> stopifnot(is(s2, "symmetricMatrix"),
++ is(st, "symmetricMatrix"))
+> checkMatrix(s.32 <- st[1:3,1:2]) ## 3 x 2 - and *not* dsTMatrix
+ norm(m [3 x 2]) : 1 I F M ok
+ Summary: ok
+as(., "nMatrix") giving full nonzero-pattern: ok
+2*m =?= m+m: ok
+m >= m for all: ok
+m < m for none: ok
+> checkMatrix(s2.32 <- s2[1:3,1:2])
+ norm(m [3 x 2]) : 1 I F M ok
+ Summary: ok
+as(., "nMatrix") giving full nonzero-pattern: ok
+2*m =?= m+m: identical
+m >= m for all: ok
+m < m for none: ok
+> I <- c(1,4:3)
+> stopifnot(is(s2.32, "generalMatrix"),
++ is(s.32, "generalMatrix"),
++ identical(as.mat(s.32), as.mat(s2.32)),
++ identical3(dm[1:3,-1], asD(s2[1:3,-1]), asD(st[1:3,-1])),
++ identical4(2, dm[4,3], s2[4,3], st[4,3]),
++ identical3(diag(dm), diag(s2), diag(st)),
++ is((cI <- s2[I,I]), "dsCMatrix"),
++ is((tI <- st[I,I]), "dsTMatrix"),
++ identical4(as.mat(dm)[I,I], as.mat(dm[I,I]), as.mat(tI), as.mat(cI))
++ )
+>
+> ## now sub-assign and check for consistency
+> ## symmetric subassign should keep symmetry
+> st[I,I] <- 0; checkMatrix(st); stopifnot(is(st,"symmetricMatrix"))
+ norm(m [4 x 4]) : 1 I F M ok
+ Summary: ok
+as(., "nMatrix") giving full nonzero-pattern: ok
+2*m =?= m+m: suboptimal 'Arith' implementation of 'dsC* o dsC*'
+identical
+m >= m for all: ok
+m < m for none: ok
+symmpart(m) + skewpart(m) == m: suboptimal 'Arith' implementation of 'dsC* o dsC*'
+ok; determinant(): ok
+> s2[I,I] <- 0; checkMatrix(s2); stopifnot(is(s2,"symmetricMatrix"))
+ norm(m [4 x 4]) : 1 I F M ok
+ Summary: ok
+as(., "nMatrix") giving full nonzero-pattern: ok
+2*m =?= m+m: suboptimal 'Arith' implementation of 'dsC* o dsC*'
+identical
+m >= m for all: ok
+m < m for none: ok
+symmpart(m) + skewpart(m) == m: suboptimal 'Arith' implementation of 'dsC* o dsC*'
+ok; determinant(): ok
+> ##
+> m <- as.mat(st)
+> m[2:1,2:1] <- 4:1
+> st[2:1,2:1] <- 4:1
+M[i,j] <- v : coercing symmetric M[] into non-symmetric
+> s2[2:1,2:1] <- 4:1
+> stopifnot(identical(m, as.mat(st)),
++ 1:4 == as.vector(s2[1:2,1:2]),
++ identical(m, as.mat(s2)))
+>
+> ## now a slightly different situation for 's2' (had bug)
+> s2 <- as(dm, "sparseMatrix")
+> s2[I,I] <- 0; diag(s2)[2:3] <- -(1:2)
+> stopifnot(is(s2,"symmetricMatrix"), diag(s2) == c(0:-2,0))
+> t2 <- as(s2, "TsparseMatrix")
+> m <- as.mat(s2)
+> s2[2:1,2:1] <- 4:1
+> t2[2:1,2:1] <- 4:1
+M[i,j] <- v : coercing symmetric M[] into non-symmetric
+> m[2:1,2:1] <- 4:1
+> assert.EQ.mat(t2, m)
+> assert.EQ.mat(s2, m)
+> ## and the same (for a different s2 !)
+> s2[2:1,2:1] <- 4:1
+> t2[2:1,2:1] <- 4:1
+> assert.EQ.mat(t2, m)# ok
+> assert.EQ.mat(s2, m)# failed in 0.9975-8
+> showProc.time()
+Time elapsed: 2.536 0.016 2.562
+>
+>
+> ## m[cbind(i,j)] <- value: (2-column matrix subassignment):
+> m.[ cbind(3:5, 1:3) ] <- 1:3
+> stopifnot(m.[3,1] == 1, m.[4,2] == 2)
+> nt. <- nt ; nt[rbind(2:3, 3:4, c(3,3))] <- FALSE
+> s. <- m. ; m.[cbind(3,4:6)] <- 0 ## assigning 0 where there *is* 0 ..
+> stopifnot(identical(nt.,nt), ## should not have changed
++ identical(s., m.))
+> x.x[ cbind(2:6, 2:6)] <- 12:16
+> stopifnot(isValid(x.x, "dsCMatrix"),
++ 12:16 == as.mat(x.x)[cbind(2:6, 2:6)])
+> (ne1 <- (mc - m.) != 0)
+5 x 7 sparse Matrix of class "lgCMatrix"
+ c1 c2 c3 c4 c5 c6 c7
+r1 . . : : . . :
+r2 . : : : : : .
+r3 | . : . . . :
+r4 . | | . . . .
+r5 . : | . : . .
+> stopifnot(identical(ne1, 0 != abs(mc - m.)))
+> (ge <- m. >= mc) # contains "=" -> result is dense
+5 x 7 Matrix of class "lgeMatrix"
+ c1 c2 c3 c4 c5 c6 c7
+r1 TRUE TRUE TRUE TRUE TRUE TRUE TRUE
+r2 TRUE TRUE TRUE TRUE TRUE TRUE TRUE
+r3 FALSE TRUE TRUE TRUE TRUE TRUE TRUE
+r4 TRUE TRUE TRUE TRUE TRUE TRUE TRUE
+r5 TRUE TRUE FALSE TRUE TRUE TRUE TRUE
+> ne. <- mc != m. # was wrong (+ warning)
+> stopifnot(identical(!(m. < mc), m. >= mc),
++ identical(m. < mc, as(!ge, "sparseMatrix")),
++ identical(ne., drop0(ne1)))
+>
+> d6 <- Diagonal(6)
+> ii <- c(1:2, 4:5)
+> d6[cbind(ii,ii)] <- 7*ii
+> stopifnot(is(d6, "ddiMatrix"), identical(d6, Diagonal(x=c(7*1:2,1,7*4:5,1))))
+>
+> for(j in 3:6) { ## even and odd j used to behave differently
++ M <- Matrix(0, j,j); m <- matrix(0, j,j)
++ T <- as(M, "TsparseMatrix")
++ TG <- as(T, "generalMatrix")
++ G <- as(M, "generalMatrix")
++ id <- cbind(1:j,1:j)
++ i2 <- cbind(1:j,j:1)
++ m[id] <- 1:j
++ M[id] <- 1:j ; stopifnot(is(M,"symmetricMatrix"))
++ T[id] <- 1:j ; stopifnot(is(T,"symmetricMatrix"))
++ G[id] <- 1:j
++ TG[id]<- 1:j
++ m[i2] <- 10
++ M[i2] <- 10 ; stopifnot(is(M,"symmetricMatrix"))
++ T[i2] <- 10 ; stopifnot(is(T,"symmetricMatrix"))
++ G[i2] <- 10
++ TG[i2]<- 10
++ ##
++ assert.EQ.mat(M, m)
++ assert.EQ.mat(T, m)
++ assert.EQ.mat(G, m)
++ assert.EQ.mat(TG,m)
++ }
+>
+>
+> ## drop, triangular, ...
+> (M3 <- Matrix(upper.tri(matrix(, 3, 3)))) # ltC; indexing used to fail
+3 x 3 sparse Matrix of class "ltCMatrix"
+
+[1,] . | |
+[2,] . . |
+[3,] . . .
+> T3 <- as(M3, "TsparseMatrix")
+> stopifnot(identical(drop(M3), M3),
++ identical4(drop(M3[,2, drop = FALSE]), M3[,2, drop = TRUE],
++ drop(T3[,2, drop = FALSE]), T3[,2, drop = TRUE]),
++ is(T3, "triangularMatrix"),
++ !is(T3[,2, drop=FALSE], "triangularMatrix")
++ )
+>
+> (T6 <- as(as(kronecker(Matrix(c(0,0,1,0),2,2), t(T3)), "lMatrix"),
++ "triangularMatrix"))
+6 x 6 sparse Matrix of class "ltTMatrix"
+
+[1,] . . . . . .
+[2,] . . . | . .
+[3,] . . . | | .
+[4,] . . . . . .
+[5,] . . . . . .
+[6,] . . . . . .
+> T6[1:4, -(1:3)] # failed (trying to coerce back to ltTMatrix)
+4 x 3 sparse Matrix of class "lgTMatrix"
+
+[1,] . . .
+[2,] | . .
+[3,] | | .
+[4,] . . .
+> stopifnot(identical(T6[1:4, -(1:3)][2:3, -3],
++ spMatrix(2,2, i=c(1,2,2), j=c(1,1,2), x=rep(TRUE,3))))
+>
+> M <- Diagonal(4); M[1,2] <- 2
+> M. <- as(M, "CsparseMatrix")
+> (R <- as(M., "RsparseMatrix"))
+4 x 4 sparse Matrix of class "dtRMatrix" (unitriangular)
+
+[1,] 1 2 . .
+[2,] . 1 . .
+[3,] . . 1 .
+[4,] . . . 1
+> (Ms <- symmpart(M.))
+4 x 4 sparse Matrix of class "dsCMatrix"
+
+[1,] 1 1 . .
+[2,] 1 1 . .
+[3,] . . 1 .
+[4,] . . . 1
+> Rs <- as(Ms, "RsparseMatrix")
+> stopifnot(isValid(M, "triangularMatrix"),
++ isValid(M.,"triangularMatrix"),
++ isValid(Ms, "dsCMatrix"),
++ isValid(R, "dtRMatrix"),
++ isValid(Rs, "dsRMatrix") )
+> stopifnot(dim(M[2:3, FALSE]) == c(2,0),
++ dim(R[2:3, FALSE]) == c(2,0),
++ identical(M [2:3,TRUE], M [2:3,]),
++ identical(M.[2:3,TRUE], M.[2:3,]),
++ identical(R [2:3,TRUE], R [2:3,]),
++ dim(R[FALSE, FALSE]) == c(0,0))
+>
+> n <- 50000L
+> Lrg <- new("dgTMatrix", Dim = c(n,n))
+> diag(Lrg) <- 1:n
+> dLrg <- as(Lrg, "diagonalMatrix")
+> stopifnot(identical(Diagonal(x = 1:n), dLrg))
+> diag(dLrg) <- 1 + diag(dLrg)
+> Clrg <- as(Lrg,"CsparseMatrix")
+> Ctrg <- as(Clrg, "triangularMatrix")
+> diag(Ctrg) <- 1 + diag(Ctrg)
+> stopifnot(identical(Diagonal(x = 1+ 1:n), dLrg),
++ identical(Ctrg, as(dLrg,"CsparseMatrix")))
+>
+> cc <- capture.output(show(dLrg))# show(<diag>) used to error for large n
+> showProc.time()
+Time elapsed: 2.521 0.016 2.545
+>
+> ## Large Matrix indexing / subassignment
+> ## ------------------------------------- (from ex. by Imran Rashid)
+> n <- 7000000
+> m <- 100000
+> nnz <- 20000
+>
+> set.seed(12)
+> f <- sparseMatrix(i = sample(n, size=nnz, replace=TRUE),
++ j = sample(m, size=nnz, replace=TRUE))
+> str(f)
+Formal class 'ngCMatrix' [package "Matrix"] with 5 slots
+ ..@ i : int [1:20000] 6692226 4657233 4490801 3688935 344371 6380246 2797160 3584813 6553304 2327896 ...
+ ..@ p : int [1:99993] 0 1 1 1 1 1 1 1 1 1 ...
+ ..@ Dim : int [1:2] 6999863 99992
+ ..@ Dimnames:List of 2
+ .. ..$ : NULL
+ .. ..$ : NULL
+ ..@ factors : list()
+> dim(f) # 6999863 x 99992
+[1] 6999863 99992
+> prod(dim(f)) # 699930301096 == 699'930'301'096 (~ 700'000 millions)
+[1] 699930301096
+> str(thisCol <- f[,5000])# logi [~ 7 mio....]
+ logi [1:6999863] FALSE FALSE FALSE FALSE FALSE FALSE ...
+> sv <- as(thisCol, "sparseVector")
+> str(sv) ## "empty" !
+Formal class 'lsparseVector' [package "Matrix"] with 3 slots
+ ..@ x : logi(0)
+ ..@ length: int 6999863
+ ..@ i : int(0)
+> validObject(spCol <- f[,5000, drop=FALSE])
+[1] TRUE
+> ##
+> ## *not* identical(): as(spCol, "sparseVector")@length is "double"prec:
+> stopifnot(all.equal(as(spCol, "sparseVector"),
++ as(sv, "nsparseVector"), tol=0))
+> if(doExtras) {#-----------------------------------------------------------------
++ f[,5762] <- thisCol # now "fine" <<<<<<<<<< FIXME uses LARGE objects -- slow --
++ ## is using replCmat() in ../R/Csparse.R, then
++ ## replTmat() in ../R/Tsparse.R
++
++ fx <- sparseMatrix(i = sample(n, size=nnz, replace=TRUE),
++ j = sample(m, size=nnz, replace=TRUE),
++ x = round(10*rnorm(nnz)))
++ class(fx)## dgCMatrix
++ fx[,6000] <- (tC <- rep(thisCol, length=nrow(fx)))# slow (as above)
++ thCol <- fx[,2000]
++ fx[,5762] <- thCol# slow
++ stopifnot(is(f, "ngCMatrix"), is(fx, "dgCMatrix"),
++ identical(thisCol, f[,5762]),# perfect
++ identical(as.logical(fx[,6000]), tC),
++ identical(thCol, fx[,5762]))
++
++ showProc.time()
++ ##
++ cat("checkMatrix() of all: \n---------\n")
++ Sys.setlocale("LC_COLLATE", "C")# to keep ls() reproducible
++ for(nm in ls()) if(is(.m <- get(nm), "Matrix")) {
++ cat(nm, "\n")
++ checkMatrix(.m, verbose = FALSE)
++ }
++ showProc.time()
++ }#--------------end if(doExtras) -----------------------------------------------
+>
+> if(!interactive()) warnings()
+NULL
+>
+> proc.time()
+ user system elapsed
+ 18.997 0.384 19.439
diff --git a/win32/deps/library/Matrix/tests/matprod.R b/win32/deps/library/Matrix/tests/matprod.R
new file mode 100644
index 0000000..5890cc7
--- /dev/null
+++ b/win32/deps/library/Matrix/tests/matprod.R
@@ -0,0 +1,435 @@
+library(Matrix)
+
+### Matrix Products including cross products
+
+source(system.file("test-tools.R", package = "Matrix"))
+
+### dimnames -- notably for matrix products
+## from ../R/Auxiliaries.R :
+.M.DN <- function(x) if(!is.null(dn <- dimnames(x))) dn else list(NULL,NULL)
+dnIdentical <- function(x,y) identical(.M.DN(x), .M.DN(y))
+chkDnProd <- function(m, M = Matrix(m), browse=FALSE) {
+ ## TODO:
+ ## if(browse) stopifnot <- f.unction(...) such that it enters browser()..
+ stopifnot(is.matrix(m), is(M, "Matrix"))
+ ## m is n x d (say)
+
+ p1 <- (tm <- t(m)) %*% m ## d x d
+ p1. <- crossprod(m)
+ stopifnot(dnIdentical(p1, p1.))
+
+ t1 <- m %*% tm ## n x n
+ t1. <- tcrossprod(m)
+ stopifnot(dnIdentical(t1, t1.))
+
+ ## Now the "Matrix" ones -- should match the "matrix" above
+ M0 <- M
+ cat("sparse: ")
+ for(sparse in c(TRUE, FALSE)) {
+ cat(sparse, "; ")
+ M <- as(M0, if(sparse)"sparseMatrix" else "denseMatrix")
+ P1 <- (tM <- t(M)) %*% M
+ P1. <- crossprod(M)
+ stopifnot(dnIdentical(P1, P1.), dnIdentical(P1, p1),
+ dnIdentical(P1., crossprod(M,M)),
+ dnIdentical(P1., crossprod(M,m)),
+ dnIdentical(P1., crossprod(m,M)))
+
+ ## P1. is "symmetricMatrix" -- semantically "must have" symm.dimnames
+ PP1 <- P1. %*% P1. ## still d x d
+ R <- triu(PP1);r <- as(R,"matrix") # upper - triangular
+ L <- tril(PP1);l <- as(L,"matrix") # lower - triangular
+ stopifnot(isSymmetric(P1.), isSymmetric(PP1),
+ is(L,"triangularMatrix"), is(R,"triangularMatrix"),
+ dnIdentical(PP1, (pp1 <- p1 %*% p1)),
+ dnIdentical(PP1, R),
+ dnIdentical(L, R))
+
+ T1 <- M %*% tM
+ T1. <- tcrossprod(M)
+ stopifnot(dnIdentical(T1, T1.), dnIdentical(T1, t1),
+ dnIdentical(T1., tcrossprod(M,M)),
+ dnIdentical(T1., tcrossprod(M,m)),
+ dnIdentical(T1., tcrossprod(m,M)),
+ dnIdentical(tcrossprod(T1., tM),
+ tcrossprod(t1., tm)),
+ dnIdentical(crossprod(T1., M),
+ crossprod(t1., m)))
+
+ ## Now, *mixing* Matrix x matrix:
+ stopifnot(dnIdentical(tM %*% m, tm %*% M))
+
+ ## Symmetric and Triangular
+ stopifnot(dnIdentical(PP1 %*% tM, pp1 %*% tm),
+ dnIdentical(R %*% tM, r %*% tm),
+ dnIdentical(L %*% tM, L %*% tm))
+ }
+ cat("\n")
+
+
+ invisible(TRUE)
+}
+
+## All these are ok {now, (2012-06-11) also for dense
+(m <- matrix(c(0, 0, 2:0), 3, 5))
+m00 <- m # *no* dimnames
+dimnames(m) <- list(LETTERS[1:3], letters[1:5])
+(m.. <- m) # has *both* dimnames
+m0. <- m.0 <- m..
+dimnames(m0.)[1] <- list(NULL); m0.
+dimnames(m.0)[2] <- list(NULL); m.0
+##
+chkDnProd(m..)
+chkDnProd(m0.)
+chkDnProd(m.0)
+chkDnProd(m00)
+
+
+
+m5 <- 1 + as(diag(-1:4)[-5,], "dgeMatrix")
+## named dimnames:
+dimnames(m5) <- list(Rows= LETTERS[1:5], paste("C", 1:6, sep=""))
+tr5 <- tril(m5[,-6])
+m. <- as(m5, "matrix")
+m5.2 <- local({t5 <- as.matrix(tr5); t5 %*% t5})
+stopifnot(isValid(tr5, "dtrMatrix"),
+ dim(m5) == 5:6,
+ class(cm5 <- crossprod(m5)) == "dpoMatrix")
+assert.EQ.mat(t(m5) %*% m5, as(cm5, "matrix"))
+assert.EQ.mat(tr5.2 <- tr5 %*% tr5, m5.2)
+stopifnot(isValid(tr5.2, "dtrMatrix"),
+ as.vector(rep(1,6) %*% cm5) == colSums(cm5),
+ as.vector(cm5 %*% rep(1,6)) == rowSums(cm5))
+## uni-diagonal dtrMatrix with "wrong" entries in diagonal
+## {the diagonal can be anything: because of diag = "U" it should never be used}:
+tru <- Diagonal(3, x=3); tru[i.lt <- lower.tri(tru, diag=FALSE)] <- c(2,-3,4)
+tru diag <- "U" ; stopifnot(diag(trm <- as.matrix(tru)) == 1)
+## TODO: Also add *upper-triangular* *packed* case !!
+stopifnot((tru %*% tru)[i.lt] ==
+ (trm %*% trm)[i.lt])
+
+## crossprod() with numeric vector RHS and LHS
+## not sensical for tcrossprod() because of 'vec' --> cbind(vec) promotion:
+assert.EQ.mat( crossprod(rep(1,5), m5), rbind( colSums(m5)))
+assert.EQ.mat( crossprod(rep(1,5), m.), rbind( colSums(m5)))
+assert.EQ.mat( crossprod(m5, rep(1,5)), cbind( colSums(m5)))
+assert.EQ.mat( crossprod(m., rep(1,5)), cbind( colSums(m5)))
+
+## classes differ
+tc.m5 <- m5 %*% t(m5) # "dge*", no dimnames (FIXME)
+(tcm5 <- tcrossprod(m5)) # "dpo*" w/ dimnames
+assert.EQ.mat(tc.m5, mm5 <- as(tcm5, "matrix"))
+## tcrossprod(x,y) :
+assert.EQ.mat(tcrossprod(m5, m5), mm5)
+assert.EQ.mat(tcrossprod(m5, m.), mm5)
+assert.EQ.mat(tcrossprod(m., m5), mm5)
+
+M50 <- m5[,FALSE, drop=FALSE]
+M05 <- t(M50)
+s05 <- as(M05, "sparseMatrix")
+s50 <- t(s05)
+assert.EQ.mat(M05, matrix(1, 0,5))
+assert.EQ.mat(M50, matrix(1, 5,0))
+assert.EQ.mat(tcrossprod(M50), tcrossprod(as(M50, "matrix")))
+assert.EQ.mat(tcrossprod(s50), tcrossprod(as(s50, "matrix")))
+assert.EQ.mat( crossprod(s50), crossprod(as(s50, "matrix")))
+stopifnot(identical( crossprod(s50), tcrossprod(s05)),
+ identical( crossprod(s05), tcrossprod(s50)))
+(M00 <- crossprod(M50))## used to fail -> .Call(dgeMatrix_crossprod, x, FALSE)
+stopifnot(identical(M00, tcrossprod(M05)),
+ all(M00 == t(M50) %*% M50), dim(M00) == 0)
+
+## simple cases with 'scalars' treated as 1x1 matrices:
+d <- Matrix(1:5)
+d %*% 2
+10 %*% t(d)
+assertError(3 %*% d) # must give an error , similar to
+assertError(5 %*% as.matrix(d)) # -> error
+
+## right and left "numeric" and "matrix" multiplication:
+(p1 <- m5 %*% c(10, 2:6))
+(p2 <- c(10, 2:5) %*% m5)
+(pd1 <- m5 %*% diag(1:6))
+(pd. <- m5 %*% Diagonal(x = 1:6))
+(pd2 <- diag (10:6) %*% m5)
+(pd..<- Diagonal(x = 10:6) %*% m5)
+stopifnot(dim(crossprod(t(m5))) == c(5,5),
+ c(class(p1),class(p2),class(pd1),class(pd2),
+ class(pd.),class(pd..)) == "dgeMatrix")
+assert.EQ.mat(p1, cbind(c(20,30,33,38,54)))
+assert.EQ.mat(pd1, m. %*% diag(1:6))
+assert.EQ.mat(pd2, diag(10:6) %*% m.)
+assert.EQ.mat(pd., as(pd1,"matrix"))
+assert.EQ.mat(pd..,as(pd2,"matrix"))
+
+## check that 'solve' and '%*%' are inverses
+set.seed(1)
+A <- Matrix(rnorm(25), nc = 5)
+y <- rnorm(5)
+all.equal((A %*% solve(A, y))@x, y)
+Atr <- new("dtrMatrix", Dim = A Dim, x = A x, uplo = "U")
+all.equal((Atr %*% solve(Atr, y))@x, y)
+
+### ------ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+### Sparse Matrix products
+### ------
+## solve() for dtC*
+mc <- round(chol(crossprod(A)), 2)
+B <- A[1:3,] # non-square on purpose
+stopifnot(all.equal(sum(rowSums(B %*% mc)), 5.82424475145))
+assert.EQ.mat(tcrossprod(B, mc), as.matrix(t(tcrossprod(mc, B))))
+
+m <- kronecker(Diagonal(2), mc)
+stopifnot(is(mc, "Cholesky"),
+ is(m, "sparseMatrix"))
+im <- solve(m)
+round(im, 3)
+itm <- solve(t(m))
+iim <- solve(im) # should be ~= 'm' of course
+iitm <- solve(itm)
+I <- Diagonal(nrow(m))
+(del <- c(mean(abs(as.numeric(im %*% m - I))),
+ mean(abs(as.numeric(m %*% im - I))),
+ mean(abs(as.numeric(im - t(itm)))),
+ mean(abs(as.numeric( m - iim))),
+ mean(abs(as.numeric(t(m)- iitm)))))
+stopifnot(is(m, "triangularMatrix"), is(m, "sparseMatrix"),
+ is(im, "dtCMatrix"), is(itm, "dtCMatrix"), is(iitm, "dtCMatrix"),
+ del < 1e-15)
+
+## crossprod(.,.) & tcrossprod(), mixing dense & sparse
+v <- c(0,0,2:0)
+(V <- Matrix(v, 5,1, sparse=TRUE))
+sv <- as(v, "sparseVector")
+a <- as.matrix(A)
+cav <- crossprod(a,v)
+tva <- tcrossprod(v,a)
+assert.EQ.mat(crossprod(A, V), cav) # gave infinite recursion
+assert.EQ.mat(crossprod(A,sv), cav)
+assert.EQ.mat(tcrossprod( sv, A), tva)
+assert.EQ.mat(tcrossprod(t(V),A), tva)
+
+M <- Matrix(0:5, 2,3) ; sM <- as(M, "sparseMatrix"); m <- as(M, "matrix")
+v <- 1:3; v2 <- 2:1
+sv <- as( v, "sparseVector")
+sv2 <- as(v2, "sparseVector")
+tvm <- tcrossprod(v, m)
+assert.EQ.mat(tcrossprod( v, M), tvm)
+assert.EQ.mat(tcrossprod( v,sM), tvm)
+assert.EQ.mat(tcrossprod(sv,sM), tvm)
+assert.EQ.mat(tcrossprod(sv, M), tvm)
+assert.EQ.mat(crossprod(M, sv2), crossprod(m, v2))
+stopifnot(identical(tcrossprod(v, M), v %*% t(M)),
+ identical(tcrossprod(v,sM), v %*% t(sM)),
+ identical(tcrossprod(v, M), crossprod(v, t(M))),
+ identical(tcrossprod(sv,sM), sv %*% t(sM)),
+ identical(crossprod(sM, sv2), t(sM) %*% sv2),
+ identical(crossprod(M, v2), t(M) %*% v2))
+
+## *unit* triangular :
+t1 <- new("dtTMatrix", x= c(3,7), i= 0:1, j=3:2, Dim= as.integer(c(4,4)))
+## from 0-diagonal to unit-diagonal {low-level step}:
+tu <- t1 ; tu diag <- "U"
+cu <- as(tu, "dtCMatrix")
+cl <- t(cu) # unit lower-triangular
+cl10 <- cl %*% Diagonal(4, x=10)
+assert.EQ.mat(cl10, as(cl, "matrix") %*% diag(4, x=10))
+stopifnot(is(cl,"dtCMatrix"), cl diag == "U")
+(cu2 <- cu %*% cu)
+cl2 <- cl %*% cl
+validObject(cl2)
+
+cu3 <- tu[-1,-1]
+assert.EQ.mat(crossprod(tru, cu3),
+ crossprod(trm, as.matrix(cu3)))
+## "FIXME" should return triangular ...
+
+cl2
+cu2. <- Diagonal(4) + Matrix(c(rep(0,9),14,0,0,6,0,0,0), 4,4)
+D4 <- Diagonal(4, x=10:7)
+stopifnot(all(cu2 == cu2.),# was wrong for ver. <= 0.999375-4
+ is(cu2, "dtCMatrix"), is(cl2, "dtCMatrix"), # triangularity preserved
+ cu2 diag == "U", cl2 diag == "U",# UNIT-triangularity preserved
+ all.equal(D4 %*% cu, D4 %*% as.matrix(cu)),
+ all.equal(cu %*% D4, as.matrix(cu) %*% D4),
+ isValid(su <- crossprod(cu), "dsCMatrix"),
+ all(D4 %*% su == D4 %*% as.mat(su)),
+ all(su %*% D4 == as.mat(su) %*% D4),
+ identical(t(cl2), cu2), # !!
+ identical( crossprod(cu), Matrix( crossprod(as.matrix(cu)),sparse=TRUE)),
+ identical(tcrossprod(cu), Matrix(tcrossprod(as.matrix(cu)),sparse=TRUE)))
+tr8 <- kronecker(rbind(c(2,0),c(1,4)), cl2)
+T8 <- tr8 %*% (tr8/2) # triangularity preserved?
+T8.2 <- (T8 %*% T8) / 4
+stopifnot(is(T8, "triangularMatrix"), T8 uplo == "L", is(T8.2, "dtCMatrix"))
+mr8 <- as(tr8,"matrix")
+m8. <- (mr8 %*% mr8 %*% mr8 %*% mr8)/16
+assert.EQ.mat(T8.2, m8.)
+
+data(KNex); mm <- KNex$mm
+M <- mm[1:500, 1:200]
+MT <- as(M, "TsparseMatrix")
+cpr <- t(mm) %*% mm
+cpr. <- crossprod(mm)
+cpr.. <- crossprod(mm, mm)
+stopifnot(is(cpr., "symmetricMatrix"),
+ identical3(cpr, as(cpr., class(cpr)), cpr..))
+## with dimnames:
+m <- Matrix(c(0, 0, 2:0), 3, 5)
+dimnames(m) <- list(LETTERS[1:3], letters[1:5])
+m
+p1 <- t(m) %*% m
+(p1. <- crossprod(m))
+t1 <- m %*% t(m)
+(t1. <- tcrossprod(m))
+stopifnot(isSymmetric(p1.),
+ isSymmetric(t1.),
+ identical(p1, as(p1., class(p1))),
+ identical(t1, as(t1., class(t1))),
+ identical(dimnames(p1), dimnames(p1.)),
+ identical(dimnames(p1), list(colnames(m), colnames(m))),
+ identical(dimnames(t1), dimnames(t1.))
+ )
+
+showMethods("%*%", class=class(M))
+
+v1 <- rep(1, ncol(M))
+str(r <- M %*% Matrix(v1))
+str(rT <- MT %*% Matrix(v1))
+stopifnot(identical(r, rT))
+str(r. <- M %*% as.matrix(v1))
+stopifnot(identical4(r, r., rT, M %*% as(v1, "matrix")))
+
+v2 <- rep(1,nrow(M))
+r2 <- t(Matrix(v2)) %*% M
+r2T <- v2 %*% MT
+str(r2. <- v2 %*% M)
+stopifnot(identical3(r2, r2., t(as(v2, "matrix")) %*% M))
+
+
+## Sparse Cov.matrices from Harri Kiiveri @ CSIRO
+a <- matrix(0,5,5)
+a[1,2] <- a[2,3] <- a[3,4] <- a[4,5] <- 1
+a <- a + t(a) + 2*diag(5)
+b <- as(a, "dsCMatrix") ## ok, but we recommend to use Matrix() ``almost always'' :
+(b. <- Matrix(a, sparse = TRUE))
+stopifnot(identical(b, b.))
+
+## calculate conditional variance matrix ( vars 3 4 5 given 1 2 )
+(B2 <- b[1:2, 1:2])
+bb <- b[1:2, 3:5]
+stopifnot(is(B2, "dsCMatrix"), # symmetric indexing keeps symmetry
+ identical(as.mat(bb), rbind(0, c(1,0,0))),
+ ## TODO: use fully-sparse cholmod_spsolve() based solution :
+ is(z.s <- solve(B2, bb), "sparseMatrix"))
+assert.EQ.mat(B2 %*% z.s, as(bb, "matrix"))
+## -> dense RHS and dense result
+z. <- solve(as(B2, "dgCMatrix"), bb)
+z <- solve( B2, as(bb,"dgeMatrix"))
+stopifnot(identical(z, z.))
+## finish calculating conditional variance matrix
+v <- b[3:5,3:5] - crossprod(bb,z)
+stopifnot(all.equal(as.mat(v),
+ matrix(c(4/3, 1:0, 1,2,1, 0:2), 3), tol = 1e-14))
+
+
+###--- "logical" Matrices : ---------------------
+
+##__ FIXME __ now works for lsparse* and nsparse* but not yet for lge* and nge* !
+
+## Robert's Example, a bit more readable
+fromTo <- rbind(c(2,10),
+ c(3, 9))
+N <- 10
+nrFT <- nrow(fromTo)
+rowi <- rep.int(1:nrFT, fromTo[,2]-fromTo[,1] + 1) - 1:1
+coli <- unlist(lapply(1:nrFT, function(x) fromTo[x,1]:fromTo[x,2])) - 1:1
+
+## "n" --- nonzero pattern Matrices
+sM <- new("ngTMatrix", i = rowi, j=coli, Dim=as.integer(c(N,N)))
+sM # nice
+
+sm <- as(sM, "matrix")
+sM %*% sM
+assert.EQ.mat(sM %*% sM, sm %*% sm)
+assert.EQ.mat(t(sM) %*% sM,
+ (t(sm) %*% sm) > 0, tol=0)
+crossprod(sM)
+tcrossprod(sM)
+stopifnot(identical(as( crossprod(sM), "ngCMatrix"), t(sM) %*% sM),
+ identical(as(tcrossprod(sM), "ngCMatrix"), sM %*% t(sM)))
+
+assert.EQ.mat( crossprod(sM), crossprod(sm) > 0)
+assert.EQ.mat(tcrossprod(sM), as(tcrossprod(sm),"matrix") > 0)
+
+## "l" --- logical Matrices -- use usual 0/1 arithmetic
+nsM <- sM
+sM <- as(sM, "lMatrix")
+sm <- as(sM, "matrix")
+stopifnot(identical(sm, as.matrix(nsM)))
+sM %*% sM
+assert.EQ.mat(sM %*% sM, sm %*% sm)
+assert.EQ.mat(t(sM) %*% sM,
+ t(sm) %*% sm, tol=0)
+crossprod(sM)
+tcrossprod(sM)
+stopifnot(identical( crossprod(sM), as(t(sM) %*% sM, "symmetricMatrix")),
+ identical(tcrossprod(sM), forceSymmetric(sM %*% t(sM))))
+assert.EQ.mat( crossprod(sM), crossprod(sm))
+assert.EQ.mat(tcrossprod(sM), as(tcrossprod(sm),"matrix"))
+
+
+## A sparse example - with *integer* matrix:
+M <- Matrix(cbind(c(1,0,-2,0,0,0,0,0,2.2,0),
+ c(2,0,0,1,0), 0, 0, c(0,0,8,0,0),0))
+t(M)
+(-4:5) %*% M
+stopifnot(as.vector(print(t(M %*% 1:6))) ==
+ c(as(M,"matrix") %*% 1:6))
+(M.M <- crossprod(M))
+MM. <- tcrossprod(M)
+stopifnot(class(MM.) == "dsCMatrix",
+ class(M.M) == "dsCMatrix")
+
+M3 <- Matrix(c(rep(c(2,0),4),3), 3,3, sparse=TRUE)
+I3 <- as(Diagonal(3), "CsparseMatrix")
+m3 <- as.matrix(M3)
+iM3 <- solve(m3)
+stopifnot(all.equal(unname(iM3), matrix(c(3/2,0,-1,0,1/2,0,-1,0,1), 3)))
+assert.EQ.mat(solve(as(M3, "sparseMatrix")), iM3)
+assert.EQ.mat(solve(I3,I3), diag(3))
+assert.EQ.mat(solve(M3, I3), iM3)# was wrong because I3 is unit-diagonal
+assert.EQ.mat(solve(m3, I3), iM3)# gave infinite recursion in (<=) 0.999375-10
+
+isValid(tru %*% I3, "triangularMatrix")
+isValid(crossprod(tru, I3), "triangularMatrix")
+isValid(crossprod(I3, tru), "triangularMatrix")
+isValid(tcrossprod(I3, tru), "triangularMatrix")
+
+## even simpler
+m <- matrix(0, 4,7); m[c(1, 3, 6, 9, 11, 22, 27)] <- 1
+(mm <- Matrix(m))
+(cm <- Matrix(crossprod(m)))
+stopifnot(identical(crossprod(mm), cm))
+(tm1 <- Matrix(tcrossprod(m))) #-> had bug in 'Matrix()' !
+(tm2 <- tcrossprod(mm))
+Im2 <- solve(tm2[-4,-4])
+P <- as(as.integer(c(4,1,3,2)),"pMatrix")
+p <- as(P, "matrix")
+P %*% mm
+assertError(mm %*% P) # dimension mismatch
+assertError(m %*% P) # ditto
+assertError(crossprod(t(mm), P)) # ditto
+stopifnot(isValid(tm1, "dsCMatrix"),
+ all.equal(tm1, tm2, tol=1e-15),
+ identical(drop0(Im2 %*% tm2[1:3,]), Matrix(cbind(diag(3),0))),
+ identical(p, as.matrix(P)),
+ identical(P %*% m, as.matrix(P) %*% m),
+ all(P %*% mm == P %*% m),
+ all(P %*% mm - P %*% m == 0),
+ all(t(mm) %*% P == t(m) %*% P),
+ identical(crossprod(m, P),
+ crossprod(mm, P)),
+ TRUE)
+
+cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''
diff --git a/win32/deps/library/Matrix/tests/matr-exp.R b/win32/deps/library/Matrix/tests/matr-exp.R
new file mode 100644
index 0000000..0666c15
--- /dev/null
+++ b/win32/deps/library/Matrix/tests/matr-exp.R
@@ -0,0 +1,79 @@
+library(Matrix)
+
+## Matrix Exponential
+
+source(system.file("test-tools.R", package = "Matrix"))
+
+## e ^ 0 = 1 - for matrices:
+assert.EQ.mat(expm(Matrix(0, 3,3)), diag(3), tol = 0)# exactly
+## e ^ diag(.) = diag(e ^ .):
+assert.EQ.mat(expm(as(diag(-1:4), "dgeMatrix")), diag(exp(-1:4)))
+set.seed(1)
+rE <- replicate(100,
+ { x <- rlnorm(12)
+ relErr(as(expm(as(diag(x), "dgeMatrix")),
+ "matrix"),
+ diag(exp(x))) })
+stopifnot(mean(rE) < 1e-15,
+ max(rE) < 1e-14)
+summary(rE)
+
+## Some small matrices
+
+m1 <- Matrix(c(1,0,1,1), nc = 2)
+e1 <- expm(m1)
+assert.EQ.mat(e1, cbind(c(exp(1),0), exp(1)))
+
+m2 <- Matrix(c(-49, -64, 24, 31), nc = 2)
+e2 <- expm(m2)
+## The true matrix exponential is 'te2':
+e_1 <- exp(-1)
+e_17 <- exp(-17)
+te2 <- rbind(c(3*e_17 - 2*e_1, -3/2*e_17 + 3/2*e_1),
+ c(4*e_17 - 4*e_1, -2 *e_17 + 3 *e_1))
+assert.EQ.mat(e2, te2, tol = 1e-13)
+## See the (average relative) difference:
+all.equal(as(e2,"matrix"), te2, tol = 0) # 1.48e-14 on "lynne"
+
+## The ``surprising identity'' det(exp(A)) == exp( tr(A) )
+## or log det(exp(A)) == tr(A) :
+stopifnot(all.equal(c(determinant(e2)$modulus), sum(diag(m2))))
+
+## a very simple nilpotent one:
+(m3 <- Matrix(cbind(0,rbind(6*diag(3),0))))# sparse
+stopifnot(all(m3 %*% m3 %*% m3 %*% m3 == 0))# <-- m3 "^" 4 == 0
+e3 <- expm(m3)
+E3 <- expm(Matrix(m3, sparse=FALSE))
+s3 <- symmpart(m3) # dsCMatrix
+es3 <- expm(s3)
+e3. <- rbind(c(1,6,18,36),
+ c(0,1, 6,18),
+ c(0,0, 1, 6),
+ c(0,0, 0, 1))
+stopifnot(is(e3, "triangularMatrix"),
+ is(es3, "symmetricMatrix"),
+ identical(e3, E3),
+ identical(as.mat(e3), e3.),
+ all.equal(as(es3,"generalMatrix"),
+ expm(as(s3,"generalMatrix")))
+ )
+
+
+## This used to be wrong {bug in octave-origin code}:
+M6 <- Matrix(c(0, -2, 0, 0, 0, 0,
+ 10, 0, 0, 0,10,-2,
+ 0, 0, 0, 0,-2, 0,
+ 0, 10,-2,-2,-2,10,
+ 0, 0, 0, 0, 0, 0,
+ 10, 0, 0, 0, 0, 0), 6, 6)
+
+exp.M6 <- expm(M6)
+as(exp.M6, "sparseMatrix")# prints a bit more nicely
+stopifnot(all.equal(t(exp.M6),
+ expm(t(M6)), tol = 1e-12),
+ all.equal(exp.M6[,3], c(0,0,1,0,-2,0), tol = 1e-12),
+ all.equal(exp.M6[,5], c(0,0,0,0, 1,0), tol = 1e-12),
+ all(exp.M6[3:4, c(1:2,5:6)] == 0)
+ )
+
+cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''
diff --git a/win32/deps/library/Matrix/tests/other-pkgs.R b/win32/deps/library/Matrix/tests/other-pkgs.R
new file mode 100644
index 0000000..23b389e
--- /dev/null
+++ b/win32/deps/library/Matrix/tests/other-pkgs.R
@@ -0,0 +1,139 @@
+####--------- Test interfaces to other non-standard Packages ---------------
+
+library(Matrix)
+
+source(system.file("test-tools.R", package = "Matrix"))# identical3() etc
+
+MatrixRversion <- pkgRversion("Matrix")
+
+###-- 1) 'graph' (from Bioconductor) ---------------------------
+###-- == ======= ---------------------------
+## do not run the test "usually" for now [Solaris problem after detach() ..]:
+if((Sys.getenv("USER")=="maechler" || nzchar(Sys.getenv("R_MATRIX_CHECK_EXTRA"))) &&
+ isTRUE(try(require(graph)))) { # may be there and fail (with R-devel)
+
+ if(packageDescription("graph")$Version <= "1.10.2") {
+ ## graph 1.10.x for x <= 2 had too many problems as(<graph>, "matrix")
+ cat("Version of 'graph' is too old --- no tests done here!\n")
+
+ } else if(pkgRversion("graph") != MatrixRversion) {
+
+ cat(sprintf("The R version (%s) of 'graph' installation differs from the Matrix one (%s)\n",
+ pkgRversion("graph"), MatrixRversion))
+
+ } else { ## do things
+
+ pdf("other-pkg-graph.pdf")
+
+ ## 1) undirected
+
+ V <- LETTERS[1:4]
+ edL <- vector("list", length=4)
+ names(edL) <- V
+ ## 1a) unweighted
+ for(i in 1:4)
+ edL[[i]] <- list(edges = 5-i)
+ gR <- new("graphNEL", nodes=V, edgeL=edL)
+ str(edges(gR))
+ sm.g <- as(gR, "sparseMatrix")
+ str(sm.g) ## dgC: TODO: want 'ds.' (symmetric)
+ validObject(sm.g)
+ show( sm.g )## (incl colnames !)
+
+ ## 1b) weighted
+ set.seed(123)
+ for(i in 1:4)
+ edL[[i]] <- list(edges = 5-i, weights=runif(1))
+ gRw <- new("graphNEL", nodes=V, edgeL=edL)
+ str(edgeWeights(gRw))
+ sm.gw <- as(gRw, "sparseMatrix")
+ str(sm.gw) ## *numeric* dgCMatrix
+ validObject(sm.gw)
+ show( sm.gw )## U[0,1] numbers in anti-diagonal
+
+ ## 2) directed
+ gU <- gR; edgemode(gU) <- "directed"
+ sgU <- as(gU, "sparseMatrix")
+ str(sgU) ## 'dgC'
+ validObject(sgU)
+ show( sgU )
+
+ ## Reverse : sparseMatrix -> graph
+ sm.g[1,2] <- 1
+ gmg <- as(sm.g, "graph")
+ validObject(gmg2 <- as(sm.g, "graphNEL"))
+ gmgw <- as(sm.gw, "graph")
+ validObject(gmgw2 <- as(sm.gw, "graphNEL"))
+ gmgU <- as(sgU, "graph")
+ validObject(gmgU2 <- as(sgU, "graphNEL"))
+ stopifnot(identical(gmg, gmg2),
+ identical(gmgw, gmgw2),
+ identical(gmgU, gmgU2))
+
+ data(CAex)
+ cc <- crossprod(CAex)
+ ## work around bug in 'graph': diagonal must be empty:
+ diag(cc) <- 0; cc <- drop0(cc)
+ image(cc)
+ gg <- as(cc, "graph")
+
+ .r <- require# cheat checks - do *not* want it in DESCRIPTION:
+ if(.r("Rgraphviz")) {
+ plot(gg, "circo")
+ detach("package:Rgraphviz", unload = TRUE)
+ }
+ stopifnot(all.equal(edgeMatrix(gg),
+ rbind(from = c(rep(1:24, each=2), 25:48),
+ to = c(rbind(25:48,49:72), 49:72))))
+
+ detach("package:graph", unload = TRUE)
+ dev.off()
+ } # {else}
+
+} ## end{graph}
+
+###-- 2) 'SparseM' ---------------------------------------------
+###-- == ======== ---------------------------------------------
+
+if(isTRUE(try(require(SparseM)))) { # may be there and fail
+
+ if(pkgRversion("SparseM") != MatrixRversion) {
+
+ cat(sprintf("The R version (%s) of 'SparseM' installation differs from the Matrix one (%s)\n",
+ pkgRversion("SparseM"), MatrixRversion))
+
+ } else { ## do things
+
+ set.seed(1)
+ a <- round(rnorm(5*4), 2)
+ a[abs(a) < 0.7] <- 0
+ A <- matrix(a,5,4)
+ print(M <- Matrix(A))
+ stopifnot(
+ validObject(A.csr <- as.matrix.csr(A)),
+ validObject(At.csr <- as.matrix.csr(t(A))),
+ identical(At.csr, t(A.csr)),
+ identical(A, as.matrix(A.csr)),
+ identical(M, as(A.csr, "CsparseMatrix")),
+ identical(t(M), as(At.csr, "CsparseMatrix"))
+ )
+
+ ## More tests, notably for triplets
+ A.coo <- as.matrix.coo(A)
+ str(T <- as(M, "TsparseMatrix")) # has 'j' sorted
+ str(T. <- as(A.coo, "TsparseMatrix")) # has 'i' sorted
+
+ T3 <- as(as(T, "matrix.coo"), "Matrix") # dgT
+ M3 <- as(as(M, "matrix.csr"), "Matrix") # dgC
+ M4 <- as(as(M, "matrix.csc"), "Matrix") # dgC
+ M5 <- as(as(M, "matrix.coo"), "Matrix") # dgT
+ uniqT <- Matrix:::uniqTsparse
+ stopifnot(identical4(uniqT(T), uniqT(T.), uniqT(T3), uniqT(M5)),
+ identical3(M, M3, M4))
+
+ if(FALSE) # detaching the package gives error ".GenericTable" not found
+ detach("package:SparseM")
+
+ }
+
+}## end{SparseM}
diff --git a/win32/deps/library/Matrix/tests/spModel.matrix.R b/win32/deps/library/Matrix/tests/spModel.matrix.R
new file mode 100644
index 0000000..a2407cb
--- /dev/null
+++ b/win32/deps/library/Matrix/tests/spModel.matrix.R
@@ -0,0 +1,190 @@
+library(Matrix)
+
+## This is example(sp....) -- much extended
+
+mEQ <- function(x,y, ...) {
+ ## first drop columns from y which are all 0 :
+ if(any(i0 <- colSums(abs(x)) == 0)) {
+ message(gettextf("x had %d zero-columns", sum(i0)))
+ x <- x[, !i0, drop=FALSE]
+ }
+ if(any(i0 <- colSums(abs(y)) == 0)) {
+ message(gettextf("y had %d zero-columns", sum(i0)))
+ y <- y[, !i0, drop=FALSE]
+ }
+ isTRUE(all.equal(x,y, tol=0, ...))
+}
+
+##' Is sparse.model.matrix() giving the "same" as dense model.matrix() ?
+##'
+##' @return logical
+##' @param frml formula
+##' @param dat data frame
+##' @param showFactors
+##' @param ...
+isEQsparseDense <- function(frml, dat,
+ showFactors = isTRUE(getOption("verboseSparse")), ...)
+{
+ ## Author: Martin Maechler, Date: 21 Jul 2009
+ stopifnot(inherits(frml, "formula"), is.data.frame(dat))
+ if(showFactors)
+ print(attr(terms(frml, data=dat), "factors"))
+ smm <- sparse.model.matrix(frml, dat, ...)
+ mm <- model.matrix(frml, dat, ...)
+ sc <- smm contrasts
+ mEQ(as(smm, "generalMatrix"), Matrix(mm, sparse=TRUE)) &
+ identical(smm assign, attr(mm, "assign")) &
+ (if(is.null(mc <- attr(mm, "contrasts"))) length(sc) == 0 else identical(sc, mc))
+}
+
+### ------------ all the "datasets" we construct for use -------------
+dd <- data.frame(a = gl(3,4), b = gl(4,1,12))# balanced 2-way
+(dd3 <- cbind(dd, c = gl(2,6), d = gl(3,8)))
+dd. <- dd3[- c(1, 13:15, 17), ]
+set.seed(17)
+dd4 <- cbind(dd, c = gl(2,6), d = gl(8,3))
+dd4 <- cbind(dd4, x = round(rnorm(nrow(dd4)), 1))
+dd4 <- dd4[- c(1, 13:15, 17), ]
+##-> 'd' has unused levels
+dM <- dd4
+dM$X <- outer(10*rpois(nrow(dM), 2), 1:3)
+dM$Y <- cbind(pmax(0, dM$x - .3), floor(4*rnorm(nrow(dM))))
+str(dM)# contains *matrices*
+
+options("contrasts") # the default: "contr.treatment"
+op <- options(sparse.colnames = TRUE) # for convenience
+
+stopifnot(identical(## non-sensical, but "should work" (with a warning each):
+ sparse.model.matrix(a~ 1, dd),
+ sparse.model.matrix( ~ 1, dd)))
+sparse.model.matrix(~ a + b, dd, contrasts = list(a="contr.sum"))
+sparse.model.matrix(~ a + b, dd, contrasts = list(b="contr.SAS"))
+xm <- sparse.model.matrix(~ x, dM) # {no warning anymore ...}
+dxm <- Matrix(model.matrix(~ x, dM), sparse=TRUE)
+stopifnot(is(xm, "sparseMatrix"), mEQ(as(xm,"generalMatrix"), dxm))
+
+## Sparse method is equivalent to the traditional one :
+stopifnot(isEQsparseDense(~ a + b, dd),
+ suppressWarnings(isEQsparseDense(~ x, dM)),
+ isEQsparseDense(~ 0 + a + b, dd),
+ identical(sparse.model.matrix(~ 0 + a + b, dd),
+ sparse.model.matrix(~ -1 + a + b, dd)),
+ isEQsparseDense(~ a + b, dd, contrasts = list(a="contr.sum")),
+ isEQsparseDense(~ a + b, dd, contrasts = list(a="contr.SAS")),
+ ## contrasts as *functions* or contrast *matrices* :
+ isEQsparseDense(~ a + b, dd,
+ contrasts = list(a=contr.sum, b=contr.treatment(4))),
+ isEQsparseDense(~ a + b, dd, contrasts =
+ list(a=contr.SAS(3),# << ok after 'contrasts<-' update
+ b = function(n, contr=TRUE, sparse=FALSE)
+ contr.sum(n=n, contr=contr, sparse=sparse))))
+
+sm <- sparse.model.matrix(~a * b, dd,
+ contrasts = list(a= contr.SAS(3, sparse = TRUE)))
+sm
+## FIXME: Move part of this to ../../MatrixModels/tests/
+##stopifnot(all(sm == model.Matrix( ~a * b, dd, contrasts= list(a= contr.SAS(3)))))
+
+##
+stopifnot(isEQsparseDense(~ a + b + c + d, dd.))
+stopifnot(isEQsparseDense(~ a + b:c + c + d, dd.))
+## no intercept -- works too
+stopifnot(isEQsparseDense(~ -1+ a + b + c + d, dd.))
+stopifnot(isEQsparseDense(~ 0 + a + b:c + c + d, dd.))
+
+
+Sparse.model.matrix <- function(...) {
+ s <- sparse.model.matrix(...)
+ as(s, "generalMatrix")# dropping 'assign',.. slots
+}
+##
+dim(mm <- Matrix(model.matrix(~ a + b + c + d, dd4), sparse=TRUE))
+dim(sm <- Sparse.model.matrix(~ a + b + c + d, dd4))
+## was (19 13), when 'drop.unused.levels' was implicitly TRUE
+dim(sm. <- Sparse.model.matrix(~ a + b + c + d, dd4, drop.unused.levels=TRUE))
+stopifnot(mEQ(sm , mm), ## (both have a zero column)
+ mEQ(sm., mm)) ## << that's ok, since mm has all-0 column !
+## look at this :
+all(mm[,"d5"] == 0) ## !!!! --- correct: a column of all 0 <--> dropped level!
+stopifnot(all.equal(sm., mm[, - which("d5" == colnames(mm))])) ## indeed !
+## i.e., sm has just dropped an all zero column --- which it should!
+
+stopifnot(isEQsparseDense(~ 1 + sin(x) + b*c + a:x, dd4, show=TRUE))
+
+stopifnot(isEQsparseDense(~ I(a) + b*c + a:x, dd4, show=TRUE))
+## no intercept -- works too
+stopifnot(isEQsparseDense(~ 0+ I(a) + b*c + a:x, dd4, show=TRUE))
+
+f <- ~ 1 + a + b*c + a*x
+attr(terms(f, data=dd4), "factors")
+dim(mm <- Matrix(model.matrix(f, data=dd4), sparse=TRUE))
+dim(sm <- Sparse.model.matrix(f, data=dd4)) # ==
+stopifnot(mEQ(sm, mm))
+
+f <- ~ a*X + X*Y + a*c
+attr(terms(f, data=dM), "factors")
+dim(mm <- Matrix(model.matrix(f, data=dM), sparse=TRUE))
+dim(sm <- Sparse.model.matrix(f, data=dM, verbose=TRUE))
+stopifnot(mEQ(sm, mm))
+
+## high order
+f <- ~ a:b:X:c:Y
+mm <- Matrix(model.matrix(f, data=dM), sparse=TRUE)
+sm <- Sparse.model.matrix(f, data=dM, verbose=2)
+stopifnot(mEQ(sm, mm))
+
+
+f <- ~ 1 + a + b*c + a*x + b*d*x + b:c:d
+attr(terms(f, data=dd4), "factors")
+dim(mm <- Matrix(model.matrix(f, data=dd4), sparse=TRUE)) ## 19 100
+dim(sm <- Sparse.model.matrix(f, data=dd4)) ## (ditto)
+dim(sm. <- Sparse.model.matrix(f, data=dd4, drop.unused.levels=TRUE)) # 19 88
+stopifnot(mEQ(sm, mm), mEQ(sm., mm))# {32, 32; 20 and 32 zero-columns ..}
+
+## now get a bit courageous:
+##
+
+## stopifnot(isEQsparseDense(~ 1 + c + a:b:d, dat=dd4))
+dim(mm <- Matrix(model.matrix(~ 1 + a + b*c + a:b:c:d, data=dd4),
+ sparse=TRUE)) ## 19 202
+dim(sm <- Sparse.model.matrix(~ 1 + a + b*c + a:b:c:d, data=dd4))
+dim(sm. <- Sparse.model.matrix(~ 1 + a + b*c + a:b:c:d, data=dd4,
+ drop.unused.levels=TRUE))
+stopifnot(mEQ(sm, mm), mEQ(sm., mm))# {173, 173, 149 and 173 zero-columns !}
+
+## stopifnot(isEQsparseDense(~ 1 + a + b*c + a:b:c:d, dat=dd4))
+dim(mm <- Matrix(model.matrix(~ 1 + a + b:c + a:b:d, data=dd4),
+ sparse=TRUE)) ## 19 107
+dim(sm <- Sparse.model.matrix(~ 1 + a + b:c + a:b:d, data=dd4))
+dim(sm. <- Sparse.model.matrix(~ 1 + a + b:c + a:b:d, data=dd4,
+ drop.unused.levels=TRUE))
+stopifnot(mEQ(sm, mm), mEQ(sm., mm))
+
+dim(mm <- Matrix(model.matrix(~ a*b*c +c*d, dd4), sparse=TRUE)) ## 19 38
+dim(sm <- Sparse.model.matrix(~ a*b*c +c*d, dd4))# (ditto)
+dim(sm. <- Sparse.model.matrix(~ a*b*c +c*d, dd4, drop.unused.levels=TRUE))
+stopifnot(mEQ(sm, mm), mEQ(sm., mm))
+
+
+f1 <- ~ (a+b+c+d)^2 + (a+b):c:d + a:b:c:d
+f2 <- ~ (a+b+c+d)^4 - a:b:c - a:b:d
+ mm1 <- Matrix(model.matrix(f1, dd4), sparse=TRUE)
+dim(mm2 <- Matrix(model.matrix(f2, dd4), sparse=TRUE))
+ sm1 <- sparse.model.matrix(f1, dd4)
+dim(sm2 <- sparse.model.matrix(f2, dd4))
+ s.1 <- sparse.model.matrix(f1, dd4, drop.unused.levels=TRUE)
+dim(s.2 <- sparse.model.matrix(f2, dd4, drop.unused.levels=TRUE))
+stopifnot(identical(mm1,mm2),
+ identical(sm1,sm2), identical(s.1,s.2),
+ mEQ(sm1,mm1), mEQ(s.1,mm1))
+
+str(dd <- data.frame(d = gl(10,6), a = ordered(gl(3,20))))
+X. <- sparse.model.matrix(~ a + d, data = dd)
+## failed because of contr.poly default in Matrix 0.999375-33
+stopifnot(dim(X.) == c(60, 12), nnzero(X.) == 234,
+ isEQsparseDense(~ 0 + d + I(as.numeric(d)^2), dd))
+## I(.) failed (upto 2010-05-07)
+
+cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''
+
+if(!interactive()) warnings()
diff --git a/win32/deps/library/Matrix/tests/validObj.R b/win32/deps/library/Matrix/tests/validObj.R
new file mode 100644
index 0000000..b1ac330
--- /dev/null
+++ b/win32/deps/library/Matrix/tests/validObj.R
@@ -0,0 +1,177 @@
+library(Matrix)
+### Do all kinds of object creation and coercion
+
+source(system.file("test-tools.R", package = "Matrix"))
+
+## the empty ones:
+checkMatrix(new("dgeMatrix"))
+checkMatrix(Matrix(,0,0))
+
+## "dge"
+assertError( new("dgeMatrix", Dim = c(2,2), x= 1:4) )# double 'Dim'
+assertError( new("dgeMatrix", Dim = as.integer(c(2,2)), x= 1:4) )# int 'x'
+assertError( new("dgeMatrix", Dim = 2:2, x=as.double(1:4)) )# length(Dim) !=2
+assertError( new("dgeMatrix", Dim = as.integer(c(2,2)), x= as.double(1:5)))
+
+checkMatrix(m1 <- Matrix(1:6, ncol=2))
+checkMatrix(m2 <- Matrix(1:7 +0, ncol=3)) # a (desired) warning
+stopifnot(all(match(is(m1), c("dgeMatrix", "ddenseMatrix", "generalMatrix",
+ "dMatrix", "denseMatrix", "compMatrix", "Matrix", "mMatrix"),0) > 0),
+ dim(t(m1)) == 2:3,
+ identical(m1, t(t(m1))))
+c.nam <- paste("C",1:2, sep='')
+dimnames(m1) <- list(NULL, c.nam)
+checkMatrix(m1) # failed in 0.999375-10
+checkMatrix(tm1 <- t(m1))
+stopifnot(colnames(m1) == c.nam,
+ identical(dimnames(tm1), list(c.nam, NULL)),
+ identical(m1, t(tm1)))
+
+## an example of *named* dimnames
+(t34N <- as(unclass(table(x = gl(3,4), y=gl(4,3))), "dgeMatrix"))
+stopifnot(identical(dimnames(t34N),
+ dimnames(as(t34N, "matrix"))),
+ identical(t34N, t(t(t34N))))
+
+## "dpo"
+checkMatrix(cm <- crossprod(m1))
+checkMatrix(cp <- as(cm, "dppMatrix"))# 'dpp' + factors
+checkMatrix(cs <- as(cm, "dsyMatrix"))# 'dsy' + factors
+checkMatrix(dcm <- as(cm, "dgeMatrix"))#'dge'
+checkMatrix(mcm <- as(cm, "dMatrix")) # 'dsy' + factors -- buglet? rather == cm?
+checkMatrix(mc. <- as(cm, "Matrix")) # dpo --> dsy -- (as above) FIXME? ??
+stopifnot(identical(mc., mcm),
+ identical(cm, (2*cm)/2),# remains dpo
+ identical(cm + cp, cp + cs),# dge
+ identical(mc., mcm),
+ all(2*cm == mcm * 2))
+
+checkMatrix(eq <- cm == cs)
+stopifnot(all(eq x),
+ identical3(pack(eq), cs == cp, cm == cp),
+ as.logical(!(cs < cp)),
+ identical4(!(cs < cp), !(cp > cs), cp <= cs, cs >= cp))
+
+## Coercion to 'dpo' should give an error if result would be invalid
+M <- Matrix(diag(4) - 1)
+assertError(as(M, "dpoMatrix"))
+M. <- as(M, "dgeMatrix")
+M.[1,2] <- 10 # -> not even symmetric anymore
+assertError(as(M., "dpoMatrix"))
+
+
+## Cholesky
+checkMatrix(ch <- chol(cm))
+checkMatrix(ch2 <- chol(as(cm, "dsyMatrix")))
+checkMatrix(ch3 <- chol(as(cm, "dgeMatrix")))
+stopifnot(is.all.equal3(as(ch, "matrix"), as(ch2, "matrix"), as(ch3, "matrix")))
+### Very basic triangular matrix stuff
+
+assertError( new("dtrMatrix", Dim = c(2,2), x= 1:4) )# double 'Dim'
+assertError( new("dtrMatrix", Dim = as.integer(c(2,2)), x= 1:4) )# int 'x'
+## This caused a segfault (before revision r1172 in ../src/dtrMatrix.c):
+assertError( new("dtrMatrix", Dim = 2:2, x=as.double(1:4)) )# length(Dim) !=2
+assertError( new("dtrMatrix", Dim = as.integer(c(2,2)), x= as.double(1:5)))
+
+tr22 <- new("dtrMatrix", Dim = as.integer(c(2,2)), x=as.double(1:4))
+tt22 <- t(tr22)
+(tPt <- tr22 + tt22)
+stopifnot(identical(10 * tPt, tPt * 10),
+ as.vector(t.22 <- (tr22 / .5)* .5) == c(1,0,3,4),
+ TRUE) ## not yet: class(t.22) == "dtrMatrix")
+
+## non-square triagonal Matrices --- are forbidden ---
+assertError(new("dtrMatrix", Dim = 2:3,
+ x=as.double(1:6), uplo="L", diag="U"))
+
+n <- 3:3
+assertError(new("dtCMatrix", Dim = c(n,n), diag = "U"))
+stopifnot(validObject(T <- new("dtTMatrix", Dim = c(n,n), diag = "U")),
+ identical(as.mat(T), diag(n)),
+ validObject(M <- new("dtCMatrix", Dim = c(n,n), diag = "U",
+ p = rep.int(0:0, n+1)))
+ )
+
+set.seed(3) ; (p9 <- as(sample(9), "pMatrix"))
+## Check that the correct error message is triggered
+ind.try <- try(p9[1,1] <- 1, silent = TRUE)
+stopifnot(grep("replacing.*sensible", ind.try[1]) == 1,
+ is.logical(p9[1,]),
+ isTRUE(p9[-c(1:6, 8:9), 1]),
+ identical(t(p9), solve(p9)),
+## identical(p9[TRUE,], as(p9, "ngTMatrix")),
+ identical(as(diag(9), "pMatrix"), as(1:9, "pMatrix"))
+ )
+assert.EQ.mat(p9[TRUE,], as.matrix(as(p9, "ngTMatrix")))
+
+## validObject --> Cparse_validate(.)
+mm <- new("dgCMatrix", Dim = c(3L, 5L),
+ i = c(2L, 0L, 1L, 2L, 0L, 1L),
+ x = c( 2, 1, 1, 2, 1, 2),
+ p = c(0:2, 4L, 4L, 6L))
+
+## Previously unsorted columns were sorted - now are flagged as invalid
+m. <- mm
+ip <- c(1:2, 4:3, 6:5) # permute the 'i' and 'x' slot just "inside column":
+m i <- m.i <- mm i[ip]
+m x <- m.x <- mm x[ip]
+stopifnot(grep("row indices are not", validObject(m., test=TRUE)) == 1)
+##
+## Make sure that validObject() objects...
+## 1) to wrong 'p'
+m. <- mm; m p[1] <- 1L
+stopifnot(grep("first element of slot p", validObject(m., test=TRUE)) == 1)
+m p <- mm p[c(1,3:2,4:6)]
+stopifnot(grep("^slot p.* non-decreasing", validObject(m., test=TRUE)) == 1)
+## 2) to non-strictly increasing i's:
+m. <- mm ; ix <- c(1:3,3,5:6)
+m i <- mm i[ix]
+m x <- mm x[ix]
+stopifnot(identical(grep("slot i is not.* increasing .*column$",
+ validObject(m., test=TRUE)), 1L))
+## ix <- c(1:3, 3:6) # now the the (i,x) slots are too large (and decreasing at end)
+## m i <- mm i[ix]
+## m x <- mm x[ix]
+## stopifnot(identical(grep("^slot i is not.* increasing .*sort",
+## (msg <- validObject(m., test=TRUE))),# seg.fault in the past
+## 1L))
+
+## over-allocation of the i- and x- slot should be allowed:
+## (though it does not really help in M[.,.] <- * yet)
+m. <- mm
+m i <- c(mm i, NA, NA, NA)
+m x <- c(mm x, 10:12)
+stopifnot(validObject(m.))
+m. # show() now works
+stopifnot(all(m. == mm), # in spite of
+ length(m i) > length(mm i),
+ identical(t(t(m.)), mm),
+ identical3(m. * m., m. * mm, mm * mm))
+m.[1,4] <- 99 ## FIXME: warning and cuts (!) the over-allocated slots
+
+## Low-level construction of invalid object:
+## Ensure that it does *NOT* segfault
+foo <- new("ngCMatrix",
+ i = as.integer(c(12204, 16799, 16799, 33517, 1128, 11930, 1128, 11930, 32183)),
+ p = rep(0:9, c(2,4,1,11,10,0,1,0,9,12)),
+ Dim = c(36952L, 49L))
+validObject(foo)# TRUE
+foo i[5] <- foo i[5] + 50000L
+msg <- validObject(foo, test=TRUE)# is -- correctly -- *not* valid anymore
+stopifnot(is.character(msg))
+## Error in validObject(foo) :
+## invalid class "ngCMatrix" object: all row indices must be between 0 and nrow-1
+getLastMsg <- function(tryRes) {
+ ## Extract "final" message from erronous try result
+ sub("\n$", "",
+ sub(".*: ", "", as.character(tryRes)))
+}
+t <- try(show(foo)) ## error
+t2 <- try(head(foo))
+stopifnot(identical(msg, getLastMsg(t)),
+ identical(1L, grep("as_cholmod_sparse", getLastMsg(t2))))
+
+
+cat('Time elapsed: ', proc.time(),'\n') # "stats"
+
+if(!interactive()) warnings()
diff --git a/win32/deps/library/Matrix/tests/write-read.R b/win32/deps/library/Matrix/tests/write-read.R
new file mode 100644
index 0000000..6381baf
--- /dev/null
+++ b/win32/deps/library/Matrix/tests/write-read.R
@@ -0,0 +1,57 @@
+library(Matrix)
+
+#### Read / Write (sparse) Matrix objects ----------------------
+
+### Rebuild the 'mm' example matrix, now in KNex data
+
+### This is no longer really important, as we now use
+### ../data/KNex.R which creates the S4 object *every time*
+data(KNex)
+
+## recreate 'mm' from list :
+sNms <- c("Dim", "i","p","x")
+L <- lapply(sNms, function(SN) slot(KNex$mm, SN)); names(L) <- sNms
+mm2 <- new(class(KNex$mm))
+for (n in sNms) slot(mm2, n) <- L[[n]]
+
+stopifnot(validObject(mm2),
+ identical(mm2, KNex$mm))
+L$y <- KNex$y
+## save(L, file = "/u/maechler/R/Pkgs/Matrix/inst/external/KNex_slots.rda")
+
+
+## recreate 'mm' from ASCI file :
+mmT <- as(KNex$mm, "dgTMatrix")
+str(mmT)
+mm3 <- cbind(i = mmT i, j = mmT j, x = mmT x)
+write.table(mm3, file = "mm-Matrix.tab", row.names=FALSE)# -> ASCII version
+
+str(mmr <- read.table("mm-Matrix.tab", header = TRUE))
+mmr$i <- as.integer(mmr$i)
+mmr$j <- as.integer(mmr$j)
+
+mmN <- with(mmr, new("dgTMatrix", Dim = c(max(i)+1:1,max(j)+1:1),
+ i = i, j = j, x = x))
+
+stopifnot(identical(mmT, mmN)) # !!
+## weaker (and hence TRUE too):
+stopifnot(all.equal(as(mmN, "matrix"),
+ as(mmT, "matrix"), tol=0))
+
+mm <- as(mmN, "dgCMatrix")
+stopifnot(all.equal(mm, KNex$mm))
+## save(mm, file = "....../Matrix/data/mm.rda", compress = TRUE)
+
+
+A <- Matrix(c(1,0,3,0,0,5), 10, 10, sparse = TRUE) # warning about [6] vs [10]
+(fname <- file.path(tempdir(), "kk.mm"))
+writeMM(A, fname)
+(B <- readMM(fname))
+validObject(B)
+Bc <- as(B, "CsparseMatrix")
+stopifnot(identical(A, Bc))
+
+fname <- system.file("external", "wrong.mtx", package = "Matrix")
+r <- try(readMM(fname))
+stopifnot(inherits(r, "try-error"), length(grep("readMM.*row.*1:nr", r)) == 1)
+## gave a much less intelligible error message
diff --git a/win32/deps/library/base/CITATION b/win32/deps/library/base/CITATION
index 03cef58..44c3b29 100644
--- a/win32/deps/library/base/CITATION
+++ b/win32/deps/library/base/CITATION
@@ -1,23 +1,24 @@
-citHeader("To cite R in publications use:")
-
-citEntry(entry="Manual",
+bibentry("Manual",
title = "R: A Language and Environment for Statistical Computing",
- author = person(last="R Development Core Team"),
+ author = person("R Core Team"),
organization = "R Foundation for Statistical Computing",
address = "Vienna, Austria",
year = version$year,
note = "{ISBN} 3-900051-07-0",
- url = "http://www.R-project.org";,
+ url = "http://www.R-project.org/";,
textVersion =
- paste("R Development Core Team (", version$year, "). ",
+ paste("R Core Team (", version$year, "). ",
"R: A language and environment for statistical computing. ",
"R Foundation for Statistical Computing, Vienna, Austria. ",
- "ISBN 3-900051-07-0, URL http://www.R-project.org.";,
- sep="")
- )
-
-citFooter("We have invested a lot of time and effort in creating R,",
+ "ISBN 3-900051-07-0, URL http://www.R-project.org/.";,
+ sep=""),
+
+ mheader = "To cite R in publications use:",
+
+ mfooter =
+ paste("We have invested a lot of time and effort in creating R,",
"please cite it when using it for data analysis.",
"See also", sQuote("citation(\"pkgname\")"),
- "for citing R packages.")
+ "for citing R packages.", sep = " ")
+ )
diff --git a/win32/deps/library/base/DESCRIPTION b/win32/deps/library/base/DESCRIPTION
index 6fc50bb..131ef4b 100644
--- a/win32/deps/library/base/DESCRIPTION
+++ b/win32/deps/library/base/DESCRIPTION
@@ -1,9 +1,9 @@
Package: base
-Version: 2.9.2
+Version: 2.15.2
Priority: base
Title: The R Base Package
-Author: R Development Core Team and contributors worldwide
+Author: R Core Team and contributors worldwide
Maintainer: R Core Team <R-core r-project org>
Description: Base R functions
-License: Part of R 2.9.2
-Built: R 2.9.2; ; 2009-08-24 12:46:30 UTC; windows
+License: Part of R 2.15.2
+Built: R 2.15.2; ; 2012-10-27 03:08:06 UTC; windows
diff --git a/win32/deps/library/base/INDEX b/win32/deps/library/base/INDEX
index e7c1b75..355b8db 100644
--- a/win32/deps/library/base/INDEX
+++ b/win32/deps/library/base/INDEX
@@ -1,12 +1,14 @@
+.Call Modern Interfaces to C/C++ code
.Device Lists of Open/Active Graphics Devices
.Internal Call an Internal Function
.Last.value Value of Last Evaluated Expression
.Library Search Paths for Packages
.Machine Numerical Characteristics of the Machine
.Platform Platform Specific Variables
-.Primitive Call a "Primitive" Internal Function
+.Primitive Look Up a Primitive Function
+.bincode Bin a Numeric Vector
.deparseOpts Options for Expression Deparsing
-.onLoad Hooks for Name Space events
+.onLoad Hooks for Namespace Events
.packages Listing of Packages
.standard_regexps Miscellaneous Internal/Programming Utilities
: Colon Operator
@@ -16,6 +18,7 @@ Arithmetic Arithmetic Operators
AsIs Inhibit Interpretation/Conversion of Objects
Bessel Bessel Functions
Comparison Relational Operators
+Constants Built-in Constants
Control Control Flow
Cstack_info Report Information on C Stack Size and Usage
DateTimeClasses Date-Time Classes
@@ -28,12 +31,13 @@ Extract Extract or Replace Parts of an Object
Filter Common Higher-Order Functions in Functional
Programming Languages
Foreign Foreign Function Interface
+ISOdatetime Date-time Conversion Functions from Numeric
+ Representations
InternalMethods Internal Generic Functions
-LETTERS Built-in Constants
Logic Logical Operators
Memory Memory Available for Data Storage
Memory-limits Memory Limits in R
-NA Not Available / "Missing" Values
+NA 'Not Available' / Missing Values
NULL The Null Object
NotYetImplemented Not Yet Implemented Functions and Unused
Arguments
@@ -43,12 +47,11 @@ Paren Parentheses and Braces
Quotes Quotes
R.Version Version Information
R.home Return the R Home Directory
-RNG Random Number Generation
+Random Random Number Generation
Random.user User-supplied Random Number Generation
Rdconv Utilities for Processing Rd Files
Recall Recursive Calling
Reserved Reserved Words in R
-S3groupGeneric S3 Group Generic Functions
Special Special Functions of Mathematics
Startup Initialization at Start of an R Session
Syntax Operator Syntax and Precedence
@@ -56,18 +59,23 @@ Sys.getenv Get Environment Variables
Sys.getpid Get the Process ID of the R Session
Sys.glob Wildcard Expansion on File Paths
Sys.info Extract System and User Information
+Sys.localeconv Find Details of the Numerical and Monetary
+ Representations in the Current Locale
+Sys.readlink Read File Symbolic Links
+Sys.setFileTime Set File Time
Sys.setenv Set or Unset Environment Variables
Sys.sleep Suspend Execution for a Time Interval
Sys.time Get Current Date and Time
Sys.timezone Time Zones
-Sys.which Find Full Paths of Executables
+Sys.which Find Full Paths to Executables
Trig Trigonometric Functions
UseMethod Class Methods
+Vectorize Vectorize a Scalar Function
[.data.frame Extract or Replace Parts of a Data Frame
[.factor Extract or Replace Parts of a Factor
abbreviate Abbreviate Strings
abs Miscellaneous Mathematical Functions
-addTaskCallback Add or remove a top-level task callback
+addTaskCallback Add or Remove a Top-Level Task Callback
agrep Approximate String Matching (Fuzzy Matching)
all Are All Values True?
all.equal Test if Two Objects are (Nearly) Equal
@@ -78,6 +86,7 @@ append Vector Merging
apply Apply Functions Over Array Margins
args Argument List of a Function
array Multi-way Arrays
+as.Date Date Conversion Functions to and from Character
as.POSIXct Date-time Conversion Functions
as.data.frame Coerce to a Data Frame
as.environment Coerce to an Environment Object
@@ -85,12 +94,11 @@ as.function Convert Object to Function
assign Assign a Value to a Name
assignOps Assignment Operators
attach Attach Set of R Objects to Search Path
-attachNamespace Loading and Unloading Name Spaces
+attachNamespace Loading and Unloading Namespaces
attr Object Attributes
attributes Object Attribute Lists
autoload On-demand Loading of Packages
backsolve Solve an Upper or Lower Triangular System
-base-deprecated Deprecated Functions in Base package
base-package The R Base Package
basename Manipulate File Paths
bindenv Binding and Environment Adjustments
@@ -98,8 +106,10 @@ body Access to and Manipulation of the Body of a
Function
bquote Partial substitution in expressions
browser Environment Browser
+browserText Functions to Retrieve Values Supplied by Calls
+ to the Browser
builtins Returns the Names of All Built-in Objects
-by Apply a Function to a Data Frame split by
+by Apply a Function to a Data Frame Split by
Factors
c Combine Values into a Vector or List
call Function Calls
@@ -119,7 +129,7 @@ class Object Classes
col Column Indexes
colSums Form Row and Column Sums and Means
commandArgs Extract Command Line Arguments
-comment Query or Set a 'Comment' Attribute
+comment Query or Set a '"comment"' Attribute
complex Complex Vectors
conditions Condition Handling and Recovery
conflicts Search for Masked Objects on the Search Path
@@ -145,15 +155,16 @@ diff Lagged Differences
difftime Time Intervals
dim Dimensions of an Object
dimnames Dimnames of an Object
-dir.create Manipulaton of Directories and file Permissions
+dir.create Manipulaton of Directories and File Permissions
do.call Execute a Function Call
double Double-Precision Vectors
dput Write an Object to a File or Recreate it
drop Drop Redundant Extent Information
+droplevels droplevels
dump Text Representations of R Objects
duplicated Determine Duplicate Elements
dyn.load Foreign Function Interface
-eapply Apply a Function over values in an environment
+eapply Apply a Function Over Values in an Environment
eigen Spectral Decomposition of a Matrix
encodeString Encode Character Vector as for Printing
environment Environment Access
@@ -170,12 +181,12 @@ file.info Extract File Information
file.path Construct Path to File
file.show Display One or More Files
files File Manipulation
+find.package Find Packages
findInterval Find Interval Numbers or Indices
force Force Evaluation of an Argument
formals Access to and Manipulation of the Formal
Arguments
format Encode in a Common Format
-format.Date Date Conversion Functions to and from Character
format.info format(.) Information
format.pval Format P Values
formatC Formatting Using C-style Formats
@@ -194,18 +205,20 @@ getLoadedDLLs Get DLLs Loaded in Current Session
getNativeSymbolInfo Obtain a Description of one or more Native
(C/Fortran) Symbols
getNumCConverters Management of .C argument conversion list
-getTaskCallbackNames Query the names of the current internal
- top-level task callbacks
+getTaskCallbackNames Query the Names of the Current Internal
+ Top-Level Task Callbacks
gettext Translate Text Messages
getwd Get or Set Working Directory
gl Generate Factor Levels
grep Pattern Matching and Replacement
+grepRaw Pattern Matching for Raw Vectors
+groupGeneric S3 Group Generic Functions
gzcon (De)compress I/O Through Connections
hexmode Display Numbers in Hexadecimal
iconv Convert Character Vector between Encodings
icuSetCollate Setup Collation by ICU
identical Test Objects for Exact Equality
-identity Identity function
+identity Identity Function
ifelse Conditional Element Selection
integer Integer Vectors
interaction Compute Factor Interactions
@@ -215,16 +228,16 @@ is.R Are we using R, rather than S?
is.finite Finite, Infinite and NaN Numbers
is.function Is an Object of Type (Primitive) Function?
is.language Is an Object a Language Object?
-is.object Is an Object "internally classed"?
+is.object Is an Object 'internally classed'?
is.recursive Is an Object Atomic or Recursive?
is.single Is an Object of Single Precision Type?
is.unsorted Test if an Object is Not Sorted
isS4 Test for an S4 object
isSymmetric Test if a Matrix or other Object is Symmetric
-jitter Add 'Jitter' (Noise) to Numbers
+jitter 'Jitter' (Add Noise) to Numbers
kappa Compute or Estimate the Condition Number of a
Matrix
-kronecker Kronecker products on arrays
+kronecker Kronecker Products on Arrays
l10n_info Localization Information
labels Find Labels from Object
lapply Apply a Function over a List or Vector
@@ -233,11 +246,10 @@ levels Levels Attributes
library Loading and Listing of Packages
library.dynam Loading DLLs from Packages
license The R License Terms
-list Lists -- Generic and Dotted Pairs
+list Lists - Generic and Dotted Pairs
list.files List the Files in a Directory/Folder
+list2env From A List, Build or Add To an Environment
load Reload Saved Datasets
-localeconv Find Details of the Numerical and Monetary
- Representations in the Current Locale
locales Query or Set Aspects of the Locale
log Logarithms and Exponentials
logical Logical Vectors
@@ -245,19 +257,20 @@ lower.tri Lower and Upper Triangular Part of a Matrix
ls List Objects
make.names Make Syntactically Valid Names
make.unique Make Character Strings Unique
-mapply Apply a function to multiple list or vector
- arguments
+mapply Apply a Function to Multiple List or Vector
+ Arguments
margin.table Compute table margin
mat.or.vec Create a Matrix or a Vector
match Value Matching
match.arg Argument Verification Using Partial Matching
match.call Argument Matching
-match.fun Function Verification for "Function Variables"
+match.fun Extract a Function Specified by Name
matmult Matrix Multiplication
matrix Matrices
max Maxima and Minima
max.col Find Maximum Position in Matrix
mean Arithmetic Mean
+memCompress In-memory Compression and Decompression
memory.profile Profile the Usage of Cons Cells
merge Merge Two Data Frames
message Diagnostic Messages
@@ -269,8 +282,10 @@ nargs The Number of Arguments to a Function
nchar Count the Number of Characters (or Bytes or
Width)
nlevels The Number of Levels of a Factor
-noquote Class for "no quote" Printing of Character
+noquote Class for 'no quote' Printing of Character
Strings
+norm Compute the Norm of a Matrix
+normalizePath Express File Paths in Canonical Form
nrow The Number of Rows/Columns of an Array
numeric Numeric Vectors
numeric_version Numeric Versions
@@ -310,10 +325,13 @@ readBin Transfer Binary Data To and From Connections
readChar Transfer Character Strings To and From
Connections
readLines Read Text Lines from a Connection
+readRDS Serialization Interface for Single Objects
+readRenviron Set Environment Variables from a File
readline Read a Line from the Terminal
real Real Vectors
reg.finalizer Finalization of Objects
regex Regular Expressions as used in R
+regmatches Extract or Replace Matched Substrings
remove Remove Objects from a Specified Environment
rep Replicate Elements of Vectors and Lists
replace Replace Values in a Vector
@@ -323,8 +341,8 @@ round.POSIXt Round / Truncate Data-Time Objects
row Row Indexes
row.names Get and Set Row Names for Data Frames
rownames Row and Column Names
-rowsum Give column sums of a matrix or data frame,
- based on a grouping variable
+rowsum Give Column Sums of a Matrix or Data Frame,
+ Based on a Grouping Variable
sQuote Quote Text
sample Random Samples and Permutations
save Save R Objects
@@ -334,7 +352,7 @@ search Give Search Path for R Objects
seek Functions to Reposition Connections
seq Sequence Generation
seq.Date Generate Regular Sequences of Dates
-seq.POSIXt Generate Regular Sequences of Dates
+seq.POSIXt Generate Regular Sequences of Times
sequence Create A Vector of Sequences
serialize Simple Serialization Interface
setTimeLimit Set CPU and/or Elapsed Time Limits
@@ -354,11 +372,13 @@ split Divide into Groups and Reassemble
sprintf Use C-style String Formatting Commands
srcfile References to source files
stop Stop Function Execution
-stopifnot Ensure the 'Truth' of R Expressions
+stopifnot Ensure the Truth of R Expressions
strptime Date-time Conversion Functions to and from
Character
strsplit Split the Elements of a Character Vector
-strtrim Trim Character Strings to Specified Widths
+strtoi Convert Strings to Integers
+strtrim Trim Character Strings to Specified Display
+ Widths
structure Attribute Specification
strwrap Wrap Character Strings to Format Paragraphs
subset Subsetting Vectors, Matrices and Data Frames
@@ -374,11 +394,12 @@ sys.source Parse and Evaluate Expressions from a File
system Invoke a System Command
system.file Find Names of R System Files
system.time CPU Time Used
+system2 Invoke a System Command
t Matrix Transpose
table Cross Tabulation and Table Creation
tabulate Tabulation for Vectors
-tapply Apply a Function Over a "Ragged" Array
-taskCallbackManager Create an R-level task callback manager
+tapply Apply a Function Over a Ragged Array
+taskCallbackManager Create an R-level Task Callback Manager
tempfile Create Names for Temporary Files
textConnection Text Connections
tilde Tilde Operator
@@ -409,3 +430,4 @@ withVisible Return both a value and its visibility
write Write Data to a File
writeLines Write Lines to a Connection
xtfrm Auxiliary Function for Sorting and Ranking
+zapsmall Rounding of Numbers
diff --git a/win32/deps/library/base/Meta/Rd.rds b/win32/deps/library/base/Meta/Rd.rds
index e982871..2a05420 100644
Binary files a/win32/deps/library/base/Meta/Rd.rds and b/win32/deps/library/base/Meta/Rd.rds differ
diff --git a/win32/deps/library/base/Meta/demo.rds b/win32/deps/library/base/Meta/demo.rds
index 4db926d..f729e47 100644
Binary files a/win32/deps/library/base/Meta/demo.rds and b/win32/deps/library/base/Meta/demo.rds differ
diff --git a/win32/deps/library/base/Meta/hsearch.rds b/win32/deps/library/base/Meta/hsearch.rds
index 18fb25f..2fa2f94 100644
Binary files a/win32/deps/library/base/Meta/hsearch.rds and b/win32/deps/library/base/Meta/hsearch.rds differ
diff --git a/win32/deps/library/base/Meta/links.rds b/win32/deps/library/base/Meta/links.rds
new file mode 100644
index 0000000..70f142b
Binary files /dev/null and b/win32/deps/library/base/Meta/links.rds differ
diff --git a/win32/deps/library/base/Meta/package.rds b/win32/deps/library/base/Meta/package.rds
index a77d121..573c2b6 100644
Binary files a/win32/deps/library/base/Meta/package.rds and b/win32/deps/library/base/Meta/package.rds differ
diff --git a/win32/deps/library/base/R/Rprofile b/win32/deps/library/base/R/Rprofile
index b48c326..9ad2407 100644
--- a/win32/deps/library/base/R/Rprofile
+++ b/win32/deps/library/base/R/Rprofile
@@ -1,5 +1,7 @@
### This is the system Rprofile file. It is always run on startup.
### Additional commands can be placed in site or user Rprofile files
+#
+# Copyright (C) 1995-2012 The R Core Team
### (see ?Rprofile).
### Notice that it is a bad idea to use this file as a template for
@@ -37,7 +39,7 @@ options(stringsAsFactors = TRUE)
if(!interactive() && is.null(getOption("showErrorCalls")))
options(showErrorCalls = TRUE)
-local({dp <- as.vector(Sys.getenv("R_DEFAULT_PACKAGES"))
+local({dp <- Sys.getenv("R_DEFAULT_PACKAGES")
if(identical(dp, "")) # marginally faster to do methods last
dp <- c("datasets", "utils", "grDevices", "graphics",
"stats", "methods")
@@ -57,10 +59,10 @@ Sys.setenv(R_LIBS_USER =
{
for(pkg in getOption("defaultPackages")) {
res <- require(pkg, quietly = TRUE, warn.conflicts = FALSE,
- character.only = TRUE, save = FALSE)
+ character.only = TRUE)
if(!res)
- warning("package ", pkg,
- ' in options("defaultPackages") was not found', call.=FALSE)
+ warning(gettextf('package %s in options("defaultPackages") was not found', sQuote(pkg)),
+ call.=FALSE, domain = NA)
}
}
@@ -68,14 +70,13 @@ Sys.setenv(R_LIBS_USER =
{
if("methods" %in% getOption("defaultPackages")) {
res <- require("methods", quietly = TRUE, warn.conflicts = FALSE,
- character.only = TRUE, save = FALSE)
+ character.only = TRUE)
if(!res)
- warning("package \"methods\"",
- ' in options("defaultPackages") was not found', call.=FALSE)
+ warning('package "methods" in options("defaultPackages") was not found', call.=FALSE)
}
}
-if(Sys.getenv("R_BATCH") != "") {
+if(nzchar(Sys.getenv("R_BATCH"))) {
.Last.sys <- function()
{
cat("> proc.time()\n")
@@ -107,24 +108,23 @@ invisible(.libPaths(c(unlist(strsplit(Sys.getenv("R_LIBS"), ";")),
)))
if(nzchar(Sys.getenv("R_PAPERSIZE"))) {
- options(papersize = as.vector(Sys.getenv("R_PAPERSIZE")))
+ options(papersize = Sys.getenv("R_PAPERSIZE"))
} else {
- if(length(grep("united.states", Sys.getlocale("LC_MONETARY"), TRUE)) ||
- length(grep("canada", Sys.getlocale("LC_MONETARY"), TRUE)))
- options(papersize = "letter")
+ if(grepl("(canada|united.states)", Sys.getlocale("LC_MONETARY"),
+ ignore.case = TRUE)) options(papersize = "letter")
else options(papersize = "a4")
}
-options(pager = if(length(grep("--ess", commandArgs()))) "console" else "internal")
-options(useFancyQuotes = (.Platform$GUI == "Rgui"))
-options(pdfviewer = file.path(R.home(), "bin", "open.exe"))
+options(pager = if(length(grep("--ess", commandArgs()))) "console" else "internal",
+ useFancyQuotes = (.Platform$GUI == "Rgui"),
+ pdfviewer = Sys.getenv("R_PDFVIEWER", file.path(R.home("bin"), "open.exe")))
-if(.Platform$GUI == "Rgui") {
- Sys.setenv(GFORTRAN_STDOUT_UNIT= "-1")
- Sys.setenv(GFORTRAN_STDERR_UNIT= "-1")
-}
+if(.Platform$GUI == "Rgui")
+ Sys.setenv(GFORTRAN_STDOUT_UNIT = "-1", GFORTRAN_STDERR_UNIT = "-1")
local({
+ br <- Sys.getenv("R_BROWSER", NA_character_)
+ if(!is.na(br)) options(browser = br)
tests_startup <- Sys.getenv("R_TESTS")
if(nzchar(tests_startup)) source(tests_startup)
})
diff --git a/win32/deps/library/base/R/base b/win32/deps/library/base/R/base
index f7d68b7..635aaf5 100644
--- a/win32/deps/library/base/R/base
+++ b/win32/deps/library/base/R/base
@@ -1,4 +1,6 @@
-## this should be keep in step with lazyLoad in R/lazyload.R
+# Copyright (C) 1995-2012 The R Core Team
+
+## this should be kept in step with code in R/lazyload.R
.Internal(eval(quote({
..lazyLoad <- function(filebase, envir = parent.frame())
{
@@ -46,10 +48,25 @@
set(n, e, envenv) # MUST do this immediately
key <- getFromFrame(n, env)
data <- lazyLoadDBfetch(key, datafile, compressed, envhook)
- parent.env(e) <- data$enclos
+ ## comment from r41494
+ ## modified the loading of old environments, so that those
+ ## serialized with parent.env NULL are loaded with the
+ ## parent.env=emptyenv(); and yes an alternative would have been
+ ## baseenv(), but that was seldom the intention of folks that
+ ## set the environment to NULL.
+ if (is.null(data$enclos))
+ parent.env(e) <- emptyenv()
+ else
+ parent.env(e) <- data$enclos
vars <- names(data$bindings)
for (i in seq_along(vars))
set(vars[i], data$bindings[[i]], e)
+ if (! is.null(data$attributes))
+ attributes(e) <-data$attributes
+ if (! is.null(data$isS4) && data$isS4)
+ .Call("R_setS4Object", e, TRUE, TRUE, PACKAGE = "base")
+ if (! is.null(data$locked) && data$locked)
+ .Internal(lockEnvironment(e, FALSE))
e
}
}
diff --git a/win32/deps/library/base/R/base.rdb b/win32/deps/library/base/R/base.rdb
index 65949a7..b49bca5 100644
Binary files a/win32/deps/library/base/R/base.rdb and b/win32/deps/library/base/R/base.rdb differ
diff --git a/win32/deps/library/base/R/base.rdx b/win32/deps/library/base/R/base.rdx
index d0e273e..b2b395c 100644
Binary files a/win32/deps/library/base/R/base.rdx and b/win32/deps/library/base/R/base.rdx differ
diff --git a/win32/deps/library/base/demo/error.catching.R b/win32/deps/library/base/demo/error.catching.R
new file mode 100644
index 0000000..55db352
--- /dev/null
+++ b/win32/deps/library/base/demo/error.catching.R
@@ -0,0 +1,36 @@
+ ##================================================================##
+ ### In longer simulations, aka computer experiments, ###
+ ### you may want to ###
+ ### 1) catch all errors and warnings (and continue) ###
+ ### 2) store the error or warning messages ###
+ ### ###
+ ### Here's a solution (see R-help mailing list, Dec 9, 2010): ###
+ ##================================================================##
+
+##' We want to catch *and* save both errors and warnings, and in the case of
+##' a warning, also keep the computed result.
+##'
+##' @title tryCatch both warnings and errors
+##' @param expr
+##' @return a list with 'value' and 'warning', where
+##' 'value' may be an error caught.
+##' @author Martin Maechler
+
+# Copyright (C) 2010 The R Core Team
+
+
+tryCatch.W.E <- function(expr)
+{
+ W <- NULL
+ w.handler <- function(w){ # warning handler
+ W <<- w
+ invokeRestart("muffleWarning")
+ }
+ list(value = withCallingHandlers(tryCatch(expr, error = function(e) e),
+ warning = w.handler),
+ warning = W)
+}
+
+str( tryCatch.W.E( log( 2 ) ) )
+str( tryCatch.W.E( log( -1) ) )
+str( tryCatch.W.E( log("a") ) )
diff --git a/win32/deps/library/base/demo/is.things.R b/win32/deps/library/base/demo/is.things.R
index 252ebcc..b5dac61 100644
--- a/win32/deps/library/base/demo/is.things.R
+++ b/win32/deps/library/base/demo/is.things.R
@@ -1,12 +1,12 @@
+# Copyright (C) 1997-2010 The R Core Team
+
## being a 'builtin' function is not the same as being in base
-## and what about objects starting with '.'?
ls.base <- ls("package:base", all=TRUE)
base.is.f <- sapply(ls.base, function(x) is.function(get(x)))
-bi <- ls.base[base.is.f]
cat("\nNumber of base objects:\t\t", length(ls.base),
"\nNumber of functions in base:\t", sum(base.is.f),
"\n\t starting with 'is.' :\t ",
- length(is.bi <- bi[substring(bi,1,3) == "is."]), "\n")
+ sum(grepl("^is\\.", ls.base[base.is.f])), "\n", sep = "")
## 0.14 : 31
## 0.50 : 33
## 0.60 : 34
@@ -19,13 +19,13 @@ cat("\nNumber of base objects:\t\t", length(ls.base),
## Do we have a method (probably)?
is.method <- function(fname) {
isFun <- function(name) (exists(name, mode="function") &&
- is.na(match(name, c("is", "as"))))
+ is.na(match(name, c("is", "as"))))
np <- length(sp <- strsplit(fname, split = "\\.")[[1]])
if(np <= 1 )
FALSE
else
(isFun(paste(sp[1:(np-1)], collapse = '.')) ||
- (np>=3 &&
+ (np >= 3 &&
isFun(paste(sp[1:(np-2)], collapse = '.'))))
}
@@ -54,6 +54,12 @@ is.ALL <- function(obj, func.names = ls(pos=length(search())),
next
}
}
+ if(any(f == c("is.nan", "is.finite", "is.infinite"))) {
+ if(!is.atomic(obj)) {
+ if(!true.only) r[[f]] <- NA
+ next
+ }
+ }
if(debug) cat(f,"")
fn <- get(f)
rr <- if(is.primitive(fn) || length(formals(fn))>0) fn(obj) else fn()
diff --git a/win32/deps/library/base/demo/recursion.R b/win32/deps/library/base/demo/recursion.R
index 8768565..3a6846c 100644
--- a/win32/deps/library/base/demo/recursion.R
+++ b/win32/deps/library/base/demo/recursion.R
@@ -1,3 +1,4 @@
+# Copyright (C) 1997-2005 The R Core Team
## Adaptive integration: Venables and Ripley pp. 105-110
## This is the basic integrator.
diff --git a/win32/deps/library/base/demo/scoping.R b/win32/deps/library/base/demo/scoping.R
index 915fb6d..745048a 100644
--- a/win32/deps/library/base/demo/scoping.R
+++ b/win32/deps/library/base/demo/scoping.R
@@ -15,6 +15,8 @@
## This is a very nifty way of creating "closures" and a little thought
## will show you that there are many ways of using this in statistics.
+# Copyright (C) 1997-8 The R Core Team
+
open.account <- function(total) {
list(
diff --git a/win32/deps/library/base/help/AnIndex b/win32/deps/library/base/help/AnIndex
index 7043ddc..1a75a9b 100644
--- a/win32/deps/library/base/help/AnIndex
+++ b/win32/deps/library/base/help/AnIndex
@@ -1,5 +1,7 @@
base-package base-package
! Logic
+!.hexmode hexmode
+!.octmode octmode
!= Comparison
" Quotes
$ Extract
@@ -15,6 +17,8 @@ $<-.data.frame Extract.data.frame
%x% kronecker
& Logic
&& Logic
+&.hexmode hexmode
+&.octmode octmode
' Quotes
( Paren
* Arithmetic
@@ -29,35 +33,45 @@ $<-.data.frame Extract.data.frame
-> assignOps
->> assignOps
.Alias base-defunct
+.amatch_bounds agrep
+.amatch_costs agrep
.ArgsEnv base-internal
.Autoloaded autoload
.AutoloadEnv autoload
.BaseNamespaceEnv environment
+.bincode bincode
.C Foreign
-.Call Foreign
-.Call.graphics Foreign
+.cache_class base-internal
+.Call CallExternal
+.Call.graphics Foreign-internal
.Class UseMethod
+.colMeans colSums
+.colSums colSums
+.conflicts.OK attach
.decode_numeric_version numeric_version
.Defunct Defunct
.deparseOpts deparseOpts
.Deprecated Deprecated
.Device dev
.Devices dev
+.difftime base-internal
.doTrace trace
.Dyn.libs base-defunct
.dynLibs library.dynam
.encode_numeric_version numeric_version
.expand_R_libs_env_var libPaths
-.Export ns-alt
-.External Foreign
-.External.graphics Foreign
-.find.package base-internal
+.Export base-defunct
+.External CallExternal
+.External.graphics Foreign-internal
+.find.package find.package
.First Startup
-.First.lib library
+.First.lib base-defunct
.First.sys Startup
+.Firstlib_as_onLoad base-internal
.Fortran Foreign
.Generic UseMethod
.GenericArgsEnv base-internal
+.getNamespace ns-internal
.getRequiredPackages base-internal
.getRequiredPackages2 base-internal
.GlobalEnv environment
@@ -65,14 +79,16 @@ $<-.data.frame Extract.data.frame
.gt base-internal
.gtn base-internal
.handleSimpleError conditions
-.Import ns-alt
-.ImportFrom ns-alt
+.Import base-defunct
+.ImportFrom base-defunct
.Internal Internal
.isMethodsDispatchOn base-internal
.isOpen srcfile
+.kappa_tri kappa
.knownS3Generics ns-internal
+.kronecker kronecker
.Last quit
-.Last.lib library
+.Last.lib ns-hooks
.Last.sys quit
.Last.value Last.value
.leap.seconds DateTimeClasses
@@ -86,6 +102,7 @@ $<-.data.frame Extract.data.frame
.mergeExportMethods ns-internal
.mergeImportMethods ns-internal
.Method UseMethod
+.methodsNamespace base-internal
.noGenerics library
.NotYetImplemented notyet
.NotYetUsed notyet
@@ -96,20 +113,24 @@ $<-.data.frame Extract.data.frame
.OptRequireMethods Startup
.packages zpackages
.packageStartupMessage message
-.path.package base-internal
+.path.package find.package
.Platform Platform
+.POSIXct base-internal
+.POSIXlt base-internal
.Primitive Primitive
-.primTrace trace
-.primUntrace trace
+.primTrace base-internal
+.primUntrace base-internal
.Provided base-defunct
.Random.seed Random
-.readRDS readRDS
+.readRDS base-defunct
.Renviron Startup
+.rowMeans colSums
+.rowSums colSums
.row_names_info base-internal
.Rprofile Startup
-.S3method ns-alt
-.S3PrimitiveGenerics zMethods
-.saveRDS readRDS
+.S3method base-defunct
+.S3PrimitiveGenerics InternalMethods
+.saveRDS base-defunct
.Script zScript
.set_row_names base-internal
.signalSimpleWarning conditions
@@ -124,6 +145,9 @@ $<-.data.frame Extract.data.frame
.__S3MethodsTable__. ns-internal
/ Arithmetic
/.difftime difftime
+0x1 NumericConstants
+1i NumericConstants
+1L NumericConstants
: Colon
:: ns-dblcolon
::: ns-dblcolon
@@ -164,18 +188,21 @@ anyDuplicated.data.frame duplicated
anyDuplicated.default duplicated
anyDuplicated.matrix duplicated
aperm aperm
+aperm.default aperm
+aperm.table aperm
append append
apply apply
Arg complex
args args
Arithmetic Arithmetic
array array
+arrayInd which
as.array array
as.array.default array
as.call call
as.character character
as.character.condition conditions
-as.character.Date format.Date
+as.character.Date as.Date
as.character.default character
as.character.error conditions
as.character.factor character
@@ -209,15 +236,15 @@ as.data.frame.raw as.data.frame
as.data.frame.table table
as.data.frame.ts as.data.frame
as.data.frame.vector as.data.frame
-as.Date format.Date
-as.Date.character format.Date
-as.Date.date format.Date
-as.Date.dates format.Date
-as.Date.default format.Date
-as.Date.factor format.Date
-as.Date.numeric format.Date
-as.Date.POSIXct format.Date
-as.Date.POSIXlt format.Date
+as.Date as.Date
+as.Date.character as.Date
+as.Date.date as.Date
+as.Date.dates as.Date
+as.Date.default as.Date
+as.Date.factor as.Date
+as.Date.numeric as.Date
+as.Date.POSIXct as.Date
+as.Date.POSIXlt as.Date
as.difftime difftime
as.double double
as.double.difftime difftime
@@ -232,12 +259,15 @@ as.hexmode hexmode
as.integer integer
as.list list
as.list.data.frame list
+as.list.Date Dates
as.list.default list
as.list.environment list
as.list.factor list
as.list.function list
as.list.numeric_version numeric_version
+as.list.POSIXct DateTimeClasses
as.logical logical
+as.logical.factor logical
as.matrix matrix
as.matrix.data.frame matrix
as.matrix.default matrix
@@ -282,6 +312,7 @@ asin Trig
asinh Hyperbolic
AsIs AsIs
asNamespace ns-internal
+asS3 isS4
asS4 isS4
assign assign
assignOps assignOps
@@ -323,6 +354,9 @@ body<- body
bquote bquote
break Control
browser browser
+browserCondition browserText
+browserSetDebug browserText
+browserText browserText
builtins builtins
by by
by.data.frame by
@@ -359,12 +393,15 @@ clipboard connections
close connections
close.connection connections
close.srcfile srcfile
+close.srcfilealias srcfile
closeAllConnections showConnections
+closure function
codes base-defunct
codes.factor base-defunct
codes.ordered base-defunct
codes<- base-defunct
col col
+collation Comparison
colMeans colSums
colnames colnames
colnames<- colnames
@@ -387,6 +424,7 @@ conflicts conflicts
Conj complex
connection connections
connections connections
+Constants Constants
contributors contributors
Control Control
copyright copyright
@@ -412,12 +450,15 @@ date-time DateTimeClasses
Dates Dates
DateTimeClasses DateTimeClasses
debug debug
+debugonce debug
default.stringsAsFactors data.frame
Defunct Defunct
+defunct Defunct
delay base-defunct
delayedAssign delayedAssign
deparse deparse
Deprecated Deprecated
+deprecated Deprecated
det det
detach detach
determinant det
@@ -441,12 +482,17 @@ dimnames<-.data.frame dimnames
dir list.files
dir.create files2
dirname basename
+DLLInfo getLoadedDLLs
+DLLInfoList getLoadedDLLs
DLLpath dynload
do.call do.call
double double
dput dput
dQuote sQuote
drop drop
+droplevels droplevels
+droplevels.data.frame droplevels
+droplevels.factor droplevels
dump dump
duplicated duplicated
duplicated.array duplicated
@@ -461,9 +507,13 @@ eapply eapply
eigen eigen
else Control
emptyenv environment
+enc2native Encoding
+enc2utf8 Encoding
+enclosure environment
encodeString encodeString
Encoding Encoding
Encoding<- Encoding
+enquote substitute
env.profile environment
environment environment
environment variables EnvVar
@@ -492,8 +542,8 @@ file.copy files
file.create files
file.exists files
file.info file.info
+file.link files
file.path file.path
-file.rcopy files
file.remove files
file.rename files
file.show file.show
@@ -501,7 +551,8 @@ file.symlink files
files files
Filter funprog
Find funprog
-findInterval findInt
+find.package find.package
+findInterval findInterval
findPackageEnv base-internal
findRestart conditions
finite is.finite
@@ -517,16 +568,20 @@ format format
format.AsIs format
format.char base-defunct
format.data.frame format
-format.Date format.Date
+format.Date as.Date
format.default format
format.difftime difftime
format.factor format
format.hexmode hexmode
format.info format.info
+format.libraryIQR library
+format.numeric_version numeric_version
format.octmode octmode
+format.packageInfo library
format.POSIXct strptime
format.POSIXlt strptime
format.pval format.pval
+format.summaryDefault summary
formatC formatc
formatDL formatDL
forwardsolve backsolve
@@ -538,6 +593,7 @@ gc gc
gc.time gc.time
gcinfo gc
gctorture gctorture
+gctorture2 gctorture
get get
getAllConnections showConnections
getCallingDLL getCallingDLL
@@ -548,6 +604,7 @@ getConnection showConnections
getDLLRegisteredRoutines getDLLRegisteredRoutines
getDLLRegisteredRoutines.character getDLLRegisteredRoutines
getDLLRegisteredRoutines.DLLInfo getDLLRegisteredRoutines
+getElement Extract
getenv base-defunct
geterrmessage stop
getExportedValue ns-reflect
@@ -574,7 +631,9 @@ globalenv environment
gregexpr grep
grep grep
grepl grep
+grepRaw grepRaw
group generic groupGeneric
+groupGeneric groupGeneric
GSC EnvVar
gsub grep
gzcon gzcon
@@ -598,10 +657,11 @@ inherits class
integer integer
interaction interaction
interactive interactive
-internal generic zMethods
-InternalGenerics zMethods
-InternalMethods zMethods
+internal generic InternalMethods
+InternalGenerics InternalMethods
+InternalMethods InternalMethods
intersect sets
+intersection sets
intToBits rawConversion
intToUtf8 utf8Conversion
inverse.rle rle
@@ -630,6 +690,7 @@ is.logical logical
is.matrix matrix
is.na NA
is.na.data.frame NA
+is.na.numeric_version numeric_version
is.na.POSIXlt DateTimeClasses
is.na<- NA
is.na<-.default NA
@@ -639,6 +700,7 @@ is.nan is.finite
is.null NULL
is.numeric numeric
is.numeric.Date numeric
+is.numeric.difftime difftime
is.numeric.POSIXt numeric
is.numeric_version numeric_version
is.object is.object
@@ -656,12 +718,13 @@ is.symbol name
is.table table
is.unsorted is.unsorted
is.vector vector
+isatty showConnections
isBaseNamespace ns-internal
isdebugged debug
isIncomplete connections
isNamespace ns-internal
-ISOdate strptime
-ISOdatetime strptime
+ISOdate ISOdatetime
+ISOdatetime ISOdatetime
isOpen connections
isRestart conditions
isS4 isS4
@@ -677,7 +740,6 @@ kappa kappa
kappa.default kappa
kappa.lm kappa
kappa.qr kappa
-kappa.tri kappa
kronecker kronecker
l10n_info l10n_info
La.chol base-defunct
@@ -690,6 +752,7 @@ LANGUAGE EnvVar
lapply lapply
last.warning warnings
lazyLoad lazyload
+lazyLoadDBexec lazyload
lazyLoadDBfetch base-internal
lbeta Special
lchoose Special
@@ -700,6 +763,7 @@ LC_MONETARY locales
LC_NUMERIC locales
LC_TIME locales
length length
+length.POSIXlt DateTimeClasses
length<- length
length<-.factor length
LETTERS Constants
@@ -716,10 +780,12 @@ library.dynam.unload library.dynam
licence license
license license
list list
+list.dirs list.files
list.files list.files
+list2env list2env
load load
loadedNamespaces ns-load
-loadingNamespaceInfo ns-lowlev
+loadingNamespaceInfo ns-internal
loadNamespace ns-load
loadURL base-defunct
local eval
@@ -741,6 +807,7 @@ machine base-defunct
make.names make.names
make.unique make.unique
makeActiveBinding bindenv
+MAKEINDEX EnvVar
manglePackageName base-defunct
Map funprog
mapply mapply
@@ -768,7 +835,9 @@ mean.default mean
mean.difftime difftime
mean.POSIXct DateTimeClasses
mean.POSIXlt DateTimeClasses
-mem.limits Memory
+mem.limits base-defunct
+memCompress memCompress
+memDecompress memCompress
Memory Memory
Memory-limits Memory-limits
memory.profile memory.profile
@@ -792,8 +861,10 @@ NA NA
name name
names names
names.default names
+names.POSIXlt DateTimeClasses
names<- names
names<-.default names
+names<-.POSIXlt DateTimeClasses
namespaceExport ns-internal
namespaceImport ns-internal
namespaceImportClasses ns-internal
@@ -817,6 +888,8 @@ NextMethod UseMethod
ngettext gettext
nlevels nlevels
noquote noquote
+norm norm
+normalizePath normalizePath
NotYetImplemented notyet
NotYetUsed notyet
NROW nrow
@@ -834,6 +907,7 @@ on.exit on.exit
open connections
open.connection connections
open.srcfile srcfile
+open.srcfilealias srcfile
open.srcfilecopy srcfile
Ops groupGeneric
Ops.data.frame groupGeneric
@@ -843,6 +917,7 @@ Ops.factor factor
Ops.numeric_version numeric_version
Ops.ordered factor
Ops.POSIXt DateTimeClasses
+option options
options options
order order
ordered factor
@@ -862,7 +937,9 @@ parse parse
parse.dcf base-defunct
parseNamespaceFile ns-internal
paste paste
+paste0 paste
path.expand path.expand
+path.package find.package
pentagamma base-defunct
pi Constants
pipe connections
@@ -879,6 +956,7 @@ POSIXct DateTimeClasses
POSIXlt DateTimeClasses
POSIXt DateTimeClasses
pretty pretty
+pretty.default pretty
prettyNum formatc
primitive Primitive
print print
@@ -897,6 +975,7 @@ print.DLLInfo getLoadedDLLs
print.DLLInfoList getLoadedDLLs
print.DLLRegisteredRoutines getDLLRegisteredRoutines
print.factor print
+print.function print
print.hexmode hexmode
print.htest print
print.libraryIQR library
@@ -917,6 +996,7 @@ print.simple.list print
print.srcfile srcfile
print.srcref srcfile
print.summary.table table
+print.summaryDefault summary
print.table print
print.tabular base-defunct
print.warnings warnings
@@ -953,6 +1033,7 @@ R.home Rhome
R.Version Version
R.version Version
R.version.string Version
+Random Random
Random.user Random-user
range range
range.default range
@@ -967,8 +1048,7 @@ rawToChar rawConversion
rbind cbind
rbind.data.frame cbind
rcond kappa
-Rd2dvi RdUtils
-Rd2txt RdUtils
+Rd2pdf RdUtils
Rdconv RdUtils
Re complex
read.dcf dcf
@@ -977,16 +1057,21 @@ readBin readBin
readChar readChar
readline readline
readLines readLines
+readRDS readRDS
+readRenviron readRenviron
real real
Recall Recall
Reduce funprog
reg.finalizer reg.finalizer
regex regex
+regexec grep
regexp regex
regexpr grep
RegisteredNativeSymbol getNativeSymbolInfo
registerS3method ns-internal
registerS3methods ns-internal
+regmatches regmatches
+regmatches<- regmatches
regular expression regex
remove rm
removeCConverter converters
@@ -1004,6 +1089,7 @@ repeat Control
replace replace
replicate lapply
require library
+requireNamespace ns-load
Reserved Reserved
reserved Reserved
restart base-defunct
@@ -1020,7 +1106,6 @@ RNGkind Random
RNGversion Random
round Round
round.Date round.POSIXt
-round.difftime difftime
round.POSIXt round.POSIXt
row row
row.names row.names
@@ -1043,7 +1128,6 @@ R_BROWSER EnvVar
R_COMPLETION EnvVar
R_DEFAULT_PACKAGES Startup
R_DOC_DIR EnvVar
-R_DVIPSCMD EnvVar
R_ENVIRON Startup
R_ENVIRON_USER Startup
R_GSCMD EnvVar
@@ -1051,18 +1135,14 @@ R_HISTFILE EnvVar
R_HISTSIZE EnvVar
R_HOME Rhome
R_INCLUDE_DIR EnvVar
-R_LATEXCMD EnvVar
R_LIBS libPaths
R_LIBS_SITE libPaths
R_LIBS_USER libPaths
-R_MAKEINDEXCMD EnvVar
R_PAPERSIZE EnvVar
-R_PDFLATEXCMD EnvVar
R_PDFVIEWER EnvVar
R_PLATFORM EnvVar
R_PROFILE Startup
R_PROFILE_USER Startup
-R_RD4DVI EnvVar
R_RD4PDF EnvVar
R_SHARE_DIR EnvVar
R_system_version numeric_version
@@ -1079,12 +1159,11 @@ sapply lapply
save save
save.image save
save.plot base-defunct
-saveNamespaceImage ns-lowlev
+saveRDS readRDS
scale scale
scale.default scale
scan scan
scan.url base-defunct
-Sd2Rd RdUtils
search search
searchpaths search
seek seek
@@ -1118,6 +1197,7 @@ simpleCondition conditions
simpleError conditions
simpleMessage conditions
simpleWarning conditions
+simplify2array lapply
sin Trig
single double
sinh Hyperbolic
@@ -1150,6 +1230,8 @@ sqrt MathFun
sQuote sQuote
srcfile srcfile
srcfile-class srcfile
+srcfilealias srcfile
+srcfilealias-class srcfile
srcfilecopy srcfile
srcfilecopy-class srcfile
srcref srcfile
@@ -1167,6 +1249,7 @@ str.POSIXt DateTimeClasses
strftime strptime
strptime strptime
strsplit strsplit
+strtoi strtoi
strtrim strtrim
structure structure
strwrap strwrap
@@ -1195,10 +1278,13 @@ Summary.factor factor
summary.factor summary
summary.matrix summary
Summary.numeric_version numeric_version
+Summary.ordered factor
Summary.POSIXct DateTimeClasses
summary.POSIXct DateTimeClasses
Summary.POSIXlt DateTimeClasses
summary.POSIXlt DateTimeClasses
+summary.srcfile srcfile
+summary.srcref srcfile
summary.table table
suppressMessages message
suppressPackageStartupMessages message
@@ -1221,15 +1307,18 @@ Sys.getlocale locales
Sys.getpid Sys.getpid
Sys.glob Sys.glob
Sys.info Sys.info
+Sys.junction files
sys.load.image base-internal
Sys.localeconv Sys.localeconv
sys.nframe sys.parent
sys.on.exit sys.parent
sys.parent sys.parent
sys.parents sys.parent
-Sys.putenv base-deprecated
+Sys.putenv base-defunct
+Sys.readlink Sys.readlink
sys.save.image base-internal
Sys.setenv Sys.setenv
+Sys.setFileTime Sys.setFileTime
Sys.setlocale locales
Sys.sleep Sys.sleep
sys.source sys.source
@@ -1243,6 +1332,7 @@ system system
system.file system.file
system.test base-defunct
system.time system.time
+system2 system2
T logical
t t
t.data.frame t
@@ -1261,10 +1351,12 @@ tetragamma base-defunct
textConnection textconnections
textConnectionValue textconnections
tilde tilde
+tilde expansion path.expand
time interval difftime
time zone timezones
time zones timezones
timezone timezones
+TMPDIR EnvVar
tolower chartr
topenv ns-topenv
toString toString
@@ -1291,6 +1383,7 @@ type typeof
typeof typeof
TZ timezones
TZDIR timezones
+umask files2
unclass class
undebug debug
union sets
@@ -1321,8 +1414,9 @@ upper.tri lower.tri
url connections
UseMethod UseMethod
utf8ToInt utf8Conversion
+vapply lapply
vector vector
-Vectorize mapply
+Vectorize Vectorize
Version base-defunct
version Version
warning warning
@@ -1349,16 +1443,21 @@ writeBin readBin
writeChar readChar
writeLines writeLines
xor Logic
+xor.hexmode hexmode
+xor.octmode octmode
xpdrows.data.frame dataframeHelpers
xtfrm xtfrm
+xtfrm.AsIs xtfrm
xtfrm.Date xtfrm
xtfrm.default xtfrm
+xtfrm.difftime xtfrm
xtfrm.factor xtfrm
xtfrm.numeric_version numeric_version
xtfrm.POSIXct xtfrm
xtfrm.POSIXlt xtfrm
xtfrm.Surv xtfrm
-zapsmall Round
+xzfile connections
+zapsmall zapsmall
[ Extract
[.AsIs AsIs
[.data.frame Extract.data.frame
@@ -1387,10 +1486,13 @@ zapsmall Round
[[.POSIXct DateTimeClasses
[[<- Extract
[[<-.data.frame Extract.data.frame
+[[<-.factor Extract.factor
[[<-.numeric_version numeric_version
^ Arithmetic
` Quotes
{ Paren
| Logic
+|.hexmode hexmode
+|.octmode octmode
|| Logic
~ tilde
diff --git a/win32/deps/library/base/help/aliases.rds b/win32/deps/library/base/help/aliases.rds
new file mode 100644
index 0000000..1bf7866
Binary files /dev/null and b/win32/deps/library/base/help/aliases.rds differ
diff --git a/win32/deps/library/base/help/base.rdb b/win32/deps/library/base/help/base.rdb
new file mode 100644
index 0000000..f39468b
Binary files /dev/null and b/win32/deps/library/base/help/base.rdb differ
diff --git a/win32/deps/library/base/help/base.rdx b/win32/deps/library/base/help/base.rdx
new file mode 100644
index 0000000..ffc4d72
Binary files /dev/null and b/win32/deps/library/base/help/base.rdx differ
diff --git a/win32/deps/library/base/help/paths.rds b/win32/deps/library/base/help/paths.rds
new file mode 100644
index 0000000..8afbb39
Binary files /dev/null and b/win32/deps/library/base/help/paths.rds differ
diff --git a/win32/deps/library/base/html/00Index.html b/win32/deps/library/base/html/00Index.html
new file mode 100644
index 0000000..ce65b04
--- /dev/null
+++ b/win32/deps/library/base/html/00Index.html
@@ -0,0 +1,2458 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: The R Base Package</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> The R Base Package
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘base’ version 2.15.2</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+<li><a href="../demo">Code demos</a>. Use <a href="../../utils/help/demo">demo()</a> to run them.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<p align="center">
+<a href="# "> </a>
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+</p>
+
+<table width="100%">
+<tr><td width="25%"><a href="base-package.html">base-package</a></td>
+<td>The R Base Package</td></tr>
+</table>
+
+<h2><a name="A">-- A --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="abbreviate.html">abbreviate</a></td>
+<td>Abbreviate Strings</td></tr>
+<tr><td width="25%"><a href="MathFun.html">abs</a></td>
+<td>Miscellaneous Mathematical Functions</td></tr>
+<tr><td width="25%"><a href="Trig.html">acos</a></td>
+<td>Trigonometric Functions</td></tr>
+<tr><td width="25%"><a href="Hyperbolic.html">acosh</a></td>
+<td>Hyperbolic Functions</td></tr>
+<tr><td width="25%"><a href="factor.html">addNA</a></td>
+<td>Factors</td></tr>
+<tr><td width="25%"><a href="taskCallback.html">addTaskCallback</a></td>
+<td>Add or Remove a Top-Level Task Callback</td></tr>
+<tr><td width="25%"><a href="agrep.html">agrep</a></td>
+<td>Approximate String Matching (Fuzzy Matching)</td></tr>
+<tr><td width="25%"><a href="list.html">alist</a></td>
+<td>Lists - Generic and Dotted Pairs</td></tr>
+<tr><td width="25%"><a href="all.html">all</a></td>
+<td>Are All Values True?</td></tr>
+<tr><td width="25%"><a href="all.equal.html">all.equal</a></td>
+<td>Test if Two Objects are (Nearly) Equal</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">all.equal.POSIXct</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="allnames.html">all.names</a></td>
+<td>Find All Names in an Expression</td></tr>
+<tr><td width="25%"><a href="allnames.html">all.vars</a></td>
+<td>Find All Names in an Expression</td></tr>
+<tr><td width="25%"><a href="any.html">any</a></td>
+<td>Are Some Values True?</td></tr>
+<tr><td width="25%"><a href="duplicated.html">anyDuplicated</a></td>
+<td>Determine Duplicate Elements</td></tr>
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+<td>Array Transposition</td></tr>
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+<td>Vector Merging</td></tr>
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+<td>Apply Functions Over Array Margins</td></tr>
+<tr><td width="25%"><a href="complex.html">Arg</a></td>
+<td>Complex Vectors</td></tr>
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+<td>Argument List of a Function</td></tr>
+<tr><td width="25%"><a href="Arithmetic.html">Arithmetic</a></td>
+<td>Arithmetic Operators</td></tr>
+<tr><td width="25%"><a href="array.html">array</a></td>
+<td>Multi-way Arrays</td></tr>
+<tr><td width="25%"><a href="which.html">arrayInd</a></td>
+<td>Which indices are TRUE?</td></tr>
+<tr><td width="25%"><a href="array.html">as.array</a></td>
+<td>Multi-way Arrays</td></tr>
+<tr><td width="25%"><a href="call.html">as.call</a></td>
+<td>Function Calls</td></tr>
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+<td>Character Vectors</td></tr>
+<tr><td width="25%"><a href="conditions.html">as.character.condition</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="as.Date.html">as.character.Date</a></td>
+<td>Date Conversion Functions to and from Character</td></tr>
+<tr><td width="25%"><a href="hexmode.html">as.character.hexmode</a></td>
+<td>Display Numbers in Hexadecimal</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">as.character.numeric_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="octmode.html">as.character.octmode</a></td>
+<td>Display Numbers in Octal</td></tr>
+<tr><td width="25%"><a href="strptime.html">as.character.POSIXt</a></td>
+<td>Date-time Conversion Functions to and from Character</td></tr>
+<tr><td width="25%"><a href="srcfile.html">as.character.srcref</a></td>
+<td>References to source files</td></tr>
+<tr><td width="25%"><a href="complex.html">as.complex</a></td>
+<td>Complex Vectors</td></tr>
+<tr><td width="25%"><a href="as.data.frame.html">as.data.frame</a></td>
+<td>Coerce to a Data Frame</td></tr>
+<tr><td width="25%"><a href="as.data.frame.html">as.data.frame.AsIs</a></td>
+<td>Coerce to a Data Frame</td></tr>
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+<td>Date Class</td></tr>
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+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">as.data.frame.POSIXct</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="table.html">as.data.frame.table</a></td>
+<td>Cross Tabulation and Table Creation</td></tr>
+<tr><td width="25%"><a href="as.Date.html">as.Date</a></td>
+<td>Date Conversion Functions to and from Character</td></tr>
+<tr><td width="25%"><a href="difftime.html">as.difftime</a></td>
+<td>Time Intervals</td></tr>
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+<td>Double-Precision Vectors</td></tr>
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+<tr><td width="25%"><a href="as.POSIXlt.html">as.double.POSIXlt</a></td>
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+<td>Coerce to an Environment Object</td></tr>
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+<td>Lists - Generic and Dotted Pairs</td></tr>
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+<td>Date Class</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">as.list.numeric_version</a></td>
+<td>Numeric Versions</td></tr>
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+<td>Class for 'no quote' Printing of Character Strings</td></tr>
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+<td>Date-Time Classes</td></tr>
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+<td>Display Numbers in Octal</td></tr>
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+<td>Factors</td></tr>
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+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="list.html">as.pairlist</a></td>
+<td>Lists - Generic and Dotted Pairs</td></tr>
+<tr><td width="25%"><a href="as.POSIXlt.html">as.POSIXct</a></td>
+<td>Date-time Conversion Functions</td></tr>
+<tr><td width="25%"><a href="as.POSIXlt.html">as.POSIXlt</a></td>
+<td>Date-time Conversion Functions</td></tr>
+<tr><td width="25%"><a href="qr.html">as.qr</a></td>
+<td>The QR Decomposition of a Matrix</td></tr>
+<tr><td width="25%"><a href="raw.html">as.raw</a></td>
+<td>Raw Vectors</td></tr>
+<tr><td width="25%"><a href="real.html">as.real</a></td>
+<td>Real Vectors</td></tr>
+<tr><td width="25%"><a href="double.html">as.single</a></td>
+<td>Double-Precision Vectors</td></tr>
+<tr><td width="25%"><a href="name.html">as.symbol</a></td>
+<td>Names and Symbols</td></tr>
+<tr><td width="25%"><a href="table.html">as.table</a></td>
+<td>Cross Tabulation and Table Creation</td></tr>
+<tr><td width="25%"><a href="vector.html">as.vector</a></td>
+<td>Vectors</td></tr>
+<tr><td width="25%"><a href="Trig.html">asin</a></td>
+<td>Trigonometric Functions</td></tr>
+<tr><td width="25%"><a href="Hyperbolic.html">asinh</a></td>
+<td>Hyperbolic Functions</td></tr>
+<tr><td width="25%"><a href="AsIs.html">AsIs</a></td>
+<td>Inhibit Interpretation/Conversion of Objects</td></tr>
+<tr><td width="25%"><a href="isS4.html">asS3</a></td>
+<td>Test for an S4 object</td></tr>
+<tr><td width="25%"><a href="isS4.html">asS4</a></td>
+<td>Test for an S4 object</td></tr>
+<tr><td width="25%"><a href="assign.html">assign</a></td>
+<td>Assign a Value to a Name</td></tr>
+<tr><td width="25%"><a href="assignOps.html">assignOps</a></td>
+<td>Assignment Operators</td></tr>
+<tr><td width="25%"><a href="Trig.html">atan</a></td>
+<td>Trigonometric Functions</td></tr>
+<tr><td width="25%"><a href="Trig.html">atan2</a></td>
+<td>Trigonometric Functions</td></tr>
+<tr><td width="25%"><a href="Hyperbolic.html">atanh</a></td>
+<td>Hyperbolic Functions</td></tr>
+<tr><td width="25%"><a href="vector.html">atomic</a></td>
+<td>Vectors</td></tr>
+<tr><td width="25%"><a href="attach.html">attach</a></td>
+<td>Attach Set of R Objects to Search Path</td></tr>
+<tr><td width="25%"><a href="ns-load.html">attachNamespace</a></td>
+<td>Loading and Unloading Namespaces</td></tr>
+<tr><td width="25%"><a href="attr.html">attr</a></td>
+<td>Object Attributes</td></tr>
+<tr><td width="25%"><a href="all.equal.html">attr.all.equal</a></td>
+<td>Test if Two Objects are (Nearly) Equal</td></tr>
+<tr><td width="25%"><a href="attributes.html">attributes</a></td>
+<td>Object Attribute Lists</td></tr>
+<tr><td width="25%"><a href="autoload.html">autoload</a></td>
+<td>On-demand Loading of Packages</td></tr>
+<tr><td width="25%"><a href="autoload.html">autoloader</a></td>
+<td>On-demand Loading of Packages</td></tr>
+<tr><td width="25%"><a href="autoload.html">Autoloads</a></td>
+<td>On-demand Loading of Packages</td></tr>
+</table>
+
+<h2><a name="B">-- B --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Quotes.html">backquote</a></td>
+<td>Quotes</td></tr>
+<tr><td width="25%"><a href="backsolve.html">backsolve</a></td>
+<td>Solve an Upper or Lower Triangular System</td></tr>
+<tr><td width="25%"><a href="Quotes.html">backtick</a></td>
+<td>Quotes</td></tr>
+<tr><td width="25%"><a href="base-package.html">base</a></td>
+<td>The R Base Package</td></tr>
+<tr><td width="25%"><a href="environment.html">baseenv</a></td>
+<td>Environment Access</td></tr>
+<tr><td width="25%"><a href="basename.html">basename</a></td>
+<td>Manipulate File Paths</td></tr>
+<tr><td width="25%"><a href="Bessel.html">Bessel</a></td>
+<td>Bessel Functions</td></tr>
+<tr><td width="25%"><a href="Bessel.html">bessel</a></td>
+<td>Bessel Functions</td></tr>
+<tr><td width="25%"><a href="Bessel.html">besselI</a></td>
+<td>Bessel Functions</td></tr>
+<tr><td width="25%"><a href="Bessel.html">besselJ</a></td>
+<td>Bessel Functions</td></tr>
+<tr><td width="25%"><a href="Bessel.html">besselK</a></td>
+<td>Bessel Functions</td></tr>
+<tr><td width="25%"><a href="Bessel.html">besselY</a></td>
+<td>Bessel Functions</td></tr>
+<tr><td width="25%"><a href="Special.html">beta</a></td>
+<td>Special Functions of Mathematics</td></tr>
+<tr><td width="25%"><a href="bindenv.html">bindenv</a></td>
+<td>Binding and Environment Adjustments</td></tr>
+<tr><td width="25%"><a href="bindenv.html">bindingIsActive</a></td>
+<td>Binding and Environment Adjustments</td></tr>
+<tr><td width="25%"><a href="bindenv.html">bindingIsLocked</a></td>
+<td>Binding and Environment Adjustments</td></tr>
+<tr><td width="25%"><a href="gettext.html">bindtextdomain</a></td>
+<td>Translate Text Messages</td></tr>
+<tr><td width="25%"><a href="body.html">body</a></td>
+<td>Access to and Manipulation of the Body of a Function</td></tr>
+<tr><td width="25%"><a href="bquote.html">bquote</a></td>
+<td>Partial substitution in expressions</td></tr>
+<tr><td width="25%"><a href="Control.html">break</a></td>
+<td>Control Flow</td></tr>
+<tr><td width="25%"><a href="browser.html">browser</a></td>
+<td>Environment Browser</td></tr>
+<tr><td width="25%"><a href="browserText.html">browserCondition</a></td>
+<td>Functions to Retrieve Values Supplied by Calls to the Browser</td></tr>
+<tr><td width="25%"><a href="browserText.html">browserSetDebug</a></td>
+<td>Functions to Retrieve Values Supplied by Calls to the Browser</td></tr>
+<tr><td width="25%"><a href="browserText.html">browserText</a></td>
+<td>Functions to Retrieve Values Supplied by Calls to the Browser</td></tr>
+<tr><td width="25%"><a href="builtins.html">builtins</a></td>
+<td>Returns the Names of All Built-in Objects</td></tr>
+<tr><td width="25%"><a href="by.html">by</a></td>
+<td>Apply a Function to a Data Frame Split by Factors</td></tr>
+<tr><td width="25%"><a href="connections.html">bzfile</a></td>
+<td>Functions to Manipulate Connections</td></tr>
+</table>
+
+<h2><a name="C">-- C --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="c.html">c</a></td>
+<td>Combine Values into a Vector or List</td></tr>
+<tr><td width="25%"><a href="Dates.html">c.Date</a></td>
+<td>Date Class</td></tr>
+<tr><td width="25%"><a href="noquote.html">c.noquote</a></td>
+<td>Class for 'no quote' Printing of Character Strings</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">c.numeric_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">c.POSIXct</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="call.html">call</a></td>
+<td>Function Calls</td></tr>
+<tr><td width="25%"><a href="callCC.html">callCC</a></td>
+<td>Call With Current Continuation</td></tr>
+<tr><td width="25%"><a href="capabilities.html">capabilities</a></td>
+<td>Report Capabilities of this Build of R</td></tr>
+<tr><td width="25%"><a href="chartr.html">casefold</a></td>
+<td>Character Translation and Casefolding</td></tr>
+<tr><td width="25%"><a href="cat.html">cat</a></td>
+<td>Concatenate and Print</td></tr>
+<tr><td width="25%"><a href="cbind.html">cbind</a></td>
+<td>Combine R Objects by Rows or Columns</td></tr>
+<tr><td width="25%"><a href="cbind.html">cbind.data.frame</a></td>
+<td>Combine R Objects by Rows or Columns</td></tr>
+<tr><td width="25%"><a href="Round.html">ceiling</a></td>
+<td>Rounding of Numbers</td></tr>
+<tr><td width="25%"><a href="char.expand.html">char.expand</a></td>
+<td>Expand a String with Respect to a Target Table</td></tr>
+<tr><td width="25%"><a href="character.html">character</a></td>
+<td>Character Vectors</td></tr>
+<tr><td width="25%"><a href="charmatch.html">charmatch</a></td>
+<td>Partial String Matching</td></tr>
+<tr><td width="25%"><a href="rawConversion.html">charToRaw</a></td>
+<td>Convert to or from Raw Vectors</td></tr>
+<tr><td width="25%"><a href="chartr.html">chartr</a></td>
+<td>Character Translation and Casefolding</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">check_tzones</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="chol.html">chol</a></td>
+<td>The Choleski Decomposition</td></tr>
+<tr><td width="25%"><a href="chol2inv.html">chol2inv</a></td>
+<td>Inverse from Choleski (or QR) Decomposition</td></tr>
+<tr><td width="25%"><a href="Special.html">choose</a></td>
+<td>Special Functions of Mathematics</td></tr>
+<tr><td width="25%"><a href="class.html">class</a></td>
+<td>Object Classes</td></tr>
+<tr><td width="25%"><a href="connections.html">clipboard</a></td>
+<td>Functions to Manipulate Connections</td></tr>
+<tr><td width="25%"><a href="connections.html">close</a></td>
+<td>Functions to Manipulate Connections</td></tr>
+<tr><td width="25%"><a href="srcfile.html">close.srcfile</a></td>
+<td>References to source files</td></tr>
+<tr><td width="25%"><a href="srcfile.html">close.srcfilealias</a></td>
+<td>References to source files</td></tr>
+<tr><td width="25%"><a href="showConnections.html">closeAllConnections</a></td>
+<td>Display Connections</td></tr>
+<tr><td width="25%"><a href="function.html">closure</a></td>
+<td>Function Definition</td></tr>
+<tr><td width="25%"><a href="col.html">col</a></td>
+<td>Column Indexes</td></tr>
+<tr><td width="25%"><a href="Comparison.html">collation</a></td>
+<td>Relational Operators</td></tr>
+<tr><td width="25%"><a href="colSums.html">colMeans</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="colnames.html">colnames</a></td>
+<td>Row and Column Names</td></tr>
+<tr><td width="25%"><a href="Colon.html">colon</a></td>
+<td>Colon Operator</td></tr>
+<tr><td width="25%"><a href="colSums.html">colSums</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="commandArgs.html">commandArgs</a></td>
+<td>Extract Command Line Arguments</td></tr>
+<tr><td width="25%"><a href="comment.html">comment</a></td>
+<td>Query or Set a '"comment"' Attribute</td></tr>
+<tr><td width="25%"><a href="Comparison.html">Comparison</a></td>
+<td>Relational Operators</td></tr>
+<tr><td width="25%"><a href="groupGeneric.html">Complex</a></td>
+<td>S3 Group Generic Functions</td></tr>
+<tr><td width="25%"><a href="complex.html">complex</a></td>
+<td>Complex Vectors</td></tr>
+<tr><td width="25%"><a href="conditions.html">computeRestarts</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="conditions.html">condition</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="conditions.html">conditionCall</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="conditions.html">conditionCall.condition</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="conditions.html">conditionMessage</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="conditions.html">conditionMessage.condition</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="conditions.html">conditions</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="conflicts.html">conflicts</a></td>
+<td>Search for Masked Objects on the Search Path</td></tr>
+<tr><td width="25%"><a href="complex.html">Conj</a></td>
+<td>Complex Vectors</td></tr>
+<tr><td width="25%"><a href="connections.html">connection</a></td>
+<td>Functions to Manipulate Connections</td></tr>
+<tr><td width="25%"><a href="connections.html">connections</a></td>
+<td>Functions to Manipulate Connections</td></tr>
+<tr><td width="25%"><a href="Constants.html">Constants</a></td>
+<td>Built-in Constants</td></tr>
+<tr><td width="25%"><a href="contributors.html">contributors</a></td>
+<td>R Project Contributors</td></tr>
+<tr><td width="25%"><a href="Control.html">Control</a></td>
+<td>Control Flow</td></tr>
+<tr><td width="25%"><a href="copyright.html">copyright</a></td>
+<td>Copyrights of Files Used to Build R</td></tr>
+<tr><td width="25%"><a href="copyright.html">copyrights</a></td>
+<td>Copyrights of Files Used to Build R</td></tr>
+<tr><td width="25%"><a href="Trig.html">cos</a></td>
+<td>Trigonometric Functions</td></tr>
+<tr><td width="25%"><a href="Hyperbolic.html">cosh</a></td>
+<td>Hyperbolic Functions</td></tr>
+<tr><td width="25%"><a href="crossprod.html">crossprod</a></td>
+<td>Matrix Crossproduct</td></tr>
+<tr><td width="25%"><a href="Cstack_info.html">Cstack_info</a></td>
+<td>Report Information on C Stack Size and Usage</td></tr>
+<tr><td width="25%"><a href="cumsum.html">cummax</a></td>
+<td>Cumulative Sums, Products, and Extremes</td></tr>
+<tr><td width="25%"><a href="cumsum.html">cummin</a></td>
+<td>Cumulative Sums, Products, and Extremes</td></tr>
+<tr><td width="25%"><a href="cumsum.html">cumprod</a></td>
+<td>Cumulative Sums, Products, and Extremes</td></tr>
+<tr><td width="25%"><a href="cumsum.html">cumsum</a></td>
+<td>Cumulative Sums, Products, and Extremes</td></tr>
+<tr><td width="25%"><a href="cut.html">cut</a></td>
+<td>Convert Numeric to Factor</td></tr>
+<tr><td width="25%"><a href="cut.POSIXt.html">cut.POSIXt</a></td>
+<td>Convert a Date or Date-Time Object to a Factor</td></tr>
+</table>
+
+<h2><a name="D">-- D --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="data.class.html">data.class</a></td>
+<td>Object Classes</td></tr>
+<tr><td width="25%"><a href="data.frame.html">data.frame</a></td>
+<td>Data Frames</td></tr>
+<tr><td width="25%"><a href="data.matrix.html">data.matrix</a></td>
+<td>Convert a Data Frame to a Numeric Matrix</td></tr>
+<tr><td width="25%"><a href="Dates.html">Date</a></td>
+<td>Date Class</td></tr>
+<tr><td width="25%"><a href="date.html">date</a></td>
+<td>System Date and Time</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">date-time</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="Dates.html">Dates</a></td>
+<td>Date Class</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">DateTimeClasses</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="debug.html">debug</a></td>
+<td>Debug a Function</td></tr>
+<tr><td width="25%"><a href="debug.html">debugonce</a></td>
+<td>Debug a Function</td></tr>
+<tr><td width="25%"><a href="data.frame.html">default.stringsAsFactors</a></td>
+<td>Data Frames</td></tr>
+<tr><td width="25%"><a href="Defunct.html">Defunct</a></td>
+<td>Marking Objects as Defunct</td></tr>
+<tr><td width="25%"><a href="Defunct.html">defunct</a></td>
+<td>Marking Objects as Defunct</td></tr>
+<tr><td width="25%"><a href="delayedAssign.html">delayedAssign</a></td>
+<td>Delay Evaluation</td></tr>
+<tr><td width="25%"><a href="deparse.html">deparse</a></td>
+<td>Expression Deparsing</td></tr>
+<tr><td width="25%"><a href="Deprecated.html">Deprecated</a></td>
+<td>Marking Objects as Deprecated</td></tr>
+<tr><td width="25%"><a href="Deprecated.html">deprecated</a></td>
+<td>Marking Objects as Deprecated</td></tr>
+<tr><td width="25%"><a href="det.html">det</a></td>
+<td>Calculate the Determinant of a Matrix</td></tr>
+<tr><td width="25%"><a href="detach.html">detach</a></td>
+<td>Detach Objects from the Search Path</td></tr>
+<tr><td width="25%"><a href="det.html">determinant</a></td>
+<td>Calculate the Determinant of a Matrix</td></tr>
+<tr><td width="25%"><a href="dput.html">dget</a></td>
+<td>Write an Object to a File or Recreate it</td></tr>
+<tr><td width="25%"><a href="diag.html">diag</a></td>
+<td>Matrix Diagonals</td></tr>
+<tr><td width="25%"><a href="diff.html">diff</a></td>
+<td>Lagged Differences</td></tr>
+<tr><td width="25%"><a href="difftime.html">difftime</a></td>
+<td>Time Intervals</td></tr>
+<tr><td width="25%"><a href="Special.html">digamma</a></td>
+<td>Special Functions of Mathematics</td></tr>
+<tr><td width="25%"><a href="dim.html">dim</a></td>
+<td>Dimensions of an Object</td></tr>
+<tr><td width="25%"><a href="dimnames.html">dimnames</a></td>
+<td>Dimnames of an Object</td></tr>
+<tr><td width="25%"><a href="list.files.html">dir</a></td>
+<td>List the Files in a Directory/Folder</td></tr>
+<tr><td width="25%"><a href="files2.html">dir.create</a></td>
+<td>Manipulaton of Directories and File Permissions</td></tr>
+<tr><td width="25%"><a href="basename.html">dirname</a></td>
+<td>Manipulate File Paths</td></tr>
+<tr><td width="25%"><a href="getLoadedDLLs.html">DLLInfo</a></td>
+<td>Get DLLs Loaded in Current Session</td></tr>
+<tr><td width="25%"><a href="getLoadedDLLs.html">DLLInfoList</a></td>
+<td>Get DLLs Loaded in Current Session</td></tr>
+<tr><td width="25%"><a href="dynload.html">DLLpath</a></td>
+<td>Foreign Function Interface</td></tr>
+<tr><td width="25%"><a href="do.call.html">do.call</a></td>
+<td>Execute a Function Call</td></tr>
+<tr><td width="25%"><a href="double.html">double</a></td>
+<td>Double-Precision Vectors</td></tr>
+<tr><td width="25%"><a href="dput.html">dput</a></td>
+<td>Write an Object to a File or Recreate it</td></tr>
+<tr><td width="25%"><a href="sQuote.html">dQuote</a></td>
+<td>Quote Text</td></tr>
+<tr><td width="25%"><a href="drop.html">drop</a></td>
+<td>Drop Redundant Extent Information</td></tr>
+<tr><td width="25%"><a href="droplevels.html">droplevels</a></td>
+<td>droplevels</td></tr>
+<tr><td width="25%"><a href="dump.html">dump</a></td>
+<td>Text Representations of R Objects</td></tr>
+<tr><td width="25%"><a href="duplicated.html">duplicated</a></td>
+<td>Determine Duplicate Elements</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">duplicated.numeric_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">duplicated.POSIXlt</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="dynload.html">dyn.load</a></td>
+<td>Foreign Function Interface</td></tr>
+<tr><td width="25%"><a href="dynload.html">dyn.unload</a></td>
+<td>Foreign Function Interface</td></tr>
+</table>
+
+<h2><a name="E">-- E --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="eapply.html">eapply</a></td>
+<td>Apply a Function Over Values in an Environment</td></tr>
+<tr><td width="25%"><a href="eigen.html">eigen</a></td>
+<td>Spectral Decomposition of a Matrix</td></tr>
+<tr><td width="25%"><a href="Control.html">else</a></td>
+<td>Control Flow</td></tr>
+<tr><td width="25%"><a href="environment.html">emptyenv</a></td>
+<td>Environment Access</td></tr>
+<tr><td width="25%"><a href="Encoding.html">enc2native</a></td>
+<td>Read or Set the Declared Encodings for a Character Vector</td></tr>
+<tr><td width="25%"><a href="Encoding.html">enc2utf8</a></td>
+<td>Read or Set the Declared Encodings for a Character Vector</td></tr>
+<tr><td width="25%"><a href="environment.html">enclosure</a></td>
+<td>Environment Access</td></tr>
+<tr><td width="25%"><a href="encodeString.html">encodeString</a></td>
+<td>Encode Character Vector as for Printing</td></tr>
+<tr><td width="25%"><a href="Encoding.html">Encoding</a></td>
+<td>Read or Set the Declared Encodings for a Character Vector</td></tr>
+<tr><td width="25%"><a href="substitute.html">enquote</a></td>
+<td>Substituting and Quoting Expressions</td></tr>
+<tr><td width="25%"><a href="environment.html">env.profile</a></td>
+<td>Environment Access</td></tr>
+<tr><td width="25%"><a href="environment.html">environment</a></td>
+<td>Environment Access</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">environment variables</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="bindenv.html">environmentIsLocked</a></td>
+<td>Binding and Environment Adjustments</td></tr>
+<tr><td width="25%"><a href="environment.html">environmentName</a></td>
+<td>Environment Access</td></tr>
+<tr><td width="25%"><a href="eval.html">eval</a></td>
+<td>Evaluate an (Unevaluated) Expression</td></tr>
+<tr><td width="25%"><a href="eval.html">eval.parent</a></td>
+<td>Evaluate an (Unevaluated) Expression</td></tr>
+<tr><td width="25%"><a href="eval.html">evalq</a></td>
+<td>Evaluate an (Unevaluated) Expression</td></tr>
+<tr><td width="25%"><a href="exists.html">exists</a></td>
+<td>Is an Object Defined?</td></tr>
+<tr><td width="25%"><a href="Log.html">exp</a></td>
+<td>Logarithms and Exponentials</td></tr>
+<tr><td width="25%"><a href="expand.grid.html">expand.grid</a></td>
+<td>Create a Data Frame from All Combinations of Factors</td></tr>
+<tr><td width="25%"><a href="Log.html">expm1</a></td>
+<td>Logarithms and Exponentials</td></tr>
+<tr><td width="25%"><a href="expression.html">expression</a></td>
+<td>Unevaluated Expressions</td></tr>
+<tr><td width="25%"><a href="Extract.html">Extract</a></td>
+<td>Extract or Replace Parts of an Object</td></tr>
+</table>
+
+<h2><a name="F">-- F --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="logical.html">F</a></td>
+<td>Logical Vectors</td></tr>
+<tr><td width="25%"><a href="factor.html">factor</a></td>
+<td>Factors</td></tr>
+<tr><td width="25%"><a href="Special.html">factorial</a></td>
+<td>Special Functions of Mathematics</td></tr>
+<tr><td width="25%"><a href="logical.html">FALSE</a></td>
+<td>Logical Vectors</td></tr>
+<tr><td width="25%"><a href="connections.html">fifo</a></td>
+<td>Functions to Manipulate Connections</td></tr>
+<tr><td width="25%"><a href="connections.html">file</a></td>
+<td>Functions to Manipulate Connections</td></tr>
+<tr><td width="25%"><a href="file.access.html">file.access</a></td>
+<td>Ascertain File Accessibility</td></tr>
+<tr><td width="25%"><a href="files.html">file.append</a></td>
+<td>File Manipulation</td></tr>
+<tr><td width="25%"><a href="file.choose.html">file.choose</a></td>
+<td>Choose a File Interactively</td></tr>
+<tr><td width="25%"><a href="files.html">file.copy</a></td>
+<td>File Manipulation</td></tr>
+<tr><td width="25%"><a href="files.html">file.create</a></td>
+<td>File Manipulation</td></tr>
+<tr><td width="25%"><a href="files.html">file.exists</a></td>
+<td>File Manipulation</td></tr>
+<tr><td width="25%"><a href="file.info.html">file.info</a></td>
+<td>Extract File Information</td></tr>
+<tr><td width="25%"><a href="files.html">file.link</a></td>
+<td>File Manipulation</td></tr>
+<tr><td width="25%"><a href="file.path.html">file.path</a></td>
+<td>Construct Path to File</td></tr>
+<tr><td width="25%"><a href="files.html">file.remove</a></td>
+<td>File Manipulation</td></tr>
+<tr><td width="25%"><a href="files.html">file.rename</a></td>
+<td>File Manipulation</td></tr>
+<tr><td width="25%"><a href="file.show.html">file.show</a></td>
+<td>Display One or More Files</td></tr>
+<tr><td width="25%"><a href="files.html">file.symlink</a></td>
+<td>File Manipulation</td></tr>
+<tr><td width="25%"><a href="files.html">files</a></td>
+<td>File Manipulation</td></tr>
+<tr><td width="25%"><a href="funprog.html">Filter</a></td>
+<td>Common Higher-Order Functions in Functional Programming Languages</td></tr>
+<tr><td width="25%"><a href="funprog.html">Find</a></td>
+<td>Common Higher-Order Functions in Functional Programming Languages</td></tr>
+<tr><td width="25%"><a href="find.package.html">find.package</a></td>
+<td>Find Packages</td></tr>
+<tr><td width="25%"><a href="findInterval.html">findInterval</a></td>
+<td>Find Interval Numbers or Indices</td></tr>
+<tr><td width="25%"><a href="conditions.html">findRestart</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="is.finite.html">finite</a></td>
+<td>Finite, Infinite and NaN Numbers</td></tr>
+<tr><td width="25%"><a href="Round.html">floor</a></td>
+<td>Rounding of Numbers</td></tr>
+<tr><td width="25%"><a href="connections.html">flush</a></td>
+<td>Functions to Manipulate Connections</td></tr>
+<tr><td width="25%"><a href="Control.html">for</a></td>
+<td>Control Flow</td></tr>
+<tr><td width="25%"><a href="force.html">force</a></td>
+<td>Force Evaluation of an Argument</td></tr>
+<tr><td width="25%"><a href="Foreign.html">Foreign</a></td>
+<td>Foreign Function Interface</td></tr>
+<tr><td width="25%"><a href="formals.html">formals</a></td>
+<td>Access to and Manipulation of the Formal Arguments</td></tr>
+<tr><td width="25%"><a href="format.html">format</a></td>
+<td>Encode in a Common Format</td></tr>
+<tr><td width="25%"><a href="as.Date.html">format.Date</a></td>
+<td>Date Conversion Functions to and from Character</td></tr>
+<tr><td width="25%"><a href="difftime.html">format.difftime</a></td>
+<td>Time Intervals</td></tr>
+<tr><td width="25%"><a href="hexmode.html">format.hexmode</a></td>
+<td>Display Numbers in Hexadecimal</td></tr>
+<tr><td width="25%"><a href="format.info.html">format.info</a></td>
+<td>format(.) Information</td></tr>
+<tr><td width="25%"><a href="library.html">format.libraryIQR</a></td>
+<td>Loading and Listing of Packages</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">format.numeric_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="octmode.html">format.octmode</a></td>
+<td>Display Numbers in Octal</td></tr>
+<tr><td width="25%"><a href="library.html">format.packageInfo</a></td>
+<td>Loading and Listing of Packages</td></tr>
+<tr><td width="25%"><a href="strptime.html">format.POSIXct</a></td>
+<td>Date-time Conversion Functions to and from Character</td></tr>
+<tr><td width="25%"><a href="format.pval.html">format.pval</a></td>
+<td>Format P Values</td></tr>
+<tr><td width="25%"><a href="summary.html">format.summaryDefault</a></td>
+<td>Object Summaries</td></tr>
+<tr><td width="25%"><a href="formatc.html">formatC</a></td>
+<td>Formatting Using C-style Formats</td></tr>
+<tr><td width="25%"><a href="formatDL.html">formatDL</a></td>
+<td>Format Description Lists</td></tr>
+<tr><td width="25%"><a href="backsolve.html">forwardsolve</a></td>
+<td>Solve an Upper or Lower Triangular System</td></tr>
+<tr><td width="25%"><a href="function.html">function</a></td>
+<td>Function Definition</td></tr>
+<tr><td width="25%"><a href="agrep.html">fuzzy matching</a></td>
+<td>Approximate String Matching (Fuzzy Matching)</td></tr>
+</table>
+
+<h2><a name="G">-- G --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Special.html">gamma</a></td>
+<td>Special Functions of Mathematics</td></tr>
+<tr><td width="25%"><a href="gc.html">gc</a></td>
+<td>Garbage Collection</td></tr>
+<tr><td width="25%"><a href="gc.time.html">gc.time</a></td>
+<td>Report Time Spent in Garbage Collection</td></tr>
+<tr><td width="25%"><a href="gc.html">gcinfo</a></td>
+<td>Garbage Collection</td></tr>
+<tr><td width="25%"><a href="gctorture.html">gctorture</a></td>
+<td>Torture Garbage Collector</td></tr>
+<tr><td width="25%"><a href="gctorture.html">gctorture2</a></td>
+<td>Torture Garbage Collector</td></tr>
+<tr><td width="25%"><a href="get.html">get</a></td>
+<td>Return the Value of a Named Object</td></tr>
+<tr><td width="25%"><a href="showConnections.html">getAllConnections</a></td>
+<td>Display Connections</td></tr>
+<tr><td width="25%"><a href="converters.html">getCConverterDescriptions</a></td>
+<td>Management of .C argument conversion list</td></tr>
+<tr><td width="25%"><a href="converters.html">getCConverterStatus</a></td>
+<td>Management of .C argument conversion list</td></tr>
+<tr><td width="25%"><a href="showConnections.html">getConnection</a></td>
+<td>Display Connections</td></tr>
+<tr><td width="25%"><a href="getDLLRegisteredRoutines.html">getDLLRegisteredRoutines</a></td>
+<td>Reflectance Information for C/Fortran routines in a DLL</td></tr>
+<tr><td width="25%"><a href="Extract.html">getElement</a></td>
+<td>Extract or Replace Parts of an Object</td></tr>
+<tr><td width="25%"><a href="stop.html">geterrmessage</a></td>
+<td>Stop Function Execution</td></tr>
+<tr><td width="25%"><a href="userhooks.html">getHook</a></td>
+<td>Functions to Get and Set Hooks for Load, Attach, Detach and Unload</td></tr>
+<tr><td width="25%"><a href="getLoadedDLLs.html">getLoadedDLLs</a></td>
+<td>Get DLLs Loaded in Current Session</td></tr>
+<tr><td width="25%"><a href="getNativeSymbolInfo.html">getNativeSymbolInfo</a></td>
+<td>Obtain a Description of one or more Native (C/Fortran) Symbols</td></tr>
+<tr><td width="25%"><a href="converters.html">getNumCConverters</a></td>
+<td>Management of .C argument conversion list</td></tr>
+<tr><td width="25%"><a href="options.html">getOption</a></td>
+<td>Options Settings</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">getRversion</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="srcfile.html">getSrcLines</a></td>
+<td>References to source files</td></tr>
+<tr><td width="25%"><a href="taskCallbackNames.html">getTaskCallbackNames</a></td>
+<td>Query the Names of the Current Internal Top-Level Task Callbacks</td></tr>
+<tr><td width="25%"><a href="gettext.html">gettext</a></td>
+<td>Translate Text Messages</td></tr>
+<tr><td width="25%"><a href="sprintf.html">gettextf</a></td>
+<td>Use C-style String Formatting Commands</td></tr>
+<tr><td width="25%"><a href="getwd.html">getwd</a></td>
+<td>Get or Set Working Directory</td></tr>
+<tr><td width="25%"><a href="gl.html">gl</a></td>
+<td>Generate Factor Levels</td></tr>
+<tr><td width="25%"><a href="environment.html">globalenv</a></td>
+<td>Environment Access</td></tr>
+<tr><td width="25%"><a href="grep.html">gregexpr</a></td>
+<td>Pattern Matching and Replacement</td></tr>
+<tr><td width="25%"><a href="grep.html">grep</a></td>
+<td>Pattern Matching and Replacement</td></tr>
+<tr><td width="25%"><a href="grep.html">grepl</a></td>
+<td>Pattern Matching and Replacement</td></tr>
+<tr><td width="25%"><a href="grepRaw.html">grepRaw</a></td>
+<td>Pattern Matching for Raw Vectors</td></tr>
+<tr><td width="25%"><a href="groupGeneric.html">group generic</a></td>
+<td>S3 Group Generic Functions</td></tr>
+<tr><td width="25%"><a href="groupGeneric.html">groupGeneric</a></td>
+<td>S3 Group Generic Functions</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">GSC</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="grep.html">gsub</a></td>
+<td>Pattern Matching and Replacement</td></tr>
+<tr><td width="25%"><a href="gzcon.html">gzcon</a></td>
+<td>(De)compress I/O Through Connections</td></tr>
+<tr><td width="25%"><a href="connections.html">gzfile</a></td>
+<td>Functions to Manipulate Connections</td></tr>
+</table>
+
+<h2><a name="H">-- H --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="hexmode.html">hexmode</a></td>
+<td>Display Numbers in Hexadecimal</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">HOME</a></td>
+<td>Environment Variables</td></tr>
+</table>
+
+<h2><a name="I">-- I --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="AsIs.html">I</a></td>
+<td>Inhibit Interpretation/Conversion of Objects</td></tr>
+<tr><td width="25%"><a href="iconv.html">iconv</a></td>
+<td>Convert Character Vector between Encodings</td></tr>
+<tr><td width="25%"><a href="iconv.html">iconvlist</a></td>
+<td>Convert Character Vector between Encodings</td></tr>
+<tr><td width="25%"><a href="icuSetCollate.html">icuSetCollate</a></td>
+<td>Setup Collation by ICU</td></tr>
+<tr><td width="25%"><a href="identical.html">identical</a></td>
+<td>Test Objects for Exact Equality</td></tr>
+<tr><td width="25%"><a href="identity.html">identity</a></td>
+<td>Identity Function</td></tr>
+<tr><td width="25%"><a href="Control.html">if</a></td>
+<td>Control Flow</td></tr>
+<tr><td width="25%"><a href="ifelse.html">ifelse</a></td>
+<td>Conditional Element Selection</td></tr>
+<tr><td width="25%"><a href="complex.html">Im</a></td>
+<td>Complex Vectors</td></tr>
+<tr><td width="25%"><a href="Control.html">in</a></td>
+<td>Control Flow</td></tr>
+<tr><td width="25%"><a href="is.finite.html">Inf</a></td>
+<td>Finite, Infinite and NaN Numbers</td></tr>
+<tr><td width="25%"><a href="class.html">inherits</a></td>
+<td>Object Classes</td></tr>
+<tr><td width="25%"><a href="integer.html">integer</a></td>
+<td>Integer Vectors</td></tr>
+<tr><td width="25%"><a href="interaction.html">interaction</a></td>
+<td>Compute Factor Interactions</td></tr>
+<tr><td width="25%"><a href="interactive.html">interactive</a></td>
+<td>Is R Running Interactively?</td></tr>
+<tr><td width="25%"><a href="InternalMethods.html">internal generic</a></td>
+<td>Internal Generic Functions</td></tr>
+<tr><td width="25%"><a href="InternalMethods.html">InternalGenerics</a></td>
+<td>Internal Generic Functions</td></tr>
+<tr><td width="25%"><a href="InternalMethods.html">InternalMethods</a></td>
+<td>Internal Generic Functions</td></tr>
+<tr><td width="25%"><a href="sets.html">intersect</a></td>
+<td>Set Operations</td></tr>
+<tr><td width="25%"><a href="sets.html">intersection</a></td>
+<td>Set Operations</td></tr>
+<tr><td width="25%"><a href="rawConversion.html">intToBits</a></td>
+<td>Convert to or from Raw Vectors</td></tr>
+<tr><td width="25%"><a href="utf8Conversion.html">intToUtf8</a></td>
+<td>Convert to or from UTF-8-encoded Character Vectors</td></tr>
+<tr><td width="25%"><a href="rle.html">inverse.rle</a></td>
+<td>Run Length Encoding</td></tr>
+<tr><td width="25%"><a href="invisible.html">invisible</a></td>
+<td>Change the Print Mode to Invisible</td></tr>
+<tr><td width="25%"><a href="conditions.html">invokeRestart</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="conditions.html">invokeRestartInteractively</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="array.html">is.array</a></td>
+<td>Multi-way Arrays</td></tr>
+<tr><td width="25%"><a href="is.recursive.html">is.atomic</a></td>
+<td>Is an Object Atomic or Recursive?</td></tr>
+<tr><td width="25%"><a href="call.html">is.call</a></td>
+<td>Function Calls</td></tr>
+<tr><td width="25%"><a href="character.html">is.character</a></td>
+<td>Character Vectors</td></tr>
+<tr><td width="25%"><a href="complex.html">is.complex</a></td>
+<td>Complex Vectors</td></tr>
+<tr><td width="25%"><a href="as.data.frame.html">is.data.frame</a></td>
+<td>Coerce to a Data Frame</td></tr>
+<tr><td width="25%"><a href="double.html">is.double</a></td>
+<td>Double-Precision Vectors</td></tr>
+<tr><td width="25%"><a href="sets.html">is.element</a></td>
+<td>Set Operations</td></tr>
+<tr><td width="25%"><a href="environment.html">is.environment</a></td>
+<td>Environment Access</td></tr>
+<tr><td width="25%"><a href="expression.html">is.expression</a></td>
+<td>Unevaluated Expressions</td></tr>
+<tr><td width="25%"><a href="factor.html">is.factor</a></td>
+<td>Factors</td></tr>
+<tr><td width="25%"><a href="is.finite.html">is.finite</a></td>
+<td>Finite, Infinite and NaN Numbers</td></tr>
+<tr><td width="25%"><a href="is.function.html">is.function</a></td>
+<td>Is an Object of Type (Primitive) Function?</td></tr>
+<tr><td width="25%"><a href="is.finite.html">is.infinite</a></td>
+<td>Finite, Infinite and NaN Numbers</td></tr>
+<tr><td width="25%"><a href="integer.html">is.integer</a></td>
+<td>Integer Vectors</td></tr>
+<tr><td width="25%"><a href="is.language.html">is.language</a></td>
+<td>Is an Object a Language Object?</td></tr>
+<tr><td width="25%"><a href="list.html">is.list</a></td>
+<td>Lists - Generic and Dotted Pairs</td></tr>
+<tr><td width="25%"><a href="dynload.html">is.loaded</a></td>
+<td>Foreign Function Interface</td></tr>
+<tr><td width="25%"><a href="logical.html">is.logical</a></td>
+<td>Logical Vectors</td></tr>
+<tr><td width="25%"><a href="matrix.html">is.matrix</a></td>
+<td>Matrices</td></tr>
+<tr><td width="25%"><a href="NA.html">is.na</a></td>
+<td>'Not Available' / Missing Values</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">is.na.numeric_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">is.na.POSIXlt</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="name.html">is.name</a></td>
+<td>Names and Symbols</td></tr>
+<tr><td width="25%"><a href="is.finite.html">is.nan</a></td>
+<td>Finite, Infinite and NaN Numbers</td></tr>
+<tr><td width="25%"><a href="NULL.html">is.null</a></td>
+<td>The Null Object</td></tr>
+<tr><td width="25%"><a href="numeric.html">is.numeric</a></td>
+<td>Numeric Vectors</td></tr>
+<tr><td width="25%"><a href="difftime.html">is.numeric.difftime</a></td>
+<td>Time Intervals</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">is.numeric_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="is.object.html">is.object</a></td>
+<td>Is an Object 'internally classed'?</td></tr>
+<tr><td width="25%"><a href="factor.html">is.ordered</a></td>
+<td>Factors</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">is.package_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="list.html">is.pairlist</a></td>
+<td>Lists - Generic and Dotted Pairs</td></tr>
+<tr><td width="25%"><a href="is.function.html">is.primitive</a></td>
+<td>Is an Object of Type (Primitive) Function?</td></tr>
+<tr><td width="25%"><a href="qr.html">is.qr</a></td>
+<td>The QR Decomposition of a Matrix</td></tr>
+<tr><td width="25%"><a href="isR.html">is.R</a></td>
+<td>Are we using R, rather than S?</td></tr>
+<tr><td width="25%"><a href="raw.html">is.raw</a></td>
+<td>Raw Vectors</td></tr>
+<tr><td width="25%"><a href="real.html">is.real</a></td>
+<td>Real Vectors</td></tr>
+<tr><td width="25%"><a href="is.recursive.html">is.recursive</a></td>
+<td>Is an Object Atomic or Recursive?</td></tr>
+<tr><td width="25%"><a href="is.single.html">is.single</a></td>
+<td>Is an Object of Single Precision Type?</td></tr>
+<tr><td width="25%"><a href="name.html">is.symbol</a></td>
+<td>Names and Symbols</td></tr>
+<tr><td width="25%"><a href="table.html">is.table</a></td>
+<td>Cross Tabulation and Table Creation</td></tr>
+<tr><td width="25%"><a href="is.unsorted.html">is.unsorted</a></td>
+<td>Test if an Object is Not Sorted</td></tr>
+<tr><td width="25%"><a href="vector.html">is.vector</a></td>
+<td>Vectors</td></tr>
+<tr><td width="25%"><a href="showConnections.html">isatty</a></td>
+<td>Display Connections</td></tr>
+<tr><td width="25%"><a href="debug.html">isdebugged</a></td>
+<td>Debug a Function</td></tr>
+<tr><td width="25%"><a href="connections.html">isIncomplete</a></td>
+<td>Functions to Manipulate Connections</td></tr>
+<tr><td width="25%"><a href="ISOdatetime.html">ISOdate</a></td>
+<td>Date-time Conversion Functions from Numeric Representations</td></tr>
+<tr><td width="25%"><a href="ISOdatetime.html">ISOdatetime</a></td>
+<td>Date-time Conversion Functions from Numeric Representations</td></tr>
+<tr><td width="25%"><a href="connections.html">isOpen</a></td>
+<td>Functions to Manipulate Connections</td></tr>
+<tr><td width="25%"><a href="conditions.html">isRestart</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="isS4.html">isS4</a></td>
+<td>Test for an S4 object</td></tr>
+<tr><td width="25%"><a href="seek.html">isSeekable</a></td>
+<td>Functions to Reposition Connections</td></tr>
+<tr><td width="25%"><a href="isSymmetric.html">isSymmetric</a></td>
+<td>Test if a Matrix or other Object is Symmetric</td></tr>
+<tr><td width="25%"><a href="Logic.html">isTRUE</a></td>
+<td>Logical Operators</td></tr>
+</table>
+
+<h2><a name="J">-- J --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="jitter.html">jitter</a></td>
+<td>'Jitter' (Add Noise) to Numbers</td></tr>
+<tr><td width="25%"><a href="weekday.POSIXt.html">julian</a></td>
+<td>Extract Parts of a POSIXt or Date Object</td></tr>
+</table>
+
+<h2><a name="K">-- K --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="kappa.html">kappa</a></td>
+<td>Compute or Estimate the Condition Number of a Matrix</td></tr>
+<tr><td width="25%"><a href="kronecker.html">kronecker</a></td>
+<td>Kronecker Products on Arrays</td></tr>
+</table>
+
+<h2><a name="L">-- L --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="l10n_info.html">l10n_info</a></td>
+<td>Localization Information</td></tr>
+<tr><td width="25%"><a href="svd.html">La.svd</a></td>
+<td>Singular Value Decomposition of a Matrix</td></tr>
+<tr><td width="25%"><a href="labels.html">labels</a></td>
+<td>Find Labels from Object</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">LANGUAGE</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="lapply.html">lapply</a></td>
+<td>Apply a Function over a List or Vector</td></tr>
+<tr><td width="25%"><a href="warnings.html">last.warning</a></td>
+<td>Print Warning Messages</td></tr>
+<tr><td width="25%"><a href="Special.html">lbeta</a></td>
+<td>Special Functions of Mathematics</td></tr>
+<tr><td width="25%"><a href="Special.html">lchoose</a></td>
+<td>Special Functions of Mathematics</td></tr>
+<tr><td width="25%"><a href="locales.html">LC_ALL</a></td>
+<td>Query or Set Aspects of the Locale</td></tr>
+<tr><td width="25%"><a href="locales.html">LC_COLLATE</a></td>
+<td>Query or Set Aspects of the Locale</td></tr>
+<tr><td width="25%"><a href="locales.html">LC_CTYPE</a></td>
+<td>Query or Set Aspects of the Locale</td></tr>
+<tr><td width="25%"><a href="locales.html">LC_MONETARY</a></td>
+<td>Query or Set Aspects of the Locale</td></tr>
+<tr><td width="25%"><a href="locales.html">LC_NUMERIC</a></td>
+<td>Query or Set Aspects of the Locale</td></tr>
+<tr><td width="25%"><a href="locales.html">LC_TIME</a></td>
+<td>Query or Set Aspects of the Locale</td></tr>
+<tr><td width="25%"><a href="length.html">length</a></td>
+<td>Length of an Object</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">length.POSIXlt</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="Constants.html">LETTERS</a></td>
+<td>Built-in Constants</td></tr>
+<tr><td width="25%"><a href="Constants.html">letters</a></td>
+<td>Built-in Constants</td></tr>
+<tr><td width="25%"><a href="levels.html">levels</a></td>
+<td>Levels Attributes</td></tr>
+<tr><td width="25%"><a href="Special.html">lfactorial</a></td>
+<td>Special Functions of Mathematics</td></tr>
+<tr><td width="25%"><a href="Special.html">lgamma</a></td>
+<td>Special Functions of Mathematics</td></tr>
+<tr><td width="25%"><a href="library.html">library</a></td>
+<td>Loading and Listing of Packages</td></tr>
+<tr><td width="25%"><a href="library.dynam.html">library.dynam</a></td>
+<td>Loading DLLs from Packages</td></tr>
+<tr><td width="25%"><a href="library.dynam.html">library.dynam.unload</a></td>
+<td>Loading DLLs from Packages</td></tr>
+<tr><td width="25%"><a href="license.html">licence</a></td>
+<td>The R License Terms</td></tr>
+<tr><td width="25%"><a href="license.html">license</a></td>
+<td>The R License Terms</td></tr>
+<tr><td width="25%"><a href="list.html">list</a></td>
+<td>Lists - Generic and Dotted Pairs</td></tr>
+<tr><td width="25%"><a href="list.files.html">list.dirs</a></td>
+<td>List the Files in a Directory/Folder</td></tr>
+<tr><td width="25%"><a href="list.files.html">list.files</a></td>
+<td>List the Files in a Directory/Folder</td></tr>
+<tr><td width="25%"><a href="list2env.html">list2env</a></td>
+<td>From A List, Build or Add To an Environment</td></tr>
+<tr><td width="25%"><a href="load.html">load</a></td>
+<td>Reload Saved Datasets</td></tr>
+<tr><td width="25%"><a href="ns-load.html">loadedNamespaces</a></td>
+<td>Loading and Unloading Namespaces</td></tr>
+<tr><td width="25%"><a href="ns-load.html">loadNamespace</a></td>
+<td>Loading and Unloading Namespaces</td></tr>
+<tr><td width="25%"><a href="eval.html">local</a></td>
+<td>Evaluate an (Unevaluated) Expression</td></tr>
+<tr><td width="25%"><a href="Sys.localeconv.html">localeconv</a></td>
+<td>Find Details of the Numerical and Monetary Representations in the Current Locale</td></tr>
+<tr><td width="25%"><a href="locales.html">locales</a></td>
+<td>Query or Set Aspects of the Locale</td></tr>
+<tr><td width="25%"><a href="bindenv.html">lockBinding</a></td>
+<td>Binding and Environment Adjustments</td></tr>
+<tr><td width="25%"><a href="bindenv.html">lockEnvironment</a></td>
+<td>Binding and Environment Adjustments</td></tr>
+<tr><td width="25%"><a href="Log.html">log</a></td>
+<td>Logarithms and Exponentials</td></tr>
+<tr><td width="25%"><a href="Log.html">log10</a></td>
+<td>Logarithms and Exponentials</td></tr>
+<tr><td width="25%"><a href="Log.html">log1p</a></td>
+<td>Logarithms and Exponentials</td></tr>
+<tr><td width="25%"><a href="Log.html">log2</a></td>
+<td>Logarithms and Exponentials</td></tr>
+<tr><td width="25%"><a href="Log.html">logb</a></td>
+<td>Logarithms and Exponentials</td></tr>
+<tr><td width="25%"><a href="Logic.html">Logic</a></td>
+<td>Logical Operators</td></tr>
+<tr><td width="25%"><a href="logical.html">logical</a></td>
+<td>Logical Vectors</td></tr>
+<tr><td width="25%"><a href="lower.tri.html">lower.tri</a></td>
+<td>Lower and Upper Triangular Part of a Matrix</td></tr>
+<tr><td width="25%"><a href="ls.html">ls</a></td>
+<td>List Objects</td></tr>
+</table>
+
+<h2><a name="M">-- M --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="make.names.html">make.names</a></td>
+<td>Make Syntactically Valid Names</td></tr>
+<tr><td width="25%"><a href="make.unique.html">make.unique</a></td>
+<td>Make Character Strings Unique</td></tr>
+<tr><td width="25%"><a href="bindenv.html">makeActiveBinding</a></td>
+<td>Binding and Environment Adjustments</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">MAKEINDEX</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="funprog.html">Map</a></td>
+<td>Common Higher-Order Functions in Functional Programming Languages</td></tr>
+<tr><td width="25%"><a href="mapply.html">mapply</a></td>
+<td>Apply a Function to Multiple List or Vector Arguments</td></tr>
+<tr><td width="25%"><a href="margin.table.html">margin.table</a></td>
+<td>Compute table margin</td></tr>
+<tr><td width="25%"><a href="mat.or.vec.html">mat.or.vec</a></td>
+<td>Create a Matrix or a Vector</td></tr>
+<tr><td width="25%"><a href="match.html">match</a></td>
+<td>Value Matching</td></tr>
+<tr><td width="25%"><a href="match.arg.html">match.arg</a></td>
+<td>Argument Verification Using Partial Matching</td></tr>
+<tr><td width="25%"><a href="match.call.html">match.call</a></td>
+<td>Argument Matching</td></tr>
+<tr><td width="25%"><a href="match.fun.html">match.fun</a></td>
+<td>Extract a Function Specified by Name</td></tr>
+<tr><td width="25%"><a href="groupGeneric.html">Math</a></td>
+<td>S3 Group Generic Functions</td></tr>
+<tr><td width="25%"><a href="Dates.html">Math.Date</a></td>
+<td>Date Class</td></tr>
+<tr><td width="25%"><a href="difftime.html">Math.difftime</a></td>
+<td>Time Intervals</td></tr>
+<tr><td width="25%"><a href="factor.html">Math.factor</a></td>
+<td>Factors</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">Math.POSIXlt</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">Math.POSIXt</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="matmult.html">matmult</a></td>
+<td>Matrix Multiplication</td></tr>
+<tr><td width="25%"><a href="matrix.html">matrix</a></td>
+<td>Matrices</td></tr>
+<tr><td width="25%"><a href="Extremes.html">max</a></td>
+<td>Maxima and Minima</td></tr>
+<tr><td width="25%"><a href="maxCol.html">max.col</a></td>
+<td>Find Maximum Position in Matrix</td></tr>
+<tr><td width="25%"><a href="mean.html">mean</a></td>
+<td>Arithmetic Mean</td></tr>
+<tr><td width="25%"><a href="Dates.html">mean.Date</a></td>
+<td>Date Class</td></tr>
+<tr><td width="25%"><a href="difftime.html">mean.difftime</a></td>
+<td>Time Intervals</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">mean.POSIXct</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="memCompress.html">memCompress</a></td>
+<td>In-memory Compression and Decompression</td></tr>
+<tr><td width="25%"><a href="memCompress.html">memDecompress</a></td>
+<td>In-memory Compression and Decompression</td></tr>
+<tr><td width="25%"><a href="Memory.html">Memory</a></td>
+<td>Memory Available for Data Storage</td></tr>
+<tr><td width="25%"><a href="Memory-limits.html">Memory-limits</a></td>
+<td>Memory Limits in R</td></tr>
+<tr><td width="25%"><a href="memory.profile.html">memory.profile</a></td>
+<td>Profile the Usage of Cons Cells</td></tr>
+<tr><td width="25%"><a href="merge.html">merge</a></td>
+<td>Merge Two Data Frames</td></tr>
+<tr><td width="25%"><a href="message.html">message</a></td>
+<td>Diagnostic Messages</td></tr>
+<tr><td width="25%"><a href="get.html">mget</a></td>
+<td>Return the Value of a Named Object</td></tr>
+<tr><td width="25%"><a href="Extremes.html">min</a></td>
+<td>Maxima and Minima</td></tr>
+<tr><td width="25%"><a href="missing.html">missing</a></td>
+<td>Does a Formal Argument have a Value?</td></tr>
+<tr><td width="25%"><a href="complex.html">Mod</a></td>
+<td>Complex Vectors</td></tr>
+<tr><td width="25%"><a href="mode.html">mode</a></td>
+<td>The (Storage) Mode of an Object</td></tr>
+<tr><td width="25%"><a href="Constants.html">month.abb</a></td>
+<td>Built-in Constants</td></tr>
+<tr><td width="25%"><a href="weekday.POSIXt.html">months</a></td>
+<td>Extract Parts of a POSIXt or Date Object</td></tr>
+</table>
+
+<h2><a name="N">-- N --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="NA.html">NA</a></td>
+<td>'Not Available' / Missing Values</td></tr>
+<tr><td width="25%"><a href="name.html">name</a></td>
+<td>Names and Symbols</td></tr>
+<tr><td width="25%"><a href="names.html">names</a></td>
+<td>The Names of an Object</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">names.POSIXlt</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="is.finite.html">NaN</a></td>
+<td>Finite, Infinite and NaN Numbers</td></tr>
+<tr><td width="25%"><a href="nargs.html">nargs</a></td>
+<td>The Number of Arguments to a Function</td></tr>
+<tr><td width="25%"><a href="getNativeSymbolInfo.html">NativeSymbol</a></td>
+<td>Obtain a Description of one or more Native (C/Fortran) Symbols</td></tr>
+<tr><td width="25%"><a href="getNativeSymbolInfo.html">NativeSymbolInfo</a></td>
+<td>Obtain a Description of one or more Native (C/Fortran) Symbols</td></tr>
+<tr><td width="25%"><a href="NA.html">NA_character_</a></td>
+<td>'Not Available' / Missing Values</td></tr>
+<tr><td width="25%"><a href="NA.html">NA_complex_</a></td>
+<td>'Not Available' / Missing Values</td></tr>
+<tr><td width="25%"><a href="NA.html">NA_integer_</a></td>
+<td>'Not Available' / Missing Values</td></tr>
+<tr><td width="25%"><a href="NA.html">NA_real_</a></td>
+<td>'Not Available' / Missing Values</td></tr>
+<tr><td width="25%"><a href="nchar.html">nchar</a></td>
+<td>Count the Number of Characters (or Bytes or Width)</td></tr>
+<tr><td width="25%"><a href="nrow.html">NCOL</a></td>
+<td>The Number of Rows/Columns of an Array</td></tr>
+<tr><td width="25%"><a href="nrow.html">ncol</a></td>
+<td>The Number of Rows/Columns of an Array</td></tr>
+<tr><td width="25%"><a href="funprog.html">Negate</a></td>
+<td>Common Higher-Order Functions in Functional Programming Languages</td></tr>
+<tr><td width="25%"><a href="environment.html">new.env</a></td>
+<td>Environment Access</td></tr>
+<tr><td width="25%"><a href="Control.html">next</a></td>
+<td>Control Flow</td></tr>
+<tr><td width="25%"><a href="UseMethod.html">NextMethod</a></td>
+<td>Class Methods</td></tr>
+<tr><td width="25%"><a href="gettext.html">ngettext</a></td>
+<td>Translate Text Messages</td></tr>
+<tr><td width="25%"><a href="nlevels.html">nlevels</a></td>
+<td>The Number of Levels of a Factor</td></tr>
+<tr><td width="25%"><a href="noquote.html">noquote</a></td>
+<td>Class for 'no quote' Printing of Character Strings</td></tr>
+<tr><td width="25%"><a href="norm.html">norm</a></td>
+<td>Compute the Norm of a Matrix</td></tr>
+<tr><td width="25%"><a href="normalizePath.html">normalizePath</a></td>
+<td>Express File Paths in Canonical Form</td></tr>
+<tr><td width="25%"><a href="notyet.html">NotYetImplemented</a></td>
+<td>Not Yet Implemented Functions and Unused Arguments</td></tr>
+<tr><td width="25%"><a href="notyet.html">NotYetUsed</a></td>
+<td>Not Yet Implemented Functions and Unused Arguments</td></tr>
+<tr><td width="25%"><a href="nrow.html">NROW</a></td>
+<td>The Number of Rows/Columns of an Array</td></tr>
+<tr><td width="25%"><a href="nrow.html">nrow</a></td>
+<td>The Number of Rows/Columns of an Array</td></tr>
+<tr><td width="25%"><a href="NULL.html">NULL</a></td>
+<td>The Null Object</td></tr>
+<tr><td width="25%"><a href="numeric.html">numeric</a></td>
+<td>Numeric Vectors</td></tr>
+<tr><td width="25%"><a href="NumericConstants.html">NumericConstants</a></td>
+<td>Numeric Constants</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">numeric_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="nchar.html">nzchar</a></td>
+<td>Count the Number of Characters (or Bytes or Width)</td></tr>
+</table>
+
+<h2><a name="O">-- O --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="ls.html">objects</a></td>
+<td>List Objects</td></tr>
+<tr><td width="25%"><a href="octmode.html">octmode</a></td>
+<td>Display Numbers in Octal</td></tr>
+<tr><td width="25%"><a href="class.html">oldClass</a></td>
+<td>Object Classes</td></tr>
+<tr><td width="25%"><a href="on.exit.html">on.exit</a></td>
+<td>Function Exit Code</td></tr>
+<tr><td width="25%"><a href="connections.html">open</a></td>
+<td>Functions to Manipulate Connections</td></tr>
+<tr><td width="25%"><a href="srcfile.html">open.srcfile</a></td>
+<td>References to source files</td></tr>
+<tr><td width="25%"><a href="srcfile.html">open.srcfilealias</a></td>
+<td>References to source files</td></tr>
+<tr><td width="25%"><a href="groupGeneric.html">Ops</a></td>
+<td>S3 Group Generic Functions</td></tr>
+<tr><td width="25%"><a href="Ops.Date.html">Ops.Date</a></td>
+<td>Operators on the Date Class</td></tr>
+<tr><td width="25%"><a href="difftime.html">Ops.difftime</a></td>
+<td>Time Intervals</td></tr>
+<tr><td width="25%"><a href="factor.html">Ops.factor</a></td>
+<td>Factors</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">Ops.numeric_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="factor.html">Ops.ordered</a></td>
+<td>Factors</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">Ops.POSIXt</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="options.html">option</a></td>
+<td>Options Settings</td></tr>
+<tr><td width="25%"><a href="options.html">options</a></td>
+<td>Options Settings</td></tr>
+<tr><td width="25%"><a href="order.html">order</a></td>
+<td>Ordering Permutation</td></tr>
+<tr><td width="25%"><a href="factor.html">ordered</a></td>
+<td>Factors</td></tr>
+<tr><td width="25%"><a href="outer.html">outer</a></td>
+<td>Outer Product of Arrays</td></tr>
+</table>
+
+<h2><a name="P">-- P --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="userhooks.html">packageEvent</a></td>
+<td>Functions to Get and Set Hooks for Load, Attach, Detach and Unload</td></tr>
+<tr><td width="25%"><a href="message.html">packageStartupMessage</a></td>
+<td>Diagnostic Messages</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">package_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="rawConversion.html">packBits</a></td>
+<td>Convert to or from Raw Vectors</td></tr>
+<tr><td width="25%"><a href="list.html">pairlist</a></td>
+<td>Lists - Generic and Dotted Pairs</td></tr>
+<tr><td width="25%"><a href="Paren.html">Paren</a></td>
+<td>Parentheses and Braces</td></tr>
+<tr><td width="25%"><a href="environment.html">parent.env</a></td>
+<td>Environment Access</td></tr>
+<tr><td width="25%"><a href="sys.parent.html">parent.frame</a></td>
+<td>Functions to Access the Function Call Stack</td></tr>
+<tr><td width="25%"><a href="parse.html">parse</a></td>
+<td>Parse Expressions</td></tr>
+<tr><td width="25%"><a href="paste.html">paste</a></td>
+<td>Concatenate Strings</td></tr>
+<tr><td width="25%"><a href="paste.html">paste0</a></td>
+<td>Concatenate Strings</td></tr>
+<tr><td width="25%"><a href="path.expand.html">path.expand</a></td>
+<td>Expand File Paths</td></tr>
+<tr><td width="25%"><a href="find.package.html">path.package</a></td>
+<td>Find Packages</td></tr>
+<tr><td width="25%"><a href="Constants.html">pi</a></td>
+<td>Built-in Constants</td></tr>
+<tr><td width="25%"><a href="connections.html">pipe</a></td>
+<td>Functions to Manipulate Connections</td></tr>
+<tr><td width="25%"><a href="pmatch.html">pmatch</a></td>
+<td>Partial String Matching</td></tr>
+<tr><td width="25%"><a href="Extremes.html">pmax</a></td>
+<td>Maxima and Minima</td></tr>
+<tr><td width="25%"><a href="Extremes.html">pmax.int</a></td>
+<td>Maxima and Minima</td></tr>
+<tr><td width="25%"><a href="Extremes.html">pmin</a></td>
+<td>Maxima and Minima</td></tr>
+<tr><td width="25%"><a href="Extremes.html">pmin.int</a></td>
+<td>Maxima and Minima</td></tr>
+<tr><td width="25%"><a href="polyroot.html">polyroot</a></td>
+<td>Find Zeros of a Real or Complex Polynomial</td></tr>
+<tr><td width="25%"><a href="pos.to.env.html">pos.to.env</a></td>
+<td>Convert Positions in the Search Path to Environments</td></tr>
+<tr><td width="25%"><a href="funprog.html">Position</a></td>
+<td>Common Higher-Order Functions in Functional Programming Languages</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">POSIXct</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">POSIXlt</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">POSIXt</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="pretty.html">pretty</a></td>
+<td>Pretty Breakpoints</td></tr>
+<tr><td width="25%"><a href="formatc.html">prettyNum</a></td>
+<td>Formatting Using C-style Formats</td></tr>
+<tr><td width="25%"><a href="Primitive.html">primitive</a></td>
+<td>Look Up a Primitive Function</td></tr>
+<tr><td width="25%"><a href="print.html">print</a></td>
+<td>Print Values</td></tr>
+<tr><td width="25%"><a href="AsIs.html">print.AsIs</a></td>
+<td>Inhibit Interpretation/Conversion of Objects</td></tr>
+<tr><td width="25%"><a href="by.html">print.by</a></td>
+<td>Apply a Function to a Data Frame Split by Factors</td></tr>
+<tr><td width="25%"><a href="conditions.html">print.condition</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="connections.html">print.connection</a></td>
+<td>Functions to Manipulate Connections</td></tr>
+<tr><td width="25%"><a href="print.dataframe.html">print.data.frame</a></td>
+<td>Printing Data Frames</td></tr>
+<tr><td width="25%"><a href="Dates.html">print.Date</a></td>
+<td>Date Class</td></tr>
+<tr><td width="25%"><a href="print.default.html">print.default</a></td>
+<td>Default Printing</td></tr>
+<tr><td width="25%"><a href="difftime.html">print.difftime</a></td>
+<td>Time Intervals</td></tr>
+<tr><td width="25%"><a href="getLoadedDLLs.html">print.DLLInfo</a></td>
+<td>Get DLLs Loaded in Current Session</td></tr>
+<tr><td width="25%"><a href="hexmode.html">print.hexmode</a></td>
+<td>Display Numbers in Hexadecimal</td></tr>
+<tr><td width="25%"><a href="library.html">print.libraryIQR</a></td>
+<td>Loading and Listing of Packages</td></tr>
+<tr><td width="25%"><a href="getDLLRegisteredRoutines.html">print.NativeRoutineList</a></td>
+<td>Reflectance Information for C/Fortran routines in a DLL</td></tr>
+<tr><td width="25%"><a href="noquote.html">print.noquote</a></td>
+<td>Class for 'no quote' Printing of Character Strings</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">print.numeric_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="octmode.html">print.octmode</a></td>
+<td>Display Numbers in Octal</td></tr>
+<tr><td width="25%"><a href="library.html">print.packageInfo</a></td>
+<td>Loading and Listing of Packages</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">print.POSIXct</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="proc.time.html">print.proc_time</a></td>
+<td>Running Time of R</td></tr>
+<tr><td width="25%"><a href="rle.html">print.rle</a></td>
+<td>Run Length Encoding</td></tr>
+<tr><td width="25%"><a href="print.html">print.simple.list</a></td>
+<td>Print Values</td></tr>
+<tr><td width="25%"><a href="srcfile.html">print.srcfile</a></td>
+<td>References to source files</td></tr>
+<tr><td width="25%"><a href="srcfile.html">print.srcref</a></td>
+<td>References to source files</td></tr>
+<tr><td width="25%"><a href="table.html">print.summary.table</a></td>
+<td>Cross Tabulation and Table Creation</td></tr>
+<tr><td width="25%"><a href="summary.html">print.summaryDefault</a></td>
+<td>Object Summaries</td></tr>
+<tr><td width="25%"><a href="print.html">print.table</a></td>
+<td>Print Values</td></tr>
+<tr><td width="25%"><a href="warnings.html">print.warnings</a></td>
+<td>Print Warning Messages</td></tr>
+<tr><td width="25%"><a href="prmatrix.html">prmatrix</a></td>
+<td>Print Matrices, Old-style</td></tr>
+<tr><td width="25%"><a href="proc.time.html">proc.time</a></td>
+<td>Running Time of R</td></tr>
+<tr><td width="25%"><a href="prod.html">prod</a></td>
+<td>Product of Vector Elements</td></tr>
+<tr><td width="25%"><a href="delayedAssign.html">promise</a></td>
+<td>Delay Evaluation</td></tr>
+<tr><td width="25%"><a href="delayedAssign.html">promises</a></td>
+<td>Delay Evaluation</td></tr>
+<tr><td width="25%"><a href="prop.table.html">prop.table</a></td>
+<td>Express Table Entries as Fraction of Marginal Table</td></tr>
+<tr><td width="25%"><a href="Special.html">psigamma</a></td>
+<td>Special Functions of Mathematics</td></tr>
+<tr><td width="25%"><a href="pushBack.html">pushBack</a></td>
+<td>Push Text Back on to a Connection</td></tr>
+<tr><td width="25%"><a href="pushBack.html">pushBackLength</a></td>
+<td>Push Text Back on to a Connection</td></tr>
+</table>
+
+<h2><a name="Q">-- Q --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="quit.html">q</a></td>
+<td>Terminate an R Session</td></tr>
+<tr><td width="25%"><a href="qr.html">qr</a></td>
+<td>The QR Decomposition of a Matrix</td></tr>
+<tr><td width="25%"><a href="qr.html">qr.coef</a></td>
+<td>The QR Decomposition of a Matrix</td></tr>
+<tr><td width="25%"><a href="qr.html">qr.default</a></td>
+<td>The QR Decomposition of a Matrix</td></tr>
+<tr><td width="25%"><a href="qr.html">qr.fitted</a></td>
+<td>The QR Decomposition of a Matrix</td></tr>
+<tr><td width="25%"><a href="qraux.html">qr.Q</a></td>
+<td>Reconstruct the Q, R, or X Matrices from a QR Object</td></tr>
+<tr><td width="25%"><a href="qr.html">qr.qty</a></td>
+<td>The QR Decomposition of a Matrix</td></tr>
+<tr><td width="25%"><a href="qr.html">qr.qy</a></td>
+<td>The QR Decomposition of a Matrix</td></tr>
+<tr><td width="25%"><a href="qraux.html">qr.R</a></td>
+<td>Reconstruct the Q, R, or X Matrices from a QR Object</td></tr>
+<tr><td width="25%"><a href="qr.html">qr.resid</a></td>
+<td>The QR Decomposition of a Matrix</td></tr>
+<tr><td width="25%"><a href="qr.html">qr.solve</a></td>
+<td>The QR Decomposition of a Matrix</td></tr>
+<tr><td width="25%"><a href="qraux.html">qr.X</a></td>
+<td>Reconstruct the Q, R, or X Matrices from a QR Object</td></tr>
+<tr><td width="25%"><a href="weekday.POSIXt.html">quarters</a></td>
+<td>Extract Parts of a POSIXt or Date Object</td></tr>
+<tr><td width="25%"><a href="quit.html">quit</a></td>
+<td>Terminate an R Session</td></tr>
+<tr><td width="25%"><a href="substitute.html">quote</a></td>
+<td>Substituting and Quoting Expressions</td></tr>
+<tr><td width="25%"><a href="Quotes.html">Quotes</a></td>
+<td>Quotes</td></tr>
+</table>
+
+<h2><a name="R">-- R --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Rhome.html">R.home</a></td>
+<td>Return the R Home Directory</td></tr>
+<tr><td width="25%"><a href="Version.html">R.Version</a></td>
+<td>Version Information</td></tr>
+<tr><td width="25%"><a href="Version.html">R.version.string</a></td>
+<td>Version Information</td></tr>
+<tr><td width="25%"><a href="Random.html">Random</a></td>
+<td>Random Number Generation</td></tr>
+<tr><td width="25%"><a href="Random-user.html">Random.user</a></td>
+<td>User-supplied Random Number Generation</td></tr>
+<tr><td width="25%"><a href="range.html">range</a></td>
+<td>Range of Values</td></tr>
+<tr><td width="25%"><a href="rank.html">rank</a></td>
+<td>Sample Ranks</td></tr>
+<tr><td width="25%"><a href="rapply.html">rapply</a></td>
+<td>Recursively Apply a Function to a List</td></tr>
+<tr><td width="25%"><a href="raw.html">raw</a></td>
+<td>Raw Vectors</td></tr>
+<tr><td width="25%"><a href="rawConnection.html">rawConnection</a></td>
+<td>Raw Connections</td></tr>
+<tr><td width="25%"><a href="rawConnection.html">rawConnectionValue</a></td>
+<td>Raw Connections</td></tr>
+<tr><td width="25%"><a href="rawConversion.html">rawShift</a></td>
+<td>Convert to or from Raw Vectors</td></tr>
+<tr><td width="25%"><a href="rawConversion.html">rawToBits</a></td>
+<td>Convert to or from Raw Vectors</td></tr>
+<tr><td width="25%"><a href="rawConversion.html">rawToChar</a></td>
+<td>Convert to or from Raw Vectors</td></tr>
+<tr><td width="25%"><a href="cbind.html">rbind</a></td>
+<td>Combine R Objects by Rows or Columns</td></tr>
+<tr><td width="25%"><a href="cbind.html">rbind.data.frame</a></td>
+<td>Combine R Objects by Rows or Columns</td></tr>
+<tr><td width="25%"><a href="kappa.html">rcond</a></td>
+<td>Compute or Estimate the Condition Number of a Matrix</td></tr>
+<tr><td width="25%"><a href="RdUtils.html">Rd2pdf</a></td>
+<td>Utilities for Processing Rd Files</td></tr>
+<tr><td width="25%"><a href="RdUtils.html">Rdconv</a></td>
+<td>Utilities for Processing Rd Files</td></tr>
+<tr><td width="25%"><a href="complex.html">Re</a></td>
+<td>Complex Vectors</td></tr>
+<tr><td width="25%"><a href="dcf.html">read.dcf</a></td>
+<td>Read and Write Data in DCF Format</td></tr>
+<tr><td width="25%"><a href="readBin.html">readBin</a></td>
+<td>Transfer Binary Data To and From Connections</td></tr>
+<tr><td width="25%"><a href="readChar.html">readChar</a></td>
+<td>Transfer Character Strings To and From Connections</td></tr>
+<tr><td width="25%"><a href="readline.html">readline</a></td>
+<td>Read a Line from the Terminal</td></tr>
+<tr><td width="25%"><a href="readLines.html">readLines</a></td>
+<td>Read Text Lines from a Connection</td></tr>
+<tr><td width="25%"><a href="readRDS.html">readRDS</a></td>
+<td>Serialization Interface for Single Objects</td></tr>
+<tr><td width="25%"><a href="readRenviron.html">readRenviron</a></td>
+<td>Set Environment Variables from a File</td></tr>
+<tr><td width="25%"><a href="real.html">real</a></td>
+<td>Real Vectors</td></tr>
+<tr><td width="25%"><a href="Recall.html">Recall</a></td>
+<td>Recursive Calling</td></tr>
+<tr><td width="25%"><a href="funprog.html">Reduce</a></td>
+<td>Common Higher-Order Functions in Functional Programming Languages</td></tr>
+<tr><td width="25%"><a href="reg.finalizer.html">reg.finalizer</a></td>
+<td>Finalization of Objects</td></tr>
+<tr><td width="25%"><a href="regex.html">regex</a></td>
+<td>Regular Expressions as used in R</td></tr>
+<tr><td width="25%"><a href="grep.html">regexec</a></td>
+<td>Pattern Matching and Replacement</td></tr>
+<tr><td width="25%"><a href="regex.html">regexp</a></td>
+<td>Regular Expressions as used in R</td></tr>
+<tr><td width="25%"><a href="grep.html">regexpr</a></td>
+<td>Pattern Matching and Replacement</td></tr>
+<tr><td width="25%"><a href="getNativeSymbolInfo.html">RegisteredNativeSymbol</a></td>
+<td>Obtain a Description of one or more Native (C/Fortran) Symbols</td></tr>
+<tr><td width="25%"><a href="regmatches.html">regmatches</a></td>
+<td>Extract or Replace Matched Substrings</td></tr>
+<tr><td width="25%"><a href="regex.html">regular expression</a></td>
+<td>Regular Expressions as used in R</td></tr>
+<tr><td width="25%"><a href="rm.html">remove</a></td>
+<td>Remove Objects from a Specified Environment</td></tr>
+<tr><td width="25%"><a href="converters.html">removeCConverter</a></td>
+<td>Management of .C argument conversion list</td></tr>
+<tr><td width="25%"><a href="taskCallback.html">removeTaskCallback</a></td>
+<td>Add or Remove a Top-Level Task Callback</td></tr>
+<tr><td width="25%"><a href="Startup.html">Renviron</a></td>
+<td>Initialization at Start of an R Session</td></tr>
+<tr><td width="25%"><a href="rep.html">rep</a></td>
+<td>Replicate Elements of Vectors and Lists</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">rep.numeric_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="Control.html">repeat</a></td>
+<td>Control Flow</td></tr>
+<tr><td width="25%"><a href="replace.html">replace</a></td>
+<td>Replace Values in a Vector</td></tr>
+<tr><td width="25%"><a href="lapply.html">replicate</a></td>
+<td>Apply a Function over a List or Vector</td></tr>
+<tr><td width="25%"><a href="library.html">require</a></td>
+<td>Loading and Listing of Packages</td></tr>
+<tr><td width="25%"><a href="ns-load.html">requireNamespace</a></td>
+<td>Loading and Unloading Namespaces</td></tr>
+<tr><td width="25%"><a href="Reserved.html">Reserved</a></td>
+<td>Reserved Words in R</td></tr>
+<tr><td width="25%"><a href="Reserved.html">reserved</a></td>
+<td>Reserved Words in R</td></tr>
+<tr><td width="25%"><a href="conditions.html">restartDescription</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="conditions.html">restartFormals</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="tracemem.html">retracemem</a></td>
+<td>Trace Copying of Objects</td></tr>
+<tr><td width="25%"><a href="function.html">return</a></td>
+<td>Function Definition</td></tr>
+<tr><td width="25%"><a href="rev.html">rev</a></td>
+<td>Reverse Elements</td></tr>
+<tr><td width="25%"><a href="rle.html">rle</a></td>
+<td>Run Length Encoding</td></tr>
+<tr><td width="25%"><a href="rm.html">rm</a></td>
+<td>Remove Objects from a Specified Environment</td></tr>
+<tr><td width="25%"><a href="Random.html">RNG</a></td>
+<td>Random Number Generation</td></tr>
+<tr><td width="25%"><a href="Random.html">RNGkind</a></td>
+<td>Random Number Generation</td></tr>
+<tr><td width="25%"><a href="Random.html">RNGversion</a></td>
+<td>Random Number Generation</td></tr>
+<tr><td width="25%"><a href="Round.html">round</a></td>
+<td>Rounding of Numbers</td></tr>
+<tr><td width="25%"><a href="round.POSIXt.html">round.Date</a></td>
+<td>Round / Truncate Data-Time Objects</td></tr>
+<tr><td width="25%"><a href="round.POSIXt.html">round.POSIXt</a></td>
+<td>Round / Truncate Data-Time Objects</td></tr>
+<tr><td width="25%"><a href="row.html">row</a></td>
+<td>Row Indexes</td></tr>
+<tr><td width="25%"><a href="row.names.html">row.names</a></td>
+<td>Get and Set Row Names for Data Frames</td></tr>
+<tr><td width="25%"><a href="colSums.html">rowMeans</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="colnames.html">rownames</a></td>
+<td>Row and Column Names</td></tr>
+<tr><td width="25%"><a href="rowsum.html">rowsum</a></td>
+<td>Give Column Sums of a Matrix or Data Frame, Based on a Grouping Variable</td></tr>
+<tr><td width="25%"><a href="colSums.html">rowSums</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="Startup.html">Rprofile</a></td>
+<td>Initialization at Start of an R Session</td></tr>
+<tr><td width="25%"><a href="Startup.html">Rprofile.site</a></td>
+<td>Initialization at Start of an R Session</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">R_BATCH</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">R_BROWSER</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">R_COMPLETION</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="Startup.html">R_DEFAULT_PACKAGES</a></td>
+<td>Initialization at Start of an R Session</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">R_DOC_DIR</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="Startup.html">R_ENVIRON</a></td>
+<td>Initialization at Start of an R Session</td></tr>
+<tr><td width="25%"><a href="Startup.html">R_ENVIRON_USER</a></td>
+<td>Initialization at Start of an R Session</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">R_GSCMD</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">R_HISTFILE</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">R_HISTSIZE</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="Rhome.html">R_HOME</a></td>
+<td>Return the R Home Directory</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">R_INCLUDE_DIR</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="libPaths.html">R_LIBS</a></td>
+<td>Search Paths for Packages</td></tr>
+<tr><td width="25%"><a href="libPaths.html">R_LIBS_SITE</a></td>
+<td>Search Paths for Packages</td></tr>
+<tr><td width="25%"><a href="libPaths.html">R_LIBS_USER</a></td>
+<td>Search Paths for Packages</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">R_PAPERSIZE</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">R_PDFVIEWER</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">R_PLATFORM</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="Startup.html">R_PROFILE</a></td>
+<td>Initialization at Start of an R Session</td></tr>
+<tr><td width="25%"><a href="Startup.html">R_PROFILE_USER</a></td>
+<td>Initialization at Start of an R Session</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">R_RD4PDF</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">R_SHARE_DIR</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">R_system_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">R_TEXI2DVICMD</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">R_UNZIPCMD</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">R_USER</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">R_ZIPCMD</a></td>
+<td>Environment Variables</td></tr>
+</table>
+
+<h2><a name="S">-- S --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="groupGeneric.html">S3groupGeneric</a></td>
+<td>S3 Group Generic Functions</td></tr>
+<tr><td width="25%"><a href="UseMethod.html">S3Methods</a></td>
+<td>Class Methods</td></tr>
+<tr><td width="25%"><a href="isS4.html">S4</a></td>
+<td>Test for an S4 object</td></tr>
+<tr><td width="25%"><a href="sample.html">sample</a></td>
+<td>Random Samples and Permutations</td></tr>
+<tr><td width="25%"><a href="lapply.html">sapply</a></td>
+<td>Apply a Function over a List or Vector</td></tr>
+<tr><td width="25%"><a href="save.html">save</a></td>
+<td>Save R Objects</td></tr>
+<tr><td width="25%"><a href="readRDS.html">saveRDS</a></td>
+<td>Serialization Interface for Single Objects</td></tr>
+<tr><td width="25%"><a href="scale.html">scale</a></td>
+<td>Scaling and Centering of Matrix-like Objects</td></tr>
+<tr><td width="25%"><a href="scan.html">scan</a></td>
+<td>Read Data Values</td></tr>
+<tr><td width="25%"><a href="search.html">search</a></td>
+<td>Give Search Path for R Objects</td></tr>
+<tr><td width="25%"><a href="search.html">searchpaths</a></td>
+<td>Give Search Path for R Objects</td></tr>
+<tr><td width="25%"><a href="seek.html">seek</a></td>
+<td>Functions to Reposition Connections</td></tr>
+<tr><td width="25%"><a href="seq.html">seq</a></td>
+<td>Sequence Generation</td></tr>
+<tr><td width="25%"><a href="seq.Date.html">seq.Date</a></td>
+<td>Generate Regular Sequences of Dates</td></tr>
+<tr><td width="25%"><a href="seq.POSIXt.html">seq.POSIXt</a></td>
+<td>Generate Regular Sequences of Times</td></tr>
+<tr><td width="25%"><a href="sequence.html">sequence</a></td>
+<td>Create A Vector of Sequences</td></tr>
+<tr><td width="25%"><a href="seq.html">seq_along</a></td>
+<td>Sequence Generation</td></tr>
+<tr><td width="25%"><a href="seq.html">seq_len</a></td>
+<td>Sequence Generation</td></tr>
+<tr><td width="25%"><a href="serialize.html">serialize</a></td>
+<td>Simple Serialization Interface</td></tr>
+<tr><td width="25%"><a href="Random.html">set.seed</a></td>
+<td>Random Number Generation</td></tr>
+<tr><td width="25%"><a href="converters.html">setCConverterStatus</a></td>
+<td>Management of .C argument conversion list</td></tr>
+<tr><td width="25%"><a href="sets.html">setdiff</a></td>
+<td>Set Operations</td></tr>
+<tr><td width="25%"><a href="sets.html">setequal</a></td>
+<td>Set Operations</td></tr>
+<tr><td width="25%"><a href="userhooks.html">setHook</a></td>
+<td>Functions to Get and Set Hooks for Load, Attach, Detach and Unload</td></tr>
+<tr><td width="25%"><a href="setTimeLimit.html">setSessionTimeLimit</a></td>
+<td>Set CPU and/or Elapsed Time Limits</td></tr>
+<tr><td width="25%"><a href="setTimeLimit.html">setTimeLimit</a></td>
+<td>Set CPU and/or Elapsed Time Limits</td></tr>
+<tr><td width="25%"><a href="getwd.html">setwd</a></td>
+<td>Get or Set Working Directory</td></tr>
+<tr><td width="25%"><a href="shell.html">shell</a></td>
+<td>Invoke a System Command, using a Shell</td></tr>
+<tr><td width="25%"><a href="shell.exec.html">shell.exec</a></td>
+<td>Open a File or URL using Windows File Associations</td></tr>
+<tr><td width="25%"><a href="showConnections.html">showConnections</a></td>
+<td>Display Connections</td></tr>
+<tr><td width="25%"><a href="shQuote.html">shQuote</a></td>
+<td>Quote Strings for Use in OS Shells</td></tr>
+<tr><td width="25%"><a href="sign.html">sign</a></td>
+<td>Sign Function</td></tr>
+<tr><td width="25%"><a href="conditions.html">signalCondition</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="Round.html">signif</a></td>
+<td>Rounding of Numbers</td></tr>
+<tr><td width="25%"><a href="conditions.html">simpleCondition</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="conditions.html">simpleError</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="conditions.html">simpleMessage</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="conditions.html">simpleWarning</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="lapply.html">simplify2array</a></td>
+<td>Apply a Function over a List or Vector</td></tr>
+<tr><td width="25%"><a href="Trig.html">sin</a></td>
+<td>Trigonometric Functions</td></tr>
+<tr><td width="25%"><a href="double.html">single</a></td>
+<td>Double-Precision Vectors</td></tr>
+<tr><td width="25%"><a href="Hyperbolic.html">sinh</a></td>
+<td>Hyperbolic Functions</td></tr>
+<tr><td width="25%"><a href="sink.html">sink</a></td>
+<td>Send R Output to a File</td></tr>
+<tr><td width="25%"><a href="slice.index.html">slice.index</a></td>
+<td>Slice Indexes in an Array</td></tr>
+<tr><td width="25%"><a href="connections.html">socketConnection</a></td>
+<td>Functions to Manipulate Connections</td></tr>
+<tr><td width="25%"><a href="socketSelect.html">socketSelect</a></td>
+<td>Wait on Socket Connections</td></tr>
+<tr><td width="25%"><a href="solve.html">solve</a></td>
+<td>Solve a System of Equations</td></tr>
+<tr><td width="25%"><a href="qr.html">solve.qr</a></td>
+<td>The QR Decomposition of a Matrix</td></tr>
+<tr><td width="25%"><a href="sort.html">sort</a></td>
+<td>Sorting or Ordering Vectors</td></tr>
+<tr><td width="25%"><a href="order.html">sort.list</a></td>
+<td>Ordering Permutation</td></tr>
+<tr><td width="25%"><a href="source.html">source</a></td>
+<td>Read R Code from a File or a Connection</td></tr>
+<tr><td width="25%"><a href="Special.html">Special</a></td>
+<td>Special Functions of Mathematics</td></tr>
+<tr><td width="25%"><a href="split.html">split</a></td>
+<td>Divide into Groups and Reassemble</td></tr>
+<tr><td width="25%"><a href="Dates.html">split.Date</a></td>
+<td>Date Class</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">split.POSIXct</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="sprintf.html">sprintf</a></td>
+<td>Use C-style String Formatting Commands</td></tr>
+<tr><td width="25%"><a href="MathFun.html">sqrt</a></td>
+<td>Miscellaneous Mathematical Functions</td></tr>
+<tr><td width="25%"><a href="sQuote.html">sQuote</a></td>
+<td>Quote Text</td></tr>
+<tr><td width="25%"><a href="srcfile.html">srcfile</a></td>
+<td>References to source files</td></tr>
+<tr><td width="25%"><a href="srcfile.html">srcfile-class</a></td>
+<td>References to source files</td></tr>
+<tr><td width="25%"><a href="srcfile.html">srcfilealias</a></td>
+<td>References to source files</td></tr>
+<tr><td width="25%"><a href="srcfile.html">srcfilealias-class</a></td>
+<td>References to source files</td></tr>
+<tr><td width="25%"><a href="srcfile.html">srcfilecopy</a></td>
+<td>References to source files</td></tr>
+<tr><td width="25%"><a href="srcfile.html">srcfilecopy-class</a></td>
+<td>References to source files</td></tr>
+<tr><td width="25%"><a href="srcfile.html">srcref</a></td>
+<td>References to source files</td></tr>
+<tr><td width="25%"><a href="srcfile.html">srcref-class</a></td>
+<td>References to source files</td></tr>
+<tr><td width="25%"><a href="Startup.html">Startup</a></td>
+<td>Initialization at Start of an R Session</td></tr>
+<tr><td width="25%"><a href="showConnections.html">stderr</a></td>
+<td>Display Connections</td></tr>
+<tr><td width="25%"><a href="showConnections.html">stdin</a></td>
+<td>Display Connections</td></tr>
+<tr><td width="25%"><a href="showConnections.html">stdout</a></td>
+<td>Display Connections</td></tr>
+<tr><td width="25%"><a href="stop.html">stop</a></td>
+<td>Stop Function Execution</td></tr>
+<tr><td width="25%"><a href="stopifnot.html">stopifnot</a></td>
+<td>Ensure the Truth of R Expressions</td></tr>
+<tr><td width="25%"><a href="mode.html">storage.mode</a></td>
+<td>The (Storage) Mode of an Object</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">str.POSIXt</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="strptime.html">strftime</a></td>
+<td>Date-time Conversion Functions to and from Character</td></tr>
+<tr><td width="25%"><a href="strptime.html">strptime</a></td>
+<td>Date-time Conversion Functions to and from Character</td></tr>
+<tr><td width="25%"><a href="strsplit.html">strsplit</a></td>
+<td>Split the Elements of a Character Vector</td></tr>
+<tr><td width="25%"><a href="strtoi.html">strtoi</a></td>
+<td>Convert Strings to Integers</td></tr>
+<tr><td width="25%"><a href="strtrim.html">strtrim</a></td>
+<td>Trim Character Strings to Specified Display Widths</td></tr>
+<tr><td width="25%"><a href="structure.html">structure</a></td>
+<td>Attribute Specification</td></tr>
+<tr><td width="25%"><a href="strwrap.html">strwrap</a></td>
+<td>Wrap Character Strings to Format Paragraphs</td></tr>
+<tr><td width="25%"><a href="grep.html">sub</a></td>
+<td>Pattern Matching and Replacement</td></tr>
+<tr><td width="25%"><a href="Extract.html">Subscript</a></td>
+<td>Extract or Replace Parts of an Object</td></tr>
+<tr><td width="25%"><a href="subset.html">subset</a></td>
+<td>Subsetting Vectors, Matrices and Data Frames</td></tr>
+<tr><td width="25%"><a href="substitute.html">substitute</a></td>
+<td>Substituting and Quoting Expressions</td></tr>
+<tr><td width="25%"><a href="substr.html">substr</a></td>
+<td>Substrings of a Character Vector</td></tr>
+<tr><td width="25%"><a href="substr.html">substring</a></td>
+<td>Substrings of a Character Vector</td></tr>
+<tr><td width="25%"><a href="sum.html">sum</a></td>
+<td>Sum of Vector Elements</td></tr>
+<tr><td width="25%"><a href="groupGeneric.html">Summary</a></td>
+<td>S3 Group Generic Functions</td></tr>
+<tr><td width="25%"><a href="summary.html">summary</a></td>
+<td>Object Summaries</td></tr>
+<tr><td width="25%"><a href="connections.html">summary.connection</a></td>
+<td>Functions to Manipulate Connections</td></tr>
+<tr><td width="25%"><a href="Dates.html">Summary.Date</a></td>
+<td>Date Class</td></tr>
+<tr><td width="25%"><a href="Dates.html">summary.Date</a></td>
+<td>Date Class</td></tr>
+<tr><td width="25%"><a href="difftime.html">Summary.difftime</a></td>
+<td>Time Intervals</td></tr>
+<tr><td width="25%"><a href="factor.html">Summary.factor</a></td>
+<td>Factors</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">Summary.numeric_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="factor.html">Summary.ordered</a></td>
+<td>Factors</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">Summary.POSIXct</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">summary.POSIXct</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">Summary.POSIXlt</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="srcfile.html">summary.srcfile</a></td>
+<td>References to source files</td></tr>
+<tr><td width="25%"><a href="srcfile.html">summary.srcref</a></td>
+<td>References to source files</td></tr>
+<tr><td width="25%"><a href="table.html">summary.table</a></td>
+<td>Cross Tabulation and Table Creation</td></tr>
+<tr><td width="25%"><a href="message.html">suppressMessages</a></td>
+<td>Diagnostic Messages</td></tr>
+<tr><td width="25%"><a href="message.html">suppressPackageStartupMessages</a></td>
+<td>Diagnostic Messages</td></tr>
+<tr><td width="25%"><a href="warning.html">suppressWarnings</a></td>
+<td>Warning Messages</td></tr>
+<tr><td width="25%"><a href="svd.html">svd</a></td>
+<td>Singular Value Decomposition of a Matrix</td></tr>
+<tr><td width="25%"><a href="sweep.html">sweep</a></td>
+<td>Sweep out Array Summaries</td></tr>
+<tr><td width="25%"><a href="switch.html">switch</a></td>
+<td>Select One of a List of Alternatives</td></tr>
+<tr><td width="25%"><a href="Syntax.html">Syntax</a></td>
+<td>Operator Syntax and Precedence</td></tr>
+<tr><td width="25%"><a href="files2.html">Sys.chmod</a></td>
+<td>Manipulaton of Directories and File Permissions</td></tr>
+<tr><td width="25%"><a href="Sys.time.html">Sys.Date</a></td>
+<td>Get Current Date and Time</td></tr>
+<tr><td width="25%"><a href="Sys.getenv.html">Sys.getenv</a></td>
+<td>Get Environment Variables</td></tr>
+<tr><td width="25%"><a href="locales.html">Sys.getlocale</a></td>
+<td>Query or Set Aspects of the Locale</td></tr>
+<tr><td width="25%"><a href="Sys.getpid.html">Sys.getpid</a></td>
+<td>Get the Process ID of the R Session</td></tr>
+<tr><td width="25%"><a href="Sys.glob.html">Sys.glob</a></td>
+<td>Wildcard Expansion on File Paths</td></tr>
+<tr><td width="25%"><a href="Sys.info.html">Sys.info</a></td>
+<td>Extract System and User Information</td></tr>
+<tr><td width="25%"><a href="files.html">Sys.junction</a></td>
+<td>File Manipulation</td></tr>
+<tr><td width="25%"><a href="Sys.localeconv.html">Sys.localeconv</a></td>
+<td>Find Details of the Numerical and Monetary Representations in the Current Locale</td></tr>
+<tr><td width="25%"><a href="sys.parent.html">sys.on.exit</a></td>
+<td>Functions to Access the Function Call Stack</td></tr>
+<tr><td width="25%"><a href="sys.parent.html">sys.parent</a></td>
+<td>Functions to Access the Function Call Stack</td></tr>
+<tr><td width="25%"><a href="Sys.readlink.html">Sys.readlink</a></td>
+<td>Read File Symbolic Links</td></tr>
+<tr><td width="25%"><a href="Sys.setenv.html">Sys.setenv</a></td>
+<td>Set or Unset Environment Variables</td></tr>
+<tr><td width="25%"><a href="Sys.setFileTime.html">Sys.setFileTime</a></td>
+<td>Set File Time</td></tr>
+<tr><td width="25%"><a href="locales.html">Sys.setlocale</a></td>
+<td>Query or Set Aspects of the Locale</td></tr>
+<tr><td width="25%"><a href="Sys.sleep.html">Sys.sleep</a></td>
+<td>Suspend Execution for a Time Interval</td></tr>
+<tr><td width="25%"><a href="sys.source.html">sys.source</a></td>
+<td>Parse and Evaluate Expressions from a File</td></tr>
+<tr><td width="25%"><a href="sys.parent.html">sys.status</a></td>
+<td>Functions to Access the Function Call Stack</td></tr>
+<tr><td width="25%"><a href="Sys.time.html">Sys.time</a></td>
+<td>Get Current Date and Time</td></tr>
+<tr><td width="25%"><a href="timezones.html">Sys.timezone</a></td>
+<td>Time Zones</td></tr>
+<tr><td width="25%"><a href="files2.html">Sys.umask</a></td>
+<td>Manipulaton of Directories and File Permissions</td></tr>
+<tr><td width="25%"><a href="Sys.setenv.html">Sys.unsetenv</a></td>
+<td>Set or Unset Environment Variables</td></tr>
+<tr><td width="25%"><a href="Sys.which.html">Sys.which</a></td>
+<td>Find Full Paths to Executables</td></tr>
+<tr><td width="25%"><a href="system.html">system</a></td>
+<td>Invoke a System Command</td></tr>
+<tr><td width="25%"><a href="system.file.html">system.file</a></td>
+<td>Find Names of R System Files</td></tr>
+<tr><td width="25%"><a href="system.time.html">system.time</a></td>
+<td>CPU Time Used</td></tr>
+<tr><td width="25%"><a href="system2.html">system2</a></td>
+<td>Invoke a System Command</td></tr>
+</table>
+
+<h2><a name="T">-- T --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="logical.html">T</a></td>
+<td>Logical Vectors</td></tr>
+<tr><td width="25%"><a href="t.html">t</a></td>
+<td>Matrix Transpose</td></tr>
+<tr><td width="25%"><a href="table.html">table</a></td>
+<td>Cross Tabulation and Table Creation</td></tr>
+<tr><td width="25%"><a href="tabulate.html">tabulate</a></td>
+<td>Tabulation for Vectors</td></tr>
+<tr><td width="25%"><a href="Trig.html">tan</a></td>
+<td>Trigonometric Functions</td></tr>
+<tr><td width="25%"><a href="Hyperbolic.html">tanh</a></td>
+<td>Hyperbolic Functions</td></tr>
+<tr><td width="25%"><a href="tapply.html">tapply</a></td>
+<td>Apply a Function Over a Ragged Array</td></tr>
+<tr><td width="25%"><a href="taskCallbackManager.html">taskCallbackManager</a></td>
+<td>Create an R-level Task Callback Manager</td></tr>
+<tr><td width="25%"><a href="crossprod.html">tcrossprod</a></td>
+<td>Matrix Crossproduct</td></tr>
+<tr><td width="25%"><a href="tempfile.html">tempdir</a></td>
+<td>Create Names for Temporary Files</td></tr>
+<tr><td width="25%"><a href="tempfile.html">tempfile</a></td>
+<td>Create Names for Temporary Files</td></tr>
+<tr><td width="25%"><a href="textconnections.html">textConnection</a></td>
+<td>Text Connections</td></tr>
+<tr><td width="25%"><a href="textconnections.html">textConnectionValue</a></td>
+<td>Text Connections</td></tr>
+<tr><td width="25%"><a href="tilde.html">tilde</a></td>
+<td>Tilde Operator</td></tr>
+<tr><td width="25%"><a href="path.expand.html">tilde expansion</a></td>
+<td>Expand File Paths</td></tr>
+<tr><td width="25%"><a href="difftime.html">time interval</a></td>
+<td>Time Intervals</td></tr>
+<tr><td width="25%"><a href="timezones.html">time zone</a></td>
+<td>Time Zones</td></tr>
+<tr><td width="25%"><a href="timezones.html">time zones</a></td>
+<td>Time Zones</td></tr>
+<tr><td width="25%"><a href="timezones.html">timezone</a></td>
+<td>Time Zones</td></tr>
+<tr><td width="25%"><a href="EnvVar.html">TMPDIR</a></td>
+<td>Environment Variables</td></tr>
+<tr><td width="25%"><a href="chartr.html">tolower</a></td>
+<td>Character Translation and Casefolding</td></tr>
+<tr><td width="25%"><a href="ns-topenv.html">topenv</a></td>
+<td>Top Level Environment</td></tr>
+<tr><td width="25%"><a href="toString.html">toString</a></td>
+<td>Convert an R Object to a Character String</td></tr>
+<tr><td width="25%"><a href="chartr.html">toupper</a></td>
+<td>Character Translation and Casefolding</td></tr>
+<tr><td width="25%"><a href="trace.html">trace</a></td>
+<td>Interactive Tracing and Debugging of Calls to a Function or Method</td></tr>
+<tr><td width="25%"><a href="traceback.html">traceback</a></td>
+<td>Print Call Stacks</td></tr>
+<tr><td width="25%"><a href="tracemem.html">tracemem</a></td>
+<td>Trace Copying of Objects</td></tr>
+<tr><td width="25%"><a href="trace.html">tracingState</a></td>
+<td>Interactive Tracing and Debugging of Calls to a Function or Method</td></tr>
+<tr><td width="25%"><a href="transform.html">transform</a></td>
+<td>Transform an Object, for Example a Data Frame</td></tr>
+<tr><td width="25%"><a href="Trig.html">Trig</a></td>
+<td>Trigonometric Functions</td></tr>
+<tr><td width="25%"><a href="Special.html">trigamma</a></td>
+<td>Special Functions of Mathematics</td></tr>
+<tr><td width="25%"><a href="logical.html">TRUE</a></td>
+<td>Logical Vectors</td></tr>
+<tr><td width="25%"><a href="Round.html">trunc</a></td>
+<td>Rounding of Numbers</td></tr>
+<tr><td width="25%"><a href="round.POSIXt.html">trunc.Date</a></td>
+<td>Round / Truncate Data-Time Objects</td></tr>
+<tr><td width="25%"><a href="round.POSIXt.html">trunc.POSIXt</a></td>
+<td>Round / Truncate Data-Time Objects</td></tr>
+<tr><td width="25%"><a href="seek.html">truncate</a></td>
+<td>Functions to Reposition Connections</td></tr>
+<tr><td width="25%"><a href="try.html">try</a></td>
+<td>Try an Expression Allowing Error Recovery</td></tr>
+<tr><td width="25%"><a href="conditions.html">tryCatch</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="typeof.html">type</a></td>
+<td>The Type of an Object</td></tr>
+<tr><td width="25%"><a href="typeof.html">typeof</a></td>
+<td>The Type of an Object</td></tr>
+<tr><td width="25%"><a href="timezones.html">TZ</a></td>
+<td>Time Zones</td></tr>
+<tr><td width="25%"><a href="timezones.html">TZDIR</a></td>
+<td>Time Zones</td></tr>
+</table>
+
+<h2><a name="U">-- U --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="files2.html">umask</a></td>
+<td>Manipulaton of Directories and File Permissions</td></tr>
+<tr><td width="25%"><a href="class.html">unclass</a></td>
+<td>Object Classes</td></tr>
+<tr><td width="25%"><a href="debug.html">undebug</a></td>
+<td>Debug a Function</td></tr>
+<tr><td width="25%"><a href="sets.html">union</a></td>
+<td>Set Operations</td></tr>
+<tr><td width="25%"><a href="unique.html">unique</a></td>
+<td>Extract Unique Elements</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">unique.numeric_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">unique.POSIXlt</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="difftime.html">units</a></td>
+<td>Time Intervals</td></tr>
+<tr><td width="25%"><a href="difftime.html">units.difftime</a></td>
+<td>Time Intervals</td></tr>
+<tr><td width="25%"><a href="system.time.html">unix.time</a></td>
+<td>CPU Time Used</td></tr>
+<tr><td width="25%"><a href="unlink.html">unlink</a></td>
+<td>Delete Files and Directories</td></tr>
+<tr><td width="25%"><a href="unlist.html">unlist</a></td>
+<td>Flatten Lists</td></tr>
+<tr><td width="25%"><a href="ns-load.html">unloadNamespace</a></td>
+<td>Loading and Unloading Namespaces</td></tr>
+<tr><td width="25%"><a href="bindenv.html">unlockBinding</a></td>
+<td>Binding and Environment Adjustments</td></tr>
+<tr><td width="25%"><a href="unname.html">unname</a></td>
+<td>Remove 'names' or 'dimnames'</td></tr>
+<tr><td width="25%"><a href="serialize.html">unserialize</a></td>
+<td>Simple Serialization Interface</td></tr>
+<tr><td width="25%"><a href="split.html">unsplit</a></td>
+<td>Divide into Groups and Reassemble</td></tr>
+<tr><td width="25%"><a href="trace.html">untrace</a></td>
+<td>Interactive Tracing and Debugging of Calls to a Function or Method</td></tr>
+<tr><td width="25%"><a href="tracemem.html">untracemem</a></td>
+<td>Trace Copying of Objects</td></tr>
+<tr><td width="25%"><a href="connections.html">unz</a></td>
+<td>Functions to Manipulate Connections</td></tr>
+<tr><td width="25%"><a href="lower.tri.html">upper.tri</a></td>
+<td>Lower and Upper Triangular Part of a Matrix</td></tr>
+<tr><td width="25%"><a href="connections.html">url</a></td>
+<td>Functions to Manipulate Connections</td></tr>
+<tr><td width="25%"><a href="UseMethod.html">UseMethod</a></td>
+<td>Class Methods</td></tr>
+<tr><td width="25%"><a href="utf8Conversion.html">utf8ToInt</a></td>
+<td>Convert to or from UTF-8-encoded Character Vectors</td></tr>
+</table>
+
+<h2><a name="V">-- V --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="lapply.html">vapply</a></td>
+<td>Apply a Function over a List or Vector</td></tr>
+<tr><td width="25%"><a href="vector.html">vector</a></td>
+<td>Vectors</td></tr>
+<tr><td width="25%"><a href="Vectorize.html">Vectorize</a></td>
+<td>Vectorize a Scalar Function</td></tr>
+<tr><td width="25%"><a href="Version.html">version</a></td>
+<td>Version Information</td></tr>
+</table>
+
+<h2><a name="W">-- W --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="warning.html">warning</a></td>
+<td>Warning Messages</td></tr>
+<tr><td width="25%"><a href="warnings.html">warnings</a></td>
+<td>Print Warning Messages</td></tr>
+<tr><td width="25%"><a href="weekday.POSIXt.html">weekdays</a></td>
+<td>Extract Parts of a POSIXt or Date Object</td></tr>
+<tr><td width="25%"><a href="which.html">which</a></td>
+<td>Which indices are TRUE?</td></tr>
+<tr><td width="25%"><a href="which.min.html">which.max</a></td>
+<td>Where is the Min() or Max() ?</td></tr>
+<tr><td width="25%"><a href="which.min.html">which.min</a></td>
+<td>Where is the Min() or Max() ?</td></tr>
+<tr><td width="25%"><a href="Control.html">while</a></td>
+<td>Control Flow</td></tr>
+<tr><td width="25%"><a href="with.html">with</a></td>
+<td>Evaluate an Expression in a Data Environment</td></tr>
+<tr><td width="25%"><a href="conditions.html">withCallingHandlers</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="with.html">within</a></td>
+<td>Evaluate an Expression in a Data Environment</td></tr>
+<tr><td width="25%"><a href="conditions.html">withRestarts</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="withVisible.html">withVisible</a></td>
+<td>Return both a value and its visibility</td></tr>
+<tr><td width="25%"><a href="write.html">write</a></td>
+<td>Write Data to a File</td></tr>
+<tr><td width="25%"><a href="dcf.html">write.dcf</a></td>
+<td>Read and Write Data in DCF Format</td></tr>
+<tr><td width="25%"><a href="readBin.html">writeBin</a></td>
+<td>Transfer Binary Data To and From Connections</td></tr>
+<tr><td width="25%"><a href="readChar.html">writeChar</a></td>
+<td>Transfer Character Strings To and From Connections</td></tr>
+<tr><td width="25%"><a href="writeLines.html">writeLines</a></td>
+<td>Write Lines to a Connection</td></tr>
+</table>
+
+<h2><a name="X">-- X --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Logic.html">xor</a></td>
+<td>Logical Operators</td></tr>
+<tr><td width="25%"><a href="hexmode.html">xor.hexmode</a></td>
+<td>Display Numbers in Hexadecimal</td></tr>
+<tr><td width="25%"><a href="octmode.html">xor.octmode</a></td>
+<td>Display Numbers in Octal</td></tr>
+<tr><td width="25%"><a href="xtfrm.html">xtfrm</a></td>
+<td>Auxiliary Function for Sorting and Ranking</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">xtfrm.numeric_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="connections.html">xzfile</a></td>
+<td>Functions to Manipulate Connections</td></tr>
+</table>
+
+<h2><a name="Z">-- Z --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="zapsmall.html">zapsmall</a></td>
+<td>Rounding of Numbers</td></tr>
+</table>
+
+<h2><a name="misc">-- misc --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Logic.html">!</a></td>
+<td>Logical Operators</td></tr>
+<tr><td width="25%"><a href="hexmode.html">!.hexmode</a></td>
+<td>Display Numbers in Hexadecimal</td></tr>
+<tr><td width="25%"><a href="octmode.html">!.octmode</a></td>
+<td>Display Numbers in Octal</td></tr>
+<tr><td width="25%"><a href="Comparison.html">!=</a></td>
+<td>Relational Operators</td></tr>
+<tr><td width="25%"><a href="Quotes.html">"</a></td>
+<td>Quotes</td></tr>
+<tr><td width="25%"><a href="Extract.html">$</a></td>
+<td>Extract or Replace Parts of an Object</td></tr>
+<tr><td width="25%"><a href="getLoadedDLLs.html">$.DLLInfo</a></td>
+<td>Get DLLs Loaded in Current Session</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">$.package_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="Extract.html">$<-</a></td>
+<td>Extract or Replace Parts of an Object</td></tr>
+<tr><td width="25%"><a href="Extract.data.frame.html">$<-.data.frame</a></td>
+<td>Extract or Replace Parts of a Data Frame</td></tr>
+<tr><td width="25%"><a href="Arithmetic.html">%%</a></td>
+<td>Arithmetic Operators</td></tr>
+<tr><td width="25%"><a href="matmult.html">%*%</a></td>
+<td>Matrix Multiplication</td></tr>
+<tr><td width="25%"><a href="Arithmetic.html">%/%</a></td>
+<td>Arithmetic Operators</td></tr>
+<tr><td width="25%"><a href="match.html">%in%</a></td>
+<td>Value Matching</td></tr>
+<tr><td width="25%"><a href="outer.html">%o%</a></td>
+<td>Outer Product of Arrays</td></tr>
+<tr><td width="25%"><a href="kronecker.html">%x%</a></td>
+<td>Kronecker Products on Arrays</td></tr>
+<tr><td width="25%"><a href="Logic.html">&</a></td>
+<td>Logical Operators</td></tr>
+<tr><td width="25%"><a href="Logic.html">&&</a></td>
+<td>Logical Operators</td></tr>
+<tr><td width="25%"><a href="hexmode.html">&.hexmode</a></td>
+<td>Display Numbers in Hexadecimal</td></tr>
+<tr><td width="25%"><a href="octmode.html">&.octmode</a></td>
+<td>Display Numbers in Octal</td></tr>
+<tr><td width="25%"><a href="Quotes.html">'</a></td>
+<td>Quotes</td></tr>
+<tr><td width="25%"><a href="Paren.html">(</a></td>
+<td>Parentheses and Braces</td></tr>
+<tr><td width="25%"><a href="Arithmetic.html">*</a></td>
+<td>Arithmetic Operators</td></tr>
+<tr><td width="25%"><a href="Arithmetic.html">**</a></td>
+<td>Arithmetic Operators</td></tr>
+<tr><td width="25%"><a href="difftime.html">*.difftime</a></td>
+<td>Time Intervals</td></tr>
+<tr><td width="25%"><a href="Arithmetic.html">+</a></td>
+<td>Arithmetic Operators</td></tr>
+<tr><td width="25%"><a href="Ops.Date.html">+.Date</a></td>
+<td>Operators on the Date Class</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">+.POSIXt</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="Arithmetic.html">-</a></td>
+<td>Arithmetic Operators</td></tr>
+<tr><td width="25%"><a href="Ops.Date.html">-.Date</a></td>
+<td>Operators on the Date Class</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">-.POSIXt</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="assignOps.html">-></a></td>
+<td>Assignment Operators</td></tr>
+<tr><td width="25%"><a href="assignOps.html">->></a></td>
+<td>Assignment Operators</td></tr>
+<tr><td width="25%"><a href="agrep.html">.amatch_bounds</a></td>
+<td>Approximate String Matching (Fuzzy Matching)</td></tr>
+<tr><td width="25%"><a href="agrep.html">.amatch_costs</a></td>
+<td>Approximate String Matching (Fuzzy Matching)</td></tr>
+<tr><td width="25%"><a href="autoload.html">.Autoloaded</a></td>
+<td>On-demand Loading of Packages</td></tr>
+<tr><td width="25%"><a href="autoload.html">.AutoloadEnv</a></td>
+<td>On-demand Loading of Packages</td></tr>
+<tr><td width="25%"><a href="environment.html">.BaseNamespaceEnv</a></td>
+<td>Environment Access</td></tr>
+<tr><td width="25%"><a href="bincode.html">.bincode</a></td>
+<td>Bin a Numeric Vector</td></tr>
+<tr><td width="25%"><a href="Foreign.html">.C</a></td>
+<td>Foreign Function Interface</td></tr>
+<tr><td width="25%"><a href="CallExternal.html">.Call</a></td>
+<td>Modern Interfaces to C/C++ code</td></tr>
+<tr><td width="25%"><a href="UseMethod.html">.Class</a></td>
+<td>Class Methods</td></tr>
+<tr><td width="25%"><a href="colSums.html">.colMeans</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="colSums.html">.colSums</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="attach.html">.conflicts.OK</a></td>
+<td>Attach Set of R Objects to Search Path</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">.decode_numeric_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="Defunct.html">.Defunct</a></td>
+<td>Marking Objects as Defunct</td></tr>
+<tr><td width="25%"><a href="deparseOpts.html">.deparseOpts</a></td>
+<td>Options for Expression Deparsing</td></tr>
+<tr><td width="25%"><a href="Deprecated.html">.Deprecated</a></td>
+<td>Marking Objects as Deprecated</td></tr>
+<tr><td width="25%"><a href="dev.html">.Device</a></td>
+<td>Lists of Open/Active Graphics Devices</td></tr>
+<tr><td width="25%"><a href="dev.html">.Devices</a></td>
+<td>Lists of Open/Active Graphics Devices</td></tr>
+<tr><td width="25%"><a href="trace.html">.doTrace</a></td>
+<td>Interactive Tracing and Debugging of Calls to a Function or Method</td></tr>
+<tr><td width="25%"><a href="library.dynam.html">.dynLibs</a></td>
+<td>Loading DLLs from Packages</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">.encode_numeric_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="libPaths.html">.expand_R_libs_env_var</a></td>
+<td>Search Paths for Packages</td></tr>
+<tr><td width="25%"><a href="CallExternal.html">.External</a></td>
+<td>Modern Interfaces to C/C++ code</td></tr>
+<tr><td width="25%"><a href="find.package.html">.find.package</a></td>
+<td>Find Packages</td></tr>
+<tr><td width="25%"><a href="Startup.html">.First</a></td>
+<td>Initialization at Start of an R Session</td></tr>
+<tr><td width="25%"><a href="Startup.html">.First.sys</a></td>
+<td>Initialization at Start of an R Session</td></tr>
+<tr><td width="25%"><a href="Foreign.html">.Fortran</a></td>
+<td>Foreign Function Interface</td></tr>
+<tr><td width="25%"><a href="UseMethod.html">.Generic</a></td>
+<td>Class Methods</td></tr>
+<tr><td width="25%"><a href="environment.html">.GlobalEnv</a></td>
+<td>Environment Access</td></tr>
+<tr><td width="25%"><a href="groupGeneric.html">.Group</a></td>
+<td>S3 Group Generic Functions</td></tr>
+<tr><td width="25%"><a href="conditions.html">.handleSimpleError</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="Internal.html">.Internal</a></td>
+<td>Call an Internal Function</td></tr>
+<tr><td width="25%"><a href="srcfile.html">.isOpen</a></td>
+<td>References to source files</td></tr>
+<tr><td width="25%"><a href="kappa.html">.kappa_tri</a></td>
+<td>Compute or Estimate the Condition Number of a Matrix</td></tr>
+<tr><td width="25%"><a href="kronecker.html">.kronecker</a></td>
+<td>Kronecker Products on Arrays</td></tr>
+<tr><td width="25%"><a href="quit.html">.Last</a></td>
+<td>Terminate an R Session</td></tr>
+<tr><td width="25%"><a href="ns-hooks.html">.Last.lib</a></td>
+<td>Hooks for Namespace Events</td></tr>
+<tr><td width="25%"><a href="quit.html">.Last.sys</a></td>
+<td>Terminate an R Session</td></tr>
+<tr><td width="25%"><a href="Last.value.html">.Last.value</a></td>
+<td>Value of Last Evaluated Expression</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">.leap.seconds</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="libPaths.html">.libPaths</a></td>
+<td>Search Paths for Packages</td></tr>
+<tr><td width="25%"><a href="libPaths.html">.Library</a></td>
+<td>Search Paths for Packages</td></tr>
+<tr><td width="25%"><a href="libPaths.html">.Library.site</a></td>
+<td>Search Paths for Packages</td></tr>
+<tr><td width="25%"><a href="zMachine.html">.Machine</a></td>
+<td>Numerical Characteristics of the Machine</td></tr>
+<tr><td width="25%"><a href="message.html">.makeMessage</a></td>
+<td>Diagnostic Messages</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">.make_numeric_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="UseMethod.html">.Method</a></td>
+<td>Class Methods</td></tr>
+<tr><td width="25%"><a href="library.html">.noGenerics</a></td>
+<td>Loading and Listing of Packages</td></tr>
+<tr><td width="25%"><a href="notyet.html">.NotYetImplemented</a></td>
+<td>Not Yet Implemented Functions and Unused Arguments</td></tr>
+<tr><td width="25%"><a href="notyet.html">.NotYetUsed</a></td>
+<td>Not Yet Implemented Functions and Unused Arguments</td></tr>
+<tr><td width="25%"><a href="ns-hooks.html">.onAttach</a></td>
+<td>Hooks for Namespace Events</td></tr>
+<tr><td width="25%"><a href="ns-hooks.html">.onLoad</a></td>
+<td>Hooks for Namespace Events</td></tr>
+<tr><td width="25%"><a href="ns-hooks.html">.onUnload</a></td>
+<td>Hooks for Namespace Events</td></tr>
+<tr><td width="25%"><a href="options.html">.Options</a></td>
+<td>Options Settings</td></tr>
+<tr><td width="25%"><a href="Startup.html">.OptRequireMethods</a></td>
+<td>Initialization at Start of an R Session</td></tr>
+<tr><td width="25%"><a href="zpackages.html">.packages</a></td>
+<td>Listing of Packages</td></tr>
+<tr><td width="25%"><a href="message.html">.packageStartupMessage</a></td>
+<td>Diagnostic Messages</td></tr>
+<tr><td width="25%"><a href="find.package.html">.path.package</a></td>
+<td>Find Packages</td></tr>
+<tr><td width="25%"><a href="Platform.html">.Platform</a></td>
+<td>Platform Specific Variables</td></tr>
+<tr><td width="25%"><a href="Primitive.html">.Primitive</a></td>
+<td>Look Up a Primitive Function</td></tr>
+<tr><td width="25%"><a href="Random.html">.Random.seed</a></td>
+<td>Random Number Generation</td></tr>
+<tr><td width="25%"><a href="Startup.html">.Renviron</a></td>
+<td>Initialization at Start of an R Session</td></tr>
+<tr><td width="25%"><a href="colSums.html">.rowMeans</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="colSums.html">.rowSums</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="Startup.html">.Rprofile</a></td>
+<td>Initialization at Start of an R Session</td></tr>
+<tr><td width="25%"><a href="InternalMethods.html">.S3PrimitiveGenerics</a></td>
+<td>Internal Generic Functions</td></tr>
+<tr><td width="25%"><a href="conditions.html">.signalSimpleWarning</a></td>
+<td>Condition Handling and Recovery</td></tr>
+<tr><td width="25%"><a href="zutils.html">.standard_regexps</a></td>
+<td>Miscellaneous Internal/Programming Utilities</td></tr>
+<tr><td width="25%"><a href="traceback.html">.Traceback</a></td>
+<td>Print Call Stacks</td></tr>
+<tr><td width="25%"><a href="userhooks.html">.userHooksEnv</a></td>
+<td>Functions to Get and Set Hooks for Load, Attach, Detach and Unload</td></tr>
+<tr><td width="25%"><a href="cbind.html">.__H__.cbind</a></td>
+<td>Combine R Objects by Rows or Columns</td></tr>
+<tr><td width="25%"><a href="cbind.html">.__H__.rbind</a></td>
+<td>Combine R Objects by Rows or Columns</td></tr>
+<tr><td width="25%"><a href="Arithmetic.html">/</a></td>
+<td>Arithmetic Operators</td></tr>
+<tr><td width="25%"><a href="difftime.html">/.difftime</a></td>
+<td>Time Intervals</td></tr>
+<tr><td width="25%"><a href="NumericConstants.html">0x1</a></td>
+<td>Numeric Constants</td></tr>
+<tr><td width="25%"><a href="NumericConstants.html">1i</a></td>
+<td>Numeric Constants</td></tr>
+<tr><td width="25%"><a href="NumericConstants.html">1L</a></td>
+<td>Numeric Constants</td></tr>
+<tr><td width="25%"><a href="Colon.html">:</a></td>
+<td>Colon Operator</td></tr>
+<tr><td width="25%"><a href="ns-dblcolon.html">::</a></td>
+<td>Double Colon and Triple Colon Operators</td></tr>
+<tr><td width="25%"><a href="ns-dblcolon.html">:::</a></td>
+<td>Double Colon and Triple Colon Operators</td></tr>
+<tr><td width="25%"><a href="Comparison.html"><</a></td>
+<td>Relational Operators</td></tr>
+<tr><td width="25%"><a href="assignOps.html"><-</a></td>
+<td>Assignment Operators</td></tr>
+<tr><td width="25%"><a href="assignOps.html"><<-</a></td>
+<td>Assignment Operators</td></tr>
+<tr><td width="25%"><a href="Comparison.html"><=</a></td>
+<td>Relational Operators</td></tr>
+<tr><td width="25%"><a href="assignOps.html">=</a></td>
+<td>Assignment Operators</td></tr>
+<tr><td width="25%"><a href="Comparison.html">==</a></td>
+<td>Relational Operators</td></tr>
+<tr><td width="25%"><a href="Comparison.html">></a></td>
+<td>Relational Operators</td></tr>
+<tr><td width="25%"><a href="Comparison.html">>=</a></td>
+<td>Relational Operators</td></tr>
+<tr><td width="25%"><a href="slotOp.html">@</a></td>
+<td>Extract Slots</td></tr>
+<tr><td width="25%"><a href="Extract.html">[</a></td>
+<td>Extract or Replace Parts of an Object</td></tr>
+<tr><td width="25%"><a href="AsIs.html">[.AsIs</a></td>
+<td>Inhibit Interpretation/Conversion of Objects</td></tr>
+<tr><td width="25%"><a href="Extract.data.frame.html">[.data.frame</a></td>
+<td>Extract or Replace Parts of a Data Frame</td></tr>
+<tr><td width="25%"><a href="Dates.html">[.Date</a></td>
+<td>Date Class</td></tr>
+<tr><td width="25%"><a href="difftime.html">[.difftime</a></td>
+<td>Time Intervals</td></tr>
+<tr><td width="25%"><a href="Extract.factor.html">[.factor</a></td>
+<td>Extract or Replace Parts of a Factor</td></tr>
+<tr><td width="25%"><a href="hexmode.html">[.hexmode</a></td>
+<td>Display Numbers in Hexadecimal</td></tr>
+<tr><td width="25%"><a href="Extract.html">[.listof</a></td>
+<td>Extract or Replace Parts of an Object</td></tr>
+<tr><td width="25%"><a href="noquote.html">[.noquote</a></td>
+<td>Class for 'no quote' Printing of Character Strings</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">[.numeric_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="octmode.html">[.octmode</a></td>
+<td>Display Numbers in Octal</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">[.POSIXct</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">[.POSIXlt</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="Extract.html">[.simple.list</a></td>
+<td>Extract or Replace Parts of an Object</td></tr>
+<tr><td width="25%"><a href="Extract.html">[<-</a></td>
+<td>Extract or Replace Parts of an Object</td></tr>
+<tr><td width="25%"><a href="Extract.data.frame.html">[<-.data.frame</a></td>
+<td>Extract or Replace Parts of a Data Frame</td></tr>
+<tr><td width="25%"><a href="Dates.html">[<-.Date</a></td>
+<td>Date Class</td></tr>
+<tr><td width="25%"><a href="Extract.factor.html">[<-.factor</a></td>
+<td>Extract or Replace Parts of a Factor</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">[<-.POSIXct</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">[<-.POSIXlt</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="Extract.html">[[</a></td>
+<td>Extract or Replace Parts of an Object</td></tr>
+<tr><td width="25%"><a href="Extract.data.frame.html">[[.data.frame</a></td>
+<td>Extract or Replace Parts of a Data Frame</td></tr>
+<tr><td width="25%"><a href="Dates.html">[[.Date</a></td>
+<td>Date Class</td></tr>
+<tr><td width="25%"><a href="Extract.factor.html">[[.factor</a></td>
+<td>Extract or Replace Parts of a Factor</td></tr>
+<tr><td width="25%"><a href="numeric_version.html">[[.numeric_version</a></td>
+<td>Numeric Versions</td></tr>
+<tr><td width="25%"><a href="DateTimeClasses.html">[[.POSIXct</a></td>
+<td>Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="Arithmetic.html">^</a></td>
+<td>Arithmetic Operators</td></tr>
+<tr><td width="25%"><a href="Quotes.html">`</a></td>
+<td>Quotes</td></tr>
+<tr><td width="25%"><a href="Paren.html">{</a></td>
+<td>Parentheses and Braces</td></tr>
+<tr><td width="25%"><a href="Logic.html">|</a></td>
+<td>Logical Operators</td></tr>
+<tr><td width="25%"><a href="hexmode.html">|.hexmode</a></td>
+<td>Display Numbers in Hexadecimal</td></tr>
+<tr><td width="25%"><a href="octmode.html">|.octmode</a></td>
+<td>Display Numbers in Octal</td></tr>
+<tr><td width="25%"><a href="Logic.html">||</a></td>
+<td>Logical Operators</td></tr>
+<tr><td width="25%"><a href="tilde.html">~</a></td>
+<td>Tilde Operator</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/base/html/R.css b/win32/deps/library/base/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/base/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/base/po/da/LC_MESSAGES/R-base.mo b/win32/deps/library/base/po/da/LC_MESSAGES/R-base.mo
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diff --git a/win32/deps/library/base/po/tr/LC_MESSAGES/R-base.mo b/win32/deps/library/base/po/tr/LC_MESSAGES/R-base.mo
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diff --git a/win32/deps/library/base/po/zh_CN/LC_MESSAGES/R-base.mo b/win32/deps/library/base/po/zh_CN/LC_MESSAGES/R-base.mo
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diff --git a/win32/deps/library/boot/CITATION b/win32/deps/library/boot/CITATION
index c4a4cc3..3de4f2a 100644
--- a/win32/deps/library/boot/CITATION
+++ b/win32/deps/library/boot/CITATION
@@ -1,8 +1,7 @@
citHeader("To cite the 'boot' package in publications use:")
-desc <- packageDescription("boot")
-year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", desc$Date)
-vers <- paste("R package version", desc$Version)
+year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", meta$Date, perl = TRUE)
+vers <- paste("R package version", meta$Version)
citEntry(entry="Manual",
title = "boot: Bootstrap R (S-Plus) Functions",
diff --git a/win32/deps/library/boot/DESCRIPTION b/win32/deps/library/boot/DESCRIPTION
index e50af77..ce99932 100644
--- a/win32/deps/library/boot/DESCRIPTION
+++ b/win32/deps/library/boot/DESCRIPTION
@@ -1,21 +1,25 @@
-Package: boot
-Priority: recommended
-Version: 1.2-38
-Date: 2009-07-28
-Author: S original <http://statwww.epfl.ch/davison/BMA/library.html> by
- Angelo Canty <cantya mcmaster ca>. R port by Brian Ripley
- <ripley stats ox ac uk>.
-Maintainer: Brian Ripley <ripley stats ox ac uk>
-Description: functions and datasets for bootstrapping from the book
- "Bootstrap Methods and Their Applications" by A. C. Davison and
- D. V. Hinkley (1997, CUP).
-Title: Bootstrap R (S-Plus) Functions (Canty)
-Depends: R (>= 2.7.0), graphics, stats
-Suggests: survival
-LazyLoad: yes
-LazyData: yes
-License: Unlimited
-Packaged: 2009-07-29 08:48:14 UTC; ripley
-Repository: CRAN
-Date/Publication: 2009-08-05 11:21:38
-Built: R 2.9.2; ; 2009-08-24 13:01:44 UTC; windows
+Package: boot
+Priority: recommended
+Version: 1.3-7
+Date: 2012-10-12
+Authors R: c(person("Angelo", "Canty", role = "aut", email =
+ "cantya mcmaster ca"), person("Brian", "Ripley", role =
+ c("aut", "trl", "cre"), email = "ripley stats ox ac uk",
+ comment = "author of parallel support"))
+Author: S original <http://statwww.epfl.ch/davison/BMA/library.html>
+ by Angelo Canty <cantya mcmaster ca>.
+ R port and many enhancements by Brian Ripley <ripley stats ox ac uk>.
+ Note that maintainers are not available to give advice on using a
+ package they did not author.
+Maintainer: Brian Ripley <ripley stats ox ac uk>
+Description: functions and datasets for bootstrapping from the
+ book "Bootstrap Methods and Their Applications" by A. C. Davison and
+ D. V. Hinkley (1997, CUP).
+Title: Bootstrap Functions (originally by Angelo Canty for S)
+Depends: R (>= 2.14.0), graphics, stats
+Suggests: MASS, survival
+LazyData: yes
+ByteCompile: yes
+License: Unlimited
+Packaged: 2012-10-12 11:52:51 UTC; ripley
+Built: R 2.15.2; ; 2012-10-27 03:14:35 UTC; windows
diff --git a/win32/deps/library/boot/INDEX b/win32/deps/library/boot/INDEX
index 9c54c23..78e8d67 100644
--- a/win32/deps/library/boot/INDEX
+++ b/win32/deps/library/boot/INDEX
@@ -1,12 +1,27 @@
-Bootstrap S-Plus Functions (Version 1.2; March 2001)
-===========================================================
+Bootstrap R Functions
+=====================
+
+Version 1.3; May 2011:
+
+The main change is support for parallel computation in functions
+boot(), censboot() and tsboot().
+
+Many of the examples have been tidied up.
+
+
+Version 1.2; March 2001:
This version corrects some minor errors in Version 1.0 of the code
distributed with the first printing of Davison and Hinkley (1997).
The author would like to thank those users who pointed out errors or
possible improvements to the code. Any further errors found should be
-reported to the author at the address below for correction in the
-next version.
+reported to the author (Angelo Canty) for correction in the next
+version.
+
+Version 1.3; May 2011:
+
+Added parallel support, some code cleanup for efficiency.
+
The package contains the following functions, all of which
have online help available.
@@ -59,17 +74,3 @@ cd4.nested A nested bootstrap referred to in Practical 5.5
corr.nested The statistic used in cd4.nested
EL.profile, EEF.profile, and lik.CI
functions defined for use in the practicals of chapter 10.
-
-
-
-Angelo J. Canty
-Department of Mathematics and Statistics
-Concordia University
-1455 Blvd de Maisonneuve, Ouest
-Montreal,
-Quebec H3G 1M8
-Canada
-
-Tel : 1-514-848-3244
-Fax : 1-514-848-4511
-email : canty cicma concordia ca
diff --git a/win32/deps/library/boot/Meta/Rd.rds b/win32/deps/library/boot/Meta/Rd.rds
index b1f3807..e99c9b2 100644
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diff --git a/win32/deps/library/boot/Meta/data.rds b/win32/deps/library/boot/Meta/data.rds
index 9db8181..1c7ad1a 100644
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diff --git a/win32/deps/library/boot/Meta/hsearch.rds b/win32/deps/library/boot/Meta/hsearch.rds
index 2301ca5..460dad6 100644
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diff --git a/win32/deps/library/boot/Meta/links.rds b/win32/deps/library/boot/Meta/links.rds
new file mode 100644
index 0000000..74163fa
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diff --git a/win32/deps/library/boot/Meta/nsInfo.rds b/win32/deps/library/boot/Meta/nsInfo.rds
index eba5895..3fa33a9 100644
Binary files a/win32/deps/library/boot/Meta/nsInfo.rds and b/win32/deps/library/boot/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/boot/Meta/package.rds b/win32/deps/library/boot/Meta/package.rds
index 4e7d7b9..bb9f155 100644
Binary files a/win32/deps/library/boot/Meta/package.rds and b/win32/deps/library/boot/Meta/package.rds differ
diff --git a/win32/deps/library/boot/NAMESPACE b/win32/deps/library/boot/NAMESPACE
index 3ee3ba8..21a096a 100644
--- a/win32/deps/library/boot/NAMESPACE
+++ b/win32/deps/library/boot/NAMESPACE
@@ -10,6 +10,7 @@ export(abc.ci, boot, boot.array, boot.ci, censboot, control, corr,
# export(lines.saddle.distn, plot.boot, print.boot, print.bootci, print.simplex)
importFrom(graphics, lines, plot)
+S3method(c, boot)
S3method(lines, saddle.distn)
S3method(plot, boot)
S3method(print, boot)
diff --git a/win32/deps/library/boot/R/boot b/win32/deps/library/boot/R/boot
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/boot/R/boot
+++ b/win32/deps/library/boot/R/boot
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/boot/R/boot.rdb b/win32/deps/library/boot/R/boot.rdb
index 3dc49fb..09508cf 100644
Binary files a/win32/deps/library/boot/R/boot.rdb and b/win32/deps/library/boot/R/boot.rdb differ
diff --git a/win32/deps/library/boot/R/boot.rdx b/win32/deps/library/boot/R/boot.rdx
index 28c3025..53c9394 100644
Binary files a/win32/deps/library/boot/R/boot.rdx and b/win32/deps/library/boot/R/boot.rdx differ
diff --git a/win32/deps/library/boot/data/Rdata.rdb b/win32/deps/library/boot/data/Rdata.rdb
index 162e6ee..7fcef03 100644
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diff --git a/win32/deps/library/boot/data/Rdata.rds b/win32/deps/library/boot/data/Rdata.rds
index 223ccf7..06eb36f 100644
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diff --git a/win32/deps/library/boot/data/Rdata.rdx b/win32/deps/library/boot/data/Rdata.rdx
index 7d77165..95f14ad 100644
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diff --git a/win32/deps/library/boot/help/AnIndex b/win32/deps/library/boot/help/AnIndex
index 7966f5f..4cf2c0b 100644
--- a/win32/deps/library/boot/help/AnIndex
+++ b/win32/deps/library/boot/help/AnIndex
@@ -13,6 +13,7 @@ boot.ci boot.ci
boot.return boot
brambles brambles
breslow breslow
+c.boot boot
calcium calcium
cane cane
capability capability
diff --git a/win32/deps/library/boot/help/aliases.rds b/win32/deps/library/boot/help/aliases.rds
new file mode 100644
index 0000000..443b311
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diff --git a/win32/deps/library/boot/help/boot.rdb b/win32/deps/library/boot/help/boot.rdb
new file mode 100644
index 0000000..97cd38c
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diff --git a/win32/deps/library/boot/help/boot.rdx b/win32/deps/library/boot/help/boot.rdx
new file mode 100644
index 0000000..97e29a8
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diff --git a/win32/deps/library/boot/help/paths.rds b/win32/deps/library/boot/help/paths.rds
new file mode 100644
index 0000000..f9fba4c
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diff --git a/win32/deps/library/boot/html/00Index.html b/win32/deps/library/boot/html/00Index.html
new file mode 100644
index 0000000..9c9a56d
--- /dev/null
+++ b/win32/deps/library/boot/html/00Index.html
@@ -0,0 +1,221 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Bootstrap Functions (originally by Angelo Canty for S)</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Bootstrap Functions (originally by Angelo Canty for S)
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘boot’ version 1.3-7</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<table width="100%">
+<tr><td width="25%"><a href="abc.ci.html">abc.ci</a></td>
+<td>Nonparametric ABC Confidence Intervals</td></tr>
+<tr><td width="25%"><a href="acme.html">acme</a></td>
+<td>Monthly Excess Returns</td></tr>
+<tr><td width="25%"><a href="aids.html">aids</a></td>
+<td>Delay in AIDS Reporting in England and Wales</td></tr>
+<tr><td width="25%"><a href="aircondit.html">aircondit</a></td>
+<td>Failures of Air-conditioning Equipment</td></tr>
+<tr><td width="25%"><a href="aircondit.html">aircondit7</a></td>
+<td>Failures of Air-conditioning Equipment</td></tr>
+<tr><td width="25%"><a href="amis.html">amis</a></td>
+<td>Car Speeding and Warning Signs</td></tr>
+<tr><td width="25%"><a href="aml.html">aml</a></td>
+<td>Remission Times for Acute Myelogenous Leukaemia</td></tr>
+<tr><td width="25%"><a href="beaver.html">beaver</a></td>
+<td>Beaver Body Temperature Data</td></tr>
+<tr><td width="25%"><a href="bigcity.html">bigcity</a></td>
+<td>Population of U.S. Cities</td></tr>
+<tr><td width="25%"><a href="boot.html">boot</a></td>
+<td>Bootstrap Resampling</td></tr>
+<tr><td width="25%"><a href="boot.array.html">boot.array</a></td>
+<td>Bootstrap Resampling Arrays</td></tr>
+<tr><td width="25%"><a href="boot.ci.html">boot.ci</a></td>
+<td>Nonparametric Bootstrap Confidence Intervals</td></tr>
+<tr><td width="25%"><a href="boot.html">boot.return</a></td>
+<td>Bootstrap Resampling</td></tr>
+<tr><td width="25%"><a href="brambles.html">brambles</a></td>
+<td>Spatial Location of Bramble Canes</td></tr>
+<tr><td width="25%"><a href="breslow.html">breslow</a></td>
+<td>Smoking Deaths Among Doctors</td></tr>
+<tr><td width="25%"><a href="boot.html">c.boot</a></td>
+<td>Bootstrap Resampling</td></tr>
+<tr><td width="25%"><a href="calcium.html">calcium</a></td>
+<td>Calcium Uptake Data</td></tr>
+<tr><td width="25%"><a href="cane.html">cane</a></td>
+<td>Sugar-cane Disease Data</td></tr>
+<tr><td width="25%"><a href="capability.html">capability</a></td>
+<td>Simulated Manufacturing Process Data</td></tr>
+<tr><td width="25%"><a href="catsM.html">catsM</a></td>
+<td>Weight Data for Domestic Cats</td></tr>
+<tr><td width="25%"><a href="cav.html">cav</a></td>
+<td>Position of Muscle Caveolae</td></tr>
+<tr><td width="25%"><a href="cd4.html">cd4</a></td>
+<td>CD4 Counts for HIV-Positive Patients</td></tr>
+<tr><td width="25%"><a href="cd4.nested.html">cd4.nested</a></td>
+<td>Nested Bootstrap of cd4 data</td></tr>
+<tr><td width="25%"><a href="censboot.html">cens.return</a></td>
+<td>Bootstrap for Censored Data</td></tr>
+<tr><td width="25%"><a href="censboot.html">censboot</a></td>
+<td>Bootstrap for Censored Data</td></tr>
+<tr><td width="25%"><a href="channing.html">channing</a></td>
+<td>Channing House Data</td></tr>
+<tr><td width="25%"><a href="bigcity.html">city</a></td>
+<td>Population of U.S. Cities</td></tr>
+<tr><td width="25%"><a href="claridge.html">claridge</a></td>
+<td>Genetic Links to Left-handedness</td></tr>
+<tr><td width="25%"><a href="cloth.html">cloth</a></td>
+<td>Number of Flaws in Cloth</td></tr>
+<tr><td width="25%"><a href="co.transfer.html">co.transfer</a></td>
+<td>Carbon Monoxide Transfer</td></tr>
+<tr><td width="25%"><a href="coal.html">coal</a></td>
+<td>Dates of Coal Mining Disasters</td></tr>
+<tr><td width="25%"><a href="control.html">control</a></td>
+<td>Control Variate Calculations</td></tr>
+<tr><td width="25%"><a href="corr.html">corr</a></td>
+<td>Correlation Coefficient</td></tr>
+<tr><td width="25%"><a href="cum3.html">cum3</a></td>
+<td>Calculate Third Order Cumulants</td></tr>
+<tr><td width="25%"><a href="cv.glm.html">cv.glm</a></td>
+<td>Cross-validation for Generalized Linear Models</td></tr>
+<tr><td width="25%"><a href="darwin.html">darwin</a></td>
+<td>Darwin's Plant Height Differences</td></tr>
+<tr><td width="25%"><a href="dogs.html">dogs</a></td>
+<td>Cardiac Data for Domestic Dogs</td></tr>
+<tr><td width="25%"><a href="downs.bc.html">downs.bc</a></td>
+<td>Incidence of Down's Syndrome in British Columbia</td></tr>
+<tr><td width="25%"><a href="ducks.html">ducks</a></td>
+<td>Behavioral and Plumage Characteristics of Hybrid Ducks</td></tr>
+<tr><td width="25%"><a href="EEF.profile.html">EEF.profile</a></td>
+<td>Empirical Likelihoods</td></tr>
+<tr><td width="25%"><a href="EEF.profile.html">EL.profile</a></td>
+<td>Empirical Likelihoods</td></tr>
+<tr><td width="25%"><a href="empinf.html">empinf</a></td>
+<td>Empirical Influence Values</td></tr>
+<tr><td width="25%"><a href="envelope.html">envelope</a></td>
+<td>Confidence Envelopes for Curves</td></tr>
+<tr><td width="25%"><a href="exp.tilt.html">exp.tilt</a></td>
+<td>Exponential Tilting</td></tr>
+<tr><td width="25%"><a href="fir.html">fir</a></td>
+<td>Counts of Balsam-fir Seedlings</td></tr>
+<tr><td width="25%"><a href="freq.array.html">freq.array</a></td>
+<td>Bootstrap Frequency Arrays</td></tr>
+<tr><td width="25%"><a href="frets.html">frets</a></td>
+<td>Head Dimensions in Brothers</td></tr>
+<tr><td width="25%"><a href="glm.diag.html">glm.diag</a></td>
+<td>Generalized Linear Model Diagnostics</td></tr>
+<tr><td width="25%"><a href="glm.diag.plots.html">glm.diag.plots</a></td>
+<td>Diagnostics plots for generalized linear models</td></tr>
+<tr><td width="25%"><a href="gravity.html">grav</a></td>
+<td>Acceleration Due to Gravity</td></tr>
+<tr><td width="25%"><a href="gravity.html">gravity</a></td>
+<td>Acceleration Due to Gravity</td></tr>
+<tr><td width="25%"><a href="hirose.html">hirose</a></td>
+<td>Failure Time of PET Film</td></tr>
+<tr><td width="25%"><a href="Imp.Estimates.html">Imp.Estimates</a></td>
+<td>Importance Sampling Estimates</td></tr>
+<tr><td width="25%"><a href="Imp.Estimates.html">imp.moments</a></td>
+<td>Importance Sampling Estimates</td></tr>
+<tr><td width="25%"><a href="Imp.Estimates.html">imp.prob</a></td>
+<td>Importance Sampling Estimates</td></tr>
+<tr><td width="25%"><a href="Imp.Estimates.html">imp.quantile</a></td>
+<td>Importance Sampling Estimates</td></tr>
+<tr><td width="25%"><a href="Imp.Estimates.html">imp.reg</a></td>
+<td>Importance Sampling Estimates</td></tr>
+<tr><td width="25%"><a href="imp.weights.html">imp.weights</a></td>
+<td>Importance Sampling Weights</td></tr>
+<tr><td width="25%"><a href="inv.logit.html">inv.logit</a></td>
+<td>Inverse Logit Function</td></tr>
+<tr><td width="25%"><a href="islay.html">islay</a></td>
+<td>Jura Quartzite Azimuths on Islay</td></tr>
+<tr><td width="25%"><a href="jack.after.boot.html">jack.after.boot</a></td>
+<td>Jackknife-after-Bootstrap Plots</td></tr>
+<tr><td width="25%"><a href="k3.linear.html">k3.linear</a></td>
+<td>Linear Skewness Estimate</td></tr>
+<tr><td width="25%"><a href="linear.approx.html">linear.approx</a></td>
+<td>Linear Approximation of Bootstrap Replicates</td></tr>
+<tr><td width="25%"><a href="lines.saddle.distn.html">lines.saddle.distn</a></td>
+<td>Add a Saddlepoint Approximation to a Plot</td></tr>
+<tr><td width="25%"><a href="logit.html">logit</a></td>
+<td>Logit of Proportions</td></tr>
+<tr><td width="25%"><a href="manaus.html">manaus</a></td>
+<td>Average Heights of the Rio Negro river at Manaus</td></tr>
+<tr><td width="25%"><a href="melanoma.html">melanoma</a></td>
+<td>Survival from Malignant Melanoma</td></tr>
+<tr><td width="25%"><a href="motor.html">motor</a></td>
+<td>Data from a Simulated Motorcycle Accident</td></tr>
+<tr><td width="25%"><a href="neuro.html">neuro</a></td>
+<td>Neurophysiological Point Process Data</td></tr>
+<tr><td width="25%"><a href="nitrofen.html">nitrofen</a></td>
+<td>Toxicity of Nitrofen in Aquatic Systems</td></tr>
+<tr><td width="25%"><a href="nodal.html">nodal</a></td>
+<td>Nodal Involvement in Prostate Cancer</td></tr>
+<tr><td width="25%"><a href="norm.ci.html">norm.ci</a></td>
+<td>Normal Approximation Confidence Intervals</td></tr>
+<tr><td width="25%"><a href="nuclear.html">nuclear</a></td>
+<td>Nuclear Power Station Construction Data</td></tr>
+<tr><td width="25%"><a href="paulsen.html">paulsen</a></td>
+<td>Neurotransmission in Guinea Pig Brains</td></tr>
+<tr><td width="25%"><a href="plot.boot.html">plot.boot</a></td>
+<td>Plots of the Output of a Bootstrap Simulation</td></tr>
+<tr><td width="25%"><a href="poisons.html">poisons</a></td>
+<td>Animal Survival Times</td></tr>
+<tr><td width="25%"><a href="polar.html">polar</a></td>
+<td>Pole Positions of New Caledonian Laterites</td></tr>
+<tr><td width="25%"><a href="print.boot.html">print.boot</a></td>
+<td>Print a Summary of a Bootstrap Object</td></tr>
+<tr><td width="25%"><a href="print.bootci.html">print.bootci</a></td>
+<td>Print Bootstrap Confidence Intervals</td></tr>
+<tr><td width="25%"><a href="print.saddle.distn.html">print.saddle.distn</a></td>
+<td>Print Quantiles of Saddlepoint Approximations</td></tr>
+<tr><td width="25%"><a href="print.simplex.html">print.simplex</a></td>
+<td>Print Solution to Linear Programming Problem</td></tr>
+<tr><td width="25%"><a href="remission.html">remission</a></td>
+<td>Cancer Remission and Cell Activity</td></tr>
+<tr><td width="25%"><a href="saddle.html">saddle</a></td>
+<td>Saddlepoint Approximations for Bootstrap Statistics</td></tr>
+<tr><td width="25%"><a href="saddle.distn.html">saddle.distn</a></td>
+<td>Saddlepoint Distribution Approximations for Bootstrap Statistics</td></tr>
+<tr><td width="25%"><a href="saddle.distn.object.html">saddle.distn.object</a></td>
+<td>Saddlepoint Distribution Approximation Objects</td></tr>
+<tr><td width="25%"><a href="salinity.html">salinity</a></td>
+<td>Water Salinity and River Discharge</td></tr>
+<tr><td width="25%"><a href="simplex.html">simplex</a></td>
+<td>Simplex Method for Linear Programming Problems</td></tr>
+<tr><td width="25%"><a href="simplex.object.html">simplex.object</a></td>
+<td>Linear Programming Solution Objects</td></tr>
+<tr><td width="25%"><a href="smooth.f.html">smooth.f</a></td>
+<td>Smooth Distributions on Data Points</td></tr>
+<tr><td width="25%"><a href="sunspot.html">sunspot</a></td>
+<td>Annual Mean Sunspot Numbers</td></tr>
+<tr><td width="25%"><a href="survival.html">survival</a></td>
+<td>Survival of Rats after Radiation Doses</td></tr>
+<tr><td width="25%"><a href="tau.html">tau</a></td>
+<td>Tau Particle Decay Modes</td></tr>
+<tr><td width="25%"><a href="tilt.boot.html">tilt.boot</a></td>
+<td>Non-parametric Tilted Bootstrap</td></tr>
+<tr><td width="25%"><a href="tsboot.html">ts.return</a></td>
+<td>Bootstrapping of Time Series</td></tr>
+<tr><td width="25%"><a href="tsboot.html">tsboot</a></td>
+<td>Bootstrapping of Time Series</td></tr>
+<tr><td width="25%"><a href="tuna.html">tuna</a></td>
+<td>Tuna Sighting Data</td></tr>
+<tr><td width="25%"><a href="urine.html">urine</a></td>
+<td>Urine Analysis Data</td></tr>
+<tr><td width="25%"><a href="var.linear.html">var.linear</a></td>
+<td>Linear Variance Estimate</td></tr>
+<tr><td width="25%"><a href="wool.html">wool</a></td>
+<td>Australian Relative Wool Prices</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/boot/html/R.css b/win32/deps/library/boot/html/R.css
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+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
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diff --git a/win32/deps/library/boot/tests/Examples/boot-Ex.Rout.save b/win32/deps/library/boot/tests/Examples/boot-Ex.Rout.save
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+++ b/win32/deps/library/boot/tests/Examples/boot-Ex.Rout.save
@@ -0,0 +1,2029 @@
+
+R Under development (unstable) (2011-07-12 r56366)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+ Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> pkgname <- "boot"
+> source(file.path(R.home("share"), "R", "examples-header.R"))
+> options(warn = 1)
+> library('boot')
+>
+> assign(".oldSearch", search(), pos = 'CheckExEnv')
+> cleanEx()
+> nameEx("Imp.Estimates")
+> ### * Imp.Estimates
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: Imp.Estimates
+> ### Title: Importance Sampling Estimates
+> ### Aliases: Imp.Estimates imp.moments imp.prob imp.quantile imp.reg
+> ### Keywords: htest nonparametric
+>
+> ### ** Examples
+>
+> # Example 9.8 of Davison and Hinkley (1997) requires tilting the
+> # resampling distribution of the studentized statistic to be centred
+> # at the observed value of the test statistic, 1.84. In this example
+> # we show how certain estimates can be found using resamples taken from
+> # the tilted distribution.
+> grav1 <- gravity[as.numeric(gravity[,2]) >= 7, ]
+> grav.fun <- function(dat, w, orig) {
++ strata <- tapply(dat[, 2], as.numeric(dat[, 2]))
++ d <- dat[, 1]
++ ns <- tabulate(strata)
++ w <- w/tapply(w, strata, sum)[strata]
++ mns <- as.vector(tapply(d * w, strata, sum)) # drop names
++ mn2 <- tapply(d * d * w, strata, sum)
++ s2hat <- sum((mn2 - mns^2)/ns)
++ c(mns[2] - mns[1], s2hat, (mns[2] - mns[1] - orig)/sqrt(s2hat))
++ }
+> grav.z0 <- grav.fun(grav1, rep(1, 26), 0)
+> grav.L <- empinf(data = grav1, statistic = grav.fun, stype = "w",
++ strata = grav1[,2], index = 3, orig = grav.z0[1])
+> grav.tilt <- exp.tilt(grav.L, grav.z0[3], strata = grav1[, 2])
+> grav.tilt.boot <- boot(grav1, grav.fun, R = 199, stype = "w",
++ strata = grav1[, 2], weights = grav.tilt$p,
++ orig = grav.z0[1])
+> # Since the weights are needed for all calculations, we shall calculate
+> # them once only.
+> grav.w <- imp.weights(grav.tilt.boot)
+> grav.mom <- imp.moments(grav.tilt.boot, w = grav.w, index = 3)
+> grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 = grav.z0[3])
+> unlist(grav.p)
+ t0 raw rat reg
+1.8401182 1.0222447 0.9778246 0.9767292
+> grav.q <- imp.quantile(grav.tilt.boot, w = grav.w, index = 3,
++ alpha = c(0.9, 0.95, 0.975, 0.99))
+> as.data.frame(grav.q)
+ alpha raw rat reg
+1 0.900 3.048484 1.170707 5.056004
+2 0.950 3.237935 1.565928 5.056004
+3 0.975 3.629448 1.895876 5.056004
+4 0.990 3.629448 2.258157 5.056004
+>
+>
+>
+> cleanEx()
+> nameEx("abc.ci")
+> ### * abc.ci
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: abc.ci
+> ### Title: Nonparametric ABC Confidence Intervals
+> ### Aliases: abc.ci
+> ### Keywords: nonparametric htest
+>
+> ### ** Examples
+>
+> # 90% and 95% confidence intervals for the correlation
+> # coefficient between the columns of the bigcity data
+>
+> abc.ci(bigcity, corr, conf=c(0.90,0.95))
+ conf
+[1,] 0.90 0.9581503 0.9917271
+[2,] 0.95 0.9493699 0.9930713
+>
+> # A 95% confidence interval for the difference between the means of
+> # the last two samples in gravity
+> mean.diff <- function(y, w)
++ { gp1 <- 1:table(as.numeric(y$series))[1]
++ sum(y[gp1, 1] * w[gp1]) - sum(y[-gp1, 1] * w[-gp1])
++ }
+> grav1 <- gravity[as.numeric(gravity[, 2]) >= 7, ]
+> abc.ci(grav1, mean.diff, strata = grav1$series)
+[1] 0.9500000 -6.7075791 -0.3939377
+>
+>
+>
+> cleanEx()
+> nameEx("boot")
+> ### * boot
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: boot
+> ### Title: Bootstrap Resampling
+> ### Aliases: boot boot.return c.boot
+> ### Keywords: nonparametric htest
+>
+> ### ** Examples
+>
+> # Usual bootstrap of the ratio of means using the city data
+> ratio <- function(d, w) sum(d$x * w)/sum(d$u * w)
+> boot(city, ratio, R = 999, stype = "w")
+
+ORDINARY NONPARAMETRIC BOOTSTRAP
+
+
+Call:
+boot(data = city, statistic = ratio, R = 999, stype = "w")
+
+
+Bootstrap Statistics :
+ original bias std. error
+t1* 1.520313 0.03959996 0.2167146
+>
+>
+> # Stratified resampling for the difference of means. In this
+> # example we will look at the difference of means between the final
+> # two series in the gravity data.
+> diff.means <- function(d, f)
++ { n <- nrow(d)
++ gp1 <- 1:table(as.numeric(d$series))[1]
++ m1 <- sum(d[gp1,1] * f[gp1])/sum(f[gp1])
++ m2 <- sum(d[-gp1,1] * f[-gp1])/sum(f[-gp1])
++ ss1 <- sum(d[gp1,1]^2 * f[gp1]) - (m1 * m1 * sum(f[gp1]))
++ ss2 <- sum(d[-gp1,1]^2 * f[-gp1]) - (m2 * m2 * sum(f[-gp1]))
++ c(m1 - m2, (ss1 + ss2)/(sum(f) - 2))
++ }
+> grav1 <- gravity[as.numeric(gravity[,2]) >= 7,]
+> boot(grav1, diff.means, R = 999, stype = "f", strata = grav1[,2])
+
+STRATIFIED BOOTSTRAP
+
+
+Call:
+boot(data = grav1, statistic = diff.means, R = 999, stype = "f",
+ strata = grav1[, 2])
+
+
+Bootstrap Statistics :
+ original bias std. error
+t1* -2.846154 0.002541003 1.546664
+t2* 16.846154 -1.457662791 6.759103
+>
+> # In this example we show the use of boot in a prediction from
+> # regression based on the nuclear data. This example is taken
+> # from Example 6.8 of Davison and Hinkley (1997). Notice also
+> # that two extra arguments to 'statistic' are passed through boot.
+> nuke <- nuclear[, c(1, 2, 5, 7, 8, 10, 11)]
+> nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, data = nuke)
+> nuke.diag <- glm.diag(nuke.lm)
+> nuke.res <- nuke.diag$res * nuke.diag$sd
+> nuke.res <- nuke.res - mean(nuke.res)
+>
+> # We set up a new data frame with the data, the standardized
+> # residuals and the fitted values for use in the bootstrap.
+> nuke.data <- data.frame(nuke, resid = nuke.res, fit = fitted(nuke.lm))
+>
+> # Now we want a prediction of plant number 32 but at date 73.00
+> new.data <- data.frame(cost = 1, date = 73.00, cap = 886, ne = 0,
++ ct = 0, cum.n = 11, pt = 1)
+> new.fit <- predict(nuke.lm, new.data)
+>
+> nuke.fun <- function(dat, inds, i.pred, fit.pred, x.pred)
++ {
++ lm.b <- glm(fit+resid[inds] ~ date+log(cap)+ne+ct+log(cum.n)+pt,
++ data = dat)
++ pred.b <- predict(lm.b, x.pred)
++ c(coef(lm.b), pred.b - (fit.pred + dat$resid[i.pred]))
++ }
+>
+> nuke.boot <- boot(nuke.data, nuke.fun, R = 999, m = 1,
++ fit.pred = new.fit, x.pred = new.data)
+> # The bootstrap prediction squared error would then be found by
+> mean(nuke.boot$t[, 8]^2)
+[1] 0.08815734
+> # Basic bootstrap prediction limits would be
+> new.fit - sort(nuke.boot$t[, 8])[c(975, 25)]
+[1] 6.160255 7.298819
+>
+>
+> # Finally a parametric bootstrap. For this example we shall look
+> # at the air-conditioning data. In this example our aim is to test
+> # the hypothesis that the true value of the index is 1 (i.e. that
+> # the data come from an exponential distribution) against the
+> # alternative that the data come from a gamma distribution with
+> # index not equal to 1.
+> air.fun <- function(data) {
++ ybar <- mean(data$hours)
++ para <- c(log(ybar), mean(log(data$hours)))
++ ll <- function(k) {
++ if (k <= 0) 1e200 else lgamma(k)-k*(log(k)-1-para[1]+para[2])
++ }
++ khat <- nlm(ll, ybar^2/var(data$hours))$estimate
++ c(ybar, khat)
++ }
+>
+> air.rg <- function(data, mle) {
++ # Function to generate random exponential variates.
++ # mle will contain the mean of the original data
++ out <- data
++ out$hours <- rexp(nrow(out), 1/mle)
++ out
++ }
+>
+> air.boot <- boot(aircondit, air.fun, R = 999, sim = "parametric",
++ ran.gen = air.rg, mle = mean(aircondit$hours))
+>
+> # The bootstrap p-value can then be approximated by
+> sum(abs(air.boot$t[,2]-1) > abs(air.boot$t0[2]-1))/(1+air.boot$R)
+[1] 0.461
+>
+>
+>
+> cleanEx()
+> nameEx("boot.array")
+> ### * boot.array
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: boot.array
+> ### Title: Bootstrap Resampling Arrays
+> ### Aliases: boot.array
+> ### Keywords: nonparametric
+>
+> ### ** Examples
+>
+> # A frequency array for a nonparametric bootstrap
+> city.boot <- boot(city, corr, R = 40, stype = "w")
+> boot.array(city.boot)
+ [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
+ [1,] 1 1 3 1 1 0 1 0 1 1
+ [2,] 0 0 1 3 1 2 1 1 1 0
+ [3,] 0 0 0 1 3 2 0 1 2 1
+ [4,] 0 2 2 2 0 1 0 1 0 2
+ [5,] 1 1 1 0 1 2 0 2 2 0
+ [6,] 0 1 2 0 2 1 0 1 2 1
+ [7,] 3 0 0 1 1 2 0 1 1 1
+ [8,] 0 4 1 1 1 0 1 2 0 0
+ [9,] 0 1 4 0 1 0 2 2 0 0
+[10,] 1 1 1 1 1 1 1 2 0 1
+[11,] 0 0 3 0 2 1 1 1 0 2
+[12,] 2 3 1 0 0 1 0 0 2 1
+[13,] 1 0 0 1 2 0 2 1 1 2
+[14,] 0 0 2 3 0 0 2 0 2 1
+[15,] 2 0 1 1 1 1 0 2 1 1
+[16,] 1 1 0 2 2 1 1 1 1 0
+[17,] 1 0 1 2 2 1 2 1 0 0
+[18,] 0 2 0 0 2 2 0 1 1 2
+[19,] 1 1 0 2 0 1 2 0 1 2
+[20,] 0 0 0 1 2 1 1 1 0 4
+[21,] 0 0 2 0 1 1 3 0 0 3
+[22,] 1 3 2 2 0 1 1 0 0 0
+[23,] 0 0 3 1 2 1 2 0 1 0
+[24,] 0 1 1 2 1 2 0 1 0 2
+[25,] 0 0 2 1 0 0 3 2 1 1
+[26,] 0 2 4 1 1 1 0 0 0 1
+[27,] 2 3 1 0 2 0 0 2 0 0
+[28,] 1 1 0 1 1 0 0 4 2 0
+[29,] 2 2 0 1 1 0 1 0 1 2
+[30,] 0 1 0 1 1 2 0 1 3 1
+[31,] 1 2 0 2 2 0 1 1 0 1
+[32,] 1 4 0 1 0 2 0 1 1 0
+[33,] 0 1 0 5 1 0 0 1 1 1
+[34,] 0 2 0 1 3 1 1 1 0 1
+[35,] 0 2 3 1 1 1 0 0 1 1
+[36,] 1 2 1 1 1 1 2 0 1 0
+[37,] 1 1 1 0 0 1 2 2 2 0
+[38,] 2 3 0 3 0 1 0 0 1 0
+[39,] 0 0 1 2 3 0 0 2 1 1
+[40,] 0 1 1 0 3 0 2 2 0 1
+>
+> perm.cor <- function(d,i) cor(d$x,d$u[i])
+> city.perm <- boot(city, perm.cor, R = 40, sim = "permutation")
+> boot.array(city.perm, indices = TRUE)
+ [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
+ [1,] 7 2 8 10 6 4 9 3 1 5
+ [2,] 10 4 6 8 5 3 2 1 9 7
+ [3,] 5 10 6 2 3 8 1 9 7 4
+ [4,] 10 1 4 8 9 5 3 6 7 2
+ [5,] 1 3 5 8 2 9 6 7 10 4
+ [6,] 10 4 3 2 1 9 8 5 7 6
+ [7,] 2 5 1 4 10 9 3 8 7 6
+ [8,] 5 9 6 3 1 2 4 10 8 7
+ [9,] 8 2 7 10 4 3 1 6 9 5
+[10,] 1 9 3 2 8 6 7 4 5 10
+[11,] 6 7 10 5 3 9 2 8 4 1
+[12,] 9 5 1 6 10 8 3 2 7 4
+[13,] 9 7 3 1 8 5 4 6 2 10
+[14,] 7 1 3 2 9 6 10 4 5 8
+[15,] 4 9 6 3 2 1 10 8 7 5
+[16,] 9 6 1 7 5 2 8 4 10 3
+[17,] 7 2 3 6 10 4 1 9 5 8
+[18,] 2 4 3 1 5 8 6 10 9 7
+[19,] 4 9 6 1 10 3 7 2 5 8
+[20,] 6 3 7 5 8 4 2 10 1 9
+[21,] 9 10 2 6 7 5 8 4 3 1
+[22,] 10 4 5 9 8 3 1 2 6 7
+[23,] 9 2 5 1 10 4 6 8 7 3
+[24,] 9 4 3 6 8 2 1 10 5 7
+[25,] 10 3 8 2 5 7 1 9 6 4
+[26,] 7 8 3 9 4 1 5 2 10 6
+[27,] 4 8 1 5 3 6 10 9 7 2
+[28,] 8 5 7 4 10 3 2 1 9 6
+[29,] 8 10 2 4 7 3 9 6 1 5
+[30,] 1 5 7 9 3 6 4 10 2 8
+[31,] 10 9 7 5 4 1 2 6 3 8
+[32,] 8 5 1 6 3 7 10 4 9 2
+[33,] 1 6 8 5 2 7 9 4 10 3
+[34,] 8 5 7 1 9 2 6 3 10 4
+[35,] 4 5 9 2 7 6 8 3 1 10
+[36,] 5 9 10 1 3 7 2 8 4 6
+[37,] 8 2 7 9 10 1 3 4 6 5
+[38,] 5 8 1 7 4 3 9 10 6 2
+[39,] 10 7 6 4 8 1 3 5 9 2
+[40,] 2 1 8 3 4 6 9 10 7 5
+>
+>
+>
+> cleanEx()
+> nameEx("boot.ci")
+> ### * boot.ci
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: boot.ci
+> ### Title: Nonparametric Bootstrap Confidence Intervals
+> ### Aliases: boot.ci
+> ### Keywords: nonparametric htest
+>
+> ### ** Examples
+>
+> # confidence intervals for the city data
+> ratio <- function(d, w) sum(d$x * w)/sum(d$u * w)
+> city.boot <- boot(city, ratio, R = 999, stype = "w", sim = "ordinary")
+> boot.ci(city.boot, conf = c(0.90, 0.95),
++ type = c("norm", "basic", "perc", "bca"))
+BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS
+Based on 999 bootstrap replicates
+
+CALL :
+boot.ci(boot.out = city.boot, conf = c(0.9, 0.95), type = c("norm",
+ "basic", "perc", "bca"))
+
+Intervals :
+Level Normal Basic
+90% ( 1.124, 1.837 ) ( 1.059, 1.740 )
+95% ( 1.056, 1.905 ) ( 0.932, 1.799 )
+
+Level Percentile BCa
+90% ( 1.301, 1.982 ) ( 1.301, 1.984 )
+95% ( 1.242, 2.109 ) ( 1.243, 2.110 )
+Calculations and Intervals on Original Scale
+>
+> # studentized confidence interval for the two sample
+> # difference of means problem using the final two series
+> # of the gravity data.
+> diff.means <- function(d, f)
++ { n <- nrow(d)
++ gp1 <- 1:table(as.numeric(d$series))[1]
++ m1 <- sum(d[gp1,1] * f[gp1])/sum(f[gp1])
++ m2 <- sum(d[-gp1,1] * f[-gp1])/sum(f[-gp1])
++ ss1 <- sum(d[gp1,1]^2 * f[gp1]) - (m1 * m1 * sum(f[gp1]))
++ ss2 <- sum(d[-gp1,1]^2 * f[-gp1]) - (m2 * m2 * sum(f[-gp1]))
++ c(m1 - m2, (ss1 + ss2)/(sum(f) - 2))
++ }
+> grav1 <- gravity[as.numeric(gravity[,2]) >= 7, ]
+> grav1.boot <- boot(grav1, diff.means, R = 999, stype = "f",
++ strata = grav1[ ,2])
+> boot.ci(grav1.boot, type = c("stud", "norm"))
+BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS
+Based on 999 bootstrap replicates
+
+CALL :
+boot.ci(boot.out = grav1.boot, type = c("stud", "norm"))
+
+Intervals :
+Level Normal Studentized
+95% (-5.880, 0.183 ) (-7.059, -0.101 )
+Calculations and Intervals on Original Scale
+>
+> # Nonparametric confidence intervals for mean failure time
+> # of the air-conditioning data as in Example 5.4 of Davison
+> # and Hinkley (1997)
+> mean.fun <- function(d, i)
++ { m <- mean(d$hours[i])
++ n <- length(i)
++ v <- (n-1)*var(d$hours[i])/n^2
++ c(m, v)
++ }
+> air.boot <- boot(aircondit, mean.fun, R = 999)
+> boot.ci(air.boot, type = c("norm", "basic", "perc", "stud"))
+BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS
+Based on 999 bootstrap replicates
+
+CALL :
+boot.ci(boot.out = air.boot, type = c("norm", "basic", "perc",
+ "stud"))
+
+Intervals :
+Level Normal Basic
+95% ( 35.5, 181.9 ) ( 26.0, 170.6 )
+
+Level Studentized Percentile
+95% ( 47.9, 294.5 ) ( 45.6, 190.2 )
+Calculations and Intervals on Original Scale
+>
+> # Now using the log transformation
+> # There are two ways of doing this and they both give the
+> # same intervals.
+>
+> # Method 1
+> boot.ci(air.boot, type = c("norm", "basic", "perc", "stud"),
++ h = log, hdot = function(x) 1/x)
+BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS
+Based on 999 bootstrap replicates
+
+CALL :
+boot.ci(boot.out = air.boot, type = c("norm", "basic", "perc",
+ "stud"), h = log, hdot = function(x) 1/x)
+
+Intervals :
+Level Normal Basic
+95% ( 4.035, 5.469 ) ( 4.118, 5.546 )
+
+Level Studentized Percentile
+95% ( 3.959, 5.808 ) ( 3.820, 5.248 )
+Calculations and Intervals on Transformed Scale
+>
+> # Method 2
+> vt0 <- air.boot$t0[2]/air.boot$t0[1]^2
+> vt <- air.boot$t[, 2]/air.boot$t[ ,1]^2
+> boot.ci(air.boot, type = c("norm", "basic", "perc", "stud"),
++ t0 = log(air.boot$t0[1]), t = log(air.boot$t[,1]),
++ var.t0 = vt0, var.t = vt)
+BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS
+Based on 999 bootstrap replicates
+
+CALL :
+boot.ci(boot.out = air.boot, type = c("norm", "basic", "perc",
+ "stud"), var.t0 = vt0, var.t = vt, t0 = log(air.boot$t0[1]),
+ t = log(air.boot$t[, 1]))
+
+Intervals :
+Level Normal Basic
+95% ( 4.069, 5.435 ) ( 4.118, 5.546 )
+
+Level Studentized Percentile
+95% ( 3.959, 5.808 ) ( 3.820, 5.248 )
+Calculations and Intervals on Original Scale
+>
+>
+>
+> cleanEx()
+> nameEx("censboot")
+> ### * censboot
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: censboot
+> ### Title: Bootstrap for Censored Data
+> ### Aliases: censboot cens.return
+> ### Keywords: survival
+>
+> ### ** Examples
+>
+> library(survival)
+Loading required package: splines
+
+Attaching package: âsurvivalâ
+
+The following object(s) are masked from âpackage:bootâ:
+
+ aml
+
+> # Example 3.9 of Davison and Hinkley (1997) does a bootstrap on some
+> # remission times for patients with a type of leukaemia. The patients
+> # were divided into those who received maintenance chemotherapy and
+> # those who did not. Here we are interested in the median remission
+> # time for the two groups.
+> data(aml, package = "boot") # not the version in survival.
+> aml.fun <- function(data) {
++ surv <- survfit(Surv(time, cens) ~ group, data = data)
++ out <- NULL
++ st <- 1
++ for (s in 1:length(surv$strata)) {
++ inds <- st:(st + surv$strata[s]-1)
++ md <- min(surv$time[inds[1-surv$surv[inds] >= 0.5]])
++ st <- st + surv$strata[s]
++ out <- c(out, md)
++ }
++ out
++ }
+> aml.case <- censboot(aml, aml.fun, R = 499, strata = aml$group)
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+>
+> # Now we will look at the same statistic using the conditional
+> # bootstrap and the weird bootstrap. For the conditional bootstrap
+> # the survival distribution is stratified but the censoring
+> # distribution is not.
+>
+> aml.s1 <- survfit(Surv(time, cens) ~ group, data = aml)
+> aml.s2 <- survfit(Surv(time-0.001*cens, 1-cens) ~ 1, data = aml)
+> aml.cond <- censboot(aml, aml.fun, R = 499, strata = aml$group,
++ F.surv = aml.s1, G.surv = aml.s2, sim = "cond")
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+>
+>
+> # For the weird bootstrap we must redefine our function slightly since
+> # the data will not contain the group number.
+> aml.fun1 <- function(data, str) {
++ surv <- survfit(Surv(data[, 1], data[, 2]) ~ str)
++ out <- NULL
++ st <- 1
++ for (s in 1:length(surv$strata)) {
++ inds <- st:(st + surv$strata[s] - 1)
++ md <- min(surv$time[inds[1-surv$surv[inds] >= 0.5]])
++ st <- st + surv$strata[s]
++ out <- c(out, md)
++ }
++ out
++ }
+> aml.wei <- censboot(cbind(aml$time, aml$cens), aml.fun1, R = 499,
++ strata = aml$group, F.surv = aml.s1, sim = "weird")
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
+ no non-missing arguments to min; returning Inf
+>
+> # Now for an example where a cox regression model has been fitted
+> # the data we will look at the melanoma data of Example 7.6 from
+> # Davison and Hinkley (1997). The fitted model assumes that there
+> # is a different survival distribution for the ulcerated and
+> # non-ulcerated groups but that the thickness of the tumour has a
+> # common effect. We will also assume that the censoring distribution
+> # is different in different age groups. The statistic of interest
+> # is the linear predictor. This is returned as the values at a
+> # number of equally spaced points in the range of interest.
+> data(melanoma, package = "boot")
+> library(splines)# for ns
+> mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4) + strata(ulcer),
++ data = melanoma)
+> mel.surv <- survfit(mel.cox)
+> agec <- cut(melanoma$age, c(0, 39, 49, 59, 69, 100))
+> mel.cens <- survfit(Surv(time - 0.001*(status == 1), status != 1) ~
++ strata(agec), data = melanoma)
+> mel.fun <- function(d) {
++ t1 <- ns(d$thickness, df=4)
++ cox <- coxph(Surv(d$time, d$status == 1) ~ t1+strata(d$ulcer))
++ ind <- !duplicated(d$thickness)
++ u <- d$thickness[!ind]
++ eta <- cox$linear.predictors[!ind]
++ sp <- smooth.spline(u, eta, df=20)
++ th <- seq(from = 0.25, to = 10, by = 0.25)
++ predict(sp, th)$y
++ }
+> mel.str <- cbind(melanoma$ulcer, agec)
+>
+> # this is slow!
+> mel.mod <- censboot(melanoma, mel.fun, R = 499, F.surv = mel.surv,
++ G.surv = mel.cens, cox = mel.cox, strata = mel.str, sim = "model")
+> # To plot the original predictor and a 95% pointwise envelope for it
+> mel.env <- envelope(mel.mod)$point
+> th <- seq(0.25, 10, by = 0.25)
+> plot(th, mel.env[1, ], ylim = c(-2, 2),
++ xlab = "thickness (mm)", ylab = "linear predictor", type = "n")
+> lines(th, mel.mod$t0, lty = 1)
+> matlines(th, t(mel.env), lty = 2)
+>
+>
+>
+> cleanEx()
+
+detaching âpackage:survivalâ, âpackage:splinesâ
+
+> nameEx("control")
+> ### * control
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: control
+> ### Title: Control Variate Calculations
+> ### Aliases: control
+> ### Keywords: nonparametric
+>
+> ### ** Examples
+>
+> # Use of control variates for the variance of the air-conditioning data
+> mean.fun <- function(d, i)
++ { m <- mean(d$hours[i])
++ n <- nrow(d)
++ v <- (n-1)*var(d$hours[i])/n^2
++ c(m, v)
++ }
+> air.boot <- boot(aircondit, mean.fun, R = 999)
+> control(air.boot, index = 2, bias.adj = TRUE)
+[1] -6.298101
+> air.cont <- control(air.boot, index = 2)
+> # Now let us try the variance on the log scale.
+> air.cont1 <- control(air.boot, t0 = log(air.boot$t0[2]),
++ t = log(air.boot$t[, 2]))
+>
+>
+>
+> cleanEx()
+> nameEx("cv.glm")
+> ### * cv.glm
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: cv.glm
+> ### Title: Cross-validation for Generalized Linear Models
+> ### Aliases: cv.glm
+> ### Keywords: regression
+>
+> ### ** Examples
+>
+> # leave-one-out and 6-fold cross-validation prediction error for
+> # the mammals data set.
+> data(mammals, package="MASS")
+> mammals.glm <- glm(log(brain) ~ log(body), data = mammals)
+> (cv.err <- cv.glm(mammals, mammals.glm)$delta)
+[1] 0.4918650 0.4916571
+> (cv.err.6 <- cv.glm(mammals, mammals.glm, K = 6)$delta)
+[1] 0.4851491 0.4834641
+>
+> # As this is a linear model we could calculate the leave-one-out
+> # cross-validation estimate without any extra model-fitting.
+> muhat <- fitted(mammals.glm)
+> mammals.diag <- glm.diag(mammals.glm)
+> (cv.err <- mean((mammals.glm$y - muhat)^2/(1 - mammals.diag$h)^2))
+[1] 0.491865
+>
+>
+> # leave-one-out and 11-fold cross-validation prediction error for
+> # the nodal data set. Since the response is a binary variable an
+> # appropriate cost function is
+> cost <- function(r, pi = 0) mean(abs(r-pi) > 0.5)
+>
+> nodal.glm <- glm(r ~ stage+xray+acid, binomial, data = nodal)
+> (cv.err <- cv.glm(nodal, nodal.glm, cost, K = nrow(nodal))$delta)
+[1] 0.1886792 0.1886792
+> (cv.11.err <- cv.glm(nodal, nodal.glm, cost, K = 11)$delta)
+[1] 0.2264151 0.2217871
+>
+>
+>
+> cleanEx()
+> nameEx("empinf")
+> ### * empinf
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: empinf
+> ### Title: Empirical Influence Values
+> ### Aliases: empinf
+> ### Keywords: nonparametric math
+>
+> ### ** Examples
+>
+> # The empirical influence values for the ratio of means in
+> # the city data.
+> ratio <- function(d, w) sum(d$x *w)/sum(d$u*w)
+> empinf(data = city, statistic = ratio)
+ [1] -1.04367815 -0.58417763 -0.37092459 -0.18958996 0.03164142 0.10544878
+ [7] 0.09236345 0.20365074 1.02178280 0.73381132
+> city.boot <- boot(city, ratio, 499, stype="w")
+> empinf(boot.out = city.boot, type = "reg")
+ 1 1 1 1 1 1
+-1.13619987 -0.69728210 -0.45301061 -0.27615882 0.02108999 0.14896336
+ 1 1 1 1
+ 0.09746429 0.20622340 1.18798956 0.90092079
+>
+> # A statistic that may be of interest in the difference of means
+> # problem is the t-statistic for testing equality of means. In
+> # the bootstrap we get replicates of the difference of means and
+> # the variance of that statistic and then want to use this output
+> # to get the empirical influence values of the t-statistic.
+> grav1 <- gravity[as.numeric(gravity[,2]) >= 7,]
+> grav.fun <- function(dat, w) {
++ strata <- tapply(dat[, 2], as.numeric(dat[, 2]))
++ d <- dat[, 1]
++ ns <- tabulate(strata)
++ w <- w/tapply(w, strata, sum)[strata]
++ mns <- as.vector(tapply(d * w, strata, sum)) # drop names
++ mn2 <- tapply(d * d * w, strata, sum)
++ s2hat <- sum((mn2 - mns^2)/ns)
++ c(mns[2] - mns[1], s2hat)
++ }
+>
+> grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w",
++ strata = grav1[, 2])
+>
+> # Since the statistic of interest is a function of the bootstrap
+> # statistics, we must calculate the bootstrap replicates and pass
+> # them to empinf using the t argument.
+> grav.z <- (grav.boot$t[,1]-grav.boot$t0[1])/sqrt(grav.boot$t[,2])
+> empinf(boot.out = grav.boot, t = grav.z)
+ 1 1 1 1 1 1 1
+-2.9326019 -1.3760327 -2.4400720 -1.2175846 0.2795352 -0.8258764 -0.8156286
+ 1 1 1 1 1 1 2
+-0.5573332 -1.1275252 -3.1603140 1.2840693 3.5434781 9.3458860 2.6692589
+ 2 2 2 2 2 2 2
+ 4.4496570 3.6948000 0.9929002 -3.0100985 -3.2237464 -2.5493305 -0.6551745
+ 2 2 2 2 2
+ 1.9065308 0.4980530 -1.6219628 -1.6980508 -1.4528364
+>
+>
+>
+> cleanEx()
+> nameEx("envelope")
+> ### * envelope
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: envelope
+> ### Title: Confidence Envelopes for Curves
+> ### Aliases: envelope
+> ### Keywords: dplot htest
+>
+> ### ** Examples
+>
+> # Testing whether the final series of measurements of the gravity data
+> # may come from a normal distribution. This is done in Examples 4.7
+> # and 4.8 of Davison and Hinkley (1997).
+> grav1 <- gravity$g[gravity$series == 8]
+> grav.z <- (grav1 - mean(grav1))/sqrt(var(grav1))
+> grav.gen <- function(dat, mle) rnorm(length(dat))
+> grav.qqboot <- boot(grav.z, sort, R = 999, sim = "parametric",
++ ran.gen = grav.gen)
+> grav.qq <- qqnorm(grav.z, plot.it = FALSE)
+> grav.qq <- lapply(grav.qq, sort)
+> plot(grav.qq, ylim = c(-3.5, 3.5), ylab = "Studentized Order Statistics",
++ xlab = "Normal Quantiles")
+> grav.env <- envelope(grav.qqboot, level = 0.9)
+> lines(grav.qq$x, grav.env$point[1, ], lty = 4)
+> lines(grav.qq$x, grav.env$point[2, ], lty = 4)
+> lines(grav.qq$x, grav.env$overall[1, ], lty = 1)
+> lines(grav.qq$x, grav.env$overall[2, ], lty = 1)
+>
+>
+>
+> cleanEx()
+> nameEx("exp.tilt")
+> ### * exp.tilt
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: exp.tilt
+> ### Title: Exponential Tilting
+> ### Aliases: exp.tilt
+> ### Keywords: nonparametric smooth
+>
+> ### ** Examples
+>
+> # Example 9.8 of Davison and Hinkley (1997) requires tilting the resampling
+> # distribution of the studentized statistic to be centred at the observed
+> # value of the test statistic 1.84. This can be achieved as follows.
+> grav1 <- gravity[as.numeric(gravity[,2]) >=7 , ]
+> grav.fun <- function(dat, w, orig) {
++ strata <- tapply(dat[, 2], as.numeric(dat[, 2]))
++ d <- dat[, 1]
++ ns <- tabulate(strata)
++ w <- w/tapply(w, strata, sum)[strata]
++ mns <- as.vector(tapply(d * w, strata, sum)) # drop names
++ mn2 <- tapply(d * d * w, strata, sum)
++ s2hat <- sum((mn2 - mns^2)/ns)
++ c(mns[2]-mns[1], s2hat, (mns[2]-mns[1]-orig)/sqrt(s2hat))
++ }
+> grav.z0 <- grav.fun(grav1, rep(1, 26), 0)
+> grav.L <- empinf(data = grav1, statistic = grav.fun, stype = "w",
++ strata = grav1[,2], index = 3, orig = grav.z0[1])
+> grav.tilt <- exp.tilt(grav.L, grav.z0[3], strata = grav1[,2])
+> boot(grav1, grav.fun, R = 499, stype = "w", weights = grav.tilt$p,
++ strata = grav1[,2], orig = grav.z0[1])
+
+STRATIFIED WEIGHTED BOOTSTRAP
+
+
+Call:
+boot(data = grav1, statistic = grav.fun, R = 499, stype = "w",
+ strata = grav1[, 2], weights = grav.tilt$p, orig = grav.z0[1])
+
+
+Bootstrap Statistics :
+ original bias std. error mean(t*)
+t1* 2.846154 -0.3661063 1.705171 5.702944
+t2* 2.392353 -0.3538294 1.002889 3.444050
+t3* 0.000000 -0.5160619 1.314298 1.473456
+>
+>
+>
+> cleanEx()
+> nameEx("glm.diag.plots")
+> ### * glm.diag.plots
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: glm.diag.plots
+> ### Title: Diagnostics plots for generalized linear models
+> ### Aliases: glm.diag.plots
+> ### Keywords: regression dplot hplot
+>
+> ### ** Examples
+>
+> # In this example we look at the leukaemia data which was looked at in
+> # Example 7.1 of Davison and Hinkley (1997)
+> data(leuk, package = "MASS")
+> leuk.mod <- glm(time ~ ag-1+log10(wbc), family = Gamma(log), data = leuk)
+> leuk.diag <- glm.diag(leuk.mod)
+> glm.diag.plots(leuk.mod, leuk.diag)
+>
+>
+>
+> cleanEx()
+> nameEx("jack.after.boot")
+> ### * jack.after.boot
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: jack.after.boot
+> ### Title: Jackknife-after-Bootstrap Plots
+> ### Aliases: jack.after.boot
+> ### Keywords: hplot nonparametric
+>
+> ### ** Examples
+>
+> # To draw the jackknife-after-bootstrap plot for the head size data as in
+> # Example 3.24 of Davison and Hinkley (1997)
+> frets.fun <- function(data, i) {
++ pcorr <- function(x) {
++ # Function to find the correlations and partial correlations between
++ # the four measurements.
++ v <- cor(x)
++ v.d <- diag(var(x))
++ iv <- solve(v)
++ iv.d <- sqrt(diag(iv))
++ iv <- - diag(1/iv.d) %*% iv %*% diag(1/iv.d)
++ q <- NULL
++ n <- nrow(v)
++ for (i in 1:(n-1))
++ q <- rbind( q, c(v[i, 1:i], iv[i,(i+1):n]) )
++ q <- rbind( q, v[n, ] )
++ diag(q) <- round(diag(q))
++ q
++ }
++ d <- data[i, ]
++ v <- pcorr(d)
++ c(v[1,], v[2,], v[3,], v[4,])
++ }
+> frets.boot <- boot(log(as.matrix(frets)), frets.fun, R = 999)
+> # we will concentrate on the partial correlation between head breadth
+> # for the first son and head length for the second. This is the 7th
+> # element in the output of frets.fun so we set index = 7
+> jack.after.boot(frets.boot, useJ = FALSE, stinf = FALSE, index = 7)
+>
+>
+>
+> cleanEx()
+> nameEx("k3.linear")
+> ### * k3.linear
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: k3.linear
+> ### Title: Linear Skewness Estimate
+> ### Aliases: k3.linear
+> ### Keywords: nonparametric
+>
+> ### ** Examples
+>
+> # To estimate the skewness of the ratio of means for the city data.
+> ratio <- function(d, w) sum(d$x * w)/sum(d$u * w)
+> k3.linear(empinf(data = city, statistic = ratio))
+[1] 7.831452e-05
+>
+>
+>
+> cleanEx()
+> nameEx("linear.approx")
+> ### * linear.approx
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: linear.approx
+> ### Title: Linear Approximation of Bootstrap Replicates
+> ### Aliases: linear.approx
+> ### Keywords: nonparametric
+>
+> ### ** Examples
+>
+> # Using the city data let us look at the linear approximation to the
+> # ratio statistic and its logarithm. We compare these with the
+> # corresponding plots for the bigcity data
+>
+> ratio <- function(d, w) sum(d$x * w)/sum(d$u * w)
+> city.boot <- boot(city, ratio, R = 499, stype = "w")
+> bigcity.boot <- boot(bigcity, ratio, R = 499, stype = "w")
+> op <- par(pty = "s", mfrow = c(2, 2))
+>
+> # The first plot is for the city data ratio statistic.
+> city.lin1 <- linear.approx(city.boot)
+> lim <- range(c(city.boot$t,city.lin1))
+> plot(city.boot$t, city.lin1, xlim = lim, ylim = lim,
++ main = "Ratio; n=10", xlab = "t*", ylab = "tL*")
+> abline(0, 1)
+>
+> # Now for the log of the ratio statistic for the city data.
+> city.lin2 <- linear.approx(city.boot,t0 = log(city.boot$t0),
++ t = log(city.boot$t))
+> lim <- range(c(log(city.boot$t),city.lin2))
+> plot(log(city.boot$t), city.lin2, xlim = lim, ylim = lim,
++ main = "Log(Ratio); n=10", xlab = "t*", ylab = "tL*")
+> abline(0, 1)
+>
+> # The ratio statistic for the bigcity data.
+> bigcity.lin1 <- linear.approx(bigcity.boot)
+> lim <- range(c(bigcity.boot$t,bigcity.lin1))
+> plot(bigcity.lin1, bigcity.boot$t, xlim = lim, ylim = lim,
++ main = "Ratio; n=49", xlab = "t*", ylab = "tL*")
+> abline(0, 1)
+>
+> # Finally the log of the ratio statistic for the bigcity data.
+> bigcity.lin2 <- linear.approx(bigcity.boot,t0 = log(bigcity.boot$t0),
++ t = log(bigcity.boot$t))
+> lim <- range(c(log(bigcity.boot$t),bigcity.lin2))
+> plot(bigcity.lin2, log(bigcity.boot$t), xlim = lim, ylim = lim,
++ main = "Log(Ratio); n=49", xlab = "t*", ylab = "tL*")
+> abline(0, 1)
+>
+> par(op)
+>
+>
+>
+> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
+> cleanEx()
+> nameEx("lines.saddle.distn")
+> ### * lines.saddle.distn
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: lines.saddle.distn
+> ### Title: Add a Saddlepoint Approximation to a Plot
+> ### Aliases: lines.saddle.distn
+> ### Keywords: aplot smooth nonparametric
+>
+> ### ** Examples
+>
+> # In this example we show how a plot such as that in Figure 9.9 of
+> # Davison and Hinkley (1997) may be produced. Note the large number of
+> # bootstrap replicates required in this example.
+> expdata <- rexp(12)
+> vfun <- function(d, i) {
++ n <- length(d)
++ (n-1)/n*var(d[i])
++ }
+> exp.boot <- boot(expdata,vfun, R = 9999)
+> exp.L <- (expdata - mean(expdata))^2 - exp.boot$t0
+> exp.tL <- linear.approx(exp.boot, L = exp.L)
+> hist(exp.tL, nclass = 50, probability = TRUE)
+> exp.t0 <- c(0, sqrt(var(exp.boot$t)))
+> exp.sp <- saddle.distn(A = exp.L/12,wdist = "m", t0 = exp.t0)
+>
+> # The saddlepoint approximation in this case is to the density of
+> # t-t0 and so t0 must be added for the plot.
+> lines(exp.sp, h = function(u, t0) u+t0, J = function(u, t0) 1,
++ t0 = exp.boot$t0)
+>
+>
+>
+> cleanEx()
+> nameEx("norm.ci")
+> ### * norm.ci
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: norm.ci
+> ### Title: Normal Approximation Confidence Intervals
+> ### Aliases: norm.ci
+> ### Keywords: htest
+>
+> ### ** Examples
+>
+> # In Example 5.1 of Davison and Hinkley (1997), normal approximation
+> # confidence intervals are found for the air-conditioning data.
+> air.mean <- mean(aircondit$hours)
+> air.n <- nrow(aircondit)
+> air.v <- air.mean^2/air.n
+> norm.ci(t0 = air.mean, var.t0 = air.v)
+ conf
+[1,] 0.95 46.93055 169.2361
+> exp(norm.ci(t0 = log(air.mean), var.t0 = 1/air.n)[2:3])
+[1] 61.38157 190.31782
+>
+> # Now a more complicated example - the ratio estimate for the city data.
+> ratio <- function(d, w)
++ sum(d$x * w)/sum(d$u *w)
+> city.v <- var.linear(empinf(data = city, statistic = ratio))
+> norm.ci(t0 = ratio(city,rep(0.1,10)), var.t0 = city.v)
+ conf
+[1,] 0.95 1.167046 1.873579
+>
+>
+>
+> cleanEx()
+> nameEx("plot.boot")
+> ### * plot.boot
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: plot.boot
+> ### Title: Plots of the Output of a Bootstrap Simulation
+> ### Aliases: plot.boot
+> ### Keywords: hplot nonparametric
+>
+> ### ** Examples
+>
+> # We fit an exponential model to the air-conditioning data and use
+> # that for a parametric bootstrap. Then we look at plots of the
+> # resampled means.
+> air.rg <- function(data, mle) rexp(length(data), 1/mle)
+>
+> air.boot <- boot(aircondit$hours, mean, R = 999, sim = "parametric",
++ ran.gen = air.rg, mle = mean(aircondit$hours))
+> plot(air.boot)
+>
+> # In the difference of means example for the last two series of the
+> # gravity data
+> grav1 <- gravity[as.numeric(gravity[, 2]) >= 7, ]
+> grav.fun <- function(dat, w) {
++ strata <- tapply(dat[, 2], as.numeric(dat[, 2]))
++ d <- dat[, 1]
++ ns <- tabulate(strata)
++ w <- w/tapply(w, strata, sum)[strata]
++ mns <- as.vector(tapply(d * w, strata, sum)) # drop names
++ mn2 <- tapply(d * d * w, strata, sum)
++ s2hat <- sum((mn2 - mns^2)/ns)
++ c(mns[2] - mns[1], s2hat)
++ }
+>
+> grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strata = grav1[, 2])
+> plot(grav.boot)
+> # now suppose we want to look at the studentized differences.
+> grav.z <- (grav.boot$t[, 1]-grav.boot$t0[1])/sqrt(grav.boot$t[, 2])
+> plot(grav.boot, t = grav.z, t0 = 0)
+>
+> # In this example we look at the one of the partial correlations for the
+> # head dimensions in the dataset frets.
+> frets.fun <- function(data, i) {
++ pcorr <- function(x) {
++ # Function to find the correlations and partial correlations between
++ # the four measurements.
++ v <- cor(x)
++ v.d <- diag(var(x))
++ iv <- solve(v)
++ iv.d <- sqrt(diag(iv))
++ iv <- - diag(1/iv.d) %*% iv %*% diag(1/iv.d)
++ q <- NULL
++ n <- nrow(v)
++ for (i in 1:(n-1))
++ q <- rbind( q, c(v[i, 1:i], iv[i,(i+1):n]) )
++ q <- rbind( q, v[n, ] )
++ diag(q) <- round(diag(q))
++ q
++ }
++ d <- data[i, ]
++ v <- pcorr(d)
++ c(v[1,], v[2,], v[3,], v[4,])
++ }
+> frets.boot <- boot(log(as.matrix(frets)), frets.fun, R = 999)
+> plot(frets.boot, index = 7, jack = TRUE, stinf = FALSE, useJ = FALSE)
+>
+>
+>
+> cleanEx()
+> nameEx("saddle")
+> ### * saddle
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: saddle
+> ### Title: Saddlepoint Approximations for Bootstrap Statistics
+> ### Aliases: saddle
+> ### Keywords: smooth nonparametric
+>
+> ### ** Examples
+>
+> # To evaluate the bootstrap distribution of the mean failure time of
+> # air-conditioning equipment at 80 hours
+> saddle(A = aircondit$hours/12, u = 80)
+$spa
+ pdf cdf
+0.01005866 0.24446677
+
+$zeta.hat
+[1] -0.02580078
+
+>
+> # Alternatively this can be done using a conditional poisson
+> saddle(A = cbind(aircondit$hours/12,1), u = c(80, 12),
++ wdist = "p", type = "cond")
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 10.090909
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.909091
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 10.090909
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.909091
+$spa
+ pdf cdf
+0.01005943 0.24438736
+
+$zeta.hat
+ A1 A2
+-0.02580805 0.89261577
+
+$zeta2.hat
+[1] 0.6931472
+
+>
+> # To use the Lugananni-Rice approximation to this
+> saddle(A = cbind(aircondit$hours/12,1), u = c(80, 12),
++ wdist = "p", type = "cond",
++ LR = TRUE)
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 10.090909
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.909091
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 10.090909
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.909091
+$spa
+ pdf cdf
+0.01005943 0.24447362
+
+$zeta.hat
+ A1 A2
+-0.02580805 0.89261577
+
+$zeta2.hat
+[1] 0.6931472
+
+>
+> # Example 9.16 of Davison and Hinkley (1997) calculates saddlepoint
+> # approximations to the distribution of the ratio statistic for the
+> # city data. Since the statistic is not in itself a linear combination
+> # of random Variables, its distribution cannot be found directly.
+> # Instead the statistic is expressed as the solution to a linear
+> # estimating equation and hence its distribution can be found. We
+> # get the saddlepoint approximation to the pdf and cdf evaluated at
+> # t = 1.25 as follows.
+> jacobian <- function(dat,t,zeta)
++ {
++ p <- exp(zeta*(dat$x-t*dat$u))
++ abs(sum(dat$u*p)/sum(p))
++ }
+> city.sp1 <- saddle(A = city$x-1.25*city$u, u = 0)
+> city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * city.sp1$spa[1]
+> city.sp1
+$spa
+ pdf cdf
+0.05565040 0.02436306
+
+$zeta.hat
+[1] -0.02435547
+
+>
+>
+>
+> cleanEx()
+> nameEx("saddle.distn")
+> ### * saddle.distn
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: saddle.distn
+> ### Title: Saddlepoint Distribution Approximations for Bootstrap Statistics
+> ### Aliases: saddle.distn
+> ### Keywords: nonparametric smooth dplot
+>
+> ### ** Examples
+>
+> # The bootstrap distribution of the mean of the air-conditioning
+> # failure data: fails to find value on R (and probably on S too)
+> air.t0 <- c(mean(aircondit$hours), sqrt(var(aircondit$hours)/12))
+> ## Not run: saddle.distn(A = aircondit$hours/12, t0 = air.t0)
+>
+> # alternatively using the conditional poisson
+> saddle.distn(A = cbind(aircondit$hours/12, 1), u = 12, wdist = "p",
++ type = "cond", t0 = air.t0)
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 11.344718
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.655282
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 11.344718
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.655282
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 11.832240
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.167760
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 11.832240
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.167760
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 7.444538
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 4.555462
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 7.444538
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 4.555462
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 5.494449
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 6.505551
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 5.494449
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 6.505551
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.594269
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 10.405731
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.594269
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 10.405731
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.544359
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 8.455641
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.544359
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 8.455641
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 4.519404
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 7.480596
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 4.519404
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 7.480596
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 11.561394
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.438606
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 11.561394
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.438606
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 11.290549
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.709451
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 11.290549
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.709451
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 11.019703
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.980297
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 11.019703
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.980297
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 10.748857
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.251143
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 10.748857
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.251143
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 10.478011
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.521989
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 10.478011
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.521989
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 10.207165
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.792835
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 10.207165
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.792835
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 9.936320
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.063680
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 9.936320
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.063680
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 9.665474
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.334526
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 9.665474
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.334526
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 8.785225
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.214775
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 8.785225
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.214775
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 8.175822
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.824178
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 8.175822
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.824178
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 7.566419
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 4.433581
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 7.566419
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 4.433581
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 6.957016
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 5.042984
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 6.957016
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 5.042984
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 6.347613
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 5.652387
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 6.347613
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 5.652387
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 5.738210
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 6.261790
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 5.738210
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 6.261790
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 5.128807
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 6.871193
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 5.128807
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 6.871193
+
+Saddlepoint Distribution Approximations
+
+Call :
+saddle.distn(A = cbind(aircondit$hours/12, 1), u = 12, wdist = "p",
+ type = "cond", t0 = air.t0)
+
+Quantiles of the Distribution
+
+ 0.1% 27.4
+ 0.5% 35.4
+ 1.0% 39.7
+ 2.5% 46.7
+ 5.0% 53.5
+10.0% 62.5
+20.0% 75.3
+50.0% 104.5
+80.0% 139.0
+90.0% 158.8
+95.0% 175.9
+97.5% 191.2
+99.0% 209.6
+99.5% 222.4
+99.9% 249.5
+
+Smoothing spline used 20 points in the range 9.8 to 304.7.
+>
+> # Distribution of the ratio of a sample of size 10 from the bigcity
+> # data, taken from Example 9.16 of Davison and Hinkley (1997).
+> ratio <- function(d, w) sum(d$x *w)/sum(d$u * w)
+> city.v <- var.linear(empinf(data = city, statistic = ratio))
+> bigcity.t0 <- c(mean(bigcity$x)/mean(bigcity$u), sqrt(city.v))
+> Afn <- function(t, data) cbind(data$x - t*data$u, 1)
+> ufn <- function(t, data) c(0,10)
+> saddle.distn(A = Afn, u = ufn, wdist = "b", type = "cond",
++ t0 = bigcity.t0, data = bigcity)
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+Warning in eval(expr, envir, enclos) :
+ non-integer counts in a binomial glm!
+
+Saddlepoint Distribution Approximations
+
+Call :
+saddle.distn(A = Afn, u = ufn, wdist = "b", type = "cond", t0 = bigcity.t0,
+ data = bigcity)
+
+Quantiles of the Distribution
+
+ 0.1% 1.070
+ 0.5% 1.092
+ 1.0% 1.104
+ 2.5% 1.122
+ 5.0% 1.139
+10.0% 1.158
+20.0% 1.184
+50.0% 1.237
+80.0% 1.304
+90.0% 1.348
+95.0% 1.392
+97.5% 1.436
+99.0% 1.494
+99.5% 1.537
+99.9% 1.636
+
+Smoothing spline used 20 points in the range 1.014 to 1.96.
+>
+> # From Example 9.16 of Davison and Hinkley (1997) again, we find the
+> # conditional distribution of the ratio given the sum of city$u.
+> Afn <- function(t, data) cbind(data$x-t*data$u, data$u, 1)
+> ufn <- function(t, data) c(0, sum(data$u), 10)
+> city.t0 <- c(mean(city$x)/mean(city$u), sqrt(city.v))
+> saddle.distn(A = Afn, u = ufn, wdist = "p", type = "cond", t0 = city.t0,
++ data = city)
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.866400
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 8.511350
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.622251
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.866400
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 8.511350
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.622251
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.210844
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.107208
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.681949
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.210844
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.107208
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.681949
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.038622
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 5.809279
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.152100
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.038622
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 5.809279
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.152100
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.452511
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 7.160314
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.387175
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.452511
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 7.160314
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.387175
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.159455
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 7.835832
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.004713
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.159455
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 7.835832
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.004713
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.155629
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.115412
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 6.728960
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.155629
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.115412
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 6.728960
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.205022
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.133273
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 7.661705
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.205022
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.133273
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 7.661705
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.722845
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.033105
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 7.244049
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.722845
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.033105
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 7.244049
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.787431
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 6.388294
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.824275
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.787431
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 6.388294
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.824275
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.415407
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 4.940756
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.643837
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.415407
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 4.940756
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.643837
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.043383
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.493218
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.463399
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.043383
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.493218
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.463399
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.671359
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.045680
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 4.282961
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.671359
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.045680
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 4.282961
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 4.299336
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.598142
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 5.102523
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 4.299336
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.598142
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 5.102523
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.433935
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 4.409277
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.156788
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.433935
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 4.409277
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.156788
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.360158
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.271008
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.368834
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.360158
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.271008
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.368834
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.319252
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.639889
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 4.040859
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.319252
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.639889
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 4.040859
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.278346
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.008770
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 4.712884
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.278346
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.008770
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 4.712884
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.237440
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.377650
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 5.384909
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.237440
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 1.377650
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 5.384909
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.196534
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.746531
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 6.056935
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.196534
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.746531
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 6.056935
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.155629
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.115412
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 6.728960
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 3.155629
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.115412
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 6.728960
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.734728
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.299661
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 6.965612
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.734728
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.299661
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 6.965612
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.228786
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.666383
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 7.104831
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 2.228786
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 0.666383
+Warning in aic(y, n, mu, weights, dev) : non-integer x = 7.104831
+
+Saddlepoint Distribution Approximations
+
+Call :
+saddle.distn(A = Afn, u = ufn, wdist = "p", type = "cond", t0 = city.t0,
+ data = city)
+
+Quantiles of the Distribution
+
+ 0.1% 1.216
+ 0.5% 1.236
+ 1.0% 1.248
+ 2.5% 1.272
+ 5.0% 1.301
+10.0% 1.340
+20.0% 1.393
+50.0% 1.502
+80.0% 1.618
+90.0% 1.680
+95.0% 1.732
+97.5% 1.777
+99.0% 1.830
+99.5% 1.866
+99.9% 1.938
+
+Smoothing spline used 20 points in the range 1.182 to 2.061.
+>
+>
+>
+> cleanEx()
+> nameEx("simplex")
+> ### * simplex
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: simplex
+> ### Title: Simplex Method for Linear Programming Problems
+> ### Aliases: simplex
+> ### Keywords: optimize
+>
+> ### ** Examples
+>
+> # This example is taken from Exercise 7.5 of Gill, Murray and Wright (1991).
+> enj <- c(200, 6000, 3000, -200)
+> fat <- c(800, 6000, 1000, 400)
+> vitx <- c(50, 3, 150, 100)
+> vity <- c(10, 10, 75, 100)
+> vitz <- c(150, 35, 75, 5)
+> simplex(a = enj, A1 = fat, b1 = 13800, A2 = rbind(vitx, vity, vitz),
++ b2 = c(600, 300, 550), maxi = TRUE)
+
+Linear Programming Results
+
+Call : simplex(a = enj, A1 = fat, b1 = 13800, A2 = rbind(vitx, vity,
+ vitz), b2 = c(600, 300, 550), maxi = TRUE)
+
+Maximization Problem with Objective Function Coefficients
+ x1 x2 x3 x4
+ 200 6000 3000 -200
+
+
+Optimal solution has the following values
+ x1 x2 x3 x4
+ 0.0 0.0 13.8 0.0
+The optimal value of the objective function is 41400.
+>
+>
+>
+> cleanEx()
+> nameEx("smooth.f")
+> ### * smooth.f
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: smooth.f
+> ### Title: Smooth Distributions on Data Points
+> ### Aliases: smooth.f
+> ### Keywords: smooth nonparametric
+>
+> ### ** Examples
+>
+> # Example 9.8 of Davison and Hinkley (1997) requires tilting the resampling
+> # distribution of the studentized statistic to be centred at the observed
+> # value of the test statistic 1.84. In the book exponential tilting was used
+> # but it is also possible to use smooth.f.
+> grav1 <- gravity[as.numeric(gravity[, 2]) >= 7, ]
+> grav.fun <- function(dat, w, orig) {
++ strata <- tapply(dat[, 2], as.numeric(dat[, 2]))
++ d <- dat[, 1]
++ ns <- tabulate(strata)
++ w <- w/tapply(w, strata, sum)[strata]
++ mns <- as.vector(tapply(d * w, strata, sum)) # drop names
++ mn2 <- tapply(d * d * w, strata, sum)
++ s2hat <- sum((mn2 - mns^2)/ns)
++ c(mns[2] - mns[1], s2hat, (mns[2]-mns[1]-orig)/sqrt(s2hat))
++ }
+> grav.z0 <- grav.fun(grav1, rep(1, 26), 0)
+> grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w",
++ strata = grav1[, 2], orig = grav.z0[1])
+> grav.sm <- smooth.f(grav.z0[3], grav.boot, index = 3)
+>
+> # Now we can run another bootstrap using these weights
+> grav.boot2 <- boot(grav1, grav.fun, R = 499, stype = "w",
++ strata = grav1[, 2], orig = grav.z0[1],
++ weights = grav.sm)
+>
+> # Estimated p-values can be found from these as follows
+> mean(grav.boot$t[, 3] >= grav.z0[3])
+[1] 0.01402806
+> imp.prob(grav.boot2, t0 = -grav.z0[3], t = -grav.boot2$t[, 3])
+$t0
+[1] -1.840118
+
+$raw
+[1] 0.02163715
+
+$rat
+[1] 0.02099078
+
+$reg
+[1] 0.02174393
+
+>
+>
+> # Note that for the importance sampling probability we must
+> # multiply everything by -1 to ensure that we find the correct
+> # probability. Raw resampling is not reliable for probabilities
+> # greater than 0.5. Thus
+> 1 - imp.prob(grav.boot2, index = 3, t0 = grav.z0[3])$raw
+[1] -0.009155757
+> # can give very strange results (negative probabilities).
+>
+>
+>
+> cleanEx()
+> nameEx("tilt.boot")
+> ### * tilt.boot
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: tilt.boot
+> ### Title: Non-parametric Tilted Bootstrap
+> ### Aliases: tilt.boot
+> ### Keywords: nonparametric
+>
+> ### ** Examples
+>
+> # Note that these examples can take a while to run.
+>
+> # Example 9.9 of Davison and Hinkley (1997).
+> grav1 <- gravity[as.numeric(gravity[,2]) >= 7, ]
+> grav.fun <- function(dat, w, orig) {
++ strata <- tapply(dat[, 2], as.numeric(dat[, 2]))
++ d <- dat[, 1]
++ ns <- tabulate(strata)
++ w <- w/tapply(w, strata, sum)[strata]
++ mns <- as.vector(tapply(d * w, strata, sum)) # drop names
++ mn2 <- tapply(d * d * w, strata, sum)
++ s2hat <- sum((mn2 - mns^2)/ns)
++ c(mns[2]-mns[1],s2hat,(mns[2]-mns[1]-orig)/sqrt(s2hat))
++ }
+> grav.z0 <- grav.fun(grav1, rep(1, 26), 0)
+> tilt.boot(grav1, grav.fun, R = c(249, 375, 375), stype = "w",
++ strata = grav1[,2], tilt = TRUE, index = 3, orig = grav.z0[1])
+
+TILTED BOOTSTRAP
+
+Exponential tilting used
+First 249 replicates untilted,
+Next 375 replicates tilted to -2.821,
+Next 375 replicates tilted to 1.636.
+
+Call:
+tilt.boot(data = grav1, statistic = grav.fun, R = c(249, 375,
+ 375), stype = "w", strata = grav1[, 2], tilt = TRUE, index = 3,
+ orig = grav.z0[1])
+
+
+Bootstrap Statistics :
+ original bias std. error
+t1* 2.846154 -0.4487564 2.500644
+t2* 2.392353 -0.3221155 1.187574
+t3* 0.000000 -0.8862944 2.208945
+>
+>
+> # Example 9.10 of Davison and Hinkley (1997) requires a balanced
+> # importance resampling bootstrap to be run. In this example we
+> # show how this might be run.
+> acme.fun <- function(data, i, bhat) {
++ d <- data[i,]
++ n <- nrow(d)
++ d.lm <- glm(d$acme~d$market)
++ beta.b <- coef(d.lm)[2]
++ d.diag <- boot::glm.diag(d.lm)
++ SSx <- (n-1)*var(d$market)
++ tmp <- (d$market-mean(d$market))*d.diag$res*d.diag$sd
++ sr <- sqrt(sum(tmp^2))/SSx
++ c(beta.b, sr, (beta.b-bhat)/sr)
++ }
+> acme.b <- acme.fun(acme, 1:nrow(acme), 0)
+> acme.boot1 <- tilt.boot(acme, acme.fun, R = c(499, 250, 250),
++ stype = "i", sim = "balanced", alpha = c(0.05, 0.95),
++ tilt = TRUE, index = 3, bhat = acme.b[1])
+>
+>
+>
+> cleanEx()
+> nameEx("tsboot")
+> ### * tsboot
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: tsboot
+> ### Title: Bootstrapping of Time Series
+> ### Aliases: tsboot ts.return
+> ### Keywords: nonparametric ts
+>
+> ### ** Examples
+>
+> lynx.fun <- function(tsb) {
++ ar.fit <- ar(tsb, order.max = 25)
++ c(ar.fit$order, mean(tsb), tsb)
++ }
+>
+> # the stationary bootstrap with mean block length 20
+> lynx.1 <- tsboot(log(lynx), lynx.fun, R = 99, l = 20, sim = "geom")
+>
+> # the fixed block bootstrap with length 20
+> lynx.2 <- tsboot(log(lynx), lynx.fun, R = 99, l = 20, sim = "fixed")
+>
+> # Now for model based resampling we need the original model
+> # Note that for all of the bootstraps which use the residuals as their
+> # data, we set orig.t to FALSE since the function applied to the residual
+> # time series will be meaningless.
+> lynx.ar <- ar(log(lynx))
+> lynx.model <- list(order = c(lynx.ar$order, 0, 0), ar = lynx.ar$ar)
+> lynx.res <- lynx.ar$resid[!is.na(lynx.ar$resid)]
+> lynx.res <- lynx.res - mean(lynx.res)
+>
+> lynx.sim <- function(res,n.sim, ran.args) {
++ # random generation of replicate series using arima.sim
++ rg1 <- function(n, res) sample(res, n, replace = TRUE)
++ ts.orig <- ran.args$ts
++ ts.mod <- ran.args$model
++ mean(ts.orig)+ts(arima.sim(model = ts.mod, n = n.sim,
++ rand.gen = rg1, res = as.vector(res)))
++ }
+>
+> lynx.3 <- tsboot(lynx.res, lynx.fun, R = 99, sim = "model", n.sim = 114,
++ orig.t = FALSE, ran.gen = lynx.sim,
++ ran.args = list(ts = log(lynx), model = lynx.model))
+>
+> # For "post-blackening" we need to define another function
+> lynx.black <- function(res, n.sim, ran.args) {
++ ts.orig <- ran.args$ts
++ ts.mod <- ran.args$model
++ mean(ts.orig) + ts(arima.sim(model = ts.mod,n = n.sim,innov = res))
++ }
+>
+> # Now we can run apply the two types of block resampling again but this
+> # time applying post-blackening.
+> lynx.1b <- tsboot(lynx.res, lynx.fun, R = 99, l = 20, sim = "fixed",
++ n.sim = 114, orig.t = FALSE, ran.gen = lynx.black,
++ ran.args = list(ts = log(lynx), model = lynx.model))
+>
+> lynx.2b <- tsboot(lynx.res, lynx.fun, R = 99, l = 20, sim = "geom",
++ n.sim = 114, orig.t = FALSE, ran.gen = lynx.black,
++ ran.args = list(ts = log(lynx), model = lynx.model))
+>
+> # To compare the observed order of the bootstrap replicates we
+> # proceed as follows.
+> table(lynx.1$t[, 1])
+
+ 2 3 4 5 7 8 10 11 12 13 14
+16 19 38 4 6 3 1 9 1 1 1
+> table(lynx.1b$t[, 1])
+
+ 2 3 4 5 6 7 8 11 12 14 15
+ 6 2 22 6 4 6 3 40 7 1 2
+> table(lynx.2$t[, 1])
+
+ 2 3 4 5 6 7 8 10 11 13
+12 18 51 5 2 3 1 2 4 1
+> table(lynx.2b$t[, 1])
+
+ 2 3 4 5 6 7 8 9 10 11 12 13 15 21
+ 2 1 21 4 1 10 4 1 3 45 3 1 2 1
+> table(lynx.3$t[, 1])
+
+ 2 3 4 5 6 7 8 9 10 11 12 13 14 15
+ 4 8 11 2 1 4 2 2 2 54 6 1 1 1
+> # Notice that the post-blackened and model-based bootstraps preserve
+> # the true order of the model (11) in many more cases than the others.
+>
+>
+>
+> cleanEx()
+> nameEx("var.linear")
+> ### * var.linear
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: var.linear
+> ### Title: Linear Variance Estimate
+> ### Aliases: var.linear
+> ### Keywords: nonparametric
+>
+> ### ** Examples
+>
+> # To estimate the variance of the ratio of means for the city data.
+> ratio <- function(d,w) sum(d$x * w)/sum(d$u * w)
+> var.linear(empinf(data = city, statistic = ratio))
+[1] 0.03248701
+>
+>
+>
+> ### * <FOOTER>
+> ###
+> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
+Time elapsed: 35.015 0.065 35.309 0 0
+> grDevices::dev.off()
+null device
+ 1
+> ###
+> ### Local variables: ***
+> ### mode: outline-minor ***
+> ### outline-regexp: "\\(> \\)?### [*]+" ***
+> ### End: ***
+> quit('no')
diff --git a/win32/deps/library/class/CITATION b/win32/deps/library/class/CITATION
index f6a6566..420318b 100644
--- a/win32/deps/library/class/CITATION
+++ b/win32/deps/library/class/CITATION
@@ -1,4 +1,4 @@
-citHeader("To cite the VR bundle (MASS, class, nnet, spatial) in publications use:")
+citHeader("To cite the class package in publications use:")
citEntry(entry="Book",
title = "Modern Applied Statistics with S",
diff --git a/win32/deps/library/class/DESCRIPTION b/win32/deps/library/class/DESCRIPTION
index e46e7b2..06090a5 100644
--- a/win32/deps/library/class/DESCRIPTION
+++ b/win32/deps/library/class/DESCRIPTION
@@ -1,23 +1,18 @@
-Bundle: VR
-Contains: MASS class nnet spatial
-Priority: recommended
-Version: 7.2-48
-Date: 2009-07-29
-Depends: R (>= 2.5.0), grDevices, graphics, stats, utils
-Suggests: lattice, nlme, survival
-Author: S original by Venables & Ripley. R port by Brian Ripley
- <ripley stats ox ac uk>, following earlier work by Kurt Hornik
- and Albrecht Gebhardt.
-Maintainer: Brian Ripley <ripley stats ox ac uk>
-BundleDescription: Functions and datasets to support Venables and
- Ripley, 'Modern Applied Statistics with S' (4th edition).
-License: GPL-2 | GPL-3
-URL: http://www.stats.ox.ac.uk/pub/MASS4/
-Packaged: 2009-07-31 13:56:57 UTC; ripley
-Repository: CRAN
-Date/Publication: 2009-08-05 11:20:53
-Package: class
-Description: Various functions for classification.
-Title: Functions for Classification
-LazyLoad: yes
-Built: R 2.9.2; i386-pc-mingw32; 2009-08-24 13:00:51 UTC; windows
+Package: class
+Priority: recommended
+Version: 7.3-5
+Date: 2012-10-08
+Depends: R (>= 2.5.0), stats, utils
+Imports: MASS
+Authors R: c(person("Brian", "Ripley", role = c("aut", "cre", "cph"),
+ email = "ripley stats ox ac uk"))
+Author: Brian Ripley <ripley stats ox ac uk>.
+Maintainer: Brian Ripley <ripley stats ox ac uk>
+Description: Various functions for classification.
+Title: Functions for Classification
+License: GPL-2 | GPL-3
+URL: http://www.stats.ox.ac.uk/pub/MASS4/
+LazyLoad: yes
+Packaged: 2012-10-08 10:07:19 UTC; ripley
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:15:17 UTC; windows
+Archs: i386, x64
diff --git a/win32/deps/library/class/LICENCE b/win32/deps/library/class/LICENCE
index e694c08..14b4e51 100644
--- a/win32/deps/library/class/LICENCE
+++ b/win32/deps/library/class/LICENCE
@@ -15,16 +15,7 @@ possible individual files also carry brief copyright notices.
Copyrights
==========
-File MASS/R/profiles.R copyright (C) 1996 D. M. Bates and W. N. Venables.
- port to R by B. D. Ripley copyright (C) 1998
- corrections copyright (C) 2000,3,6 B. D. Ripley
-
-Our understanding is that the dataset files MASS/data/*.rda are not copyright.
-
-Files spatial/data/*.dat were generated or digitized by B. D. Ripley: no
-copyright is asserted.
-
-All other files are copyright (C) 1994-2007 W. N. Venables and
+All files are copyright (C) 1994-2009 W. N. Venables and
B. D. Ripley. Those parts which were distributed with the first
edition are also copyright (C) 1994 Springer-Verlag New York Inc, with
all rights assigned to W. N. Venables and B. D. Ripley.
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index 88674a0..9438b87 100644
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diff --git a/win32/deps/library/class/R/class b/win32/deps/library/class/R/class
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/class/R/class
+++ b/win32/deps/library/class/R/class
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
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new file mode 100644
index 0000000..0c3931c
--- /dev/null
+++ b/win32/deps/library/class/html/00Index.html
@@ -0,0 +1,58 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Functions for Classification</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Functions for Classification
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘class’ version 7.3-5</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+<li><a href="../NEWS">Package NEWS</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<table width="100%">
+<tr><td width="25%"><a href="batchSOM.html">batchSOM</a></td>
+<td>Self-Organizing Maps: Batch Algorithm</td></tr>
+<tr><td width="25%"><a href="condense.html">condense</a></td>
+<td>Condense training set for k-NN classifier</td></tr>
+<tr><td width="25%"><a href="knn.html">knn</a></td>
+<td>k-Nearest Neighbour Classification</td></tr>
+<tr><td width="25%"><a href="knn.cv.html">knn.cv</a></td>
+<td>k-Nearest Neighbour Cross-Validatory Classification</td></tr>
+<tr><td width="25%"><a href="knn1.html">knn1</a></td>
+<td>1-nearest neighbour classification</td></tr>
+<tr><td width="25%"><a href="lvq1.html">lvq1</a></td>
+<td>Learning Vector Quantization 1</td></tr>
+<tr><td width="25%"><a href="lvq2.html">lvq2</a></td>
+<td>Learning Vector Quantization 2.1</td></tr>
+<tr><td width="25%"><a href="lvq3.html">lvq3</a></td>
+<td>Learning Vector Quantization 3</td></tr>
+<tr><td width="25%"><a href="lvqinit.html">lvqinit</a></td>
+<td>Initialize a LVQ Codebook</td></tr>
+<tr><td width="25%"><a href="lvqtest.html">lvqtest</a></td>
+<td>Classify Test Set from LVQ Codebook</td></tr>
+<tr><td width="25%"><a href="multiedit.html">multiedit</a></td>
+<td>Multiedit for k-NN Classifier</td></tr>
+<tr><td width="25%"><a href="olvq1.html">olvq1</a></td>
+<td>Optimized Learning Vector Quantization 1</td></tr>
+<tr><td width="25%"><a href="somgrid.html">plot.SOM</a></td>
+<td>Plot SOM Fits</td></tr>
+<tr><td width="25%"><a href="somgrid.html">plot.somgrid</a></td>
+<td>Plot SOM Fits</td></tr>
+<tr><td width="25%"><a href="reduce.nn.html">reduce.nn</a></td>
+<td>Reduce Training Set for a k-NN Classifier</td></tr>
+<tr><td width="25%"><a href="SOM.html">SOM</a></td>
+<td>Self-Organizing Maps: Online Algorithm</td></tr>
+<tr><td width="25%"><a href="somgrid.html">somgrid</a></td>
+<td>Plot SOM Fits</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/class/html/R.css b/win32/deps/library/class/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/class/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
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+++ b/win32/deps/library/class/tests/Examples/class-Ex.Rout.save
@@ -0,0 +1,580 @@
+
+R version 2.10.0 Patched (2009-11-23 r50545)
+Copyright (C) 2009 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+ Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> pkgname <- "class"
+> source(file.path(R.home("share"), "R", "examples-header.R"))
+> options(warn = 1)
+> library('class')
+>
+> assign(".oldSearch", search(), pos = 'CheckExEnv')
+> cleanEx()
+> nameEx("SOM")
+> ### * SOM
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: SOM
+> ### Title: Self-Organizing Maps: Online Algorithm
+> ### Aliases: SOM
+> ### Keywords: classif
+>
+> ### ** Examples
+>
+> require(graphics)
+> data(crabs, package = "MASS")
+>
+> lcrabs <- log(crabs[, 4:8])
+> crabs.grp <- factor(c("B", "b", "O", "o")[rep(1:4, rep(50,4))])
+> gr <- somgrid(topo = "hexagonal")
+> crabs.som <- SOM(lcrabs, gr)
+> plot(crabs.som)
+>
+> ## 2-phase training
+> crabs.som2 <- SOM(lcrabs, gr,
++ alpha = list(seq(0.05, 0, len = 1e4), seq(0.02, 0, len = 1e5)),
++ radii = list(seq(8, 1, len = 1e4), seq(4, 1, len = 1e5)))
+> plot(crabs.som2)
+>
+>
+>
+> cleanEx()
+> nameEx("batchSOM")
+> ### * batchSOM
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: batchSOM
+> ### Title: Self-Organizing Maps: Batch Algorithm
+> ### Aliases: batchSOM
+> ### Keywords: classif
+>
+> ### ** Examples
+>
+> require(graphics)
+> data(crabs, package = "MASS")
+>
+> lcrabs <- log(crabs[, 4:8])
+> crabs.grp <- factor(c("B", "b", "O", "o")[rep(1:4, rep(50,4))])
+> gr <- somgrid(topo = "hexagonal")
+> crabs.som <- batchSOM(lcrabs, gr, c(4, 4, 2, 2, 1, 1, 1, 0, 0))
+> plot(crabs.som)
+>
+> bins <- as.numeric(knn1(crabs.som$code, lcrabs, 0:47))
+> plot(crabs.som$grid, type = "n")
+> symbols(crabs.som$grid$pts[, 1], crabs.som$grid$pts[, 2],
++ circles = rep(0.4, 48), inches = FALSE, add = TRUE)
+> text(crabs.som$grid$pts[bins, ] + rnorm(400, 0, 0.1),
++ as.character(crabs.grp))
+>
+>
+>
+> cleanEx()
+> nameEx("condense")
+> ### * condense
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: condense
+> ### Title: Condense training set for k-NN classifier
+> ### Aliases: condense
+> ### Keywords: classif
+>
+> ### ** Examples
+>
+> train <- rbind(iris3[1:25,,1], iris3[1:25,,2], iris3[1:25,,3])
+> test <- rbind(iris3[26:50,,1], iris3[26:50,,2], iris3[26:50,,3])
+> cl <- factor(c(rep("s",25), rep("c",25), rep("v",25)))
+> keep <- condense(train, cl)
+[1] 20
+[1] 20 44
+[1] 20 44 65
+[1] 20 44 65 74
+[1] 20 28 44 65 74
+[1] 20 28 44 65 73 74
+[1] 20 28 44 65 73 74 75
+[1] 20 28 44 48 65 73 74 75
+[1] 20 28 44 46 48 65 73 74 75
+ [1] 20 28 44 46 48 57 65 73 74 75
+ [1] 20 28 35 44 46 48 57 65 73 74 75
+ [1] 20 28 35 44 46 48 57 65 70 73 74 75
+> knn(train[keep, , drop=FALSE], test, cl[keep])
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c v c c c c
+[39] c c c c c c c c c c c c v v c v v v v v c v v v v c v v v v v v v v v v c
+Levels: c s v
+> keep2 <- reduce.nn(train, keep, cl)
+> knn(train[keep2, , drop=FALSE], test, cl[keep2])
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c v c c c c
+[39] c c c c c c c c c c c c v v c v v v v v c v v v v c v v v v v v v v v v c
+Levels: c s v
+>
+>
+>
+> cleanEx()
+> nameEx("knn")
+> ### * knn
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: knn
+> ### Title: k-Nearest Neighbour Classification
+> ### Aliases: knn
+> ### Keywords: classif
+>
+> ### ** Examples
+>
+> train <- rbind(iris3[1:25,,1], iris3[1:25,,2], iris3[1:25,,3])
+> test <- rbind(iris3[26:50,,1], iris3[26:50,,2], iris3[26:50,,3])
+> cl <- factor(c(rep("s",25), rep("c",25), rep("v",25)))
+> knn(train, test, cl, k = 3, prob=TRUE)
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c v c c c c c v c c c c
+[39] c c c c c c c c c c c c v c c v v v v v v v v v v c v v v v v v v v v v v
+attr(,"prob")
+ [1] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [8] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.6666667
+[29] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.6666667 1.0000000
+[36] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+[43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+[50] 1.0000000 1.0000000 0.6666667 0.7500000 1.0000000 1.0000000 1.0000000
+[57] 1.0000000 1.0000000 0.5000000 1.0000000 1.0000000 1.0000000 1.0000000
+[64] 0.6666667 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+[71] 1.0000000 0.6666667 1.0000000 1.0000000 0.6666667
+Levels: c s v
+> attributes(.Last.value)
+$levels
+[1] "c" "s" "v"
+
+$class
+[1] "factor"
+
+$prob
+ [1] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [8] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.6666667
+[29] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.6666667 1.0000000
+[36] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+[43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+[50] 1.0000000 1.0000000 0.6666667 0.7500000 1.0000000 1.0000000 1.0000000
+[57] 1.0000000 1.0000000 0.5000000 1.0000000 1.0000000 1.0000000 1.0000000
+[64] 0.6666667 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+[71] 1.0000000 0.6666667 1.0000000 1.0000000 0.6666667
+
+>
+>
+>
+> cleanEx()
+> nameEx("knn.cv")
+> ### * knn.cv
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: knn.cv
+> ### Title: k-Nearest Neighbour Cross-Validatory Classification
+> ### Aliases: knn.cv
+> ### Keywords: classif
+>
+> ### ** Examples
+>
+> train <- rbind(iris3[,,1], iris3[,,2], iris3[,,3])
+> cl <- factor(c(rep("s",50), rep("c",50), rep("v",50)))
+> knn.cv(train, cl, k = 3, prob = TRUE)
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s s s s s s s s s s s s s
+ [38] s s s s s s s s s s s s s c c c c c c c c c c c c c c c c c c c c v c v c
+ [75] c c c c c c c c c v c c c c c c c c c c c c c c c c v v v v v v c v v v v
+[112] v v v v v v v v c v v v v v v v v v v v v v c v v v v v v v v v v v v v v
+[149] v v
+attr(,"prob")
+ [1] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [8] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [29] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [36] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [50] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [57] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [64] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.6666667 1.0000000
+ [71] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [78] 0.6666667 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [85] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [92] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [99] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+[106] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.7500000 1.0000000
+[113] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+[120] 1.0000000 1.0000000 1.0000000 1.0000000 0.7500000 1.0000000 1.0000000
+[127] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+[134] 0.6666667 0.6666667 1.0000000 1.0000000 1.0000000 0.6666667 1.0000000
+[141] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+[148] 1.0000000 1.0000000 1.0000000
+Levels: c s v
+> attributes(.Last.value)
+$levels
+[1] "c" "s" "v"
+
+$class
+[1] "factor"
+
+$prob
+ [1] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [8] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [29] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [36] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [50] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [57] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [64] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.6666667 1.0000000
+ [71] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [78] 0.6666667 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [85] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [92] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+ [99] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+[106] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.7500000 1.0000000
+[113] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+[120] 1.0000000 1.0000000 1.0000000 1.0000000 0.7500000 1.0000000 1.0000000
+[127] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+[134] 0.6666667 0.6666667 1.0000000 1.0000000 1.0000000 0.6666667 1.0000000
+[141] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
+[148] 1.0000000 1.0000000 1.0000000
+
+>
+>
+>
+> cleanEx()
+> nameEx("knn1")
+> ### * knn1
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: knn1
+> ### Title: 1-nearest neighbour classification
+> ### Aliases: knn1
+> ### Keywords: classif
+>
+> ### ** Examples
+>
+> train <- rbind(iris3[1:25,,1], iris3[1:25,,2], iris3[1:25,,3])
+> test <- rbind(iris3[26:50,,1], iris3[26:50,,2], iris3[26:50,,3])
+> cl <- factor(c(rep("s",25), rep("c",25), rep("v",25)))
+> knn1(train, test, cl)
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c v c c c c
+[39] c c c c c c c c c c c c v v c v v v v v c v v v v c v v v v v v v v v v v
+Levels: c s v
+>
+>
+>
+> cleanEx()
+> nameEx("lvq1")
+> ### * lvq1
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: lvq1
+> ### Title: Learning Vector Quantization 1
+> ### Aliases: lvq1
+> ### Keywords: classif
+>
+> ### ** Examples
+>
+> train <- rbind(iris3[1:25,,1], iris3[1:25,,2], iris3[1:25,,3])
+> test <- rbind(iris3[26:50,,1], iris3[26:50,,2], iris3[26:50,,3])
+> cl <- factor(c(rep("s",25), rep("c",25), rep("v",25)))
+> cd <- lvqinit(train, cl, 10)
+> lvqtest(cd, train)
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c c c c c c
+[39] c c c c c v c v c v c c v v v v v v v v v v v v v v v v v v v v v v v v v
+Levels: c s v
+> cd0 <- olvq1(train, cl, cd)
+> lvqtest(cd0, train)
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c c c c c c
+[39] c c c c c c c c c c c c v v v v v v v v v v v v v v v v v v v v v v v c v
+Levels: c s v
+> cd1 <- lvq1(train, cl, cd0)
+> lvqtest(cd1, train)
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c c c c c c
+[39] c c c c c c c v c c c c v v v v v v v v v v v v v v v v v v v v v v v c v
+Levels: c s v
+>
+>
+>
+> cleanEx()
+> nameEx("lvq2")
+> ### * lvq2
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: lvq2
+> ### Title: Learning Vector Quantization 2.1
+> ### Aliases: lvq2
+> ### Keywords: classif
+>
+> ### ** Examples
+>
+> train <- rbind(iris3[1:25,,1], iris3[1:25,,2], iris3[1:25,,3])
+> test <- rbind(iris3[26:50,,1], iris3[26:50,,2], iris3[26:50,,3])
+> cl <- factor(c(rep("s",25), rep("c",25), rep("v",25)))
+> cd <- lvqinit(train, cl, 10)
+> lvqtest(cd, train)
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c c c c c c
+[39] c c c c c v c v c v c c v v v v v v v v v v v v v v v v v v v v v v v v v
+Levels: c s v
+> cd0 <- olvq1(train, cl, cd)
+> lvqtest(cd0, train)
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c c c c c c
+[39] c c c c c c c c c c c c v v v v v v v v v v v v v v v v v v v v v v v c v
+Levels: c s v
+> cd2 <- lvq2(train, cl, cd0)
+> lvqtest(cd2, train)
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c c c c c c
+[39] c c c c c c c c c c c c v v v v v v v v v v v v v v v v v v v v v v v c v
+Levels: c s v
+>
+>
+>
+> cleanEx()
+> nameEx("lvq3")
+> ### * lvq3
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: lvq3
+> ### Title: Learning Vector Quantization 3
+> ### Aliases: lvq3
+> ### Keywords: classif
+>
+> ### ** Examples
+>
+> train <- rbind(iris3[1:25,,1], iris3[1:25,,2], iris3[1:25,,3])
+> test <- rbind(iris3[26:50,,1], iris3[26:50,,2], iris3[26:50,,3])
+> cl <- factor(c(rep("s",25), rep("c",25), rep("v",25)))
+> cd <- lvqinit(train, cl, 10)
+> lvqtest(cd, train)
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c c c c c c
+[39] c c c c c v c v c v c c v v v v v v v v v v v v v v v v v v v v v v v v v
+Levels: c s v
+> cd0 <- olvq1(train, cl, cd)
+> lvqtest(cd0, train)
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c c c c c c
+[39] c c c c c c c c c c c c v v v v v v v v v v v v v v v v v v v v v v v c v
+Levels: c s v
+> cd3 <- lvq3(train, cl, cd0)
+> lvqtest(cd3, train)
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c c c c c c
+[39] c c c c c c c c c c c c v v v v v v v v v v v v v v v v v v v v v v v c v
+Levels: c s v
+>
+>
+>
+> cleanEx()
+> nameEx("lvqinit")
+> ### * lvqinit
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: lvqinit
+> ### Title: Initialize a LVQ Codebook
+> ### Aliases: lvqinit
+> ### Keywords: classif
+>
+> ### ** Examples
+>
+> train <- rbind(iris3[1:25,,1], iris3[1:25,,2], iris3[1:25,,3])
+> test <- rbind(iris3[26:50,,1], iris3[26:50,,2], iris3[26:50,,3])
+> cl <- factor(c(rep("s",25), rep("c",25), rep("v",25)))
+> cd <- lvqinit(train, cl, 10)
+> lvqtest(cd, train)
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c c c c c c
+[39] c c c c c v c v c v c c v v v v v v v v v v v v v v v v v v v v v v v v v
+Levels: c s v
+> cd1 <- olvq1(train, cl, cd)
+> lvqtest(cd1, train)
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c c c c c c
+[39] c c c c c c c c c c c c v v v v v v v v v v v v v v v v v v v v v v v c v
+Levels: c s v
+>
+>
+>
+> cleanEx()
+> nameEx("lvqtest")
+> ### * lvqtest
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: lvqtest
+> ### Title: Classify Test Set from LVQ Codebook
+> ### Aliases: lvqtest
+> ### Keywords: classif
+>
+> ### ** Examples
+>
+> # The function is currently defined as
+> function(codebk, test) knn1(codebk$x, test, codebk$cl)
+function (codebk, test)
+knn1(codebk$x, test, codebk$cl)
+>
+>
+>
+> cleanEx()
+> nameEx("multiedit")
+> ### * multiedit
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: multiedit
+> ### Title: Multiedit for k-NN Classifier
+> ### Aliases: multiedit
+> ### Keywords: classif
+>
+> ### ** Examples
+>
+> tr <- sample(1:50, 25)
+> train <- rbind(iris3[tr,,1], iris3[tr,,2], iris3[tr,,3])
+> test <- rbind(iris3[-tr,,1], iris3[-tr,,2], iris3[-tr,,3])
+> cl <- factor(c(rep(1,25),rep(2,25), rep(3,25)), labels=c("s", "c", "v"))
+> table(cl, knn(train, test, cl, 3))
+
+cl s c v
+ s 25 0 0
+ c 0 23 2
+ v 0 1 24
+> ind1 <- multiedit(train, cl, 3)
+pass 1 size 70
+pass 2 size 67
+pass 3 size 65
+pass 4 size 62
+pass 5 size 61
+pass 6 size 61
+pass 7 size 59
+pass 8 size 59
+pass 9 size 59
+pass 10 size 58
+pass 11 size 58
+pass 12 size 58
+pass 13 size 58
+pass 14 size 58
+> length(ind1)
+[1] 58
+> table(cl, knn(train[ind1, , drop=FALSE], test, cl[ind1], 1))
+
+cl s c v
+ s 25 0 0
+ c 0 25 0
+ v 0 2 23
+> ntrain <- train[ind1,]; ncl <- cl[ind1]
+> ind2 <- condense(ntrain, ncl)
+[1] 15
+[1] 15 26
+[1] 15 26 50
+> length(ind2)
+[1] 3
+> table(cl, knn(ntrain[ind2, , drop=FALSE], test, ncl[ind2], 1))
+
+cl s c v
+ s 25 0 0
+ c 0 25 0
+ v 0 5 20
+>
+>
+>
+> cleanEx()
+> nameEx("olvq1")
+> ### * olvq1
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: olvq1
+> ### Title: Optimized Learning Vector Quantization 1
+> ### Aliases: olvq1
+> ### Keywords: classif
+>
+> ### ** Examples
+>
+> train <- rbind(iris3[1:25,,1], iris3[1:25,,2], iris3[1:25,,3])
+> test <- rbind(iris3[26:50,,1], iris3[26:50,,2], iris3[26:50,,3])
+> cl <- factor(c(rep("s",25), rep("c",25), rep("v",25)))
+> cd <- lvqinit(train, cl, 10)
+> lvqtest(cd, train)
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c c c c c c
+[39] c c c c c v c v c v c c v v v v v v v v v v v v v v v v v v v v v v v v v
+Levels: c s v
+> cd1 <- olvq1(train, cl, cd)
+> lvqtest(cd1, train)
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c c c c c c
+[39] c c c c c c c c c c c c v v v v v v v v v v v v v v v v v v v v v v v c v
+Levels: c s v
+>
+>
+>
+> cleanEx()
+> nameEx("reduce.nn")
+> ### * reduce.nn
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: reduce.nn
+> ### Title: Reduce Training Set for a k-NN Classifier
+> ### Aliases: reduce.nn
+> ### Keywords: classif
+>
+> ### ** Examples
+>
+> train <- rbind(iris3[1:25,,1], iris3[1:25,,2], iris3[1:25,,3])
+> test <- rbind(iris3[26:50,,1], iris3[26:50,,2], iris3[26:50,,3])
+> cl <- factor(c(rep("s",25), rep("c",25), rep("v",25)))
+> keep <- condense(train, cl)
+[1] 20
+[1] 20 44
+[1] 20 44 65
+[1] 20 44 65 74
+[1] 20 28 44 65 74
+[1] 20 28 44 65 73 74
+[1] 20 28 44 65 73 74 75
+[1] 20 28 44 48 65 73 74 75
+[1] 20 28 44 46 48 65 73 74 75
+ [1] 20 28 44 46 48 57 65 73 74 75
+ [1] 20 28 35 44 46 48 57 65 73 74 75
+ [1] 20 28 35 44 46 48 57 65 70 73 74 75
+> knn(train[keep,], test, cl[keep])
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c v c c c c
+[39] c c c c c c c c c c c c v v c v v v v v c v v v v c v v v v v v v v v v c
+Levels: c s v
+> keep2 <- reduce.nn(train, keep, cl)
+> knn(train[keep2,], test, cl[keep2])
+ [1] s s s s s s s s s s s s s s s s s s s s s s s s s c c c c c c c c v c c c c
+[39] c c c c c c c c c c c c v v c v v v v v c v v v v c v v v v v v v v v v c
+Levels: c s v
+>
+>
+>
+> ### * <FOOTER>
+> ###
+> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
+Time elapsed: 0.285 0.016 0.302 0 0
+> grDevices::dev.off()
+null device
+ 1
+> ###
+> ### Local variables: ***
+> ### mode: outline-minor ***
+> ### outline-regexp: "\\(> \\)?### [*]+" ***
+> ### End: ***
+> quit('no')
diff --git a/win32/deps/library/cluster/CITATION b/win32/deps/library/cluster/CITATION
index 9420a74..76acd57 100644
--- a/win32/deps/library/cluster/CITATION
+++ b/win32/deps/library/cluster/CITATION
@@ -1,28 +1,27 @@
## -*- R -*-
citHeader("To cite the R package 'cluster' in publications use:")
-citEntry(entry = "unpublished",
- title = "Cluster Analysis Basics and Extensions",
- author = personList(
- person(first="Martin", last="Maechler",
- email="maechler stat math ethz ch"),
- person(first="Peter", last="Rousseeuw",
- email="rousse uia ua ac be"),
- person(first="Anja", last="Struyf",
- email="Anja Struyf uia ua ac be"),
- person(first="Mia", last="Hubert",
- email="Mia Hubert uia ua ac be")),
- year = 2005,
- note = paste("Rousseeuw et al provided the S original",
- "which has been ported to R by Kurt Hornik",
- "and has since been enhanced by Martin Maechler:",
- "speed improvements, silhouette() functionality, bug fixes, etc. ",
- "See the 'Changelog' file (in the package source)"),
-## FIXME: rather give the URL to the manual on CRAN ???
-## url = "http://stat.ethz.ch/CRAN/src/contrib/........";,
- textVersion = paste(
- "Maechler, M., Rousseeuw, P., Struyf, A., Hubert, M. (2005). ",
- "Cluster Analysis Basics and Extensions;",
- "unpublished")
- )
+if(!exists("meta") || is.null(meta)) meta <- packageDescription("cluster")
+year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", meta$Date)
+vers <- paste("R package version", meta$Version)
+citEntry(entry = "Manual",
+ title = "cluster: Cluster Analysis Basics and Extensions",
+ author = c(
+ person("Martin", "Maechler", email="maechler stat math ethz ch",
+ role = c("aut", "cre"),
+ comment = "enhancements, speed improvements, bug fixes, since 2000"),
+ person("Peter", "Rousseeuw", email="rousse uia ua ac be", role="aut"),
+ person("Anja", "Struyf", email="Anja Struyf uia ua ac be", role="aut"),
+ person("Mia", "Hubert", email="Mia Hubert uia ua ac be", role="aut"),
+ person("Kurt", "Hornik", role=c("trl","ctb"), comment = "R port; and much initial help file fixing, 1998--2000")
+ ),
+ year = year,
+ note = paste(vers,"---",
+ "For new features, see the 'Changelog' file (in the package source)"),
+## FIXME: rather give the URL to the manual on CRAN ???
+## url = "http://stat.ethz.ch/CRAN/src/contrib/........";,
+ textVersion = paste(
+ "Maechler, M., Rousseeuw, P., Struyf, A., Hubert, M., Hornik, K.(",
+ year, "). cluster: Cluster Analysis Basics and Extensions. ",
+ vers, ".", sep=""))
diff --git a/win32/deps/library/cluster/DESCRIPTION b/win32/deps/library/cluster/DESCRIPTION
index 24eba91..77b786d 100644
--- a/win32/deps/library/cluster/DESCRIPTION
+++ b/win32/deps/library/cluster/DESCRIPTION
@@ -1,20 +1,22 @@
-Package: cluster
-Version: 1.12.0
-Date: 2009-05-13
-Priority: recommended
-Author: Martin Maechler, based on S original by Peter Rousseeuw
- <rousse uia ua ac be>, Anja Struyf uia ua ac be and
- Mia Hubert uia ua ac be, and initial R port by
- Kurt Hornik R-project org
-Maintainer: Martin Maechler <maechler stat math ethz ch>
-Title: Cluster Analysis Extended Rousseeuw et al.
-Description: Cluster Analysis, extended original from Peter Rousseeuw,
- Anja Struyf and Mia Hubert.
-Depends: R (>= 2.5.0), stats, graphics, utils
-LazyLoad: yes
-LazyData: yes
-License: GPL (>= 2)
-Packaged: 2009-05-13 12:25:09 UTC; maechler
-Repository: CRAN
-Date/Publication: 2009-05-13 19:17:08
-Built: R 2.9.2; i386-pc-mingw32; 2009-08-24 13:02:40 UTC; windows
+Package: cluster
+Version: 1.14.3
+Date: 2012-10-12
+Priority: recommended
+Author: Martin Maechler, based on S original by Peter Rousseeuw <rousse uia ua ac be>,
+ Anja Struyf uia ua ac be and Mia Hubert uia ua ac be,
+ and initial R port by Kurt Hornik R-project org
+Maintainer: Martin Maechler <maechler stat math ethz ch>
+Title: Cluster Analysis Extended Rousseeuw et al.
+Description: Cluster Analysis, extended original from
+ Peter Rousseeuw, Anja Struyf and Mia Hubert.
+Depends: R (>= 2.10.0), stats, graphics, utils
+Suggests: MASS
+SuggestsNote: two small examples using MASS' cov.rob() and mvrnorm()
+LazyLoad: yes
+LazyData: yes
+ByteCompile: yes
+BuildResaveData: no
+License: GPL (>= 2)
+Packaged: 2012-10-12 22:25:05 UTC; maechler
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:14:44 UTC; windows
+Archs: i386, x64
diff --git a/win32/deps/library/cluster/Meta/Rd.rds b/win32/deps/library/cluster/Meta/Rd.rds
index e1e8f5b..c7f5134 100644
Binary files a/win32/deps/library/cluster/Meta/Rd.rds and b/win32/deps/library/cluster/Meta/Rd.rds differ
diff --git a/win32/deps/library/cluster/Meta/data.rds b/win32/deps/library/cluster/Meta/data.rds
index 8eec852..629f3cb 100644
Binary files a/win32/deps/library/cluster/Meta/data.rds and b/win32/deps/library/cluster/Meta/data.rds differ
diff --git a/win32/deps/library/cluster/Meta/hsearch.rds b/win32/deps/library/cluster/Meta/hsearch.rds
index 2c61d3b..4f404da 100644
Binary files a/win32/deps/library/cluster/Meta/hsearch.rds and b/win32/deps/library/cluster/Meta/hsearch.rds differ
diff --git a/win32/deps/library/cluster/Meta/links.rds b/win32/deps/library/cluster/Meta/links.rds
new file mode 100644
index 0000000..917a86a
Binary files /dev/null and b/win32/deps/library/cluster/Meta/links.rds differ
diff --git a/win32/deps/library/cluster/Meta/nsInfo.rds b/win32/deps/library/cluster/Meta/nsInfo.rds
index e71bb8e..9b51e78 100644
Binary files a/win32/deps/library/cluster/Meta/nsInfo.rds and b/win32/deps/library/cluster/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/cluster/Meta/package.rds b/win32/deps/library/cluster/Meta/package.rds
index cca3cb5..03c9a2d 100644
Binary files a/win32/deps/library/cluster/Meta/package.rds and b/win32/deps/library/cluster/Meta/package.rds differ
diff --git a/win32/deps/library/cluster/NAMESPACE b/win32/deps/library/cluster/NAMESPACE
index 0c1ac3e..2f68a81 100644
--- a/win32/deps/library/cluster/NAMESPACE
+++ b/win32/deps/library/cluster/NAMESPACE
@@ -1,4 +1,4 @@
-useDynLib(cluster)
+useDynLib(cluster, .registration=TRUE)
## S3 Generics:
export(clusplot, pltree, silhouette, volume)
@@ -7,12 +7,13 @@ export(clusplot, pltree, silhouette, volume)
export(agnes, clara, daisy, diana, fanny, mona, pam)
## and the rest
export(bannerplot, ellipsoidhull, ellipsoidPoints,
+ clusGap, maxSE,
lower.to.upper.tri.inds, upper.to.lower.tri.inds,
meanabsdev, sizeDiss, sortSilhouette)
## Methods also useful as 'standalone functions':
export(predict.ellipsoid)
-export(coef.hclust)
+export(coef.hclust, coefHier)
## things from (ex-)mva -- not really needed..
#importFrom(stats, as.hclust, as.dist, as.dendrogram, cutree)
@@ -34,7 +35,7 @@ S3method(volume, ellipsoid)
## register all the method for generics elsewhere in case namespace is
## loaded but not currently attached.
-S3method(as.dendrogram, agnes)
+S3method(as.dendrogram, twins)
S3method(coef, hclust)
S3method(coef, twins)
@@ -43,6 +44,7 @@ S3method(plot, diana)
S3method(plot, mona)
S3method(plot, partition)
S3method(plot, silhouette)
+S3method(plot, clusGap)
#exported: S3method(predict, ellipsoid)
@@ -54,6 +56,7 @@ S3method(print, ellipsoid)
S3method(print, fanny)
S3method(print, mona)
S3method(print, pam)
+S3method(print, clusGap)
S3method(print, summary.agnes)
S3method(print, summary.clara)
S3method(print, summary.diana)
diff --git a/win32/deps/library/cluster/R/cluster b/win32/deps/library/cluster/R/cluster
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/cluster/R/cluster
+++ b/win32/deps/library/cluster/R/cluster
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/cluster/R/cluster.rdb b/win32/deps/library/cluster/R/cluster.rdb
index 3112d67..6911e18 100644
Binary files a/win32/deps/library/cluster/R/cluster.rdb and b/win32/deps/library/cluster/R/cluster.rdb differ
diff --git a/win32/deps/library/cluster/R/cluster.rdx b/win32/deps/library/cluster/R/cluster.rdx
index 2c39ab2..51c5d7c 100644
Binary files a/win32/deps/library/cluster/R/cluster.rdx and b/win32/deps/library/cluster/R/cluster.rdx differ
diff --git a/win32/deps/library/cluster/data/Rdata.rdb b/win32/deps/library/cluster/data/Rdata.rdb
index 3edea71..84f17b5 100644
Binary files a/win32/deps/library/cluster/data/Rdata.rdb and b/win32/deps/library/cluster/data/Rdata.rdb differ
diff --git a/win32/deps/library/cluster/data/Rdata.rds b/win32/deps/library/cluster/data/Rdata.rds
index 9514bdc..83c12a8 100644
Binary files a/win32/deps/library/cluster/data/Rdata.rds and b/win32/deps/library/cluster/data/Rdata.rds differ
diff --git a/win32/deps/library/cluster/data/Rdata.rdx b/win32/deps/library/cluster/data/Rdata.rdx
index f7cac94..184666a 100644
Binary files a/win32/deps/library/cluster/data/Rdata.rdx and b/win32/deps/library/cluster/data/Rdata.rdx differ
diff --git a/win32/deps/library/cluster/help/AnIndex b/win32/deps/library/cluster/help/AnIndex
index 122e8a3..336353a 100644
--- a/win32/deps/library/cluster/help/AnIndex
+++ b/win32/deps/library/cluster/help/AnIndex
@@ -6,11 +6,13 @@ bannerplot bannerplot
chorSub chorSub
clara clara
clara.object clara.object
-clusplot clusplot
+clusGap clusGap
+clusplot clusplot.partition
clusplot.default clusplot.default
clusplot.partition clusplot.partition
coef.hclust coef.hclust
coef.twins coef.hclust
+coefHier coef.hclust
daisy daisy
diana diana
diana.object diana
@@ -21,6 +23,7 @@ fanny fanny
fanny.object fanny.object
flower flower
lower.to.upper.tri.inds lower.to.upper.tri.inds
+maxSE clusGap
meanabsdev cluster-internal
mona mona
mona.object mona.object
@@ -30,6 +33,7 @@ partition partition.object
partition.object partition.object
plantTraits plantTraits
plot.agnes plot.agnes
+plot.clusGap clusGap
plot.diana plot.diana
plot.mona plot.mona
plot.partition plot.partition
@@ -40,6 +44,7 @@ pluton pluton
predict.ellipsoid predict.ellipsoid
print.agnes print.agnes
print.clara print.clara
+print.clusGap clusGap
print.diana print.diana
print.dissimilarity print.dissimilarity
print.ellipsoid ellipsoidhull
diff --git a/win32/deps/library/cluster/help/aliases.rds b/win32/deps/library/cluster/help/aliases.rds
new file mode 100644
index 0000000..ac09ac2
Binary files /dev/null and b/win32/deps/library/cluster/help/aliases.rds differ
diff --git a/win32/deps/library/cluster/help/cluster.rdb b/win32/deps/library/cluster/help/cluster.rdb
new file mode 100644
index 0000000..78e660e
Binary files /dev/null and b/win32/deps/library/cluster/help/cluster.rdb differ
diff --git a/win32/deps/library/cluster/help/cluster.rdx b/win32/deps/library/cluster/help/cluster.rdx
new file mode 100644
index 0000000..9628136
Binary files /dev/null and b/win32/deps/library/cluster/help/cluster.rdx differ
diff --git a/win32/deps/library/cluster/help/paths.rds b/win32/deps/library/cluster/help/paths.rds
new file mode 100644
index 0000000..6baac32
Binary files /dev/null and b/win32/deps/library/cluster/help/paths.rds differ
diff --git a/win32/deps/library/cluster/html/00Index.html b/win32/deps/library/cluster/html/00Index.html
new file mode 100644
index 0000000..d3d2583
--- /dev/null
+++ b/win32/deps/library/cluster/html/00Index.html
@@ -0,0 +1,187 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Cluster Analysis Extended Rousseeuw et al.</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Cluster Analysis Extended Rousseeuw et al.
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘cluster’ version 1.14.3</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<table width="100%">
+<tr><td width="25%"><a href="agnes.html">agnes</a></td>
+<td>Agglomerative Nesting (Hierarchical Clustering)</td></tr>
+<tr><td width="25%"><a href="agnes.object.html">agnes.object</a></td>
+<td>Agglomerative Nesting (AGNES) Object</td></tr>
+<tr><td width="25%"><a href="agriculture.html">agriculture</a></td>
+<td>European Union Agricultural Workforces</td></tr>
+<tr><td width="25%"><a href="animals.html">animals</a></td>
+<td>Attributes of Animals</td></tr>
+<tr><td width="25%"><a href="bannerplot.html">bannerplot</a></td>
+<td>Plot Banner (of Hierarchical Clustering)</td></tr>
+<tr><td width="25%"><a href="chorSub.html">chorSub</a></td>
+<td>Subset of C-horizon of Kola Data</td></tr>
+<tr><td width="25%"><a href="clara.html">clara</a></td>
+<td>Clustering Large Applications</td></tr>
+<tr><td width="25%"><a href="clara.object.html">clara.object</a></td>
+<td>Clustering Large Applications (CLARA) Object</td></tr>
+<tr><td width="25%"><a href="clusGap.html">clusGap</a></td>
+<td>Gap Statistic for Estimating the Number of Clusters</td></tr>
+<tr><td width="25%"><a href="clusplot.partition.html">clusplot</a></td>
+<td>Bivariate Cluster Plot (of a Partitioning Object)</td></tr>
+<tr><td width="25%"><a href="clusplot.default.html">clusplot.default</a></td>
+<td>Bivariate Cluster Plot (clusplot) Default Method</td></tr>
+<tr><td width="25%"><a href="clusplot.partition.html">clusplot.partition</a></td>
+<td>Bivariate Cluster Plot (of a Partitioning Object)</td></tr>
+<tr><td width="25%"><a href="coef.hclust.html">coef.hclust</a></td>
+<td>Agglomerative / Divisive Coefficient for 'hclust' Objects</td></tr>
+<tr><td width="25%"><a href="coef.hclust.html">coef.twins</a></td>
+<td>Agglomerative / Divisive Coefficient for 'hclust' Objects</td></tr>
+<tr><td width="25%"><a href="coef.hclust.html">coefHier</a></td>
+<td>Agglomerative / Divisive Coefficient for 'hclust' Objects</td></tr>
+<tr><td width="25%"><a href="daisy.html">daisy</a></td>
+<td>Dissimilarity Matrix Calculation</td></tr>
+<tr><td width="25%"><a href="diana.html">diana</a></td>
+<td>DIvisive ANAlysis Clustering</td></tr>
+<tr><td width="25%"><a href="diana.html">diana.object</a></td>
+<td>DIvisive ANAlysis Clustering</td></tr>
+<tr><td width="25%"><a href="dissimilarity.object.html">dissimilarity.object</a></td>
+<td>Dissimilarity Matrix Object</td></tr>
+<tr><td width="25%"><a href="ellipsoidhull.html">ellipsoidhull</a></td>
+<td>Compute the Ellipsoid Hull or Spanning Ellipsoid of a Point Set</td></tr>
+<tr><td width="25%"><a href="predict.ellipsoid.html">ellipsoidPoints</a></td>
+<td>Predict Method for Ellipsoid Objects</td></tr>
+<tr><td width="25%"><a href="fanny.html">fanny</a></td>
+<td>Fuzzy Analysis Clustering</td></tr>
+<tr><td width="25%"><a href="fanny.object.html">fanny.object</a></td>
+<td>Fuzzy Analysis (FANNY) Object</td></tr>
+<tr><td width="25%"><a href="flower.html">flower</a></td>
+<td>Flower Characteristics</td></tr>
+<tr><td width="25%"><a href="lower.to.upper.tri.inds.html">lower.to.upper.tri.inds</a></td>
+<td>Permute Indices for Triangular Matrices</td></tr>
+<tr><td width="25%"><a href="clusGap.html">maxSE</a></td>
+<td>Gap Statistic for Estimating the Number of Clusters</td></tr>
+<tr><td width="25%"><a href="mona.html">mona</a></td>
+<td>MONothetic Analysis Clustering of Binary Variables</td></tr>
+<tr><td width="25%"><a href="mona.object.html">mona.object</a></td>
+<td>Monothetic Analysis (MONA) Object</td></tr>
+<tr><td width="25%"><a href="pam.html">pam</a></td>
+<td>Partitioning Around Medoids</td></tr>
+<tr><td width="25%"><a href="pam.object.html">pam.object</a></td>
+<td>Partitioning Around Medoids (PAM) Object</td></tr>
+<tr><td width="25%"><a href="partition.object.html">partition</a></td>
+<td>Partitioning Object</td></tr>
+<tr><td width="25%"><a href="partition.object.html">partition.object</a></td>
+<td>Partitioning Object</td></tr>
+<tr><td width="25%"><a href="plantTraits.html">plantTraits</a></td>
+<td>Plant Species Traits Data</td></tr>
+<tr><td width="25%"><a href="plot.agnes.html">plot.agnes</a></td>
+<td>Plots of an Agglomerative Hierarchical Clustering</td></tr>
+<tr><td width="25%"><a href="clusGap.html">plot.clusGap</a></td>
+<td>Gap Statistic for Estimating the Number of Clusters</td></tr>
+<tr><td width="25%"><a href="plot.diana.html">plot.diana</a></td>
+<td>Plots of a Divisive Hierarchical Clustering</td></tr>
+<tr><td width="25%"><a href="plot.mona.html">plot.mona</a></td>
+<td>Banner of Monothetic Divisive Hierarchical Clusterings</td></tr>
+<tr><td width="25%"><a href="plot.partition.html">plot.partition</a></td>
+<td>Plot of a Partition of the Data Set</td></tr>
+<tr><td width="25%"><a href="silhouette.html">plot.silhouette</a></td>
+<td>Compute or Extract Silhouette Information from Clustering</td></tr>
+<tr><td width="25%"><a href="pltree.html">pltree</a></td>
+<td>Clustering Trees - Generic Function</td></tr>
+<tr><td width="25%"><a href="pltree.twins.html">pltree.twins</a></td>
+<td>Clustering Tree of a Hierarchical Clustering</td></tr>
+<tr><td width="25%"><a href="pluton.html">pluton</a></td>
+<td>Isotopic Composition Plutonium Batches</td></tr>
+<tr><td width="25%"><a href="predict.ellipsoid.html">predict.ellipsoid</a></td>
+<td>Predict Method for Ellipsoid Objects</td></tr>
+<tr><td width="25%"><a href="print.agnes.html">print.agnes</a></td>
+<td>Print Method for AGNES Objects</td></tr>
+<tr><td width="25%"><a href="print.clara.html">print.clara</a></td>
+<td>Print Method for CLARA Objects</td></tr>
+<tr><td width="25%"><a href="clusGap.html">print.clusGap</a></td>
+<td>Gap Statistic for Estimating the Number of Clusters</td></tr>
+<tr><td width="25%"><a href="print.diana.html">print.diana</a></td>
+<td>Print Method for DIANA Objects</td></tr>
+<tr><td width="25%"><a href="print.dissimilarity.html">print.dissimilarity</a></td>
+<td>Print and Summary Methods for Dissimilarity Objects</td></tr>
+<tr><td width="25%"><a href="ellipsoidhull.html">print.ellipsoid</a></td>
+<td>Compute the Ellipsoid Hull or Spanning Ellipsoid of a Point Set</td></tr>
+<tr><td width="25%"><a href="print.fanny.html">print.fanny</a></td>
+<td>Print and Summary Methods for FANNY Objects</td></tr>
+<tr><td width="25%"><a href="print.mona.html">print.mona</a></td>
+<td>Print Method for MONA Objects</td></tr>
+<tr><td width="25%"><a href="print.pam.html">print.pam</a></td>
+<td>Print Method for PAM Objects</td></tr>
+<tr><td width="25%"><a href="summary.agnes.html">print.summary.agnes</a></td>
+<td>Summary Method for 'agnes' Objects</td></tr>
+<tr><td width="25%"><a href="summary.clara.html">print.summary.clara</a></td>
+<td>Summary Method for 'clara' Objects</td></tr>
+<tr><td width="25%"><a href="summary.diana.html">print.summary.diana</a></td>
+<td>Summary Method for 'diana' Objects</td></tr>
+<tr><td width="25%"><a href="print.dissimilarity.html">print.summary.dissimilarity</a></td>
+<td>Print and Summary Methods for Dissimilarity Objects</td></tr>
+<tr><td width="25%"><a href="print.fanny.html">print.summary.fanny</a></td>
+<td>Print and Summary Methods for FANNY Objects</td></tr>
+<tr><td width="25%"><a href="summary.mona.html">print.summary.mona</a></td>
+<td>Summary Method for 'mona' Objects</td></tr>
+<tr><td width="25%"><a href="summary.pam.html">print.summary.pam</a></td>
+<td>Summary Method for PAM Objects</td></tr>
+<tr><td width="25%"><a href="silhouette.html">print.summary.silhouette</a></td>
+<td>Compute or Extract Silhouette Information from Clustering</td></tr>
+<tr><td width="25%"><a href="ruspini.html">ruspini</a></td>
+<td>Ruspini Data</td></tr>
+<tr><td width="25%"><a href="silhouette.html">silhouette</a></td>
+<td>Compute or Extract Silhouette Information from Clustering</td></tr>
+<tr><td width="25%"><a href="silhouette.html">silhouette.clara</a></td>
+<td>Compute or Extract Silhouette Information from Clustering</td></tr>
+<tr><td width="25%"><a href="silhouette.html">silhouette.default</a></td>
+<td>Compute or Extract Silhouette Information from Clustering</td></tr>
+<tr><td width="25%"><a href="silhouette.html">silhouette.partition</a></td>
+<td>Compute or Extract Silhouette Information from Clustering</td></tr>
+<tr><td width="25%"><a href="sizeDiss.html">sizeDiss</a></td>
+<td>Sample Size of Dissimilarity Like Object</td></tr>
+<tr><td width="25%"><a href="silhouette.html">sortSilhouette</a></td>
+<td>Compute or Extract Silhouette Information from Clustering</td></tr>
+<tr><td width="25%"><a href="summary.agnes.html">summary.agnes</a></td>
+<td>Summary Method for 'agnes' Objects</td></tr>
+<tr><td width="25%"><a href="summary.clara.html">summary.clara</a></td>
+<td>Summary Method for 'clara' Objects</td></tr>
+<tr><td width="25%"><a href="summary.diana.html">summary.diana</a></td>
+<td>Summary Method for 'diana' Objects</td></tr>
+<tr><td width="25%"><a href="print.dissimilarity.html">summary.dissimilarity</a></td>
+<td>Print and Summary Methods for Dissimilarity Objects</td></tr>
+<tr><td width="25%"><a href="print.fanny.html">summary.fanny</a></td>
+<td>Print and Summary Methods for FANNY Objects</td></tr>
+<tr><td width="25%"><a href="summary.mona.html">summary.mona</a></td>
+<td>Summary Method for 'mona' Objects</td></tr>
+<tr><td width="25%"><a href="summary.pam.html">summary.pam</a></td>
+<td>Summary Method for PAM Objects</td></tr>
+<tr><td width="25%"><a href="silhouette.html">summary.silhouette</a></td>
+<td>Compute or Extract Silhouette Information from Clustering</td></tr>
+<tr><td width="25%"><a href="twins.object.html">twins</a></td>
+<td>Hierarchical Clustering Object</td></tr>
+<tr><td width="25%"><a href="twins.object.html">twins.object</a></td>
+<td>Hierarchical Clustering Object</td></tr>
+<tr><td width="25%"><a href="lower.to.upper.tri.inds.html">upper.to.lower.tri.inds</a></td>
+<td>Permute Indices for Triangular Matrices</td></tr>
+<tr><td width="25%"><a href="volume.ellipsoid.html">volume</a></td>
+<td>Compute the Volume of Planar Object</td></tr>
+<tr><td width="25%"><a href="volume.ellipsoid.html">volume.ellipsoid</a></td>
+<td>Compute the Volume of Planar Object</td></tr>
+<tr><td width="25%"><a href="votes.repub.html">votes.repub</a></td>
+<td>Votes for Republican Candidate in Presidential Elections</td></tr>
+<tr><td width="25%"><a href="xclara.html">xclara</a></td>
+<td>Bivariate Data Set with 3 Clusters</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/cluster/html/R.css b/win32/deps/library/cluster/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/cluster/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/cluster/libs/i386/cluster.dll b/win32/deps/library/cluster/libs/i386/cluster.dll
new file mode 100644
index 0000000..c2c6345
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diff --git a/win32/deps/library/cluster/po/de/LC_MESSAGES/R-cluster.mo b/win32/deps/library/cluster/po/de/LC_MESSAGES/R-cluster.mo
new file mode 100644
index 0000000..94ca3bf
Binary files /dev/null and b/win32/deps/library/cluster/po/de/LC_MESSAGES/R-cluster.mo differ
diff --git a/win32/deps/library/cluster/po/en quot/LC_MESSAGES/R-cluster.mo b/win32/deps/library/cluster/po/en quot/LC_MESSAGES/R-cluster.mo
new file mode 100644
index 0000000..59240c5
Binary files /dev/null and b/win32/deps/library/cluster/po/en quot/LC_MESSAGES/R-cluster.mo differ
diff --git a/win32/deps/library/cluster/po/pl/LC_MESSAGES/R-cluster.mo b/win32/deps/library/cluster/po/pl/LC_MESSAGES/R-cluster.mo
new file mode 100644
index 0000000..61ea628
Binary files /dev/null and b/win32/deps/library/cluster/po/pl/LC_MESSAGES/R-cluster.mo differ
diff --git a/win32/deps/library/cluster/tests/agnes-ex.R b/win32/deps/library/cluster/tests/agnes-ex.R
new file mode 100644
index 0000000..7dc1cb7
--- /dev/null
+++ b/win32/deps/library/cluster/tests/agnes-ex.R
@@ -0,0 +1,35 @@
+library(cluster)
+options(digits = 6)
+data(votes.repub)
+
+.proctime00 <- proc.time()
+
+agn1 <- agnes(votes.repub, metric = "manhattan", stand = TRUE)
+summary(agn1)
+Dvr <- daisy(votes.repub)
+agn2 <- agnes(Dvr, method = "complete")
+summary(agn2)
+## almost same:
+(ag2. <- agnes(Dvr, method= "complete", keep.diss=FALSE))
+ag22 <- agnes(votes.repub, method= "complete", keep.diss=FALSE,keep.data=FALSE)
+stopifnot(identical(agn2[-5:-6], ag2.[-5:-6]),
+ identical(Dvr, daisy(votes.repub)), # DUP=FALSE (!)
+ identical(ag2.[-6], ag22[-6])
+ )
+
+data(agriculture)
+summary(agnes(agriculture))
+
+data(ruspini)
+summary(ar0 <- agnes(ruspini, keep.diss=FALSE, keep.data=FALSE))
+summary(ar1 <- agnes(ruspini, metric = "manhattan"))
+str(ar1)
+
+cat('Time elapsed: ', proc.time() - .proctime00,'\n')
+
+summary(ar2 <- agnes(ruspini, metric="manhattan", method = "weighted"))
+print (ar3 <- agnes(ruspini, metric="manhattan", method = "flexible",
+ par.meth = 0.5))
+stopifnot(all.equal(ar2[1:4], ar3[1:4], tol=1e-12))
+
+cat('Time elapsed: ', proc.time() - .proctime00,'\n')
diff --git a/win32/deps/library/cluster/tests/agnes-ex.Rout.save b/win32/deps/library/cluster/tests/agnes-ex.Rout.save
new file mode 100644
index 0000000..e7a7cdb
--- /dev/null
+++ b/win32/deps/library/cluster/tests/agnes-ex.Rout.save
@@ -0,0 +1,610 @@
+
+R version 2.8.1 Patched (2009-01-19 r47658)
+Copyright (C) 2009 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(cluster)
+> options(digits = 6)
+> data(votes.repub)
+>
+> .proctime00 <- proc.time()
+>
+> agn1 <- agnes(votes.repub, metric = "manhattan", stand = TRUE)
+> summary(agn1)
+Object of class 'agnes' from call:
+ agnes(x = votes.repub, metric = "manhattan", stand = TRUE)
+Agglomerative coefficient: 0.797756
+Order of objects:
+ [1] Alabama Georgia Arkansas Louisiana Mississippi
+ [6] South Carolina Alaska Vermont Arizona Montana
+[11] Nevada Colorado Idaho Wyoming Utah
+[16] California Oregon Washington Minnesota Connecticut
+[21] New York New Jersey Illinois Ohio Indiana
+[26] Michigan Pennsylvania New Hampshire Wisconsin Delaware
+[31] Kentucky Maryland Missouri New Mexico West Virginia
+[36] Iowa South Dakota North Dakota Kansas Nebraska
+[41] Maine Massachusetts Rhode Island Florida North Carolina
+[46] Tennessee Virginia Oklahoma Hawaii Texas
+Merge:
+ [,1] [,2]
+ [1,] -7 -32
+ [2,] -13 -35
+ [3,] -12 -50
+ [4,] 1 -30
+ [5,] 2 -14
+ [6,] -26 -28
+ [7,] -5 -37
+ [8,] -15 -41
+ [9,] -22 -38
+[10,] -25 -31
+[11,] 7 -47
+[12,] -21 -39
+[13,] -16 -27
+[14,] 4 5
+[15,] -42 -46
+[16,] -20 10
+[17,] 14 9
+[18,] -3 6
+[19,] -6 3
+[20,] -33 15
+[21,] 17 -29
+[22,] -17 16
+[23,] 8 -34
+[24,] 21 -49
+[25,] 22 -48
+[26,] -8 25
+[27,] 19 -44
+[28,] 11 -23
+[29,] 28 24
+[30,] -11 -43
+[31,] 18 27
+[32,] 23 13
+[33,] 29 26
+[34,] 20 -36
+[35,] -1 -10
+[36,] 32 -19
+[37,] 31 33
+[38,] -9 34
+[39,] 37 36
+[40,] 35 -4
+[41,] -2 -45
+[42,] 40 -18
+[43,] -24 -40
+[44,] 39 12
+[45,] 44 38
+[46,] 41 45
+[47,] 42 43
+[48,] 46 30
+[49,] 47 48
+Height:
+ [1] 27.36345 31.15453 35.61832 51.44421 35.69152 87.45523 31.58222 47.53682
+ [9] 16.34184 11.49397 22.11426 16.35662 10.46294 19.03961 28.41137 11.70132
+[17] 12.72838 19.07671 20.90246 8.38200 11.10094 12.92659 9.23004 11.37867
+[25] 15.97442 12.70819 16.91515 17.74499 24.83533 18.78225 17.03525 15.77893
+[33] 12.71848 18.52818 30.74557 12.55524 17.14634 22.33846 12.80419 27.38835
+[41] 37.23685 12.79160 38.76377 29.38432 16.63215 14.75762 25.59605 53.03627
+[49] 21.07684
+
+1225 dissimilarities, summarized :
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+ 8.382 25.540 34.510 45.060 56.020 167.600
+Metric : manhattan
+Number of objects : 50
+
+Available components:
+[1] "order" "height" "ac" "merge" "diss" "call"
+[7] "method" "order.lab" "data"
+> Dvr <- daisy(votes.repub)
+> agn2 <- agnes(Dvr, method = "complete")
+> summary(agn2)
+Object of class 'agnes' from call:
+ agnes(x = Dvr, method = "complete")
+Agglomerative coefficient: 0.88084
+Order of objects:
+ [1] Alabama Georgia Louisiana Arkansas Florida
+ [6] Texas Mississippi South Carolina Alaska Michigan
+[11] Connecticut New York New Hampshire Indiana Ohio
+[16] Illinois New Jersey Pennsylvania Minnesota North Dakota
+[21] Wisconsin Iowa South Dakota Kansas Nebraska
+[26] Arizona Nevada Montana Oklahoma Colorado
+[31] Idaho Wyoming Utah California Oregon
+[36] Washington Missouri New Mexico West Virginia Delaware
+[41] Kentucky Maryland North Carolina Tennessee Virginia
+[46] Hawaii Maine Massachusetts Rhode Island Vermont
+Merge:
+ [,1] [,2]
+ [1,] -12 -50
+ [2,] -7 -32
+ [3,] -14 -35
+ [4,] -13 -30
+ [5,] -25 -31
+ [6,] -37 -47
+ [7,] -21 -39
+ [8,] -3 -28
+ [9,] 4 -38
+[10,] -16 -27
+[11,] -15 -41
+[12,] 8 -26
+[13,] -2 -22
+[14,] -33 -42
+[15,] 14 -46
+[16,] 1 -44
+[17,] -11 -19
+[18,] 2 -29
+[19,] -5 6
+[20,] -17 -20
+[21,] -34 -49
+[22,] 5 -48
+[23,] 18 3
+[24,] 11 10
+[25,] 23 9
+[26,] -23 21
+[27,] -8 20
+[28,] 12 -36
+[29,] -6 16
+[30,] 13 25
+[31,] 28 29
+[32,] -1 -10
+[33,] 19 22
+[34,] 17 7
+[35,] -4 -9
+[36,] 30 26
+[37,] 35 -43
+[38,] 32 -18
+[39,] -24 -40
+[40,] 36 24
+[41,] 27 15
+[42,] 31 33
+[43,] 38 37
+[44,] 40 42
+[45,] 34 -45
+[46,] 43 39
+[47,] 44 41
+[48,] 47 45
+[49,] 46 48
+Height:
+ [1] 48.2397 60.8984 72.9221 56.1363 58.8227 116.7048 63.0951 281.9508
+ [9] 28.1437 47.1690 19.4218 32.9438 36.7643 20.2258 39.1728 20.8792
+[17] 25.3229 56.3813 42.2230 33.6978 64.5254 26.1547 37.4564 25.9221
+[25] 80.4894 23.4206 27.8273 43.4492 48.0483 43.7055 17.1992 31.1988
+[33] 70.4868 33.2328 22.1831 54.3057 21.1413 35.1129 121.4022 43.3829
+[41] 33.4744 66.7591 29.5099 30.1541 178.4119 32.7611 55.3633 22.6334
+[49] 83.1040
+
+1225 dissimilarities, summarized :
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+ 17.20 48.34 64.68 82.23 105.50 282.00
+Metric : euclidean
+Number of objects : 50
+
+Available components:
+[1] "order" "height" "ac" "merge" "diss" "call"
+[7] "method" "order.lab"
+> ## almost same:
+> (ag2. <- agnes(Dvr, method= "complete", keep.diss=FALSE))
+Call: agnes(x = Dvr, method = "complete", keep.diss = FALSE)
+Agglomerative coefficient: 0.88084
+Order of objects:
+ [1] Alabama Georgia Louisiana Arkansas Florida
+ [6] Texas Mississippi South Carolina Alaska Michigan
+[11] Connecticut New York New Hampshire Indiana Ohio
+[16] Illinois New Jersey Pennsylvania Minnesota North Dakota
+[21] Wisconsin Iowa South Dakota Kansas Nebraska
+[26] Arizona Nevada Montana Oklahoma Colorado
+[31] Idaho Wyoming Utah California Oregon
+[36] Washington Missouri New Mexico West Virginia Delaware
+[41] Kentucky Maryland North Carolina Tennessee Virginia
+[46] Hawaii Maine Massachusetts Rhode Island Vermont
+Height (summary):
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+ 17.2 28.1 39.2 52.3 58.8 282.0
+
+Available components:
+[1] "order" "height" "ac" "merge" "diss" "call"
+[7] "method" "order.lab"
+> ag22 <- agnes(votes.repub, method= "complete", keep.diss=FALSE,keep.data=FALSE)
+> stopifnot(identical(agn2[-5:-6], ag2.[-5:-6]),
++ identical(Dvr, daisy(votes.repub)), # DUP=FALSE (!)
++ identical(ag2.[-6], ag22[-6])
++ )
+>
+> data(agriculture)
+> summary(agnes(agriculture))
+Object of class 'agnes' from call:
+ agnes(x = agriculture)
+Agglomerative coefficient: 0.781893
+Order of objects:
+ [1] B NL D F UK DK L I GR P E IRL
+Merge:
+ [,1] [,2]
+ [1,] -1 -10
+ [2,] -2 -9
+ [3,] 1 -3
+ [4,] 3 -6
+ [5,] -5 -7
+ [6,] 4 -12
+ [7,] 6 2
+ [8,] -4 -11
+ [9,] 7 -8
+[10,] 8 5
+[11,] 9 10
+Height:
+ [1] 1.64924 2.24836 2.76918 4.02677 4.78835 2.22036 5.29409 14.77963
+ [9] 5.16236 8.55075 3.14006
+
+66 dissimilarities, summarized :
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+ 1.649 4.357 7.987 9.594 13.250 24.040
+Metric : euclidean
+Number of objects : 12
+
+Available components:
+[1] "order" "height" "ac" "merge" "diss" "call"
+[7] "method" "order.lab" "data"
+>
+> data(ruspini)
+> summary(ar0 <- agnes(ruspini, keep.diss=FALSE, keep.data=FALSE))
+Object of class 'agnes' from call:
+ agnes(x = ruspini, keep.diss = FALSE, keep.data = FALSE)
+Agglomerative coefficient: 0.947954
+Order of objects:
+ [1] 1 2 3 5 4 6 8 7 9 10 14 15 17 16 18 19 11 12 13 20 61 62 66 63 64
+[26] 68 65 67 69 70 71 72 75 73 74 21 22 23 24 27 28 29 30 25 26 32 35 31 36 39
+[51] 40 33 34 37 38 41 42 43 44 45 49 51 53 50 54 52 55 56 57 59 60 58 46 47 48
+Merge:
+ [,1] [,2]
+ [1,] -18 -19
+ [2,] -55 -56
+ [3,] -27 -28
+ [4,] -49 -51
+ [5,] -33 -34
+ [6,] -23 -24
+ [7,] -67 -69
+ [8,] -59 -60
+ [9,] -29 -30
+[10,] -36 -39
+[11,] -32 -35
+[12,] -50 -54
+[13,] -25 -26
+[14,] -16 1
+[15,] -70 -71
+[16,] -64 -68
+[17,] -37 -38
+[18,] 12 -52
+[19,] -62 -66
+[20,] -12 -13
+[21,] -9 -10
+[22,] -42 -43
+[23,] -15 -17
+[24,] -47 -48
+[25,] -21 -22
+[26,] 7 15
+[27,] 2 -57
+[28,] 4 -53
+[29,] 10 -40
+[30,] 3 9
+[31,] -73 -74
+[32,] -72 -75
+[33,] -11 20
+[34,] 13 11
+[35,] -6 -8
+[36,] -14 23
+[37,] -2 -3
+[38,] -65 26
+[39,] 5 17
+[40,] 25 6
+[41,] 36 14
+[42,] 34 -31
+[43,] -4 35
+[44,] 28 18
+[45,] 27 8
+[46,] 19 -63
+[47,] -46 24
+[48,] -1 37
+[49,] 16 38
+[50,] 40 30
+[51,] 42 29
+[52,] 33 -20
+[53,] 49 32
+[54,] 51 39
+[55,] 21 41
+[56,] 48 -5
+[57,] 45 -58
+[58,] 53 31
+[59,] 43 -7
+[60,] 50 54
+[61,] 44 57
+[62,] -41 22
+[63,] -61 46
+[64,] 55 52
+[65,] 63 58
+[66,] -44 -45
+[67,] 59 64
+[68,] 56 67
+[69,] 66 61
+[70,] 60 62
+[71,] 69 47
+[72,] 70 71
+[73,] 68 65
+[74,] 73 72
+Height:
+ [1] 9.26758 6.40312 12.13789 22.37868 7.63441 6.32456 14.58991
+ [8] 21.63544 4.12311 12.07902 6.36396 4.24264 7.23741 3.56155
+[15] 1.41421 16.38921 5.85486 4.12311 10.69547 67.75052 15.48443
+[22] 4.12311 8.94386 17.00500 3.60555 9.53375 6.46443 2.82843
+[29] 4.48680 3.60555 10.91541 5.83095 14.34411 5.65685 101.14200
+[36] 4.47214 6.98022 2.23607 9.56136 2.00000 5.61339 2.82843
+[43] 14.95692 3.16228 6.19728 3.00000 7.28356 9.97147 3.00000
+[50] 5.47542 11.07404 2.23607 6.60456 3.60555 24.90532 15.45463
+[57] 4.24264 64.42555 17.02939 22.56493 2.23607 5.22383 8.28122
+[64] 3.16228 3.81721 15.20808 2.00000 5.19258 8.51123 2.82843
+[71] 12.62990 34.72475 9.14005 4.47214
+
+Available components:
+[1] "order" "height" "ac" "merge" "diss" "call"
+[7] "method" "order.lab"
+> summary(ar1 <- agnes(ruspini, metric = "manhattan"))
+Object of class 'agnes' from call:
+ agnes(x = ruspini, metric = "manhattan")
+Agglomerative coefficient: 0.946667
+Order of objects:
+ [1] 1 2 3 5 4 6 8 7 9 10 14 16 18 19 15 17 11 12 13 20 61 62 66 63 73
+[26] 74 64 68 65 67 69 70 71 72 75 21 22 23 24 27 28 29 30 25 26 32 35 31 36 39
+[51] 40 33 34 37 38 41 42 43 44 45 49 51 53 50 54 52 55 56 57 59 60 58 46 47 48
+Merge:
+ [,1] [,2]
+ [1,] -55 -56
+ [2,] -27 -28
+ [3,] -18 -19
+ [4,] -49 -51
+ [5,] -36 -39
+ [6,] -33 -34
+ [7,] -32 -35
+ [8,] -23 -24
+ [9,] -67 -69
+[10,] -59 -60
+[11,] -50 -54
+[12,] -29 -30
+[13,] -25 -26
+[14,] -16 3
+[15,] -70 -71
+[16,] -64 -68
+[17,] -62 -66
+[18,] 11 -52
+[19,] -37 -38
+[20,] -12 -13
+[21,] -9 -10
+[22,] 9 15
+[23,] 1 -57
+[24,] -47 -48
+[25,] -42 -43
+[26,] -21 -22
+[27,] -15 -17
+[28,] 4 -53
+[29,] 2 12
+[30,] 5 -40
+[31,] 6 19
+[32,] 13 7
+[33,] -11 20
+[34,] -73 -74
+[35,] -72 -75
+[36,] -6 -8
+[37,] -65 22
+[38,] -14 14
+[39,] -2 -3
+[40,] 32 -31
+[41,] 38 27
+[42,] 26 8
+[43,] 28 18
+[44,] -46 24
+[45,] -4 36
+[46,] 23 10
+[47,] -1 39
+[48,] 42 29
+[49,] 33 -20
+[50,] 37 35
+[51,] 40 30
+[52,] 17 -63
+[53,] 16 50
+[54,] 51 31
+[55,] 46 -58
+[56,] 21 41
+[57,] 47 -5
+[58,] 45 -7
+[59,] 52 34
+[60,] -44 -45
+[61,] 48 54
+[62,] 43 55
+[63,] 59 53
+[64,] 56 49
+[65,] -41 25
+[66,] -61 63
+[67,] 57 58
+[68,] 67 64
+[69,] 60 62
+[70,] 61 65
+[71,] 69 44
+[72,] 70 71
+[73,] 68 66
+[74,] 73 72
+Height:
+ [1] 11.50000 9.00000 16.00000 26.25000 10.00000 8.00000 16.66667
+ [8] 28.70833 5.00000 15.50000 8.66667 4.00000 2.00000 9.25000
+[15] 6.00000 20.50000 7.50000 5.00000 12.33333 94.33333 22.78571
+[22] 5.00000 12.50000 18.00000 8.00000 20.20000 5.00000 13.78571
+[29] 8.25000 4.00000 5.50000 5.00000 12.40000 8.00000 125.71357
+[36] 6.00000 9.50000 3.00000 11.87500 2.00000 7.00000 4.00000
+[43] 18.72917 4.00000 7.50000 3.00000 9.25000 12.40000 3.00000
+[50] 7.50000 14.43750 3.00000 7.50000 5.00000 32.38333 21.00000
+[57] 6.00000 85.49616 18.00000 28.75000 3.00000 6.50000 9.55556
+[64] 4.00000 5.00000 19.61111 2.00000 6.00000 11.00000 4.00000
+[71] 15.40000 47.02381 10.00000 6.00000
+
+2775 dissimilarities, summarized :
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+ 2.00 52.50 97.00 90.95 128.00 187.00
+Metric : manhattan
+Number of objects : 75
+
+Available components:
+[1] "order" "height" "ac" "merge" "diss" "call"
+[7] "method" "order.lab" "data"
+> str(ar1)
+List of 9
+ $ order : int [1:75] 1 2 3 5 4 6 8 7 9 10 ...
+ $ height : num [1:74] 11.5 9 16 26.2 10 ...
+ $ ac : num 0.947
+ $ merge : int [1:74, 1:2] -55 -27 -18 -49 -36 -33 -32 -23 -67 -59 ...
+ $ diss :Classes 'dissimilarity', 'dist' atomic [1:2775] 11 12 29 13 25 43 33 22 27 39 ...
+ .. ..- attr(*, "Size")= int 75
+ .. ..- attr(*, "Metric")= chr "manhattan"
+ .. ..- attr(*, "Labels")= chr [1:75] "1" "2" "3" "4" ...
+ $ call : language agnes(x = ruspini, metric = "manhattan")
+ $ method : chr "average"
+ $ order.lab: chr [1:75] "1" "2" "3" "5" ...
+ $ data : num [1:75, 1:2] 4 5 10 9 13 13 12 15 18 19 ...
+ ..- attr(*, "dimnames")=List of 2
+ .. ..$ : chr [1:75] "1" "2" "3" "4" ...
+ .. ..$ : chr [1:2] "x" "y"
+ - attr(*, "class")= chr [1:2] "agnes" "twins"
+>
+> cat('Time elapsed: ', proc.time() - .proctime00,'\n')
+Time elapsed: 0.11 0.02 0.136 0 0
+>
+> summary(ar2 <- agnes(ruspini, metric="manhattan", method = "weighted"))
+Object of class 'agnes' from call:
+ agnes(x = ruspini, metric = "manhattan", method = "weighted")
+Agglomerative coefficient: 0.942387
+Order of objects:
+ [1] 1 2 3 5 9 10 14 16 18 19 15 17 4 6 8 7 11 12 13 20 61 64 68 65 67
+[26] 69 70 71 62 66 63 72 75 73 74 21 22 23 24 27 28 29 30 25 26 32 35 31 36 39
+[51] 40 33 34 37 38 41 42 43 44 45 49 51 53 50 54 52 55 56 57 59 60 58 46 47 48
+Merge:
+ [,1] [,2]
+ [1,] -55 -56
+ [2,] -27 -28
+ [3,] -18 -19
+ [4,] -49 -51
+ [5,] -36 -39
+ [6,] -33 -34
+ [7,] -32 -35
+ [8,] -23 -24
+ [9,] -67 -69
+[10,] -59 -60
+[11,] -50 -54
+[12,] -29 -30
+[13,] -25 -26
+[14,] -16 3
+[15,] -70 -71
+[16,] -64 -68
+[17,] -62 -66
+[18,] 11 -52
+[19,] -37 -38
+[20,] -12 -13
+[21,] -9 -10
+[22,] 9 15
+[23,] 1 -57
+[24,] -47 -48
+[25,] -42 -43
+[26,] -21 -22
+[27,] -15 -17
+[28,] 4 -53
+[29,] 2 12
+[30,] 5 -40
+[31,] 6 19
+[32,] 13 7
+[33,] -11 20
+[34,] -73 -74
+[35,] -72 -75
+[36,] -14 14
+[37,] -6 -8
+[38,] -65 22
+[39,] 36 27
+[40,] -2 -3
+[41,] 32 -31
+[42,] 28 18
+[43,] 26 8
+[44,] -46 24
+[45,] -4 37
+[46,] 23 10
+[47,] -1 40
+[48,] 16 38
+[49,] 43 29
+[50,] 17 -63
+[51,] 41 30
+[52,] 33 -20
+[53,] 35 34
+[54,] 46 -58
+[55,] 47 -5
+[56,] 51 31
+[57,] 21 39
+[58,] 45 -7
+[59,] -44 -45
+[60,] -61 48
+[61,] 42 54
+[62,] 49 56
+[63,] -41 25
+[64,] 55 57
+[65,] 60 50
+[66,] 65 53
+[67,] 58 52
+[68,] 59 61
+[69,] 64 67
+[70,] 62 63
+[71,] 68 44
+[72,] 70 71
+[73,] 69 66
+[74,] 73 72
+Height:
+ [1] 11.5000 9.0000 15.2500 21.7734 5.0000 15.8750 8.0000 4.0000
+ [9] 2.0000 9.0000 6.0000 32.1172 10.0000 8.0000 16.0000 27.9062
+[17] 7.5000 5.0000 13.2500 97.9766 18.3125 5.0000 11.8750 8.2500
+[25] 4.0000 5.5000 5.0000 22.3438 5.0000 12.5000 23.7812 8.0000
+[33] 14.5000 8.0000 114.9764 6.0000 9.5000 3.0000 11.8750 2.0000
+[41] 7.0000 4.0000 20.2031 4.0000 7.5000 3.0000 9.2500 12.6250
+[49] 3.0000 7.5000 15.6875 3.0000 7.5000 5.0000 33.5469 21.0000
+[57] 6.0000 69.4453 18.0000 28.4375 3.0000 6.5000 9.5000 4.0000
+[65] 5.0000 19.1250 2.0000 6.0000 10.5000 4.0000 15.0000 41.5312
+[73] 10.0000 6.0000
+
+2775 dissimilarities, summarized :
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+ 2.00 52.50 97.00 90.95 128.00 187.00
+Metric : manhattan
+Number of objects : 75
+
+Available components:
+[1] "order" "height" "ac" "merge" "diss" "call"
+[7] "method" "order.lab" "data"
+> print (ar3 <- agnes(ruspini, metric="manhattan", method = "flexible",
++ par.meth = 0.5))
+Call: agnes(x = ruspini, metric = "manhattan", method = "flexible", par.method = 0.5)
+Agglomerative coefficient: 0.942387
+Order of objects:
+ [1] 1 2 3 5 9 10 14 16 18 19 15 17 4 6 8 7 11 12 13 20 61 64 68 65 67
+[26] 69 70 71 62 66 63 72 75 73 74 21 22 23 24 27 28 29 30 25 26 32 35 31 36 39
+[51] 40 33 34 37 38 41 42 43 44 45 49 51 53 50 54 52 55 56 57 59 60 58 46 47 48
+Height (summary):
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+ 2.00 5.00 8.12 14.20 15.60 115.00
+
+Available components:
+[1] "order" "height" "ac" "merge" "diss" "call"
+[7] "method" "order.lab" "data"
+> stopifnot(all.equal(ar2[1:4], ar3[1:4], tol=1e-12))
+>
+> cat('Time elapsed: ', proc.time() - .proctime00,'\n')
+Time elapsed: 0.123 0.028 0.157 0 0
+>
diff --git a/win32/deps/library/cluster/tests/clara-NAs.R b/win32/deps/library/cluster/tests/clara-NAs.R
new file mode 100644
index 0000000..8892fa8
--- /dev/null
+++ b/win32/deps/library/cluster/tests/clara-NAs.R
@@ -0,0 +1,46 @@
+library(cluster)
+
+x <- cbind(c(0, -4, -22, -14, 0, NA, -28, 1, 10, -1,
+ 100 + c(13, 0, 2, 4, 7, 8, 1)),
+ c(-5, -14, NA, -35, -30, NA, 7, 2, -18, 13,
+ 47, 64, 48, NA, NA, 44, 65))
+x
+(d <- dist(x,'manhattan'))
+summary(d, na.rm = TRUE) # max = 270
+## First call with "trace" (seg.fault typically later ...):
+try( clara(x, k=2, metric="manhattan", sampsize=10, trace = 3) )
+## Originally:already shows the problem: nbest[] = c(0,0,...,0) must be WRONG!!
+## Now: gives the proper error message.
+
+## S-plus 6.1.2 (rel.2 for Linux, 2002) gives
+##> cc <- clara(x, k=2, metric="manhattan", samples=2, sampsize=10)
+## Problem in .Fortran("clara",: Internal error: data for decrementing
+## ref.count didn't point to a valid arena (0x0), while calling subroutine clara
+
+## The large example from clara.R -- made small enough to still provoke
+## the "** dysta2() ... OUT" problem {no longer!}
+x <- matrix(c(0, 3, -4, 62, 1, 3, -7, 45, 36, 46, 45, 54, -10,
+ 51, 49, -5, 13, -6, 49, 52, 57, 39, -1, 55, 68, -3, 51, 11, NA,
+ 9, -3, 50, NA, 58, 9, 52, 12, NA, 47, -12, -6, -9, 5, 30, 38,
+ 54, -5, 39, 50, 50, 54, 43, 7, 64, 55, 4, 0, 72, 54, 37, 59,
+ -1, 8, 43, 50, -2, 56, -8, 43, 6, 4, 48, -2, 14, 45, 49, 56,
+ 51, 45, 11, 10, 42, 50, 2, -12, 3, 1, 2, 2, -14, -4, 8, 0, 3,
+ -11, 8, 5, 14, -1, 9, 0, 19, 10, -2, -9, 9, 2, 16, 10, 4, 1,
+ 12, 7, -4, 27, -8, -9, -9, 2, 8, NA, 13, -23, -3, -5, 1, 15,
+ -3, 5, -9, -5, 14, 8, 7, -4, 26, 20, 10, 8, 17, 4, 14, 23, -2,
+ 23, 2, 16, 5, 5, -3, 12, 5, 14, -2, 4, 2, -2, 7, 9, 1, -15, -1,
+ 9, 23, 1, 7, 13, 2, -11, 16, 12, -11, -14, 2, 6, -8),
+ ncol = 2)
+str(x) # 88 x 2
+try(clara(x, 2, samples = 20, trace = 3))# 2nd sample did show dysta2() problem
+## To see error message for > 1 missing:
+try(clara(rbind(NA,x), 2))
+
+x <- x[-33,]
+## still had the ** dysta2() .. OUT" problem {no longer!}
+clara(x, 2, samples = 12, trace = 3)
+
+data(xclara)
+set.seed(123)
+xclara[sample(nrow(xclara), 50),] <- NA
+try( clara(xclara, k = 3) ) #-> "nice" error message depicting first 12 missing obs
diff --git a/win32/deps/library/cluster/tests/clara-NAs.Rout.save b/win32/deps/library/cluster/tests/clara-NAs.Rout.save
new file mode 100644
index 0000000..acfeb1e
--- /dev/null
+++ b/win32/deps/library/cluster/tests/clara-NAs.Rout.save
@@ -0,0 +1,635 @@
+
+R version 2.15.1 Patched (2012-10-12 r60924) -- "Roasted Marshmallows"
+Copyright (C) 2012 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(cluster)
+>
+> x <- cbind(c(0, -4, -22, -14, 0, NA, -28, 1, 10, -1,
++ 100 + c(13, 0, 2, 4, 7, 8, 1)),
++ c(-5, -14, NA, -35, -30, NA, 7, 2, -18, 13,
++ 47, 64, 48, NA, NA, 44, 65))
+> x
+ [,1] [,2]
+ [1,] 0 -5
+ [2,] -4 -14
+ [3,] -22 NA
+ [4,] -14 -35
+ [5,] 0 -30
+ [6,] NA NA
+ [7,] -28 7
+ [8,] 1 2
+ [9,] 10 -18
+[10,] -1 13
+[11,] 113 47
+[12,] 100 64
+[13,] 102 48
+[14,] 104 NA
+[15,] 107 NA
+[16,] 108 44
+[17,] 101 65
+> (d <- dist(x,'manhattan'))
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
+2 13
+3 44 36
+4 44 31 16
+5 25 20 44 19
+6 NA NA NA NA NA
+7 40 45 12 56 65 NA
+8 8 21 46 52 33 NA 34
+9 23 18 64 41 22 NA 63 29
+10 19 30 42 61 44 NA 33 13 42
+11 165 178 270 209 190 NA 181 157 168 148
+12 169 182 244 213 194 NA 185 161 172 152 30
+13 155 168 248 199 180 NA 171 147 158 138 12 18
+14 208 216 252 236 208 NA 264 206 188 210 18 8 4
+15 214 222 258 242 214 NA 270 212 194 216 12 14 10 6
+16 157 170 260 201 182 NA 173 149 160 140 8 28 10 8 2
+17 171 184 246 215 196 NA 187 163 174 154 30 2 18 6 12 28
+> summary(d, na.rm = TRUE) # max = 270
+ Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
+ 2.00 27.25 147.50 114.60 188.50 270.00 16
+> ## First call with "trace" (seg.fault typically later ...):
+> try( clara(x, k=2, metric="manhattan", sampsize=10, trace = 3) )
+calling .C(cl_clara, ..., DUP = FALSE):
+C clara(): (nsam,nran,n) = (10,5,17); 'large_sample',
+C clara(): sample 1 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 1
+ {295} [ntt=7, nunfs=0] .. nsel[1:10]= 6 7 8 9 10 12 13 14 16 17 -> dysta2()
+ dysta2() gave dyst_toomany_NA --> new sample
+C clara(): sample 2 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 3
+ {295} [ntt=7, nunfs=1] .. nsel[1:10]= 1 4 7 9 11 12 13 15 16 17 -> dysta2()
+. clara(): s:= max dys[1..45] = 270;
+clara()'s bswap2(*, s=270): new repr. 7
+ new repr. 1
+ after build: medoids are 1 7
+ and min.dist dysma[1:n] are
+ 0 44 40 23 12 18 0 10 10 18
+ --> sky = sum_j D_j= 175
+ swp new 8 <-> 7 old; decreasing diss. by -18
+ Last swap: new 8 <-> 7 old; decreasing diss. by 1
+end{bswap}: sky = 157
+ selec() -> 'NAfs' obj= 5.47059
+C clara(): sample 3 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 6
+ {295} [ntt=7, nunfs=2] .. nsel[1:10]= 1 2 3 5 8 9 10 11 13 17 -> dysta2()
+. clara(): s:= max dys[1..45] = 270;
+clara()'s bswap2(*, s=270): new repr. 5
+ new repr. 9
+ after build: medoids are 5 9
+ and min.dist dysma[1:n] are
+ 8 21 46 33 0 29 13 12 0 18
+ --> sky = sum_j D_j= 180
+ swp new 1 <-> 5 old; decreasing diss. by -18
+ Last swap: new 1 <-> 5 old; decreasing diss. by 1
+end{bswap}: sky = 162
+ selec() -> 'NAfs' obj= 5.47059
+C clara(): sample 4 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 5
+ {295} [ntt=7, nunfs=3] .. nsel[1:10]= 1 2 3 4 7 8 9 10 13 14 -> dysta2()
+. clara(): s:= max dys[1..45] = 264;
+clara()'s bswap2(*, s=264): new repr. 1
+ new repr. 10
+ after build: medoids are 1 10
+ and min.dist dysma[1:n] are
+ 0 13 44 44 40 8 23 19 4 0
+ --> sky = sum_j D_j= 195
+ Last swap: new 9 <-> 10 old; decreasing diss. by 0
+end{bswap}: sky = 195
+ selec() -> 'NAfs' obj= 5.47059
+C clara(): sample 5 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 16
+ {295} [ntt=7, nunfs=4] .. nsel[1:10]= 2 3 4 6 7 8 9 10 11 17 -> dysta2()
+ dysta2() gave dyst_toomany_NA --> new sample
+Error in clara(x, k = 2, metric = "manhattan", sampsize = 10, trace = 3) :
+ Observation 6 has *only* NAs --> omit it for clustering
+> ## Originally:already shows the problem: nbest[] = c(0,0,...,0) must be WRONG!!
+> ## Now: gives the proper error message.
+>
+> ## S-plus 6.1.2 (rel.2 for Linux, 2002) gives
+> ##> cc <- clara(x, k=2, metric="manhattan", samples=2, sampsize=10)
+> ## Problem in .Fortran("clara",: Internal error: data for decrementing
+> ## ref.count didn't point to a valid arena (0x0), while calling subroutine clara
+>
+> ## The large example from clara.R -- made small enough to still provoke
+> ## the "** dysta2() ... OUT" problem {no longer!}
+> x <- matrix(c(0, 3, -4, 62, 1, 3, -7, 45, 36, 46, 45, 54, -10,
++ 51, 49, -5, 13, -6, 49, 52, 57, 39, -1, 55, 68, -3, 51, 11, NA,
++ 9, -3, 50, NA, 58, 9, 52, 12, NA, 47, -12, -6, -9, 5, 30, 38,
++ 54, -5, 39, 50, 50, 54, 43, 7, 64, 55, 4, 0, 72, 54, 37, 59,
++ -1, 8, 43, 50, -2, 56, -8, 43, 6, 4, 48, -2, 14, 45, 49, 56,
++ 51, 45, 11, 10, 42, 50, 2, -12, 3, 1, 2, 2, -14, -4, 8, 0, 3,
++ -11, 8, 5, 14, -1, 9, 0, 19, 10, -2, -9, 9, 2, 16, 10, 4, 1,
++ 12, 7, -4, 27, -8, -9, -9, 2, 8, NA, 13, -23, -3, -5, 1, 15,
++ -3, 5, -9, -5, 14, 8, 7, -4, 26, 20, 10, 8, 17, 4, 14, 23, -2,
++ 23, 2, 16, 5, 5, -3, 12, 5, 14, -2, 4, 2, -2, 7, 9, 1, -15, -1,
++ 9, 23, 1, 7, 13, 2, -11, 16, 12, -11, -14, 2, 6, -8),
++ ncol = 2)
+> str(x) # 88 x 2
+ num [1:88, 1:2] 0 3 -4 62 1 3 -7 45 36 46 ...
+> try(clara(x, 2, samples = 20, trace = 3))# 2nd sample did show dysta2() problem
+calling .C(cl_clara, ..., DUP = FALSE):
+C clara(): (nsam,nran,n) = (44,20,88);
+C clara(): sample 1 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 2
+ {295} [ntt=44, nunfs=0] .. nsel[1:44]= 2 3 4 6 9 10 12 14 15 18 19 20 24 25 26 28 31 35 38 42 47 48 51 53 54 57 60 61 64 66 68 70 71 73 74 75 76 77 78 79 80 81 82 88 -> dysta2()
+. clara(): s:= max dys[1..946] = 78.6448;
+clara()'s bswap2(*, s=78.6448): new repr. 19
+ new repr. 9
+ after build: medoids are 9 19
+ and min.dist dysma[1:n] are
+ 21.2 7.07 9.9 2.83 5.66 5 5.1 9.22 0 11.3
+ 1.41 6.71 6.32 8.49 7.07 12.7 1.41 33.9 0 14.1
+ 7.07 18.9 5.39 4.24 15.5 31.1 5.66 5.66 5.66 4.24
+ 1.41 8.49 11.3 22.6 2.83 4.12 13 0 3.61 5
+ 1.41 17 9.22 12.7
+ --> sky = sum_j D_j= 385.677
+ Last swap: new 6 <-> 9 old; decreasing diss. by 0.939294
+end{bswap}: sky = 385.677
+ selec() -> 'NAfs' obj= 1.64279
+C clara(): sample 2 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 12
+ {295} [ntt=44, nunfs=1] .. nsel[1:44]= 1 2 3 5 6 7 9 12 17 19 26 27 28 29 30 38 39 42 43 45 47 50 52 54 55 56 58 59 60 61 62 64 67 68 71 74 75 76 77 79 80 81 83 84 -> dysta2()
+. clara(): s:= max dys[1..946] = 81.7435;
+clara()'s bswap2(*, s=81.7435): new repr. 16
+ new repr. 43
+ after build: medoids are 16 43
+ and min.dist dysma[1:n] are
+ 1.41 21.2 7.07 1.41 2.83 17 5.66 5 14.1 1.41
+ 7.07 15 12.7 14.1 14.1 0 4.24 14.1 8.49 9.9
+ 7.07 2 8.6 14.1 12.1 4.24 1.41 5.66 5.66 5.66
+ 5.66 5.66 4.24 1.41 11.3 2.83 5.83 11 0 5.1
+ 1.41 17 0 17
+ --> sky = sum_j D_j= 331.98
+ Last swap: new 17 <-> 43 old; decreasing diss. by 0.492109
+end{bswap}: sky = 331.98
+ selec() -> 'NAfs' obj= 1.59799
+C clara(): sample 3 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 14
+ {295} [ntt=44, nunfs=2] .. nsel[1:44]= 1 3 4 6 7 9 12 14 15 16 18 19 20 29 30 31 32 36 38 39 40 44 46 47 48 49 51 53 54 56 57 60 62 64 65 66 67 73 75 77 79 81 82 87 -> dysta2()
+. clara(): s:= max dys[1..946] = 77.8781;
+clara()'s bswap2(*, s=77.8781): new repr. 19
+ new repr. 35
+ after build: medoids are 19 35
+ and min.dist dysma[1:n] are
+ 1.41 7.07 9.9 2.83 17 5.66 6.4 5.1 4.12 4.24
+ 11.3 1.41 2.83 14.1 14.1 1.41 6 5.66 0 3.16
+ 5.66 18.4 8.06 7.07 16.3 6 7.21 4.24 14 4.24
+ 31.1 5.66 5.66 5.66 0 4.24 4.24 22.6 7.07 0
+ 5.1 17 8.25 7.07
+ --> sky = sum_j D_j= 338.587
+end{bswap}: sky = 338.587
+ selec() -> 'NAfs' obj= 1.57294
+C clara(): sample 4 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 70
+ {295} [ntt=44, nunfs=3] .. nsel[1:44]= 1 3 8 9 14 15 16 17 19 20 22 23 28 30 31 32 34 35 36 37 38 39 40 41 45 46 47 49 54 56 57 65 66 67 69 70 71 74 76 77 78 84 86 88 -> dysta2()
+. clara(): s:= max dys[1..946] = 77.8781;
+clara()'s bswap2(*, s=77.8781): new repr. 21
+ new repr. 32
+ after build: medoids are 21 32
+ and min.dist dysma[1:n] are
+ 1.41 7.07 7.81 5.66 5.1 4.12 4.24 14.1 1.41 2.83
+ 4.24 0 12.7 14.1 1.41 6 8.06 33.9 5.66 8.49
+ 0 3.16 5.66 5.66 9.9 8.06 7.07 6 14 4.24
+ 31.1 0 4.24 4.24 4.24 8.49 11.3 2.83 9.06 0
+ 7.07 17 1.41 12.7
+ --> sky = sum_j D_j= 325.933
+end{bswap}: sky = 325.933
+ selec() -> 'NAfs' obj= 1.57294
+C clara(): sample 5 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 80
+ {295} [ntt=44, nunfs=4] .. nsel[1:44]= 1 2 3 5 7 8 11 13 14 20 22 23 26 28 30 31 33 34 37 38 39 41 45 46 47 50 51 52 57 59 61 64 67 71 76 77 79 80 81 82 85 86 87 88 -> dysta2()
+ dysta2() gave dyst_toomany_NA --> new sample
+C clara(): sample 6 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 5
+ {295} [ntt=44, nunfs=5] .. nsel[1:44]= 2 3 4 5 6 8 10 12 19 20 21 23 24 25 29 30 31 32 33 37 39 41 42 45 46 48 50 53 54 59 61 66 68 69 71 72 73 79 80 82 84 85 86 87 -> dysta2()
+ dysta2() gave dyst_toomany_NA --> new sample
+C clara(): sample 7 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 17
+ {295} [ntt=44, nunfs=6] .. nsel[1:44]= 2 3 6 7 8 12 14 16 17 18 20 22 26 27 29 30 31 32 33 35 36 37 42 44 45 46 49 52 54 58 59 61 62 63 65 67 70 74 75 77 78 79 87 88 -> dysta2()
+ dysta2() gave dyst_toomany_NA --> new sample
+C clara(): sample 8 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 67
+ {295} [ntt=44, nunfs=7] .. nsel[1:44]= 2 3 6 7 8 9 11 13 14 18 30 31 32 34 35 37 38 40 43 44 47 48 49 52 54 55 56 58 59 60 66 67 68 70 71 72 73 75 80 83 84 85 87 88 -> dysta2()
+. clara(): s:= max dys[1..946] = 85.5102;
+clara()'s bswap2(*, s=85.5102): new repr. 17
+ new repr. 9
+ after build: medoids are 9 17
+ and min.dist dysma[1:n] are
+ 21.2 7.07 2.83 17 9.9 5.66 2.83 1.41 0 11.3
+ 14.1 1.41 9.9 9.22 33.9 8.49 0 5.66 8.49 18.4
+ 7.07 13.9 1.41 8.25 13.9 5.66 4.24 1.41 4.24 5.66
+ 4.24 4.24 1.41 8.49 11.3 0 22.6 11.3 1.41 7.07
+ 17 21.2 7.07 12.7
+ --> sky = sum_j D_j= 384.698
+end{bswap}: sky = 384.698
+ selec() -> 'NAfs' obj= 1.54909
+C clara(): sample 9 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 67
+ {295} [ntt=44, nunfs=8] .. nsel[1:44]= 2 4 6 7 8 11 12 13 14 15 17 19 20 21 24 27 29 30 31 33 34 35 36 39 42 45 46 48 50 51 52 54 55 58 60 61 62 65 67 78 80 84 86 88 -> dysta2()
+ dysta2() gave dyst_toomany_NA --> new sample
+C clara(): sample 10 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 5
+ {295} [ntt=44, nunfs=9] .. nsel[1:44]= 1 3 5 6 7 9 10 14 15 16 17 18 19 20 21 23 28 29 30 32 33 36 37 39 40 44 46 47 51 53 54 55 56 57 65 69 70 74 76 81 82 84 86 87 -> dysta2()
+ dysta2() gave dyst_toomany_NA --> new sample
+C clara(): sample 11 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 66
+ {295} [ntt=44, nunfs=10] .. nsel[1:44]= 1 3 4 5 6 11 13 14 15 18 19 21 28 30 31 32 33 34 39 40 41 42 43 46 47 57 58 59 63 65 66 67 71 72 73 74 75 78 79 80 83 84 87 88 -> dysta2()
+ dysta2() gave dyst_toomany_NA --> new sample
+C clara(): sample 12 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 21
+ {295} [ntt=44, nunfs=11] .. nsel[1:44]= 4 5 6 8 9 10 13 14 15 16 17 21 23 25 27 28 30 35 36 41 44 46 47 49 50 54 55 56 57 59 61 62 64 65 66 68 71 72 74 75 76 81 83 84 -> dysta2()
+. clara(): s:= max dys[1..946] = 78.3135;
+clara()'s bswap2(*, s=78.3135): new repr. 5
+ new repr. 2
+ after build: medoids are 2 5
+ and min.dist dysma[1:n] are
+ 26.2 0 3.61 9.49 0 13.5 11 20.5 13.9 6.32
+ 15 21.6 2.24 32.1 26.6 12.8 12 24.4 17.9 8.6
+ 10.8 18.1 7.21 20.5 14.9 29.4 26.2 3.61 23 21.1
+ 23 3.61 7 16.6 3.61 9.22 9.49 12.6 13 9.85
+ 22.2 14.2 15.7 11
+ --> sky = sum_j D_j= 623.732
+ swp new 43 <-> 5 old; decreasing diss. by -205.358
+ Last swap: new 43 <-> 5 old; decreasing diss. by 1
+end{bswap}: sky = 418.375
+ selec() -> 'NAfs' obj= 3.10025
+C clara(): sample 13 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 4
+ {295} [ntt=44, nunfs=12] .. nsel[1:44]= 3 4 5 14 15 16 17 19 20 21 24 25 26 29 30 31 34 35 38 40 41 43 47 49 50 52 55 57 58 60 61 63 64 65 66 68 72 73 74 79 81 83 86 88 -> dysta2()
+. clara(): s:= max dys[1..946] = 84.1487;
+clara()'s bswap2(*, s=84.1487): new repr. 19
+ new repr. 34
+ after build: medoids are 19 34
+ and min.dist dysma[1:n] are
+ 7.07 9.9 1.41 5.1 4.12 4.24 14.1 1.41 2.83 8.06
+ 5.39 8.49 7.07 14.1 14.1 1.41 8.06 33.9 0 5.66
+ 5.66 8.49 7.07 6 4 7.62 10.3 31.1 1.41 5.66
+ 5.66 15.6 5.66 0 4.24 1.41 0 22.6 2.83 5.1
+ 17 2 1.41 12.7
+ --> sky = sum_j D_j= 340.1
+end{bswap}: sky = 340.1
+ selec() -> 'NAfs' obj= 1.57294
+C clara(): sample 14 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 78
+ {295} [ntt=44, nunfs=13] .. nsel[1:44]= 5 7 8 9 10 11 12 18 19 21 23 27 28 29 31 32 33 35 36 38 39 46 50 51 52 56 57 58 59 60 64 65 66 68 72 73 75 77 78 80 84 86 87 88 -> dysta2()
+ dysta2() gave dyst_toomany_NA --> new sample
+C clara(): sample 15 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 73
+ {295} [ntt=44, nunfs=14] .. nsel[1:44]= 2 3 8 10 18 25 26 27 29 31 33 34 35 41 42 43 44 46 47 48 49 53 54 56 57 58 59 60 63 69 70 71 72 73 75 76 77 79 81 84 85 86 87 88 -> dysta2()
+ dysta2() gave dyst_toomany_NA --> new sample
+C clara(): sample 16 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 43
+ {295} [ntt=44, nunfs=15] .. nsel[1:44]= 5 6 7 8 9 12 14 16 18 22 23 24 27 28 29 30 34 35 36 39 40 41 43 45 56 57 59 60 62 64 65 67 69 70 71 73 74 75 79 81 83 85 86 87 -> dysta2()
+. clara(): s:= max dys[1..946] = 75.1665;
+clara()'s bswap2(*, s=75.1665): new repr. 15
+ new repr. 41
+ after build: medoids are 15 41
+ and min.dist dysma[1:n] are
+ 12.7 17 2.83 6.4 15.7 5 7.07 9.9 25.5 13.6
+ 14.1 5 15 1.41 0 0 8.06 19.8 8.49 4.24
+ 8.49 19.8 5.66 12.6 9.9 45.3 5.66 14.8 8.49 9.9
+ 2 10 9.9 22.6 25.5 8.49 11.3 5.83 5.1 2.83
+ 0 7.07 15.6 21.2
+ --> sky = sum_j D_j= 479.721
+end{bswap}: sky = 479.721
+ selec() -> 'NAfs' obj= 2.17131
+C clara(): sample 17 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 22
+ {295} [ntt=44, nunfs=16] .. nsel[1:44]= 4 6 9 10 11 12 13 16 19 22 26 27 29 30 33 34 37 38 39 42 43 48 51 54 55 57 60 61 62 63 64 66 69 72 73 75 76 77 78 81 82 85 86 87 -> dysta2()
+ dysta2() gave dyst_toomany_NA --> new sample
+C clara(): sample 18 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 39
+ {295} [ntt=44, nunfs=17] .. nsel[1:44]= 1 4 8 13 15 19 20 23 25 26 27 28 30 31 33 34 36 37 39 41 42 43 44 45 46 47 50 54 55 57 59 60 62 64 65 66 67 72 73 78 79 81 82 85 -> dysta2()
+ dysta2() gave dyst_toomany_NA --> new sample
+C clara(): sample 19 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 72
+ {295} [ntt=44, nunfs=18] .. nsel[1:44]= 1 4 5 6 10 12 13 14 17 18 19 22 23 25 27 30 31 32 33 38 39 40 41 42 44 45 46 48 55 57 58 59 60 61 66 67 69 70 72 74 83 84 85 86 -> dysta2()
+ dysta2() gave dyst_toomany_NA --> new sample
+C clara(): sample 20 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 48
+ {295} [ntt=44, nunfs=19] .. nsel[1:44]= 1 3 4 5 7 10 11 13 14 20 22 23 31 32 33 34 35 36 37 40 41 42 43 44 48 50 52 53 55 56 62 63 68 71 72 73 74 75 81 82 83 84 86 88 -> dysta2()
+ dysta2() gave dyst_toomany_NA --> new sample
+Error in clara(x, 2, samples = 20, trace = 3) :
+ Observation 33 has *only* NAs --> omit it for clustering
+> ## To see error message for > 1 missing:
+> try(clara(rbind(NA,x), 2))
+Error in clara(rbind(NA, x), 2) : Observations 1,34
+ have *only* NAs --> na.omit() them for clustering!
+>
+> x <- x[-33,]
+> ## still had the ** dysta2() .. OUT" problem {no longer!}
+> clara(x, 2, samples = 12, trace = 3)
+calling .C(cl_clara, ..., DUP = FALSE):
+C clara(): (nsam,nran,n) = (44,12,87); 'large_sample',
+C clara(): sample 1 finding 1st... new k{ran}:
+.. kall: FALSE,
+... nrx [0:1]= 0 0
+... nsel[0:0]= 2
+ {295} [ntt=43, nunfs=0] .. nsel[1:44]= 1 7 8 11 14 16 17 21 22 26 29 30 32 33 34 36 37 39 40 41 43 44 45 46 48 49 51 52 54 55 56 58 62 64 66 68 69 71 74 82 83 84 85 86 -> dysta2()
+. clara(): s:= max dys[1..946] = 76.5376;
+clara()'s bswap2(*, s=76.5376): new repr. 17
+ new repr. 40
+ after build: medoids are 17 40
+ and min.dist dysma[1:n] are
+ 1.41 17 6.4 2.83 7.07 4.24 14.1 7.28 4.24 7.07
+ 14.1 14.1 4 8.06 33.9 8.49 0 5.66 5.66 14.1
+ 18.4 9.9 6.4 7.07 8 2 8.6 4.24 12.1 4.24
+ 31.1 5.66 15.6 2 4.24 4.24 8.49 0 5.83 0
+ 17 21.2 1.41 7.07
+ --> sky = sum_j D_j= 384.62
+end{bswap}: sky = 384.62
+ 1st proper or new best: obj= 4.93331
+C clara(): sample 2 finding 1st... new k{ran}:
+.. kall: T,
+... nrx [0:1]= 37 82
+... nsel[0:0]= 70
+ {295} [ntt=43, nunfs=0] .. nsel[1:44]= 4 8 10 11 13 15 16 18 20 21 22 23 24 25 31 32 33 34 35 36 37 40 41 43 45 46 48 50 52 55 62 64 65 68 69 71 72 77 81 82 84 85 86 87 -> dysta2()
+. clara(): s:= max dys[1..946] = 82.7103;
+clara()'s bswap2(*, s=82.7103): new repr. 21
+ new repr. 40
+ after build: medoids are 21 40
+ and min.dist dysma[1:n] are
+ 9.9 6.4 4.47 2.83 1.41 2.24 4.24 11.3 4.47 7.28
+ 4.24 0 5 8.49 1.41 4 8.06 33.9 5.66 8.49
+ 0 5.66 14.1 18.4 6.4 7.07 8 5.66 4.24 4.24
+ 15.6 2 4.24 4.24 8.49 0 22.6 5.1 8.94 0
+ 21.2 1.41 7.07 12.7
+ --> sky = sum_j D_j= 321.274
+end{bswap}: sky = 321.274
+ obj= 4.93331
+C clara(): sample 3 finding 1st... new k{ran}:
+.. kall: T,
+... nrx [0:1]= 37 82
+... nsel[0:0]= 38
+ {295} [ntt=43, nunfs=0] .. nsel[1:44]= 2 5 10 11 14 18 21 22 23 24 25 26 27 29 33 34 36 37 39 41 42 43 45 47 49 50 55 57 58 60 62 64 67 68 71 73 75 77 79 82 83 84 85 87 -> dysta2()
+. clara(): s:= max dys[1..946] = 85.5102;
+clara()'s bswap2(*, s=85.5102): new repr. 18
+ new repr. 32
+ after build: medoids are 18 32
+ and min.dist dysma[1:n] are
+ 21.2 1.41 4 2.83 5.1 11.3 8.06 4.24 0 5.39
+ 8.49 7.07 13 14.1 8.06 33.9 8.49 0 5.66 14.1
+ 8.49 18.4 8.06 16.3 4 7.21 4.24 1.41 4.47 5.66
+ 15.6 0 1.41 4.24 0 2.83 9.06 7.07 1.41 2
+ 17 21.2 1.41 12.7
+ --> sky = sum_j D_j= 350.699
+ Last swap: new 40 <-> 32 old; decreasing diss. by 0.7867
+end{bswap}: sky = 350.699
+ 1st proper or new best: obj= 4.80308
+C clara(): sample 4 finding 1st... new k{ran}:
+.. kall: T,
+... nrx [0:1]= 37 64
+... nsel[0:0]= 85
+ {295} [ntt=43, nunfs=0] .. nsel[1:44]= 2 4 5 6 8 10 11 12 15 18 21 24 25 26 28 31 33 37 40 42 43 47 49 50 52 54 55 57 58 59 60 61 62 63 64 71 72 73 74 78 79 81 82 86 -> dysta2()
+. clara(): s:= max dys[1..946] = 78.3135;
+clara()'s bswap2(*, s=78.3135): new repr. 18
+ new repr. 43
+ after build: medoids are 18 43
+ and min.dist dysma[1:n] are
+ 21.2 9.9 1.41 2.83 6.4 4.47 2.83 5 2.24 11.3
+ 7.28 5 8.49 7.07 12.7 1.41 8.06 0 5.66 8.49
+ 18.4 17.8 2 5.66 4.24 12.1 4.24 1.41 5.66 5.66
+ 5.66 5.66 15.6 5.66 2 0 22.6 2.83 5.83 5.1
+ 1.41 8.94 0 7.07
+ --> sky = sum_j D_j= 297.276
+end{bswap}: sky = 297.276
+ obj= 4.93331
+C clara(): sample 5 finding 1st... new k{ran}:
+.. kall: T,
+... nrx [0:1]= 37 64
+... nsel[0:0]= 84
+ {295} [ntt=43, nunfs=0] .. nsel[1:44]= 4 6 9 10 12 13 15 16 17 18 20 21 24 26 27 31 34 35 36 37 40 41 42 43 45 51 52 53 54 55 56 62 64 65 67 68 69 71 72 73 74 77 79 82 -> dysta2()
+. clara(): s:= max dys[1..946] = 76.5376;
+clara()'s bswap2(*, s=76.5376): new repr. 20
+ new repr. 44
+ after build: medoids are 20 44
+ and min.dist dysma[1:n] are
+ 9.9 2.83 5.66 4.47 5 1.41 2.24 4.24 14.1 11.3
+ 4.47 7.28 5 7.07 15 1.41 33.9 5.66 8.49 0
+ 5.66 14.1 8.49 18.4 6.4 8.6 4.24 14.1 12.1 4.24
+ 31.1 15.6 2 4.24 1.41 4.24 8.49 0 22.6 2.83
+ 5.83 5.1 1.41 0
+ --> sky = sum_j D_j= 350.799
+end{bswap}: sky = 350.799
+ obj= 4.93331
+C clara(): sample 6 finding 1st... new k{ran}:
+.. kall: T,
+... nrx [0:1]= 37 64
+... nsel[0:0]= 33
+ {295} [ntt=43, nunfs=0] .. nsel[1:44]= 1 5 7 9 11 13 14 15 17 18 22 26 27 28 34 35 36 37 38 43 46 47 48 50 51 54 55 56 57 61 63 64 66 69 71 73 74 75 76 77 78 80 81 82 -> dysta2()
+. clara(): s:= max dys[1..946] = 82.0244;
+clara()'s bswap2(*, s=82.0244): new repr. 18
+ new repr. 19
+ after build: medoids are 18 19
+ and min.dist dysma[1:n] are
+ 1.41 1.41 17 5.66 2.83 1.41 5.66 5.39 14.1 11.3
+ 4.24 7.07 12.6 12.7 33.9 5.66 8.49 0 0 17
+ 7.07 13.6 5.83 9.9 4.47 11.3 4.24 31.1 1.41 5.66
+ 5.66 3.16 4.24 8.49 0 2.83 6.32 8.25 0 8.49
+ 2.83 17 5.1 4.24
+ --> sky = sum_j D_j= 339.187
+end{bswap}: sky = 339.187
+ 1st proper or new best: obj= 4.79624
+C clara(): sample 7 finding 1st... new k{ran}:
+.. kall: T,
+... nrx [0:1]= 37 38
+... nsel[0:0]= 26
+ {295} [ntt=43, nunfs=0] .. nsel[1:44]= 1 3 4 5 9 10 11 18 19 21 23 24 25 30 37 38 39 40 46 47 50 54 55 56 59 62 65 66 67 68 70 71 72 74 75 76 79 80 81 82 83 84 85 86 -> dysta2()
+. clara(): s:= max dys[1..946] = 82.7103;
+clara()'s bswap2(*, s=82.7103): new repr. 15
+ new repr. 16
+ after build: medoids are 15 16
+ and min.dist dysma[1:n] are
+ 1.41 7.07 9.9 1.41 5.66 1.41 2.83 11.3 1.41 11.2
+ 0 8.54 8.49 14.1 0 0 5.66 5.66 7.07 13.6
+ 9.9 11.3 4.24 31.1 5.66 15.6 4.24 4.24 1.41 4.24
+ 11.3 0 22.6 6.32 8.25 0 1.41 17 5.1 4.24
+ 17 21.2 1.41 7.07
+ --> sky = sum_j D_j= 331.596
+end{bswap}: sky = 331.596
+ obj= 4.79624
+C clara(): sample 8 finding 1st... new k{ran}:
+.. kall: T,
+... nrx [0:1]= 37 38
+... nsel[0:0]= 74
+ {295} [ntt=43, nunfs=0] .. nsel[1:44]= 4 5 10 12 15 16 17 19 20 21 22 23 24 25 26 27 28 29 31 37 38 39 41 42 44 45 46 49 50 51 56 57 61 62 63 64 68 73 75 77 78 80 81 85 -> dysta2()
+. clara(): s:= max dys[1..946] = 84.1487;
+clara()'s bswap2(*, s=84.1487): new repr. 20
+ new repr. 36
+ after build: medoids are 20 36
+ and min.dist dysma[1:n] are
+ 9.9 1.41 4 6.4 4.12 4.24 14.1 1.41 2.83 8.06
+ 4.24 0 5.39 8.49 7.07 13 12.7 14.1 1.41 0
+ 3.16 5.66 14.1 8.49 9.9 8.06 7.07 4 7.21 7.62
+ 31.1 1.41 5.66 15.6 5.66 0 4.24 2.83 9.06 7.07
+ 5.1 17 8.25 1.41
+ --> sky = sum_j D_j= 312.667
+end{bswap}: sky = 312.667
+ obj= 4.80308
+C clara(): sample 9 finding 1st... new k{ran}:
+.. kall: T,
+... nrx [0:1]= 37 38
+... nsel[0:0]= 67
+ {295} [ntt=43, nunfs=0] .. nsel[1:44]= 1 3 5 9 11 13 17 22 23 25 29 31 32 34 37 38 40 42 43 44 47 49 53 55 56 58 62 63 66 68 69 70 71 72 73 74 75 76 78 81 82 84 85 86 -> dysta2()
+. clara(): s:= max dys[1..946] = 82.7103;
+clara()'s bswap2(*, s=82.7103): new repr. 15
+ new repr. 16
+ after build: medoids are 15 16
+ and min.dist dysma[1:n] are
+ 1.41 7.07 1.41 5.66 2.83 1.41 14.1 4.24 0 8.49
+ 14.1 1.41 7.62 33.9 0 0 5.66 8.49 17 9.9
+ 13.6 5.83 17 4.24 31.1 7.07 15.6 5.66 4.24 4.24
+ 8.49 11.3 0 22.6 2.83 6.32 8.25 0 2.83 5.1
+ 4.24 21.2 1.41 7.07
+ --> sky = sum_j D_j= 355.134
+end{bswap}: sky = 355.134
+ obj= 4.79624
+C clara(): sample 10 finding 1st... new k{ran}:
+.. kall: T,
+... nrx [0:1]= 37 38
+... nsel[0:0]= 85
+ {295} [ntt=43, nunfs=0] .. nsel[1:44]= 2 4 8 11 13 22 24 25 26 27 29 31 34 36 37 38 39 41 42 44 47 48 49 50 53 57 58 59 60 61 62 63 64 66 67 70 71 72 75 77 79 82 84 87 -> dysta2()
+. clara(): s:= max dys[1..946] = 85.5102;
+clara()'s bswap2(*, s=85.5102): new repr. 15
+ new repr. 33
+ after build: medoids are 15 33
+ and min.dist dysma[1:n] are
+ 21.2 9.9 7.81 2.83 1.41 4.24 5.39 8.49 7.07 13
+ 14.1 1.41 33.9 8.49 0 3.16 5.66 14.1 8.49 9.9
+ 16.3 6 4 7.21 14 1.41 4.47 5.66 5.66 5.66
+ 15.6 5.66 0 4.24 1.41 11.3 0 22.6 9.06 7.07
+ 1.41 2 21.2 12.7
+ --> sky = sum_j D_j= 365.357
+end{bswap}: sky = 365.357
+ obj= 4.80308
+C clara(): sample 11 finding 1st... new k{ran}:
+.. kall: T,
+... nrx [0:1]= 37 38
+... nsel[0:0]= 87
+ {295} [ntt=43, nunfs=0] .. nsel[1:44]= 2 7 8 9 10 12 16 17 20 22 23 24 26 27 29 34 35 36 37 38 41 44 47 48 49 50 51 52 53 54 59 60 61 63 67 68 69 75 76 78 80 81 84 85 -> dysta2()
+. clara(): s:= max dys[1..946] = 80.9938;
+clara()'s bswap2(*, s=80.9938): new repr. 19
+ new repr. 20
+ after build: medoids are 19 20
+ and min.dist dysma[1:n] are
+ 21.2 17 7.28 5.66 1.41 9.22 4.24 14.1 5.1 4.24
+ 0 8.54 7.07 12.6 14.1 33.9 5.66 8.49 0 0
+ 14.1 9.9 13.6 5.83 5.83 9.9 4.47 4.24 17 11.3
+ 5.66 5.66 5.66 5.66 1.41 4.24 8.49 8.25 0 2.83
+ 17 5.1 21.2 1.41
+ --> sky = sum_j D_j= 368.774
+end{bswap}: sky = 368.774
+ obj= 4.79624
+C clara(): sample 12 finding 1st... new k{ran}:
+.. kall: T,
+... nrx [0:1]= 37 38
+... nsel[0:0]= 44
+ {295} [ntt=43, nunfs=0] .. nsel[1:44]= 1 2 3 7 11 12 14 18 19 20 21 24 28 30 31 32 33 34 37 38 39 40 42 49 51 52 53 55 59 63 68 69 70 72 74 76 77 78 79 81 84 85 86 87 -> dysta2()
+. clara(): s:= max dys[1..946] = 80.9938;
+clara()'s bswap2(*, s=80.9938): new repr. 19
+ new repr. 24
+ after build: medoids are 19 24
+ and min.dist dysma[1:n] are
+ 1.41 21.2 7.07 17 2.83 4.12 9.06 11.3 1.41 6.32
+ 7 5.39 12.7 14.1 1.41 2 8.54 33.9 0 5.83
+ 5.66 5.66 8.49 0 9.9 4.24 14.6 4.24 5.66 5.66
+ 4.24 8.49 11.3 22.6 5.1 0 3.16 5.83 1.41 10
+ 21.2 1.41 7.07 12.7
+ --> sky = sum_j D_j= 351.374
+end{bswap}: sky = 351.374
+ obj= 5.11334
+C clara(): best sample _found_ ; nbest[1:44] =
+ c(1,5,7,9,11,13,14,15,17,18,22,26,27,28,34,35,36,37,38,43,46,47,48,50,51,54,55,56,57,61,63,64,66,69,71,73,74,75,76,77,78,80,81,82)
+ --> dysta2(nbest), resul(), end
+Call: clara(x = x, k = 2, samples = 12, trace = 3)
+Medoids:
+ [,1] [,2]
+[1,] NA 1
+[2,] 47 15
+Objective function: 4.79624
+Clustering vector: int [1:87] 1 1 1 1 1 1 1 1 1 2 1 1 1 2 1 1 1 1 ...
+Cluster sizes: 74 13
+Best sample:
+ [1] 1 5 7 9 11 13 14 15 17 18 22 26 27 28 34 35 36 37 38 43 46 47 48 50 51
+[26] 54 55 56 57 61 63 64 66 69 71 73 74 75 76 77 78 80 81 82
+
+Available components:
+ [1] "sample" "medoids" "i.med" "clustering" "objective"
+ [6] "clusinfo" "diss" "call" "silinfo" "data"
+>
+> data(xclara)
+> set.seed(123)
+> xclara[sample(nrow(xclara), 50),] <- NA
+> try( clara(xclara, k = 3) ) #-> "nice" error message depicting first 12 missing obs
+Error in clara(xclara, k = 3) :
+ 50 observations (74,126,137,308,411,423,438,451,642,686,689,735 ...)
+ have *only* NAs --> na.omit() them for clustering!
+>
+> proc.time()
+ user system elapsed
+ 0.228 0.024 0.240
diff --git a/win32/deps/library/cluster/tests/clara-ex.R b/win32/deps/library/cluster/tests/clara-ex.R
new file mode 100644
index 0000000..4333342
--- /dev/null
+++ b/win32/deps/library/cluster/tests/clara-ex.R
@@ -0,0 +1,23 @@
+#### These are *NOT* compared with output in the released version of
+### 'cluster' currently
+
+library(cluster)
+
+data(xclara)
+## Try 100 times *different* random samples -- for reliability:
+if(R.version$major != "1" || as.numeric(R.version$minor) >= 7) RNGversion("1.6")
+
+nSim <- 100
+nCl <- 3 # = no.classes
+set.seed(421)# (reproducibility)
+## unknown problem: this is still platform dependent to some extent:
+cl <- matrix(NA,nrow(xclara), nSim)
+for(i in 1:nSim) cl[,i] <- clara(xclara, nCl, rngR = TRUE)$cluster
+tcl <- apply(cl,1, tabulate, nbins = nCl)
+## those that are not always in same cluster (5 out of 3000 for this seed):
+(iDoubt <- which(apply(tcl,2, function(n) all(n < nSim))))
+if(length(iDoubt)) { # (not for all seeds)
+ tabD <- tcl[,iDoubt, drop=FALSE]
+ dimnames(tabD) <- list(cluster = paste(1:nCl), obs = format(iDoubt))
+ t(tabD) # how many times in which clusters
+}
diff --git a/win32/deps/library/cluster/tests/clara.R b/win32/deps/library/cluster/tests/clara.R
new file mode 100644
index 0000000..c6c87e0
--- /dev/null
+++ b/win32/deps/library/cluster/tests/clara.R
@@ -0,0 +1,107 @@
+library(cluster)
+
+## generate 1500 objects, divided into 2 clusters.
+set.seed(144)
+x <- rbind(cbind(rnorm(700, 0,8), rnorm(700, 0,8)),
+ cbind(rnorm(800,50,8), rnorm(800,10,8)))
+
+isEq <- function(x,y, epsF = 100)
+ is.logical(r <- all.equal(x,y, tol = epsF * .Machine$double.eps)) && r
+
+.proctime00 <- proc.time()
+
+## full size sample {should be = pam()}:
+n0 <- length(iSml <- c(1:70, 701:720))
+summary(clara0 <- clara(x[iSml,], k = 2, sampsize = n0))
+ pam0 <- pam (x[iSml,], k = 2)
+stopifnot(identical(clara0$clustering, pam0$clustering)
+ , isEq(clara0$objective, unname(pam0$objective[2]))
+ )
+
+summary(clara2 <- clara(x, 2))
+
+clInd <- c("objective", "i.med", "medoids", "clusinfo")
+clInS <- c(clInd, "sample")
+## clara() {as original code} always draws the *same* random samples !!!!
+clara(x, 2, samples = 50)[clInd]
+for(i in 1:20)
+ print(clara(x[sample(nrow(x)),], 2, samples = 50)[clInd])
+
+clara(x, 2, samples = 101)[clInd]
+clara(x, 2, samples = 149)[clInd]
+clara(x, 2, samples = 200)[clInd]
+## Note that this last one is practically identical to the slower pam() one
+
+(ii <- sample(length(x), 20))
+## This was bogous (and lead to seg.faults); now properly gives error.
+## but for these, now see ./clara-NAs.R
+if(FALSE) { ## ~~~~~~~~~~~~~
+ x[ii] <- NA
+ try( clara(x, 2, samples = 50) )
+}
+
+###-- Larger example: 2000 objects, divided into 5 clusters.
+x5 <- rbind(cbind(rnorm(400, 0,4), rnorm(400, 0,4)),
+ cbind(rnorm(400,10,8), rnorm(400,40,6)),
+ cbind(rnorm(400,30,4), rnorm(400, 0,4)),
+ cbind(rnorm(400,40,4), rnorm(400,20,2)),
+ cbind(rnorm(400,50,4), rnorm(400,50,4)))
+## plus 1 random dimension
+x5 <- cbind(x5, rnorm(nrow(x5)))
+
+clara(x5, 5)
+summary(clara(x5, 5, samples = 50))
+## 3 "half" samples:
+clara(x5, 5, samples = 999)
+clara(x5, 5, samples = 1000)
+clara(x5, 5, samples = 1001)
+
+clara(x5, 5, samples = 2000)#full sample
+
+###--- Start a version of example(clara) -------
+
+## xclara : artificial data with 3 clusters of 1000 bivariate objects each.
+data(xclara)
+(clx3 <- clara(xclara, 3))
+## Plot similar to Figure 5 in Struyf et al (1996)
+plot(clx3)
+
+## The rngR = TRUE case is currently in the non-strict tests
+## ./clara-ex.R
+## ~~~~~~~~~~~~
+
+###--- End version of example(clara) -------
+
+## small example(s):
+data(ruspini)
+
+clara(ruspini,4)
+
+rus <- data.matrix(ruspini); storage.mode(rus) <- "double"
+ru2 <- rus[c(1:7,21:28, 45:51, 61:69),]
+ru3 <- rus[c(1:4,21:25, 45:48, 61:63),]
+ru4 <- rus[c(1:2,21:22, 45:47),]
+ru5 <- rus[c(1:2,21, 45),]
+daisy(ru5, "manhattan")
+## Dissimilarities : 11 118 143 107 132 89
+
+## no problem anymore, since 2002-12-28:
+## sampsize >= k+1 is now enforced:
+## clara(ru5, k=3, met="manhattan", sampsize=3,trace=2)[clInS]
+clara(ru5, k=3, met="manhattan", sampsize=4,trace=1)[clInS]
+
+daisy(ru4, "manhattan")
+## this one (k=3) gave problems, from ss = 6 on ___ still after 2002-12-28 ___ :
+for(ss in 4:nrow(ru4)){
+ cat("---\n\nsample size = ",ss,"\n")
+ print(clara(ru4,k=3,met="manhattan",sampsize=ss)[clInS])
+}
+for(ss in 5:nrow(ru3)){
+ cat("---\n\nsample size = ",ss,"\n")
+ print(clara(ru3,k=4,met="manhattan",sampsize=ss)[clInS])
+}
+
+## Last Line:
+cat('Time elapsed: ', proc.time() - .proctime00,'\n')
+## Lynne (P IV, 1.6 GHz): 18.81; then (no NA; R 1.9.0-alpha): 15.07
+## nb-mm (P III,700 MHz): 27.97
diff --git a/win32/deps/library/cluster/tests/clara.Rout.save b/win32/deps/library/cluster/tests/clara.Rout.save
new file mode 100644
index 0000000..786c0ef
--- /dev/null
+++ b/win32/deps/library/cluster/tests/clara.Rout.save
@@ -0,0 +1,1491 @@
+
+R version 2.13.0 Patched (2011-04-16 r55459)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(cluster)
+>
+> ## generate 1500 objects, divided into 2 clusters.
+> set.seed(144)
+> x <- rbind(cbind(rnorm(700, 0,8), rnorm(700, 0,8)),
++ cbind(rnorm(800,50,8), rnorm(800,10,8)))
+>
+> isEq <- function(x,y, epsF = 100)
++ is.logical(r <- all.equal(x,y, tol = epsF * .Machine$double.eps)) && r
+>
+> .proctime00 <- proc.time()
+>
+> ## full size sample {should be = pam()}:
+> n0 <- length(iSml <- c(1:70, 701:720))
+> summary(clara0 <- clara(x[iSml,], k = 2, sampsize = n0))
+Object of class 'clara' from call:
+ clara(x = x[iSml, ], k = 2, sampsize = n0)
+Medoids:
+ [,1] [,2]
+[1,] -1.499522 -1.944452
+[2,] 48.629631 12.998515
+Objective function: 10.23588
+Numerical information per cluster:
+ size max_diss av_diss isolation
+[1,] 70 24.81995 10.25745 0.4744879
+[2,] 20 19.07782 10.16040 0.3647145
+Average silhouette width per cluster:
+[1] 0.7144587 0.7090915
+Average silhouette width of best sample: 0.713266
+
+Best sample:
+ [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
+[26] 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50
+[51] 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
+[76] 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
+Clustering vector:
+ [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+[39] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2
+[77] 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+
+Silhouette plot information for best sample:
+ cluster neighbor sil_width
+45 1 2 0.8033727
+60 1 2 0.8021017
+55 1 2 0.8005931
+66 1 2 0.8002776
+58 1 2 0.7991899
+11 1 2 0.7991773
+41 1 2 0.7973302
+26 1 2 0.7962397
+63 1 2 0.7962229
+13 1 2 0.7949705
+67 1 2 0.7942590
+54 1 2 0.7936184
+17 1 2 0.7916087
+16 1 2 0.7913570
+39 1 2 0.7912755
+6 1 2 0.7840455
+34 1 2 0.7833568
+49 1 2 0.7819733
+9 1 2 0.7789087
+23 1 2 0.7785009
+32 1 2 0.7757325
+22 1 2 0.7655369
+61 1 2 0.7639754
+12 1 2 0.7639644
+5 1 2 0.7606436
+18 1 2 0.7579145
+56 1 2 0.7566307
+3 1 2 0.7537894
+24 1 2 0.7531180
+50 1 2 0.7517817
+48 1 2 0.7501998
+25 1 2 0.7499655
+59 1 2 0.7472022
+19 1 2 0.7445038
+65 1 2 0.7398395
+28 1 2 0.7377377
+38 1 2 0.7370935
+7 1 2 0.7335940
+40 1 2 0.7310012
+14 1 2 0.7294895
+62 1 2 0.7254478
+70 1 2 0.7163214
+4 1 2 0.7157257
+21 1 2 0.7148663
+64 1 2 0.7108496
+2 1 2 0.7062831
+15 1 2 0.7015120
+52 1 2 0.6978313
+37 1 2 0.6954023
+31 1 2 0.6932905
+33 1 2 0.6888478
+10 1 2 0.6805028
+20 1 2 0.6766854
+43 1 2 0.6761461
+8 1 2 0.6749706
+27 1 2 0.6671817
+35 1 2 0.6632888
+68 1 2 0.6587599
+30 1 2 0.6554989
+36 1 2 0.6228481
+53 1 2 0.6203313
+57 1 2 0.6191666
+42 1 2 0.6142020
+47 1 2 0.6024151
+1 1 2 0.5814464
+69 1 2 0.5091186
+46 1 2 0.4961302
+44 1 2 0.4849961
+29 1 2 0.4569316
+51 1 2 0.4230181
+81 2 1 0.7965942
+71 2 1 0.7961971
+85 2 1 0.7919593
+74 2 1 0.7869047
+82 2 1 0.7795304
+78 2 1 0.7788873
+79 2 1 0.7729041
+72 2 1 0.7492980
+88 2 1 0.7447973
+87 2 1 0.7404399
+76 2 1 0.7352351
+77 2 1 0.7216838
+86 2 1 0.7165677
+84 2 1 0.6952406
+73 2 1 0.6942882
+83 2 1 0.6621568
+80 2 1 0.6368446
+90 2 1 0.5743228
+75 2 1 0.5597232
+89 2 1 0.4482549
+
+4005 dissimilarities, summarized :
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+ 0.18647 11.58500 20.05800 27.81500 45.57800 85.23200
+Metric : euclidean
+Number of objects : 90
+
+Available components:
+ [1] "sample" "medoids" "i.med" "clustering" "objective"
+ [6] "clusinfo" "diss" "call" "silinfo" "data"
+> pam0 <- pam (x[iSml,], k = 2)
+> stopifnot(identical(clara0$clustering, pam0$clustering)
++ , isEq(clara0$objective, unname(pam0$objective[2]))
++ )
+>
+> summary(clara2 <- clara(x, 2))
+Object of class 'clara' from call:
+ clara(x = x, k = 2)
+Medoids:
+ [,1] [,2]
+[1,] 2.012828 -1.896095
+[2,] 51.494628 10.274769
+Objective function: 10.23445
+Numerical information per cluster:
+ size max_diss av_diss isolation
+[1,] 700 36.84408 10.49814 0.7230478
+[2,] 800 30.89896 10.00373 0.6063775
+Average silhouette width per cluster:
+[1] 0.7562366 0.7203254
+Average silhouette width of best sample: 0.733384
+
+Best sample:
+ [1] 21 23 50 97 142 168 191 192 197 224 325 328 433 458 471
+[16] 651 712 714 722 797 805 837 909 919 926 999 1006 1018 1019 1049
+[31] 1081 1084 1132 1144 1150 1201 1207 1250 1291 1307 1330 1374 1426 1428
+Clustering vector:
+ [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [38] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [75] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [112] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [149] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [186] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [223] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [260] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [297] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [334] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [371] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [408] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [445] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [482] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [519] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [556] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [593] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [630] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [667] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2
+ [704] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+ [741] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+ [778] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+ [815] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+ [852] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+ [889] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+ [926] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+ [963] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+[1000] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+[1037] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+[1074] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+[1111] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+[1148] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+[1185] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+[1222] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+[1259] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+[1296] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+[1333] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+[1370] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+[1407] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+[1444] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+[1481] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+
+Silhouette plot information for best sample:
+ cluster neighbor sil_width
+325 1 2 0.8261589
+191 1 2 0.8206687
+23 1 2 0.8149640
+97 1 2 0.8048084
+433 1 2 0.8017745
+458 1 2 0.8008324
+471 1 2 0.7958547
+328 1 2 0.7689099
+142 1 2 0.7619508
+21 1 2 0.7607528
+197 1 2 0.7606641
+50 1 2 0.7509131
+192 1 2 0.7098473
+651 1 2 0.7035969
+224 1 2 0.6843886
+168 1 2 0.5337006
+1084 2 1 0.8180447
+1081 2 1 0.8171686
+1201 2 1 0.8170847
+1291 2 1 0.8167148
+1307 2 1 0.8166841
+1144 2 1 0.8159947
+999 2 1 0.8135303
+1426 2 1 0.8023538
+1049 2 1 0.8022891
+1250 2 1 0.8014300
+712 2 1 0.7859324
+837 2 1 0.7792784
+1018 2 1 0.7764837
+919 2 1 0.7651939
+1374 2 1 0.7648534
+1428 2 1 0.7516819
+1330 2 1 0.7505861
+1006 2 1 0.7368113
+714 2 1 0.7237565
+1150 2 1 0.7046060
+1132 2 1 0.6940608
+909 2 1 0.6859682
+926 2 1 0.6725631
+722 2 1 0.6572791
+797 2 1 0.6395698
+1019 2 1 0.6083662
+805 2 1 0.2814164
+1207 2 1 0.2694097
+
+946 dissimilarities, summarized :
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+ 0.48462 12.32300 26.49900 32.21300 52.39100 77.17500
+Metric : euclidean
+Number of objects : 44
+
+Available components:
+ [1] "sample" "medoids" "i.med" "clustering" "objective"
+ [6] "clusinfo" "diss" "call" "silinfo" "data"
+>
+> clInd <- c("objective", "i.med", "medoids", "clusinfo")
+> clInS <- c(clInd, "sample")
+> ## clara() {as original code} always draws the *same* random samples !!!!
+> clara(x, 2, samples = 50)[clInd]
+$objective
+[1] 10.06735
+
+$i.med
+[1] 177 1115
+
+$medoids
+ [,1] [,2]
+[1,] -0.2538744 -1.209148
+[2,] 50.0372683 9.501125
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 700 34.67208 10.193945 0.6743054
+[2,] 800 29.51964 9.956571 0.5741003
+
+> for(i in 1:20)
++ print(clara(x[sample(nrow(x)),], 2, samples = 50)[clInd])
+$objective
+[1] 10.05727
+
+$i.med
+[1] 936 192
+
+$medoids
+ [,1] [,2]
+[1,] 50.03726827 9.501124850
+[2,] -0.03900399 -0.009078886
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 800 29.51964 9.956571 0.5791419
+[2,] 700 34.06055 10.172348 0.6682295
+
+$objective
+[1] 10.05296
+
+$i.med
+[1] 468 1394
+
+$medoids
+ [,1] [,2]
+[1,] -0.3292826 -0.2398794
+[2,] 50.0372683 9.5011249
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 700 33.98451 10.163128 0.6624677
+[2,] 800 29.51964 9.956571 0.5754330
+
+$objective
+[1] 10.05852
+
+$i.med
+[1] 1171 379
+
+$medoids
+ [,1] [,2]
+[1,] 50.9444060 9.6723175
+[2,] -0.3292826 -0.2398794
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 800 30.10388 9.966988 0.5764486
+[2,] 700 33.98451 10.163128 0.6507574
+
+$objective
+[1] 10.07051
+
+$i.med
+[1] 75 1254
+
+$medoids
+ [,1] [,2]
+[1,] -0.9493373 0.3552542
+[2,] 50.5455985 9.3904972
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 700 33.12704 10.191999 0.6336273
+[2,] 800 29.66384 9.964205 0.5673860
+
+$objective
+[1] 10.0613
+
+$i.med
+[1] 199 134
+
+$medoids
+ [,1] [,2]
+[1,] -0.03900399 -0.009078886
+[2,] 49.59384120 9.792964832
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 700 34.06055 10.172348 0.6732466
+[2,] 800 29.57491 9.964138 0.5845827
+
+$objective
+[1] 10.06101
+
+$i.med
+[1] 1453 1122
+
+$medoids
+ [,1] [,2]
+[1,] 50.0372683 9.50112485
+[2,] -0.9691441 0.03342515
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 800 29.51964 9.956571 0.5690241
+[2,] 700 33.31923 10.180359 0.6422655
+
+$objective
+[1] 10.08603
+
+$i.med
+[1] 613 318
+
+$medoids
+ [,1] [,2]
+[1,] 50.0627056 9.478225
+[2,] -0.2902194 1.026496
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 800 29.51131 9.957225 0.5780037
+[2,] 700 33.21560 10.233240 0.6505552
+
+$objective
+[1] 10.07293
+
+$i.med
+[1] 618 406
+
+$medoids
+ [,1] [,2]
+[1,] 50.3621263 9.0207185
+[2,] -0.2092816 -0.5916053
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 800 29.25143 9.990206 0.5682446
+[2,] 700 34.30301 10.167473 0.6663777
+
+$objective
+[1] 10.0592
+
+$i.med
+[1] 1279 1349
+
+$medoids
+ [,1] [,2]
+[1,] 50.1502433 10.60358224
+[2,] -0.9691441 0.03342515
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 800 30.54975 9.953191 0.5852356
+[2,] 700 33.31923 10.180359 0.6382900
+
+$objective
+[1] 10.06241
+
+$i.med
+[1] 1293 21
+
+$medoids
+ [,1] [,2]
+[1,] 50.5809098 9.7418386
+[2,] -0.9493373 0.3552542
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 800 29.98892 9.949013 0.5725461
+[2,] 700 33.12704 10.191999 0.6324587
+
+$objective
+[1] 10.0592
+
+$i.med
+[1] 337 675
+
+$medoids
+ [,1] [,2]
+[1,] -0.9691441 0.03342515
+[2,] 50.1502433 10.60358224
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 700 33.31923 10.180359 0.6382900
+[2,] 800 30.54975 9.953191 0.5852356
+
+$objective
+[1] 10.05697
+
+$i.med
+[1] 22 574
+
+$medoids
+ [,1] [,2]
+[1,] 50.5809098 9.74183863
+[2,] -0.9691441 0.03342515
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 800 29.98892 9.949013 0.5716937
+[2,] 700 33.31923 10.180359 0.6351809
+
+$objective
+[1] 10.05096
+
+$i.med
+[1] 739 808
+
+$medoids
+ [,1] [,2]
+[1,] 50.5809098 9.7418386
+[2,] -0.2092816 -0.5916053
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 800 29.98892 9.949013 0.5785936
+[2,] 700 34.30301 10.167473 0.6618278
+
+$objective
+[1] 10.06135
+
+$i.med
+[1] 1431 485
+
+$medoids
+ [,1] [,2]
+[1,] 50.0627056 9.47822525
+[2,] -0.9691441 0.03342515
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 800 29.51131 9.957225 0.5686352
+[2,] 700 33.31923 10.180359 0.6420076
+
+$objective
+[1] 10.05324
+
+$i.med
+[1] 10 1221
+
+$medoids
+ [,1] [,2]
+[1,] 50.58090982 9.741838628
+[2,] -0.03900399 -0.009078886
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 800 29.98892 9.949013 0.5817385
+[2,] 700 34.06055 10.172348 0.6607218
+
+$objective
+[1] 10.06101
+
+$i.med
+[1] 1249 1411
+
+$medoids
+ [,1] [,2]
+[1,] -0.9691441 0.03342515
+[2,] 50.0372683 9.50112485
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 700 33.31923 10.180359 0.6422655
+[2,] 800 29.51964 9.956571 0.5690241
+
+$objective
+[1] 10.05296
+
+$i.med
+[1] 610 21
+
+$medoids
+ [,1] [,2]
+[1,] -0.3292826 -0.2398794
+[2,] 50.0372683 9.5011249
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 700 33.98451 10.163128 0.6624677
+[2,] 800 29.51964 9.956571 0.5754330
+
+$objective
+[1] 10.06486
+
+$i.med
+[1] 1101 397
+
+$medoids
+ [,1] [,2]
+[1,] -0.9691441 0.03342515
+[2,] 50.1066826 9.35514422
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 700 33.31923 10.180359 0.6417479
+[2,] 800 29.42336 9.963794 0.5667111
+
+$objective
+[1] 10.07521
+
+$i.med
+[1] 838 356
+
+$medoids
+ [,1] [,2]
+[1,] 50.36212634 9.020718482
+[2,] -0.03900399 -0.009078886
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 800 29.25143 9.990206 0.5712766
+[2,] 700 34.06055 10.172348 0.6651980
+
+$objective
+[1] 10.05906
+
+$i.med
+[1] 1270 1024
+
+$medoids
+ [,1] [,2]
+[1,] 50.5455985 9.3904972
+[2,] -0.2092816 -0.5916053
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 800 29.66384 9.964205 0.5734673
+[2,] 700 34.30301 10.167473 0.6631526
+
+>
+> clara(x, 2, samples = 101)[clInd]
+$objective
+[1] 10.05727
+
+$i.med
+[1] 286 1115
+
+$medoids
+ [,1] [,2]
+[1,] -0.03900399 -0.009078886
+[2,] 50.03726827 9.501124850
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 700 34.06055 10.172348 0.6682295
+[2,] 800 29.51964 9.956571 0.5791419
+
+> clara(x, 2, samples = 149)[clInd]
+$objective
+[1] 10.05319
+
+$i.med
+[1] 238 1272
+
+$medoids
+ [,1] [,2]
+[1,] -0.2092816 -0.5916053
+[2,] 50.1502433 10.6035822
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 700 34.30301 10.167473 0.6649301
+[2,] 800 30.54975 9.953191 0.5921768
+
+> clara(x, 2, samples = 200)[clInd]
+$objective
+[1] 10.05319
+
+$i.med
+[1] 238 1272
+
+$medoids
+ [,1] [,2]
+[1,] -0.2092816 -0.5916053
+[2,] 50.1502433 10.6035822
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 700 34.30301 10.167473 0.6649301
+[2,] 800 30.54975 9.953191 0.5921768
+
+> ## Note that this last one is practically identical to the slower pam() one
+>
+> (ii <- sample(length(x), 20))
+ [1] 249 452 2663 2537 2235 2421 1004 1834 2602 397 717 2805 1575 1281 283
+[16] 1657 1749 820 269 519
+> ## This was bogous (and lead to seg.faults); now properly gives error.
+> ## but for these, now see ./clara-NAs.R
+> if(FALSE) { ## ~~~~~~~~~~~~~
++ x[ii] <- NA
++ try( clara(x, 2, samples = 50) )
++ }
+>
+> ###-- Larger example: 2000 objects, divided into 5 clusters.
+> x5 <- rbind(cbind(rnorm(400, 0,4), rnorm(400, 0,4)),
++ cbind(rnorm(400,10,8), rnorm(400,40,6)),
++ cbind(rnorm(400,30,4), rnorm(400, 0,4)),
++ cbind(rnorm(400,40,4), rnorm(400,20,2)),
++ cbind(rnorm(400,50,4), rnorm(400,50,4)))
+> ## plus 1 random dimension
+> x5 <- cbind(x5, rnorm(nrow(x5)))
+>
+> clara(x5, 5)
+Call: clara(x = x5, k = 5)
+Medoids:
+ [,1] [,2] [,3]
+[1,] 0.5850466 -2.222194 -0.63631241
+[2,] 8.0131143 42.708122 -0.31693240
+[3,] 42.6657812 21.123133 -0.62411426
+[4,] 50.6470292 48.480686 -0.09146223
+[5,] 28.6470950 -2.544131 -0.22186047
+Objective function: 6.100721
+Clustering vector: int [1:2000] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...
+Cluster sizes: 400 396 408 401 395
+Best sample:
+ [1] 23 130 178 202 267 297 338 357 376 387 439 441 638 647 662
+[16] 719 723 802 874 880 994 1038 1056 1097 1184 1215 1225 1268 1271 1282
+[31] 1346 1442 1446 1474 1496 1515 1585 1590 1605 1641 1680 1687 1696 1728 1742
+[46] 1761 1857 1909 1951 1956
+
+Available components:
+ [1] "sample" "medoids" "i.med" "clustering" "objective"
+ [6] "clusinfo" "diss" "call" "silinfo" "data"
+> summary(clara(x5, 5, samples = 50))
+Object of class 'clara' from call:
+ clara(x = x5, k = 5, samples = 50)
+Medoids:
+ [,1] [,2] [,3]
+[1,] -0.8427864 0.1606105 -0.70362181
+[2,] 12.0389703 39.0303445 0.19158023
+[3,] 39.6341676 20.7182868 0.43978514
+[4,] 50.6470292 48.4806864 -0.09146223
+[5,] 30.6814242 -0.1072177 -0.25861548
+Objective function: 5.743812
+Numerical information per cluster:
+ size max_diss av_diss isolation
+[1,] 400 15.20728 5.207177 0.4823345
+[2,] 397 24.25898 8.677062 0.7324727
+[3,] 406 18.39064 4.369617 0.8109074
+[4,] 401 18.28050 5.260543 0.6119680
+[5,] 396 12.69653 5.243478 0.5598344
+Average silhouette width per cluster:
+[1] 0.7433532 0.6956424 0.7315944 0.7336104 0.7079360
+Average silhouette width of best sample: 0.7188531
+
+Best sample:
+ [1] 106 130 145 213 275 316 434 444 486 501 630 693 713 739 773
+[16] 804 808 821 823 899 914 948 961 972 980 987 1076 1114 1126 1127
+[31] 1169 1175 1203 1225 1228 1242 1269 1397 1405 1421 1595 1606 1658 1703 1777
+[46] 1834 1857 1881 1937 1999
+Clustering vector:
+ [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [38] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [75] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [112] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [149] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [186] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [223] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [260] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [297] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [334] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [371] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2
+ [408] 2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+ [445] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+ [482] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+ [519] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+ [556] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+ [593] 2 2 2 2 3 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+ [630] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+ [667] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+ [704] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+ [741] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+ [778] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 5 5 5 5 5 5 5 5 5 5 5 5 5 5
+ [815] 5 3 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
+ [852] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 3 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
+ [889] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
+ [926] 5 5 5 5 5 5 5 5 5 3 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
+ [963] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
+[1000] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
+[1037] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
+[1074] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 3 5 5 5 5 5 5 5 5 5 5 5 5 5 5
+[1111] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
+[1148] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
+[1185] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
+[1222] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
+[1259] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
+[1296] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
+[1333] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
+[1370] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
+[1407] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
+[1444] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
+[1481] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
+[1518] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
+[1555] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
+[1592] 3 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
+[1629] 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
+[1666] 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
+[1703] 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
+[1740] 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
+[1777] 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
+[1814] 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
+[1851] 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
+[1888] 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
+[1925] 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
+[1962] 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
+[1999] 4 4
+
+Silhouette plot information for best sample:
+ cluster neighbor sil_width
+130 1 5 0.8123353
+275 1 5 0.7945197
+316 1 5 0.7561799
+213 1 5 0.7459412
+106 1 5 0.6869957
+145 1 5 0.6641473
+630 2 3 0.7819320
+739 2 3 0.7774128
+486 2 3 0.7559683
+713 2 3 0.7316982
+444 2 3 0.7204625
+501 2 3 0.7091146
+773 2 1 0.6886472
+693 2 3 0.5855803
+434 2 3 0.5099654
+1225 3 5 0.8105776
+1203 3 5 0.7965773
+1595 3 5 0.7842711
+1269 3 5 0.7799931
+1242 3 5 0.7625442
+1397 3 5 0.7315512
+1228 3 5 0.7262025
+1421 3 5 0.6011616
+1405 3 5 0.5914707
+1999 4 3 0.8050046
+1857 4 3 0.8030709
+1658 4 3 0.7941141
+1777 4 3 0.7865209
+1937 4 3 0.7831996
+1881 4 3 0.7504779
+1834 4 3 0.6614223
+1606 4 3 0.6373808
+1703 4 3 0.5813025
+804 5 3 0.8021043
+987 5 3 0.7999064
+1076 5 3 0.7907769
+948 5 3 0.7905304
+961 5 3 0.7716289
+823 5 3 0.7657693
+808 5 3 0.7510670
+914 5 3 0.7358231
+1175 5 3 0.7337485
+1169 5 3 0.7254812
+972 5 3 0.7118795
+821 5 3 0.7101558
+899 5 1 0.6580927
+1114 5 3 0.6552887
+1127 5 3 0.6292428
+1126 5 3 0.5362475
+980 5 1 0.4671695
+
+1225 dissimilarities, summarized :
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+ 0.69682 19.31600 34.09200 33.07000 46.25400 92.25300
+Metric : euclidean
+Number of objects : 50
+
+Available components:
+ [1] "sample" "medoids" "i.med" "clustering" "objective"
+ [6] "clusinfo" "diss" "call" "silinfo" "data"
+> ## 3 "half" samples:
+> clara(x5, 5, samples = 999)
+Call: clara(x = x5, k = 5, samples = 999)
+Medoids:
+ [,1] [,2] [,3]
+[1,] 0.2143499 0.3891695 0.45577894
+[2,] 10.9779485 39.6788652 -0.23487762
+[3,] 40.2944064 20.2221253 0.21417849
+[4,] 50.7170411 49.7645642 -0.43318939
+[5,] 29.7257398 -0.5981739 -0.05616701
+Objective function: 5.659041
+Clustering vector: int [1:2000] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...
+Cluster sizes: 400 397 407 401 395
+Best sample:
+ [1] 1 2 103 147 155 176 179 247 262 288 365 369 372 470 486
+[16] 573 759 779 785 791 797 822 875 883 913 954 1107 1114 1154 1156
+[31] 1171 1175 1206 1213 1218 1233 1243 1394 1439 1444 1512 1741 1777 1798 1800
+[46] 1818 1845 1946 1948 1973
+
+Available components:
+ [1] "sample" "medoids" "i.med" "clustering" "objective"
+ [6] "clusinfo" "diss" "call" "silinfo" "data"
+> clara(x5, 5, samples = 1000)
+Call: clara(x = x5, k = 5, samples = 1000)
+Medoids:
+ [,1] [,2] [,3]
+[1,] 0.2143499 0.3891695 0.45577894
+[2,] 10.9779485 39.6788652 -0.23487762
+[3,] 40.2944064 20.2221253 0.21417849
+[4,] 50.7170411 49.7645642 -0.43318939
+[5,] 29.7257398 -0.5981739 -0.05616701
+Objective function: 5.659041
+Clustering vector: int [1:2000] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...
+Cluster sizes: 400 397 407 401 395
+Best sample:
+ [1] 1 2 103 147 155 176 179 247 262 288 365 369 372 470 486
+[16] 573 759 779 785 791 797 822 875 883 913 954 1107 1114 1154 1156
+[31] 1171 1175 1206 1213 1218 1233 1243 1394 1439 1444 1512 1741 1777 1798 1800
+[46] 1818 1845 1946 1948 1973
+
+Available components:
+ [1] "sample" "medoids" "i.med" "clustering" "objective"
+ [6] "clusinfo" "diss" "call" "silinfo" "data"
+> clara(x5, 5, samples = 1001)
+Call: clara(x = x5, k = 5, samples = 1001)
+Medoids:
+ [,1] [,2] [,3]
+[1,] 0.2143499 0.3891695 0.45577894
+[2,] 10.9779485 39.6788652 -0.23487762
+[3,] 40.2944064 20.2221253 0.21417849
+[4,] 50.7170411 49.7645642 -0.43318939
+[5,] 29.7257398 -0.5981739 -0.05616701
+Objective function: 5.659041
+Clustering vector: int [1:2000] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...
+Cluster sizes: 400 397 407 401 395
+Best sample:
+ [1] 1 2 103 147 155 176 179 247 262 288 365 369 372 470 486
+[16] 573 759 779 785 791 797 822 875 883 913 954 1107 1114 1154 1156
+[31] 1171 1175 1206 1213 1218 1233 1243 1394 1439 1444 1512 1741 1777 1798 1800
+[46] 1818 1845 1946 1948 1973
+
+Available components:
+ [1] "sample" "medoids" "i.med" "clustering" "objective"
+ [6] "clusinfo" "diss" "call" "silinfo" "data"
+>
+> clara(x5, 5, samples = 2000)#full sample
+Call: clara(x = x5, k = 5, samples = 2000)
+Medoids:
+ [,1] [,2] [,3]
+[1,] 0.2143499 0.3891695 0.45577894
+[2,] 10.5993345 39.8970536 -0.39199265
+[3,] 40.3370139 20.3148331 -0.06033818
+[4,] 50.7170411 49.7645642 -0.43318939
+[5,] 29.7257398 -0.5981739 -0.05616701
+Objective function: 5.65785
+Clustering vector: int [1:2000] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...
+Cluster sizes: 400 397 407 401 395
+Best sample:
+ [1] 84 106 164 226 284 288 329 423 430 450 469 593 603 654 742
+[16] 887 929 970 974 1035 1043 1096 1171 1187 1192 1302 1307 1327 1371 1431
+[31] 1433 1439 1440 1452 1513 1522 1525 1548 1565 1593 1620 1639 1654 1688 1740
+[46] 1761 1832 1845 1895 1899
+
+Available components:
+ [1] "sample" "medoids" "i.med" "clustering" "objective"
+ [6] "clusinfo" "diss" "call" "silinfo" "data"
+>
+> ###--- Start a version of example(clara) -------
+>
+> ## xclara : artificial data with 3 clusters of 1000 bivariate objects each.
+> data(xclara)
+> (clx3 <- clara(xclara, 3))
+Call: clara(x = xclara, k = 3)
+Medoids:
+ V1 V2
+[1,] 5.553391 13.306260
+[2,] 43.198760 60.360720
+[3,] 74.591890 -6.969018
+Objective function: 13.225
+Clustering vector: int [1:3000] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...
+Cluster sizes: 900 1148 952
+Best sample:
+ [1] 20 30 46 91 92 169 179 187 209 223 382 450 555 971 1004
+[16] 1025 1058 1277 1281 1302 1319 1361 1362 1513 1591 1623 1628 1729 1752 1791
+[31] 1907 1917 1946 2064 2089 2498 2527 2537 2545 2591 2672 2722 2729 2790 2797
+[46] 2852
+
+Available components:
+ [1] "sample" "medoids" "i.med" "clustering" "objective"
+ [6] "clusinfo" "diss" "call" "silinfo" "data"
+> ## Plot similar to Figure 5 in Struyf et al (1996)
+> plot(clx3)
+>
+> ## The rngR = TRUE case is currently in the non-strict tests
+> ## ./clara-ex.R
+> ## ~~~~~~~~~~~~
+>
+> ###--- End version of example(clara) -------
+>
+> ## small example(s):
+> data(ruspini)
+>
+> clara(ruspini,4)
+Call: clara(x = ruspini, k = 4)
+Medoids:
+ x y
+10 19 65
+32 44 149
+52 99 119
+67 66 18
+Objective function: 11.51066
+Clustering vector: Named int [1:75] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...
+ - attr(*, "names")= chr [1:75] "1" "2" "3" "4" "5" "6" "7" ...
+Cluster sizes: 20 23 17 15
+Best sample:
+ [1] 2 3 4 5 6 7 8 9 10 16 18 19 20 21 22 23 25 29 30 32 34 35 36 37 41
+[26] 42 43 44 46 47 49 50 52 53 54 58 59 60 61 63 65 66 67 69 71 72 73 75
+
+Available components:
+ [1] "sample" "medoids" "i.med" "clustering" "objective"
+ [6] "clusinfo" "diss" "call" "silinfo" "data"
+>
+> rus <- data.matrix(ruspini); storage.mode(rus) <- "double"
+> ru2 <- rus[c(1:7,21:28, 45:51, 61:69),]
+> ru3 <- rus[c(1:4,21:25, 45:48, 61:63),]
+> ru4 <- rus[c(1:2,21:22, 45:47),]
+> ru5 <- rus[c(1:2,21, 45),]
+> daisy(ru5, "manhattan")
+Dissimilarities :
+ 1 2 21
+2 11
+21 118 107
+45 143 132 89
+
+Metric : manhattan
+Number of objects : 4
+> ## Dissimilarities : 11 118 143 107 132 89
+>
+> ## no problem anymore, since 2002-12-28:
+> ## sampsize >= k+1 is now enforced:
+> ## clara(ru5, k=3, met="manhattan", sampsize=3,trace=2)[clInS]
+> clara(ru5, k=3, met="manhattan", sampsize=4,trace=1)[clInS]
+calling .C(cl_clara, ..., DUP = FALSE):
+C clara(): (nsam,nran,n) = (4,5,4); 'full_sample',
+C clara(): sample 1 C clara(): best sample _found_ --> dysta2(nbest), resul(), end
+$objective
+[1] 2.75
+
+$i.med
+[1] 2 3 4
+
+$medoids
+ x y
+2 5 63
+21 28 147
+45 85 115
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 2 11 5.5 0.1028037
+[2,] 1 0 0.0 0.0000000
+[3,] 1 0 0.0 0.0000000
+
+$sample
+[1] "1" "2" "21" "45"
+
+>
+> daisy(ru4, "manhattan")
+Dissimilarities :
+ 1 2 21 22 45 46
+2 11
+21 118 107
+22 124 113 6
+45 143 132 89 87
+46 124 113 108 106 19
+47 115 104 103 101 28 9
+
+Metric : manhattan
+Number of objects : 7
+> ## this one (k=3) gave problems, from ss = 6 on ___ still after 2002-12-28 ___ :
+> for(ss in 4:nrow(ru4)){
++ cat("---\n\nsample size = ",ss,"\n")
++ print(clara(ru4,k=3,met="manhattan",sampsize=ss)[clInS])
++ }
+---
+
+sample size = 4
+$objective
+[1] 7.714286
+
+$i.med
+[1] 1 4 7
+
+$medoids
+ x y
+1 4 53
+22 32 149
+47 78 94
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 2 11 5.50000 0.09565217
+[2,] 2 6 3.00000 0.05940594
+[3,] 3 28 12.33333 0.27722772
+
+$sample
+[1] "1" "22" "45" "47"
+
+---
+
+sample size = 5
+$objective
+[1] 7.714286
+
+$i.med
+[1] 2 3 7
+
+$medoids
+ x y
+2 5 63
+21 28 147
+47 78 94
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 2 11 5.50000 0.10576923
+[2,] 2 6 3.00000 0.05825243
+[3,] 3 28 12.33333 0.27184466
+
+$sample
+[1] "2" "21" "22" "45" "47"
+
+---
+
+sample size = 6
+$objective
+[1] 6.428571
+
+$i.med
+[1] 2 4 6
+
+$medoids
+ x y
+2 5 63
+22 32 149
+46 85 96
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 2 11 5.500000 0.09734513
+[2,] 2 6 3.000000 0.05660377
+[3,] 3 19 9.333333 0.17924528
+
+$sample
+[1] "2" "21" "22" "45" "46" "47"
+
+---
+
+sample size = 7
+$objective
+[1] 6.428571
+
+$i.med
+[1] 2 4 6
+
+$medoids
+ x y
+2 5 63
+22 32 149
+46 85 96
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 2 11 5.500000 0.09734513
+[2,] 2 6 3.000000 0.05660377
+[3,] 3 19 9.333333 0.17924528
+
+$sample
+[1] "1" "2" "21" "22" "45" "46" "47"
+
+> for(ss in 5:nrow(ru3)){
++ cat("---\n\nsample size = ",ss,"\n")
++ print(clara(ru3,k=4,met="manhattan",sampsize=ss)[clInS])
++ }
+---
+
+sample size = 5
+$objective
+[1] 13.625
+
+$i.med
+[1] 4 5 10 15
+
+$medoids
+ x y
+4 9 77
+21 28 147
+45 85 115
+62 77 12
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 4 29 16.50 0.3258427
+[2,] 5 14 9.00 0.1573034
+[3,] 4 30 19.25 0.3370787
+[4,] 3 15 10.00 0.1351351
+
+$sample
+[1] "3" "4" "21" "45" "62"
+
+---
+
+sample size = 6
+$objective
+[1] 9.0625
+
+$i.med
+[1] 3 7 13 15
+
+$medoids
+ x y
+3 10 59
+23 35 153
+48 74 96
+62 77 12
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 4 19 10.00 0.1881188
+[2,] 5 13 5.60 0.1354167
+[3,] 4 30 11.75 0.3448276
+[4,] 3 15 10.00 0.1724138
+
+$sample
+[1] "3" "21" "23" "45" "48" "62"
+
+---
+
+sample size = 7
+$objective
+[1] 9.0625
+
+$i.med
+[1] 3 7 13 15
+
+$medoids
+ x y
+3 10 59
+23 35 153
+48 74 96
+62 77 12
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 4 19 10.00 0.1881188
+[2,] 5 13 5.60 0.1354167
+[3,] 4 30 11.75 0.3448276
+[4,] 3 15 10.00 0.1724138
+
+$sample
+[1] "2" "3" "21" "23" "45" "48" "62"
+
+---
+
+sample size = 8
+$objective
+[1] 8.8125
+
+$i.med
+[1] 3 7 12 15
+
+$medoids
+ x y
+3 10 59
+23 35 153
+47 78 94
+62 77 12
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 4 19 10.00 0.1844660
+[2,] 5 13 5.60 0.1274510
+[3,] 4 28 10.75 0.3373494
+[4,] 3 15 10.00 0.1807229
+
+$sample
+[1] "3" "21" "23" "46" "47" "48" "61" "62"
+
+---
+
+sample size = 9
+$objective
+[1] 9.3125
+
+$i.med
+[1] 2 6 11 16
+
+$medoids
+ x y
+2 5 63
+22 32 149
+46 85 96
+63 83 21
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 4 18 9.50 0.1592920
+[2,] 5 8 5.40 0.0754717
+[3,] 4 19 9.75 0.2467532
+[4,] 3 30 15.00 0.3896104
+
+$sample
+[1] "2" "21" "22" "23" "45" "46" "47" "61" "63"
+
+---
+
+sample size = 10
+$objective
+[1] 8.5625
+
+$i.med
+[1] 3 7 11 15
+
+$medoids
+ x y
+3 10 59
+23 35 153
+46 85 96
+62 77 12
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 4 19 10.00 0.1696429
+[2,] 5 13 5.60 0.1214953
+[3,] 4 19 9.75 0.2065217
+[4,] 3 15 10.00 0.1630435
+
+$sample
+ [1] "2" "3" "22" "23" "45" "46" "47" "61" "62" "63"
+
+---
+
+sample size = 11
+$objective
+[1] 8.6875
+
+$i.med
+[1] 2 7 12 15
+
+$medoids
+ x y
+2 5 63
+23 35 153
+47 78 94
+62 77 12
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 4 18 9.50 0.1730769
+[2,] 5 13 5.60 0.1274510
+[3,] 4 28 10.75 0.3373494
+[4,] 3 15 10.00 0.1807229
+
+$sample
+ [1] "1" "2" "3" "4" "23" "24" "25" "45" "47" "48" "62"
+
+---
+
+sample size = 12
+$objective
+[1] 8.8125
+
+$i.med
+[1] 3 7 12 15
+
+$medoids
+ x y
+3 10 59
+23 35 153
+47 78 94
+62 77 12
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 4 19 10.00 0.1844660
+[2,] 5 13 5.60 0.1274510
+[3,] 4 28 10.75 0.3373494
+[4,] 3 15 10.00 0.1807229
+
+$sample
+ [1] "2" "3" "22" "23" "24" "25" "46" "47" "48" "61" "62" "63"
+
+---
+
+sample size = 13
+$objective
+[1] 8.4375
+
+$i.med
+[1] 2 7 11 15
+
+$medoids
+ x y
+2 5 63
+23 35 153
+46 85 96
+62 77 12
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 4 18 9.50 0.1592920
+[2,] 5 13 5.60 0.1214953
+[3,] 4 19 9.75 0.2065217
+[4,] 3 15 10.00 0.1630435
+
+$sample
+ [1] "1" "2" "4" "22" "23" "24" "25" "45" "46" "47" "61" "62" "63"
+
+---
+
+sample size = 14
+$objective
+[1] 8.4375
+
+$i.med
+[1] 2 7 11 15
+
+$medoids
+ x y
+2 5 63
+23 35 153
+46 85 96
+62 77 12
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 4 18 9.50 0.1592920
+[2,] 5 13 5.60 0.1214953
+[3,] 4 19 9.75 0.2065217
+[4,] 3 15 10.00 0.1630435
+
+$sample
+ [1] "2" "3" "4" "22" "23" "24" "25" "45" "46" "47" "48" "61" "62" "63"
+
+---
+
+sample size = 15
+$objective
+[1] 8.375
+
+$i.med
+[1] 2 6 11 15
+
+$medoids
+ x y
+2 5 63
+22 32 149
+46 85 96
+62 77 12
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 4 18 9.50 0.1592920
+[2,] 5 8 5.40 0.0754717
+[3,] 4 19 9.75 0.2065217
+[4,] 3 15 10.00 0.1630435
+
+$sample
+ [1] "2" "3" "4" "21" "22" "23" "24" "25" "45" "46" "47" "48" "61" "62" "63"
+
+---
+
+sample size = 16
+$objective
+[1] 8.375
+
+$i.med
+[1] 2 6 11 15
+
+$medoids
+ x y
+2 5 63
+22 32 149
+46 85 96
+62 77 12
+
+$clusinfo
+ size max_diss av_diss isolation
+[1,] 4 18 9.50 0.1592920
+[2,] 5 8 5.40 0.0754717
+[3,] 4 19 9.75 0.2065217
+[4,] 3 15 10.00 0.1630435
+
+$sample
+ [1] "1" "2" "3" "4" "21" "22" "23" "24" "25" "45" "46" "47" "48" "61" "62"
+[16] "63"
+
+>
+> ## Last Line:
+> cat('Time elapsed: ', proc.time() - .proctime00,'\n')
+Time elapsed: 2.83 0 2.82 0 0
+> ## Lynne (P IV, 1.6 GHz): 18.81; then (no NA; R 1.9.0-alpha): 15.07
+> ## nb-mm (P III,700 MHz): 27.97
+>
diff --git a/win32/deps/library/cluster/tests/clusplot-out.R b/win32/deps/library/cluster/tests/clusplot-out.R
new file mode 100644
index 0000000..164f221
--- /dev/null
+++ b/win32/deps/library/cluster/tests/clusplot-out.R
@@ -0,0 +1,29 @@
+library(cluster)
+
+### clusplot() & pam() RESULT checking ...
+
+## plotting votes.diss(dissimilarity) in a bivariate plot and
+## partitioning into 2 clusters
+data(votes.repub)
+votes.diss <- daisy(votes.repub)
+for(k in 2:4) {
+ votes.clus <- pam(votes.diss, k, diss = TRUE)$clustering
+ print(clusplot(votes.diss, votes.clus, diss = TRUE, shade = TRUE))
+}
+
+## plotting iris (dataframe) in a 2-dimensional plot and partitioning
+## into 3 clusters.
+data(iris)
+iris.x <- iris[, 1:4]
+
+for(k in 2:5)
+ print(clusplot(iris.x, pam(iris.x, k)$clustering, diss = FALSE))
+
+
+.Random.seed <- c(0L,rep(7654L,3))
+## generate 25 objects, divided into 2 clusters.
+x <- rbind(cbind(rnorm(10,0,0.5), rnorm(10,0,0.5)),
+ cbind(rnorm(15,5,0.5), rnorm(15,5,0.5)))
+print.default(clusplot(px2 <- pam(x, 2)))
+
+clusplot(px2, labels = 2, col.p = 1 + px2$clustering)
diff --git a/win32/deps/library/cluster/tests/clusplot-out.Rout.save b/win32/deps/library/cluster/tests/clusplot-out.Rout.save
new file mode 100644
index 0000000..ed1cc13
--- /dev/null
+++ b/win32/deps/library/cluster/tests/clusplot-out.Rout.save
@@ -0,0 +1,121 @@
+
+R version 2.12.0 Patched (2010-10-19 r53372)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: i686-pc-linux-gnu (32-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(cluster)
+>
+> ### clusplot() & pam() RESULT checking ...
+>
+> ## plotting votes.diss(dissimilarity) in a bivariate plot and
+> ## partitioning into 2 clusters
+> data(votes.repub)
+> votes.diss <- daisy(votes.repub)
+> for(k in 2:4) {
++ votes.clus <- pam(votes.diss, k, diss = TRUE)$clustering
++ print(clusplot(votes.diss, votes.clus, diss = TRUE, shade = TRUE))
++ }
+$Distances
+ [,1] [,2]
+[1,] 0.0000 154.8601
+[2,] 154.8601 0.0000
+
+$Shading
+[1] 22.12103 20.87897
+
+$Distances
+ [,1] [,2] [,3]
+[1,] 0.0000 NA 140.8008
+[2,] NA 0 NA
+[3,] 140.8008 NA 0.0000
+
+$Shading
+[1] 25.602967 5.292663 15.104370
+
+$Distances
+ [,1] [,2] [,3] [,4]
+[1,] 0.0000 NA 117.2287 280.7259
+[2,] NA 0 NA NA
+[3,] 117.2287 NA 0.0000 NA
+[4,] 280.7259 NA NA 0.0000
+
+$Shading
+[1] 15.431339 3.980743 10.145454 19.442464
+
+>
+> ## plotting iris (dataframe) in a 2-dimensional plot and partitioning
+> ## into 3 clusters.
+> data(iris)
+> iris.x <- iris[, 1:4]
+>
+> for(k in 2:5)
++ print(clusplot(iris.x, pam(iris.x, k)$clustering, diss = FALSE))
+$Distances
+ [,1] [,2]
+[1,] 0.0000000 0.5452161
+[2,] 0.5452161 0.0000000
+
+$Shading
+[1] 18.93861 24.06139
+
+$Distances
+ [,1] [,2] [,3]
+[1,] 0.000000 1.433071 2.851715
+[2,] 1.433071 0.000000 NA
+[3,] 2.851715 NA 0.000000
+
+$Shading
+[1] 18.987588 17.166940 9.845472
+
+$Distances
+ [,1] [,2] [,3] [,4]
+[1,] 0.000000 2.24157 1.6340329 3.0945887
+[2,] 2.241570 0.00000 NA NA
+[3,] 1.634033 NA 0.0000000 0.9461858
+[4,] 3.094589 NA 0.9461858 0.0000000
+
+$Shading
+[1] 12.881766 14.912379 13.652381 7.553474
+
+$Distances
+ [,1] [,2] [,3] [,4] [,5]
+[1,] 0.000000 1.9899160 1.552387 3.11516148 3.96536391
+[2,] 1.989916 0.0000000 NA NA 0.94713417
+[3,] 1.552387 NA 0.000000 1.17348334 2.22769309
+[4,] 3.115161 NA 1.173483 0.00000000 0.04539385
+[5,] 3.965364 0.9471342 2.227693 0.04539385 0.00000000
+
+$Shading
+[1] 10.369738 11.560147 10.088431 14.857590 5.124093
+
+>
+>
+> .Random.seed <- c(0L,rep(7654L,3))
+> ## generate 25 objects, divided into 2 clusters.
+> x <- rbind(cbind(rnorm(10,0,0.5), rnorm(10,0,0.5)),
++ cbind(rnorm(15,5,0.5), rnorm(15,5,0.5)))
+> print.default(clusplot(px2 <- pam(x, 2)))
+$Distances
+ [,1] [,2]
+[1,] 0.000000 5.516876
+[2,] 5.516876 0.000000
+
+$Shading
+[1] 20.18314 22.81686
+
+>
+> clusplot(px2, labels = 2, col.p = 1 + px2$clustering)
+>
diff --git a/win32/deps/library/cluster/tests/daisy-ex.R b/win32/deps/library/cluster/tests/daisy-ex.R
new file mode 100644
index 0000000..66338f9
--- /dev/null
+++ b/win32/deps/library/cluster/tests/daisy-ex.R
@@ -0,0 +1,110 @@
+## For different cluster versions
+
+require(cluster)
+
+if(interactive()) {
+ (pkgPath <- .find.package("cluster", verbose = TRUE))
+ (verC <- readLines(Dfile <- file.path(pkgPath, "DESCRIPTION"), n = 2)[2])
+}
+
+## trivial cases should 'work':
+daisy(cbind(1))
+(d10 <- daisy(matrix(0., 1,0))); str(d10)
+d01 <- daisy(matrix(0., 0,1))
+if(paste(R.version$major, R.version$minor, sep=".") >= "2.1.0")
+ print(d01)
+str(d01)
+d32 <- data.frame(eins=c("A"=1,"B"=1,"C"=1), zwei=c(2,2,2))
+daisy(d32)
+daisy(d32, stand = TRUE)
+daisy(d32, type = list(ordratio="zwei"))
+
+
+str(d5 <- data.frame(a= c(0, 0, 0,1,0,0, 0,0,1, 0,NA),
+ b= c(NA,0, 1,1,0,1, 0,1,0, 1,0),
+ c= c(0, 1, 1,0,1,NA,1,0,1, 0,NA),
+ d= c(1, 1, 0,1,0,0, 0,0,0, 1,0),
+ e= c(1, NA,0,1,0,0, 0,0,NA,1,1)))
+(d0 <- daisy(d5))
+(d1 <- daisy(d5, type = list(asymm = 1:5)))
+(d2 <- daisy(d5, type = list(symm = 1:2, asymm= 3:5)))
+(d2.<- daisy(d5, type = list( asymm= 3:5)))
+stopifnot(identical(c(d2), c(d2.)))
+(dS <- daisy(d5, stand = TRUE))# gave error in some versions
+stopifnot(all.equal(as.vector(summary(c(dS), digits=9)),
+ c(0, 2.6142638, 3.4938562, 3.2933687, 4.0591077, 5.5580177),
+ tol = 1e-7))# 7.88e-9
+
+d5[,4] <- 1 # binary with only one instead of two values
+(d0 <- daisy(d5))
+(d1 <- daisy(d5, type = list(asymm = 1:5)))# 2 NAs
+(d2 <- daisy(d5, type = list(symm = 1:2, asymm= 3:5)))
+(d2.<- daisy(d5, type = list( asymm= 3:5)))
+## better leave away the constant variable: it has no effect:
+stopifnot(identical(c(d1), c(daisy(d5[,-4], type = list(asymm = 1:4)))))
+
+###---- Trivial "binary only" matrices (not data frames) did fail:
+
+x <- matrix(0, 2, 2)
+dimnames(x)[[2]] <- c("A", "B")## colnames<- is missing in S+
+daisy(x, type = list(symm= "B", asymm="A"))
+daisy(x, type = list(symm= "B"))# 0 too
+
+x2 <- x; x2[2,2] <- 1
+daisy(x2, type= list(symm = "B"))# |-> 0.5 (gives 1 in S+)
+daisy(x2, type= list(symm = "B", asymm="A"))# 1
+
+x3 <- x; x3[] <- diag(2)
+daisy(x3) # warning: both as interval scaled -> sqrt(2)
+daisy(x3, type= list(symm="B", asymm="A"))# 1
+daisy(x3, type= list(symm =c("B","A"))) # 1, S+: sqrt(2)
+daisy(x3, type= list(asymm=c("B","A"))) # 1, S+ : sqrt(2)
+
+x4 <- rbind(x3, 1)
+daisy(x4, type= list(symm="B", asymm="A"))# 1 0.5 0.5
+daisy(x4, type= list(symm=c("B","A"))) # dito; S+ : 1.41 1 1
+daisy(x4, type= list(asymm=c("A","B"))) # dito, dito
+
+
+
+## ----------- example(daisy) -----------------------
+
+data(flower)
+data(agriculture)
+
+## Example 1 in ref:
+## Dissimilarities using Euclidean metric and without standardization
+(d.agr <- daisy(agriculture, metric = "euclidean", stand = FALSE))
+(d.agr2 <- daisy(agriculture, metric = "manhattan"))
+
+
+## Example 2 in ref
+(dfl0 <- daisy(flower))
+stopifnot(identical(c(dfl0),
+ c(daisy(flower, type = list(symm = 1)))) &&
+ identical(c(dfl0),
+ c(daisy(flower, type = list(symm = 2)))) &&
+ identical(c(dfl0),
+ c(daisy(flower, type = list(symm = 3)))) &&
+ identical(c(dfl0),
+ c(daisy(flower, type = list(symm = c(1,3)))))
+ )
+
+(dfl1 <- daisy(flower, type = list(asymm = 3)))
+(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ordratio = 7)))
+(dfl3 <- daisy(flower, type = list(asymm = 1:3)))
+
+## --- animals
+data(animals)
+d0 <- daisy(animals)
+
+d1 <- daisy(animals - 1, type=list(asymm=c(2,4)))
+(d2 <- daisy(animals - 1, type=list(symm = c(1,3,5,6), asymm=c(2,4))))
+stopifnot(c(d1) == c(d2))
+
+d3 <- daisy(2 - animals, type=list(asymm=c(2,4)))
+(d4 <- daisy(2 - animals, type=list(symm = c(1,3,5,6), asymm=c(2,4))))
+stopifnot(c(d3) == c(d4))
+
+pairs(cbind(d0,d2,d4),
+ main = "Animals -- symmetric and asymm. dissimilarities")
diff --git a/win32/deps/library/cluster/tests/daisy-ex.Rout.save b/win32/deps/library/cluster/tests/daisy-ex.Rout.save
new file mode 100644
index 0000000..0ca1ef1
--- /dev/null
+++ b/win32/deps/library/cluster/tests/daisy-ex.Rout.save
@@ -0,0 +1,927 @@
+
+R version 2.14.0 alpha (2011-10-06 r57181)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> ## For different cluster versions
+>
+> require(cluster)
+Loading required package: cluster
+>
+> if(interactive()) {
++ (pkgPath <- .find.package("cluster", verbose = TRUE))
++ (verC <- readLines(Dfile <- file.path(pkgPath, "DESCRIPTION"), n = 2)[2])
++ }
+>
+> ## trivial cases should 'work':
+> daisy(cbind(1))
+Dissimilarities :
+dissimilarity(0)
+
+Metric : euclidean
+Number of objects : 1
+> (d10 <- daisy(matrix(0., 1,0))); str(d10)
+Dissimilarities :
+dissimilarity(0)
+
+Metric : euclidean
+Number of objects : 1
+Classes 'dissimilarity', 'dist' atomic (0)
+ ..- attr(*, "Size")= int 1
+ ..- attr(*, "Metric")= chr "euclidean"
+> d01 <- daisy(matrix(0., 0,1))
+> if(paste(R.version$major, R.version$minor, sep=".") >= "2.1.0")
++ print(d01)
+Dissimilarities :
+dissimilarity(0)
+
+Metric : euclidean
+Number of objects : 0
+> str(d01)
+Classes 'dissimilarity', 'dist' atomic (0)
+ ..- attr(*, "Size")= int 0
+ ..- attr(*, "Metric")= chr "euclidean"
+> d32 <- data.frame(eins=c("A"=1,"B"=1,"C"=1), zwei=c(2,2,2))
+> daisy(d32)
+Dissimilarities :
+ A B
+B 0
+C 0 0
+
+Metric : euclidean
+Number of objects : 3
+> daisy(d32, stand = TRUE)
+Dissimilarities :
+ A B
+B 0
+C 0 0
+
+Metric : euclidean
+Number of objects : 3
+Warning message:
+In daisy(d32, stand = TRUE) :
+ 'x' has constant columns 1, 2; these are standardized to 0
+> daisy(d32, type = list(ordratio="zwei"))
+Dissimilarities :
+ A B
+B 0
+C 0 0
+
+Metric : mixed ; Types = I, T
+Number of objects : 3
+>
+>
+> str(d5 <- data.frame(a= c(0, 0, 0,1,0,0, 0,0,1, 0,NA),
++ b= c(NA,0, 1,1,0,1, 0,1,0, 1,0),
++ c= c(0, 1, 1,0,1,NA,1,0,1, 0,NA),
++ d= c(1, 1, 0,1,0,0, 0,0,0, 1,0),
++ e= c(1, NA,0,1,0,0, 0,0,NA,1,1)))
+'data.frame': 11 obs. of 5 variables:
+ $ a: num 0 0 0 1 0 0 0 0 1 0 ...
+ $ b: num NA 0 1 1 0 1 0 1 0 1 ...
+ $ c: num 0 1 1 0 1 NA 1 0 1 0 ...
+ $ d: num 1 1 0 1 0 0 0 0 0 1 ...
+ $ e: num 1 NA 0 1 0 0 0 0 NA 1 ...
+> (d0 <- daisy(d5))
+Dissimilarities :
+ 1 2 3 4 5 6 7 8
+2 1.290994
+3 1.936492 1.581139
+4 1.118034 1.936492 2.000000
+5 1.936492 1.118034 1.000000 2.236068
+6 1.825742 1.825742 0.000000 1.936492 1.118034
+7 1.936492 1.118034 1.000000 2.236068 0.000000 1.118034
+8 1.581139 1.936492 1.000000 1.732051 1.414214 0.000000 1.414214
+9 2.236068 1.581139 1.581139 1.936492 1.118034 1.825742 1.118034 1.936492
+10 0.000000 1.581139 1.732051 1.000000 2.000000 1.581139 2.000000 1.414214
+11 1.581139 1.581139 1.825742 1.825742 1.290994 1.825742 1.290994 1.825742
+ 9 10
+2
+3
+4
+5
+6
+7
+8
+9
+10 2.236068
+11 0.000000 1.825742
+
+Metric : euclidean
+Number of objects : 11
+Warning message:
+In daisy(d5) : binary variable(s) 1, 2, 3, 4, 5 treated as interval scaled
+> (d1 <- daisy(d5, type = list(asymm = 1:5)))
+Dissimilarities :
+ 1 2 3 4 5 6 7
+2 0.5000000
+3 1.0000000 0.6666667
+4 0.3333333 0.7500000 0.8000000
+5 1.0000000 0.5000000 0.5000000 1.0000000
+6 1.0000000 1.0000000 0.0000000 0.7500000 1.0000000
+7 1.0000000 0.5000000 0.5000000 1.0000000 0.0000000 1.0000000
+8 1.0000000 1.0000000 0.5000000 0.7500000 1.0000000 0.0000000 1.0000000
+9 1.0000000 0.6666667 0.6666667 0.7500000 0.5000000 1.0000000 0.5000000
+10 0.0000000 0.6666667 0.7500000 0.2500000 1.0000000 0.6666667 1.0000000
+11 0.5000000 1.0000000 1.0000000 0.6666667 1.0000000 1.0000000 1.0000000
+ 8 9 10
+2
+3
+4
+5
+6
+7
+8
+9 1.0000000
+10 0.6666667 1.0000000
+11 1.0000000 NA 0.6666667
+
+Metric : mixed ; Types = A, A, A, A, A
+Number of objects : 11
+> (d2 <- daisy(d5, type = list(symm = 1:2, asymm= 3:5)))
+Dissimilarities :
+ 1 2 3 4 5 6 7
+2 0.3333333
+3 0.7500000 0.5000000
+4 0.3333333 0.7500000 0.8000000
+5 0.7500000 0.2500000 0.3333333 1.0000000
+6 0.6666667 0.6666667 0.0000000 0.7500000 0.5000000
+7 0.7500000 0.2500000 0.3333333 1.0000000 0.0000000 0.5000000
+8 0.6666667 0.7500000 0.3333333 0.7500000 0.6666667 0.0000000 0.6666667
+9 1.0000000 0.5000000 0.6666667 0.7500000 0.3333333 1.0000000 0.3333333
+10 0.0000000 0.5000000 0.6000000 0.2500000 0.8000000 0.5000000 0.8000000
+11 0.5000000 0.5000000 1.0000000 0.6666667 0.5000000 1.0000000 0.5000000
+ 8 9 10
+2
+3
+4
+5
+6
+7
+8
+9 1.0000000
+10 0.5000000 1.0000000
+11 1.0000000 0.0000000 0.6666667
+
+Metric : mixed ; Types = S, S, A, A, A
+Number of objects : 11
+> (d2.<- daisy(d5, type = list( asymm= 3:5)))
+Dissimilarities :
+ 1 2 3 4 5 6 7
+2 0.3333333
+3 0.7500000 0.5000000
+4 0.3333333 0.7500000 0.8000000
+5 0.7500000 0.2500000 0.3333333 1.0000000
+6 0.6666667 0.6666667 0.0000000 0.7500000 0.5000000
+7 0.7500000 0.2500000 0.3333333 1.0000000 0.0000000 0.5000000
+8 0.6666667 0.7500000 0.3333333 0.7500000 0.6666667 0.0000000 0.6666667
+9 1.0000000 0.5000000 0.6666667 0.7500000 0.3333333 1.0000000 0.3333333
+10 0.0000000 0.5000000 0.6000000 0.2500000 0.8000000 0.5000000 0.8000000
+11 0.5000000 0.5000000 1.0000000 0.6666667 0.5000000 1.0000000 0.5000000
+ 8 9 10
+2
+3
+4
+5
+6
+7
+8
+9 1.0000000
+10 0.5000000 1.0000000
+11 1.0000000 0.0000000 0.6666667
+
+Metric : mixed ; Types = I, I, A, A, A
+Number of objects : 11
+Warning message:
+In daisy(d5, type = list(asymm = 3:5)) :
+ binary variable(s) 1, 2 treated as interval scaled
+> stopifnot(identical(c(d2), c(d2.)))
+> (dS <- daisy(d5, stand = TRUE))# gave error in some versions
+Dissimilarities :
+ 1 2 3 4 5 6 7 8
+2 2.614264
+3 4.010913 3.291786
+4 3.493856 4.725761 4.757684
+5 4.010913 2.415752 2.000000 5.160965
+6 3.823025 3.801028 0.000000 4.813384 2.236068
+7 4.010913 2.415752 2.000000 5.160965 0.000000 2.236068
+8 3.310837 3.995202 2.025000 4.305222 2.846160 0.000000 2.846160
+9 5.558018 4.247692 4.148136 3.995202 3.493856 4.789855 3.493856 4.725761
+10 0.000000 3.182103 3.587469 3.125000 4.107303 3.310837 4.107303 2.961302
+11 3.416389 3.416389 3.674376 3.801028 2.614264 3.674376 2.614264 3.674376
+ 9 10
+2
+3
+4
+5
+6
+7
+8
+9
+10 5.307417
+11 0.000000 3.801028
+
+Metric : euclidean
+Number of objects : 11
+Warning message:
+In daisy(d5, stand = TRUE) :
+ binary variable(s) 1, 2, 3, 4, 5 treated as interval scaled
+> stopifnot(all.equal(as.vector(summary(c(dS), digits=9)),
++ c(0, 2.6142638, 3.4938562, 3.2933687, 4.0591077, 5.5580177),
++ tol = 1e-7))# 7.88e-9
+>
+> d5[,4] <- 1 # binary with only one instead of two values
+> (d0 <- daisy(d5))
+Dissimilarities :
+ 1 2 3 4 5 6 7 8
+2 1.290994
+3 1.581139 1.118034
+4 1.118034 1.936492 1.732051
+5 1.581139 0.000000 1.000000 2.000000
+6 1.290994 1.290994 0.000000 1.581139 1.118034
+7 1.581139 0.000000 1.000000 2.000000 0.000000 1.118034
+8 1.118034 1.581139 1.000000 1.414214 1.414214 0.000000 1.414214
+9 1.825742 1.118034 1.581139 1.581139 1.118034 1.825742 1.118034 1.936492
+10 0.000000 1.581139 1.414214 1.000000 1.732051 1.118034 1.732051 1.000000
+11 0.000000 0.000000 1.825742 1.290994 1.290994 1.825742 1.290994 1.825742
+ 9 10
+2
+3
+4
+5
+6
+7
+8
+9
+10 1.936492
+11 0.000000 1.290994
+
+Metric : euclidean
+Number of objects : 11
+Warning message:
+In daisy(d5) : binary variable(s) 1, 2, 3, 5 treated as interval scaled
+> (d1 <- daisy(d5, type = list(asymm = 1:5)))# 2 NAs
+Dissimilarities :
+ 1 2 3 4 5 6 7
+2 1.0000000
+3 1.0000000 0.5000000
+4 0.5000000 1.0000000 0.7500000
+5 1.0000000 0.0000000 0.5000000 1.0000000
+6 1.0000000 1.0000000 0.0000000 0.6666667 1.0000000
+7 1.0000000 0.0000000 0.5000000 1.0000000 0.0000000 1.0000000
+8 1.0000000 1.0000000 0.5000000 0.6666667 1.0000000 0.0000000 1.0000000
+9 1.0000000 0.5000000 0.6666667 0.6666667 0.5000000 1.0000000 0.5000000
+10 0.0000000 1.0000000 0.6666667 0.3333333 1.0000000 0.5000000 1.0000000
+11 0.0000000 NA 1.0000000 0.5000000 1.0000000 1.0000000 1.0000000
+ 8 9 10
+2
+3
+4
+5
+6
+7
+8
+9 1.0000000
+10 0.5000000 1.0000000
+11 1.0000000 NA 0.5000000
+
+Metric : mixed ; Types = A, A, A, A, A
+Number of objects : 11
+Warning message:
+In daisy(d5, type = list(asymm = 1:5)) :
+ at least one binary variable has not 2 different levels.
+> (d2 <- daisy(d5, type = list(symm = 1:2, asymm= 3:5)))
+Dissimilarities :
+ 1 2 3 4 5 6 7
+2 0.5000000
+3 0.6666667 0.3333333
+4 0.5000000 1.0000000 0.7500000
+5 0.6666667 0.0000000 0.3333333 1.0000000
+6 0.5000000 0.5000000 0.0000000 0.6666667 0.5000000
+7 0.6666667 0.0000000 0.3333333 1.0000000 0.0000000 0.5000000
+8 0.5000000 0.6666667 0.3333333 0.6666667 0.6666667 0.0000000 0.6666667
+9 1.0000000 0.3333333 0.6666667 0.6666667 0.3333333 1.0000000 0.3333333
+10 0.0000000 0.6666667 0.5000000 0.3333333 0.7500000 0.3333333 0.7500000
+11 0.0000000 0.0000000 1.0000000 0.5000000 0.5000000 1.0000000 0.5000000
+ 8 9 10
+2
+3
+4
+5
+6
+7
+8
+9 1.0000000
+10 0.3333333 1.0000000
+11 1.0000000 0.0000000 0.5000000
+
+Metric : mixed ; Types = S, S, A, A, A
+Number of objects : 11
+Warning message:
+In daisy(d5, type = list(symm = 1:2, asymm = 3:5)) :
+ at least one binary variable has not 2 different levels.
+> (d2.<- daisy(d5, type = list( asymm= 3:5)))
+Dissimilarities :
+ 1 2 3 4 5 6 7
+2 0.5000000
+3 0.6666667 0.3333333
+4 0.5000000 1.0000000 0.7500000
+5 0.6666667 0.0000000 0.3333333 1.0000000
+6 0.5000000 0.5000000 0.0000000 0.6666667 0.5000000
+7 0.6666667 0.0000000 0.3333333 1.0000000 0.0000000 0.5000000
+8 0.5000000 0.6666667 0.3333333 0.6666667 0.6666667 0.0000000 0.6666667
+9 1.0000000 0.3333333 0.6666667 0.6666667 0.3333333 1.0000000 0.3333333
+10 0.0000000 0.6666667 0.5000000 0.3333333 0.7500000 0.3333333 0.7500000
+11 0.0000000 0.0000000 1.0000000 0.5000000 0.5000000 1.0000000 0.5000000
+ 8 9 10
+2
+3
+4
+5
+6
+7
+8
+9 1.0000000
+10 0.3333333 1.0000000
+11 1.0000000 0.0000000 0.5000000
+
+Metric : mixed ; Types = I, I, A, A, A
+Number of objects : 11
+Warning messages:
+1: In daisy(d5, type = list(asymm = 3:5)) :
+ at least one binary variable has not 2 different levels.
+2: In daisy(d5, type = list(asymm = 3:5)) :
+ binary variable(s) 1, 2 treated as interval scaled
+> ## better leave away the constant variable: it has no effect:
+> stopifnot(identical(c(d1), c(daisy(d5[,-4], type = list(asymm = 1:4)))))
+>
+> ###---- Trivial "binary only" matrices (not data frames) did fail:
+>
+> x <- matrix(0, 2, 2)
+> dimnames(x)[[2]] <- c("A", "B")## colnames<- is missing in S+
+> daisy(x, type = list(symm= "B", asymm="A"))
+Dissimilarities :
+ 1
+2 0
+
+Metric : mixed ; Types = A, S
+Number of objects : 2
+Warning message:
+In daisy(x, type = list(symm = "B", asymm = "A")) :
+ at least one binary variable has not 2 different levels.
+> daisy(x, type = list(symm= "B"))# 0 too
+Dissimilarities :
+ 1
+2 0
+
+Metric : mixed ; Types = I, S
+Number of objects : 2
+Warning message:
+In daisy(x, type = list(symm = "B")) :
+ at least one binary variable has not 2 different levels.
+>
+> x2 <- x; x2[2,2] <- 1
+> daisy(x2, type= list(symm = "B"))# |-> 0.5 (gives 1 in S+)
+Dissimilarities :
+ 1
+2 0.5
+
+Metric : mixed ; Types = I, S
+Number of objects : 2
+> daisy(x2, type= list(symm = "B", asymm="A"))# 1
+Dissimilarities :
+ 1
+2 1
+
+Metric : mixed ; Types = A, S
+Number of objects : 2
+Warning message:
+In daisy(x2, type = list(symm = "B", asymm = "A")) :
+ at least one binary variable has not 2 different levels.
+>
+> x3 <- x; x3[] <- diag(2)
+> daisy(x3) # warning: both as interval scaled -> sqrt(2)
+Dissimilarities :
+ 1
+2 1.414214
+
+Metric : euclidean
+Number of objects : 2
+> daisy(x3, type= list(symm="B", asymm="A"))# 1
+Dissimilarities :
+ 1
+2 1
+
+Metric : mixed ; Types = A, S
+Number of objects : 2
+> daisy(x3, type= list(symm =c("B","A"))) # 1, S+: sqrt(2)
+Dissimilarities :
+ 1
+2 1
+
+Metric : mixed ; Types = S, S
+Number of objects : 2
+> daisy(x3, type= list(asymm=c("B","A"))) # 1, S+ : sqrt(2)
+Dissimilarities :
+ 1
+2 1
+
+Metric : mixed ; Types = A, A
+Number of objects : 2
+>
+> x4 <- rbind(x3, 1)
+> daisy(x4, type= list(symm="B", asymm="A"))# 1 0.5 0.5
+Dissimilarities :
+ 1 2
+2 1.0
+3 0.5 0.5
+
+Metric : mixed ; Types = A, S
+Number of objects : 3
+> daisy(x4, type= list(symm=c("B","A"))) # dito; S+ : 1.41 1 1
+Dissimilarities :
+ 1 2
+2 1.0
+3 0.5 0.5
+
+Metric : mixed ; Types = S, S
+Number of objects : 3
+> daisy(x4, type= list(asymm=c("A","B"))) # dito, dito
+Dissimilarities :
+ 1 2
+2 1.0
+3 0.5 0.5
+
+Metric : mixed ; Types = A, A
+Number of objects : 3
+>
+>
+>
+> ## ----------- example(daisy) -----------------------
+>
+> data(flower)
+> data(agriculture)
+>
+> ## Example 1 in ref:
+> ## Dissimilarities using Euclidean metric and without standardization
+> (d.agr <- daisy(agriculture, metric = "euclidean", stand = FALSE))
+Dissimilarities :
+ B DK D GR E F IRL
+DK 5.408327
+D 2.061553 3.405877
+GR 22.339651 22.570113 22.661200
+E 9.818350 11.182576 10.394710 12.567418
+F 3.448188 3.512834 2.657066 20.100995 8.060397
+IRL 12.747549 13.306014 13.080138 9.604166 3.140064 10.564563
+I 5.803447 5.470832 5.423099 17.383325 5.727128 2.773085 7.920859
+L 4.275512 2.220360 2.300000 24.035391 12.121056 4.060788 14.569145
+NL 1.649242 5.096077 2.435159 20.752349 8.280097 2.202272 11.150785
+P 17.236299 17.864490 17.664088 5.162364 7.430343 15.164432 4.601087
+UK 2.828427 8.052950 4.850773 21.485344 8.984431 5.303772 12.103718
+ I L NL P
+DK
+D
+GR
+E
+F
+IRL
+I
+L 6.660330
+NL 4.204759 4.669047
+P 12.515990 19.168985 15.670673
+UK 6.723095 7.102112 3.124100 16.323296
+
+Metric : euclidean
+Number of objects : 12
+> (d.agr2 <- daisy(agriculture, metric = "manhattan"))
+Dissimilarities :
+ B DK D GR E F IRL I L NL P
+DK 7.5
+D 2.7 4.8
+GR 30.4 31.9 31.5
+E 13.6 15.1 14.7 16.8
+F 4.3 3.8 3.4 28.1 11.3
+IRL 17.2 18.7 18.3 13.2 3.6 14.9
+I 6.0 7.5 7.1 24.4 7.6 3.7 11.2
+L 5.0 2.5 2.3 33.8 17.0 5.7 20.6 9.4
+NL 2.0 6.3 3.1 28.4 11.6 3.1 15.2 4.4 5.4
+P 23.7 25.2 24.8 6.7 10.1 21.4 6.5 17.7 27.1 21.7
+UK 3.2 10.7 5.9 28.0 11.2 7.5 14.8 8.8 8.2 4.4 21.3
+
+Metric : manhattan
+Number of objects : 12
+>
+>
+> ## Example 2 in ref
+> (dfl0 <- daisy(flower))
+Dissimilarities :
+ 1 2 3 4 5 6 7
+2 0.8875408
+3 0.5272467 0.5147059
+4 0.3517974 0.5504493 0.5651552
+5 0.4115605 0.6226307 0.3726307 0.6383578
+6 0.2269199 0.6606209 0.3003268 0.4189951 0.3443627
+7 0.2876225 0.5999183 0.4896242 0.3435866 0.4197712 0.1892974
+8 0.4234069 0.4641340 0.6038399 0.2960376 0.4673203 0.5714869 0.4107843
+9 0.5808824 0.4316585 0.4463644 0.8076797 0.3306781 0.5136846 0.5890931
+10 0.6094363 0.4531046 0.4678105 0.5570670 0.3812908 0.4119281 0.5865196
+11 0.3278595 0.7096814 0.5993873 0.6518791 0.3864788 0.4828840 0.5652369
+12 0.4267565 0.5857843 0.6004902 0.5132761 0.5000817 0.5248366 0.6391340
+13 0.5196487 0.5248366 0.5395425 0.7464461 0.2919118 0.4524510 0.5278595
+14 0.2926062 0.5949346 0.6096405 0.3680147 0.5203431 0.3656863 0.5049837
+15 0.6221814 0.3903595 0.5300654 0.5531454 0.4602124 0.5091503 0.3345588
+16 0.6935866 0.3575163 0.6222222 0.3417892 0.7301471 0.5107843 0.4353758
+17 0.7765114 0.1904412 0.5801471 0.4247141 0.6880719 0.5937092 0.5183007
+18 0.4610294 0.4515114 0.7162173 0.4378268 0.4755310 0.6438317 0.4692402
+ 8 9 10 11 12 13 14
+2
+3
+4
+5
+6
+7
+8
+9 0.6366422
+10 0.6639706 0.4256127
+11 0.4955474 0.4308007 0.3948121
+12 0.4216503 0.4194036 0.3812092 0.2636029
+13 0.5754085 0.2181781 0.3643791 0.3445670 0.2331699
+14 0.4558007 0.4396650 0.3609477 0.2838644 0.1591503 0.3784314
+15 0.4512255 0.2545343 0.4210784 0.4806781 0.4295752 0.3183007 0.4351307
+16 0.6378268 0.6494690 0.3488562 0.7436683 0.6050654 0.5882353 0.4598039
+17 0.4707516 0.6073938 0.3067810 0.7015931 0.5629902 0.5461601 0.5427288
+18 0.1417892 0.5198529 0.8057598 0.5359477 0.5495507 0.5733252 0.5698121
+ 15 16 17
+2
+3
+4
+5
+6
+7
+8
+9
+10
+11
+12
+13
+14
+15
+16 0.3949346
+17 0.3528595 0.1670752
+18 0.5096814 0.7796160 0.6125408
+
+Metric : mixed ; Types = N, N, N, N, O, O, I, I
+Number of objects : 18
+> stopifnot(identical(c(dfl0),
++ c(daisy(flower, type = list(symm = 1)))) &&
++ identical(c(dfl0),
++ c(daisy(flower, type = list(symm = 2)))) &&
++ identical(c(dfl0),
++ c(daisy(flower, type = list(symm = 3)))) &&
++ identical(c(dfl0),
++ c(daisy(flower, type = list(symm = c(1,3)))))
++ )
+>
+> (dfl1 <- daisy(flower, type = list(asymm = 3)))
+Dissimilarities :
+ 1 2 3 4 5 6 7
+2 0.8875408
+3 0.5272467 0.5882353
+4 0.3517974 0.5504493 0.5651552
+5 0.4115605 0.7115780 0.4258637 0.6383578
+6 0.2269199 0.7549953 0.3432306 0.4189951 0.3935574
+7 0.2876225 0.6856209 0.5595705 0.3435866 0.4797386 0.2163399
+8 0.4234069 0.4641340 0.6038399 0.2960376 0.4673203 0.5714869 0.4107843
+9 0.5808824 0.4933240 0.5101307 0.8076797 0.3779178 0.5870682 0.6732493
+10 0.6094363 0.5178338 0.5346405 0.5570670 0.4357610 0.4707750 0.6703081
+11 0.3278595 0.7096814 0.5993873 0.6518791 0.3864788 0.4828840 0.5652369
+12 0.4267565 0.5857843 0.6004902 0.5132761 0.5000817 0.5248366 0.6391340
+13 0.5196487 0.5998133 0.6166200 0.7464461 0.3336134 0.5170868 0.6032680
+14 0.2926062 0.5949346 0.6096405 0.3680147 0.5203431 0.3656863 0.5049837
+15 0.6221814 0.4461251 0.6057890 0.5531454 0.5259570 0.5818861 0.3823529
+16 0.6935866 0.4085901 0.7111111 0.3417892 0.8344538 0.5837535 0.4975724
+17 0.7765114 0.2176471 0.6630252 0.4247141 0.7863679 0.6785247 0.5923436
+18 0.4610294 0.4515114 0.7162173 0.4378268 0.4755310 0.6438317 0.4692402
+ 8 9 10 11 12 13 14
+2
+3
+4
+5
+6
+7
+8
+9 0.6366422
+10 0.6639706 0.4864146
+11 0.4955474 0.4308007 0.3948121
+12 0.4216503 0.4194036 0.3812092 0.2636029
+13 0.5754085 0.2493464 0.4164332 0.3445670 0.2331699
+14 0.4558007 0.4396650 0.3609477 0.2838644 0.1591503 0.3784314
+15 0.4512255 0.2908964 0.4812325 0.4806781 0.4295752 0.3637722 0.4351307
+16 0.6378268 0.7422502 0.3986928 0.7436683 0.6050654 0.6722689 0.4598039
+17 0.4707516 0.6941643 0.3506069 0.7015931 0.5629902 0.6241830 0.5427288
+18 0.1417892 0.5198529 0.8057598 0.5359477 0.5495507 0.5733252 0.5698121
+ 15 16 17
+2
+3
+4
+5
+6
+7
+8
+9
+10
+11
+12
+13
+14
+15
+16 0.4513539
+17 0.4032680 0.1909430
+18 0.5096814 0.7796160 0.6125408
+
+Metric : mixed ; Types = N, N, A, N, O, O, I, I
+Number of objects : 18
+> (dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ordratio = 7)))
+Dissimilarities :
+ 1 2 3 4 5 6 7
+2 0.9007353
+3 0.6176471 0.5882353
+4 0.4226891 0.5455882 0.6403361
+5 0.4806723 0.7369748 0.5264706 0.7605042
+6 0.2823529 0.7470588 0.3911765 0.4764706 0.4980392
+7 0.3310924 0.6983193 0.6676471 0.4109244 0.5745098 0.2764706
+8 0.5100840 0.4544118 0.6789916 0.3327731 0.5705882 0.6563025 0.4932773
+9 0.5808824 0.5084034 0.5252101 0.8257353 0.3882353 0.6100840 0.6756303
+10 0.6323529 0.5067227 0.5235294 0.5522059 0.4722689 0.4739496 0.6941176
+11 0.3389706 0.7117647 0.6014706 0.6588235 0.4066176 0.4919118 0.5742647
+12 0.4441176 0.5816176 0.5963235 0.5139706 0.5264706 0.5220588 0.6544118
+13 0.5286765 0.6252101 0.6420168 0.7735294 0.3336134 0.5504202 0.6159664
+14 0.3044118 0.5963235 0.6110294 0.3742647 0.5411765 0.3573529 0.5147059
+15 0.6242647 0.4588235 0.6184874 0.5691176 0.5386555 0.6025210 0.3823529
+16 0.6845588 0.3831933 0.6857143 0.3147059 0.8344538 0.5504202 0.4848739
+17 0.7897059 0.2176471 0.6630252 0.4198529 0.8117647 0.6705882 0.6050420
+18 0.5268908 0.4647059 0.8336134 0.5210084 0.5537815 0.7588235 0.5386555
+ 8 9 10 11 12 13 14
+2
+3
+4
+5
+6
+7
+8
+9 0.6595588
+10 0.6639706 0.5126050
+11 0.5073529 0.4419118 0.4066176
+12 0.4272059 0.4367647 0.3867647 0.2698529
+13 0.6073529 0.2596639 0.4529412 0.3647059 0.2595588
+14 0.4669118 0.4514706 0.3720588 0.2845588 0.1647059 0.3992647
+15 0.4720588 0.2932773 0.5050420 0.4897059 0.4448529 0.3764706 0.4448529
+16 0.6058824 0.7319328 0.3621849 0.7235294 0.5786765 0.6722689 0.4389706
+17 0.4610294 0.7092437 0.3394958 0.7036765 0.5588235 0.6495798 0.5441176
+18 0.1882353 0.5198529 0.8286765 0.5470588 0.5669118 0.5823529 0.5816176
+ 15 16 17
+2
+3
+4
+5
+6
+7
+8
+9
+10
+11
+12
+13
+14
+15
+16 0.4386555
+17 0.4159664 0.1655462
+18 0.5117647 0.7705882 0.6257353
+
+Metric : mixed ; Types = A, N, A, N, O, O, T, I
+Number of objects : 18
+> (dfl3 <- daisy(flower, type = list(asymm = 1:3)))
+Dissimilarities :
+ 1 2 3 4 5 6 7
+2 0.8875408
+3 0.6025677 0.5882353
+4 0.4020542 0.6290850 0.6458917
+5 0.4703548 0.7115780 0.4968410 0.7295518
+6 0.2593371 0.7549953 0.4004357 0.4788515 0.4591503
+7 0.3287115 0.7998911 0.6528322 0.4581155 0.5596950 0.2523965
+8 0.4838936 0.5304388 0.6901027 0.3947168 0.5340803 0.6531279 0.5477124
+9 0.5808824 0.4933240 0.5101307 0.8076797 0.3779178 0.5870682 0.6732493
+10 0.6094363 0.5178338 0.5346405 0.5570670 0.4357610 0.4707750 0.6703081
+11 0.3278595 0.7096814 0.5993873 0.6518791 0.3864788 0.4828840 0.5652369
+12 0.4267565 0.5857843 0.6004902 0.5132761 0.5000817 0.5248366 0.6391340
+13 0.5196487 0.5998133 0.6166200 0.7464461 0.3336134 0.5170868 0.6032680
+14 0.2926062 0.5949346 0.6096405 0.3680147 0.5203431 0.3656863 0.5049837
+15 0.6221814 0.5204793 0.6057890 0.6321662 0.5259570 0.5818861 0.4460784
+16 0.6935866 0.4766885 0.7111111 0.3906162 0.8344538 0.5837535 0.5805011
+17 0.7765114 0.2539216 0.6630252 0.4853875 0.7863679 0.6785247 0.6910675
+18 0.5268908 0.5160131 0.8185341 0.5837691 0.5434641 0.7358077 0.6256536
+ 8 9 10 11 12 13 14
+2
+3
+4
+5
+6
+7
+8
+9 0.6366422
+10 0.6639706 0.4864146
+11 0.4955474 0.4308007 0.3948121
+12 0.4216503 0.4194036 0.3812092 0.2636029
+13 0.5754085 0.2493464 0.4164332 0.3445670 0.2331699
+14 0.4558007 0.4396650 0.3609477 0.2838644 0.1591503 0.3784314
+15 0.5156863 0.2908964 0.4812325 0.4806781 0.4295752 0.3637722 0.4351307
+16 0.7289449 0.7422502 0.3986928 0.7436683 0.6050654 0.6722689 0.4598039
+17 0.5380019 0.6941643 0.3506069 0.7015931 0.5629902 0.6241830 0.5427288
+18 0.1890523 0.5198529 0.8057598 0.5359477 0.5495507 0.5733252 0.5698121
+ 15 16 17
+2
+3
+4
+5
+6
+7
+8
+9
+10
+11
+12
+13
+14
+15
+16 0.5265795
+17 0.4704793 0.2227669
+18 0.5824930 0.8909897 0.7000467
+
+Metric : mixed ; Types = A, A, A, N, O, O, I, I
+Number of objects : 18
+>
+> ## --- animals
+> data(animals)
+> d0 <- daisy(animals)
+Warning message:
+In daisy(animals) :
+ binary variable(s) 1, 2, 3, 4, 5, 6 treated as interval scaled
+>
+> d1 <- daisy(animals - 1, type=list(asymm=c(2,4)))
+Warning message:
+In daisy(animals - 1, type = list(asymm = c(2, 4))) :
+ binary variable(s) 1, 3, 5, 6 treated as interval scaled
+> (d2 <- daisy(animals - 1, type=list(symm = c(1,3,5,6), asymm=c(2,4))))
+Dissimilarities :
+ ant bee cat cpl chi cow duc
+bee 0.4000000
+cat 1.0000000 0.8000000
+cpl 0.5000000 0.4000000 0.5000000
+chi 0.8000000 0.6666667 0.4000000 0.8000000
+cow 0.7500000 0.6000000 0.2500000 0.7500000 0.2000000
+duc 0.6000000 0.6000000 0.6000000 1.0000000 0.5000000 0.4000000
+eag 0.8333333 0.8333333 0.5000000 0.8333333 0.5000000 0.6666667 0.3333333
+ele 0.6000000 0.8333333 0.6000000 1.0000000 0.2000000 0.4000000 0.3333333
+fly 0.4000000 0.4000000 0.8000000 0.4000000 1.0000000 1.0000000 0.6000000
+fro 0.5000000 0.8000000 0.7500000 0.7500000 0.5000000 0.7500000 0.6000000
+her 0.2500000 0.6000000 0.7500000 0.7500000 0.6000000 0.5000000 0.4000000
+lio 0.7500000 0.6000000 0.2500000 0.7500000 0.0000000 0.0000000 0.4000000
+liz 0.5000000 0.8000000 0.5000000 0.5000000 0.8000000 0.7500000 0.6000000
+lob 0.0000000 0.5000000 1.0000000 0.3333333 1.0000000 1.0000000 0.7500000
+man 0.8000000 0.6666667 0.4000000 0.8000000 0.0000000 0.2000000 0.5000000
+rab 0.7500000 0.6000000 0.2500000 0.7500000 0.2000000 0.0000000 0.4000000
+sal 0.3333333 0.7500000 0.6666667 0.6666667 0.7500000 0.6666667 0.5000000
+spi 0.5000000 0.4000000 0.5000000 0.0000000 0.7500000 0.7500000 1.0000000
+wha 0.6000000 0.8333333 0.6000000 1.0000000 0.2000000 0.4000000 0.3333333
+ eag ele fly fro her lio liz
+bee
+cat
+cpl
+chi
+cow
+duc
+eag
+ele 0.3333333
+fly 0.5000000 0.8333333
+fro 0.4000000 0.2500000 0.6000000
+her 0.6666667 0.4000000 0.6000000 0.2500000
+lio 0.6000000 0.2500000 1.0000000 0.6666667 0.5000000
+liz 0.5000000 0.6000000 0.4000000 0.2500000 0.2500000 0.7500000
+lob 0.8000000 0.7500000 0.2500000 0.5000000 0.3333333 1.0000000 0.3333333
+man 0.5000000 0.2000000 1.0000000 0.5000000 0.6000000 0.0000000 0.8000000
+rab 0.6666667 0.4000000 1.0000000 0.7500000 0.5000000 0.0000000 0.7500000
+sal 0.6000000 0.5000000 0.5000000 0.2500000 0.0000000 0.6666667 0.0000000
+spi 0.8000000 1.0000000 0.4000000 0.6666667 0.7500000 0.7500000 0.5000000
+wha 0.3333333 0.0000000 0.8333333 0.2500000 0.4000000 0.2500000 0.6000000
+ lob man rab sal spi
+bee
+cat
+cpl
+chi
+cow
+duc
+eag
+ele
+fly
+fro
+her
+lio
+liz
+lob
+man 1.0000000
+rab 1.0000000 0.2000000
+sal 0.3333333 0.7500000 0.6666667
+spi 0.3333333 0.7500000 0.7500000 0.6666667
+wha 0.7500000 0.2000000 0.4000000 0.5000000 1.0000000
+
+Metric : mixed ; Types = S, A, S, A, S, S
+Number of objects : 20
+> stopifnot(c(d1) == c(d2))
+>
+> d3 <- daisy(2 - animals, type=list(asymm=c(2,4)))
+Warning message:
+In daisy(2 - animals, type = list(asymm = c(2, 4))) :
+ binary variable(s) 1, 3, 5, 6 treated as interval scaled
+> (d4 <- daisy(2 - animals, type=list(symm = c(1,3,5,6), asymm=c(2,4))))
+Dissimilarities :
+ ant bee cat cpl chi cow duc
+bee 0.3333333
+cat 0.6666667 0.6666667
+cpl 0.3333333 0.3333333 0.3333333
+chi 0.6666667 0.6666667 0.3333333 0.6666667
+cow 0.5000000 0.5000000 0.1666667 0.5000000 0.1666667
+duc 0.5000000 0.6000000 0.5000000 0.8333333 0.5000000 0.3333333
+eag 0.8333333 1.0000000 0.5000000 0.8333333 0.6000000 0.6666667 0.4000000
+ele 0.5000000 0.8333333 0.5000000 0.8333333 0.2000000 0.3333333 0.3333333
+fly 0.3333333 0.4000000 0.6666667 0.3333333 1.0000000 0.8333333 0.6000000
+fro 0.4000000 0.8000000 0.6000000 0.6000000 0.5000000 0.6000000 0.6000000
+her 0.1666667 0.5000000 0.5000000 0.5000000 0.5000000 0.3333333 0.3333333
+lio 0.6000000 0.6000000 0.2000000 0.6000000 0.0000000 0.0000000 0.4000000
+liz 0.3333333 0.6666667 0.3333333 0.3333333 0.6666667 0.5000000 0.5000000
+lob 0.0000000 0.4000000 0.6000000 0.2000000 0.8000000 0.6000000 0.6000000
+man 0.6666667 0.6666667 0.3333333 0.6666667 0.0000000 0.1666667 0.5000000
+rab 0.5000000 0.5000000 0.1666667 0.5000000 0.1666667 0.0000000 0.3333333
+sal 0.2000000 0.6000000 0.4000000 0.4000000 0.6000000 0.4000000 0.4000000
+spi 0.4000000 0.4000000 0.4000000 0.0000000 0.6000000 0.6000000 1.0000000
+wha 0.5000000 0.8333333 0.5000000 0.8333333 0.2000000 0.3333333 0.3333333
+ eag ele fly fro her lio liz
+bee
+cat
+cpl
+chi
+cow
+duc
+eag
+ele 0.4000000
+fly 0.6000000 0.8333333
+fro 0.5000000 0.2500000 0.6000000
+her 0.6666667 0.3333333 0.5000000 0.2000000
+lio 0.6000000 0.2000000 1.0000000 0.5000000 0.4000000
+liz 0.5000000 0.5000000 0.3333333 0.2000000 0.1666667 0.6000000
+lob 0.8000000 0.6000000 0.2000000 0.4000000 0.2000000 0.7500000 0.2000000
+man 0.6000000 0.2000000 1.0000000 0.5000000 0.5000000 0.0000000 0.6666667
+rab 0.6666667 0.3333333 0.8333333 0.6000000 0.3333333 0.0000000 0.5000000
+sal 0.6000000 0.4000000 0.4000000 0.2000000 0.0000000 0.5000000 0.0000000
+spi 0.8000000 0.8000000 0.4000000 0.5000000 0.6000000 0.6000000 0.4000000
+wha 0.4000000 0.0000000 0.8333333 0.2500000 0.3333333 0.2000000 0.5000000
+ lob man rab sal spi
+bee
+cat
+cpl
+chi
+cow
+duc
+eag
+ele
+fly
+fro
+her
+lio
+liz
+lob
+man 0.8000000
+rab 0.6000000 0.1666667
+sal 0.2000000 0.6000000 0.4000000
+spi 0.2500000 0.6000000 0.6000000 0.5000000
+wha 0.6000000 0.2000000 0.3333333 0.4000000 0.8000000
+
+Metric : mixed ; Types = S, A, S, A, S, S
+Number of objects : 20
+> stopifnot(c(d3) == c(d4))
+>
+> pairs(cbind(d0,d2,d4),
++ main = "Animals -- symmetric and asymm. dissimilarities")
+>
diff --git a/win32/deps/library/cluster/tests/diana-boots.R b/win32/deps/library/cluster/tests/diana-boots.R
new file mode 100644
index 0000000..2f96742
--- /dev/null
+++ b/win32/deps/library/cluster/tests/diana-boots.R
@@ -0,0 +1,31 @@
+library(cluster)
+
+## Kind of a bootstrap -- calling many diana()s
+dianaBoot <- function(data, B = 500, frac.sub = c(0.7, min = 0.2),
+ digits = 4)
+{
+ stopifnot((n <- nrow(data)) >= 10, B >= 10, frac.sub > 0,
+ (m <- round(frac.sub[["min"]]*n)) >= 2,
+ (mm <- round(frac.sub[1]*n)) > m)
+ for(b in 1:B) {
+ d.r <- data[sample(n, max(m, min(n, rpois(1, lambda = mm)))) ,]
+ dia. <- diana(d.r, keep.diss=FALSE, keep.data=FALSE)
+ print(dia.[1:3], digits = digits)
+ }
+}
+
+.p0 <- proc.time()
+data(ruspini)
+set.seed(134)
+dianaBoot(ruspini)
+cat('Time elapsed: ', (.p1 <- proc.time()) - .p0,'\n')
+
+data(agriculture)
+set.seed(707)
+dianaBoot(agriculture)
+cat('Time elapsed: ', (.p2 <- proc.time()) - .p1,'\n')
+
+data(swiss); swiss.x <- as.matrix(swiss[,-1])
+set.seed(312)
+dianaBoot(swiss.x)
+cat('Time elapsed: ', (.p3 <- proc.time()) - .p2,'\n')
diff --git a/win32/deps/library/cluster/tests/diana-ex.R b/win32/deps/library/cluster/tests/diana-ex.R
new file mode 100644
index 0000000..66ac4c7
--- /dev/null
+++ b/win32/deps/library/cluster/tests/diana-ex.R
@@ -0,0 +1,31 @@
+library(cluster)
+options(digits = 6)
+data(votes.repub)
+di.votes <- daisy(votes.repub)
+
+.p00 <- proc.time()
+summary(diana(votes.repub, metric = "manhattan", stand = TRUE))
+summary(diana(di.votes, keep.diss = FALSE))
+cat('Time elapsed: ', proc.time() - .p00,'\n')
+
+data(agriculture)
+data(ruspini)
+
+.p0 <- proc.time()
+dia.agr <- diana(agriculture)
+drusp0 <- diana(ruspini, keep.diss=FALSE, keep.data=FALSE)
+drusp1 <- diana(ruspini, metric = "manhattan")
+cat('Time elapsed: ', proc.time() - .p0,'\n')
+
+summary(dia.agr)
+summary(drusp0)
+summary(drusp1)
+str (drusp1)
+
+## From system.file("scripts/ch11.R", package = "MASS")
+data(swiss)
+swiss.x <- as.matrix(swiss[,-1])
+.p1 <- proc.time()
+dCH <- diana(swiss.x)
+cat('Time elapsed: ', proc.time() - .p1,'\n')
+str(as.dendrogram(as.hclust(dCH)))# keep back-compatible
diff --git a/win32/deps/library/cluster/tests/diana-ex.Rout.save b/win32/deps/library/cluster/tests/diana-ex.Rout.save
new file mode 100644
index 0000000..efb4041
--- /dev/null
+++ b/win32/deps/library/cluster/tests/diana-ex.Rout.save
@@ -0,0 +1,545 @@
+
+R version 2.14.1 RC (2011-12-20 r57943)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(cluster)
+> options(digits = 6)
+> data(votes.repub)
+> di.votes <- daisy(votes.repub)
+>
+> .p00 <- proc.time()
+> summary(diana(votes.repub, metric = "manhattan", stand = TRUE))
+Merge:
+ [,1] [,2]
+ [1,] -7 -32
+ [2,] -13 -35
+ [3,] -12 -50
+ [4,] 1 -30
+ [5,] -26 -28
+ [6,] -5 -37
+ [7,] -22 -38
+ [8,] -21 -39
+ [9,] -16 -27
+[10,] 4 2
+[11,] -25 -48
+[12,] -42 -46
+[13,] -6 -14
+[14,] -34 -41
+[15,] -8 -20
+[16,] 5 -31
+[17,] 10 7
+[18,] -17 -47
+[19,] -3 -44
+[20,] -33 12
+[21,] 15 18
+[22,] 17 -29
+[23,] 22 -49
+[24,] 21 11
+[25,] 23 -15
+[26,] -11 -19
+[27,] 3 9
+[28,] 8 -23
+[29,] 19 16
+[30,] 27 14
+[31,] 6 25
+[32,] -1 -10
+[33,] 31 13
+[34,] 29 -36
+[35,] -2 -45
+[36,] -9 -43
+[37,] 24 20
+[38,] 32 -4
+[39,] -24 -40
+[40,] 38 -18
+[41,] 33 30
+[42,] 34 37
+[43,] 35 26
+[44,] 41 28
+[45,] 40 36
+[46,] 42 44
+[47,] 45 39
+[48,] 43 46
+[49,] 47 48
+Order of objects:
+ [1] Alabama Georgia Arkansas Louisiana Florida
+ [6] Texas Mississippi South Carolina Alaska Vermont
+[11] Hawaii Maine Arizona Utah Montana
+[16] Nevada New Mexico Oklahoma Delaware Maryland
+[21] Kentucky Washington Missouri West Virginia North Carolina
+[26] Tennessee Virginia California Oregon Connecticut
+[31] New York New Jersey Illinois Ohio Michigan
+[36] Pennsylvania New Hampshire Wisconsin Iowa Colorado
+[41] Indiana Idaho Wyoming Kansas Nebraska
+[46] North Dakota South Dakota Massachusetts Rhode Island Minnesota
+Height:
+ [1] 27.36345 33.96925 39.65826 48.53428 31.89965 72.59850 35.69152
+ [8] 167.58020 31.58222 43.84601 24.48796 85.55248 18.39339 25.67631
+[15] 11.49397 17.45552 28.62550 42.54480 16.48510 20.04450 17.87516
+[22] 21.98373 14.21808 33.61071 18.39733 14.75762 56.55675 11.70132
+[29] 27.05887 8.38200 11.36820 13.25237 9.23004 17.83484 12.70819
+[36] 20.66714 21.03997 23.66586 28.60541 15.31703 40.33905 10.46294
+[43] 24.83525 12.80419 26.36292 16.25192 47.25773 12.79160 24.87206
+Divisive coefficient:
+[1] 0.886918
+
+1225 dissimilarities, summarized :
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+ 8.382 25.540 34.510 45.060 56.020 167.600
+Metric : manhattan
+Number of objects : 50
+
+Available components:
+[1] "order" "height" "dc" "merge" "diss" "call"
+[7] "order.lab" "data"
+> summary(diana(di.votes, keep.diss = FALSE))
+Merge:
+ [,1] [,2]
+ [1,] -12 -50
+ [2,] -13 -32
+ [3,] -14 -35
+ [4,] -7 -29
+ [5,] -21 -39
+ [6,] -3 -28
+ [7,] -25 -48
+ [8,] -16 -27
+ [9,] -15 -41
+[10,] 2 -30
+[11,] 6 -26
+[12,] -33 -42
+[13,] 12 -46
+[14,] 1 -44
+[15,] 10 3
+[16,] -22 -38
+[17,] -11 -19
+[18,] -5 -47
+[19,] -17 -20
+[20,] -2 -45
+[21,] 14 -31
+[22,] -37 -49
+[23,] 9 8
+[24,] 4 15
+[25,] -8 19
+[26,] -6 21
+[27,] 5 -23
+[28,] 24 16
+[29,] 26 -36
+[30,] 11 29
+[31,] -1 -10
+[32,] 28 22
+[33,] 23 -34
+[34,] 7 13
+[35,] -4 -9
+[36,] 20 17
+[37,] -24 -40
+[38,] 31 -43
+[39,] 32 33
+[40,] 25 34
+[41,] 30 18
+[42,] 35 -18
+[43,] 38 42
+[44,] 39 27
+[45,] 41 40
+[46,] 36 44
+[47,] 43 37
+[48,] 46 45
+[49,] 47 48
+Order of objects:
+ [1] Alabama Georgia Texas Arkansas Florida
+ [6] Louisiana Mississippi South Carolina Alaska Vermont
+[11] Hawaii Maine Connecticut New Hampshire Illinois
+[16] New York New Jersey Indiana Ohio Michigan
+[21] Pennsylvania Oregon Wisconsin Iowa South Dakota
+[26] Kansas Nebraska North Dakota Massachusetts Rhode Island
+[31] Minnesota Arizona Nevada Montana Colorado
+[36] Idaho Wyoming Utah New Mexico Oklahoma
+[41] California Washington Delaware Kentucky Maryland
+[46] Missouri West Virginia North Carolina Tennessee Virginia
+Height:
+ [1] 48.2397 63.1862 72.9221 56.1363 72.9221 116.7048 63.0951 281.9508
+ [9] 33.8330 58.0384 32.7611 106.7448 20.5216 39.1728 19.8436 27.0243
+[17] 31.4966 20.2258 47.1690 31.6595 49.2428 36.7667 64.4821 26.1547
+[25] 37.4564 25.9221 50.7201 77.1184 22.6334 44.4594 178.4119 23.4206
+[33] 27.8273 48.0483 43.7055 17.1992 31.1988 34.0510 48.0483 70.4868
+[41] 33.2328 81.0764 43.3829 33.4744 66.7591 25.3953 54.7306 29.5099
+[49] 30.1541
+Divisive coefficient:
+[1] 0.878225
+
+Available components:
+[1] "order" "height" "dc" "merge" "diss" "call"
+[7] "order.lab"
+> cat('Time elapsed: ', proc.time() - .p00,'\n')
+Time elapsed: 0.014 0.001 0.015 0 0
+>
+> data(agriculture)
+> data(ruspini)
+>
+> .p0 <- proc.time()
+> dia.agr <- diana(agriculture)
+> drusp0 <- diana(ruspini, keep.diss=FALSE, keep.data=FALSE)
+> drusp1 <- diana(ruspini, metric = "manhattan")
+> cat('Time elapsed: ', proc.time() - .p0,'\n')
+Time elapsed: 0.006 0.001 0.006 0 0
+>
+> summary(dia.agr)
+Merge:
+ [,1] [,2]
+ [1,] -1 -10
+ [2,] -2 -9
+ [3,] 1 -3
+ [4,] -6 -8
+ [5,] -5 -7
+ [6,] 3 -12
+ [7,] -4 -11
+ [8,] 6 4
+ [9,] 8 2
+[10,] 7 5
+[11,] 9 10
+Order of objects:
+ [1] B NL D UK F I DK L GR P E IRL
+Height:
+ [1] 1.64924 2.43516 4.85077 6.72309 2.77308 8.05295 2.22036 24.03539
+ [9] 5.16236 12.56742 3.14006
+Divisive coefficient:
+[1] 0.871106
+
+66 dissimilarities, summarized :
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+ 1.649 4.357 7.987 9.594 13.250 24.040
+Metric : euclidean
+Number of objects : 12
+
+Available components:
+[1] "order" "height" "dc" "merge" "diss" "call"
+[7] "order.lab" "data"
+> summary(drusp0)
+Merge:
+ [,1] [,2]
+ [1,] -18 -19
+ [2,] -55 -56
+ [3,] -27 -28
+ [4,] -49 -51
+ [5,] -33 -34
+ [6,] -23 -24
+ [7,] -59 -60
+ [8,] -29 -30
+ [9,] -67 -69
+[10,] -36 -39
+[11,] -32 -35
+[12,] -50 -54
+[13,] -37 -38
+[14,] -70 -71
+[15,] -64 -68
+[16,] -62 -66
+[17,] -12 -13
+[18,] -16 1
+[19,] -9 -10
+[20,] -42 -43
+[21,] -15 -17
+[22,] -47 -48
+[23,] 12 -52
+[24,] -21 -22
+[25,] 9 14
+[26,] 2 -57
+[27,] -73 -74
+[28,] 6 -25
+[29,] -26 11
+[30,] 4 -53
+[31,] 3 8
+[32,] -11 17
+[33,] -6 -8
+[34,] -2 -3
+[35,] 10 -40
+[36,] -14 21
+[37,] -65 25
+[38,] -4 33
+[39,] 36 18
+[40,] 29 5
+[41,] 26 7
+[42,] -1 34
+[43,] 24 28
+[44,] 16 -63
+[45,] -46 22
+[46,] -31 35
+[47,] 27 -75
+[48,] 37 -72
+[49,] 43 31
+[50,] 30 23
+[51,] 13 20
+[52,] 15 48
+[53,] 32 -20
+[54,] 41 -58
+[55,] 42 -5
+[56,] 40 46
+[57,] -44 -45
+[58,] 19 39
+[59,] 38 -7
+[60,] 51 -41
+[61,] -61 44
+[62,] 50 54
+[63,] 52 47
+[64,] 61 63
+[65,] 49 56
+[66,] 59 53
+[67,] 55 58
+[68,] 57 62
+[69,] 65 60
+[70,] 67 66
+[71,] 68 45
+[72,] 69 71
+[73,] 70 64
+[74,] 73 72
+Order of objects:
+ [1] 1 2 3 5 9 10 14 15 17 16 18 19 4 6 8 7 11 12 13 20 61 62 66 63 64
+[26] 68 65 67 69 70 71 72 73 74 75 21 22 23 24 25 27 28 29 30 26 32 35 33 34 31
+[51] 36 39 40 37 38 42 43 41 44 45 49 51 53 50 54 52 55 56 57 59 60 58 46 47 48
+Height:
+ [1] 10.04988 6.40312 16.12452 29.12044 4.12311 17.02939 8.48528
+ [8] 4.24264 9.21954 4.12311 1.41421 40.24922 8.94427 6.32456
+[15] 19.02630 28.84441 6.32456 4.12311 14.14214 102.07840 21.40093
+[22] 4.12311 10.81665 27.07397 3.60555 13.60147 8.54400 2.82843
+[29] 5.09902 3.60555 12.80625 22.80351 5.65685 12.36932 154.49595
+[36] 4.47214 10.77033 2.23607 5.83095 13.03840 2.00000 6.32456
+[43] 2.82843 28.16026 6.08276 3.00000 9.43398 2.23607 16.27882
+[50] 11.04536 3.00000 6.70820 36.61967 3.60555 13.34166 4.24264
+[57] 20.02498 94.57801 17.02939 35.35534 2.23607 6.32456 13.15295
+[64] 3.16228 4.47214 22.20360 2.00000 5.38516 9.84886 2.82843
+[71] 15.29706 47.63402 11.00000 4.47214
+Divisive coefficient:
+[1] 0.960566
+
+Available components:
+[1] "order" "height" "dc" "merge" "diss" "call"
+[7] "order.lab"
+> summary(drusp1)
+Merge:
+ [,1] [,2]
+ [1,] -55 -56
+ [2,] -27 -28
+ [3,] -18 -19
+ [4,] -49 -51
+ [5,] -33 -34
+ [6,] -32 -35
+ [7,] -23 -24
+ [8,] -59 -60
+ [9,] -50 -54
+[10,] -29 -30
+[11,] -67 -69
+[12,] -37 -38
+[13,] 11 -71
+[14,] -64 -68
+[15,] -62 -66
+[16,] -12 -13
+[17,] -16 3
+[18,] -9 -10
+[19,] -47 -48
+[20,] 9 -52
+[21,] -42 -43
+[22,] -39 -40
+[23,] -21 -22
+[24,] 13 -70
+[25,] -15 -17
+[26,] 1 -57
+[27,] -26 6
+[28,] 4 -53
+[29,] 7 -25
+[30,] 2 10
+[31,] -11 16
+[32,] -6 -8
+[33,] -31 -36
+[34,] -74 -75
+[35,] -2 -3
+[36,] -46 19
+[37,] -65 24
+[38,] -14 17
+[39,] -4 32
+[40,] 38 25
+[41,] -1 35
+[42,] 26 8
+[43,] 27 5
+[44,] 23 30
+[45,] 28 20
+[46,] 15 -63
+[47,] 43 33
+[48,] 44 29
+[49,] 46 -73
+[50,] 31 -20
+[51,] 42 -58
+[52,] -44 -45
+[53,] 12 22
+[54,] 37 -72
+[55,] 14 54
+[56,] 39 -7
+[57,] 41 -5
+[58,] 53 21
+[59,] 18 40
+[60,] 48 47
+[61,] -61 49
+[62,] 45 51
+[63,] 58 -41
+[64,] 55 34
+[65,] 61 64
+[66,] 57 59
+[67,] 56 50
+[68,] 52 62
+[69,] 60 63
+[70,] 66 67
+[71,] 68 36
+[72,] 69 71
+[73,] 70 65
+[74,] 73 72
+Order of objects:
+ [1] 1 2 3 5 9 10 14 16 18 19 15 17 4 6 8 7 11 12 13 20 61 62 66 63 73
+[26] 64 68 65 67 69 71 70 72 74 75 21 22 27 28 29 30 23 24 25 26 32 35 33 34 31
+[51] 36 37 38 39 40 42 43 41 44 45 49 51 53 50 54 52 55 56 57 59 60 58 46 47 48
+Height:
+ [1] 12 9 22 36 5 24 11 5 2 12 6 54 12 8 20 40 8 5 16
+[20] 142 30 5 15 16 33 5 19 11 4 5 6 18 32 9 187 6 14 2
+[39] 8 4 16 3 8 26 7 3 13 3 16 9 51 5 18 6 24 6 32
+[58] 123 18 48 3 8 15 4 6 31 2 7 13 4 18 67 11 6
+Divisive coefficient:
+[1] 0.958075
+
+2775 dissimilarities, summarized :
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+ 2.00 52.50 97.00 90.95 128.00 187.00
+Metric : manhattan
+Number of objects : 75
+
+Available components:
+[1] "order" "height" "dc" "merge" "diss" "call"
+[7] "order.lab" "data"
+> str (drusp1)
+List of 8
+ $ order : int [1:75] 1 2 3 5 9 10 14 16 18 19 ...
+ $ height : num [1:74] 12 9 22 36 5 24 11 5 2 12 ...
+ $ dc : num 0.958
+ $ merge : int [1:74, 1:2] -55 -27 -18 -49 -33 -32 -23 -59 -50 -29 ...
+ $ diss :Classes 'dissimilarity', 'dist' atomic [1:2775] 11 12 29 13 25 43 33 22 27 39 ...
+ .. ..- attr(*, "Size")= int 75
+ .. ..- attr(*, "Metric")= chr "manhattan"
+ .. ..- attr(*, "Labels")= chr [1:75] "1" "2" "3" "4" ...
+ $ call : language diana(x = ruspini, metric = "manhattan")
+ $ order.lab: chr [1:75] "1" "2" "3" "5" ...
+ $ data : int [1:75, 1:2] 4 5 10 9 13 13 12 15 18 19 ...
+ ..- attr(*, "dimnames")=List of 2
+ .. ..$ : chr [1:75] "1" "2" "3" "4" ...
+ .. ..$ : chr [1:2] "x" "y"
+ - attr(*, "class")= chr [1:2] "diana" "twins"
+>
+> ## From system.file("scripts/ch11.R", package = "MASS")
+> data(swiss)
+> swiss.x <- as.matrix(swiss[,-1])
+> .p1 <- proc.time()
+> dCH <- diana(swiss.x)
+> cat('Time elapsed: ', proc.time() - .p1,'\n')
+Time elapsed: 0.001 0 0.001 0 0
+> str(as.dendrogram(as.hclust(dCH)))# keep back-compatible
+--[dendrogram w/ 2 branches and 47 members at h = 127]
+ |--[dendrogram w/ 2 branches and 31 members at h = 99.2]
+ | |--[dendrogram w/ 2 branches and 11 members at h = 60.9]
+ | | |--[dendrogram w/ 2 branches and 8 members at h = 29.1]
+ | | | |--[dendrogram w/ 2 branches and 5 members at h = 22.7]
+ | | | | |--[dendrogram w/ 2 branches and 4 members at h = 17.4]
+ | | | | | |--[dendrogram w/ 2 branches and 3 members at h = 11.7]
+ | | | | | | |--leaf "Courtelary"
+ | | | | | | `--[dendrogram w/ 2 branches and 2 members at h = 7.48]
+ | | | | | | |--leaf "Le Locle"
+ | | | | | | `--leaf "ValdeTravers"
+ | | | | | `--leaf "La Chauxdfnd"
+ | | | | `--leaf "La Vallee"
+ | | | `--[dendrogram w/ 2 branches and 3 members at h = 19]
+ | | | |--[dendrogram w/ 2 branches and 2 members at h = 11.5]
+ | | | | |--leaf "Lausanne"
+ | | | | `--leaf "Neuchatel"
+ | | | `--leaf "Vevey"
+ | | `--[dendrogram w/ 2 branches and 3 members at h = 56.1]
+ | | |--leaf "V. De Geneve"
+ | | `--[dendrogram w/ 2 branches and 2 members at h = 21.4]
+ | | |--leaf "Rive Droite"
+ | | `--leaf "Rive Gauche"
+ | `--[dendrogram w/ 2 branches and 20 members at h = 48.4]
+ | |--leaf "Moutier"
+ | `--[dendrogram w/ 2 branches and 19 members at h = 44.3]
+ | |--[dendrogram w/ 2 branches and 18 members at h = 39.1]
+ | | |--[dendrogram w/ 2 branches and 6 members at h = 21.9]
+ | | | |--[dendrogram w/ 2 branches and 4 members at h = 12.1]
+ | | | | |--[dendrogram w/ 2 branches and 2 members at h = 10.8]
+ | | | | | |--leaf "Neuveville"
+ | | | | | `--leaf "Boudry"
+ | | | | `--[dendrogram w/ 2 branches and 2 members at h = 4.56]
+ | | | | |--leaf "Grandson"
+ | | | | `--leaf "Val de Ruz"
+ | | | `--[dendrogram w/ 2 branches and 2 members at h = 13.5]
+ | | | |--leaf "Nyone"
+ | | | `--leaf "Yverdon"
+ | | `--[dendrogram w/ 2 branches and 12 members at h = 20.4]
+ | | |--[dendrogram w/ 2 branches and 7 members at h = 15.1]
+ | | | |--[dendrogram w/ 2 branches and 5 members at h = 11.6]
+ | | | | |--[dendrogram w/ 2 branches and 4 members at h = 8.05]
+ | | | | | |--[dendrogram w/ 2 branches and 3 members at h = 6.79]
+ | | | | | | |--[dendrogram w/ 2 branches and 2 members at h = 4.79]
+ | | | | | | | |--leaf "Aigle"
+ | | | | | | | `--leaf "Morges"
+ | | | | | | `--leaf "Rolle"
+ | | | | | `--leaf "Avenches"
+ | | | | `--leaf "Orbe"
+ | | | `--[dendrogram w/ 2 branches and 2 members at h = 6.04]
+ | | | |--leaf "Moudon"
+ | | | `--leaf "Payerne"
+ | | `--[dendrogram w/ 2 branches and 5 members at h = 17.3]
+ | | |--[dendrogram w/ 2 branches and 4 members at h = 11.2]
+ | | | |--[dendrogram w/ 2 branches and 2 members at h = 7.57]
+ | | | | |--leaf "Aubonne"
+ | | | | `--leaf "Oron"
+ | | | `--[dendrogram w/ 2 branches and 2 members at h = 6.35]
+ | | | |--leaf "Cossonay"
+ | | | `--leaf "Lavaux"
+ | | `--leaf "Paysd'enhaut"
+ | `--leaf "Echallens"
+ `--[dendrogram w/ 2 branches and 16 members at h = 56.2]
+ |--[dendrogram w/ 2 branches and 5 members at h = 20.4]
+ | |--[dendrogram w/ 2 branches and 3 members at h = 12.7]
+ | | |--leaf "Delemont"
+ | | `--[dendrogram w/ 2 branches and 2 members at h = 9.4]
+ | | |--leaf "Franches-Mnt"
+ | | `--leaf "Porrentruy"
+ | `--[dendrogram w/ 2 branches and 2 members at h = 13]
+ | |--leaf "Gruyere"
+ | `--leaf "Sarine"
+ `--[dendrogram w/ 2 branches and 11 members at h = 30]
+ |--[dendrogram w/ 2 branches and 5 members at h = 12.9]
+ | |--[dendrogram w/ 2 branches and 4 members at h = 11.9]
+ | | |--[dendrogram w/ 2 branches and 3 members at h = 8.45]
+ | | | |--leaf "Broye"
+ | | | `--[dendrogram w/ 2 branches and 2 members at h = 4.14]
+ | | | |--leaf "Glane"
+ | | | `--leaf "Veveyse"
+ | | `--leaf "Sion"
+ | `--leaf "Monthey"
+ `--[dendrogram w/ 2 branches and 6 members at h = 16]
+ |--[dendrogram w/ 2 branches and 4 members at h = 7.42]
+ | |--[dendrogram w/ 2 branches and 3 members at h = 5.94]
+ | | |--[dendrogram w/ 2 branches and 2 members at h = 2.05]
+ | | | |--leaf "Conthey"
+ | | | `--leaf "Sierre"
+ | | `--leaf "Herens"
+ | `--leaf "Entremont"
+ `--[dendrogram w/ 2 branches and 2 members at h = 5.09]
+ |--leaf "Martigwy"
+ `--leaf "St Maurice"
+>
diff --git a/win32/deps/library/cluster/tests/ellipsoid-ex.R b/win32/deps/library/cluster/tests/ellipsoid-ex.R
new file mode 100644
index 0000000..252fd06
--- /dev/null
+++ b/win32/deps/library/cluster/tests/ellipsoid-ex.R
@@ -0,0 +1,27 @@
+library(cluster)
+
+eh <- ellipsoidhull(cbind(x=1:4, y = 1:4)) #singular
+eh
+
+set.seed(157)
+for(n in 4:10) { ## n=2 and 3 still differ -- platform dependently!
+ cat("n = ",n,"\n")
+ x2 <- rnorm(n)
+ print(ellipsoidhull(cbind(1:n, x2)))
+ print(ellipsoidhull(cbind(1:n, x2, 4*x2 + rnorm(n))))
+}
+
+set.seed(1)
+x <- rt(100, df = 4)
+y <- 100 + 5 * x + rnorm(100)
+ellipsoidhull(cbind(x,y))
+z <- 10 - 8 * x + y + rnorm(100)
+(e3 <- ellipsoidhull(cbind(x,y,z)))
+d3o <- cbind(x,y + rt(100,3), 2 * x^2 + rt(100, 2))
+(e. <- ellipsoidhull(d3o, ret.sq = TRUE))
+stopifnot(all.equal(e.$sqdist,
+ with(e., mahalanobis(d3o, center=loc, cov=cov)),
+ tol = 1e-13))
+d5 <- cbind(d3o, 2*abs(y)^1.5 + rt(100,3), 3*x - sqrt(abs(y)))
+(e5 <- ellipsoidhull(d5, ret.sq = TRUE))
+tail(sort(e5$sqdist)) ## 4 values 5.00039 ... 5.0099
diff --git a/win32/deps/library/cluster/tests/ellipsoid-ex.Rout.save b/win32/deps/library/cluster/tests/ellipsoid-ex.Rout.save
new file mode 100644
index 0000000..a2ab64a
--- /dev/null
+++ b/win32/deps/library/cluster/tests/ellipsoid-ex.Rout.save
@@ -0,0 +1,207 @@
+
+R version 2.13.0 Patched (2011-04-16 r55459)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(cluster)
+>
+> eh <- ellipsoidhull(cbind(x=1:4, y = 1:4)) #singular
+Error in Fortran routine computing the spanning ellipsoid,
+ probably collinear data
+Warning message:
+In ellipsoidhull(cbind(x = 1:4, y = 1:4)) :
+ possibly not converged in 5000 iterations
+> eh
+'ellipsoid' in 2 dimensions:
+ center = ( 2.5 2.5 ); squared ave.radius d^2 = 0
+ and shape matrix =
+ x y
+x 1.25 1.25
+y 1.25 1.25
+ hence, area = 0
+
+** Warning: ** the algorithm did not terminate reliably!
+ most probably because of collinear data
+>
+> set.seed(157)
+> for(n in 4:10) { ## n=2 and 3 still differ -- platform dependently!
++ cat("n = ",n,"\n")
++ x2 <- rnorm(n)
++ print(ellipsoidhull(cbind(1:n, x2)))
++ print(ellipsoidhull(cbind(1:n, x2, 4*x2 + rnorm(n))))
++ }
+n = 4
+'ellipsoid' in 2 dimensions:
+ center = ( 2.66215 0.82086 ); squared ave.radius d^2 = 2
+ and shape matrix =
+ x2
+ 1.55901 0.91804
+x2 0.91804 0.67732
+ hence, area = 2.9008
+'ellipsoid' in 3 dimensions:
+ center = ( 2.50000 0.74629 2.95583 ); squared ave.radius d^2 = 3
+ and shape matrix =
+ x2
+ 1.25000 0.72591 1.8427
+x2 0.72591 0.52562 1.5159
+ 1.84268 1.51588 4.7918
+ hence, volume = 1.3843
+n = 5
+'ellipsoid' in 2 dimensions:
+ center = ( 3.0726 1.2307 ); squared ave.radius d^2 = 2
+ and shape matrix =
+ x2
+ 2.21414 0.45527
+x2 0.45527 2.39853
+ hence, area = 14.194
+'ellipsoid' in 3 dimensions:
+ center = ( 2.7989 1.1654 4.6782 ); squared ave.radius d^2 = 3
+ and shape matrix =
+ x2
+ 1.92664 0.40109 1.4317
+x2 0.40109 1.76625 6.9793
+ 1.43170 6.97928 28.0530
+ hence, volume = 11.532
+n = 6
+'ellipsoid' in 2 dimensions:
+ center = ( 3.04367 0.97016 ); squared ave.radius d^2 = 2
+ and shape matrix =
+ x2
+ 4.39182 0.30833
+x2 0.30833 0.59967
+ hence, area = 10.011
+'ellipsoid' in 3 dimensions:
+ center = ( 3.3190 0.7678 3.2037 ); squared ave.radius d^2 = 3
+ and shape matrix =
+ x2
+ 2.786928 -0.044373 -1.1467
+x2 -0.044373 0.559495 1.5496
+ -1.146728 1.549620 5.5025
+ hence, volume = 10.741
+n = 7
+'ellipsoid' in 2 dimensions:
+ center = ( 3.98294 -0.16567 ); squared ave.radius d^2 = 2
+ and shape matrix =
+ x2
+ 4.62064 -0.83135
+x2 -0.83135 0.37030
+ hence, area = 6.3453
+'ellipsoid' in 3 dimensions:
+ center = ( 4.24890 -0.25918 -0.76499 ); squared ave.radius d^2 = 3
+ and shape matrix =
+ x2
+ 4.6494 -0.93240 -4.0758
+x2 -0.9324 0.39866 1.9725
+ -4.0758 1.97253 10.4366
+ hence, volume = 6.9939
+n = 8
+'ellipsoid' in 2 dimensions:
+ center = ( 3.6699 -0.4532 ); squared ave.radius d^2 = 2
+ and shape matrix =
+ x2
+ 9.4327 -2.5269
+x2 -2.5269 3.7270
+ hence, area = 33.702
+'ellipsoid' in 3 dimensions:
+ center = ( 4.22030 -0.37953 -1.53922 ); squared ave.radius d^2 = 3
+ and shape matrix =
+ x2
+ 7.5211 -1.4804 -6.6587
+x2 -1.4804 2.6972 11.8198
+ -6.6587 11.8198 52.6243
+ hence, volume = 36.383
+n = 9
+'ellipsoid' in 2 dimensions:
+ center = ( 5.324396 -0.037779 ); squared ave.radius d^2 = 2
+ and shape matrix =
+ x2
+ 10.1098 -1.3708
+x2 -1.3708 2.1341
+ hence, area = 27.885
+'ellipsoid' in 3 dimensions:
+ center = ( 5.44700 -0.12504 -1.13538 ); squared ave.radius d^2 = 3
+ and shape matrix =
+ x2
+ 7.0364 -1.2424 -5.5741
+x2 -1.2424 1.7652 7.3654
+ -5.5741 7.3654 31.5558
+ hence, volume = 27.782
+n = 10
+'ellipsoid' in 2 dimensions:
+ center = ( 4.85439 0.28401 ); squared ave.radius d^2 = 2
+ and shape matrix =
+ x2
+ 13.932 0.64900
+x2 0.649 0.95132
+ hence, area = 22.508
+'ellipsoid' in 3 dimensions:
+ center = ( 5.12537 0.25024 0.86441 ); squared ave.radius d^2 = 3
+ and shape matrix =
+ x2
+ 9.29343 0.56973 1.4143
+x2 0.56973 0.76519 1.8941
+ 1.41427 1.89409 6.3803
+ hence, volume = 31.936
+>
+> set.seed(1)
+> x <- rt(100, df = 4)
+> y <- 100 + 5 * x + rnorm(100)
+> ellipsoidhull(cbind(x,y))
+'ellipsoid' in 2 dimensions:
+ center = ( -1.3874 93.0589 ); squared ave.radius d^2 = 2
+ and shape matrix =
+ x y
+x 32.924 160.54
+y 160.543 785.88
+ hence, area = 62.993
+> z <- 10 - 8 * x + y + rnorm(100)
+> (e3 <- ellipsoidhull(cbind(x,y,z)))
+'ellipsoid' in 3 dimensions:
+ center = ( -0.71678 96.09950 111.61029 ); squared ave.radius d^2 = 3
+ and shape matrix =
+ x y z
+x 26.005 126.41 -80.284
+y 126.410 616.94 -387.459
+z -80.284 -387.46 254.006
+ hence, volume = 130.45
+> d3o <- cbind(x,y + rt(100,3), 2 * x^2 + rt(100, 2))
+> (e. <- ellipsoidhull(d3o, ret.sq = TRUE))
+'ellipsoid' in 3 dimensions:
+ center = ( 0.32491 101.68998 39.48045 ); squared ave.radius d^2 = 3
+ and shape matrix =
+ x
+x 19.655 94.364 48.739
+ 94.364 490.860 181.022
+ 48.739 181.022 1551.980
+ hence, volume = 9463.8
+> stopifnot(all.equal(e.$sqdist,
++ with(e., mahalanobis(d3o, center=loc, cov=cov)),
++ tol = 1e-13))
+> d5 <- cbind(d3o, 2*abs(y)^1.5 + rt(100,3), 3*x - sqrt(abs(y)))
+> (e5 <- ellipsoidhull(d5, ret.sq = TRUE))
+'ellipsoid' in 5 dimensions:
+ center = ( -0.32451 98.54780 37.33619 1973.88383 -10.81891 ); squared ave.radius d^2 = 5
+ and shape matrix =
+ x
+x 17.8372 87.0277 8.3389 2607.9 49.117
+ 87.0277 446.9453 -2.0502 12745.4 239.470
+ 8.3389 -2.0502 1192.8439 2447.8 24.458
+ 2607.9264 12745.3826 2447.8006 384472.1 7179.239
+ 49.1172 239.4703 24.4582 7179.2 135.260
+ hence, volume = 10218
+> tail(sort(e5$sqdist)) ## 4 values 5.00039 ... 5.0099
+[1] 4.999915 5.000005 5.000010 5.000088 5.001444 5.009849
+>
diff --git a/win32/deps/library/cluster/tests/fanny-ex.R b/win32/deps/library/cluster/tests/fanny-ex.R
new file mode 100644
index 0000000..81e8416
--- /dev/null
+++ b/win32/deps/library/cluster/tests/fanny-ex.R
@@ -0,0 +1,72 @@
+.libPaths() # show full library tree {also as check of R CMD check!}
+library(cluster)
+
+####---------- Tests for FANNY i.e., fanny() --------------------------
+####
+### -- thanks to ../.Rbuildignore , the output of this is
+### -- only compared to saved values for the maintainer
+
+###--- An extension of example(fanny) : -------------------
+set.seed(21)
+## generate 10+15 objects in two clusters, plus 3 objects lying
+## between those clusters.
+x <- rbind(cbind(rnorm(10, 0, 0.5), rnorm(10, 0, 0.5)),
+ cbind(rnorm(15, 5, 0.5), rnorm(15, 5, 0.5)),
+ cbind(rnorm( 3,3.2,0.5), rnorm( 3,3.2,0.5)))
+
+.proctime00 <- proc.time()
+
+(fannyx <- fanny(x, 2))
+summary(fannyx)
+str(fannyx)
+## Different platforms differ (even gcc 3.0.1 vs 3.2 on same platform)!
+## {70 or 71 iterations}
+## ==> No "fanny-ex.Rout.save" is distributed !
+## --------------------------------------------
+summary(fanny(x,3))# one extra cluster
+
+(fanny(x,2, memb.exp = 1.5))
+(fanny(x,2, memb.exp = 1.2))
+(fanny(x,2, memb.exp = 1.1))
+(fanny(x,2, memb.exp = 3))
+
+data(ruspini) # < to run under R 1.9.1
+summary(fanny(ruspini, 3), digits = 9)
+summary(fanny(ruspini, 4), digits = 9)# 'correct' #{clusters}
+summary(fanny(ruspini, 5), digits = 9)
+
+cat('Time elapsed: ', proc.time() - .proctime00,'\n')
+data(chorSub)
+p4cl <- pam(chorSub, k = 4, cluster.only = TRUE)
+## The first two are "completely fuzzy" -- and now give a warnings
+f4.20 <- fanny(chorSub, k = 4, trace.lev = 1) ; f4.20$coef
+f4.18 <- fanny(chorSub, k = 4, memb.exp = 1.8) # same problem
+f4.18. <- fanny(chorSub, k = 4, memb.exp = 1.8,
+ iniMem.p = f4.20$membership) # very quick convergence
+stopifnot(all.equal(f4.18[-c(7,9)], f4.18.[-c(7,9)], tol = 5e-7))
+
+f4.16 <- fanny(chorSub, k = 4, memb.exp = 1.6) # now gives 4 crisp clusters
+f4.16. <- fanny(chorSub, k = 4, memb.exp = 1.6,
+ iniMem.p = f4.18$membership, trace.lev = 2)# "converges" immediately - WRONGLY!
+f4.16.2 <- fanny(chorSub, k = 4, memb.exp = 1.6,
+ iniMem.p = cluster:::as.membership(p4cl),
+ tol = 1e-10, trace.lev = 2)## looks much better:
+stopifnot(f4.16$clustering == f4.16.2$clustering,
+ all.equal(f4.16[-c(1,7,9)], f4.16.2[-c(1,7,9)], tol = 1e-7),
+ all.equal(f4.16$membership, f4.16.2$membership, tol = 0.001))
+## the memberships are quite close but have only converged to precision 0.000228
+
+f4.14 <- fanny(chorSub, k = 4, memb.exp = 1.4)
+f4.12 <- fanny(chorSub, k = 4, memb.exp = 1.2)
+
+table(f4.12$clustering, f4.14$clustering)# close but different
+table(f4.16$clustering, f4.14$clustering)# dito
+table(f4.12$clustering, f4.16$clustering)# hence differ even more
+
+symnum(cbind(f4.16$membership, 1, f4.12$membership),
+ cutpoints= c(0., 0.2, 0.6, 0.8, 0.9, 0.95, 1 -1e-7, 1 +1e-7),
+ symbols = c(" ", ".", ",", "+", "*", "B","1"))
+
+
+## Last Line:
+cat('Time elapsed: ', proc.time() - .proctime00,'\n')
diff --git a/win32/deps/library/cluster/tests/mona.R b/win32/deps/library/cluster/tests/mona.R
new file mode 100644
index 0000000..5231a16
--- /dev/null
+++ b/win32/deps/library/cluster/tests/mona.R
@@ -0,0 +1,23 @@
+library(cluster)
+
+data(animals)
+(mani <- mona(animals))
+
+str(mani)
+
+if(require(MASS)) {
+
+ if(R.version$major != "1" || as.numeric(R.version$minor) >= 7)
+ RNGversion("1.6")
+ set.seed(253)
+ n <- 512; p <- 3
+ Sig <- diag(p); Sig[] <- 0.8 ^ abs(col(Sig) - row(Sig))
+ x3 <- mvrnorm(n, rep(0,p), Sig) >= 0
+ x <- cbind(x3, rbinom(n, size=1, prob = 1/2))
+
+ print(sapply(as.data.frame(x), table))
+
+ mx <- mona(x)
+ str(mx)
+ print(lapply(mx[c(1,3,4)], table))
+}
diff --git a/win32/deps/library/cluster/tests/mona.Rout.save b/win32/deps/library/cluster/tests/mona.Rout.save
new file mode 100644
index 0000000..5c29183
--- /dev/null
+++ b/win32/deps/library/cluster/tests/mona.Rout.save
@@ -0,0 +1,118 @@
+
+R version 2.15.1 Patched (2012-10-12 r60924) -- "Roasted Marshmallows"
+Copyright (C) 2012 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(cluster)
+>
+> data(animals)
+> (mani <- mona(animals))
+Revised data:
+ war fly ver end gro hai
+ant 0 0 0 0 1 0
+bee 0 1 0 0 1 1
+cat 1 0 1 0 0 1
+cpl 0 0 0 0 0 1
+chi 1 0 1 1 1 1
+cow 1 0 1 0 1 1
+duc 1 1 1 0 1 0
+eag 1 1 1 1 0 0
+ele 1 0 1 1 1 0
+fly 0 1 0 0 0 0
+fro 0 0 1 1 0 0
+her 0 0 1 0 1 0
+lio 1 0 1 1 1 1
+liz 0 0 1 0 0 0
+lob 0 0 0 0 0 0
+man 1 0 1 1 1 1
+rab 1 0 1 0 1 1
+sal 0 0 1 0 0 0
+spi 0 0 0 0 0 1
+wha 1 0 1 1 1 0
+Order of objects:
+ [1] ant cpl spi lob bee fly fro her liz sal cat cow rab chi lio man ele wha duc
+[20] eag
+Variable used:
+ [1] gro NULL hai fly gro ver end gro NULL war gro NULL end NULL NULL
+[16] hai NULL fly end
+Separation step:
+ [1] 4 0 5 3 4 2 3 4 0 1 4 0 3 0 0 4 0 2 3
+
+Available components:
+[1] "data" "order" "variable" "step" "call" "order.lab"
+>
+> str(mani)
+List of 6
+ $ data : int [1:20, 1:6] 0 0 1 0 1 1 1 1 1 0 ...
+ ..- attr(*, "dimnames")=List of 2
+ .. ..$ : chr [1:20] "ant" "bee" "cat" "cpl" ...
+ .. ..$ : chr [1:6] "war" "fly" "ver" "end" ...
+ $ order : int [1:20] 1 4 19 15 2 10 11 12 14 18 ...
+ $ variable : chr [1:19] "gro" "NULL" "hai" "fly" ...
+ $ step : int [1:19] 4 0 5 3 4 2 3 4 0 1 ...
+ $ call : language mona(x = animals)
+ $ order.lab: chr [1:20] "ant" "cpl" "spi" "lob" ...
+ - attr(*, "class")= chr "mona"
+>
+> if(require(MASS)) {
++
++ if(R.version$major != "1" || as.numeric(R.version$minor) >= 7)
++ RNGversion("1.6")
++ set.seed(253)
++ n <- 512; p <- 3
++ Sig <- diag(p); Sig[] <- 0.8 ^ abs(col(Sig) - row(Sig))
++ x3 <- mvrnorm(n, rep(0,p), Sig) >= 0
++ x <- cbind(x3, rbinom(n, size=1, prob = 1/2))
++
++ print(sapply(as.data.frame(x), table))
++
++ mx <- mona(x)
++ str(mx)
++ print(lapply(mx[c(1,3,4)], table))
++ }
+Loading required package: MASS
+ V1 V2 V3 V4
+0 244 245 261 238
+1 268 267 251 274
+List of 5
+ $ data : int [1:512, 1:4] 0 0 0 0 1 1 1 0 1 0 ...
+ $ order : int [1:512] 1 137 154 204 353 398 30 52 69 85 ...
+ $ variable: int [1:511] 0 0 0 0 0 3 0 0 0 0 ...
+ $ step : int [1:511] 0 0 0 0 0 4 0 0 0 0 ...
+ $ call : language mona(x = x)
+ - attr(*, "class")= chr "mona"
+$data
+
+ 0 1
+ 988 1060
+
+$variable
+
+ 0 1 2 3 4
+496 4 1 5 5
+
+$step
+
+ 0 1 2 3 4
+496 1 2 4 8
+
+Warning message:
+In RNGkind("Marsaglia-Multicarry", "Buggy Kinderman-Ramage") :
+ Buggy version of Kinderman-Ramage generator used
+>
+> proc.time()
+ user system elapsed
+ 0.248 0.020 0.262
diff --git a/win32/deps/library/cluster/tests/pam.R b/win32/deps/library/cluster/tests/pam.R
new file mode 100644
index 0000000..7a5d6f7
--- /dev/null
+++ b/win32/deps/library/cluster/tests/pam.R
@@ -0,0 +1,165 @@
+library(cluster)
+## Compare on these:
+nms <- c("clustering", "objective", "isolation", "clusinfo", "silinfo")
+nm2 <- c("medoids", "id.med", nms)
+nm3 <- nm2[- pmatch("obj", nm2)]
+
+(x <- x0 <- cbind(V1 = (-3:4)^2, V2 = c(0:6,NA), V3 = c(1,2,NA,7,NA,8:9,8)))
+(px <- pam(x,2, metric="manhattan"))
+stopifnot(identical(x,x0))# DUP=FALSE ..
+pd <- pam(dist(x,"manhattan"), 2)
+px2 <- pam(x,2, metric="manhattan", keep.diss=FALSE, keep.data=FALSE)
+pdC <- pam(x,2, metric="manhattan", cluster.only = TRUE)
+
+stopifnot(identical(px[nms], pd[nms]),
+ identical(px[nms], px2[nms]),
+ identical(pdC, px2$clustering),
+ ## and for default dist "euclidean":
+ identical(pam(x, 2)[nms],
+ pam(dist(x),2)[nms])
+ )
+
+set.seed(253)
+## generate 250 objects, divided into 2 clusters.
+x <- rbind(cbind(rnorm(120, 0,8), rnorm(120, 0,8)),
+ cbind(rnorm(130,50,8), rnorm(130,10,8)))
+
+.proctime00 <- proc.time()
+
+summary(px2 <- pam(x, 2))
+pdx <- pam(dist(x), 2)
+all.equal(px2[nms], pdx[nms], tol = 1e-12) ## TRUE
+pdxK <- pam(dist(x), 2, keep.diss = TRUE)
+stopifnot(identical(pdx[nm2], pdxK[nm2]))
+
+spdx <- silhouette(pdx)
+summary(spdx)
+spdx
+postscript("pam-tst.ps")
+if(FALSE)
+ plot(spdx)# the silhouette
+## is now identical :
+plot(pdx)# failed in 1.7.0 -- now only does silhouette
+
+par(mfrow = 2:1)
+## new 'dist' argument for clusplot():
+plot(pdx, dist=dist(x))
+## but this should work automagically (via eval()) as well:
+plot(pdx)
+## or this
+clusplot(pdx)
+
+data(ruspini)
+summary(pr4 <- pam(ruspini, 4))
+(pr3 <- pam(ruspini, 3))
+(pr5 <- pam(ruspini, 5))
+
+data(votes.repub)
+summary(pv3 <- pam(votes.repub, 3))
+(pv4 <- pam(votes.repub, 4))
+(pv6 <- pam(votes.repub, 6, trace = 3))
+
+cat('Time elapsed: ', proc.time() - .proctime00,'\n')
+
+## re-starting with medoids from pv6 shouldn't change:
+pv6. <- pam(votes.repub, 6, medoids = pv6$id.med, trace = 3)
+identical(pv6[nm3], pv6.[nm3])
+
+## This example seg.faulted at some point:
+d.st <- data.frame(V1= c(9, 12, 12, 15, 9, 9, 13, 11, 15, 10, 13, 13,
+ 13, 15, 8, 13, 13, 10, 7, 9, 6, 11, 3),
+ V2= c(5, 9, 3, 5, 1, 1, 2, NA, 10, 1, 4, 7,
+ 4, NA, NA, 5, 2, 4, 3, 3, 6, 1, 1),
+ V3 = c(63, 41, 59, 50, 290, 226, 60, 36, 32, 121, 70, 51,
+ 79, 32, 42, 39, 76, 60, 56, 88, 57, 309, 254),
+ V4 = c(146, 43, 78, 88, 314, 149, 78, NA, 238, 153, 159, 222,
+ 203, NA, NA, 74, 100, 111, 9, 180, 50, 256, 107))
+dd <- daisy(d.st, stand = TRUE)
+(r0 <- pam(dd, 5))# cluster 5 = { 23 } -- on single observation
+## This gave only 3 different medoids -> and seg.fault:
+(r5 <- pam(dd, 5, medoids = c(1,3,20,2,5), trace = 2)) # now "fine"
+
+dev.off()
+
+##------------------------ Testing pam() with new "pamonce" argument:
+
+## This is from "next version of Matrix" test-tools-1.R:
+showSys.time <- function(expr) {
+ ## prepend 'Time' for R CMD Rdiff
+ st <- system.time(expr)
+ writeLines(paste("Time", capture.output(print(st))))
+ invisible(st)
+}
+show2Ratios <- function(...) {
+ stopifnot(length(rgs <- list(...)) == 2,
+ nchar(ns <- names(rgs)) > 0)
+ r <- round(cbind(..1, ..2)[c(1,3),], 3)
+ dimnames(r) <- list(paste("Time ", rownames(r)), ns)
+ r
+}
+
+
+n <- 1000
+## If not enough cases, all CPU times equals 0.
+n <- 500 # for now, and automatic testing
+
+sd <- 0.5
+set.seed(13)
+n2 <- as.integer(round(n * 1.5))
+x <- rbind(cbind(rnorm( n,0,sd), rnorm( n,0,sd)),
+ cbind(rnorm(n2,5,sd), rnorm(n2,5,sd)),
+ cbind(rnorm(n2,7,sd), rnorm(n2,7,sd)),
+ cbind(rnorm(n2,9,sd), rnorm(n2,9,sd)))
+
+
+## original algorithm
+st0 <- showSys.time(pamx <- pam(x, 4, trace.lev=2))# 8.157 0.024 8.233
+ ## bswapPamOnce algorithm
+st1 <- showSys.time(pamxonce <- pam(x, 4, pamonce=TRUE, trace.lev=2))# 6.122 0.024 6.181
+## bswapPamOnceDistIndice
+st2 <- showSys.time(pamxonce2 <- pam(x, 4, pamonce = 2, trace.lev=2))# 4.101 0.024 4.151
+show2Ratios('2:orig' = st2/st0, '1:orig' = st1/st0)
+
+## only call element is not equal
+(icall <- which(names(pamx) == "call"))
+pamx[[icall]]
+stopifnot(all.equal(pamx [-icall], pamxonce [-icall]),
+ all.equal(pamxonce[-icall], pamxonce2[-icall]))
+
+## Same using specified medoids
+(med0 <- 1 + round(n* c(0,1, 2.5, 4)))# lynne (~ 2010, AMD Phenom II X4 925)
+st0 <- showSys.time(pamxst <- pam(x, 4, medoids = med0, trace.lev=2))# 13.071 0.024 13.177
+st1 <- showSys.time(pamxoncest <- pam(x, 4, medoids = med0, pamonce=TRUE, trace.lev=2))# 8.503 0.024 8.578
+st2 <- showSys.time(pamxonce2st <- pam(x, 4, medoids = med0, pamonce=2, trace.lev=2))# 5.587 0.025 5.647
+show2Ratios('2:orig' = st2/st0, '1:orig' = st1/st0)
+
+## only call element is not equal
+stopifnot(all.equal(pamxst [-icall], pamxoncest [-icall]),
+ all.equal(pamxoncest[-icall], pamxonce2st[-icall]))
+
+## Different starting values
+med0 <- 1:4 # lynne (~ 2010, AMD Phenom II X4 925)
+st0 <- showSys.time(pamxst <- pam(x, 4, medoids = med0, trace.lev=2))# 13.416 0.023 13.529
+st1 <- showSys.time(pamxoncest <- pam(x, 4, medoids = med0, pamonce=TRUE, trace.lev=2))# 8.384 0.024 8.459
+st2 <- showSys.time(pamxonce2st <- pam(x, 4, medoids = med0, pamonce=2, trace.lev=2))# 5.455 0.030 5.520
+show2Ratios('2:orig' = st2/st0, '1:orig' = st1/st0)
+
+## only call element is not equal
+stopifnot(all.equal(pamxst [-icall], pamxoncest [-icall]),
+ all.equal(pamxoncest[-icall], pamxonce2st[-icall]))
+
+
+## Medoid bug --- MM: Fixed, well "0L+ hack", in my pam.q, on 2012-01-31
+## ----------
+med0 <- (1:6)
+st0 <- showSys.time(pamxst <- pam(x, 6, medoids = med0 , trace.lev=2))
+stopifnot(identical(med0, 1:6))
+med0 <- (1:6)
+st1 <- showSys.time(pamxst.1 <- pam(x, 6, medoids = med0 , pamonce=1, trace.lev=2))
+stopifnot(identical(med0, 1:6))
+stopifnot(all.equal(pamxst[-icall], pamxst.1 [-icall]))
+
+
+## Last Line:
+cat('Time elapsed: ', proc.time() - .proctime00,'\n')
+
diff --git a/win32/deps/library/cluster/tests/pam.Rout.save b/win32/deps/library/cluster/tests/pam.Rout.save
new file mode 100644
index 0000000..3511314
--- /dev/null
+++ b/win32/deps/library/cluster/tests/pam.Rout.save
@@ -0,0 +1,1343 @@
+
+R version 2.14.1 Patched (2012-01-24 r58194)
+Copyright (C) 2012 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(cluster)
+> ## Compare on these:
+> nms <- c("clustering", "objective", "isolation", "clusinfo", "silinfo")
+> nm2 <- c("medoids", "id.med", nms)
+> nm3 <- nm2[- pmatch("obj", nm2)]
+>
+> (x <- x0 <- cbind(V1 = (-3:4)^2, V2 = c(0:6,NA), V3 = c(1,2,NA,7,NA,8:9,8)))
+ V1 V2 V3
+[1,] 9 0 1
+[2,] 4 1 2
+[3,] 1 2 NA
+[4,] 0 3 7
+[5,] 1 4 NA
+[6,] 4 5 8
+[7,] 9 6 9
+[8,] 16 NA 8
+> (px <- pam(x,2, metric="manhattan"))
+Medoids:
+ ID V1 V2 V3
+[1,] 2 4 1 2
+[2,] 6 4 5 8
+Clustering vector:
+[1] 1 1 1 2 2 2 2 2
+Objective function:
+build swap
+6.375 6.375
+
+Available components:
+ [1] "medoids" "id.med" "clustering" "objective" "isolation"
+ [6] "clusinfo" "silinfo" "diss" "call" "data"
+> stopifnot(identical(x,x0))# DUP=FALSE ..
+> pd <- pam(dist(x,"manhattan"), 2)
+> px2 <- pam(x,2, metric="manhattan", keep.diss=FALSE, keep.data=FALSE)
+> pdC <- pam(x,2, metric="manhattan", cluster.only = TRUE)
+>
+> stopifnot(identical(px[nms], pd[nms]),
++ identical(px[nms], px2[nms]),
++ identical(pdC, px2$clustering),
++ ## and for default dist "euclidean":
++ identical(pam(x, 2)[nms],
++ pam(dist(x),2)[nms])
++ )
+>
+> set.seed(253)
+> ## generate 250 objects, divided into 2 clusters.
+> x <- rbind(cbind(rnorm(120, 0,8), rnorm(120, 0,8)),
++ cbind(rnorm(130,50,8), rnorm(130,10,8)))
+>
+> .proctime00 <- proc.time()
+>
+> summary(px2 <- pam(x, 2))
+Medoids:
+ ID
+[1,] 61 -0.7697828 -0.2330187
+[2,] 163 49.1392167 9.4097259
+Clustering vector:
+ [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [38] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [75] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+[112] 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+[149] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+[186] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+[223] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+Objective function:
+ build swap
+13.25843 10.20817
+
+Numerical information per cluster:
+ size max_diss av_diss diameter separation
+[1,] 120 31.04843 10.18584 53.22082 9.419035
+[2,] 130 26.94337 10.22878 47.86442 9.419035
+
+Isolated clusters:
+ L-clusters: character(0)
+ L*-clusters: character(0)
+
+Silhouette plot information:
+ cluster neighbor sil_width
+117 1 2 0.80638966
+75 1 2 0.80600824
+81 1 2 0.80556624
+107 1 2 0.80535252
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+233 2 1 0.37013099
+167 2 1 0.32442373
+Average silhouette width per cluster:
+[1] 0.7196104 0.7148520
+Average silhouette width of total data set:
+[1] 0.717136
+
+Available components:
+ [1] "medoids" "id.med" "clustering" "objective" "isolation"
+ [6] "clusinfo" "silinfo" "diss" "call" "data"
+> pdx <- pam(dist(x), 2)
+> all.equal(px2[nms], pdx[nms], tol = 1e-12) ## TRUE
+[1] TRUE
+> pdxK <- pam(dist(x), 2, keep.diss = TRUE)
+> stopifnot(identical(pdx[nm2], pdxK[nm2]))
+>
+> spdx <- silhouette(pdx)
+> summary(spdx)
+Silhouette of 250 units in 2 clusters from pam(x = dist(x), k = 2) :
+ Cluster sizes and average silhouette widths:
+ 120 130
+0.7196104 0.7148520
+Individual silhouette widths:
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+0.08929 0.69140 0.74400 0.71710 0.77810 0.80640
+> spdx
+ cluster neighbor sil_width
+117 1 2 0.80638966
+75 1 2 0.80600824
+81 1 2 0.80556624
+107 1 2 0.80535252
+6 1 2 0.80526675
+100 1 2 0.80385505
+68 1 2 0.80369702
+113 1 2 0.80331774
+61 1 2 0.80315322
+57 1 2 0.80313945
+12 1 2 0.80161573
+59 1 2 0.80047745
+82 1 2 0.79630964
+67 1 2 0.79559589
+63 1 2 0.79488886
+47 1 2 0.79458809
+21 1 2 0.79379540
+9 1 2 0.79343081
+95 1 2 0.79332153
+4 1 2 0.79136081
+3 1 2 0.79130879
+39 1 2 0.79052367
+120 1 2 0.78877423
+90 1 2 0.78767224
+85 1 2 0.78588359
+106 1 2 0.78504452
+92 1 2 0.78303000
+83 1 2 0.78245915
+19 1 2 0.78228359
+14 1 2 0.78139236
+10 1 2 0.77825678
+49 1 2 0.77597087
+64 1 2 0.77482761
+44 1 2 0.77397394
+89 1 2 0.77297318
+119 1 2 0.77238705
+108 1 2 0.77137189
+104 1 2 0.76871378
+32 1 2 0.76856251
+115 1 2 0.76843312
+27 1 2 0.76811698
+88 1 2 0.76810713
+109 1 2 0.76681303
+62 1 2 0.76655954
+36 1 2 0.76547988
+66 1 2 0.76535606
+74 1 2 0.76491406
+26 1 2 0.76441455
+24 1 2 0.76436188
+65 1 2 0.76381352
+40 1 2 0.76061109
+52 1 2 0.75748679
+54 1 2 0.75746436
+13 1 2 0.75594073
+56 1 2 0.75353784
+96 1 2 0.75268786
+116 1 2 0.75267215
+110 1 2 0.75266614
+112 1 2 0.75150872
+78 1 2 0.75083708
+7 1 2 0.74905187
+86 1 2 0.74190424
+18 1 2 0.74162144
+111 1 2 0.74085474
+69 1 2 0.74044653
+76 1 2 0.73911707
+50 1 2 0.73847075
+93 1 2 0.73616384
+31 1 2 0.73462007
+33 1 2 0.73455252
+43 1 2 0.73396232
+102 1 2 0.72930751
+118 1 2 0.72778023
+15 1 2 0.72588122
+53 1 2 0.72542363
+8 1 2 0.72535191
+77 1 2 0.72467809
+16 1 2 0.72446952
+48 1 2 0.72331213
+105 1 2 0.72325095
+37 1 2 0.72055248
+101 1 2 0.71783562
+22 1 2 0.71217552
+23 1 2 0.71078375
+84 1 2 0.70573352
+17 1 2 0.70221946
+38 1 2 0.69947240
+2 1 2 0.69718780
+98 1 2 0.69601237
+1 1 2 0.69373841
+35 1 2 0.69179546
+70 1 2 0.69074915
+28 1 2 0.68434091
+97 1 2 0.68351978
+5 1 2 0.67662675
+72 1 2 0.67420722
+34 1 2 0.67315267
+11 1 2 0.67226046
+103 1 2 0.67188668
+87 1 2 0.67172802
+58 1 2 0.67090513
+46 1 2 0.66835116
+60 1 2 0.66565445
+80 1 2 0.65983842
+73 1 2 0.65093947
+55 1 2 0.64709226
+20 1 2 0.64439401
+45 1 2 0.63403361
+51 1 2 0.63303101
+42 1 2 0.62906268
+94 1 2 0.60916406
+91 1 2 0.59905996
+41 1 2 0.57245485
+29 1 2 0.55594781
+99 1 2 0.55035955
+79 1 2 0.50808544
+71 1 2 0.46663954
+25 1 2 0.43797346
+114 1 2 0.16645003
+30 1 2 0.08928664
+121 2 1 0.80353953
+137 2 1 0.80253721
+146 2 1 0.80106653
+173 2 1 0.80039417
+216 2 1 0.79969919
+124 2 1 0.79964913
+163 2 1 0.79901674
+157 2 1 0.79779188
+242 2 1 0.79744315
+227 2 1 0.79708130
+207 2 1 0.79653829
+130 2 1 0.79574204
+188 2 1 0.79496670
+250 2 1 0.79302877
+145 2 1 0.79190501
+126 2 1 0.79156003
+166 2 1 0.79068795
+222 2 1 0.78986170
+232 2 1 0.78839216
+176 2 1 0.78819086
+198 2 1 0.78782877
+225 2 1 0.78747329
+230 2 1 0.78689375
+205 2 1 0.78683641
+160 2 1 0.78643596
+150 2 1 0.78484046
+136 2 1 0.78455577
+228 2 1 0.78198238
+206 2 1 0.78137390
+152 2 1 0.78044944
+200 2 1 0.77843458
+149 2 1 0.77822272
+221 2 1 0.77758324
+226 2 1 0.77611981
+129 2 1 0.77531368
+199 2 1 0.77491451
+154 2 1 0.77136276
+241 2 1 0.77076783
+179 2 1 0.77010597
+174 2 1 0.76893758
+214 2 1 0.76776510
+181 2 1 0.76763087
+213 2 1 0.76683151
+215 2 1 0.76639087
+236 2 1 0.76637552
+218 2 1 0.76563050
+182 2 1 0.76450873
+219 2 1 0.76370712
+208 2 1 0.76090426
+151 2 1 0.75957536
+164 2 1 0.75914844
+248 2 1 0.75849775
+224 2 1 0.75826151
+168 2 1 0.75782023
+189 2 1 0.75555083
+128 2 1 0.75550519
+125 2 1 0.75510766
+177 2 1 0.75128941
+147 2 1 0.75086382
+158 2 1 0.75029192
+245 2 1 0.74993652
+186 2 1 0.74741247
+165 2 1 0.74681005
+156 2 1 0.74478894
+122 2 1 0.74315425
+247 2 1 0.74107328
+220 2 1 0.74054057
+183 2 1 0.73818743
+184 2 1 0.73743259
+169 2 1 0.73712431
+180 2 1 0.73419669
+240 2 1 0.73390938
+134 2 1 0.73382823
+190 2 1 0.73379720
+217 2 1 0.73311931
+171 2 1 0.73110365
+143 2 1 0.72986022
+153 2 1 0.72891371
+223 2 1 0.72887340
+238 2 1 0.72789416
+175 2 1 0.72311665
+138 2 1 0.72290131
+235 2 1 0.72157157
+237 2 1 0.71591233
+132 2 1 0.71549875
+204 2 1 0.71381083
+201 2 1 0.71263881
+170 2 1 0.70812568
+191 2 1 0.70747428
+243 2 1 0.70588929
+193 2 1 0.70499170
+141 2 1 0.70489885
+161 2 1 0.70303117
+249 2 1 0.69300988
+229 2 1 0.69231982
+196 2 1 0.69162302
+211 2 1 0.69128644
+246 2 1 0.68757678
+159 2 1 0.68619850
+133 2 1 0.68605444
+194 2 1 0.68538064
+155 2 1 0.68278455
+234 2 1 0.68202095
+127 2 1 0.68111027
+144 2 1 0.67559517
+131 2 1 0.65959281
+139 2 1 0.65895024
+209 2 1 0.65844942
+148 2 1 0.65180336
+185 2 1 0.64989675
+212 2 1 0.63954685
+192 2 1 0.63470144
+123 2 1 0.63005333
+202 2 1 0.61735843
+135 2 1 0.61493992
+210 2 1 0.60680456
+140 2 1 0.58410004
+187 2 1 0.58193543
+239 2 1 0.57088679
+203 2 1 0.56761998
+244 2 1 0.55321123
+231 2 1 0.55043439
+197 2 1 0.52364031
+195 2 1 0.51955678
+142 2 1 0.47466260
+162 2 1 0.46155841
+172 2 1 0.45167576
+178 2 1 0.42686872
+233 2 1 0.37013099
+167 2 1 0.32442373
+attr(,"Ordered")
+[1] TRUE
+attr(,"call")
+pam(x = dist(x), k = 2)
+attr(,"class")
+[1] "silhouette"
+> postscript("pam-tst.ps")
+> if(FALSE)
++ plot(spdx)# the silhouette
+> ## is now identical :
+> plot(pdx)# failed in 1.7.0 -- now only does silhouette
+>
+> par(mfrow = 2:1)
+> ## new 'dist' argument for clusplot():
+> plot(pdx, dist=dist(x))
+> ## but this should work automagically (via eval()) as well:
+> plot(pdx)
+> ## or this
+> clusplot(pdx)
+>
+> data(ruspini)
+> summary(pr4 <- pam(ruspini, 4))
+Medoids:
+ ID x y
+10 10 19 65
+32 32 44 149
+52 52 99 119
+70 70 69 21
+Clustering vector:
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
+ 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2
+27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52
+ 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3
+53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
+ 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
+Objective function:
+ build swap
+17.22898 11.48637
+
+Numerical information per cluster:
+ size max_diss av_diss diameter separation
+[1,] 20 24.04163 12.55362 40.24922 40.49691
+[2,] 23 26.92582 10.44238 36.61967 24.04163
+[3,] 17 33.97058 13.84800 47.63402 24.04163
+[4,] 15 17.02939 8.98767 27.07397 40.49691
+
+Isolated clusters:
+ L-clusters: character(0)
+ L*-clusters: [1] 1 4
+
+Silhouette plot information:
+ cluster neighbor sil_width
+10 1 4 0.8056096
+6 1 4 0.7954977
+9 1 4 0.7923048
+11 1 4 0.7831672
+8 1 2 0.7811793
+12 1 4 0.7658171
+3 1 4 0.7587961
+14 1 4 0.7569107
+2 1 4 0.7456150
+16 1 4 0.7436018
+13 1 4 0.7398841
+4 1 2 0.7361533
+18 1 4 0.7080079
+15 1 4 0.7006854
+19 1 4 0.7000938
+1 1 4 0.6798381
+5 1 4 0.6646571
+20 1 4 0.6619626
+17 1 4 0.6148541
+7 1 2 0.5900575
+26 2 3 0.8357433
+32 2 3 0.8332753
+27 2 3 0.8290271
+25 2 3 0.8285547
+28 2 3 0.8192636
+35 2 3 0.8186309
+33 2 3 0.8175087
+23 2 3 0.8089969
+22 2 3 0.8025389
+34 2 3 0.8013310
+31 2 3 0.7949677
+36 2 3 0.7943536
+24 2 3 0.7930770
+29 2 3 0.7897346
+30 2 3 0.7892027
+21 2 3 0.7698024
+37 2 3 0.7684502
+39 2 3 0.7631648
+38 2 3 0.7438848
+40 2 3 0.7083130
+42 2 3 0.5291270
+43 2 3 0.4931623
+41 2 3 0.4290814
+54 3 2 0.7741745
+57 3 2 0.7703455
+55 3 2 0.7641810
+50 3 2 0.7619943
+52 3 2 0.7616220
+56 3 2 0.7575313
+59 3 2 0.7327828
+49 3 2 0.7317002
+51 3 2 0.7209864
+60 3 2 0.7206840
+58 3 2 0.7019611
+53 3 2 0.6775322
+45 3 2 0.5974787
+46 3 2 0.5740823
+47 3 2 0.4835635
+48 3 2 0.4247331
+44 3 2 0.4196093
+70 4 1 0.8548947
+67 4 1 0.8527439
+65 4 1 0.8503105
+69 4 1 0.8391810
+71 4 1 0.8381065
+66 4 1 0.8229841
+62 4 1 0.8153092
+64 4 1 0.8061254
+73 4 1 0.7950213
+63 4 1 0.7795369
+72 4 1 0.7748121
+61 4 1 0.7701103
+68 4 1 0.7620559
+74 4 1 0.7596815
+75 4 1 0.7425538
+Average silhouette width per cluster:
+[1] 0.7262347 0.7548344 0.6691154 0.8042285
+Average silhouette width of total data set:
+[1] 0.737657
+
+2775 dissimilarities, summarized :
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+ 1.4142 40.1060 75.5910 71.5380 99.1690 154.5000
+Metric : euclidean
+Number of objects : 75
+
+Available components:
+ [1] "medoids" "id.med" "clustering" "objective" "isolation"
+ [6] "clusinfo" "silinfo" "diss" "call" "data"
+> (pr3 <- pam(ruspini, 3))
+Medoids:
+ ID x y
+17 17 30 52
+32 32 44 149
+52 52 99 119
+Clustering vector:
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
+ 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2
+27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52
+ 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3
+53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
+ 3 3 3 3 3 3 3 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+Objective function:
+ build swap
+25.68229 21.59293
+
+Available components:
+ [1] "medoids" "id.med" "clustering" "objective" "isolation"
+ [6] "clusinfo" "silinfo" "diss" "call" "data"
+> (pr5 <- pam(ruspini, 5))
+Medoids:
+ ID x y
+10 10 19 65
+32 32 44 149
+52 52 99 119
+47 47 78 94
+70 70 69 21
+Clustering vector:
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
+ 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2
+27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52
+ 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 4 4 4 3 3 3 3
+53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
+ 3 3 3 3 3 3 3 3 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
+Objective function:
+ build swap
+12.09864 10.39579
+
+Available components:
+ [1] "medoids" "id.med" "clustering" "objective" "isolation"
+ [6] "clusinfo" "silinfo" "diss" "call" "data"
+>
+> data(votes.repub)
+> summary(pv3 <- pam(votes.repub, 3))
+Medoids:
+ ID X1856 X1860 X1864 X1868 X1872 X1876 X1880 X1884 X1888 X1892 X1896
+Alabama 1 NA NA NA 51.44 53.19 40.02 36.98 38.44 32.28 3.95 28.13
+Alaska 2 NA NA NA NA NA NA NA NA NA NA NA
+New Mexico 31 NA NA NA NA NA NA NA NA NA NA NA
+ X1900 X1904 X1908 X1912 X1916 X1920 X1924 X1928 X1932 X1936 X1940
+Alabama 34.67 20.65 24.38 8.26 21.97 30.98 27.01 48.49 14.15 12.82 14.34
+Alaska NA NA NA NA NA NA NA NA NA NA NA
+New Mexico NA NA NA 35.91 46.53 54.68 48.52 59.01 35.76 36.50 43.28
+ X1944 X1948 X1952 X1956 X1960 X1964 X1968 X1972 X1976
+Alabama 18.20 19.04 35.02 39.39 41.75 69.5 14.0 72.4 43.48
+Alaska NA NA NA NA 50.94 34.1 45.3 58.1 62.91
+New Mexico 46.44 42.93 55.39 57.81 49.41 41.0 51.8 61.0 51.04
+Clustering vector:
+ Alabama Alaska Arizona Arkansas California
+ 1 2 3 1 2
+ Colorado Connecticut Delaware Florida Georgia
+ 2 2 3 1 1
+ Hawaii Idaho Illinois Indiana Iowa
+ 2 3 2 3 3
+ Kansas Kentucky Louisiana Maine Maryland
+ 2 3 1 2 3
+ Massachusetts Michigan Minnesota Mississippi Missouri
+ 3 2 3 1 3
+ Montana Nebraska Nevada New Hampshire New Jersey
+ 3 3 2 2 2
+ New Mexico New York North Carolina North Dakota Ohio
+ 3 3 3 2 3
+ Oklahoma Oregon Pennsylvania Rhode Island South Carolina
+ 3 3 2 3 2
+ South Dakota Tennessee Texas Utah Vermont
+ 3 3 2 3 2
+ Virginia Washington West Virginia Wisconsin Wyoming
+ 2 3 3 3 3
+Objective function:
+ build swap
+38.32548 38.32548
+
+Numerical information per cluster:
+ size max_diss av_diss diameter separation
+[1,] 6 78.92731 51.59134 116.7048 50.14189
+[2,] 18 86.54675 38.47068 271.2455 19.42184
+[3,] 26 60.03879 35.16361 124.8324 19.42184
+
+Isolated clusters:
+ L-clusters: character(0)
+ L*-clusters: character(0)
+
+Silhouette plot information:
+ cluster neighbor sil_width
+Louisiana 1 3 0.54689535
+Alabama 1 3 0.52839272
+Georgia 1 3 0.52730253
+Mississippi 1 2 0.52454810
+Florida 1 3 0.25211631
+Arkansas 1 3 0.24131701
+Alaska 2 3 0.15699268
+Hawaii 2 3 0.08479842
+Vermont 2 3 -0.02620975
+Maine 2 3 -0.03284950
+Michigan 2 3 -0.11524982
+Pennsylvania 2 3 -0.15341477
+New Hampshire 2 3 -0.17099889
+Connecticut 2 3 -0.19095000
+New Jersey 2 3 -0.19281567
+Kansas 2 3 -0.19719316
+California 2 3 -0.24006293
+Illinois 2 3 -0.25236336
+North Dakota 2 3 -0.25464430
+Virginia 2 3 -0.26262534
+Nevada 2 3 -0.27016336
+Colorado 2 3 -0.27885043
+Texas 2 1 -0.47297583
+South Carolina 2 1 -0.50899710
+New Mexico 3 2 0.39555584
+Washington 3 2 0.32989454
+Oklahoma 3 2 0.30953823
+Wyoming 3 2 0.30163169
+Idaho 3 2 0.29915132
+Montana 3 2 0.29105494
+Missouri 3 2 0.29038462
+Oregon 3 2 0.27710695
+Maryland 3 2 0.27437520
+West Virginia 3 2 0.27089938
+Utah 3 2 0.26964380
+Tennessee 3 2 0.26846440
+Arizona 3 2 0.25968564
+Delaware 3 2 0.25920434
+Kentucky 3 2 0.25868341
+South Dakota 3 2 0.25615670
+Indiana 3 2 0.25031548
+Wisconsin 3 2 0.21808013
+Ohio 3 2 0.21477474
+Nebraska 3 2 0.20965953
+North Carolina 3 2 0.19201537
+Minnesota 3 2 0.18955165
+New York 3 2 0.18820394
+Iowa 3 2 0.17296046
+Rhode Island 3 2 0.12599915
+Massachusetts 3 2 0.12106770
+Average silhouette width per cluster:
+[1] 0.4367620 -0.1876985 0.2497715
+Average silhouette width of total data set:
+[1] 0.1147212
+
+1225 dissimilarities, summarized :
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+ 17.199 48.343 64.681 82.227 105.490 281.950
+Metric : euclidean
+Number of objects : 50
+
+Available components:
+ [1] "medoids" "id.med" "clustering" "objective" "isolation"
+ [6] "clusinfo" "silinfo" "diss" "call" "data"
+> (pv4 <- pam(votes.repub, 4))
+Medoids:
+ ID X1856 X1860 X1864 X1868 X1872 X1876 X1880 X1884 X1888 X1892 X1896
+Alabama 1 NA NA NA 51.44 53.19 40.02 36.98 38.44 32.28 3.95 28.13
+Alaska 2 NA NA NA NA NA NA NA NA NA NA NA
+New Mexico 31 NA NA NA NA NA NA NA NA NA NA NA
+Iowa 15 49.13 54.87 64.23 61.92 64.18 58.58 56.85 52.42 52.36 49.60 55.46
+ X1900 X1904 X1908 X1912 X1916 X1920 X1924 X1928 X1932 X1936 X1940
+Alabama 34.67 20.65 24.38 8.26 21.97 30.98 27.01 48.49 14.15 12.82 14.34
+Alaska NA NA NA NA NA NA NA NA NA NA NA
+New Mexico NA NA NA 35.91 46.53 54.68 48.52 59.01 35.76 36.50 43.28
+Iowa 57.99 63.37 55.62 24.30 54.06 70.91 55.06 61.80 39.98 42.70 52.03
+ X1944 X1948 X1952 X1956 X1960 X1964 X1968 X1972 X1976
+Alabama 18.20 19.04 35.02 39.39 41.75 69.5 14.0 72.4 43.48
+Alaska NA NA NA NA 50.94 34.1 45.3 58.1 62.91
+New Mexico 46.44 42.93 55.39 57.81 49.41 41.0 51.8 61.0 51.04
+Iowa 51.99 47.58 63.76 59.06 56.71 38.1 53.0 57.6 50.51
+Clustering vector:
+ Alabama Alaska Arizona Arkansas California
+ 1 2 3 1 2
+ Colorado Connecticut Delaware Florida Georgia
+ 2 2 3 1 1
+ Hawaii Idaho Illinois Indiana Iowa
+ 2 3 4 3 4
+ Kansas Kentucky Louisiana Maine Maryland
+ 4 3 1 2 3
+ Massachusetts Michigan Minnesota Mississippi Missouri
+ 4 2 4 1 3
+ Montana Nebraska Nevada New Hampshire New Jersey
+ 3 4 2 2 2
+ New Mexico New York North Carolina North Dakota Ohio
+ 3 3 3 4 4
+ Oklahoma Oregon Pennsylvania Rhode Island South Carolina
+ 3 3 4 4 2
+ South Dakota Tennessee Texas Utah Vermont
+ 4 3 2 3 2
+ Virginia Washington West Virginia Wisconsin Wyoming
+ 2 3 3 4 3
+Objective function:
+ build swap
+35.84182 35.84182
+
+Available components:
+ [1] "medoids" "id.med" "clustering" "objective" "isolation"
+ [6] "clusinfo" "silinfo" "diss" "call" "data"
+> (pv6 <- pam(votes.repub, 6, trace = 3))
+C pam(): computing 1226 dissimilarities: [Ok]
+pam()'s bswap(*, s=281.951, pamonce=0): build 6 medoids:
+ new repr. 2
+ new repr. 1
+ new repr. 31
+ new repr. 15
+ new repr. 46
+ new repr. 40
+ after build: medoids are 1 2 15 31 40 46
+ and min.dist dysma[1:n] are
+ 0 0 37.7 56 35.8 28.5 28.6 31.7 54.1 48.2
+ 51.7 33.2 27.3 30.5 0 35.1 25.4 60.9 36.9 26.7
+ 48.4 28.1 33.2 63.1 21.1 28.6 37.5 35.8 29.8 31.3
+ 0 32 29.9 35.7 30.9 35.1 27.8 35.7 50.2 0
+ 26.2 30.2 45.2 34.1 33.8 0 28.5 35.1 34.2 28.8
+ swp new 10 <-> 1 old; decreasing diss. 1579.03 by -2.57067
+end{bswap()}, end{cstat()}
+Medoids:
+ ID X1856 X1860 X1864 X1868 X1872 X1876 X1880 X1884 X1888 X1892
+Georgia 10 NA NA NA 35.72 43.77 27.94 34.33 33.84 28.33 21.80
+Alaska 2 NA NA NA NA NA NA NA NA NA NA
+Virginia 46 0.19 1.15 NA NA 50.48 40.62 39.52 48.90 49.47 38.75
+New Mexico 31 NA NA NA NA NA NA NA NA NA NA
+Iowa 15 49.13 54.87 64.23 61.92 64.18 58.58 56.85 52.42 52.36 49.60
+South Carolina 40 NA NA NA 57.93 75.95 50.26 33.97 23.72 17.27 18.99
+ X1896 X1900 X1904 X1908 X1912 X1916 X1920 X1924 X1928 X1932
+Georgia 36.82 28.56 18.32 31.40 4.27 7.07 28.57 18.19 43.37 7.77
+Alaska NA NA NA NA NA NA NA NA NA NA
+Virginia 45.90 43.81 36.67 38.36 17.00 32.05 37.85 32.79 53.91 30.09
+New Mexico NA NA NA NA 35.91 46.53 54.68 48.52 59.01 35.76
+Iowa 55.46 57.99 63.37 55.62 24.30 54.06 70.91 55.06 61.80 39.98
+South Carolina 13.51 7.04 4.63 5.97 1.06 2.43 3.90 2.21 8.54 1.89
+ X1936 X1940 X1944 X1948 X1952 X1956 X1960 X1964 X1968 X1972
+Georgia 12.60 14.84 18.25 18.31 30.34 33.22 37.44 54.1 30.4 75.0
+Alaska NA NA NA NA NA NA 50.94 34.1 45.3 58.1
+Virginia 29.39 31.55 37.39 41.04 56.32 55.37 52.44 46.5 41.4 67.8
+New Mexico 36.50 43.28 46.44 42.93 55.39 57.81 49.41 41.0 51.8 61.0
+Iowa 42.70 52.03 51.99 47.58 63.76 59.06 56.71 38.1 53.0 57.6
+South Carolina 1.43 4.37 4.46 3.78 49.28 25.18 48.76 58.9 38.1 70.8
+ X1976
+Georgia 33.02
+Alaska 62.91
+Virginia 50.73
+New Mexico 51.04
+Iowa 50.51
+South Carolina 43.54
+Clustering vector:
+ Alabama Alaska Arizona Arkansas California
+ 1 2 3 3 2
+ Colorado Connecticut Delaware Florida Georgia
+ 2 2 4 3 1
+ Hawaii Idaho Illinois Indiana Iowa
+ 2 4 5 4 5
+ Kansas Kentucky Louisiana Maine Maryland
+ 5 4 1 2 4
+ Massachusetts Michigan Minnesota Mississippi Missouri
+ 5 2 5 6 4
+ Montana Nebraska Nevada New Hampshire New Jersey
+ 4 5 2 2 2
+ New Mexico New York North Carolina North Dakota Ohio
+ 4 4 3 5 5
+ Oklahoma Oregon Pennsylvania Rhode Island South Carolina
+ 4 4 5 5 6
+ South Dakota Tennessee Texas Utah Vermont
+ 5 3 2 4 2
+ Virginia Washington West Virginia Wisconsin Wyoming
+ 3 4 4 5 4
+Objective function:
+ build swap
+31.58067 31.52926
+
+Available components:
+ [1] "medoids" "id.med" "clustering" "objective" "isolation"
+ [6] "clusinfo" "silinfo" "diss" "call" "data"
+>
+> cat('Time elapsed: ', proc.time() - .proctime00,'\n')
+Time elapsed: 1.24 0.012 1.258 0 0
+>
+> ## re-starting with medoids from pv6 shouldn't change:
+> pv6. <- pam(votes.repub, 6, medoids = pv6$id.med, trace = 3)
+C pam(): computing 1226 dissimilarities: [Ok]
+pam()'s bswap(*, s=281.951, pamonce=0): medoids given
+ after build: medoids are 2 10 15 31 40 46
+ and min.dist dysma[1:n] are
+ 48.2 0 37.7 56 35.8 28.5 28.6 31.7 54.1 0
+ 51.7 33.2 27.3 30.5 0 35.1 25.4 58.3 36.9 26.7
+ 48.4 28.1 33.2 63.1 21.1 28.6 37.5 35.8 29.8 31.3
+ 0 32 29.9 35.7 30.9 35.1 27.8 35.7 50.2 0
+ 26.2 30.2 45.2 34.1 33.8 0 28.5 35.1 34.2 28.8
+end{bswap()}, end{cstat()}
+> identical(pv6[nm3], pv6.[nm3])
+[1] TRUE
+>
+> ## This example seg.faulted at some point:
+> d.st <- data.frame(V1= c(9, 12, 12, 15, 9, 9, 13, 11, 15, 10, 13, 13,
++ 13, 15, 8, 13, 13, 10, 7, 9, 6, 11, 3),
++ V2= c(5, 9, 3, 5, 1, 1, 2, NA, 10, 1, 4, 7,
++ 4, NA, NA, 5, 2, 4, 3, 3, 6, 1, 1),
++ V3 = c(63, 41, 59, 50, 290, 226, 60, 36, 32, 121, 70, 51,
++ 79, 32, 42, 39, 76, 60, 56, 88, 57, 309, 254),
++ V4 = c(146, 43, 78, 88, 314, 149, 78, NA, 238, 153, 159, 222,
++ 203, NA, NA, 74, 100, 111, 9, 180, 50, 256, 107))
+> dd <- daisy(d.st, stand = TRUE)
+> (r0 <- pam(dd, 5))# cluster 5 = { 23 } -- on single observation
+Medoids:
+ ID
+[1,] 15 15
+[2,] 8 8
+[3,] 14 14
+[4,] 22 22
+[5,] 23 23
+Clustering vector:
+ [1] 1 2 2 3 4 4 2 2 3 2 2 2 2 3 1 2 2 2 1 1 1 4 5
+Objective function:
+ build swap
+0.9368049 0.8621860
+
+Available components:
+[1] "medoids" "id.med" "clustering" "objective" "isolation"
+[6] "clusinfo" "silinfo" "diss" "call"
+> ## This gave only 3 different medoids -> and seg.fault:
+> (r5 <- pam(dd, 5, medoids = c(1,3,20,2,5), trace = 2)) # now "fine"
+pam()'s bswap(*, s=8.51931, pamonce=0): medoids given
+ after build: medoids are 1 2 3 5 20
+ swp new 14 <-> 2 old; decreasing diss. 29.8745 by -5.50096
+ swp new 15 <-> 1 old; decreasing diss. 24.3735 by -2.20162
+ swp new 6 <-> 20 old; decreasing diss. 22.1719 by -2.12745
+ swp new 8 <-> 3 old; decreasing diss. 20.0444 by -0.201608
+end{bswap()}, end{cstat()}
+Medoids:
+ ID
+[1,] 15 15
+[2,] 8 8
+[3,] 14 14
+[4,] 5 5
+[5,] 6 6
+Clustering vector:
+ [1] 1 2 2 3 4 5 2 2 3 5 2 2 2 3 1 2 2 2 1 1 1 4 5
+Objective function:
+ build swap
+1.2988899 0.8627319
+
+Available components:
+[1] "medoids" "id.med" "clustering" "objective" "isolation"
+[6] "clusinfo" "silinfo" "diss" "call"
+>
+> dev.off()
+null device
+ 1
+>
+> ##------------------------ Testing pam() with new "pamonce" argument:
+>
+> ## This is from "next version of Matrix" test-tools-1.R:
+> showSys.time <- function(expr) {
++ ## prepend 'Time' for R CMD Rdiff
++ st <- system.time(expr)
++ writeLines(paste("Time", capture.output(print(st))))
++ invisible(st)
++ }
+> show2Ratios <- function(...) {
++ stopifnot(length(rgs <- list(...)) == 2,
++ nchar(ns <- names(rgs)) > 0)
++ r <- round(cbind(..1, ..2)[c(1,3),], 3)
++ dimnames(r) <- list(paste("Time ", rownames(r)), ns)
++ r
++ }
+>
+>
+> n <- 1000
+> ## If not enough cases, all CPU times equals 0.
+> n <- 500 # for now, and automatic testing
+>
+> sd <- 0.5
+> set.seed(13)
+> n2 <- as.integer(round(n * 1.5))
+> x <- rbind(cbind(rnorm( n,0,sd), rnorm( n,0,sd)),
++ cbind(rnorm(n2,5,sd), rnorm(n2,5,sd)),
++ cbind(rnorm(n2,7,sd), rnorm(n2,7,sd)),
++ cbind(rnorm(n2,9,sd), rnorm(n2,9,sd)))
+>
+>
+> ## original algorithm
+> st0 <- showSys.time(pamx <- pam(x, 4, trace.lev=2))# 8.157 0.024 8.233
+C pam(): computing 3779876 dissimilarities: [Ok]
+pam()'s bswap(*, s=15.7788, pamonce=0): build 4 medoids:
+ new repr. 1268
+ new repr. 414
+ new repr. 2153
+ new repr. 915
+ after build: medoids are 414 915 1268 2153
+ swp new 1793 <-> 1268 old; decreasing diss. 1862.37 by -129.13
+end{bswap()}, end{cstat()}
+Time user system elapsed
+Time 1.516 0.012 1.536
+> ## bswapPamOnce algorithm
+> st1 <- showSys.time(pamxonce <- pam(x, 4, pamonce=TRUE, trace.lev=2))# 6.122 0.024 6.181
+C pam(): computing 3779876 dissimilarities: [Ok]
+pam()'s bswap(*, s=15.7788, pamonce=1): build 4 medoids:
+ new repr. 1268
+ new repr. 414
+ new repr. 2153
+ new repr. 915
+ after build: medoids are 414 915 1268 2153
+ swp new 1793 <-> 1268 old; decreasing diss. 1862.37 by -129.13
+end{bswap()}, end{cstat()}
+Time user system elapsed
+Time 1.400 0.008 1.413
+> ## bswapPamOnceDistIndice
+> st2 <- showSys.time(pamxonce2 <- pam(x, 4, pamonce = 2, trace.lev=2))# 4.101 0.024 4.151
+C pam(): computing 3779876 dissimilarities: [Ok]
+pam()'s bswap(*, s=15.7788, pamonce=2): build 4 medoids:
+ new repr. 1268
+ new repr. 414
+ new repr. 2153
+ new repr. 915
+ after build: medoids are 414 915 1268 2153
+ swp new 1793 <-> 1268 old; decreasing diss. 1862.37 by -129.13
+end{bswap()}, end{cstat()}
+Time user system elapsed
+Time 1.064 0.000 1.069
+> show2Ratios('2:orig' = st2/st0, '1:orig' = st1/st0)
+ 2:orig 1:orig
+Time user.self 0.702 0.923
+Time elapsed 0.696 0.920
+>
+> ## only call element is not equal
+> (icall <- which(names(pamx) == "call"))
+[1] 9
+> pamx[[icall]]
+pam(x = x, k = 4, trace.lev = 2)
+> stopifnot(all.equal(pamx [-icall], pamxonce [-icall]),
++ all.equal(pamxonce[-icall], pamxonce2[-icall]))
+>
+> ## Same using specified medoids
+> (med0 <- 1 + round(n* c(0,1, 2.5, 4)))# lynne (~ 2010, AMD Phenom II X4 925)
+[1] 1 501 1251 2001
+> st0 <- showSys.time(pamxst <- pam(x, 4, medoids = med0, trace.lev=2))# 13.071 0.024 13.177
+C pam(): computing 3779876 dissimilarities: [Ok]
+pam()'s bswap(*, s=15.7788, pamonce=0): medoids given
+ after build: medoids are 1 501 1251 2001
+ swp new 915 <-> 501 old; decreasing diss. 2126.83 by -197.507
+ swp new 1793 <-> 1251 old; decreasing diss. 1929.32 by -101.336
+ swp new 414 <-> 1 old; decreasing diss. 1827.98 by -86.3404
+ swp new 2153 <-> 2001 old; decreasing diss. 1741.64 by -8.40201
+end{bswap()}, end{cstat()}
+Time user system elapsed
+Time 2.432 0.000 2.439
+> st1 <- showSys.time(pamxoncest <- pam(x, 4, medoids = med0, pamonce=TRUE, trace.lev=2))# 8.503 0.024 8.578
+C pam(): computing 3779876 dissimilarities: [Ok]
+pam()'s bswap(*, s=15.7788, pamonce=1): medoids given
+ after build: medoids are 1 501 1251 2001
+ swp new 915 <-> 501 old; decreasing diss. 2126.83 by -197.507
+ swp new 1793 <-> 1251 old; decreasing diss. 1929.32 by -101.336
+ swp new 414 <-> 1 old; decreasing diss. 1827.98 by -86.3404
+ swp new 2153 <-> 2001 old; decreasing diss. 1741.64 by -8.40201
+end{bswap()}, end{cstat()}
+Time user system elapsed
+Time 2.112 0.000 2.118
+> st2 <- showSys.time(pamxonce2st <- pam(x, 4, medoids = med0, pamonce=2, trace.lev=2))# 5.587 0.025 5.647
+C pam(): computing 3779876 dissimilarities: [Ok]
+pam()'s bswap(*, s=15.7788, pamonce=2): medoids given
+ after build: medoids are 1 501 1251 2001
+ swp new 915 <-> 501 old; decreasing diss. 2126.83 by -197.507
+ swp new 1793 <-> 1251 old; decreasing diss. 1929.32 by -101.336
+ swp new 414 <-> 1 old; decreasing diss. 1827.98 by -86.3404
+ swp new 2153 <-> 2001 old; decreasing diss. 1741.64 by -8.40201
+end{bswap()}, end{cstat()}
+Time user system elapsed
+Time 1.288 0.000 1.289
+> show2Ratios('2:orig' = st2/st0, '1:orig' = st1/st0)
+ 2:orig 1:orig
+Time user.self 0.530 0.868
+Time elapsed 0.528 0.868
+>
+> ## only call element is not equal
+> stopifnot(all.equal(pamxst [-icall], pamxoncest [-icall]),
++ all.equal(pamxoncest[-icall], pamxonce2st[-icall]))
+>
+> ## Different starting values
+> med0 <- 1:4 # lynne (~ 2010, AMD Phenom II X4 925)
+> st0 <- showSys.time(pamxst <- pam(x, 4, medoids = med0, trace.lev=2))# 13.416 0.023 13.529
+C pam(): computing 3779876 dissimilarities: [Ok]
+pam()'s bswap(*, s=15.7788, pamonce=0): medoids given
+ after build: medoids are 1 2 3 4
+ swp new 1421 <-> 4 old; decreasing diss. 21009.4 by -15939.9
+ swp new 2153 <-> 3 old; decreasing diss. 5069.52 by -1657.88
+ swp new 915 <-> 2 old; decreasing diss. 3411.65 by -1592.06
+ swp new 414 <-> 1 old; decreasing diss. 1819.59 by -86.3404
+ swp new 1793 <-> 1421 old; decreasing diss. 1733.25 by -0.00639415
+end{bswap()}, end{cstat()}
+Time user system elapsed
+Time 3.008 0.000 3.016
+> st1 <- showSys.time(pamxoncest <- pam(x, 4, medoids = med0, pamonce=TRUE, trace.lev=2))# 8.384 0.024 8.459
+C pam(): computing 3779876 dissimilarities: [Ok]
+pam()'s bswap(*, s=15.7788, pamonce=1): medoids given
+ after build: medoids are 1 2 3 4
+ swp new 1421 <-> 4 old; decreasing diss. 21009.4 by -15939.9
+ swp new 2153 <-> 3 old; decreasing diss. 5069.52 by -1657.88
+ swp new 915 <-> 2 old; decreasing diss. 3411.65 by -1592.06
+ swp new 414 <-> 1 old; decreasing diss. 1819.59 by -86.3404
+ swp new 1793 <-> 1421 old; decreasing diss. 1733.25 by -0.00639415
+end{bswap()}, end{cstat()}
+Time user system elapsed
+Time 2.441 0.000 2.448
+> st2 <- showSys.time(pamxonce2st <- pam(x, 4, medoids = med0, pamonce=2, trace.lev=2))# 5.455 0.030 5.520
+C pam(): computing 3779876 dissimilarities: [Ok]
+pam()'s bswap(*, s=15.7788, pamonce=2): medoids given
+ after build: medoids are 1 2 3 4
+ swp new 1421 <-> 4 old; decreasing diss. 21009.4 by -15939.9
+ swp new 2153 <-> 3 old; decreasing diss. 5069.52 by -1657.88
+ swp new 915 <-> 2 old; decreasing diss. 3411.65 by -1592.06
+ swp new 414 <-> 1 old; decreasing diss. 1819.59 by -86.3404
+ swp new 1793 <-> 1421 old; decreasing diss. 1733.25 by -0.00639415
+end{bswap()}, end{cstat()}
+Time user system elapsed
+Time 1.468 0.000 1.470
+> show2Ratios('2:orig' = st2/st0, '1:orig' = st1/st0)
+ 2:orig 1:orig
+Time user.self 0.488 0.812
+Time elapsed 0.487 0.812
+>
+> ## only call element is not equal
+> stopifnot(all.equal(pamxst [-icall], pamxoncest [-icall]),
++ all.equal(pamxoncest[-icall], pamxonce2st[-icall]))
+>
+>
+> ## Medoid bug --- MM: Fixed, well "0L+ hack", in my pam.q, on 2012-01-31
+> ## ----------
+> med0 <- (1:6)
+> st0 <- showSys.time(pamxst <- pam(x, 6, medoids = med0 , trace.lev=2))
+C pam(): computing 3779876 dissimilarities: [Ok]
+pam()'s bswap(*, s=15.7788, pamonce=0): medoids given
+ after build: medoids are 1 2 3 4 5 6
+ swp new 1421 <-> 6 old; decreasing diss. 20991.1 by -15949.5
+ swp new 2153 <-> 4 old; decreasing diss. 5041.66 by -1676.25
+ swp new 915 <-> 3 old; decreasing diss. 3365.41 by -1671.37
+ swp new 325 <-> 2 old; decreasing diss. 1694.04 by -53.8582
+ swp new 2720 <-> 5 old; decreasing diss. 1640.18 by -26.6572
+ swp new 2696 <-> 2153 old; decreasing diss. 1613.53 by -19.0531
+ swp new 52 <-> 1 old; decreasing diss. 1594.47 by -13.965
+ swp new 2709 <-> 2720 old; decreasing diss. 1580.51 by -5.81848
+ swp new 199 <-> 325 old; decreasing diss. 1574.69 by -2.65496
+ swp new 438 <-> 52 old; decreasing diss. 1572.03 by -1.77054
+ swp new 2082 <-> 2696 old; decreasing diss. 1570.26 by -0.187256
+end{bswap()}, end{cstat()}
+Time user system elapsed
+Time 8.140 0.000 8.161
+> stopifnot(identical(med0, 1:6))
+> med0 <- (1:6)
+> st1 <- showSys.time(pamxst.1 <- pam(x, 6, medoids = med0 , pamonce=1, trace.lev=2))
+C pam(): computing 3779876 dissimilarities: [Ok]
+pam()'s bswap(*, s=15.7788, pamonce=1): medoids given
+ after build: medoids are 1 2 3 4 5 6
+ swp new 1421 <-> 6 old; decreasing diss. 20991.1 by -15949.5
+ swp new 2153 <-> 4 old; decreasing diss. 5041.66 by -1676.25
+ swp new 915 <-> 3 old; decreasing diss. 3365.41 by -1671.37
+ swp new 325 <-> 2 old; decreasing diss. 1694.04 by -53.8582
+ swp new 2720 <-> 5 old; decreasing diss. 1640.18 by -26.6572
+ swp new 2696 <-> 2153 old; decreasing diss. 1613.53 by -19.0531
+ swp new 52 <-> 1 old; decreasing diss. 1594.47 by -13.965
+ swp new 2709 <-> 2720 old; decreasing diss. 1580.51 by -5.81848
+ swp new 199 <-> 325 old; decreasing diss. 1574.69 by -2.65496
+ swp new 438 <-> 52 old; decreasing diss. 1572.03 by -1.77054
+ swp new 2082 <-> 2696 old; decreasing diss. 1570.26 by -0.187256
+end{bswap()}, end{cstat()}
+Time user system elapsed
+Time 6.817 0.000 6.833
+> stopifnot(identical(med0, 1:6))
+> stopifnot(all.equal(pamxst[-icall], pamxst.1 [-icall]))
+>
+>
+> ## Last Line:
+> cat('Time elapsed: ', proc.time() - .proctime00,'\n')
+Time elapsed: 33.318 0.032 33.446 0 0
+>
+>
diff --git a/win32/deps/library/cluster/tests/silhouette-default.R b/win32/deps/library/cluster/tests/silhouette-default.R
new file mode 100644
index 0000000..32130c6
--- /dev/null
+++ b/win32/deps/library/cluster/tests/silhouette-default.R
@@ -0,0 +1,83 @@
+## This came from a bug report on R-help by ge yreyt <tothri2000 yahoo ca>
+## Date: Mon, 9 Jun 2003 16:06:53 -0400 (EDT)
+library(cluster)
+if(FALSE) # manual testing
+library(cluster, lib="~/R/Pkgs/cluster.Rcheck")
+
+data(iris)
+
+.proctime00 <- proc.time()
+
+mdist <- as.dist(1 - cor(t(iris[,1:4])))#dissimlarity
+## this is always the same:
+hc <- diana(mdist, diss = TRUE, stand = FALSE)
+
+maxk <- 15 # at most 15 clusters
+silh.wid <- numeric(maxk) # myind[k] := the silh.value for k clusters
+silh.wid[1] <- NA # 1-cluster: silhouette not defined
+
+op <- par(mfrow = c(4,4), mar = .1+ c(2,1,2,1), mgp=c(1.5, .6,0))
+for(k in 2:maxk) {
+ cat("\n", k,":\n==\n")
+ k.gr <- cutree(as.hclust(hc), k = k)
+ cat("grouping table: "); print(table(k.gr))
+ si <- silhouette(k.gr, mdist)
+ cat("silhouette:\n"); print(summary(si))
+ plot(si, main = paste("k =",k),
+ col = 2:(k+1), do.n.k=FALSE, do.clus.stat=FALSE)
+ silh.wid[k] <- summary(si)$avg.width
+ ## ===
+}
+par(op)
+
+summary(si.p <- silhouette(50 - k.gr, mdist))
+stopifnot(identical(si.p[,3], si[,3]),
+ identical(si.p[, 1:2], 50 - si[, 1:2]))
+
+# the widths:
+silh.wid
+#select the number of k clusters with the largest si value :
+(myk <- which.min(silh.wid)) # -> 8 (here)
+
+postscript(file="silhouette-ex.ps")
+## MM: plot to see how the decision is made
+plot(silh.wid, type = 'b', col= "blue", xlab = "k")
+axis(1, at=myk, col.axis= "red", font.axis= 2)
+
+##--- PAM()'s silhouette should give same as silh*.default()!
+Eq <- function(x,y, tol = 1e-12) x == y | abs(x - y) < tol * abs((x+y)/2)
+
+for(k in 2:40) {
+ cat("\n", k,":\n==\n")
+ p.k <- pam(mdist, k = k)
+ k.gr <- p.k$clustering
+ si.p <- silhouette(p.k)
+ si.g <- silhouette(k.gr, mdist)
+ ## since the obs.order may differ (within cluster):
+ si.g <- si.g[ as.integer(rownames(si.p)), ]
+ cat("grouping table: "); print(table(k.gr))
+ if(!isTRUE(all.equal(c(si.g), c(si.p)))) {
+ cat("silhouettes differ:")
+ if(any(neq <- !Eq(si.g[,3], si.p[,3]))) {
+ cat("\n")
+ print( cbind(si.p[], si.g[,2:3])[ neq, ] )
+ } else cat(" -- but not in col.3 !\n")
+ }
+}
+
+
+## "pathological" case where a_i == b_i == 0 :
+D6 <- structure(c(0, 0, 0, 0.4, 1, 0.05, 1, 1, 0, 1, 1, 0, 0.25, 1, 1),
+ Labels = LETTERS[1:6], Size = 6, call = as.name("manually"),
+ class = "dist", Diag = FALSE, Upper = FALSE)
+D6
+kl6 <- c(1,1, 2,2, 3,3)
+silhouette(kl6, D6)# had one NaN
+summary(silhouette(kl6, D6))
+plot(silhouette(kl6, D6))# gives error in earlier cluster versions
+
+dev.off()
+
+## Last Line:
+cat('Time elapsed: ', proc.time() - .proctime00,'\n')
+
diff --git a/win32/deps/library/cluster/tests/silhouette-default.Rout.save b/win32/deps/library/cluster/tests/silhouette-default.Rout.save
new file mode 100644
index 0000000..10e0f1e
--- /dev/null
+++ b/win32/deps/library/cluster/tests/silhouette-default.Rout.save
@@ -0,0 +1,616 @@
+
+R Under development (unstable) (2011-08-28 r56813)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: i686-pc-linux-gnu (32-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> ## This came from a bug report on R-help by ge yreyt <tothri2000 yahoo ca>
+> ## Date: Mon, 9 Jun 2003 16:06:53 -0400 (EDT)
+> library(cluster)
+> if(FALSE) # manual testing
++ library(cluster, lib="~/R/Pkgs/cluster.Rcheck")
+>
+> data(iris)
+>
+> .proctime00 <- proc.time()
+>
+> mdist <- as.dist(1 - cor(t(iris[,1:4])))#dissimlarity
+> ## this is always the same:
+> hc <- diana(mdist, diss = TRUE, stand = FALSE)
+>
+> maxk <- 15 # at most 15 clusters
+> silh.wid <- numeric(maxk) # myind[k] := the silh.value for k clusters
+> silh.wid[1] <- NA # 1-cluster: silhouette not defined
+>
+> op <- par(mfrow = c(4,4), mar = .1+ c(2,1,2,1), mgp=c(1.5, .6,0))
+> for(k in 2:maxk) {
++ cat("\n", k,":\n==\n")
++ k.gr <- cutree(as.hclust(hc), k = k)
++ cat("grouping table: "); print(table(k.gr))
++ si <- silhouette(k.gr, mdist)
++ cat("silhouette:\n"); print(summary(si))
++ plot(si, main = paste("k =",k),
++ col = 2:(k+1), do.n.k=FALSE, do.clus.stat=FALSE)
++ silh.wid[k] <- summary(si)$avg.width
++ ## ===
++ }
+
+ 2 :
+==
+grouping table: k.gr
+ 1 2
+ 50 100
+silhouette:
+Silhouette of 150 units in 2 clusters from silhouette.default(x = k.gr, dist = mdist) :
+ Cluster sizes and average silhouette widths:
+ 50 100
+0.9829965 0.9362626
+Individual silhouette widths:
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+ 0.5884 0.9437 0.9611 0.9518 0.9815 0.9918
+
+ 3 :
+==
+grouping table: k.gr
+ 1 2 3
+50 50 50
+silhouette:
+Silhouette of 150 units in 3 clusters from silhouette.default(x = k.gr, dist = mdist) :
+ Cluster sizes and average silhouette widths:
+ 50 50 50
+0.9773277 0.6926798 0.7467236
+Individual silhouette widths:
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+0.03353 0.76940 0.86120 0.80560 0.97560 0.98920
+
+ 4 :
+==
+grouping table: k.gr
+ 1 2 3 4
+35 15 50 50
+silhouette:
+Silhouette of 150 units in 4 clusters from silhouette.default(x = k.gr, dist = mdist) :
+ Cluster sizes and average silhouette widths:
+ 35 15 50 50
+0.5653722 0.5226372 0.6926798 0.7467236
+Individual silhouette widths:
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+0.03353 0.56620 0.75100 0.66400 0.84240 0.89390
+
+ 5 :
+==
+grouping table: k.gr
+ 1 2 3 4 5
+35 15 29 21 50
+silhouette:
+Silhouette of 150 units in 5 clusters from silhouette.default(x = k.gr, dist = mdist) :
+ Cluster sizes and average silhouette widths:
+ 35 15 29 21 50
+0.5653722 0.5226372 0.5776362 0.4625437 0.5296735
+Individual silhouette widths:
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+-0.5404 0.3937 0.6252 0.5372 0.7392 0.8136
+
+ 6 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6
+35 15 29 21 29 21
+silhouette:
+Silhouette of 150 units in 6 clusters from silhouette.default(x = k.gr, dist = mdist) :
+ Cluster sizes and average silhouette widths:
+ 35 15 29 21 29 21
+0.5653722 0.5226372 0.5776362 0.3732981 0.3383135 0.5945444
+Individual silhouette widths:
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+-0.1094 0.3351 0.5257 0.4968 0.6938 0.8136
+
+ 7 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7
+35 14 1 29 21 29 21
+silhouette:
+Silhouette of 150 units in 7 clusters from silhouette.default(x = k.gr, dist = mdist) :
+ Cluster sizes and average silhouette widths:
+ 35 14 1 29 21 29 21
+0.4165289 0.6671435 0.0000000 0.5776362 0.3732981 0.3383135 0.5945444
+Individual silhouette widths:
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+-0.3264 0.3001 0.5234 0.4720 0.6970 0.8301
+
+ 8 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8
+35 14 1 29 10 11 29 21
+silhouette:
+Silhouette of 150 units in 8 clusters from silhouette.default(x = k.gr, dist = mdist) :
+ Cluster sizes and average silhouette widths:
+ 35 14 1 29 10 11 29 21
+0.4165289 0.6671435 0.0000000 0.4209012 0.6943265 0.7262601 0.2053018 0.5945444
+Individual silhouette widths:
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+-0.6258 0.2576 0.5842 0.4633 0.7132 0.8887
+
+ 9 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9
+35 14 1 26 10 11 3 29 21
+silhouette:
+Silhouette of 150 units in 9 clusters from silhouette.default(x = k.gr, dist = mdist) :
+ Cluster sizes and average silhouette widths:
+ 35 14 1 26 10 11 3 29
+0.4165289 0.6671435 0.0000000 0.5318152 0.6673269 0.6944652 0.7957279 0.2053018
+ 21
+0.5945444
+Individual silhouette widths:
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+-0.6258 0.3150 0.5896 0.4859 0.7263 0.8870
+
+ 10 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10
+35 14 1 26 10 11 3 16 13 21
+silhouette:
+Silhouette of 150 units in 10 clusters from silhouette.default(x = k.gr, dist = mdist) :
+ Cluster sizes and average silhouette widths:
+ 35 14 1 26 10 11 3 16
+0.4165289 0.6671435 0.0000000 0.5318152 0.6319149 0.6145837 0.7957279 0.4640123
+ 13 21
+0.6615431 0.4228530
+Individual silhouette widths:
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+-0.5870 0.3535 0.6068 0.5208 0.7349 0.8803
+
+ 11 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11
+35 14 1 26 10 11 3 16 13 11 10
+silhouette:
+Silhouette of 150 units in 11 clusters from silhouette.default(x = k.gr, dist = mdist) :
+ Cluster sizes and average silhouette widths:
+ 35 14 1 26 10 11 3 16
+0.4165289 0.6671435 0.0000000 0.5318152 0.6319149 0.6145837 0.7957279 0.4064279
+ 13 11 10
+0.5866228 0.4297258 0.6590274
+Individual silhouette widths:
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+-0.3264 0.3730 0.5984 0.5244 0.7302 0.8505
+
+ 12 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12
+35 11 3 1 26 10 11 3 16 13 11 10
+silhouette:
+Silhouette of 150 units in 12 clusters from silhouette.default(x = k.gr, dist = mdist) :
+ Cluster sizes and average silhouette widths:
+ 35 11 3 1 26 10 11 3
+0.2883758 0.7044155 0.4092330 0.0000000 0.5318152 0.6319149 0.6145837 0.7957279
+ 16 13 11 10
+0.4064279 0.5866228 0.4297258 0.6590274
+Individual silhouette widths:
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+-0.6007 0.3395 0.5817 0.4921 0.7216 0.8700
+
+ 13 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13
+28 11 3 7 1 26 10 11 3 16 13 11 10
+silhouette:
+Silhouette of 150 units in 13 clusters from silhouette.default(x = k.gr, dist = mdist) :
+ Cluster sizes and average silhouette widths:
+ 28 11 3 7 1 26 10 11
+0.3783869 0.6827810 0.4092330 0.4285753 0.0000000 0.5318152 0.6319149 0.6145837
+ 3 16 13 11 10
+0.7957279 0.4064279 0.5866228 0.4297258 0.6590274
+Individual silhouette widths:
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+-0.4013 0.3314 0.5704 0.5138 0.7274 0.8531
+
+ 14 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14
+19 11 3 9 7 1 26 10 11 3 16 13 11 10
+silhouette:
+Silhouette of 150 units in 14 clusters from silhouette.default(x = k.gr, dist = mdist) :
+ Cluster sizes and average silhouette widths:
+ 19 11 3 9 7 1 26 10
+0.5419530 0.6171802 0.3959926 0.4525348 0.1669077 0.0000000 0.5318152 0.6319149
+ 11 3 16 13 11 10
+0.6145837 0.7957279 0.4064279 0.5866228 0.4297258 0.6590274
+Individual silhouette widths:
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+-0.5929 0.3795 0.5875 0.5217 0.7263 0.8505
+
+ 15 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
+19 11 3 9 7 1 18 10 11 8 3 16 13 11 10
+silhouette:
+Silhouette of 150 units in 15 clusters from silhouette.default(x = k.gr, dist = mdist) :
+ Cluster sizes and average silhouette widths:
+ 19 11 3 9 7 1 18 10
+0.5419530 0.6171802 0.3959926 0.4525348 0.1669077 0.0000000 0.6616381 0.5871805
+ 11 8 3 16 13 11 10
+0.5171407 0.6705138 0.7444822 0.4064279 0.5866228 0.4297258 0.6590274
+Individual silhouette widths:
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+-0.5929 0.3859 0.6211 0.5335 0.7478 0.8551
+> par(op)
+>
+> summary(si.p <- silhouette(50 - k.gr, mdist))
+Silhouette of 150 units in 15 clusters from silhouette.default(x = 50 - k.gr, dist = mdist) :
+ Cluster sizes, ids = (35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49), and average silhouette widths:
+ 10 11 13 16 3 8 11 10
+0.6590274 0.4297258 0.5866228 0.4064279 0.7444822 0.6705138 0.5171407 0.5871805
+ 18 1 7 9 3 11 19
+0.6616381 0.0000000 0.1669077 0.4525348 0.3959926 0.6171802 0.5419530
+Individual silhouette widths:
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+-0.5929 0.3859 0.6211 0.5335 0.7478 0.8551
+> stopifnot(identical(si.p[,3], si[,3]),
++ identical(si.p[, 1:2], 50 - si[, 1:2]))
+>
+> # the widths:
+> silh.wid
+ [1] NA 0.9518406 0.8055770 0.6639850 0.5371742 0.4967654 0.4720384
+ [8] 0.4633064 0.4858965 0.5207776 0.5243911 0.4920638 0.5138220 0.5217026
+[15] 0.5335255
+> #select the number of k clusters with the largest si value :
+> (myk <- which.min(silh.wid)) # -> 8 (here)
+[1] 8
+>
+> postscript(file="silhouette-ex.ps")
+> ## MM: plot to see how the decision is made
+> plot(silh.wid, type = 'b', col= "blue", xlab = "k")
+> axis(1, at=myk, col.axis= "red", font.axis= 2)
+>
+> ##--- PAM()'s silhouette should give same as silh*.default()!
+> Eq <- function(x,y, tol = 1e-12) x == y | abs(x - y) < tol * abs((x+y)/2)
+>
+> for(k in 2:40) {
++ cat("\n", k,":\n==\n")
++ p.k <- pam(mdist, k = k)
++ k.gr <- p.k$clustering
++ si.p <- silhouette(p.k)
++ si.g <- silhouette(k.gr, mdist)
++ ## since the obs.order may differ (within cluster):
++ si.g <- si.g[ as.integer(rownames(si.p)), ]
++ cat("grouping table: "); print(table(k.gr))
++ if(!isTRUE(all.equal(c(si.g), c(si.p)))) {
++ cat("silhouettes differ:")
++ if(any(neq <- !Eq(si.g[,3], si.p[,3]))) {
++ cat("\n")
++ print( cbind(si.p[], si.g[,2:3])[ neq, ] )
++ } else cat(" -- but not in col.3 !\n")
++ }
++ }
+
+ 2 :
+==
+grouping table: k.gr
+ 1 2
+ 50 100
+
+ 3 :
+==
+grouping table: k.gr
+ 1 2 3
+50 50 50
+
+ 4 :
+==
+grouping table: k.gr
+ 1 2 3 4
+50 43 37 20
+
+ 5 :
+==
+grouping table: k.gr
+ 1 2 3 4 5
+50 25 35 20 20
+
+ 6 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6
+33 17 25 35 20 20
+
+ 7 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7
+33 17 17 14 18 31 20
+
+ 8 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8
+21 13 16 17 14 18 31 20
+
+ 9 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9
+21 13 16 12 20 11 19 17 21
+
+ 10 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10
+21 13 16 18 10 15 14 7 16 20
+
+ 11 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11
+21 13 16 19 10 14 7 6 15 13 16
+
+ 12 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12
+21 13 16 17 10 12 9 3 5 15 13 16
+
+ 13 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13
+21 12 16 1 18 11 12 9 3 15 13 4 15
+
+ 14 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14
+20 10 7 13 18 10 12 9 3 7 10 13 4 14
+
+ 15 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
+20 11 5 13 1 18 10 12 9 3 7 10 13 4 14
+
+ 16 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
+20 11 5 13 1 12 8 9 11 9 3 7 10 13 4 14
+
+ 17 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
+20 11 5 13 1 12 8 7 9 10 3 3 9 13 4 13 9
+
+ 18 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
+20 11 5 9 4 1 12 8 7 9 10 3 3 9 13 4 13 9
+
+ 19 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
+20 11 5 9 4 1 10 8 8 9 8 3 3 9 13 3 4 13 9
+
+ 20 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
+20 11 5 9 4 1 10 8 8 9 8 3 3 9 12 3 4 6 9 8
+
+ 21 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
+20 11 5 9 4 1 10 8 8 7 8 3 3 7 11 3 4 6 9 8 5
+
+ 22 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
+ 9 11 5 9 11 4 1 10 8 8 7 8 3 3 7 11 3 4 6 9 8 5
+
+ 23 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
+ 9 11 5 9 11 4 1 10 8 8 7 8 3 3 7 11 3 4 6 8 8 5 1
+
+ 24 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
+15 10 5 10 3 3 3 1 10 8 8 7 8 3 3 7 11 3 4 6 8 8 5 1
+
+ 25 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
+ 8 4 5 9 11 7 2 3 1 10 8 8 7 8 3 3 7 11 3 4 6 8 8 5 1
+
+ 26 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
+ 8 4 5 9 11 7 2 3 1 10 8 8 7 8 3 3 7 7 3 4 6 8 8 4 5 1
+
+ 27 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
+ 8 4 5 9 11 7 2 3 1 10 8 7 7 8 3 2 7 7 3 2 4 6 8 8 4 5
+27
+ 1
+
+ 28 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
+ 8 4 4 9 11 7 2 3 1 1 10 8 7 7 8 3 2 7 7 3 2 4 6 8 8 4
+27 28
+ 5 1
+
+ 29 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
+ 8 4 4 9 11 7 2 3 1 1 10 8 7 7 8 2 2 7 7 3 2 1 4 6 8 8
+27 28 29
+ 4 5 1
+
+ 30 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
+ 8 4 11 10 6 3 2 3 1 1 1 10 8 7 7 8 2 2 7 7 3 2 1 4 6 8
+27 28 29 30
+ 8 4 5 1
+
+ 31 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
+ 8 4 11 10 6 3 2 3 1 1 1 10 8 7 7 8 2 2 7 7 3 2 1 4 6 7
+27 28 29 30 31
+ 7 4 5 1 2
+
+ 32 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
+ 7 4 3 10 10 6 2 2 3 1 1 1 10 8 7 7 8 2 2 7 7 3 2 1 4 6
+27 28 29 30 31 32
+ 7 7 4 5 1 2
+
+ 33 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
+ 7 4 3 10 10 6 2 2 3 1 1 1 10 8 7 7 8 2 2 7 7 3 2 1 1 6
+27 28 29 30 31 32 33
+ 7 3 7 4 5 1 2
+
+ 34 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
+ 7 4 3 8 9 6 2 3 3 1 1 2 1 10 8 7 7 8 2 2 7 7 3 2 1 1
+27 28 29 30 31 32 33 34
+ 6 7 3 7 4 5 1 2
+
+ 35 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
+ 7 4 3 8 9 6 2 3 3 1 1 2 1 10 8 7 7 8 2 2 5 7 3 2 1 1
+27 28 29 30 31 32 33 34 35
+ 6 5 3 7 4 4 5 1 2
+
+ 36 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
+ 7 4 3 8 9 6 2 3 3 1 1 2 1 10 8 7 6 8 2 2 5 7 1 3 2 1
+27 28 29 30 31 32 33 34 35 36
+ 1 6 5 3 7 4 4 5 1 2
+
+ 37 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
+ 7 4 3 8 9 6 2 3 3 1 1 2 1 10 8 3 5 6 8 2 2 5 7 1 3 2
+27 28 29 30 31 32 33 34 35 36 37
+ 1 1 6 5 3 7 4 5 1 3 2
+
+ 38 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
+ 7 4 3 8 9 6 2 3 3 1 1 2 1 10 8 3 5 6 5 2 2 5 3 7 1 3
+27 28 29 30 31 32 33 34 35 36 37 38
+ 2 1 1 6 5 3 7 4 5 1 3 2
+
+ 39 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
+ 7 4 3 8 9 6 2 3 3 1 1 2 1 7 3 8 3 5 6 5 2 2 5 3 7 1
+27 28 29 30 31 32 33 34 35 36 37 38 39
+ 3 2 1 1 6 5 3 7 4 5 1 3 2
+
+ 40 :
+==
+grouping table: k.gr
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
+ 5 4 3 7 10 6 2 2 3 3 1 1 2 1 7 3 8 3 5 6 5 2 2 5 3 7
+27 28 29 30 31 32 33 34 35 36 37 38 39 40
+ 1 3 2 1 1 6 5 3 7 4 5 1 3 2
+>
+>
+> ## "pathological" case where a_i == b_i == 0 :
+> D6 <- structure(c(0, 0, 0, 0.4, 1, 0.05, 1, 1, 0, 1, 1, 0, 0.25, 1, 1),
++ Labels = LETTERS[1:6], Size = 6, call = as.name("manually"),
++ class = "dist", Diag = FALSE, Upper = FALSE)
+> D6
+ A B C D E
+B 0.00
+C 0.00 0.05
+D 0.00 1.00 1.00
+E 0.40 1.00 1.00 0.25
+F 1.00 0.00 0.00 1.00 1.00
+> kl6 <- c(1,1, 2,2, 3,3)
+> silhouette(kl6, D6)# had one NaN
+ cluster neighbor sil_width
+[1,] 1 2 0.000
+[2,] 1 3 1.000
+[3,] 2 1 -0.975
+[4,] 2 1 -0.500
+[5,] 3 2 -0.375
+[6,] 3 1 -0.500
+attr(,"Ordered")
+[1] FALSE
+attr(,"call")
+silhouette.default(x = kl6, dist = D6)
+attr(,"class")
+[1] "silhouette"
+> summary(silhouette(kl6, D6))
+Silhouette of 6 units in 3 clusters from silhouette.default(x = kl6, dist = D6) :
+ Cluster sizes and average silhouette widths:
+ 2 2 2
+ 0.5000 -0.7375 -0.4375
+Individual silhouette widths:
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+-0.97500 -0.50000 -0.43750 -0.22500 -0.09375 1.00000
+> plot(silhouette(kl6, D6))# gives error in earlier cluster versions
+>
+> dev.off()
+pdf
+ 2
+>
+> ## Last Line:
+> cat('Time elapsed: ', proc.time() - .proctime00,'\n')
+Time elapsed: 3.453 0.03 3.503 0 0
+>
+>
diff --git a/win32/deps/library/cluster/tests/sweep-ex.R b/win32/deps/library/cluster/tests/sweep-ex.R
new file mode 100644
index 0000000..2058103
--- /dev/null
+++ b/win32/deps/library/cluster/tests/sweep-ex.R
@@ -0,0 +1,69 @@
+#### NOT part of the cluster package!
+
+#### Find out what exactly sweep() in ../src/spannel.f is doing
+#### in order to eventually replace it with BLAS calls !
+
+### subroutine sweep (cov,nord,ixlo,nel,deter)
+### ===============================
+### is called only once as
+### call sweep(cov,ndep,0,i,deter)
+### where i in 0:ndep
+
+sweep1 <- function(cov, i, det = 1)
+{
+ ## Purpose:
+ ## -------------------------------------------------------------------------
+ ## Arguments:
+ ## -------------------------------------------------------------------------
+ ## Author: Martin Maechler, Date: 22 Jan 2002, 08:58
+ if(!is.matrix(cov) || 0 != diff(D <- dim(cov)))
+ stop("'cov' must be a square matrix")
+ if((nord <- as.integer(D[1] - 1)) < 1)## cov[0:nord, 0:nord]
+ stop("'cov' must be at least 2 x 2")
+ if(0 > (i <- as.integer(i)) || i > nord)
+ stop("'i' must be in 0:nord, where nord = nrow(cov)-1")
+ storage.mode(cov) <- "double"
+ .C(cluster:::cl_sweep,
+ cov,
+ nord,
+ ixlo = 0:0,
+ i = i,
+ deter=det)
+}
+
+sweepAll <- function(cov, det = 1)
+{
+ ## Purpose:
+ ## -------------------------------------------------------------------------
+ ## Arguments:
+ ## -------------------------------------------------------------------------
+ ## Author: Martin Maechler, Date: 22 Jan 2002, 08:58
+ if(!is.matrix(cov) || 0 != diff(D <- dim(cov)))
+ stop("'cov' must be a square matrix")
+ if((nord <- as.integer(D[1] - 1)) < 1)## cov[0:nord, 0:nord]
+ stop("'cov' must be at least 2 x 2")
+ storage.mode(cov) <- "double"
+ for(i in 0:nord) {
+ .C(cluster:::cl_sweep,
+ cov,
+ nord,
+ ixlo = 0:0,
+ i = i,
+ deter = det,
+ DUP = FALSE) # i.e. work on 'cov' and 'det' directly
+ if(det <= 0)
+ cat("** i = ", i, "; deter = ", format(det)," <= 0\n",sep="")
+ }
+ list(cov = cov, deter = det)
+}
+
+require(cluster)
+
+## Examples with errors
+m1 <- cov(cbind(1, 1:5))
+try(sweepAll(m1))# deter = 0; cov[2,2] = Inf
+
+## ok
+(m2 <- cov(cbind(1:5, c(2:5,1), c(4:2,2,6))))
+qr(m2, tol = .001)$rank
+sweepAll(m2) ## deter = 0
diff --git a/win32/deps/library/codetools/DESCRIPTION b/win32/deps/library/codetools/DESCRIPTION
index db1aa89..ac052d9 100644
--- a/win32/deps/library/codetools/DESCRIPTION
+++ b/win32/deps/library/codetools/DESCRIPTION
@@ -1,11 +1,13 @@
-Package: codetools
-Version: 0.2-2
-Priority: recommended
-Author: Luke Tierney <luke stat uiowa edu>
-Description: Code analysis tools for R
-Title: Code Analysis Tools for R
-Depends: R (>= 2.1)
-Maintainer: Luke Tierney <luke stat uiowa edu>
-License: GPL
-Packaged: Fri Mar 6 16:54:30 2009; luke
-Built: R 2.9.2; ; 2009-08-24 13:03:30 UTC; windows
+Package: codetools
+Version: 0.2-8
+Priority: recommended
+Author: Luke Tierney <luke stat uiowa edu>
+Description: Code analysis tools for R
+Title: Code Analysis Tools for R
+Depends: R (>= 2.1)
+Maintainer: Luke Tierney <luke stat uiowa edu>
+License: GPL
+Packaged: 2011-02-14 20:49:48 UTC; luke
+Repository: CRAN
+Date/Publication: 2011-02-15 09:52:32
+Built: R 2.15.2; ; 2012-10-27 03:14:53 UTC; windows
diff --git a/win32/deps/library/codetools/Meta/Rd.rds b/win32/deps/library/codetools/Meta/Rd.rds
index 92d4203..7b9be01 100644
Binary files a/win32/deps/library/codetools/Meta/Rd.rds and b/win32/deps/library/codetools/Meta/Rd.rds differ
diff --git a/win32/deps/library/codetools/Meta/hsearch.rds b/win32/deps/library/codetools/Meta/hsearch.rds
index 315649d..193978b 100644
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diff --git a/win32/deps/library/codetools/Meta/links.rds b/win32/deps/library/codetools/Meta/links.rds
new file mode 100644
index 0000000..6acabbd
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diff --git a/win32/deps/library/codetools/Meta/nsInfo.rds b/win32/deps/library/codetools/Meta/nsInfo.rds
index 6010fb9..39c4b80 100644
Binary files a/win32/deps/library/codetools/Meta/nsInfo.rds and b/win32/deps/library/codetools/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/codetools/Meta/package.rds b/win32/deps/library/codetools/Meta/package.rds
index 9c1a5ee..95f810e 100644
Binary files a/win32/deps/library/codetools/Meta/package.rds and b/win32/deps/library/codetools/Meta/package.rds differ
diff --git a/win32/deps/library/codetools/R/codetools b/win32/deps/library/codetools/R/codetools
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/codetools/R/codetools
+++ b/win32/deps/library/codetools/R/codetools
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/codetools/R/codetools.rdb b/win32/deps/library/codetools/R/codetools.rdb
index 7589773..277849f 100644
Binary files a/win32/deps/library/codetools/R/codetools.rdb and b/win32/deps/library/codetools/R/codetools.rdb differ
diff --git a/win32/deps/library/codetools/R/codetools.rdx b/win32/deps/library/codetools/R/codetools.rdx
index 703b800..475e49a 100644
Binary files a/win32/deps/library/codetools/R/codetools.rdx and b/win32/deps/library/codetools/R/codetools.rdx differ
diff --git a/win32/deps/library/codetools/help/aliases.rds b/win32/deps/library/codetools/help/aliases.rds
new file mode 100644
index 0000000..f39355c
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diff --git a/win32/deps/library/codetools/help/codetools.rdb b/win32/deps/library/codetools/help/codetools.rdb
new file mode 100644
index 0000000..93503e4
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diff --git a/win32/deps/library/codetools/help/codetools.rdx b/win32/deps/library/codetools/help/codetools.rdx
new file mode 100644
index 0000000..8678b4d
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diff --git a/win32/deps/library/codetools/help/paths.rds b/win32/deps/library/codetools/help/paths.rds
new file mode 100644
index 0000000..e9a4c27
Binary files /dev/null and b/win32/deps/library/codetools/help/paths.rds differ
diff --git a/win32/deps/library/codetools/html/00Index.html b/win32/deps/library/codetools/html/00Index.html
new file mode 100644
index 0000000..cf493a5
--- /dev/null
+++ b/win32/deps/library/codetools/html/00Index.html
@@ -0,0 +1,63 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Code Analysis Tools for R</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Code Analysis Tools for R
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘codetools’ version 0.2-8</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<table width="100%">
+<tr><td width="25%"><a href="checkUsage.html">checkUsage</a></td>
+<td>Check R Code for Possible Problems</td></tr>
+<tr><td width="25%"><a href="checkUsage.html">checkUsageEnv</a></td>
+<td>Check R Code for Possible Problems</td></tr>
+<tr><td width="25%"><a href="checkUsage.html">checkUsagePackage</a></td>
+<td>Check R Code for Possible Problems</td></tr>
+<tr><td width="25%"><a href="codetools.html">codetools</a></td>
+<td>Low Level Code Analysis Tools for R</td></tr>
+<tr><td width="25%"><a href="codetools.html">collectLocals</a></td>
+<td>Low Level Code Analysis Tools for R</td></tr>
+<tr><td width="25%"><a href="codetools.html">collectUsage</a></td>
+<td>Low Level Code Analysis Tools for R</td></tr>
+<tr><td width="25%"><a href="codetools.html">constantFold</a></td>
+<td>Low Level Code Analysis Tools for R</td></tr>
+<tr><td width="25%"><a href="codetools.html">findFuncLocals</a></td>
+<td>Low Level Code Analysis Tools for R</td></tr>
+<tr><td width="25%"><a href="findGlobals.html">findGlobals</a></td>
+<td>Find Global Functions and Variables Used by a Closure</td></tr>
+<tr><td width="25%"><a href="codetools.html">findLocals</a></td>
+<td>Low Level Code Analysis Tools for R</td></tr>
+<tr><td width="25%"><a href="codetools.html">findLocalsList</a></td>
+<td>Low Level Code Analysis Tools for R</td></tr>
+<tr><td width="25%"><a href="codetools.html">flattenAssignment</a></td>
+<td>Low Level Code Analysis Tools for R</td></tr>
+<tr><td width="25%"><a href="codetools.html">getAssignedVar</a></td>
+<td>Low Level Code Analysis Tools for R</td></tr>
+<tr><td width="25%"><a href="codetools.html">isConstantValue</a></td>
+<td>Low Level Code Analysis Tools for R</td></tr>
+<tr><td width="25%"><a href="codetools.html">makeCodeWalker</a></td>
+<td>Low Level Code Analysis Tools for R</td></tr>
+<tr><td width="25%"><a href="codetools.html">makeConstantFolder</a></td>
+<td>Low Level Code Analysis Tools for R</td></tr>
+<tr><td width="25%"><a href="codetools.html">makeLocalsCollector</a></td>
+<td>Low Level Code Analysis Tools for R</td></tr>
+<tr><td width="25%"><a href="codetools.html">makeUsageCollector</a></td>
+<td>Low Level Code Analysis Tools for R</td></tr>
+<tr><td width="25%"><a href="showTree.html">showTree</a></td>
+<td>Print Lisp-Style Representation of R Expression</td></tr>
+<tr><td width="25%"><a href="codetools.html">walkCode</a></td>
+<td>Low Level Code Analysis Tools for R</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/codetools/html/R.css b/win32/deps/library/codetools/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/codetools/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/codetools/tests/tests.R b/win32/deps/library/codetools/tests/tests.R
new file mode 100644
index 0000000..1206c3c
--- /dev/null
+++ b/win32/deps/library/codetools/tests/tests.R
@@ -0,0 +1,90 @@
+library(codetools)
+assert <- function(e)
+ if (! e) stop(paste("assertion failed:", deparse(substitute(e))))
+local({
+ st <- function(e) {
+ v <- NULL
+ write <- function(x)
+ v <<- paste(v, as.character(x), sep = "")
+ showTree(e, write = write)
+ v
+ }
+ assert(identical(st(quote(f(x))), "(f x)\n"))
+ assert(identical(st(quote((x+y)*z)), "(* (\"(\" (+ x y)) z)\n"))
+ assert(identical(st(quote(-3)), "(- 3)\n"))
+})
+assert(identical(constantFold(quote(3)), 3))
+assert(identical(constantFold(quote(1+2)), 3))
+assert(identical(constantFold(quote(1+2+x)), NULL))
+assert(identical(constantFold(quote(pi)), pi))
+assert(identical(constantFold(quote(pi), "pi"), NULL))
+assert(identical(constantFold(quote(pi), "pi", FALSE), FALSE))
+assert(identical(getAssignedVar(quote("v"<-x)), "v"))
+assert(identical(getAssignedVar(quote(v<-x)), "v"))
+assert(identical(getAssignedVar(quote(f(v)<-x)), "v"))
+assert(identical(getAssignedVar(quote(f(g(v,2),1)<-x)), "v"))
+assert(identical(findLocals(quote(x<-1)), "x"))
+assert(identical(findLocals(quote(f(x)<-1)), "x"))
+assert(identical(findLocals(quote(f(g(x,2),1)<-1)), "x"))
+assert(identical(findLocals(quote(x<-y<-1)), c("x","y")))
+assert(identical(findLocals(quote(local(x<-1,e))), "x"))
+assert(identical(findLocals(quote(local(x<-1))), character(0)))
+assert(identical(findLocals(quote({local<-1;local(x<-1)})), c("local", "x")))
+assert(identical(findLocals(quote(local(x<-1,e)), "local"), "x"))
+local({
+ f <- function (f, x, y) {
+ local <- f
+ local(x <- y)
+ x
+ }
+ assert(identical(findLocals(body(f)), c("local","x")))
+})
+local({
+ env <- new.env()
+ assign("local", 1, env)
+ assert(identical(findLocals(quote(local(x<-1,e)), env), "x"))
+})
+assert(identical(findLocals(quote(assign(x, 3))), character(0)))
+assert(identical(findLocals(quote(assign("x", 3))), "x"))
+assert(identical(findLocals(quote(assign("x", 3, 4))), character(0)))
+local({
+ f<-function() { x <- 1; y <- 2}
+ assert(identical(sort(findFuncLocals(formals(f),body(f))), c("x","y")))
+ f<-function(u = x <- 1) y <- 2
+ assert(identical(sort(findFuncLocals(formals(f),body(f))), c("x","y")))
+})
+assert(identical(flattenAssignment(quote(x)), list(NULL, NULL)))
+assert(identical(flattenAssignment(quote(f(x, 1))),
+ list(list(quote(x)),
+ list(quote("f<-"(x, 1, value = `*tmpv*`))))))
+assert(identical(flattenAssignment(quote(f(g(x, 2), 1))),
+ list(list(quote(x), quote(g(`*tmp*`, 2))),
+ list(quote("f<-"(`*tmp*`, 1, value = `*tmpv*`)),
+ quote("g<-"(x, 2, value = `*tmpv*`))))))
+assert(identical(flattenAssignment(quote(f(g(h(x, 3), 2), 1))),
+ list(list(quote(x),
+ quote(h(`*tmp*`, 3)),
+ quote(g(`*tmp*`, 2))),
+ list(quote("f<-"(`*tmp*`, 1, value = `*tmpv*`)),
+ quote("g<-"(`*tmp*`, 2, value = `*tmpv*`)),
+ quote("h<-"(x, 3, value = `*tmpv*`))))))
+assert(identical(flattenAssignment(quote(f(g(h(k(x, 4), 3), 2), 1))),
+ list(list(quote(x),
+ quote(k(`*tmp*`, 4)),
+ quote(h(`*tmp*`, 3)),
+ quote(g(`*tmp*`, 2))),
+ list(quote("f<-"(`*tmp*`, 1, value = `*tmpv*`)),
+ quote("g<-"(`*tmp*`, 2, value = `*tmpv*`)),
+ quote("h<-"(`*tmp*`, 3, value = `*tmpv*`)),
+ quote("k<-"(x, 4, value = `*tmpv*`))))))
+if (getRversion() >= "2.13.0")
+ assert(identical(flattenAssignment(quote(base::diag(x))),
+ list(list(quote(x)),
+ list(quote(base::`diag<-`(x, value = `*tmpv*`))))))
+assert(! "y" %in% findGlobals(function() if (is.R()) x else y))
+assert(identical(findGlobals(function() if (FALSE) x), "if"))
+# **** need more test cases here
+assert(identical(sort(findGlobals(function(x) { z <- 1; x + y + z})),
+ sort(c("<-", "{", "+", "y"))))
+
+assert(identical(findGlobals(function() Quote(x)), "Quote"))
diff --git a/win32/deps/library/compiler/DESCRIPTION b/win32/deps/library/compiler/DESCRIPTION
new file mode 100644
index 0000000..6cd5286
--- /dev/null
+++ b/win32/deps/library/compiler/DESCRIPTION
@@ -0,0 +1,9 @@
+Package: compiler
+Version: 2.15.2
+Priority: base
+Title: The R Compiler Package
+Author: Luke Tierney <luke-tierney uiowa edu>
+Maintainer: R Core Team <R-core r-project org>
+Description: Byte code compiler for R
+License: Part of R 2.15.2
+Built: R 2.15.2; ; 2012-10-27 03:04:39 UTC; windows
diff --git a/win32/deps/library/compiler/INDEX b/win32/deps/library/compiler/INDEX
new file mode 100644
index 0000000..3ddbb04
--- /dev/null
+++ b/win32/deps/library/compiler/INDEX
@@ -0,0 +1 @@
+compile Byte Code Compiler
diff --git a/win32/deps/library/compiler/Meta/Rd.rds b/win32/deps/library/compiler/Meta/Rd.rds
new file mode 100644
index 0000000..bb7465e
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index 0000000..0fc8dd1
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diff --git a/win32/deps/library/compiler/Meta/links.rds b/win32/deps/library/compiler/Meta/links.rds
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index 0000000..26a7d1d
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index 0000000..cd61040
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diff --git a/win32/deps/library/compiler/Meta/package.rds b/win32/deps/library/compiler/Meta/package.rds
new file mode 100644
index 0000000..4c055e8
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diff --git a/win32/deps/library/compiler/NAMESPACE b/win32/deps/library/compiler/NAMESPACE
new file mode 100644
index 0000000..79fe63f
--- /dev/null
+++ b/win32/deps/library/compiler/NAMESPACE
@@ -0,0 +1,4 @@
+export(cmpfun,cmpfile,loadcmp,compile,disassemble)
+export(enableJIT,compilePKGS)
+export(getCompilerOption,setCompilerOptions)
+
diff --git a/win32/deps/library/compiler/R/compiler b/win32/deps/library/compiler/R/compiler
new file mode 100644
index 0000000..ac8cebe
--- /dev/null
+++ b/win32/deps/library/compiler/R/compiler
@@ -0,0 +1,9 @@
+local({
+ info <- loadingNamespaceInfo()
+ ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
+ if (is.null(ns))
+ stop("cannot find namespace environment");
+ barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
+ dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
+ lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
+})
diff --git a/win32/deps/library/compiler/R/compiler.rdb b/win32/deps/library/compiler/R/compiler.rdb
new file mode 100644
index 0000000..436da35
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diff --git a/win32/deps/library/compiler/R/compiler.rdx b/win32/deps/library/compiler/R/compiler.rdx
new file mode 100644
index 0000000..e5b22e5
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diff --git a/win32/deps/library/compiler/help/AnIndex b/win32/deps/library/compiler/help/AnIndex
new file mode 100644
index 0000000..3c096a9
--- /dev/null
+++ b/win32/deps/library/compiler/help/AnIndex
@@ -0,0 +1,9 @@
+cmpfile compile
+cmpfun compile
+compile compile
+compilePKGS compile
+disassemble compile
+enableJIT compile
+getCompilerOption compile
+loadcmp compile
+setCompilerOptions compile
diff --git a/win32/deps/library/compiler/help/aliases.rds b/win32/deps/library/compiler/help/aliases.rds
new file mode 100644
index 0000000..0f3c605
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diff --git a/win32/deps/library/compiler/help/compiler.rdb b/win32/deps/library/compiler/help/compiler.rdb
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index 0000000..c44ad67
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diff --git a/win32/deps/library/compiler/help/compiler.rdx b/win32/deps/library/compiler/help/compiler.rdx
new file mode 100644
index 0000000..3fcc542
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diff --git a/win32/deps/library/compiler/help/paths.rds b/win32/deps/library/compiler/help/paths.rds
new file mode 100644
index 0000000..d716a13
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diff --git a/win32/deps/library/compiler/html/00Index.html b/win32/deps/library/compiler/html/00Index.html
new file mode 100644
index 0000000..30834d3
--- /dev/null
+++ b/win32/deps/library/compiler/html/00Index.html
@@ -0,0 +1,41 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: The R Compiler Package</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> The R Compiler Package
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘compiler’ version 2.15.2</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<table width="100%">
+<tr><td width="25%"><a href="compile.html">cmpfile</a></td>
+<td>Byte Code Compiler</td></tr>
+<tr><td width="25%"><a href="compile.html">cmpfun</a></td>
+<td>Byte Code Compiler</td></tr>
+<tr><td width="25%"><a href="compile.html">compile</a></td>
+<td>Byte Code Compiler</td></tr>
+<tr><td width="25%"><a href="compile.html">compilePKGS</a></td>
+<td>Byte Code Compiler</td></tr>
+<tr><td width="25%"><a href="compile.html">disassemble</a></td>
+<td>Byte Code Compiler</td></tr>
+<tr><td width="25%"><a href="compile.html">enableJIT</a></td>
+<td>Byte Code Compiler</td></tr>
+<tr><td width="25%"><a href="compile.html">getCompilerOption</a></td>
+<td>Byte Code Compiler</td></tr>
+<tr><td width="25%"><a href="compile.html">loadcmp</a></td>
+<td>Byte Code Compiler</td></tr>
+<tr><td width="25%"><a href="compile.html">setCompilerOptions</a></td>
+<td>Byte Code Compiler</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/compiler/html/R.css b/win32/deps/library/compiler/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/compiler/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
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diff --git a/win32/deps/library/compiler/tests/assign.R b/win32/deps/library/compiler/tests/assign.R
new file mode 100644
index 0000000..96291b0
--- /dev/null
+++ b/win32/deps/library/compiler/tests/assign.R
@@ -0,0 +1,148 @@
+##
+## Assignment tests
+##
+
+library(compiler)
+
+## Local assignment
+
+### symbol
+x <- 1
+eval(compile(quote(x <- 2)))
+stopifnot(x == 2)
+
+### closure
+`f<-` <- function(x, i, value) { x[i] <- value; x }
+x <- 1
+eval(compile(quote(f(x, 1) <- 2)))
+stopifnot(x == 2)
+
+### SPECIAL
+`f<-` <- `[<-`
+x <- 1
+eval(compile(quote(f(x, 1) <- 2)))
+stopifnot(x == 2)
+
+### BUILTIN
+`f<-` <- `names<-`
+x <- 1
+eval(compile(quote(f(x) <- "foo")))
+stopifnot(identical(x, structure(1, names = "foo")))
+
+## Super assignment
+
+### symbol
+x <- 1
+eval(compile(quote((function() x <<- 2)())))
+stopifnot(x == 2)
+
+### closure
+`f<-` <- function(x, i, value) { x[i] <- value; x }
+x <- 1
+eval(compile(quote((function() f(x, 1) <<- 2)())))
+stopifnot(x == 2)
+
+### SPECIAL
+`f<-` <- `[<-`
+x <- 1
+eval(compile(quote((function() f(x, 1) <<- 2)())))
+stopifnot(x == 2)
+
+### BUILTIN
+`f<-` <- `names<-`
+x <- 1
+eval(compile(quote((function() f(x) <<- "foo")())))
+stopifnot(identical(x, structure(1, names = "foo")))
+
+## Dollargets
+
+### Default
+x <- list(a = 1)
+eval(compile(quote(x$a <- 2)))
+stopifnot(identical(x, list(a = 2)))
+
+### Dispatch
+x <- structure(list(a = 1), class = "foo")
+y <- NULL
+`$<-.foo` <- function(x, tag, value) { y <<- list(tag, value); x }
+eval(compile(quote(x$a <- 2)))
+stopifnot(identical(y, list("a", 2)))
+
+## Subassign
+
+### Default
+x <- 1
+eval(compile(quote(x[1] <- 2)))
+stopifnot(identical(x, 2))
+
+### Dispatching
+x <- structure(list(NULL), class = "foo")
+y <- NULL
+`[<-.foo` <- function(x, k, value) { y <<- rep(value, k); x }
+eval(compile(quote(x[2] <- 3)))
+stopifnot(identical(y, rep(3, 2)))
+
+#### Missing args
+x <- c(1, 2, 3)
+eval(compile(quote(x[] <- c(4, 5, 6))))
+stopifnot(identical(x, c(4, 5, 6)))
+
+### Named args
+x <- structure(list(NULL), class = "foo")
+y <- NULL
+`[<-.foo` <- function(x, k, value) { y <<- names(sys.call()[-1]); x }
+eval(compile(quote(x[k = 2] <- 3)))
+stopifnot(identical(y, c("", "k", "value")))
+
+## Subassign2
+
+### Default
+x <- list(NULL)
+eval(compile(quote(x[[1]] <- list(1))))
+stopifnot(identical(x, list(list(1))))
+
+### Dispatching
+x <- structure(list(), class = "foo")
+y <- 1
+`[[<-.foo` <- function(x, i, value) { y[i] <<- value; x }
+eval(compile(quote(x[[1]] <- 3)))
+stopifnot(identical(y, 3))
+
+## Nested assignments
+x <- list(a = list(b = 1))
+eval(compile(quote(x$a$b <- 2)))
+stopifnot(identical(x, list(a = list(b = 2))))
+
+x <- list(1, list(2))
+eval(compile(quote(x[[1]][] <- 2)))
+eval(compile(quote(x[[2]][[1]] <- 3)))
+stopifnot(identical(x, list(2, list(3))))
+
+
+## checkAssign
+checkAssign <- compiler:::checkAssign
+cenv <- compiler:::makeCenv(.GlobalEnv)
+cntxt <- compiler:::make.toplevelContext(cenv, list(suppressAll = TRUE))
+stopifnot(identical(checkAssign(quote(x <- 1), cntxt), TRUE))
+stopifnot(identical(checkAssign(quote("x" <- 1), cntxt), TRUE))
+stopifnot(identical(checkAssign(quote(3 <- 1), cntxt), FALSE))
+stopifnot(identical(checkAssign(quote(f(x) <- 1), cntxt), TRUE))
+stopifnot(identical(checkAssign(quote((f())(x) <- 1), cntxt), FALSE))
+stopifnot(identical(checkAssign(quote(f(g(x)) <- 1), cntxt), TRUE))
+stopifnot(identical(checkAssign(quote(f(g("x")) <- 1), cntxt), FALSE))
+
+
+## flattenPlace
+flattenPlace <- compiler:::flattenPlace
+stopifnot(identical(flattenPlace(quote(f(g(h(x, k), j), i))),
+ list(quote(f(`*tmp*`, i)),
+ quote(g(`*tmp*`, j)),
+ quote(h(`*tmp*`, k)))))
+
+## getAssignFun
+getAssignFun <- compiler:::getAssignFun
+stopifnot(identical(getAssignFun(quote(f)), quote(`f<-`)))
+stopifnot(identical(getAssignFun("f"), NULL))
+stopifnot(identical(getAssignFun(quote(f(x))), NULL))
+stopifnot(identical(getAssignFun(quote(base::diag)), quote(base::`diag<-`)))
+stopifnot(identical(getAssignFun(quote(base:::diag)), quote(base:::`diag<-`)))
diff --git a/win32/deps/library/compiler/tests/basics.R b/win32/deps/library/compiler/tests/basics.R
new file mode 100644
index 0000000..fc158a4
--- /dev/null
+++ b/win32/deps/library/compiler/tests/basics.R
@@ -0,0 +1,101 @@
+library(compiler)
+
+## very minimal
+x <- 2
+stopifnot(eval(compile(quote(x + 1))) == 3)
+
+## simple code generation
+checkCode <- function(expr, code, optimize = 2) {
+ v <- compile(expr, options = list(optimize = optimize))
+ d <- .Internal(disassemble(v))[[2]][-1]
+ dd <- as.integer(eval(substitute(code), getNamespace("compiler")))
+ identical(d, dd)
+}
+x <- 2
+stopifnot(checkCode(quote(x + 1),
+ c(GETVAR.OP, 1L,
+ LDCONST.OP, 2L,
+ ADD.OP, 0L,
+ RETURN.OP)))
+f <- function(x) x
+checkCode(quote({f(1); f(2)}),
+ c(GETFUN.OP, 1L,
+ PUSHCONSTARG.OP, 2L,
+ CALL.OP, 3L,
+ POP.OP,
+ GETFUN.OP, 1L,
+ PUSHCONSTARG.OP, 4L,
+ CALL.OP, 5L,
+ RETURN.OP))
+
+
+## names and ... args
+f <- function(...) list(...)
+stopifnot(identical(f(1, 2), cmpfun(f)(1, 2)))
+
+f <- function(...) list(x = ...)
+stopifnot(identical(f(1, 2), cmpfun(f)(1, 2)))
+
+
+## substitute and argument constant folding
+f <- function(x) substitute(x)
+g <- function() f(1 + 2)
+v1 <- g()
+f <- cmpfun(f)
+g <- cmpfun(g)
+v2 <- g()
+stopifnot(identical(v1, v2))
+
+
+## simple loops
+sr <- function(x) {
+ n <- length(x)
+ i <- 1
+ s <- 0
+ repeat {
+ if (i > n) break
+ s <- s + x[i]
+ i <- i + 1
+ }
+ s
+}
+sw <- function(x) {
+ n <- length(x)
+ i <- 1
+ s <- 0
+ while (i <= n) {
+ s <- s + x[i]
+ i <- i + 1
+ }
+ s
+}
+sf <- function(x) {
+ s <- 0
+ for (y in x)
+ s <- s + y
+ s
+}
+src <- cmpfun(sr)
+swc <- cmpfun(sw)
+sfc <- cmpfun(sf)
+x <- 1 : 5
+stopifnot(src(x) == sr(x))
+stopifnot(swc(x) == sw(x))
+stopifnot(sfc(x) == sf(x))
+
+
+## Check that the handlers have been associated with the correct package
+h <- ls(compiler:::inlineHandlers, all = TRUE)
+p <- sub("package:", "", sapply(h, find))
+pp <- sapply(h, function(n) get(n, compiler:::inlineHandlers)$package)
+stopifnot(identical(p, pp))
+
+
+## Check assumption about simple .Internals
+stopifnot(all(sapply(compiler:::safeStatsInternals,
+ function(f)
+ compiler:::is.simpleInternal(get(f, "package:stats")))))
+
+stopifnot(all(sapply(compiler:::safeBaseInternals,
+ function(f)
+ compiler:::is.simpleInternal(get(f, "package:base")))))
diff --git a/win32/deps/library/compiler/tests/const.R b/win32/deps/library/compiler/tests/const.R
new file mode 100644
index 0000000..cfa8cbd
--- /dev/null
+++ b/win32/deps/library/compiler/tests/const.R
@@ -0,0 +1,65 @@
+
+library(compiler)
+
+##
+## Test code for constant folding
+##
+
+makeCenv <- compiler:::makeCenv
+checkConst <- compiler:::checkConst
+constantFoldSym <- compiler:::constantFoldSym
+constantFold <- compiler:::constantFold
+
+## using a global environment
+ce <- makeCenv(.GlobalEnv)
+stopifnot(identical(constantFoldSym(quote(pi), list(env = ce, optimize = 3)),
+ checkConst(base::pi)))
+stopifnot(identical(constantFoldSym(quote(pi), list(env = ce, optimize = 2)),
+ NULL))
+stopifnot(identical(constantFoldSym(quote(pi), list(env = ce, optimize = 1)),
+ NULL))
+stopifnot(identical(constantFoldSym(quote(pi), list(env = ce, optimize = 0)),
+ NULL))
+stopifnot(identical(constantFold(quote(1 + 2), list(optimize = 3, env = ce)),
+ checkConst(1 + 2)))
+stopifnot(identical(constantFold(quote(1 + 2), list(optimize = 2, env = ce)),
+ checkConst(1 + 2)))
+stopifnot(identical(constantFold(quote(1 + 2), list(optimize = 1, env = ce)),
+ NULL))
+stopifnot(identical(constantFold(quote(1 + 2), list(optimize = 0, env = ce)),
+ NULL))
+stopifnot(identical(constantFold(quote(sqrt(2)), list(optimize = 3, env = ce)),
+ checkConst(sqrt(2))))
+stopifnot(identical(constantFold(quote(sqrt(2)), list(optimize = 2, env = ce)),
+ NULL))
+stopifnot(identical(constantFold(quote(sqrt(2)), list(optimize = 1, env = ce)),
+ NULL))
+stopifnot(identical(constantFold(quote(sqrt(2)), list(optimize = 0, env = ce)),
+ NULL))
+
+## using a namespace environment
+ce <- makeCenv(getNamespace("stats"))
+stopifnot(identical(constantFoldSym(quote(pi), list(env = ce, optimize = 3)),
+ list(value = base::pi)))
+stopifnot(identical(constantFoldSym(quote(pi), list(env = ce, optimize = 2)),
+ list(value = base::pi)))
+stopifnot(identical(constantFoldSym(quote(pi), list(env = ce, optimize = 1)),
+ checkConst(base::pi)))
+stopifnot(identical(constantFoldSym(quote(pi), list(env = ce, optimize = 0)),
+ NULL))
+stopifnot(identical(constantFold(quote(1 + 2), list(optimize = 3, env = ce)),
+ checkConst(1 + 2)))
+stopifnot(identical(constantFold(quote(1 + 2), list(optimize = 2, env = ce)),
+ checkConst(1 + 2)))
+stopifnot(identical(constantFold(quote(1 + 2), list(optimize = 1, env = ce)),
+ checkConst(1 + 2)))
+stopifnot(identical(constantFold(quote(1 + 2), list(optimize = 0, env = ce)),
+ NULL))
+stopifnot(identical(constantFold(quote(sqrt(2)), list(optimize = 3, env = ce)),
+ checkConst(sqrt(2))))
+stopifnot(identical(constantFold(quote(sqrt(2)), list(optimize = 2, env = ce)),
+ checkConst(sqrt(2))))
+stopifnot(identical(constantFold(quote(sqrt(2)), list(optimize = 1, env = ce)),
+ checkConst(sqrt(2))))
+stopifnot(identical(constantFold(quote(sqrt(2)), list(optimize = 0, env = ce)),
+ NULL))
diff --git a/win32/deps/library/compiler/tests/envir.R b/win32/deps/library/compiler/tests/envir.R
new file mode 100644
index 0000000..ffe5d63
--- /dev/null
+++ b/win32/deps/library/compiler/tests/envir.R
@@ -0,0 +1,90 @@
+
+library(compiler)
+
+##
+## Tests for findHomeNS()
+##
+
+findHomeNS <- compiler:::findHomeNS
+
+## return value for an undefinded variable should be NULL
+stopifnot(is.null(findHomeNS("foo", getNamespace("stats"))))
+stopifnot(is.null(findHomeNS("foo", parent.env(getNamespace("stats")))))
+stopifnot(is.null(findHomeNS("foo", getNamespace("base"))))
+
+## + is found in .BaseNamespaceEnv for stats or base
+stopifnot(identical(findHomeNS("+", getNamespace("stats")),
+ .BaseNamespaceEnv))
+stopifnot(identical(findHomeNS("+", parent.env(getNamespace("stats"))),
+ .BaseNamespaceEnv))
+stopifnot(identical(findHomeNS("+", getNamespace("base")),
+ .BaseNamespaceEnv))
+
+## dnorm is defined in stats
+stopifnot(identical(findHomeNS("dnorm", getNamespace("stats")),
+ getNamespace("stats")))
+stopifnot(identical(findHomeNS("dnorm", parent.env(getNamespace("stats"))),
+ getNamespace("stats")))
+stopifnot(is.null(findHomeNS("dnorm", getNamespace("base"))))
+
+## plot is available via the stats namespace since stats imports graphics
+stopifnot(identical(findHomeNS("plot", getNamespace("stats")),
+ getNamespace("graphics")))
+stopifnot(identical(findHomeNS("plot", parent.env(getNamespace("stats"))),
+ getNamespace("graphics")))
+stopifnot(is.null(findHomeNS("plot", getNamespace("base"))))
+
+## palette is one of a small set of selective imports from grDevices
+stopifnot(identical(findHomeNS("palette", getNamespace("stats")),
+ getNamespace("grDevices")))
+stopifnot(identical(findHomeNS("palette", parent.env(getNamespace("stats"))),
+ getNamespace("grDevices")))
+stopifnot(is.null(findHomeNS("palette", getNamespace("base"))))
+
+
+##
+## Tests for getAssignedVar
+##
+
+getAssignedVar <- compiler:::getAssignedVar
+stopifnot(identical(getAssignedVar(quote("v"<-x)), "v"))
+stopifnot(identical(getAssignedVar(quote(v<-x)), "v"))
+stopifnot(identical(getAssignedVar(quote(f(v)<-x)), "v"))
+stopifnot(identical(getAssignedVar(quote(f(g(v,2),1)<-x)), "v"))
+
+
+##
+## Tests for findLocals
+##
+
+findLocals <- compiler:::findLocals
+cenv <- compiler:::makeCenv(.GlobalEnv)
+cntxt <- compiler:::make.toplevelContext(cenv, NULL)
+
+stopifnot(identical(findLocals(quote(x<-1), cntxt), "x"))
+stopifnot(identical(findLocals(quote(f(x)<-1), cntxt), "x"))
+stopifnot(identical(findLocals(quote(f(g(x,2),1)<-1), cntxt), "x"))
+stopifnot(identical(findLocals(quote(x<-y<-1), cntxt), c("x","y")))
+stopifnot(identical(findLocals(quote(local(x<-1,e)), cntxt), "x"))
+stopifnot(identical(findLocals(quote(local(x<-1)), cntxt), character(0)))
+stopifnot(identical(findLocals(quote({local<-1;local(x<-1)}), cntxt),
+ c("local", "x")))
+
+local({
+ f <- function (f, x, y) {
+ local <- f
+ local(x <- y)
+ x
+ }
+ stopifnot(identical(findLocals(body(f), cntxt), c("local","x")))
+})
+
+local({
+ cenv <- compiler:::addCenvVars(cenv, "local")
+ cntxt <- compiler:::make.toplevelContext(cenv, NULL)
+ stopifnot(identical(findLocals(quote(local(x<-1,e)), cntxt), "x"))
+})
+
+stopifnot(identical(findLocals(quote(assign(x, 3)), cntxt), character(0)))
+stopifnot(identical(findLocals(quote(assign("x", 3)), cntxt), "x"))
+stopifnot(identical(findLocals(quote(assign("x", 3, 4)), cntxt), character(0)))
diff --git a/win32/deps/library/compiler/tests/jit.R b/win32/deps/library/compiler/tests/jit.R
new file mode 100644
index 0000000..0b6262e
--- /dev/null
+++ b/win32/deps/library/compiler/tests/jit.R
@@ -0,0 +1,16 @@
+library(compiler)
+
+oldJIT <- enableJIT(3)
+
+## need a test of level 1 to make sure functions are compiled
+
+## need more tests here
+
+repeat { break }
+
+while(TRUE) break
+
+for (i in 1:10) i
+
+enableJIT(oldJIT)
+
diff --git a/win32/deps/library/compiler/tests/loop.R b/win32/deps/library/compiler/tests/loop.R
new file mode 100644
index 0000000..583b10b
--- /dev/null
+++ b/win32/deps/library/compiler/tests/loop.R
@@ -0,0 +1,26 @@
+library(compiler)
+
+f <- function(x) x
+
+g <- function(x) repeat if (x) f(return(1)) else return(2)
+gc <- cmpfun(g)
+stopifnot(identical(g(TRUE), gc(TRUE)))
+stopifnot(identical(g(FALSE), gc(FALSE)))
+
+h <- function(x) { repeat if (x) f(return(1)) else break; 2 }
+hc <- cmpfun(h)
+stopifnot(identical(h(TRUE), hc(TRUE)))
+stopifnot(identical(h(FALSE), hc(FALSE)))
+
+k <- function(x) { repeat if (x) return(1) else f(break); 2 }
+kc <- cmpfun(k)
+stopifnot(identical(k(TRUE), kc(TRUE)))
+stopifnot(identical(k(FALSE), kc(FALSE)))
+
+## **** need more variations on this.
+
+## this would give an error prior to fixing a binding cache bug
+f <- function(x) { for (y in x) { z <- y; g(break) } ; z }
+g <- function(x) x
+cmpfun(f)(c(1,2,3))
+
diff --git a/win32/deps/library/compiler/tests/switch.R b/win32/deps/library/compiler/tests/switch.R
new file mode 100644
index 0000000..42c846e
--- /dev/null
+++ b/win32/deps/library/compiler/tests/switch.R
@@ -0,0 +1,86 @@
+library(compiler)
+
+ev <- function(expr)
+ tryCatch(withVisible(eval(expr, parent.frame(), baseenv())),
+ error = function(e) conditionMessage(e))
+
+f <- function(x) switch(x, x = 1, y = , z = 3, , w =, 6, v = )
+fc <- cmpfun(f)
+
+stopifnot(identical(ev(quote(fc("x"))), ev(quote(f("x")))))
+stopifnot(identical(ev(quote(fc("A"))), ev(quote(f("A")))))
+
+stopifnot(identical(ev(quote(fc(0))), ev(quote(f(0)))))
+stopifnot(identical(ev(quote(fc(1))), ev(quote(f(1)))))
+stopifnot(identical(ev(quote(fc(2))), ev(quote(f(2)))))
+stopifnot(identical(ev(quote(fc(3))), ev(quote(f(3)))))
+stopifnot(identical(ev(quote(fc(4))), ev(quote(f(4)))))
+stopifnot(identical(ev(quote(fc(5))), ev(quote(f(5)))))
+stopifnot(identical(ev(quote(fc(6))), ev(quote(f(6)))))
+stopifnot(identical(ev(quote(fc(7))), ev(quote(f(7)))))
+stopifnot(identical(ev(quote(fc(8))), ev(quote(f(8)))))
+
+
+g <- function(x) switch(x, x = 1, y = , z = 3, w =, 5, v = )
+gc <- cmpfun(g)
+
+stopifnot(identical(ev(quote(gc("x"))), ev(quote(g("x")))))
+stopifnot(identical(ev(quote(gc("y"))), ev(quote(g("y")))))
+stopifnot(identical(ev(quote(gc("z"))), ev(quote(g("z")))))
+stopifnot(identical(ev(quote(gc("w"))), ev(quote(g("w")))))
+stopifnot(identical(ev(quote(gc("v"))), ev(quote(g("v")))))
+stopifnot(identical(ev(quote(gc("A"))), ev(quote(g("A")))))
+
+stopifnot(identical(ev(quote(gc(0))), ev(quote(g(0)))))
+stopifnot(identical(ev(quote(gc(1))), ev(quote(g(1)))))
+stopifnot(identical(ev(quote(gc(2))), ev(quote(g(2)))))
+stopifnot(identical(ev(quote(gc(3))), ev(quote(g(3)))))
+stopifnot(identical(ev(quote(gc(4))), ev(quote(g(4)))))
+stopifnot(identical(ev(quote(gc(5))), ev(quote(g(5)))))
+stopifnot(identical(ev(quote(gc(6))), ev(quote(g(6)))))
+stopifnot(identical(ev(quote(gc(7))), ev(quote(g(7)))))
+
+
+h <- function(x) switch(x, x = 1, y = , z = 3)
+hc <- cmpfun(h)
+
+stopifnot(identical(ev(quote(hc("x"))), ev(quote(h("x")))))
+stopifnot(identical(ev(quote(hc("y"))), ev(quote(h("y")))))
+stopifnot(identical(ev(quote(hc("z"))), ev(quote(h("z")))))
+stopifnot(identical(ev(quote(hc("A"))), ev(quote(h("A")))))
+
+stopifnot(identical(ev(quote(hc(0))), ev(quote(h(0)))))
+stopifnot(identical(ev(quote(hc(1))), ev(quote(h(1)))))
+stopifnot(identical(ev(quote(hc(2))), ev(quote(h(2)))))
+stopifnot(identical(ev(quote(hc(3))), ev(quote(h(3)))))
+stopifnot(identical(ev(quote(hc(4))), ev(quote(h(4)))))
+
+
+k <- function(x) switch(x, x = 1, y = 2, z = 3)
+kc <- cmpfun(k)
+
+stopifnot(identical(ev(quote(kc("x"))), ev(quote(k("x")))))
+stopifnot(identical(ev(quote(kc("y"))), ev(quote(k("y")))))
+stopifnot(identical(ev(quote(kc("z"))), ev(quote(k("z")))))
+stopifnot(identical(ev(quote(kc("A"))), ev(quote(k("A")))))
+
+stopifnot(identical(ev(quote(kc(0))), ev(quote(k(0)))))
+stopifnot(identical(ev(quote(kc(1))), ev(quote(k(1)))))
+stopifnot(identical(ev(quote(kc(2))), ev(quote(k(2)))))
+stopifnot(identical(ev(quote(kc(3))), ev(quote(k(3)))))
+stopifnot(identical(ev(quote(kc(4))), ev(quote(k(4)))))
+
+
+l <- function(x) switch(x, "a", "b", "c")
+lc <- cmpfun(l)
+
+ce <- function(expr) tryCatch(expr, error = function(e) "Error")
+
+## both of these should raise errors but the messages will differ
+stopifnot(identical(ce(lc("A")), ce(l("A"))))
+
+stopifnot(identical(ev(quote(lc(0))), ev(quote(l(0)))))
+stopifnot(identical(ev(quote(lc(1))), ev(quote(l(1)))))
+stopifnot(identical(ev(quote(lc(2))), ev(quote(l(2)))))
+stopifnot(identical(ev(quote(lc(3))), ev(quote(l(3)))))
+stopifnot(identical(ev(quote(lc(4))), ev(quote(l(4)))))
diff --git a/win32/deps/library/datasets/DESCRIPTION b/win32/deps/library/datasets/DESCRIPTION
index 15a42e1..03afe20 100644
--- a/win32/deps/library/datasets/DESCRIPTION
+++ b/win32/deps/library/datasets/DESCRIPTION
@@ -1,9 +1,9 @@
Package: datasets
-Version: 2.9.2
+Version: 2.15.2
Priority: base
Title: The R Datasets Package
-Author: R Development Core Team and contributors worldwide
+Author: R Core Team and contributors worldwide
Maintainer: R Core Team <R-core r-project org>
Description: Base R datasets
-License: Part of R 2.9.2
-Built: R 2.9.2; ; 2009-08-24 12:45:11 UTC; windows
+License: Part of R 2.15.2
+Built: R 2.15.2; ; 2012-10-27 03:07:02 UTC; windows
diff --git a/win32/deps/library/datasets/INDEX b/win32/deps/library/datasets/INDEX
index e795575..e9a37cc 100644
--- a/win32/deps/library/datasets/INDEX
+++ b/win32/deps/library/datasets/INDEX
@@ -1,7 +1,7 @@
AirPassengers Monthly Airline Passenger Numbers 1949-1960
BJsales Sales Data with Leading Indicator
BOD Biochemical Oxygen Demand
-CO2 Carbon Dioxide uptake in grass plants
+CO2 Carbon Dioxide Uptake in Grass Plants
ChickWeight Weight versus age of chicks on different diets
DNase Elisa assay of DNase
EuStockMarkets Daily Closing Prices of Major European Stock
@@ -10,7 +10,7 @@ Formaldehyde Determination of Formaldehyde
HairEyeColor Hair and Eye Color of Statistics Students
Harman23.cor Harman Example 2.3
Harman74.cor Harman Example 7.4
-Indometh Pharmacokinetics of Indomethicin
+Indometh Pharmacokinetics of Indomethacin
InsectSprays Effectiveness of Insect Sprays
JohnsonJohnson Quarterly Earnings per Johnson & Johnson Share
LakeHuron Level of Lake Huron 1875-1972
@@ -20,8 +20,8 @@ Nile Flow of the River Nile
Orange Growth of Orange Trees
OrchardSprays Potency of Orchard Sprays
PlantGrowth Results from an Experiment on Plant Growth
-Puromycin Reaction velocity of an enzymatic reaction
-Theoph Pharmacokinetics of theophylline
+Puromycin Reaction Velocity of an Enzymatic Reaction
+Theoph Pharmacokinetics of Theophylline
Titanic Survival of passengers on the Titanic
ToothGrowth The Effect of Vitamin C on Tooth Growth in
Guinea Pigs
@@ -41,7 +41,7 @@ ability.cov Ability and Intelligence Tests
airmiles Passenger Miles on Commercial US Airlines,
1937-1960
airquality New York Air Quality Measurements
-anscombe Anscombe's Quartet of "Identical" Simple Linear
+anscombe Anscombe's Quartet of 'Identical' Simple Linear
Regressions
attenu The Joyner-Boore Attenuation Data
attitude The Chatterjee-Price Attitude Data
@@ -66,7 +66,7 @@ islands Areas of the World's Major Landmasses
lh Luteinizing Hormone in Blood Samples
longley Longley's Economic Regression Data
lynx Annual Canadian Lynx trappings 1821-1934
-morley Michaelson-Morley Speed of Light Data
+morley Michelson Speed of Light Data
mtcars Motor Trend Car Road Tests
nhtemp Average Yearly Temperatures in New Haven
nottem Average Monthly Temperatures at Nottingham,
diff --git a/win32/deps/library/datasets/Meta/Rd.rds b/win32/deps/library/datasets/Meta/Rd.rds
index 6f896bb..4e28191 100644
Binary files a/win32/deps/library/datasets/Meta/Rd.rds and b/win32/deps/library/datasets/Meta/Rd.rds differ
diff --git a/win32/deps/library/datasets/Meta/data.rds b/win32/deps/library/datasets/Meta/data.rds
index 3c0510a..e89c28f 100644
Binary files a/win32/deps/library/datasets/Meta/data.rds and b/win32/deps/library/datasets/Meta/data.rds differ
diff --git a/win32/deps/library/datasets/Meta/hsearch.rds b/win32/deps/library/datasets/Meta/hsearch.rds
index e47e79e..36d475f 100644
Binary files a/win32/deps/library/datasets/Meta/hsearch.rds and b/win32/deps/library/datasets/Meta/hsearch.rds differ
diff --git a/win32/deps/library/datasets/Meta/links.rds b/win32/deps/library/datasets/Meta/links.rds
new file mode 100644
index 0000000..a6e5e04
Binary files /dev/null and b/win32/deps/library/datasets/Meta/links.rds differ
diff --git a/win32/deps/library/datasets/Meta/nsInfo.rds b/win32/deps/library/datasets/Meta/nsInfo.rds
new file mode 100644
index 0000000..b825b2a
Binary files /dev/null and b/win32/deps/library/datasets/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/datasets/Meta/package.rds b/win32/deps/library/datasets/Meta/package.rds
index 3efed75..53dd299 100644
Binary files a/win32/deps/library/datasets/Meta/package.rds and b/win32/deps/library/datasets/Meta/package.rds differ
diff --git a/win32/deps/library/datasets/NAMESPACE b/win32/deps/library/datasets/NAMESPACE
new file mode 100644
index 0000000..5d0f475
--- /dev/null
+++ b/win32/deps/library/datasets/NAMESPACE
@@ -0,0 +1,2 @@
+# This package exports nothing (it uses lazydata)
+# exportPattern(".")
diff --git a/win32/deps/library/datasets/data/Rdata.rdb b/win32/deps/library/datasets/data/Rdata.rdb
index 2cfcc31..8a37907 100644
Binary files a/win32/deps/library/datasets/data/Rdata.rdb and b/win32/deps/library/datasets/data/Rdata.rdb differ
diff --git a/win32/deps/library/datasets/data/Rdata.rds b/win32/deps/library/datasets/data/Rdata.rds
index baa235e..9119841 100644
Binary files a/win32/deps/library/datasets/data/Rdata.rds and b/win32/deps/library/datasets/data/Rdata.rds differ
diff --git a/win32/deps/library/datasets/data/Rdata.rdx b/win32/deps/library/datasets/data/Rdata.rdx
index ea14f07..b94434b 100644
Binary files a/win32/deps/library/datasets/data/Rdata.rdx and b/win32/deps/library/datasets/data/Rdata.rdx differ
diff --git a/win32/deps/library/datasets/help/aliases.rds b/win32/deps/library/datasets/help/aliases.rds
new file mode 100644
index 0000000..1e1f980
Binary files /dev/null and b/win32/deps/library/datasets/help/aliases.rds differ
diff --git a/win32/deps/library/datasets/help/datasets.rdb b/win32/deps/library/datasets/help/datasets.rdb
new file mode 100644
index 0000000..82f6008
Binary files /dev/null and b/win32/deps/library/datasets/help/datasets.rdb differ
diff --git a/win32/deps/library/datasets/help/datasets.rdx b/win32/deps/library/datasets/help/datasets.rdx
new file mode 100644
index 0000000..1ede2a0
Binary files /dev/null and b/win32/deps/library/datasets/help/datasets.rdx differ
diff --git a/win32/deps/library/datasets/help/paths.rds b/win32/deps/library/datasets/help/paths.rds
new file mode 100644
index 0000000..9e914ab
Binary files /dev/null and b/win32/deps/library/datasets/help/paths.rds differ
diff --git a/win32/deps/library/datasets/html/00Index.html b/win32/deps/library/datasets/html/00Index.html
new file mode 100644
index 0000000..0bab6ab
--- /dev/null
+++ b/win32/deps/library/datasets/html/00Index.html
@@ -0,0 +1,367 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: The R Datasets Package</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> The R Datasets Package
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘datasets’ version 2.15.2</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<p align="center">
+<a href="# "> </a>
+<a href="#A">A</a>
+<a href="#B">B</a>
+<a href="#C">C</a>
+<a href="#D">D</a>
+<a href="#E">E</a>
+<a href="#F">F</a>
+<a href="#H">H</a>
+<a href="#I">I</a>
+<a href="#J">J</a>
+<a href="#L">L</a>
+<a href="#M">M</a>
+<a href="#N">N</a>
+<a href="#O">O</a>
+<a href="#P">P</a>
+<a href="#Q">Q</a>
+<a href="#R">R</a>
+<a href="#S">S</a>
+<a href="#T">T</a>
+<a href="#U">U</a>
+<a href="#V">V</a>
+<a href="#W">W</a>
+</p>
+
+<table width="100%">
+<tr><td width="25%"><a href="datasets-package.html">datasets-package</a></td>
+<td>The R Datasets Package</td></tr>
+</table>
+
+<h2><a name="A">-- A --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="ability.cov.html">ability.cov</a></td>
+<td>Ability and Intelligence Tests</td></tr>
+<tr><td width="25%"><a href="airmiles.html">airmiles</a></td>
+<td>Passenger Miles on Commercial US Airlines, 1937-1960</td></tr>
+<tr><td width="25%"><a href="AirPassengers.html">AirPassengers</a></td>
+<td>Monthly Airline Passenger Numbers 1949-1960</td></tr>
+<tr><td width="25%"><a href="airquality.html">airquality</a></td>
+<td>New York Air Quality Measurements</td></tr>
+<tr><td width="25%"><a href="anscombe.html">anscombe</a></td>
+<td>Anscombe's Quartet of 'Identical' Simple Linear Regressions</td></tr>
+<tr><td width="25%"><a href="attenu.html">attenu</a></td>
+<td>The Joyner-Boore Attenuation Data</td></tr>
+<tr><td width="25%"><a href="attitude.html">attitude</a></td>
+<td>The Chatterjee-Price Attitude Data</td></tr>
+<tr><td width="25%"><a href="austres.html">austres</a></td>
+<td>Quarterly Time Series of the Number of Australian Residents</td></tr>
+</table>
+
+<h2><a name="B">-- B --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="beavers.html">beaver1</a></td>
+<td>Body Temperature Series of Two Beavers</td></tr>
+<tr><td width="25%"><a href="beavers.html">beaver2</a></td>
+<td>Body Temperature Series of Two Beavers</td></tr>
+<tr><td width="25%"><a href="beavers.html">beavers</a></td>
+<td>Body Temperature Series of Two Beavers</td></tr>
+<tr><td width="25%"><a href="BJsales.html">BJsales</a></td>
+<td>Sales Data with Leading Indicator</td></tr>
+<tr><td width="25%"><a href="BJsales.html">BJsales.lead</a></td>
+<td>Sales Data with Leading Indicator</td></tr>
+<tr><td width="25%"><a href="BOD.html">BOD</a></td>
+<td>Biochemical Oxygen Demand</td></tr>
+</table>
+
+<h2><a name="C">-- C --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="cars.html">cars</a></td>
+<td>Speed and Stopping Distances of Cars</td></tr>
+<tr><td width="25%"><a href="ChickWeight.html">ChickWeight</a></td>
+<td>Weight versus age of chicks on different diets</td></tr>
+<tr><td width="25%"><a href="chickwts.html">chickwts</a></td>
+<td>Chicken Weights by Feed Type</td></tr>
+<tr><td width="25%"><a href="zCO2.html">CO2</a></td>
+<td>Carbon Dioxide Uptake in Grass Plants</td></tr>
+<tr><td width="25%"><a href="co2.html">co2</a></td>
+<td>Mauna Loa Atmospheric CO2 Concentration</td></tr>
+<tr><td width="25%"><a href="crimtab.html">crimtab</a></td>
+<td>Student's 3000 Criminals Data</td></tr>
+</table>
+
+<h2><a name="D">-- D --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="datasets-package.html">datasets</a></td>
+<td>The R Datasets Package</td></tr>
+<tr><td width="25%"><a href="discoveries.html">discoveries</a></td>
+<td>Yearly Numbers of Important Discoveries</td></tr>
+<tr><td width="25%"><a href="DNase.html">DNase</a></td>
+<td>Elisa assay of DNase</td></tr>
+</table>
+
+<h2><a name="E">-- E --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="esoph.html">esoph</a></td>
+<td>Smoking, Alcohol and (O)esophageal Cancer</td></tr>
+<tr><td width="25%"><a href="euro.html">euro</a></td>
+<td>Conversion Rates of Euro Currencies</td></tr>
+<tr><td width="25%"><a href="euro.html">euro.cross</a></td>
+<td>Conversion Rates of Euro Currencies</td></tr>
+<tr><td width="25%"><a href="eurodist.html">eurodist</a></td>
+<td>Distances Between European Cities</td></tr>
+<tr><td width="25%"><a href="EuStockMarkets.html">EuStockMarkets</a></td>
+<td>Daily Closing Prices of Major European Stock Indices, 1991-1998</td></tr>
+</table>
+
+<h2><a name="F">-- F --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="faithful.html">faithful</a></td>
+<td>Old Faithful Geyser Data</td></tr>
+<tr><td width="25%"><a href="UKLungDeaths.html">fdeaths</a></td>
+<td>Monthly Deaths from Lung Diseases in the UK</td></tr>
+<tr><td width="25%"><a href="Formaldehyde.html">Formaldehyde</a></td>
+<td>Determination of Formaldehyde</td></tr>
+<tr><td width="25%"><a href="freeny.html">freeny</a></td>
+<td>Freeny's Revenue Data</td></tr>
+<tr><td width="25%"><a href="freeny.html">freeny.x</a></td>
+<td>Freeny's Revenue Data</td></tr>
+<tr><td width="25%"><a href="freeny.html">freeny.y</a></td>
+<td>Freeny's Revenue Data</td></tr>
+</table>
+
+<h2><a name="H">-- H --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="HairEyeColor.html">HairEyeColor</a></td>
+<td>Hair and Eye Color of Statistics Students</td></tr>
+<tr><td width="25%"><a href="Harman23.cor.html">Harman23.cor</a></td>
+<td>Harman Example 2.3</td></tr>
+<tr><td width="25%"><a href="Harman74.cor.html">Harman74.cor</a></td>
+<td>Harman Example 7.4</td></tr>
+</table>
+
+<h2><a name="I">-- I --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Indometh.html">Indometh</a></td>
+<td>Pharmacokinetics of Indomethacin</td></tr>
+<tr><td width="25%"><a href="infert.html">infert</a></td>
+<td>Infertility after Spontaneous and Induced Abortion</td></tr>
+<tr><td width="25%"><a href="InsectSprays.html">InsectSprays</a></td>
+<td>Effectiveness of Insect Sprays</td></tr>
+<tr><td width="25%"><a href="iris.html">iris</a></td>
+<td>Edgar Anderson's Iris Data</td></tr>
+<tr><td width="25%"><a href="iris.html">iris3</a></td>
+<td>Edgar Anderson's Iris Data</td></tr>
+<tr><td width="25%"><a href="islands.html">islands</a></td>
+<td>Areas of the World's Major Landmasses</td></tr>
+</table>
+
+<h2><a name="J">-- J --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="JohnsonJohnson.html">JohnsonJohnson</a></td>
+<td>Quarterly Earnings per Johnson & Johnson Share</td></tr>
+</table>
+
+<h2><a name="L">-- L --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="LakeHuron.html">LakeHuron</a></td>
+<td>Level of Lake Huron 1875-1972</td></tr>
+<tr><td width="25%"><a href="UKLungDeaths.html">ldeaths</a></td>
+<td>Monthly Deaths from Lung Diseases in the UK</td></tr>
+<tr><td width="25%"><a href="lh.html">lh</a></td>
+<td>Luteinizing Hormone in Blood Samples</td></tr>
+<tr><td width="25%"><a href="LifeCycleSavings.html">LifeCycleSavings</a></td>
+<td>Intercountry Life-Cycle Savings Data</td></tr>
+<tr><td width="25%"><a href="Loblolly.html">Loblolly</a></td>
+<td>Growth of Loblolly pine trees</td></tr>
+<tr><td width="25%"><a href="longley.html">longley</a></td>
+<td>Longley's Economic Regression Data</td></tr>
+<tr><td width="25%"><a href="lynx.html">lynx</a></td>
+<td>Annual Canadian Lynx trappings 1821-1934</td></tr>
+</table>
+
+<h2><a name="M">-- M --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="UKLungDeaths.html">mdeaths</a></td>
+<td>Monthly Deaths from Lung Diseases in the UK</td></tr>
+<tr><td width="25%"><a href="morley.html">morley</a></td>
+<td>Michelson Speed of Light Data</td></tr>
+<tr><td width="25%"><a href="mtcars.html">mtcars</a></td>
+<td>Motor Trend Car Road Tests</td></tr>
+</table>
+
+<h2><a name="N">-- N --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="nhtemp.html">nhtemp</a></td>
+<td>Average Yearly Temperatures in New Haven</td></tr>
+<tr><td width="25%"><a href="Nile.html">Nile</a></td>
+<td>Flow of the River Nile</td></tr>
+<tr><td width="25%"><a href="nottem.html">nottem</a></td>
+<td>Average Monthly Temperatures at Nottingham, 1920-1939</td></tr>
+</table>
+
+<h2><a name="O">-- O --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="occupationalStatus.html">occupationalStatus</a></td>
+<td>Occupational Status of Fathers and their Sons</td></tr>
+<tr><td width="25%"><a href="Orange.html">Orange</a></td>
+<td>Growth of Orange Trees</td></tr>
+<tr><td width="25%"><a href="OrchardSprays.html">OrchardSprays</a></td>
+<td>Potency of Orchard Sprays</td></tr>
+</table>
+
+<h2><a name="P">-- P --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="PlantGrowth.html">PlantGrowth</a></td>
+<td>Results from an Experiment on Plant Growth</td></tr>
+<tr><td width="25%"><a href="precip.html">precip</a></td>
+<td>Annual Precipitation in US Cities</td></tr>
+<tr><td width="25%"><a href="presidents.html">presidents</a></td>
+<td>Quarterly Approval Ratings of US Presidents</td></tr>
+<tr><td width="25%"><a href="pressure.html">pressure</a></td>
+<td>Vapor Pressure of Mercury as a Function of Temperature</td></tr>
+<tr><td width="25%"><a href="Puromycin.html">Puromycin</a></td>
+<td>Reaction Velocity of an Enzymatic Reaction</td></tr>
+</table>
+
+<h2><a name="Q">-- Q --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="quakes.html">quakes</a></td>
+<td>Locations of Earthquakes off Fiji</td></tr>
+</table>
+
+<h2><a name="R">-- R --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="randu.html">randu</a></td>
+<td>Random Numbers from Congruential Generator RANDU</td></tr>
+<tr><td width="25%"><a href="rivers.html">rivers</a></td>
+<td>Lengths of Major North American Rivers</td></tr>
+<tr><td width="25%"><a href="rock.html">rock</a></td>
+<td>Measurements on Petroleum Rock Samples</td></tr>
+</table>
+
+<h2><a name="S">-- S --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="UKDriverDeaths.html">Seatbelts</a></td>
+<td>Road Casualties in Great Britain 1969-84</td></tr>
+<tr><td width="25%"><a href="sleep.html">sleep</a></td>
+<td>Student's Sleep Data</td></tr>
+<tr><td width="25%"><a href="stackloss.html">stack.loss</a></td>
+<td>Brownlee's Stack Loss Plant Data</td></tr>
+<tr><td width="25%"><a href="stackloss.html">stack.x</a></td>
+<td>Brownlee's Stack Loss Plant Data</td></tr>
+<tr><td width="25%"><a href="stackloss.html">stackloss</a></td>
+<td>Brownlee's Stack Loss Plant Data</td></tr>
+<tr><td width="25%"><a href="state.html">state</a></td>
+<td>US State Facts and Figures</td></tr>
+<tr><td width="25%"><a href="state.html">state.abb</a></td>
+<td>US State Facts and Figures</td></tr>
+<tr><td width="25%"><a href="state.html">state.area</a></td>
+<td>US State Facts and Figures</td></tr>
+<tr><td width="25%"><a href="state.html">state.center</a></td>
+<td>US State Facts and Figures</td></tr>
+<tr><td width="25%"><a href="state.html">state.division</a></td>
+<td>US State Facts and Figures</td></tr>
+<tr><td width="25%"><a href="state.html">state.name</a></td>
+<td>US State Facts and Figures</td></tr>
+<tr><td width="25%"><a href="state.html">state.region</a></td>
+<td>US State Facts and Figures</td></tr>
+<tr><td width="25%"><a href="state.html">state.x77</a></td>
+<td>US State Facts and Figures</td></tr>
+<tr><td width="25%"><a href="sunspot.month.html">sunspot.month</a></td>
+<td>Monthly Sunspot Data, 1749-1997</td></tr>
+<tr><td width="25%"><a href="sunspot.year.html">sunspot.year</a></td>
+<td>Yearly Sunspot Data, 1700-1988</td></tr>
+<tr><td width="25%"><a href="sunspots.html">sunspots</a></td>
+<td>Monthly Sunspot Numbers, 1749-1983</td></tr>
+<tr><td width="25%"><a href="swiss.html">swiss</a></td>
+<td>Swiss Fertility and Socioeconomic Indicators (1888) Data</td></tr>
+</table>
+
+<h2><a name="T">-- T --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Theoph.html">Theoph</a></td>
+<td>Pharmacokinetics of Theophylline</td></tr>
+<tr><td width="25%"><a href="Titanic.html">Titanic</a></td>
+<td>Survival of passengers on the Titanic</td></tr>
+<tr><td width="25%"><a href="ToothGrowth.html">ToothGrowth</a></td>
+<td>The Effect of Vitamin C on Tooth Growth in Guinea Pigs</td></tr>
+<tr><td width="25%"><a href="treering.html">treering</a></td>
+<td>Yearly Treering Data, -6000-1979</td></tr>
+<tr><td width="25%"><a href="trees.html">trees</a></td>
+<td>Girth, Height and Volume for Black Cherry Trees</td></tr>
+</table>
+
+<h2><a name="U">-- U --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="UCBAdmissions.html">UCBAdmissions</a></td>
+<td>Student Admissions at UC Berkeley</td></tr>
+<tr><td width="25%"><a href="UKDriverDeaths.html">UKDriverDeaths</a></td>
+<td>Road Casualties in Great Britain 1969-84</td></tr>
+<tr><td width="25%"><a href="UKgas.html">UKgas</a></td>
+<td>UK Quarterly Gas Consumption</td></tr>
+<tr><td width="25%"><a href="UKLungDeaths.html">UKLungDeaths</a></td>
+<td>Monthly Deaths from Lung Diseases in the UK</td></tr>
+<tr><td width="25%"><a href="USAccDeaths.html">USAccDeaths</a></td>
+<td>Accidental Deaths in the US 1973-1978</td></tr>
+<tr><td width="25%"><a href="USArrests.html">USArrests</a></td>
+<td>Violent Crime Rates by US State</td></tr>
+<tr><td width="25%"><a href="USJudgeRatings.html">USJudgeRatings</a></td>
+<td>Lawyers' Ratings of State Judges in the US Superior Court</td></tr>
+<tr><td width="25%"><a href="USPersonalExpenditure.html">USPersonalExpenditure</a></td>
+<td>Personal Expenditure Data</td></tr>
+<tr><td width="25%"><a href="uspop.html">uspop</a></td>
+<td>Populations Recorded by the US Census</td></tr>
+</table>
+
+<h2><a name="V">-- V --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="VADeaths.html">VADeaths</a></td>
+<td>Death Rates in Virginia (1940)</td></tr>
+<tr><td width="25%"><a href="volcano.html">volcano</a></td>
+<td>Topographic Information on Auckland's Maunga Whau Volcano</td></tr>
+</table>
+
+<h2><a name="W">-- W --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="warpbreaks.html">warpbreaks</a></td>
+<td>The Number of Breaks in Yarn during Weaving</td></tr>
+<tr><td width="25%"><a href="women.html">women</a></td>
+<td>Average Heights and Weights for American Women</td></tr>
+<tr><td width="25%"><a href="WorldPhones.html">WorldPhones</a></td>
+<td>The World's Telephones</td></tr>
+<tr><td width="25%"><a href="WWWusage.html">WWWusage</a></td>
+<td>Internet Usage per Minute</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/datasets/html/R.css b/win32/deps/library/datasets/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/datasets/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/fields/DESCRIPTION b/win32/deps/library/fields/DESCRIPTION
index a796ae3..9a71d62 100644
--- a/win32/deps/library/fields/DESCRIPTION
+++ b/win32/deps/library/fields/DESCRIPTION
@@ -1,25 +1,33 @@
Package: fields
-Version: 6.01
-Date: September 4, 2009
+Version: 6.7
+Date: October 13, 2012
Title: Tools for spatial data
Author: Reinhard Furrer, Douglas Nychka and Stephen Sain
Maintainer: Doug Nychka <nychka ucar edu>
Description: Fields is for curve, surface and function fitting with an
emphasis on splines, spatial data and spatial statistics. The
major methods include cubic, robust, and thin plate splines,
- multivariate Kriging and Kriging for large data sets. A major
- feature is that any covariance function implemented in R can be
- used for spatial prediction. There are also many useful
- functions for plotting and working with spatial data as images.
- This package also contains an implementation of a sparse matrix
- methods for large data sets and currently requires the sparse
- matrix (spam) package for testing (but not for the standard
- spatial functions.) Use help(fields) to get started and for an
- overview.
+ and Kriging for large data sets. The splines and Kriging
+ methods are supporting by functions that can determine the
+ smoothing parameter (nugget and sill variance) by cross
+ validation and also by restricted maximum likelihood. A major
+ feature is that any covariance function implemented in R with
+ the fields interface can be used for spatial prediction. Some
+ tailored optimization functions are supplied for find the MLEs
+ for the Matern family of covariances. There are also many
+ useful functions for plotting and working with spatial data as
+ images. This package also contains an implementation of a
+ sparse matrix methods for large data sets and currently
+ requires the sparse matrix (spam) package for testing (but not
+ for the standard spatial functions.) Use help(fields) to get
+ started and for an overview. The fields source code is heavily
+ commented and should provide useful explanation of numerical
+ details in addition to the manual pages.
License: GPL (>= 2)
URL: http://www.image.ucar.edu/Software/Fields
-Depends: methods, spam
-Packaged: 2009-09-22 19:37:06 UTC; nychka
+Depends: R (>= 2.13), methods, spam
+Packaged: 2012-10-16 17:40:42 UTC; nychka
Repository: CRAN
-Date/Publication: 2009-09-22 20:23:49
-Built: R 2.9.2; i386-pc-mingw32; 2010-01-13 23:29:00 UTC; windows
+Date/Publication: 2012-10-16 18:52:38
+Built: R 2.15.2; x86_64-w64-mingw32; 2013-01-24 20:19:29 UTC; windows
+Archs: i386, x64
diff --git a/win32/deps/library/fields/INDEX b/win32/deps/library/fields/INDEX
index 3d561f5..1e4246d 100644
--- a/win32/deps/library/fields/INDEX
+++ b/win32/deps/library/fields/INDEX
@@ -1,125 +1,122 @@
-%d*%-methods Multiplying diagonal matrices in Package
- 'fields'
-BD Data frame of the effect of buffer compositions
- on DNA strand displacement amplification. A 4-d
- regression data set with with replication. This
- is a useful test data set for exercising
- function fitting methods.
-CO2 Simulated global CO2 observations
-COmonthlyMet Monthly surface meterology for Colorado
- 1895-1997
-Exp.cov Exponential family, radial basis
- functions,cubic spline, compactly supported
- Wendland family and stationary covariances.
-Exponential Covariance functions
-Krig Kriging surface estimate
-Krig.Amatrix Smoother (or "hat") matrix relating predicted
- values to the dependent (Y) values.
-Krig.engine.default Basic linear algebra utilities and other
- computations supporting the Krig function.
-Krig.null.function Default function to create fixed matrix part of
- spatial process model.
-RCMexample 3-hour precipitation fields from a regional
- climate model
-RMprecip Monthly total precipitation (mm) for August
- 1963 in the Rocky Mountain Region and some
- gridded 4km elevation data sets.
-Tps Thin plate spline regression
-US Plot of the US with state boundaries
-US.dat Outline of coterminous US and states.
-W.info Gives indexing imfomration for a wavelet
- decompostion
-Wendland Wendland family of covariance functions and
- supporting numerical functions
-Wimage.cov Functions for W-transform based covariance
- models
-Wimage.info Finds key indices related to a 2-d
- multiresolution
-Wimage.info.plot Plot to check 2-d multiresolution indexing
-Wtransform Quadratic W wavelet transform for 1-d vectors
- or rectangular or cylindrical images
-add.image Adds an image to an existing plot.
-arrow.plot Adds arrows to a plot
-as.image Creates image from irregular x,y,z
-as.surface Creates an "surface" object from grid values.
-bplot boxplot
-bplot.xy Boxplots for conditional distribution
-colorbar.plot Adds color scale strips to an existing plot.
-cover.design Computes Space-Filling "Coverage" designs using
- Swapping Algorithm
-drape.plot Perspective plot draped with colors in the
- facets.
-fields fields - tools for spatial data
-fields.diagonalize Fields supporting functions
-fields.hints fields - graphics hints
-fields.tests Testing fields functions
-flame Response surface experiment ionizing a reagent
-gcv.Krig Finds profile likelihood and GCV estimates of
- smoothing parameters for splines and Kriging.
-grid list Some simple functions for working with gridded
- data and the grid format (grid.list) used in
- fields.
-image.plot Draws image plot with a legend strip for the
- color scale based on either a regular grid or a
- grid of quadrilaterals.
-image.smooth Kernel smoother for irregular 2-d data
-image2lz Some simple functions for subsetting images
-interp.surface Fast bilinear interpolator from a grid.
-krig.image Spatial process estimate for large irregular
- 2-d dats sets.
-lennon Gray image of John Lennon.
-mKrig "micro Krig" Spatial process estimate of a
- curve or surface, "kriging" with a known
- covariance function.
-mKrig.grid Using MKrig for predicting on a grid.
-minitri Mini triathlon results
-ozone Data set of ozone measurements at 20 Chicago
- monitoring stations.
-ozone2 Daily 8-hour ozone averages for sites in the
- Midwest
-plot.Krig Diagnostic and summary plots of a Kriging or
- spline object
-plot.Wimage Plots 2-d wavelet coefficents by level and type
-plot.surface Plots a surface
-poisson.cov Poisson spherical covariance function
-poly.image Image plot for cells that are irregular
- quadrilaterals.
-predict.Krig Evaluation of Krig spatial process estimate.
-predict.se Standard errors of predictions
-predict.se.Krig Standard errors of predictions for Krig spatial
- process estimate
-predict.surface Evaluates a fitted function or its standard
- errors as a surface object
-print.Krig Print kriging fit results.
-pushpin Adds a "push pin" to an existing 3-d plot
-qsreg Quantile or Robust spline regression
-quilt.plot Image plot for irregular spatial data.
-rat.diet Experiment studying an appetite supressant in
- rats.
-rdist Euclidean distance matrix
-rdist.earth Great circle distance matrix
-ribbon.plot Adds to an existing plot, a ribbon of color,
- based on values from a color scale, along a
- sequence of line segments.
-set.panel Specify a panel of plots
-sim.Krig.standard Conditonal simulation of a spatial process
-sim.rf Simulates a random field
-smooth.2d Kernel smoother for irregular 2-d data
-spind2spam Conversion of formats for sparse matrices
-splint Cubic spline interpolation
-sreg Smoothing spline regression
-stationary.image.cov Exponential, Matern and general covariance
- functions for 2-d gridded locations.
-stats Calculate summary statistics
-stats.bin Bins data and finds some summary statistics.
-summary.Krig Summary for Krig spatial process estimate
-summary.ncdf Summarizes a netCDF file handle
-surface.Krig Plots a surface and contours
-tim.colors Some useful color tables for images.
-transformx Linear transformation
-vgram Finds a traditional or robust variogram for
- spatial data.
-vgram.matrix Computes a variogram from an image
-world Plot of the world
-xline Draw a vertical line
-yline Draw horizontal lines
+BD Data frame of the effect of buffer compositions
+ on DNA strand displacement amplification. A 4-d
+ regression data set with with replication. This
+ is a useful test data set for exercising
+ function fitting methods.
+CO2 Simulated global CO2 observations
+COmonthlyMet Monthly surface meterology for Colorado
+ 1895-1997
+Exp.cov Exponential family, radial basis
+ functions,cubic spline, compactly supported
+ Wendland family and stationary covariances.
+Exponential Covariance functions
+Krig Kriging surface estimate
+Krig.Amatrix Smoother (or "hat") matrix relating predicted
+ values to the dependent (Y) values.
+Krig.engine.default Basic linear algebra utilities and other
+ computations supporting the Krig function.
+Krig.null.function Default function to create fixed matrix part of
+ spatial process model.
+NorthAmericanRainfall Observed North American summer precipitation
+ from the historical climate network.
+RCMexample 3-hour precipitation fields from a regional
+ climate model
+REML.test Maximum Likelihood estimates for some Matern
+ covariance parameters.
+RMprecip Monthly total precipitation (mm) for August
+ 1963 in the Rocky Mountain Region and some
+ gridded 4km elevation data sets.
+Tps Thin plate spline regression
+US Plot of the US with state boundaries
+US.dat Outline of coterminous US and states.
+Wendland Wendland family of covariance functions and
+ supporting numerical functions
+WorldBankCO2 Carbon emissions and demographic covariables by
+ country for 1999.
+add.image Adds an image to an existing plot.
+arrow.plot Adds arrows to a plot
+as.image Creates image from irregular x,y,z
+as.surface Creates an "surface" object from grid values.
+bplot boxplot
+bplot.xy Boxplots for conditional distribution
+colorbar.plot Adds color scale strips to an existing plot.
+cover.design Computes Space-Filling "Coverage" designs using
+ Swapping Algorithm
+drape.plot Perspective plot draped with colors in the
+ facets.
+fields fields - tools for spatial data
+fields.diagonalize2 Fields supporting functions
+fields.hints fields - graphics hints
+fields.tests Testing fields functions
+flame Response surface experiment ionizing a reagent
+gcv.Krig Finds profile likelihood and GCV estimates of
+ smoothing parameters for splines and Kriging.
+grid list Some simple functions for working with gridded
+ data and the grid format (grid.list) used in
+ fields.
+image.plot Draws image plot with a legend strip for the
+ color scale based on either a regular grid or a
+ grid of quadrilaterals.
+image.smooth Kernel smoother for irregular 2-d data
+image2lz Some simple functions for subsetting images
+interp.surface Fast bilinear interpolator from a grid.
+lennon Gray image of John Lennon.
+mKrig "micro Krig" Spatial process estimate of a
+ curve or surface, "kriging" with a known
+ covariance function.
+mKrig.MLE maximizes likelihood for the process marginal
+ variance (rho) and nugget standard deviation
+ (sigma) parameters (e.g. lambda) over a list of
+ covariance models or a grid of covariance
+ parameter values.
+mKrig.grid Using MKrig for predicting on a grid.
+minitri Mini triathlon results
+ozone Data set of ozone measurements at 20 Chicago
+ monitoring stations.
+ozone2 Daily 8-hour ozone averages for sites in the
+ Midwest
+plot.Krig Diagnostic and summary plots of a Kriging or
+ spline object
+plot.surface Plots a surface
+poly.image Image plot for cells that are irregular
+ quadrilaterals.
+predict.Krig Evaluation of Krig spatial process estimate.
+predict.derivative Predicted derivatives
+predict.se Standard errors of predictions
+predict.se.Krig Standard errors of predictions for Krig spatial
+ process estimate
+predict.surface Evaluates a fitted function or its standard
+ errors as a surface object
+print.Krig Print kriging fit results.
+pushpin Adds a "push pin" to an existing 3-d plot
+quilt.plot Image plot for irregular spatial data.
+rat.diet Experiment studying an appetite supressant in
+ rats.
+rdist Euclidean distance matrix
+rdist.earth Great circle distance matrix
+ribbon.plot Adds to an existing plot, a ribbon of color,
+ based on values from a color scale, along a
+ sequence of line segments.
+set.panel Specify a panel of plots
+sim.Krig.standard Conditonal simulation of a spatial process
+sim.rf Simulates a random field
+smooth.2d Kernel smoother for irregular 2-d data
+spind2spam Conversion of formats for sparse matrices
+splint Cubic spline interpolation
+sreg Smoothing spline regression
+stationary.image.cov Exponential, Matern and general covariance
+ functions for 2-d gridded locations.
+stats Calculate summary statistics
+stats.bin Bins data and finds some summary statistics.
+summary.Krig Summary for Krig spatial process estimate
+summary.ncdf Summarizes a netCDF file handle
+surface.Krig Plots a surface and contours
+tim.colors Some useful color tables for images and tools
+ to handle them.
+transformx Linear transformation
+vgram Finds a traditional or robust variogram for
+ spatial data.
+vgram.matrix Computes a variogram from an image
+world Plot of the world
+xline Draw a vertical line
+yline Draw horizontal lines
diff --git a/win32/deps/library/fields/LICENSE b/win32/deps/library/fields/LICENSE
new file mode 100644
index 0000000..3a847ba
--- /dev/null
+++ b/win32/deps/library/fields/LICENSE
@@ -0,0 +1,11 @@
+All R code and documentation in this package (fields) is licensed
+under the terms of the GPL license.
+
+NOTE:
+
+The sparse matrix methods used in fields are supported by the package
+spam and there are a subset of fortran routines in spam where some
+licensing issues are unclear. Please refer to the spam license
+information for details. Note that many functions in fields e.g. Tps,
+Krig, all the graphical functions, do not require this package so much
+of fields will be functional under a GPL license.
diff --git a/win32/deps/library/fields/MD5 b/win32/deps/library/fields/MD5
index 6935c71..8a4f8e9 100644
--- a/win32/deps/library/fields/MD5
+++ b/win32/deps/library/fields/MD5
@@ -1,115 +1,37 @@
-0560fb103dec40ad9a3dbb2848cc31d4 *CONTENTS
-7b72cfcf8b0d5e9b74f444e2cafea8dc *DESCRIPTION
-b39f7e1fd93048e25f2382b45e794c6e *INDEX
-1890ec32d42ba4f7a5ba4de7d857979a *Meta/Rd.rds
-a61a5faf8d28a8df20768392d50c5eb3 *Meta/data.rds
-fd133af4457148790b53103dce248d82 *Meta/hsearch.rds
-94a99e4b1e5160e970be0a6958dd6947 *Meta/package.rds
-b4257847c0d1a8c2a1a03dd31b157616 *R-ex/Rex.zip
-6e60a4480e0345d65902fc23b54bffd6 *R/fields
-fe06b9c0d095236767019bd4b16a67ae *R/fields.rdb
-f939626673d754ab205ea2ae29ddbf3c *R/fields.rdx
-9325aad5173d112f712ec09f22ddb2ca *chtml/fields.chm
-115c24a6041c8e2fd17102d18840c609 *data/CO2.rda
-08003b5b82b618cd116a0ad59c7a202a *data/COmonthlyMet.rda
-3adbae86a62efba890a88654302c9e8f *data/PRISMelevation.rda
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-97b306efd6b89771023e321be8ea6893 *libs/fields.dll
-0e7d9deae29c5babdd00755eaef91e9b *man/fields.Rd.gz
+0f6cd40458aafe676451ba8ad7498977 *DESCRIPTION
+ad2be08a47ce2d189e1a518366a86832 *INDEX
+9fdcee37301b4808ab63d8f9dbcd9bd9 *LICENSE
+996b82515235ee8add680c4930c74433 *Meta/Rd.rds
+555c38561f2a652e126f66ccfeaaed77 *Meta/data.rds
+1f7371b7e8ab52a51f5d2d9646d4d796 *Meta/hsearch.rds
+c1b1dd957b3551bb42a0bdecf58dc950 *Meta/links.rds
+1c56a07a334ee8ad603a2ffb4db78b5e *Meta/nsInfo.rds
+3b572eb7a14de6f671e6191d0a01f024 *Meta/package.rds
+e5db63a0f2482b78082007ba4ceea935 *NAMESPACE
+240d28d145138a75831809e31a480bad *R/fields
+8a19f0bc2c5a3342da679ee01c63c11d *R/fields.rdb
+6def3359456254864ee60211eda810f9 *R/fields.rdx
+def2e3c5b2487cf369719ecedc0ec009 *data/CO2.rda
+74f28573008f6b64fae8e5b724bd36a3 *data/COmonthlyMet.rda
+652f70fc0c2630a0a698419bb91fc736 *data/NorthAmericanRainfall.rda
+0c0be8a07fa347d68fc36fc6a117c759 *data/PRISMelevation.rda
+d5ae9ea8fb3cff4c92c686e2b8e2a669 *data/RCMexample.rda
+ec8555f8006ae1cbdf3937be5609b37e *data/RMelevation.rda
+5f0f32a5ee0dbc877a28c20bdeb6f64d *data/US.dat.rda
+5baf657b81b2ee2809dc96ecde12794d *data/WorldBankCO2.rda
+66b8754c3221f29585a9b52f84a34e9f *data/datalist
+f560c509a3416dcb22274af12ebf5d07 *data/lennon.rda
+3abfd104c2c387a4ebb62742932ca0a6 *data/ozone2.rda
+43a5afaacf0deb2f95d4288968aa7168 *data/rat.diet.rda
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+383e200004bad37b10e11e1ba0f10d66 *help/aliases.rds
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+933ffb5b8362960f5e294ebc9733dd49 *help/paths.rds
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+444535b9cb76ddff1bab1e1865a3fb14 *html/R.css
+3226ccc98c3cfed7f5f63e52706b06c3 *libs/i386/fields.dll
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diff --git a/win32/deps/library/fields/Meta/Rd.rds b/win32/deps/library/fields/Meta/Rd.rds
index 05148cd..a2a0c98 100644
Binary files a/win32/deps/library/fields/Meta/Rd.rds and b/win32/deps/library/fields/Meta/Rd.rds differ
diff --git a/win32/deps/library/fields/Meta/data.rds b/win32/deps/library/fields/Meta/data.rds
index 251b5cf..493df35 100644
Binary files a/win32/deps/library/fields/Meta/data.rds and b/win32/deps/library/fields/Meta/data.rds differ
diff --git a/win32/deps/library/fields/Meta/hsearch.rds b/win32/deps/library/fields/Meta/hsearch.rds
index 1dd5d90..6e1f973 100644
Binary files a/win32/deps/library/fields/Meta/hsearch.rds and b/win32/deps/library/fields/Meta/hsearch.rds differ
diff --git a/win32/deps/library/fields/Meta/links.rds b/win32/deps/library/fields/Meta/links.rds
new file mode 100644
index 0000000..604951a
Binary files /dev/null and b/win32/deps/library/fields/Meta/links.rds differ
diff --git a/win32/deps/library/fields/Meta/nsInfo.rds b/win32/deps/library/fields/Meta/nsInfo.rds
new file mode 100644
index 0000000..fabbe2f
Binary files /dev/null and b/win32/deps/library/fields/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/fields/Meta/package.rds b/win32/deps/library/fields/Meta/package.rds
index 03617f1..5f60b15 100644
Binary files a/win32/deps/library/fields/Meta/package.rds and b/win32/deps/library/fields/Meta/package.rds differ
diff --git a/win32/deps/library/fields/NAMESPACE b/win32/deps/library/fields/NAMESPACE
new file mode 100644
index 0000000..d8d6bdf
--- /dev/null
+++ b/win32/deps/library/fields/NAMESPACE
@@ -0,0 +1,12 @@
+exportPattern("^[^\\.]")
+
+S3method(print, Krig)
+S3method(print, mKrig)
+S3method(summary, Krig)
+S3method(summary, mKrig)
+
+useDynLib(fields,evlpoly, evlpoly2, multeb, dmaket, ddfind, inpoly, igpoly,
+ rcss, radbas, multrb, css)
+
+import("spam")
+
diff --git a/win32/deps/library/fields/R/fields b/win32/deps/library/fields/R/fields
index be99e29..ac8cebe 100644
--- a/win32/deps/library/fields/R/fields
+++ b/win32/deps/library/fields/R/fields
@@ -1,18 +1,9 @@
-.First.lib <- function(libname, pkgname)
-{
- fullName <- paste("package", pkgname, sep=":")
- myEnv <- as.environment(match(fullName, search()))
- barepackage <- sub("([^-]+)_.*", "\\1", pkgname)
- dbbase <- file.path(libname, pkgname, "R", barepackage)
- rm(.First.lib, envir = myEnv)
- lazyLoad(dbbase, myEnv)
- if(exists(".First.lib", envir = myEnv, inherits = FALSE)) {
- f <- get(".First.lib", envir = myEnv, inherits = FALSE)
- if(is.function(f))
- f(libname, pkgname)
- else
- stop(gettextf("package '%s' has a non-function '.First.lib'",
- pkgname),
- domain = NA)
- }
-}
+local({
+ info <- loadingNamespaceInfo()
+ ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
+ if (is.null(ns))
+ stop("cannot find namespace environment");
+ barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
+ dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
+ lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
+})
diff --git a/win32/deps/library/fields/R/fields.rdb b/win32/deps/library/fields/R/fields.rdb
index 3e11efb..e569313 100644
Binary files a/win32/deps/library/fields/R/fields.rdb and b/win32/deps/library/fields/R/fields.rdb differ
diff --git a/win32/deps/library/fields/R/fields.rdx b/win32/deps/library/fields/R/fields.rdx
index ab4fe1c..73bce55 100644
Binary files a/win32/deps/library/fields/R/fields.rdx and b/win32/deps/library/fields/R/fields.rdx differ
diff --git a/win32/deps/library/fields/data/CO2.rda b/win32/deps/library/fields/data/CO2.rda
index df4e593..949589d 100644
Binary files a/win32/deps/library/fields/data/CO2.rda and b/win32/deps/library/fields/data/CO2.rda differ
diff --git a/win32/deps/library/fields/data/COmonthlyMet.rda b/win32/deps/library/fields/data/COmonthlyMet.rda
index a8255aa..69fa997 100644
Binary files a/win32/deps/library/fields/data/COmonthlyMet.rda and b/win32/deps/library/fields/data/COmonthlyMet.rda differ
diff --git a/win32/deps/library/fields/data/NorthAmericanRainfall.rda b/win32/deps/library/fields/data/NorthAmericanRainfall.rda
new file mode 100644
index 0000000..ed4d528
Binary files /dev/null and b/win32/deps/library/fields/data/NorthAmericanRainfall.rda differ
diff --git a/win32/deps/library/fields/data/PRISMelevation.rda b/win32/deps/library/fields/data/PRISMelevation.rda
index 902d4f0..4005686 100644
Binary files a/win32/deps/library/fields/data/PRISMelevation.rda and b/win32/deps/library/fields/data/PRISMelevation.rda differ
diff --git a/win32/deps/library/fields/data/RCMexample.rda b/win32/deps/library/fields/data/RCMexample.rda
index bf4c2f3..9c45a50 100644
Binary files a/win32/deps/library/fields/data/RCMexample.rda and b/win32/deps/library/fields/data/RCMexample.rda differ
diff --git a/win32/deps/library/fields/data/RMelevation.rda b/win32/deps/library/fields/data/RMelevation.rda
index 4771db9..ad90f87 100644
Binary files a/win32/deps/library/fields/data/RMelevation.rda and b/win32/deps/library/fields/data/RMelevation.rda differ
diff --git a/win32/deps/library/fields/data/US.dat.rda b/win32/deps/library/fields/data/US.dat.rda
index 0268828..48393aa 100644
Binary files a/win32/deps/library/fields/data/US.dat.rda and b/win32/deps/library/fields/data/US.dat.rda differ
diff --git a/win32/deps/library/fields/data/WorldBankCO2.rda b/win32/deps/library/fields/data/WorldBankCO2.rda
new file mode 100644
index 0000000..dc6015f
Binary files /dev/null and b/win32/deps/library/fields/data/WorldBankCO2.rda differ
diff --git a/win32/deps/library/fields/data/datalist b/win32/deps/library/fields/data/datalist
new file mode 100644
index 0000000..5fbcd9e
--- /dev/null
+++ b/win32/deps/library/fields/data/datalist
@@ -0,0 +1,11 @@
+CO2: CO2 CO2.true
+COmonthlyMet: CO.elev CO.id CO.loc CO.names CO.ppt CO.ppt.MAM CO.ppt.MAM.climate CO.tmax CO.tmax.MAM CO.tmax.MAM.climate CO.tmean.MAM.climate CO.tmin CO.tmin.MAM CO.tmin.MAM.climate CO.years
+PRISMelevation
+RCMexample
+RMelevation
+US.dat
+WorldBankCO2
+lennon
+ozone2
+rat.diet
+world.dat
diff --git a/win32/deps/library/fields/data/lennon.rda b/win32/deps/library/fields/data/lennon.rda
index 7a21eb4..11f395c 100644
Binary files a/win32/deps/library/fields/data/lennon.rda and b/win32/deps/library/fields/data/lennon.rda differ
diff --git a/win32/deps/library/fields/data/ozone2.rda b/win32/deps/library/fields/data/ozone2.rda
index bf33a0d..fd08710 100644
Binary files a/win32/deps/library/fields/data/ozone2.rda and b/win32/deps/library/fields/data/ozone2.rda differ
diff --git a/win32/deps/library/fields/data/rat.diet.rda b/win32/deps/library/fields/data/rat.diet.rda
new file mode 100644
index 0000000..d8a31c6
Binary files /dev/null and b/win32/deps/library/fields/data/rat.diet.rda differ
diff --git a/win32/deps/library/fields/data/world.dat.rda b/win32/deps/library/fields/data/world.dat.rda
index 8eefba5..be48ea0 100644
Binary files a/win32/deps/library/fields/data/world.dat.rda and b/win32/deps/library/fields/data/world.dat.rda differ
diff --git a/win32/deps/library/fields/help/AnIndex b/win32/deps/library/fields/help/AnIndex
index 1c20dae..2f6370a 100644
--- a/win32/deps/library/fields/help/AnIndex
+++ b/win32/deps/library/fields/help/AnIndex
@@ -1,9 +1,5 @@
+fields-package fields
%d*% Krig.engine.default
-%d*%,matrix,matrix-method diag_mult
-%d*%,matrix,numeric-method diag_mult
-%d*%,numeric,matrix-method diag_mult
-%d*%,numeric,numeric-method diag_mult
-%d*%-methods diag_mult
add.image add.image
arrow.plot arrow.plot
as.image as.image
@@ -12,7 +8,6 @@ average.image image2lz
BD BD
bisection.search fields-internal
bplot bplot
-bplot.obj fields-internal
bplot.xy bplot.xy
cat.matrix fields-internal
cat.to.list fields-internal
@@ -33,26 +28,29 @@ CO.tmin.MAM CO
CO.tmin.MAM.climate CO
CO.years CO
CO2 CO2
+CO2.true CO2
coef.Krig Krig
+color.scale tim.colors
colorbar.plot colorbar.plot
COmonthlyMet CO
-conjugate.gradient fields-internal
COR fields-internal
cover.design cover.design
crop.image image2lz
+css FORTRAN.internal
cubic.cov exp.cov
D4transform.image fields-internal
+ddfind FORTRAN.internal
describe fields-internal
-describe.bplot fields-internal
designer.colors tim.colors
discretize.image grid.list
+dmaket FORTRAN.internal
double.exp fields-internal
drape.color drape.plot
drape.plot drape.plot
-draw.bplot fields-internal
-draw.bplot.obj fields-internal
dyadic.2check fields-internal
dyadic.check fields-internal
+evlpoly FORTRAN.internal
+evlpoly2 FORTRAN.internal
Exp.cov exp.cov
Exp.earth.cov fields-internal
Exp.image.cov image.cov
@@ -66,6 +64,7 @@ fields.convert.grid grid.list
fields.D Wendland
fields.derivative.poly fields-stuff
fields.diagonalize fields-stuff
+fields.diagonalize2 fields-stuff
fields.duplicated.matrix fields-stuff
fields.evlpoly fields-stuff
fields.evlpoly2 fields-stuff
@@ -85,17 +84,19 @@ gcv.Krig gcv.Krig
gcv.sreg gcv.Krig
get.rectangle image2lz
golden.section.search fields-internal
-grey.level fields-internal
grid list grid.list
grid.list grid.list
half.image image2lz
+igpoly FORTRAN.internal
image.plot image.plot
image.plot.info fields-internal
image.plot.plt fields-internal
image.smooth image.smooth
image2lz image2lz
+in.land.grid world
in.poly image2lz
in.poly.grid image2lz
+inpoly FORTRAN.internal
interp.surface interp.surface
interp.surface.grid interp.surface
Krig Krig
@@ -116,7 +117,6 @@ Krig.find.REML fields-internal
Krig.flplike fields-internal
Krig.fs2hat fields-internal
Krig.ftrace fields-internal
-krig.image krig.image
krig.image.parameters fields-internal
Krig.make.u Krig.engine.default
Krig.make.W Krig.engine.default
@@ -129,53 +129,58 @@ Krig.updateY fields-internal
Krig.which.lambda fields-internal
Krig.ynew fields-internal
lennon lennon
-lonlat2xy fields-internal
make.surface.grid grid.list
Matern Exponential
Matern.cor.to.range Exponential
matern.image.cov image.cov
+MaternGLS.test REML.test
+MaternGLSProfile.test REML.test
+MaternQR.test REML.test
+MaternQRProfile.test REML.test
minimax.crit fields-internal
minitri minitri
mKrig mKrig
mKrig.coef mKrig
mKrig.grid fields.grid
+mKrig.MLE mKrig.MLE
mKrig.trace mKrig
+MLE.Matern REML.test
+MLE.Matern.fast REML.test
+MLE.objective.fn REML.test
+multeb FORTRAN.internal
+multrb FORTRAN.internal
+NorthAmericanRainfall NorthAmericanRainfall
ozone ozone
ozone2 ozone2
parse.grid.list grid.list
-periodic.cov.1d fields-internal
-periodic.cov.cyl fields-internal
-periodic.plane.3d fields-internal
plot.Krig plot.Krig
plot.krig.image fields-internal
-plot.qsreg fields-internal
plot.sim.krig.image fields-internal
plot.spatial.design fields-internal
plot.sreg plot.Krig
plot.surface plot.surface
plot.vgram.matrix vgram.matrix
-plot.Wimage plot.Wimage
-poisson.cov poisson.cov
poly.image poly.image
poly.image.regrid poly.image
+predict.derivative predict.derivative
+predict.derivative.default predict.derivative
predict.derivative.Krig predict.Krig
predict.interp.surface fields-internal
predict.Krig predict.Krig
predict.krig.image fields-internal
predict.mKrig mKrig
-predict.qsreg fields-internal
predict.se predict.se
predict.se.Krig predict.se.Krig
predict.se.KrigA predict.se.Krig
predict.se.mKrig predict.se.Krig
predict.sreg fields-internal
predict.surface predict.surface
+predict.surface.derivative predict.surface
predict.surface.se predict.surface
predict.Tps fields-internal
print.Krig print.Krig
print.krig.image fields-internal
print.mKrig mKrig
-print.qsreg fields-internal
print.spatial.design fields-internal
print.sreg fields-internal
print.summary.Krig fields-internal
@@ -186,22 +191,19 @@ PRISMelevation RMprecip
pushpin pushpin
qr.q2ty fields-internal
qr.yq2 fields-internal
-qsreg qsreg
-qsreg.fit fields-internal
-qsreg.psi fields-internal
-qsreg.rho fields-internal
-qsreg.trace fields-internal
quilt.plot quilt.plot
Rad.cov exp.cov
Rad.image.cov image.cov
Rad.simple.cov exp.cov
+radbas FORTRAN.internal
radbas.constant fields-internal
RadialBasis Exponential
rat.diet rat.diet
RCMexample RCMexample
+rcss FORTRAN.internal
rdist rdist
rdist.earth rdist.earth
-replace.args.function fields-internal
+REML.test REML.test
resid.Krig Krig
ribbon.plot ribbon.plot
RMelevation RMprecip
@@ -232,14 +234,13 @@ stationary.image.cov image.cov
stationary.taper.cov exp.cov
stats stats
stats.bin stats.bin
-stats.bplot fields-internal
stats.sim.krig.image fields-internal
summary.gcv.Krig fields-internal
summary.gcv.sreg fields-internal
summary.Krig summary.Krig
summary.krig.image fields-internal
+summary.mKrig mKrig
summary.ncdf summary.ncdf
-summary.qsreg fields-internal
summary.spatial.design fields-internal
summary.sreg fields-internal
surface fields-internal
@@ -258,46 +259,16 @@ US US
US.dat US.dat
vgram vgram
vgram.matrix vgram.matrix
-W.i2s W.info
-W.info W.info
-W.s2i W.info
-WD4 fields-internal
-WD42d fields-internal
-WD42di fields-internal
-WD4i fields-internal
Wendland Wendland
Wendland.beta Wendland
wendland.cov exp.cov
wendland.eval Wendland
Wendland2.2 Wendland
-Wimage.cov Wimage.cov
-Wimage.i2s Wimage.info
-Wimage.info Wimage.info
-Wimage.info.plot Wimage.info.plot
-Wimage.s2i Wimage.info
-Wimage.sim Wimage.cov
world world
world.color world
world.dat fields-internal
-WQS fields-internal
-WQS.basis fields-internal
-WQS.periodic fields-internal
-WQS.periodic.basis fields-internal
-WQS.periodic.T fields-internal
-WQS.T fields-internal
-WQS2d fields-internal
-WQS2d.cylinder fields-internal
-WQS2di fields-internal
-WQS2di.cylinder fields-internal
-WQSdi fields-internal
-WQSi fields-internal
-WQSi.periodic fields-internal
-WQSi.periodic.T fields-internal
-WQSi.T fields-internal
-Wtransform Wtransform
-Wtransform.cylinder.image Wtransform
-Wtransform.image Wtransform
-Wtransform.image.cov Wimage.cov
+world.land world
+WorldBankCO2 WorldBank
xline xline
yline yline
[.spatial.design fields-internal
diff --git a/win32/deps/library/fields/help/aliases.rds b/win32/deps/library/fields/help/aliases.rds
new file mode 100644
index 0000000..4c73950
Binary files /dev/null and b/win32/deps/library/fields/help/aliases.rds differ
diff --git a/win32/deps/library/fields/help/fields.rdb b/win32/deps/library/fields/help/fields.rdb
new file mode 100644
index 0000000..6f5f566
Binary files /dev/null and b/win32/deps/library/fields/help/fields.rdb differ
diff --git a/win32/deps/library/fields/help/fields.rdx b/win32/deps/library/fields/help/fields.rdx
new file mode 100644
index 0000000..b6bf6b5
Binary files /dev/null and b/win32/deps/library/fields/help/fields.rdx differ
diff --git a/win32/deps/library/fields/help/paths.rds b/win32/deps/library/fields/help/paths.rds
new file mode 100644
index 0000000..3853a95
Binary files /dev/null and b/win32/deps/library/fields/help/paths.rds differ
diff --git a/win32/deps/library/fields/html/00Index.html b/win32/deps/library/fields/html/00Index.html
index 747967c..fba3d26 100644
--- a/win32/deps/library/fields/html/00Index.html
+++ b/win32/deps/library/fields/html/00Index.html
@@ -1,25 +1,25 @@
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html><head><title>R: Tools for spatial data</title>
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><link rel="stylesheet" type="text/css" href="../../R.css">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
</head><body>
-<h1>Tools for spatial data <img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]"></h1>
-
+<h1> Tools for spatial data
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
<hr>
-
<div align="center">
-<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg"
-alt="[Package List]" width="30" height="30" border="0"></a>
-<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg"
-alt="[Top]" width="30" height="30" border="0"></a>
-</div>
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘fields’ version 6.7</h2>
-<h2>Documentation for package ‘fields’ version 6.01</h2>
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+</ul>
<h2>Help Pages</h2>
<p align="center">
-<a href="#"></a>
+<a href="# "> </a>
<a href="#A">A</a>
<a href="#B">B</a>
<a href="#C">C</a>
@@ -32,6 +32,7 @@ alt="[Top]" width="30" height="30" border="0"></a>
<a href="#K">K</a>
<a href="#L">L</a>
<a href="#M">M</a>
+<a href="#N">N</a>
<a href="#O">O</a>
<a href="#P">P</a>
<a href="#Q">Q</a>
@@ -43,24 +44,12 @@ alt="[Top]" width="30" height="30" border="0"></a>
<a href="#W">W</a>
<a href="#X">X</a>
<a href="#Y">Y</a>
+<a href="#misc">misc</a>
</p>
-
-<h2><a name="">-- --</a></h2>
-
<table width="100%">
-<tr><td width="25%"><a href="Krig.engine.default.html">%d*%</a></td>
-<td>Basic linear algebra utilities and other computations supporting the Krig function.</td></tr>
-<tr><td width="25%"><a href="diag_mult.html">%d*%,matrix,matrix-method</a></td>
-<td>Multiplying diagonal matrices in Package 'fields'</td></tr>
-<tr><td width="25%"><a href="diag_mult.html">%d*%,matrix,numeric-method</a></td>
-<td>Multiplying diagonal matrices in Package 'fields'</td></tr>
-<tr><td width="25%"><a href="diag_mult.html">%d*%,numeric,matrix-method</a></td>
-<td>Multiplying diagonal matrices in Package 'fields'</td></tr>
-<tr><td width="25%"><a href="diag_mult.html">%d*%,numeric,numeric-method</a></td>
-<td>Multiplying diagonal matrices in Package 'fields'</td></tr>
-<tr><td width="25%"><a href="diag_mult.html">%d*%-methods</a></td>
-<td>Multiplying diagonal matrices in Package 'fields'</td></tr>
+<tr><td width="25%"><a href="fields.html">fields-package</a></td>
+<td>fields - tools for spatial data</td></tr>
</table>
<h2><a name="A">-- A --</a></h2>
@@ -124,8 +113,12 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Monthly surface meterology for Colorado 1895-1997</td></tr>
<tr><td width="25%"><a href="CO2.html">CO2</a></td>
<td>Simulated global CO2 observations</td></tr>
+<tr><td width="25%"><a href="CO2.html">CO2.true</a></td>
+<td>Simulated global CO2 observations</td></tr>
<tr><td width="25%"><a href="Krig.html">coef.Krig</a></td>
<td>Kriging surface estimate</td></tr>
+<tr><td width="25%"><a href="tim.colors.html">color.scale</a></td>
+<td>Some useful color tables for images and tools to handle them.</td></tr>
<tr><td width="25%"><a href="colorbar.plot.html">colorbar.plot</a></td>
<td>Adds color scale strips to an existing plot.</td></tr>
<tr><td width="25%"><a href="CO.html">COmonthlyMet</a></td>
@@ -142,7 +135,7 @@ alt="[Top]" width="30" height="30" border="0"></a>
<table width="100%">
<tr><td width="25%"><a href="tim.colors.html">designer.colors</a></td>
-<td>Some useful color tables for images.</td></tr>
+<td>Some useful color tables for images and tools to handle them.</td></tr>
<tr><td width="25%"><a href="grid.list.html">discretize.image</a></td>
<td>Some simple functions for working with gridded data and the grid format (grid.list) used in fields.</td></tr>
<tr><td width="25%"><a href="drape.plot.html">drape.color</a></td>
@@ -181,6 +174,8 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Fields supporting functions</td></tr>
<tr><td width="25%"><a href="fields-stuff.html">fields.diagonalize</a></td>
<td>Fields supporting functions</td></tr>
+<tr><td width="25%"><a href="fields-stuff.html">fields.diagonalize2</a></td>
+<td>Fields supporting functions</td></tr>
<tr><td width="25%"><a href="fields-stuff.html">fields.duplicated.matrix</a></td>
<td>Fields supporting functions</td></tr>
<tr><td width="25%"><a href="fields-stuff.html">fields.evlpoly</a></td>
@@ -240,6 +235,8 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Kernel smoother for irregular 2-d data</td></tr>
<tr><td width="25%"><a href="image2lz.html">image2lz</a></td>
<td>Some simple functions for subsetting images</td></tr>
+<tr><td width="25%"><a href="world.html">in.land.grid</a></td>
+<td>Plot of the world</td></tr>
<tr><td width="25%"><a href="image2lz.html">in.poly</a></td>
<td>Some simple functions for subsetting images</td></tr>
<tr><td width="25%"><a href="image2lz.html">in.poly.grid</a></td>
@@ -269,8 +266,6 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Basic linear algebra utilities and other computations supporting the Krig function.</td></tr>
<tr><td width="25%"><a href="Krig.engine.default.html">Krig.engine.knots</a></td>
<td>Basic linear algebra utilities and other computations supporting the Krig function.</td></tr>
-<tr><td width="25%"><a href="krig.image.html">krig.image</a></td>
-<td>Spatial process estimate for large irregular 2-d dats sets.</td></tr>
<tr><td width="25%"><a href="Krig.engine.default.html">Krig.make.u</a></td>
<td>Basic linear algebra utilities and other computations supporting the Krig function.</td></tr>
<tr><td width="25%"><a href="Krig.engine.default.html">Krig.make.W</a></td>
@@ -301,6 +296,14 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Covariance functions</td></tr>
<tr><td width="25%"><a href="image.cov.html">matern.image.cov</a></td>
<td>Exponential, Matern and general covariance functions for 2-d gridded locations.</td></tr>
+<tr><td width="25%"><a href="REML.test.html">MaternGLS.test</a></td>
+<td>Maximum Likelihood estimates for some Matern covariance parameters.</td></tr>
+<tr><td width="25%"><a href="REML.test.html">MaternGLSProfile.test</a></td>
+<td>Maximum Likelihood estimates for some Matern covariance parameters.</td></tr>
+<tr><td width="25%"><a href="REML.test.html">MaternQR.test</a></td>
+<td>Maximum Likelihood estimates for some Matern covariance parameters.</td></tr>
+<tr><td width="25%"><a href="REML.test.html">MaternQRProfile.test</a></td>
+<td>Maximum Likelihood estimates for some Matern covariance parameters.</td></tr>
<tr><td width="25%"><a href="minitri.html">minitri</a></td>
<td>Mini triathlon results</td></tr>
<tr><td width="25%"><a href="mKrig.html">mKrig</a></td>
@@ -309,8 +312,23 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>"micro Krig" Spatial process estimate of a curve or surface, "kriging" with a known covariance function.</td></tr>
<tr><td width="25%"><a href="fields.grid.html">mKrig.grid</a></td>
<td>Using MKrig for predicting on a grid.</td></tr>
+<tr><td width="25%"><a href="mKrig.MLE.html">mKrig.MLE</a></td>
+<td>maximizes likelihood for the process marginal variance (rho) and nugget standard deviation (sigma) parameters (e.g. lambda) over a list of covariance models or a grid of covariance parameter values.</td></tr>
<tr><td width="25%"><a href="mKrig.html">mKrig.trace</a></td>
<td>"micro Krig" Spatial process estimate of a curve or surface, "kriging" with a known covariance function.</td></tr>
+<tr><td width="25%"><a href="REML.test.html">MLE.Matern</a></td>
+<td>Maximum Likelihood estimates for some Matern covariance parameters.</td></tr>
+<tr><td width="25%"><a href="REML.test.html">MLE.Matern.fast</a></td>
+<td>Maximum Likelihood estimates for some Matern covariance parameters.</td></tr>
+<tr><td width="25%"><a href="REML.test.html">MLE.objective.fn</a></td>
+<td>Maximum Likelihood estimates for some Matern covariance parameters.</td></tr>
+</table>
+
+<h2><a name="N">-- N --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="NorthAmericanRainfall.html">NorthAmericanRainfall</a></td>
+<td>Observed North American summer precipitation from the historical climate network.</td></tr>
</table>
<h2><a name="O">-- O --</a></h2>
@@ -335,14 +353,14 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Plots a surface</td></tr>
<tr><td width="25%"><a href="vgram.matrix.html">plot.vgram.matrix</a></td>
<td>Computes a variogram from an image</td></tr>
-<tr><td width="25%"><a href="plot.Wimage.html">plot.Wimage</a></td>
-<td>Plots 2-d wavelet coefficents by level and type</td></tr>
-<tr><td width="25%"><a href="poisson.cov.html">poisson.cov</a></td>
-<td>Poisson spherical covariance function</td></tr>
<tr><td width="25%"><a href="poly.image.html">poly.image</a></td>
<td>Image plot for cells that are irregular quadrilaterals.</td></tr>
<tr><td width="25%"><a href="poly.image.html">poly.image.regrid</a></td>
<td>Image plot for cells that are irregular quadrilaterals.</td></tr>
+<tr><td width="25%"><a href="predict.derivative.html">predict.derivative</a></td>
+<td>Predicted derivatives</td></tr>
+<tr><td width="25%"><a href="predict.derivative.html">predict.derivative.default</a></td>
+<td>Predicted derivatives</td></tr>
<tr><td width="25%"><a href="predict.Krig.html">predict.derivative.Krig</a></td>
<td>Evaluation of Krig spatial process estimate.</td></tr>
<tr><td width="25%"><a href="predict.Krig.html">predict.Krig</a></td>
@@ -359,6 +377,8 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Standard errors of predictions for Krig spatial process estimate</td></tr>
<tr><td width="25%"><a href="predict.surface.html">predict.surface</a></td>
<td>Evaluates a fitted function or its standard errors as a surface object</td></tr>
+<tr><td width="25%"><a href="predict.surface.html">predict.surface.derivative</a></td>
+<td>Evaluates a fitted function or its standard errors as a surface object</td></tr>
<tr><td width="25%"><a href="predict.surface.html">predict.surface.se</a></td>
<td>Evaluates a fitted function or its standard errors as a surface object</td></tr>
<tr><td width="25%"><a href="print.Krig.html">print.Krig</a></td>
@@ -374,8 +394,6 @@ alt="[Top]" width="30" height="30" border="0"></a>
<h2><a name="Q">-- Q --</a></h2>
<table width="100%">
-<tr><td width="25%"><a href="qsreg.html">qsreg</a></td>
-<td>Quantile or Robust spline regression</td></tr>
<tr><td width="25%"><a href="quilt.plot.html">quilt.plot</a></td>
<td>Image plot for irregular spatial data.</td></tr>
</table>
@@ -399,6 +417,8 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Euclidean distance matrix</td></tr>
<tr><td width="25%"><a href="rdist.earth.html">rdist.earth</a></td>
<td>Great circle distance matrix</td></tr>
+<tr><td width="25%"><a href="REML.test.html">REML.test</a></td>
+<td>Maximum Likelihood estimates for some Matern covariance parameters.</td></tr>
<tr><td width="25%"><a href="Krig.html">resid.Krig</a></td>
<td>Kriging surface estimate</td></tr>
<tr><td width="25%"><a href="ribbon.plot.html">ribbon.plot</a></td>
@@ -448,6 +468,8 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Bins data and finds some summary statistics.</td></tr>
<tr><td width="25%"><a href="summary.Krig.html">summary.Krig</a></td>
<td>Summary for Krig spatial process estimate</td></tr>
+<tr><td width="25%"><a href="mKrig.html">summary.mKrig</a></td>
+<td>"micro Krig" Spatial process estimate of a curve or surface, "kriging" with a known covariance function.</td></tr>
<tr><td width="25%"><a href="summary.ncdf.html">summary.ncdf</a></td>
<td>Summarizes a netCDF file handle</td></tr>
<tr><td width="25%"><a href="surface.Krig.html">surface.Krig</a></td>
@@ -462,13 +484,13 @@ alt="[Top]" width="30" height="30" border="0"></a>
<tr><td width="25%"><a href="fields.tests.html">test.for.zero</a></td>
<td>Testing fields functions</td></tr>
<tr><td width="25%"><a href="tim.colors.html">tim.colors</a></td>
-<td>Some useful color tables for images.</td></tr>
+<td>Some useful color tables for images and tools to handle them.</td></tr>
<tr><td width="25%"><a href="Tps.html">Tps</a></td>
<td>Thin plate spline regression</td></tr>
<tr><td width="25%"><a href="transformx.html">transformx</a></td>
<td>Linear transformation</td></tr>
<tr><td width="25%"><a href="tim.colors.html">two.colors</a></td>
-<td>Some useful color tables for images.</td></tr>
+<td>Some useful color tables for images and tools to handle them.</td></tr>
</table>
<h2><a name="U">-- U --</a></h2>
@@ -492,12 +514,6 @@ alt="[Top]" width="30" height="30" border="0"></a>
<h2><a name="W">-- W --</a></h2>
<table width="100%">
-<tr><td width="25%"><a href="W.info.html">W.i2s</a></td>
-<td>Gives indexing imfomration for a wavelet decompostion</td></tr>
-<tr><td width="25%"><a href="W.info.html">W.info</a></td>
-<td>Gives indexing imfomration for a wavelet decompostion</td></tr>
-<tr><td width="25%"><a href="W.info.html">W.s2i</a></td>
-<td>Gives indexing imfomration for a wavelet decompostion</td></tr>
<tr><td width="25%"><a href="Wendland.html">Wendland</a></td>
<td>Wendland family of covariance functions and supporting numerical functions</td></tr>
<tr><td width="25%"><a href="Wendland.html">Wendland.beta</a></td>
@@ -508,30 +524,14 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Wendland family of covariance functions and supporting numerical functions</td></tr>
<tr><td width="25%"><a href="Wendland.html">Wendland2.2</a></td>
<td>Wendland family of covariance functions and supporting numerical functions</td></tr>
-<tr><td width="25%"><a href="Wimage.cov.html">Wimage.cov</a></td>
-<td>Functions for W-transform based covariance models</td></tr>
-<tr><td width="25%"><a href="Wimage.info.html">Wimage.i2s</a></td>
-<td>Finds key indices related to a 2-d multiresolution</td></tr>
-<tr><td width="25%"><a href="Wimage.info.html">Wimage.info</a></td>
-<td>Finds key indices related to a 2-d multiresolution</td></tr>
-<tr><td width="25%"><a href="Wimage.info.plot.html">Wimage.info.plot</a></td>
-<td>Plot to check 2-d multiresolution indexing</td></tr>
-<tr><td width="25%"><a href="Wimage.info.html">Wimage.s2i</a></td>
-<td>Finds key indices related to a 2-d multiresolution</td></tr>
-<tr><td width="25%"><a href="Wimage.cov.html">Wimage.sim</a></td>
-<td>Functions for W-transform based covariance models</td></tr>
<tr><td width="25%"><a href="world.html">world</a></td>
<td>Plot of the world</td></tr>
<tr><td width="25%"><a href="world.html">world.color</a></td>
<td>Plot of the world</td></tr>
-<tr><td width="25%"><a href="Wtransform.html">Wtransform</a></td>
-<td>Quadratic W wavelet transform for 1-d vectors or rectangular or cylindrical images</td></tr>
-<tr><td width="25%"><a href="Wtransform.html">Wtransform.cylinder.image</a></td>
-<td>Quadratic W wavelet transform for 1-d vectors or rectangular or cylindrical images</td></tr>
-<tr><td width="25%"><a href="Wtransform.html">Wtransform.image</a></td>
-<td>Quadratic W wavelet transform for 1-d vectors or rectangular or cylindrical images</td></tr>
-<tr><td width="25%"><a href="Wimage.cov.html">Wtransform.image.cov</a></td>
-<td>Functions for W-transform based covariance models</td></tr>
+<tr><td width="25%"><a href="world.html">world.land</a></td>
+<td>Plot of the world</td></tr>
+<tr><td width="25%"><a href="WorldBank.html">WorldBankCO2</a></td>
+<td>Carbon emissions and demographic covariables by country for 1999.</td></tr>
</table>
<h2><a name="X">-- X --</a></h2>
@@ -547,4 +547,11 @@ alt="[Top]" width="30" height="30" border="0"></a>
<tr><td width="25%"><a href="yline.html">yline</a></td>
<td>Draw horizontal lines</td></tr>
</table>
+
+<h2><a name="misc">-- misc --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Krig.engine.default.html">%d*%</a></td>
+<td>Basic linear algebra utilities and other computations supporting the Krig function.</td></tr>
+</table>
</body></html>
diff --git a/win32/deps/library/fields/html/R.css b/win32/deps/library/fields/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/fields/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/fields/libs/i386/fields.dll b/win32/deps/library/fields/libs/i386/fields.dll
new file mode 100644
index 0000000..cf44910
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diff --git a/win32/deps/library/fields/libs/i386/symbols.rds b/win32/deps/library/fields/libs/i386/symbols.rds
new file mode 100644
index 0000000..91be258
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diff --git a/win32/deps/library/fields/libs/x64/fields.dll b/win32/deps/library/fields/libs/x64/fields.dll
new file mode 100644
index 0000000..65fbe59
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diff --git a/win32/deps/library/fields/libs/x64/symbols.rds b/win32/deps/library/fields/libs/x64/symbols.rds
new file mode 100644
index 0000000..b6a5e71
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diff --git a/win32/deps/library/foreign/DESCRIPTION b/win32/deps/library/foreign/DESCRIPTION
index 8fa16ea..e74fbf3 100644
--- a/win32/deps/library/foreign/DESCRIPTION
+++ b/win32/deps/library/foreign/DESCRIPTION
@@ -1,21 +1,46 @@
-Package: foreign
-Priority: recommended
-Version: 0.8-37
-Date: 2009-08-13
-Title: Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase,
- ...
-Depends: R (>= 2.6.0), stats
-Imports: methods, utils
-Maintainer: R-core <R-core r-project org>
-Author: R-core members, Saikat DebRoy <saikat stat wisc edu>, Roger
- Bivand <Roger Bivand nhh no> and others: see COPYRIGHTS file in
- the sources.
-Description: Functions for reading and writing data stored by
- statistical packages such as Minitab, S, SAS, SPSS, Stata,
- Systat, ..., and for reading and writing .dbf (dBase) files.
-LazyLoad: yes
-License: GPL (>= 2)
-Packaged: 2009-08-13 12:15:02 UTC; ripley
-Repository: CRAN
-Date/Publication: 2009-08-13 12:33:14
-Built: R 2.9.2; i386-pc-mingw32; 2009-08-24 13:03:41 UTC; windows
+Package: foreign
+Priority: recommended
+Version: 0.8-51
+Date: 2012-10-08
+Title: Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase,
+ ...
+Depends: R (>= 2.14.0), stats
+Imports: methods, utils
+Authors R: structure( c(person("R Core Team", email =
+ "R-core R-project org", role = c("aut", "cph", "cre")),
+ person("Roger", "Bivand", role = c("ctb", "cph")),
+ person(c("Vincent", "J."), "Carey", role = c("ctb", "cph")),
+ person("Saikat", "DebRoy", role = c("ctb", "cph")),
+ person("Stephen", "Eglen", role = c("ctb", "cph")),
+ person("Rajarshi", "Guha", role = c("ctb", "cph")),
+ person("Nicholas", "Lewin-Koh", role = c("ctb", "cph")),
+ person("Mark", "Myatt", role = c("ctb", "cph")), person("Ben",
+ "Pfaff", role = "ctb"), person("Frank", "Warmerdam", role =
+ c("ctb", "cph")), person("Stephen", "Weigand", role = c("ctb",
+ "cph")), person("Free Software Foundation, Inc.", role =
+ "cph")), footer = "See the COPYRIGHTS file in the sources for
+ details on contributions and copyrights.")
+Description: Functions for reading and writing data stored by statistical
+ packages such as Minitab, S, SAS, SPSS, Stata, Systat, ...,
+ and for reading and writing dBase files.
+LazyLoad: yes
+License: GPL (>= 2)
+BugReports: http://bugs.r-project.org
+Packaged: 2012-10-11 13:26:23 UTC; ripley
+Author: R Core Team [aut, cph, cre],
+ Roger Bivand [ctb, cph],
+ Vincent J. Carey [ctb, cph],
+ Saikat DebRoy [ctb, cph],
+ Stephen Eglen [ctb, cph],
+ Rajarshi Guha [ctb, cph],
+ Nicholas Lewin-Koh [ctb, cph],
+ Mark Myatt [ctb, cph],
+ Ben Pfaff [ctb],
+ Frank Warmerdam [ctb, cph],
+ Stephen Weigand [ctb, cph],
+ Free Software Foundation, Inc. [cph].
+ See the COPYRIGHTS file in the sources for details on contributions
+ and copyrights.
+Maintainer: R Core Team <R-core R-project org>
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:14:55 UTC; windows
+Archs: i386, x64
diff --git a/win32/deps/library/foreign/LICENCE b/win32/deps/library/foreign/LICENCE
index 1a9ecbd..c86bc17 100644
--- a/win32/deps/library/foreign/LICENCE
+++ b/win32/deps/library/foreign/LICENCE
@@ -2,6 +2,6 @@ This software is distributed under the terms of the GNU General Public
License as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
-A copy of the GNU General Public License is in file COPYING in the
-sources of this package, and is also available at
+A copy of version 2 of the GNU General Public License is in file GPL-2
+in the sources of this package, and is also available at
http://www.r-project.org/Licenses/
diff --git a/win32/deps/library/foreign/Meta/Rd.rds b/win32/deps/library/foreign/Meta/Rd.rds
index b262d45..01e9b89 100644
Binary files a/win32/deps/library/foreign/Meta/Rd.rds and b/win32/deps/library/foreign/Meta/Rd.rds differ
diff --git a/win32/deps/library/foreign/Meta/hsearch.rds b/win32/deps/library/foreign/Meta/hsearch.rds
index 346dc67..e293bf7 100644
Binary files a/win32/deps/library/foreign/Meta/hsearch.rds and b/win32/deps/library/foreign/Meta/hsearch.rds differ
diff --git a/win32/deps/library/foreign/Meta/links.rds b/win32/deps/library/foreign/Meta/links.rds
new file mode 100644
index 0000000..061d4d0
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diff --git a/win32/deps/library/foreign/Meta/nsInfo.rds b/win32/deps/library/foreign/Meta/nsInfo.rds
index bea2288..2ab2dd3 100644
Binary files a/win32/deps/library/foreign/Meta/nsInfo.rds and b/win32/deps/library/foreign/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/foreign/Meta/package.rds b/win32/deps/library/foreign/Meta/package.rds
index 2acce49..a1fb8a5 100644
Binary files a/win32/deps/library/foreign/Meta/package.rds and b/win32/deps/library/foreign/Meta/package.rds differ
diff --git a/win32/deps/library/foreign/R/foreign b/win32/deps/library/foreign/R/foreign
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/foreign/R/foreign
+++ b/win32/deps/library/foreign/R/foreign
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/foreign/R/foreign.rdb b/win32/deps/library/foreign/R/foreign.rdb
index 5d4cc36..a5f326a 100644
Binary files a/win32/deps/library/foreign/R/foreign.rdb and b/win32/deps/library/foreign/R/foreign.rdb differ
diff --git a/win32/deps/library/foreign/R/foreign.rdx b/win32/deps/library/foreign/R/foreign.rdx
index f6fb78b..fb3e8c2 100644
Binary files a/win32/deps/library/foreign/R/foreign.rdx and b/win32/deps/library/foreign/R/foreign.rdx differ
diff --git a/win32/deps/library/foreign/help/aliases.rds b/win32/deps/library/foreign/help/aliases.rds
new file mode 100644
index 0000000..3b211dc
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diff --git a/win32/deps/library/foreign/help/foreign.rdb b/win32/deps/library/foreign/help/foreign.rdb
new file mode 100644
index 0000000..649c096
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diff --git a/win32/deps/library/foreign/help/foreign.rdx b/win32/deps/library/foreign/help/foreign.rdx
new file mode 100644
index 0000000..214cdf7
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diff --git a/win32/deps/library/foreign/help/paths.rds b/win32/deps/library/foreign/help/paths.rds
new file mode 100644
index 0000000..8a304a1
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diff --git a/win32/deps/library/foreign/html/00Index.html b/win32/deps/library/foreign/html/00Index.html
new file mode 100644
index 0000000..f8b8264
--- /dev/null
+++ b/win32/deps/library/foreign/html/00Index.html
@@ -0,0 +1,59 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase,
+...</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase,
+...
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘foreign’ version 0.8-51</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<table width="100%">
+<tr><td width="25%"><a href="read.S.html">data.restore</a></td>
+<td>Read an S3 Binary or data.dump File</td></tr>
+<tr><td width="25%"><a href="lookup.xport.html">lookup.xport</a></td>
+<td>Lookup Information on a SAS XPORT Format Library</td></tr>
+<tr><td width="25%"><a href="read.arff.html">read.arff</a></td>
+<td>Read Data from ARFF Files</td></tr>
+<tr><td width="25%"><a href="read.dbf.html">read.dbf</a></td>
+<td>Read a DBF File</td></tr>
+<tr><td width="25%"><a href="read.dta.html">read.dta</a></td>
+<td>Read Stata Binary Files</td></tr>
+<tr><td width="25%"><a href="read.epiinfo.html">read.epiinfo</a></td>
+<td>Read Epi Info Data Files</td></tr>
+<tr><td width="25%"><a href="read.mtp.html">read.mtp</a></td>
+<td>Read a Minitab Portable Worksheet</td></tr>
+<tr><td width="25%"><a href="read.octave.html">read.octave</a></td>
+<td>Read Octave Text Data Files</td></tr>
+<tr><td width="25%"><a href="read.S.html">read.S</a></td>
+<td>Read an S3 Binary or data.dump File</td></tr>
+<tr><td width="25%"><a href="read.spss.html">read.spss</a></td>
+<td>Read an SPSS Data File</td></tr>
+<tr><td width="25%"><a href="read.ssd.html">read.ssd</a></td>
+<td>Obtain a Data Frame from a SAS Permanent Dataset, via read.xport</td></tr>
+<tr><td width="25%"><a href="read.systat.html">read.systat</a></td>
+<td>Obtain a Data Frame from a Systat File</td></tr>
+<tr><td width="25%"><a href="read.xport.html">read.xport</a></td>
+<td>Read a SAS XPORT Format Library</td></tr>
+<tr><td width="25%"><a href="write.arff.html">write.arff</a></td>
+<td>Write Data into ARFF Files</td></tr>
+<tr><td width="25%"><a href="write.dbf.html">write.dbf</a></td>
+<td>Write a DBF File</td></tr>
+<tr><td width="25%"><a href="write.dta.html">write.dta</a></td>
+<td>Write Files in Stata Binary Format</td></tr>
+<tr><td width="25%"><a href="write.foreign.html">write.foreign</a></td>
+<td>Write Text Files and Code to Read Them</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/foreign/html/R.css b/win32/deps/library/foreign/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/foreign/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/foreign/libs/i386/foreign.dll b/win32/deps/library/foreign/libs/i386/foreign.dll
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diff --git a/win32/deps/library/foreign/po/fr/LC_MESSAGES/R-foreign.mo b/win32/deps/library/foreign/po/fr/LC_MESSAGES/R-foreign.mo
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diff --git a/win32/deps/library/foreign/po/pl/LC_MESSAGES/R-foreign.mo b/win32/deps/library/foreign/po/pl/LC_MESSAGES/R-foreign.mo
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diff --git a/win32/deps/library/foreign/po/pl/LC_MESSAGES/foreign.mo b/win32/deps/library/foreign/po/pl/LC_MESSAGES/foreign.mo
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diff --git a/win32/deps/library/foreign/tests/Alfalfa.xpt b/win32/deps/library/foreign/tests/Alfalfa.xpt
new file mode 100644
index 0000000..319df52
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diff --git a/win32/deps/library/foreign/tests/S3.R b/win32/deps/library/foreign/tests/S3.R
new file mode 100644
index 0000000..1de22f4
--- /dev/null
+++ b/win32/deps/library/foreign/tests/S3.R
@@ -0,0 +1,9 @@
+library(foreign)
+read.S("mySobj")
+data.restore("dumpdata", print = TRUE)
+print(myobj)
+data.restore("tsdumpdata", print = TRUE, verbose = TRUE)
+sunspot
+utils::str(carbon.dioxide)
+carbon.dioxide[1:60]
+q()
diff --git a/win32/deps/library/foreign/tests/S3.Rout.save b/win32/deps/library/foreign/tests/S3.Rout.save
new file mode 100644
index 0000000..1f2f105
--- /dev/null
+++ b/win32/deps/library/foreign/tests/S3.Rout.save
@@ -0,0 +1,59 @@
+
+R : Copyright 2004, The R Foundation for Statistical Computing
+Version 2.1.0 Under development (unstable) (2004-12-02), ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for a HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(foreign)
+> read.S("mySobj")
+ factor ints floats
+1 a 1 1.1
+2 bc 2 1.2
+3 def 3 1.3
+> data.restore("dumpdata", print = TRUE)
+"myobj": structure
+[1] "dumpdata"
+> print(myobj)
+ factor ints floats logs
+1 a NA 1.1 TRUE
+2 bc 2 1.2 NA
+3 def 3 1.3 FALSE
+> data.restore("tsdumpdata", print = TRUE, verbose = TRUE)
+"sunspot": structure
+ sunspot structure 3
+ .Data numeric 37
+ .Tsp numeric 3
+ class character 2
+"carbon.dioxide": structure
+ carbon.dioxide structure 3
+ .Data numeric 384
+ .Tsp numeric 3
+ class character 2
+[1] "tsdumpdata"
+> sunspot
+Time Series:
+Start = 1936
+End = 1972
+Frequency = 1
+ [1] 40 115 100 80 60 40 23 10 10 25 75 145 130 130 80 65 20 10 5
+[20] 10 60 190 180 175 120 50 35 20 10 15 30 60 105 105 105 80 65
+> utils::str(carbon.dioxide)
+ Time-Series [1:384] from 1959 to 1991: 315 316 316 318 318 ...
+> carbon.dioxide[1:60]
+ [1] 315.42 316.32 316.49 317.56 318.13 318.00 316.39 314.66 313.68 313.18
+[11] 314.66 315.43 316.27 316.81 317.42 318.87 319.87 319.43 318.01 315.75
+[21] 314.00 313.68 314.84 316.03 316.73 317.54 318.38 319.31 320.42 319.61
+[31] 318.42 316.64 314.83 315.15 315.95 316.85 317.78 318.40 319.53 320.41
+[41] 320.85 320.45 319.44 317.25 316.12 315.27 316.53 317.53 318.58 318.92
+[51] 319.70 321.22 322.08 321.31 319.58 317.61 316.05 315.83 316.91 318.20
+> q()
diff --git a/win32/deps/library/foreign/tests/arff.R b/win32/deps/library/foreign/tests/arff.R
new file mode 100644
index 0000000..3b1e4ef
--- /dev/null
+++ b/win32/deps/library/foreign/tests/arff.R
@@ -0,0 +1,5 @@
+library("foreign")
+df <- read.arff("contact-lenses.arff")
+summary(df)
+str(df)
+q()
diff --git a/win32/deps/library/foreign/tests/arff.Rout.save b/win32/deps/library/foreign/tests/arff.Rout.save
new file mode 100644
index 0000000..4d91355
--- /dev/null
+++ b/win32/deps/library/foreign/tests/arff.Rout.save
@@ -0,0 +1,36 @@
+
+R version 2.5.0 Under development (unstable) (2007-03-25 r40887)
+Copyright (C) 2007 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library("foreign")
+> df <- read.arff("contact-lenses.arff")
+> summary(df)
+ age spectacle-prescrip astigmatism tear-prod-rate
+ pre-presbyopic:8 hypermetrope:12 no :12 normal :12
+ presbyopic :8 myope :12 yes:12 reduced:12
+ young :8
+ contact-lenses
+ hard: 4
+ none:15
+ soft: 5
+> str(df)
+'data.frame': 24 obs. of 5 variables:
+ $ age : Factor w/ 3 levels "pre-presbyopic",..: 3 3 3 3 3 3 3 3 1 1 ...
+ $ spectacle-prescrip: Factor w/ 2 levels "hypermetrope",..: 2 2 2 2 1 1 1 1 2 2 ...
+ $ astigmatism : Factor w/ 2 levels "no","yes": 1 1 2 2 1 1 2 2 1 1 ...
+ $ tear-prod-rate : Factor w/ 2 levels "normal","reduced": 2 1 2 1 2 1 2 1 2 1 ...
+ $ contact-lenses : Factor w/ 3 levels "hard","none",..: 2 3 2 1 2 3 2 1 2 3 ...
+> q()
diff --git a/win32/deps/library/foreign/tests/auto8.dta b/win32/deps/library/foreign/tests/auto8.dta
new file mode 100644
index 0000000..48803e6
Binary files /dev/null and b/win32/deps/library/foreign/tests/auto8.dta differ
diff --git a/win32/deps/library/foreign/tests/compressed.dta b/win32/deps/library/foreign/tests/compressed.dta
new file mode 100644
index 0000000..7bd31e5
Binary files /dev/null and b/win32/deps/library/foreign/tests/compressed.dta differ
diff --git a/win32/deps/library/foreign/tests/contact-lenses.arff b/win32/deps/library/foreign/tests/contact-lenses.arff
new file mode 100644
index 0000000..34fe9b0
--- /dev/null
+++ b/win32/deps/library/foreign/tests/contact-lenses.arff
@@ -0,0 +1,85 @@
+% 1. Title: Database for fitting contact lenses
+%
+% 2. Sources:
+% (a) Cendrowska, J. "PRISM: An algorithm for inducing modular rules",
+% International Journal of Man-Machine Studies, 1987, 27, 349-370
+% (b) Donor: Benoit Julien (Julien ce cmu edu)
+% (c) Date: 1 August 1990
+%
+% 3. Past Usage:
+% 1. See above.
+% 2. Witten, I. H. & MacDonald, B. A. (1988). Using concept
+% learning for knowledge acquisition. International Journal of
+% Man-Machine Studies, 27, (pp. 349-370).
+%
+% Notes: This database is complete (all possible combinations of
+% attribute-value pairs are represented).
+%
+% Each instance is complete and correct.
+%
+% 9 rules cover the training set.
+%
+% 4. Relevant Information Paragraph:
+% The examples are complete and noise free.
+% The examples highly simplified the problem. The attributes do not
+% fully describe all the factors affecting the decision as to which type,
+% if any, to fit.
+%
+% 5. Number of Instances: 24
+%
+% 6. Number of Attributes: 4 (all nominal)
+%
+% 7. Attribute Information:
+% -- 3 Classes
+% 1 : the patient should be fitted with hard contact lenses,
+% 2 : the patient should be fitted with soft contact lenses,
+% 1 : the patient should not be fitted with contact lenses.
+%
+% 1. age of the patient: (1) young, (2) pre-presbyopic, (3) presbyopic
+% 2. spectacle prescription: (1) myope, (2) hypermetrope
+% 3. astigmatic: (1) no, (2) yes
+% 4. tear production rate: (1) reduced, (2) normal
+%
+% 8. Number of Missing Attribute Values: 0
+%
+% 9. Class Distribution:
+% 1. hard contact lenses: 4
+% 2. soft contact lenses: 5
+% 3. no contact lenses: 15
+
+ relation contact-lenses
+
+ attribute age {young, pre-presbyopic, presbyopic}
+ attribute spectacle-prescrip {myope, hypermetrope}
+ attribute astigmatism {no, yes}
+ attribute tear-prod-rate {reduced, normal}
+ attribute contact-lenses {soft, hard, none}
+
+ data
+%
+% 24 instances
+%
+young,myope,no,reduced,none
+young,myope,no,normal,soft
+young,myope,yes,reduced,none
+young,myope,yes,normal,hard
+young,hypermetrope,no,reduced,none
+young,hypermetrope,no,normal,soft
+young,hypermetrope,yes,reduced,none
+young,hypermetrope,yes,normal,hard
+pre-presbyopic,myope,no,reduced,none
+pre-presbyopic,myope,no,normal,soft
+pre-presbyopic,myope,yes,reduced,none
+pre-presbyopic,myope,yes,normal,hard
+pre-presbyopic,hypermetrope,no,reduced,none
+pre-presbyopic,hypermetrope,no,normal,soft
+pre-presbyopic,hypermetrope,yes,reduced,none
+pre-presbyopic,hypermetrope,yes,normal,none
+presbyopic,myope,no,reduced,none
+presbyopic,myope,no,normal,none
+presbyopic,myope,yes,reduced,none
+presbyopic,myope,yes,normal,hard
+presbyopic,hypermetrope,no,reduced,none
+presbyopic,hypermetrope,no,normal,soft
+presbyopic,hypermetrope,yes,reduced,none
+presbyopic,hypermetrope,yes,normal,none
diff --git a/win32/deps/library/foreign/tests/create-dumpdata.S b/win32/deps/library/foreign/tests/create-dumpdata.S
new file mode 100644
index 0000000..71c1004
--- /dev/null
+++ b/win32/deps/library/foreign/tests/create-dumpdata.S
@@ -0,0 +1,5 @@
+## file ./dumpdata was created by these (S-PLUS 6.2.1 for Linux):
+myobj <- data.frame(factor = factor(1:3, labels=c("a", "bc", "def")),
+ ints = 1:3, floats = 1+(1:3)/10, logs= c(T,NA,F))
+myobj[1,2] <- NA
+data.dump("myobj",file="dumpdata", oldStyle=TRUE)
diff --git a/win32/deps/library/foreign/tests/datefactor.dta b/win32/deps/library/foreign/tests/datefactor.dta
new file mode 100644
index 0000000..e7a465c
Binary files /dev/null and b/win32/deps/library/foreign/tests/datefactor.dta differ
diff --git a/win32/deps/library/foreign/tests/download.R b/win32/deps/library/foreign/tests/download.R
new file mode 100644
index 0000000..bb72592
--- /dev/null
+++ b/win32/deps/library/foreign/tests/download.R
@@ -0,0 +1,9 @@
+library(foreign)
+if(!nzchar(Sys.getenv("R_FOREIGN_FULL_TEST"))) q("no")
+
+read.dta("http://www.principlesofeconometrics.com/stata/airline.dta";)
+
+str(read.spss("http://psyweb.psy.ox.ac.uk/dapweb/teaching/graduate/data/crime.sav";,
+ to.data.frame=TRUE))
+
+q()
diff --git a/win32/deps/library/foreign/tests/dumpdata b/win32/deps/library/foreign/tests/dumpdata
new file mode 100644
index 0000000..af2d127
--- /dev/null
+++ b/win32/deps/library/foreign/tests/dumpdata
@@ -0,0 +1,60 @@
+myobj
+structure
+4
+.Data
+list
+4
+factor
+structure
+3
+.Data
+integer
+3
+1
+2
+3
+.Label
+character
+3
+a
+bc
+def
+class
+character
+1
+factor
+ints
+integer
+3
+N
+2
+3
+floats
+numeric
+3
+1.1
+1.2
+1.3
+logs
+logical
+3
+1
+N
+0
+.Names
+character
+4
+factor
+ints
+floats
+logs
+row.names
+character
+3
+1
+2
+3
+class
+character
+1
+data.frame
diff --git a/win32/deps/library/foreign/tests/electric.por b/win32/deps/library/foreign/tests/electric.por
new file mode 100644
index 0000000..ac42a38
--- /dev/null
+++ b/win32/deps/library/foreign/tests/electric.por
@@ -0,0 +1,123 @@
+ÁÃÉââÖãÉÅ@@@@@@@@@@@@@@@@@@@ASCII SPSS PORT FILE
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+*.8I/0/2A.F/66/9/0/1/N0/37/1/1O/39/E/7H/0/25.F/7E/9/0/1/N0/38/1/1G/2E/A/AK/K/26.
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diff --git a/win32/deps/library/foreign/tests/electric.sav b/win32/deps/library/foreign/tests/electric.sav
new file mode 100644
index 0000000..2fcbb2d
Binary files /dev/null and b/win32/deps/library/foreign/tests/electric.sav differ
diff --git a/win32/deps/library/foreign/tests/ex1-51.mtp b/win32/deps/library/foreign/tests/ex1-51.mtp
new file mode 100644
index 0000000..257b748
--- /dev/null
+++ b/win32/deps/library/foreign/tests/ex1-51.mtp
@@ -0,0 +1,15 @@
+Minitab Portable Worksheet P1.1 1994 522 Release 9.1 .
+% 3 1 26 0 control .
+ 1.202599976E+03 8.300999756E+02 3.723999939E+02 3.454999695E+02 3.211999817E+02
+ 2.442999878E+02 1.629999847E+02 1.477999878E+02 9.499999237E+01 8.699999237E+01
+ 8.119999695E+01 6.849999237E+01 4.729999924E+01 4.109999847E+01 3.659999847E+01
+ 2.899999809E+01 2.859999847E+01 2.629999924E+01 2.609999847E+01 2.439999962E+01
+ 2.169999886E+01 1.729999924E+01 1.149999905E+01 4.899999619E+00 4.899999619E+00
+ 0.999999940E+00 .
+% 3 2 26 0 seeded .
+ 2.745599854E+03 1.697799927E+03 1.655999878E+03 9.779999390E+02 7.033999634E+02
+ 4.890999756E+02 4.299999695E+02 3.340999756E+02 3.027999878E+02 2.746999817E+02
+ 2.746999817E+02 2.549999847E+02 2.424999847E+02 2.006999969E+02 1.985999908E+02
+ 1.295999908E+02 1.189999924E+02 1.182999954E+02 1.152999954E+02 9.239999390E+01
+ 4.059999847E+01 3.269999695E+01 3.139999962E+01 1.749999809E+01 7.699999809E+00
+ 4.099999905E+00 .
diff --git a/win32/deps/library/foreign/tests/minitab.R b/win32/deps/library/foreign/tests/minitab.R
new file mode 100644
index 0000000..9099863
--- /dev/null
+++ b/win32/deps/library/foreign/tests/minitab.R
@@ -0,0 +1,7 @@
+library(foreign)
+ex1.51 <- read.mtp("ex1-51.mtp")
+summary(ex1.51)
+str(ex1.51)
+ex1.51 <- data.frame(ex1.51)
+summary(ex1.51)
+q()
diff --git a/win32/deps/library/foreign/tests/minitab.Rout.save b/win32/deps/library/foreign/tests/minitab.Rout.save
new file mode 100644
index 0000000..e5a963a
--- /dev/null
+++ b/win32/deps/library/foreign/tests/minitab.Rout.save
@@ -0,0 +1,37 @@
+
+R version 2.9.0 Under development (unstable) (2009-01-28 r47758)
+Copyright (C) 2009 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(foreign)
+> ex1.51 <- read.mtp("ex1-51.mtp")
+> summary(ex1.51)
+ Length Class Mode
+control 26 -none- numeric
+seeded 26 -none- numeric
+> str(ex1.51)
+List of 2
+ $ control: num [1:26] 1203 830 372 346 321 ...
+ $ seeded : num [1:26] 2746 1698 1656 978 703 ...
+> ex1.51 <- data.frame(ex1.51)
+> summary(ex1.51)
+ control seeded
+ Min. : 1.00 Min. : 4.10
+ 1st Qu.: 24.82 1st Qu.: 98.12
+ Median : 44.20 Median : 221.60
+ Mean : 164.59 Mean : 441.98
+ 3rd Qu.: 159.20 3rd Qu.: 406.02
+ Max. :1202.60 Max. :2745.60
+> q()
diff --git a/win32/deps/library/foreign/tests/mySobj b/win32/deps/library/foreign/tests/mySobj
new file mode 100644
index 0000000..97e7273
Binary files /dev/null and b/win32/deps/library/foreign/tests/mySobj differ
diff --git a/win32/deps/library/foreign/tests/octave.R b/win32/deps/library/foreign/tests/octave.R
new file mode 100644
index 0000000..6fafe7f
--- /dev/null
+++ b/win32/deps/library/foreign/tests/octave.R
@@ -0,0 +1,5 @@
+library("foreign")
+otd <- read.octave("octave.dat")
+summary(otd)
+str(otd)
+q()
diff --git a/win32/deps/library/foreign/tests/octave.Rout.save b/win32/deps/library/foreign/tests/octave.Rout.save
new file mode 100644
index 0000000..fbd7547
--- /dev/null
+++ b/win32/deps/library/foreign/tests/octave.Rout.save
@@ -0,0 +1,61 @@
+
+R version 2.12.0 Under development (unstable) (2010-03-25 r51410)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library("foreign")
+> otd <- read.octave("octave.dat")
+> summary(otd)
+ Length Class Mode
+a_string 2 -none- character
+a_bool 1 -none- logical
+a_struct 3 -none- list
+a_cell 4 -none- list
+a_complex_scalar 1 -none- complex
+a_list 3 -none- list
+a_complex_matrix 4 -none- complex
+a_range 5 -none- numeric
+a_scalar 1 -none- numeric
+a_complex_3_d_array 8 -none- complex
+a_3_d_array 8 -none- numeric
+a_matrix 4 -none- numeric
+a_bool_matrix 4 -none- logical
+> str(otd)
+List of 13
+ $ a_string : chr [1:2] "foo" "bar"
+ $ a_bool : logi FALSE
+ $ a_struct :List of 3
+ ..$ a: num 1
+ ..$ b: num [1:2, 1:2] 1 3 2 4
+ ..$ c: chr "foo"
+ $ a_cell :List of 4
+ ..$ : num 1
+ ..$ : chr "foo"
+ ..$ : num [1:2, 1:2] 1 3 2 4
+ ..$ : chr "bar"
+ ..- attr(*, "dim")= int [1:2] 2 2
+ $ a_complex_scalar : cplx 0+1i
+ $ a_list :List of 3
+ ..$ : num 1
+ ..$ : num [1:2, 1:2] 1 3 2 4
+ ..$ : chr "foo"
+ $ a_complex_matrix : cplx [1:2, 1:2] 1+2i 5+0i 3-4i ...
+ $ a_range : num [1:5] 1 2 3 4 5
+ $ a_scalar : num 1
+ $ a_complex_3_d_array: cplx [1:2, 1:2, 1:2] 1+1i 3+1i 2+1i ...
+ $ a_3_d_array : num [1:2, 1:2, 1:2] 1 3 2 4 5 7 6 8
+ $ a_matrix : num [1:2, 1:2] 1 3 2 4
+ $ a_bool_matrix : logi [1:2, 1:2] TRUE FALSE FALSE TRUE
+> q()
diff --git a/win32/deps/library/foreign/tests/octave.dat b/win32/deps/library/foreign/tests/octave.dat
new file mode 100644
index 0000000..c5b75b1
--- /dev/null
+++ b/win32/deps/library/foreign/tests/octave.dat
@@ -0,0 +1,122 @@
+# Created by Octave 2.1.60, Mon Dec 27 12:13:21 2004 CET <hornik mithrandir>
+# name: a_string
+# type: string
+# elements: 2
+# length: 3
+foo
+# length: 3
+bar
+# name: a_bool
+# type: bool
+0
+# name: a_struct
+# type: struct
+# length: 3
+# name: a
+# type: scalar
+1
+# name: b
+# type: matrix
+# rows: 2
+# columns: 2
+ 1 2
+ 3 4
+# name: c
+# type: string
+# elements: 1
+# length: 3
+foo
+# name: a_cell
+# type: cell
+# rows: 2
+# columns: 2
+# name: <cell-element>
+# type: scalar
+1
+# name: <cell-element>
+# type: string
+# elements: 1
+# length: 3
+foo
+
+# name: <cell-element>
+# type: matrix
+# rows: 2
+# columns: 2
+ 1 2
+ 3 4
+# name: <cell-element>
+# type: string
+# elements: 1
+# length: 3
+bar
+
+# name: a_complex_scalar
+# type: complex scalar
+(0,1)
+# name: a_list
+# type: list
+# length: 3
+# name: _0
+# type: scalar
+1
+# name: _1
+# type: matrix
+# rows: 2
+# columns: 2
+ 1 2
+ 3 4
+# name: _2
+# type: string
+# elements: 1
+# length: 3
+foo
+# name: a_complex_matrix
+# type: complex matrix
+# rows: 2
+# columns: 2
+ (1,2) (3,-4)
+ (5,0) (-6,0)
+# name: a_range
+# type: range
+# base, limit, increment
+1 5 1
+# name: a_scalar
+# type: scalar
+1
+# name: a_complex_3_d_array
+# type: complex matrix
+# ndims: 3
+ 2 2 2
+ (1,1)
+ (3,1)
+ (2,1)
+ (4,1)
+ (5,-1)
+ (7,-1)
+ (6,-1)
+ (8,-1)
+# name: a_3_d_array
+# type: matrix
+# ndims: 3
+ 2 2 2
+ 1
+ 3
+ 2
+ 4
+ 5
+ 7
+ 6
+ 8
+# name: a_matrix
+# type: matrix
+# rows: 2
+# columns: 2
+ 1 2
+ 3 4
+# name: a_bool_matrix
+# type: bool matrix
+# rows: 2
+# columns: 2
+ 1 0
+ 0 1
diff --git a/win32/deps/library/foreign/tests/octave.m b/win32/deps/library/foreign/tests/octave.m
new file mode 100644
index 0000000..521708f
--- /dev/null
+++ b/win32/deps/library/foreign/tests/octave.m
@@ -0,0 +1,22 @@
+## Run this through (a recent enough version of) Octave to (re)create
+## 'octave.dat', using 'octave < octave.m'.
+
+a_scalar = 1;
+a_complex_scalar = i;
+a_matrix = [1, 2; 3, 4];
+a_complex_matrix = [1+2i, 3-4i; 5, -6];
+a_range = 1 : 5;
+a_string = [ "foo"; "bar" ];
+a_3_d_array = zeros(2, 2, 2);
+a_3_d_array(:,:,1) = a_matrix;
+a_3_d_array(:,:,2) = a_matrix + 4;
+a_complex_3_d_array = a_3_d_array;
+a_complex_3_d_array(:,:,1) = a_complex_3_d_array(:,:,1) + i;
+a_complex_3_d_array(:,:,2) = a_complex_3_d_array(:,:,2) - i;
+a_struct = struct("a", a_scalar, "b", a_matrix, "c", "foo");
+a_list = list(a_scalar, a_matrix, "foo");
+a_cell = { a_scalar, a_matrix; "foo", "bar" };
+a_bool = false;
+a_bool_matrix = [ true, false ; false, true ];
+
+save -ascii "octave.dat" a_*;
diff --git a/win32/deps/library/foreign/tests/pbc.por b/win32/deps/library/foreign/tests/pbc.por
new file mode 100644
index 0000000..81c1af5
--- /dev/null
+++ b/win32/deps/library/foreign/tests/pbc.por
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diff --git a/win32/deps/library/foreign/tests/pbc.sav b/win32/deps/library/foreign/tests/pbc.sav
new file mode 100644
index 0000000..3eb0747
Binary files /dev/null and b/win32/deps/library/foreign/tests/pbc.sav differ
diff --git a/win32/deps/library/foreign/tests/pbc.sys b/win32/deps/library/foreign/tests/pbc.sys
new file mode 100644
index 0000000..8ee17e4
Binary files /dev/null and b/win32/deps/library/foreign/tests/pbc.sys differ
diff --git a/win32/deps/library/foreign/tests/pbcold.sav b/win32/deps/library/foreign/tests/pbcold.sav
new file mode 100644
index 0000000..6cdd469
Binary files /dev/null and b/win32/deps/library/foreign/tests/pbcold.sav differ
diff --git a/win32/deps/library/foreign/tests/pc5.dta b/win32/deps/library/foreign/tests/pc5.dta
new file mode 100644
index 0000000..dd9fe9c
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diff --git a/win32/deps/library/foreign/tests/sample100.por b/win32/deps/library/foreign/tests/sample100.por
new file mode 100644
index 0000000..691463c
--- /dev/null
+++ b/win32/deps/library/foreign/tests/sample100.por
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diff --git a/win32/deps/library/foreign/tests/sample100.sav b/win32/deps/library/foreign/tests/sample100.sav
new file mode 100644
index 0000000..4821574
Binary files /dev/null and b/win32/deps/library/foreign/tests/sample100.sav differ
diff --git a/win32/deps/library/foreign/tests/sas.R b/win32/deps/library/foreign/tests/sas.R
new file mode 100644
index 0000000..2281737
--- /dev/null
+++ b/win32/deps/library/foreign/tests/sas.R
@@ -0,0 +1,11 @@
+if(!nzchar(Sys.getenv("R_FOREIGN_FULL_TEST"))) q("no")
+library("foreign")
+setwd(tempdir())
+tfile <- "int1982ag.zip"
+download.file("ftp://cusk.nmfs.noaa.gov/mrfss/intercept/ag/int1982ag.zip";,
+ tfile, quiet=TRUE, mode="wb")
+zip.file.extract("int1982ag.xpt", tfile)
+dfs <- read.xport("int1982ag.xpt")
+foo <- dfs$I3_19822
+nrow(foo)
+stopifnot(nrow(foo) == 3650)
diff --git a/win32/deps/library/foreign/tests/spss.R b/win32/deps/library/foreign/tests/spss.R
new file mode 100644
index 0000000..cdb5878
--- /dev/null
+++ b/win32/deps/library/foreign/tests/spss.R
@@ -0,0 +1,52 @@
+library(foreign)
+
+sample100 <- read.spss("sample100.sav",FALSE)
+summary(sample100)
+str(sample100)
+d.sample100 <- data.frame(sample100)
+summary(d.sample100)
+s100 <- sample100
+sample100 <- read.spss("sample100.por",FALSE)
+stopifnot(identical(s100, sample100)) # no need for further summary() etc
+
+pbc <- read.spss("pbc.sav",FALSE)
+summary(pbc)
+str(pbc)
+d.pbc <- data.frame(pbc)
+summary(d.pbc)
+pbco <- read.spss("pbcold.sav",FALSE)
+stopifnot(identical(pbc, pbco))
+## summary(pbco)
+## str(pbco)
+## d.pbco <- data.frame(pbco)
+## summary(d.pbco)
+pbc. <- read.spss("pbc.por",FALSE)
+summary(pbc.)
+str(pbc.) # has variable.labels
+stopifnot(all.equal(d.pbc, data.frame(pbc.), tol=1e-15))
+
+electric.s <- read.spss("electric.sav",TRUE,TRUE)
+electric.p <- read.spss("electric.por",TRUE,TRUE)
+electric.s4 <- read.spss("electric.sav",TRUE,TRUE,max.value.labels = 4)
+summary(electric.s)
+ii <- c(2,10)
+vl <- list(FIRSTCHD = c("OTHER CHD"= 6, "FATAL MI"= 5, "NONFATALMI"= 3,
+ "SUDDEN DEATH" = 2, "NO CHD" = 1),
+ DAYOFWK = c(SATURDAY=7, FRIDAY=6, THURSDAY=5,
+ WEDNSDAY=4, TUESDAY=3, MONDAY=2, SUNDAY=1))
+stopifnot(identical(electric.s, electric.p),
+ identical(electric.s[-ii], electric.s4[-ii]),
+ identical(vl, lapply(electric.s4[ii], attr, "value.labels")),
+ identical(lapply(vl, names),
+ lapply(electric.s[ii], function(.) rev(levels(.)))))
+
+
+## after "long label patch":
+
+invisible(Sys.setlocale (locale="C")) ## to resolve locale problem
+ldat <- read.spss("spss_long.sav", to.data.frame=TRUE)
+ldat
+nnms <- nms <- names(ldat)
+names(nnms) <- nms
+stopifnot(identical(nms, c("variable1", "variable2")),
+ identical(nnms, attr(ldat, "variable.labels")))
diff --git a/win32/deps/library/foreign/tests/spss.Rout.save b/win32/deps/library/foreign/tests/spss.Rout.save
new file mode 100644
index 0000000..3f5065b
--- /dev/null
+++ b/win32/deps/library/foreign/tests/spss.Rout.save
@@ -0,0 +1,327 @@
+
+R Under development (unstable) (2012-02-09 r58309)
+Copyright (C) 2012 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: i386-apple-darwin9.8.0/i386 (32-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(foreign)
+>
+> sample100 <- read.spss("sample100.sav",FALSE)
+> summary(sample100)
+ Length Class Mode
+YEAR 100 -none- numeric
+DISTRICT 100 -none- numeric
+CAMPUS 100 -none- numeric
+DNAME 100 -none- character
+CNAME 100 -none- character
+SEX 100 -none- character
+DISADVG 100 -none- character
+ETHNICTY 100 -none- character
+STUID 100 -none- character
+TLIMTH 100 -none- numeric
+GRADE 100 -none- numeric
+> str(sample100)
+List of 11
+ $ YEAR : num [1:100] 99 94 94 95 96 97 98 99 94 95 ...
+ $ DISTRICT: num [1:100] 57914 57914 57914 57914 57914 ...
+ $ CAMPUS : num [1:100] 57914045 57914106 57914110 57914123 57914117 ...
+ $ DNAME : chr [1:100] "MESQUITE ISD " "MESQUITE ISD " "MESQUITE ISD " "MESQUITE ISD " ...
+ $ CNAME : chr [1:100] "A C NEW MIDDLE " "MCWHORTER EL " "RUTHERFORD EL " "JOEY M PIRRUNG " ...
+ $ SEX : chr [1:100] "F" "F" " " "F" ...
+ $ DISADVG : chr [1:100] "NO " "NO " " " "NO " ...
+ $ ETHNICTY: chr [1:100] "WHITE " "WHITE " " " "HISPANIC" ...
+ $ STUID : chr [1:100] "00614371S" "00614372S" "00614373S" "00614373S" ...
+ $ TLIMTH : num [1:100] 90 86 67 77 77 79 86 87 89 85 ...
+ $ GRADE : num [1:100] 8 3 3 4 5 6 7 8 3 4 ...
+ - attr(*, "label.table")=List of 11
+ ..$ YEAR : NULL
+ ..$ DISTRICT: NULL
+ ..$ CAMPUS : NULL
+ ..$ DNAME : NULL
+ ..$ CNAME : NULL
+ ..$ SEX : NULL
+ ..$ DISADVG : NULL
+ ..$ ETHNICTY: NULL
+ ..$ STUID : NULL
+ ..$ TLIMTH : NULL
+ ..$ GRADE : NULL
+ - attr(*, "variable.labels")= Named chr [1:11] "YEAR OF ADMINISTRATION" "COUNTY DISTRICT NUMBER" "COUNTY DISTRICT CAMPUS NUMBER" "DISTRICT NAME" ...
+ ..- attr(*, "names")= chr [1:11] "YEAR" "DISTRICT" "CAMPUS" "DNAME" ...
+> d.sample100 <- data.frame(sample100)
+> summary(d.sample100)
+ YEAR DISTRICT CAMPUS DNAME
+ Min. : 94.0 Min. : 57905 Min. : 57905126 DALLAS ISD : 1
+ 1st Qu.: 95.0 1st Qu.: 57914 1st Qu.: 57914046 HARMONY ISD : 1
+ Median : 96.0 Median : 57914 Median : 57914112 MESQUITE ISD :96
+ Mean : 115.4 Mean : 59644 Mean : 59644015 SUNNYVALE ISD : 2
+ 3rd Qu.: 98.0 3rd Qu.: 57914 3rd Qu.: 57914125
+ Max. :2000.0 Max. :230905 Max. :230905101
+
+ CNAME SEX DISADVG ETHNICTY STUID
+ J C AUSTIN EL :23 : 4 : 4 : 4 00614373S: 6
+ R S KIMBROUGH M:12 F:62 NO :90 HISPANIC: 3 00614378S: 6
+ WILKINSON MIDDL: 9 M:34 YES: 6 OTHER : 2 00614379S: 6
+ VERNON PRICE EL: 7 WHITE :91 00614389S: 6
+ TISINGER EL : 6 00614397S: 6
+ THOMPSON EL : 5 00614403S: 6
+ (Other) :38 (Other) :64
+ TLIMTH GRADE
+ Min. :54.00 Min. :3.00
+ 1st Qu.:74.00 1st Qu.:4.00
+ Median :84.00 Median :5.00
+ Mean :80.16 Mean :5.37
+ 3rd Qu.:87.00 3rd Qu.:7.00
+ Max. :93.00 Max. :8.00
+
+> s100 <- sample100
+> sample100 <- read.spss("sample100.por",FALSE)
+> stopifnot(identical(s100, sample100)) # no need for further summary() etc
+>
+> pbc <- read.spss("pbc.sav",FALSE)
+> summary(pbc)
+ Length Class Mode
+AGE 418 -none- numeric
+ALB 418 -none- numeric
+ALKPHOS 418 -none- numeric
+ASCITES 418 -none- numeric
+BILI 418 -none- numeric
+CHOL 418 -none- numeric
+EDEMA 418 -none- numeric
+EDTRT 418 -none- numeric
+HEPMEG 418 -none- numeric
+TIME 418 -none- numeric
+PLATELET 418 -none- numeric
+PROTIME 418 -none- numeric
+SEX 418 -none- numeric
+SGOT 418 -none- numeric
+SPIDERS 418 -none- numeric
+STAGE 418 -none- numeric
+STATUS 418 -none- numeric
+TRT 418 -none- numeric
+TRIG 418 -none- numeric
+COPPER 418 -none- numeric
+> str(pbc)
+List of 20
+ $ AGE : num [1:418] 58.8 56.4 70.1 54.7 38.1 ...
+ $ ALB : num [1:418] 2.6 4.14 3.48 2.54 3.53 3.98 4.09 4 3.08 2.74 ...
+ $ ALKPHOS : num [1:418] 1718 7395 516 6122 671 ...
+ $ ASCITES : num [1:418] 1 0 0 0 0 0 0 0 0 1 ...
+ $ BILI : num [1:418] 14.5 1.1 1.4 1.8 3.4 0.8 1 0.3 3.2 12.6 ...
+ $ CHOL : num [1:418] 261 302 176 244 279 248 322 280 562 200 ...
+ $ EDEMA : num [1:418] 1 0 1 1 0 0 0 0 0 1 ...
+ $ EDTRT : num [1:418] 1 0 0.5 0.5 0 0 0 0 0 1 ...
+ $ HEPMEG : num [1:418] 1 1 0 1 1 1 1 0 0 0 ...
+ $ TIME : num [1:418] 400 4500 1012 1925 1504 ...
+ $ PLATELET: num [1:418] 190 221 151 183 136 -9 204 373 251 302 ...
+ $ PROTIME : num [1:418] 12.2 10.6 12 10.3 10.9 11 9.7 11 11 11.5 ...
+ $ SEX : num [1:418] 1 1 0 1 1 1 1 1 1 1 ...
+ $ SGOT : num [1:418] 137.9 113.5 96.1 60.6 113.2 ...
+ $ SPIDERS : num [1:418] 1 1 0 1 1 0 0 0 1 1 ...
+ $ STAGE : num [1:418] 4 3 4 4 3 3 3 3 2 4 ...
+ $ STATUS : num [1:418] 1 0 1 1 0 1 0 1 1 1 ...
+ $ TRT : num [1:418] 1 1 1 1 2 2 2 2 1 2 ...
+ $ TRIG : num [1:418] 172 88 55 92 72 63 213 189 88 143 ...
+ $ COPPER : num [1:418] 156 54 210 64 143 50 52 52 79 140 ...
+ - attr(*, "label.table")=List of 20
+ ..$ AGE : NULL
+ ..$ ALB : NULL
+ ..$ ALKPHOS : NULL
+ ..$ ASCITES : NULL
+ ..$ BILI : NULL
+ ..$ CHOL : NULL
+ ..$ EDEMA : NULL
+ ..$ EDTRT : NULL
+ ..$ HEPMEG : NULL
+ ..$ TIME : NULL
+ ..$ PLATELET: NULL
+ ..$ PROTIME : NULL
+ ..$ SEX : NULL
+ ..$ SGOT : NULL
+ ..$ SPIDERS : NULL
+ ..$ STAGE : NULL
+ ..$ STATUS : NULL
+ ..$ TRT : NULL
+ ..$ TRIG : NULL
+ ..$ COPPER : NULL
+> d.pbc <- data.frame(pbc)
+> summary(d.pbc)
+ AGE ALB ALKPHOS ASCITES
+ Min. :26.28 Min. :1.960 Min. : -9 Min. :-9.000
+ 1st Qu.:42.83 1st Qu.:3.243 1st Qu.: -9 1st Qu.:-9.000
+ Median :51.00 Median :3.530 Median : 1009 Median : 0.000
+ Mean :50.74 Mean :3.497 Mean : 1478 Mean :-2.225
+ 3rd Qu.:58.24 3rd Qu.:3.770 3rd Qu.: 1708 3rd Qu.: 0.000
+ Max. :78.44 Max. :4.640 Max. :13862 Max. : 1.000
+ BILI CHOL EDEMA EDTRT
+ Min. : 0.300 Min. : -9.0 Min. :0.0000 Min. :0.0000
+ 1st Qu.: 0.800 1st Qu.: -9.0 1st Qu.:0.0000 1st Qu.:0.0000
+ Median : 1.400 Median : 252.5 Median :0.0000 Median :0.0000
+ Mean : 3.221 Mean : 248.2 Mean :0.1196 Mean :0.1005
+ 3rd Qu.: 3.400 3rd Qu.: 347.8 3rd Qu.:0.0000 3rd Qu.:0.0000
+ Max. :28.000 Max. :1775.0 Max. :1.0000 Max. :1.0000
+ HEPMEG TIME PLATELET PROTIME SEX
+ Min. :-9.0 Min. : 41 Min. : -9.0 Min. : 9.00 Min. :-9.000
+ 1st Qu.:-9.0 1st Qu.:1093 1st Qu.:181.0 1st Qu.:10.00 1st Qu.:-9.000
+ Median : 0.0 Median :1730 Median :248.0 Median :10.60 Median : 1.000
+ Mean :-1.9 Mean :1918 Mean :250.0 Mean :10.73 Mean :-1.622
+ 3rd Qu.: 1.0 3rd Qu.:2614 3rd Qu.:315.5 3rd Qu.:11.10 3rd Qu.: 1.000
+ Max. : 1.0 Max. :4795 Max. :721.0 Max. :18.00 Max. : 1.000
+ SGOT SPIDERS STAGE STATUS
+ Min. : -9.00 Min. :-9.000 Min. :-9.00000 Min. :0.0000
+ 1st Qu.: -9.00 1st Qu.:-9.000 1st Qu.:-9.00000 1st Qu.:0.0000
+ Median : 90.45 Median : 0.000 Median : 3.00000 Median :0.0000
+ Mean : 89.20 Mean :-2.067 Mean :-0.01914 Mean :0.3852
+ 3rd Qu.:135.75 3rd Qu.: 0.000 3rd Qu.: 4.00000 3rd Qu.:1.0000
+ Max. :457.25 Max. : 1.000 Max. : 4.00000 Max. :1.0000
+ TRT TRIG COPPER
+ Min. :-9.000 Min. : -9.0 Min. : -9.00
+ 1st Qu.:-9.000 1st Qu.: -9.0 1st Qu.: -9.00
+ Median : 1.000 Median : 85.0 Median : 50.50
+ Mean :-1.167 Mean : 81.2 Mean : 70.09
+ 3rd Qu.: 2.000 3rd Qu.:127.8 3rd Qu.:100.75
+ Max. : 2.000 Max. :598.0 Max. :588.00
+> pbco <- read.spss("pbcold.sav",FALSE)
+> stopifnot(identical(pbc, pbco))
+> ## summary(pbco)
+> ## str(pbco)
+> ## d.pbco <- data.frame(pbco)
+> ## summary(d.pbco)
+> pbc. <- read.spss("pbc.por",FALSE)
+> summary(pbc.)
+ Length Class Mode
+AGE 418 -none- numeric
+ALB 418 -none- numeric
+ALKPHOS 418 -none- numeric
+ASCITES 418 -none- numeric
+BILI 418 -none- numeric
+CHOL 418 -none- numeric
+EDEMA 418 -none- numeric
+EDTRT 418 -none- numeric
+HEPMEG 418 -none- numeric
+TIME 418 -none- numeric
+PLATELET 418 -none- numeric
+PROTIME 418 -none- numeric
+SEX 418 -none- numeric
+SGOT 418 -none- numeric
+SPIDERS 418 -none- numeric
+STAGE 418 -none- numeric
+STATUS 418 -none- numeric
+TRT 418 -none- numeric
+TRIG 418 -none- numeric
+COPPER 418 -none- numeric
+> str(pbc.) # has variable.labels
+List of 20
+ $ AGE : num [1:418] 58.8 56.4 70.1 54.7 38.1 ...
+ $ ALB : num [1:418] 2.6 4.14 3.48 2.54 3.53 3.98 4.09 4 3.08 2.74 ...
+ $ ALKPHOS : num [1:418] 1718 7395 516 6122 671 ...
+ $ ASCITES : num [1:418] 1 0 0 0 0 0 0 0 0 1 ...
+ $ BILI : num [1:418] 14.5 1.1 1.4 1.8 3.4 0.8 1 0.3 3.2 12.6 ...
+ $ CHOL : num [1:418] 261 302 176 244 279 248 322 280 562 200 ...
+ $ EDEMA : num [1:418] 1 0 1 1 0 0 0 0 0 1 ...
+ $ EDTRT : num [1:418] 1 0 0.5 0.5 0 0 0 0 0 1 ...
+ $ HEPMEG : num [1:418] 1 1 0 1 1 1 1 0 0 0 ...
+ $ TIME : num [1:418] 400 4500 1012 1925 1504 ...
+ $ PLATELET: num [1:418] 190 221 151 183 136 -9 204 373 251 302 ...
+ $ PROTIME : num [1:418] 12.2 10.6 12 10.3 10.9 11 9.7 11 11 11.5 ...
+ $ SEX : num [1:418] 1 1 0 1 1 1 1 1 1 1 ...
+ $ SGOT : num [1:418] 137.9 113.5 96.1 60.6 113.2 ...
+ $ SPIDERS : num [1:418] 1 1 0 1 1 0 0 0 1 1 ...
+ $ STAGE : num [1:418] 4 3 4 4 3 3 3 3 2 4 ...
+ $ STATUS : num [1:418] 1 0 1 1 0 1 0 1 1 1 ...
+ $ TRT : num [1:418] 1 1 1 1 2 2 2 2 1 2 ...
+ $ TRIG : num [1:418] 172 88 55 92 72 63 213 189 88 143 ...
+ $ COPPER : num [1:418] 156 54 210 64 143 50 52 52 79 140 ...
+ - attr(*, "label.table")=List of 20
+ ..$ AGE : NULL
+ ..$ ALB : NULL
+ ..$ ALKPHOS : NULL
+ ..$ ASCITES : NULL
+ ..$ BILI : NULL
+ ..$ CHOL : NULL
+ ..$ EDEMA : NULL
+ ..$ EDTRT : NULL
+ ..$ HEPMEG : NULL
+ ..$ TIME : NULL
+ ..$ PLATELET: NULL
+ ..$ PROTIME : NULL
+ ..$ SEX : NULL
+ ..$ SGOT : NULL
+ ..$ SPIDERS : NULL
+ ..$ STAGE : NULL
+ ..$ STATUS : NULL
+ ..$ TRT : NULL
+ ..$ TRIG : NULL
+ ..$ COPPER : NULL
+ - attr(*, "variable.labels")= Named chr [1:20] " " " " " " " " ...
+ ..- attr(*, "names")= chr [1:20] "AGE" "ALB" "ALKPHOS" "ASCITES" ...
+> stopifnot(all.equal(d.pbc, data.frame(pbc.), tol=1e-15))
+>
+> electric.s <- read.spss("electric.sav",TRUE,TRUE)
+> electric.p <- read.spss("electric.por",TRUE,TRUE)
+> electric.s4 <- read.spss("electric.sav",TRUE,TRUE,max.value.labels = 4)
+> summary(electric.s)
+ CASEID FIRSTCHD AGE DBP58
+ Min. : 1.00 NO CHD :120 Min. :40.0 Min. : 65.00
+ 1st Qu.: 73.75 SUDDEN DEATH: 36 1st Qu.:45.0 1st Qu.: 80.00
+ Median : 144.50 NONFATALMI : 72 Median :48.0 Median : 87.00
+ Mean : 572.94 FATAL MI : 9 Mean :47.8 Mean : 88.79
+ 3rd Qu.:1042.25 OTHER CHD : 3 3rd Qu.:51.0 3rd Qu.: 96.50
+ Max. :2098.00 Max. :54.0 Max. :160.00
+ NA's :1
+ EDUYR CHOL58 CGT58 HT58
+ Min. : 6.00 Min. :106.0 Min. : 0.00 Min. :60.90
+ 1st Qu.: 9.75 1st Qu.:228.8 1st Qu.: 0.00 1st Qu.:66.50
+ Median :12.00 Median :261.0 Median :10.00 Median :68.15
+ Mean :11.66 Mean :264.1 Mean :11.58 Mean :68.51
+ 3rd Qu.:14.00 3rd Qu.:293.2 3rd Qu.:20.00 3rd Qu.:70.20
+ Max. :18.00 Max. :515.0 Max. :60.00 Max. :77.00
+ NA's :28 NA's :1
+ WT58 DAYOFWK VITAL10 FAMHXCVR CHD
+ Min. :123.0 SUNDAY : 19 ALIVE:179 NO :178 Min. :0.0
+ 1st Qu.:156.0 TUESDAY : 19 DEAD : 61 YES: 62 1st Qu.:0.0
+ Median :171.0 WEDNSDAY: 17 Median :0.5
+ Mean :173.4 SATURDAY: 16 Mean :0.5
+ 3rd Qu.:187.0 THURSDAY: 15 3rd Qu.:1.0
+ Max. :278.0 (Other) : 24 Max. :1.0
+ NA's :130
+> ii <- c(2,10)
+> vl <- list(FIRSTCHD = c("OTHER CHD"= 6, "FATAL MI"= 5, "NONFATALMI"= 3,
++ "SUDDEN DEATH" = 2, "NO CHD" = 1),
++ DAYOFWK = c(SATURDAY=7, FRIDAY=6, THURSDAY=5,
++ WEDNSDAY=4, TUESDAY=3, MONDAY=2, SUNDAY=1))
+> stopifnot(identical(electric.s, electric.p),
++ identical(electric.s[-ii], electric.s4[-ii]),
++ identical(vl, lapply(electric.s4[ii], attr, "value.labels")),
++ identical(lapply(vl, names),
++ lapply(electric.s[ii], function(.) rev(levels(.)))))
+>
+>
+> ## after "long label patch":
+>
+> invisible(Sys.setlocale (locale="C")) ## to resolve locale problem
+> ldat <- read.spss("spss_long.sav", to.data.frame=TRUE)
+> ldat
+ variable1 variable2
+1 1 1
+2 2 1
+3 2 3
+> nnms <- nms <- names(ldat)
+> names(nnms) <- nms
+> stopifnot(identical(nms, c("variable1", "variable2")),
++ identical(nnms, attr(ldat, "variable.labels")))
+>
+> proc.time()
+ user system elapsed
+ 0.732 0.076 0.785
diff --git a/win32/deps/library/foreign/tests/spss_long.sav b/win32/deps/library/foreign/tests/spss_long.sav
new file mode 100644
index 0000000..b87faaa
Binary files /dev/null and b/win32/deps/library/foreign/tests/spss_long.sav differ
diff --git a/win32/deps/library/foreign/tests/stata.R b/win32/deps/library/foreign/tests/stata.R
new file mode 100644
index 0000000..082f443
--- /dev/null
+++ b/win32/deps/library/foreign/tests/stata.R
@@ -0,0 +1,33 @@
+library(foreign)
+pc5 <- read.dta("pc5.dta")
+summary(pc5)
+str(pc5)
+compressed<-read.dta("compressed.dta")
+summary(compressed)
+all.equal(summary(pc5), summary(compressed))
+sun6 <- read.dta("sun6.dta")
+summary(sun6)
+str(sun6)
+all.equal(summary(sun6),summary(pc5))
+df<-read.dta("datefactor.dta")
+summary(df)
+data(esoph)
+write.dta(esoph,esophile<-tempfile())
+esoph2<-read.dta(esophile)
+all.equal(ordered(esoph2$alcgp),esoph$alcgp)
+write.dta(esoph,esophile,convert.factors="string")
+esoph2<-read.dta(esophile)
+all.equal(as.character(esoph$alcgp),esoph2$alcgp)
+write.dta(esoph,esophile,convert.factors="code")
+esoph2<-read.dta(esophile)
+all.equal(as.numeric(esoph$alcgp),as.numeric(esoph2$alcgp))
+
+se<-read.dta("stata7se.dta")
+print(se)
+v8<-read.dta("stata8mac.dta")
+print(v8)
+
+stata8<-read.dta("auto8.dta",missing.type=TRUE,convert.underscore=FALSE)
+str(stata8)
+
+q()
diff --git a/win32/deps/library/foreign/tests/stata.Rout.save b/win32/deps/library/foreign/tests/stata.Rout.save
new file mode 100644
index 0000000..d471fbe
--- /dev/null
+++ b/win32/deps/library/foreign/tests/stata.Rout.save
@@ -0,0 +1,308 @@
+
+R version 2.13.0 Under development (unstable) (2011-03-05 r54672)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(foreign)
+> pc5 <- read.dta("pc5.dta")
+Warning message:
+In read.dta("pc5.dta") : cannot read factor labels from Stata 5 files
+> summary(pc5)
+ age alb alkphos ascites
+ Min. :26.28 Min. :1.960 Min. : -9 Min. :-9.000
+ 1st Qu.:42.71 1st Qu.:3.330 1st Qu.: 423 1st Qu.: 0.000
+ Median :50.47 Median :3.570 Median : 1009 Median : 0.000
+ Mean :50.45 Mean :3.543 Mean : 1525 Mean :-2.074
+ 3rd Qu.:56.99 3rd Qu.:3.820 3rd Qu.: 1677 3rd Qu.: 0.000
+ Max. :78.44 Max. :4.640 Max. :13862 Max. : 1.000
+ bili chol edema edemarx
+ Min. : 0.300 Min. : -9.0 Min. :0.00000 Min. :0.00000
+ 1st Qu.: 0.700 1st Qu.: -9.0 1st Qu.:0.00000 1st Qu.:0.00000
+ Median : 1.200 Median : 256.0 Median :0.00000 Median :0.00000
+ Mean : 2.688 Mean : 245.8 Mean :0.09256 Mean :0.07815
+ 3rd Qu.: 3.000 3rd Qu.: 346.0 3rd Qu.:0.00000 3rd Qu.:0.00000
+ Max. :28.000 Max. :1775.0 Max. :1.00000 Max. :1.00000
+ hepmeg time plate protime sex
+ Min. :-9.00 Min. : 41 Min. : -9 Min. : 9.00 Min. :-9.000
+ 1st Qu.: 0.00 1st Qu.:1434 1st Qu.:181 1st Qu.:10.00 1st Qu.: 0.000
+ Median : 0.00 Median :1487 Median :249 Median :10.60 Median : 1.000
+ Mean :-1.75 Mean :1760 Mean :252 Mean :10.67 Mean :-1.434
+ 3rd Qu.: 1.00 3rd Qu.:2153 3rd Qu.:321 3rd Qu.:11.00 3rd Qu.: 1.000
+ Max. : 1.00 Max. :4795 Max. :721 Max. :18.00 Max. : 1.000
+ sgot spiders stage cens
+ Min. : -9.00 Min. :-9.000 Min. :-9.0000 Min. :0.0000
+ 1st Qu.: 44.20 1st Qu.: 0.000 1st Qu.: 1.0000 1st Qu.:0.0000
+ Median : 88.35 Median : 0.000 Median : 3.0000 Median :0.0000
+ Mean : 88.22 Mean :-1.914 Mean : 0.1351 Mean :0.2443
+ 3rd Qu.:130.20 3rd Qu.: 0.000 3rd Qu.: 3.0000 3rd Qu.:0.0000
+ Max. :457.25 Max. : 1.000 Max. : 4.0000 Max. :1.0000
+ rx trig copper id
+ Min. :-9.0000 Min. : -9.00 Min. : -9.00 Min. : 1.0
+ 1st Qu.: 1.0000 1st Qu.: -9.00 1st Qu.: 10.00 1st Qu.: 99.5
+ Median : 1.0000 Median : 85.00 Median : 48.00 Median :195.0
+ Mean :-0.9788 Mean : 81.44 Mean : 65.26 Mean :199.6
+ 3rd Qu.: 2.0000 3rd Qu.:126.00 3rd Qu.: 88.00 3rd Qu.:302.5
+ Max. : 2.0000 Max. :598.00 Max. :588.00 Max. :418.0
+ first late t0
+ Min. :0.0000 Min. :0.0000 Min. : 0.0
+ 1st Qu.:0.0000 1st Qu.:0.0000 1st Qu.: 0.0
+ Median :0.0000 Median :0.0000 Median : 0.0
+ Mean :0.3657 Mean :0.3657 Mean : 543.8
+ 3rd Qu.:1.0000 3rd Qu.:1.0000 3rd Qu.:1487.0
+ Max. :1.0000 Max. :1.0000 Max. :1487.0
+> str(pc5)
+'data.frame': 659 obs. of 24 variables:
+ $ age : num 58.8 56.4 56.4 70.1 54.7 ...
+ $ alb : num 2.6 4.14 4.14 3.48 2.54 ...
+ $ alkphos: num 1718 7395 7395 516 6122 ...
+ $ ascites: num 1 0 0 0 0 0 0 0 0 0 ...
+ $ bili : num 14.5 1.1 1.1 1.4 1.8 ...
+ $ chol : num 261 302 302 176 244 244 279 279 248 248 ...
+ $ edema : num 1 0 0 1 1 1 0 0 0 0 ...
+ $ edemarx: num 1 0 0 0.5 0.5 0.5 0 0 0 0 ...
+ $ hepmeg : num 1 1 1 0 1 1 1 1 1 1 ...
+ $ time : num 400 1487 4500 1012 1487 ...
+ $ plate : num 190 221 221 151 183 183 136 136 -9 -9 ...
+ $ protime: num 12.2 10.6 10.6 12 10.3 ...
+ $ sex : num 1 1 1 0 1 1 1 1 1 1 ...
+ $ sgot : num 137.9 113.5 113.5 96.1 60.6 ...
+ $ spiders: num 1 1 1 0 1 1 1 1 0 0 ...
+ $ stage : num 4 3 3 4 4 4 3 3 3 3 ...
+ $ cens : num 1 0 0 1 0 1 0 0 0 1 ...
+ $ rx : num 1 1 1 1 1 1 2 2 2 2 ...
+ $ trig : num 172 88 88 55 92 92 72 72 63 63 ...
+ $ copper : num 156 54 54 210 64 64 143 143 50 50 ...
+ $ id : num 1 2 2 3 4 4 5 5 6 6 ...
+ $ first : num 0 1 0 0 1 0 1 0 1 0 ...
+ $ late : num 0 0 1 0 0 1 0 1 0 1 ...
+ $ t0 : num 0 0 1487 0 0 ...
+ - attr(*, "datalabel")= chr ""
+ - attr(*, "time.stamp")= chr "14 Feb 1997 14:22"
+ - attr(*, "formats")= chr "%9.0g" "%9.0g" "%9.0g" "%9.0g" ...
+ - attr(*, "types")= int 102 102 102 102 102 102 102 102 102 102 ...
+ - attr(*, "val.labels")= chr "" "" "" "" ...
+ - attr(*, "var.labels")= chr "" "" "" "" ...
+ - attr(*, "version")= int 5
+> compressed<-read.dta("compressed.dta")
+> summary(compressed)
+ age alb alkphos ascites
+ Min. :26.28 Min. :1.960 Min. : -9 Min. :-9.000
+ 1st Qu.:42.71 1st Qu.:3.330 1st Qu.: 423 1st Qu.: 0.000
+ Median :50.47 Median :3.570 Median : 1009 Median : 0.000
+ Mean :50.45 Mean :3.543 Mean : 1525 Mean :-2.074
+ 3rd Qu.:56.99 3rd Qu.:3.820 3rd Qu.: 1677 3rd Qu.: 0.000
+ Max. :78.44 Max. :4.640 Max. :13862 Max. : 1.000
+ bili chol edema edemarx
+ Min. : 0.300 Min. : -9.0 Min. :0.00000 Min. :0.00000
+ 1st Qu.: 0.700 1st Qu.: -9.0 1st Qu.:0.00000 1st Qu.:0.00000
+ Median : 1.200 Median : 256.0 Median :0.00000 Median :0.00000
+ Mean : 2.688 Mean : 245.8 Mean :0.09256 Mean :0.07815
+ 3rd Qu.: 3.000 3rd Qu.: 346.0 3rd Qu.:0.00000 3rd Qu.:0.00000
+ Max. :28.000 Max. :1775.0 Max. :1.00000 Max. :1.00000
+ hepmeg time plate protime sex
+ Min. :-9.00 Min. : 41 Min. : -9 Min. : 9.00 Min. :-9.000
+ 1st Qu.: 0.00 1st Qu.:1434 1st Qu.:181 1st Qu.:10.00 1st Qu.: 0.000
+ Median : 0.00 Median :1487 Median :249 Median :10.60 Median : 1.000
+ Mean :-1.75 Mean :1760 Mean :252 Mean :10.67 Mean :-1.434
+ 3rd Qu.: 1.00 3rd Qu.:2153 3rd Qu.:321 3rd Qu.:11.00 3rd Qu.: 1.000
+ Max. : 1.00 Max. :4795 Max. :721 Max. :18.00 Max. : 1.000
+ sgot spiders stage cens
+ Min. : -9.00 Min. :-9.000 Min. :-9.0000 Min. :0.0000
+ 1st Qu.: 44.20 1st Qu.: 0.000 1st Qu.: 1.0000 1st Qu.:0.0000
+ Median : 88.35 Median : 0.000 Median : 3.0000 Median :0.0000
+ Mean : 88.22 Mean :-1.914 Mean : 0.1351 Mean :0.2443
+ 3rd Qu.:130.20 3rd Qu.: 0.000 3rd Qu.: 3.0000 3rd Qu.:0.0000
+ Max. :457.25 Max. : 1.000 Max. : 4.0000 Max. :1.0000
+ rx trig copper id
+ Min. :-9.0000 Min. : -9.00 Min. : -9.00 Min. : 1.0
+ 1st Qu.: 1.0000 1st Qu.: -9.00 1st Qu.: 10.00 1st Qu.: 99.5
+ Median : 1.0000 Median : 85.00 Median : 48.00 Median :195.0
+ Mean :-0.9788 Mean : 81.44 Mean : 65.26 Mean :199.6
+ 3rd Qu.: 2.0000 3rd Qu.:126.00 3rd Qu.: 88.00 3rd Qu.:302.5
+ Max. : 2.0000 Max. :598.00 Max. :588.00 Max. :418.0
+ first late t0
+ Min. :0.0000 Min. :0.0000 Min. : 0.0
+ 1st Qu.:0.0000 1st Qu.:0.0000 1st Qu.: 0.0
+ Median :0.0000 Median :0.0000 Median : 0.0
+ Mean :0.3657 Mean :0.3657 Mean : 543.8
+ 3rd Qu.:1.0000 3rd Qu.:1.0000 3rd Qu.:1487.0
+ Max. :1.0000 Max. :1.0000 Max. :1487.0
+> all.equal(summary(pc5), summary(compressed))
+[1] TRUE
+> sun6 <- read.dta("sun6.dta")
+> summary(sun6)
+ age alb alkphos ascites
+ Min. :26.28 Min. :1.960 Min. : -9 Min. :-9.000
+ 1st Qu.:42.71 1st Qu.:3.330 1st Qu.: 423 1st Qu.: 0.000
+ Median :50.47 Median :3.570 Median : 1009 Median : 0.000
+ Mean :50.45 Mean :3.543 Mean : 1525 Mean :-2.074
+ 3rd Qu.:56.99 3rd Qu.:3.820 3rd Qu.: 1677 3rd Qu.: 0.000
+ Max. :78.44 Max. :4.640 Max. :13862 Max. : 1.000
+ bili chol edema edemarx
+ Min. : 0.300 Min. : -9.0 Min. :0.00000 Min. :0.00000
+ 1st Qu.: 0.700 1st Qu.: -9.0 1st Qu.:0.00000 1st Qu.:0.00000
+ Median : 1.200 Median : 256.0 Median :0.00000 Median :0.00000
+ Mean : 2.688 Mean : 245.8 Mean :0.09256 Mean :0.07815
+ 3rd Qu.: 3.000 3rd Qu.: 346.0 3rd Qu.:0.00000 3rd Qu.:0.00000
+ Max. :28.000 Max. :1775.0 Max. :1.00000 Max. :1.00000
+ hepmeg time plate protime sex
+ Min. :-9.00 Min. : 41 Min. : -9 Min. : 9.00 Min. :-9.000
+ 1st Qu.: 0.00 1st Qu.:1434 1st Qu.:181 1st Qu.:10.00 1st Qu.: 0.000
+ Median : 0.00 Median :1487 Median :249 Median :10.60 Median : 1.000
+ Mean :-1.75 Mean :1760 Mean :252 Mean :10.67 Mean :-1.434
+ 3rd Qu.: 1.00 3rd Qu.:2153 3rd Qu.:321 3rd Qu.:11.00 3rd Qu.: 1.000
+ Max. : 1.00 Max. :4795 Max. :721 Max. :18.00 Max. : 1.000
+ sgot spiders stage cens
+ Min. : -9.00 Min. :-9.000 Min. :-9.0000 Min. :0.0000
+ 1st Qu.: 44.20 1st Qu.: 0.000 1st Qu.: 1.0000 1st Qu.:0.0000
+ Median : 88.35 Median : 0.000 Median : 3.0000 Median :0.0000
+ Mean : 88.22 Mean :-1.914 Mean : 0.1351 Mean :0.2443
+ 3rd Qu.:130.20 3rd Qu.: 0.000 3rd Qu.: 3.0000 3rd Qu.:0.0000
+ Max. :457.25 Max. : 1.000 Max. : 4.0000 Max. :1.0000
+ rx trig copper id
+ Min. :-9.0000 Min. : -9.00 Min. : -9.00 Min. : 1.0
+ 1st Qu.: 1.0000 1st Qu.: -9.00 1st Qu.: 10.00 1st Qu.: 99.5
+ Median : 1.0000 Median : 85.00 Median : 48.00 Median :195.0
+ Mean :-0.9788 Mean : 81.44 Mean : 65.26 Mean :199.6
+ 3rd Qu.: 2.0000 3rd Qu.:126.00 3rd Qu.: 88.00 3rd Qu.:302.5
+ Max. : 2.0000 Max. :598.00 Max. :588.00 Max. :418.0
+ first late t0
+ Min. :0.0000 Min. :0.0000 Min. : 0.0
+ 1st Qu.:0.0000 1st Qu.:0.0000 1st Qu.: 0.0
+ Median :0.0000 Median :0.0000 Median : 0.0
+ Mean :0.3657 Mean :0.3657 Mean : 543.8
+ 3rd Qu.:1.0000 3rd Qu.:1.0000 3rd Qu.:1487.0
+ Max. :1.0000 Max. :1.0000 Max. :1487.0
+> str(sun6)
+'data.frame': 659 obs. of 24 variables:
+ $ age : num 58.8 56.4 56.4 70.1 54.7 ...
+ $ alb : num 2.6 4.14 4.14 3.48 2.54 ...
+ $ alkphos: num 1718 7395 7395 516 6122 ...
+ $ ascites: int 1 0 0 0 0 0 0 0 0 0 ...
+ $ bili : num 14.5 1.1 1.1 1.4 1.8 ...
+ $ chol : int 261 302 302 176 244 244 279 279 248 248 ...
+ $ edema : int 1 0 0 1 1 1 0 0 0 0 ...
+ $ edemarx: num 1 0 0 0.5 0.5 0.5 0 0 0 0 ...
+ $ hepmeg : int 1 1 1 0 1 1 1 1 1 1 ...
+ $ time : int 400 1487 4500 1012 1487 1925 1487 1504 1487 2503 ...
+ $ plate : int 190 221 221 151 183 183 136 136 -9 -9 ...
+ $ protime: num 12.2 10.6 10.6 12 10.3 ...
+ $ sex : int 1 1 1 0 1 1 1 1 1 1 ...
+ $ sgot : num 137.9 113.5 113.5 96.1 60.6 ...
+ $ spiders: int 1 1 1 0 1 1 1 1 0 0 ...
+ $ stage : int 4 3 3 4 4 4 3 3 3 3 ...
+ $ cens : int 1 0 0 1 0 1 0 0 0 1 ...
+ $ rx : int 1 1 1 1 1 1 2 2 2 2 ...
+ $ trig : int 172 88 88 55 92 92 72 72 63 63 ...
+ $ copper : int 156 54 54 210 64 64 143 143 50 50 ...
+ $ id : int 1 2 2 3 4 4 5 5 6 6 ...
+ $ first : int 0 1 0 0 1 0 1 0 1 0 ...
+ $ late : int 0 0 1 0 0 1 0 1 0 1 ...
+ $ t0 : int 0 0 1487 0 0 1487 0 1487 0 1487 ...
+ - attr(*, "datalabel")= chr ""
+ - attr(*, "time.stamp")= chr "14 Sep 2000 10:40"
+ - attr(*, "formats")= chr "%9.0g" "%9.0g" "%9.0g" "%9.0g" ...
+ - attr(*, "types")= int 102 102 102 98 102 105 98 102 98 105 ...
+ - attr(*, "val.labels")= chr "" "" "" "" ...
+ - attr(*, "var.labels")= chr "" "" "" "" ...
+ - attr(*, "version")= int 6
+> all.equal(summary(sun6),summary(pc5))
+[1] TRUE
+> df<-read.dta("datefactor.dta")
+> summary(df)
+ hlth159 id adate
+ EXCELLENT: 0 Min. : 1.00 Min. :1960-01-02
+ VERY GOOD: 6 1st Qu.: 8.25 1st Qu.:1960-01-09
+ GOOD : 8 Median :15.50 Median :1960-01-16
+ FAIR : 4 Mean :15.50 Mean :1960-01-16
+ POOR : 1 3rd Qu.:22.75 3rd Qu.:1960-01-23
+ NA's :11 Max. :30.00 Max. :1960-01-31
+> data(esoph)
+> write.dta(esoph,esophile<-tempfile())
+> esoph2<-read.dta(esophile)
+> all.equal(ordered(esoph2$alcgp),esoph$alcgp)
+[1] TRUE
+> write.dta(esoph,esophile,convert.factors="string")
+> esoph2<-read.dta(esophile)
+> all.equal(as.character(esoph$alcgp),esoph2$alcgp)
+[1] TRUE
+> write.dta(esoph,esophile,convert.factors="code")
+> esoph2<-read.dta(esophile)
+> all.equal(as.numeric(esoph$alcgp),as.numeric(esoph2$alcgp))
+[1] TRUE
+>
+> se<-read.dta("stata7se.dta")
+> print(se)
+ race number
+1 white 2
+2 asian 5
+3 hispanic 5
+4 white 4
+5 black 5
+6 white 6
+7 black 7
+> v8<-read.dta("stata8mac.dta")
+> print(v8)
+ race number
+1 white 2
+2 asian 5
+3 hispanic 5
+4 white 4
+5 black 5
+6 white 6
+7 black 7
+>
+> stata8<-read.dta("auto8.dta",missing.type=TRUE,convert.underscore=FALSE)
+> str(stata8)
+'data.frame': 74 obs. of 13 variables:
+ $ make : chr "AMC Concord" "AMC Pacer" "AMC Spirit" "Buick Century" ...
+ $ price : int 4099 4749 3799 4816 7827 5788 4453 5189 10372 4082 ...
+ $ mpg : int 22 17 22 20 15 18 26 20 16 19 ...
+ $ rep78 : int 3 3 NA 3 4 3 NA 3 3 3 ...
+ $ headroom : num 2.5 3 3 4.5 4 4 3 2 3.5 3.5 ...
+ $ trunk : int 11 11 12 16 20 21 10 16 17 13 ...
+ $ weight : int 2930 3350 2640 3250 4080 3670 2230 3280 3880 3400 ...
+ $ length : int 186 173 168 196 222 218 170 200 207 200 ...
+ $ turn : int 40 40 35 40 43 43 34 42 43 42 ...
+ $ displacement: int 121 258 121 196 350 231 304 196 231 231 ...
+ $ gear_ratio : num 3.58 2.53 3.08 2.93 2.41 ...
+ $ foreign : Factor w/ 2 levels "Domestic","Foreign": 1 1 1 1 1 1 1 1 1 1 ...
+ $ testmiss : num NA NA NA NA NA NA NA NA NA NA ...
+ - attr(*, "datalabel")= chr "1978 Automobile Data"
+ - attr(*, "time.stamp")= chr "20 May 2003 14:39"
+ - attr(*, "formats")= chr "%-18s" "%8.0gc" "%8.0g" "%8.0g" ...
+ - attr(*, "types")= int 18 252 252 252 254 252 252 252 252 252 ...
+ - attr(*, "val.labels")= chr "" "" "" "" ...
+ - attr(*, "var.labels")= chr "Make and Model" "Price" "Mileage (mpg)" "Repair Record 1978" ...
+ - attr(*, "version")= int 8
+ - attr(*, "label.table")=List of 1
+ ..$ origin: Named num 0 1
+ .. ..- attr(*, "names")= chr "Domestic" "Foreign"
+ - attr(*, "missing")=List of 13
+ ..$ make : NULL
+ ..$ price : num NA NA NA NA NA NA NA NA NA NA ...
+ ..$ mpg : num NA NA NA NA NA NA NA NA NA NA ...
+ ..$ rep78 : num NA NA 0 NA NA NA 0 NA NA NA ...
+ ..$ headroom : num NA NA NA NA NA NA NA NA NA NA ...
+ ..$ trunk : num NA NA NA NA NA NA NA NA NA NA ...
+ ..$ weight : num NA NA NA NA NA NA NA NA NA NA ...
+ ..$ length : num NA NA NA NA NA NA NA NA NA NA ...
+ ..$ turn : num NA NA NA NA NA NA NA NA NA NA ...
+ ..$ displacement: num NA NA NA NA NA NA NA NA NA NA ...
+ ..$ gear_ratio : num NA NA NA NA NA NA NA NA NA NA ...
+ ..$ foreign : num NA NA NA NA NA NA NA NA NA NA ...
+ ..$ testmiss : num 18 18 18 18 18 18 18 18 18 18 ...
+>
+> q()
diff --git a/win32/deps/library/foreign/tests/stata7se.dta b/win32/deps/library/foreign/tests/stata7se.dta
new file mode 100644
index 0000000..239addf
Binary files /dev/null and b/win32/deps/library/foreign/tests/stata7se.dta differ
diff --git a/win32/deps/library/foreign/tests/stata8mac.dta b/win32/deps/library/foreign/tests/stata8mac.dta
new file mode 100644
index 0000000..0203e72
Binary files /dev/null and b/win32/deps/library/foreign/tests/stata8mac.dta differ
diff --git a/win32/deps/library/foreign/tests/sun6.dta b/win32/deps/library/foreign/tests/sun6.dta
new file mode 100644
index 0000000..2745888
Binary files /dev/null and b/win32/deps/library/foreign/tests/sun6.dta differ
diff --git a/win32/deps/library/foreign/tests/test.xpt b/win32/deps/library/foreign/tests/test.xpt
new file mode 100644
index 0000000..2eb345a
Binary files /dev/null and b/win32/deps/library/foreign/tests/test.xpt differ
diff --git a/win32/deps/library/foreign/tests/tsdumpdata b/win32/deps/library/foreign/tests/tsdumpdata
new file mode 100644
index 0000000..2bd65dc
--- /dev/null
+++ b/win32/deps/library/foreign/tests/tsdumpdata
@@ -0,0 +1,455 @@
+sunspot
+structure
+3
+.Data
+numeric
+37
+40
+115
+100
+80
+60
+40
+23
+10
+10
+25
+75
+145
+130
+130
+80
+65
+20
+10
+5
+10
+60
+190
+180
+175
+120
+50
+35
+20
+10
+15
+30
+60
+105
+105
+105
+80
+65
+.Tsp
+numeric
+3
+1936
+1972
+1
+class
+character
+2
+ts
+numeric
+carbon.dioxide
+structure
+3
+.Data
+numeric
+384
+315.42
+316.32
+316.49
+317.56
+318.13
+318
+316.39
+314.66
+313.68
+313.18
+314.66
+315.43
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+318.58
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+319.7
+321.22
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+321.31
+319.58
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+321.4
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+325.04
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+346.22
+347.68
+348.82
+350.29
+351.58
+352.08
+353.45
+354.08
+353.66
+352.25
+350.3
+348.58
+348.74
+349.93
+351.21
+352.62
+352.93
+353.54
+355.27
+355.52
+354.97
+353.74
+351.51
+349.63
+349.82
+351.12
+352.35
+353.47
+354.51
+355.18
+355.98
+356.94
+355.99
+354.58
+352.68
+350.72
+350.92
+352.55
+353.91
+.Tsp
+numeric
+3
+1959
+1990.9166666666667
+12
+class
+character
+2
+ts
+numeric
diff --git a/win32/deps/library/foreign/tests/xport.R b/win32/deps/library/foreign/tests/xport.R
new file mode 100644
index 0000000..7585c6e
--- /dev/null
+++ b/win32/deps/library/foreign/tests/xport.R
@@ -0,0 +1,9 @@
+library(foreign)
+lookup.xport("Alfalfa.xpt")
+Alfalfa <- read.xport("Alfalfa.xpt")
+summary(Alfalfa)
+## test data provided by FRohde birchdavis com
+lookup.xport("test.xpt")
+testdata <- read.xport("test.xpt")
+summary(testdata)
+q()
diff --git a/win32/deps/library/foreign/tests/xport.Rout.save b/win32/deps/library/foreign/tests/xport.Rout.save
new file mode 100644
index 0000000..e920982
--- /dev/null
+++ b/win32/deps/library/foreign/tests/xport.Rout.save
@@ -0,0 +1,115 @@
+
+R : Copyright 2003, The R Development Core Team
+Version 1.7.0 Patched (2003-04-24)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type `license()' or `licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type `contributors()' for more information.
+
+Type `demo()' for some demos, `help()' for on-line help, or
+`help.start()' for a HTML browser interface to help.
+Type `q()' to quit R.
+
+> library(foreign)
+> lookup.xport("Alfalfa.xpt")
+$SPEC
+$SPEC$headpad
+[1] 1360
+
+$SPEC$type
+[1] "character" "numeric" "numeric" "numeric" "numeric" "numeric"
+
+$SPEC$width
+[1] 8 8 8 8 8 8
+
+$SPEC$index
+[1] 1 2 3 4 5 6
+
+$SPEC$position
+[1] 0 8 16 24 32 40
+
+$SPEC$name
+[1] "POP" "SAMPLE" "REP" "SEEDWT" "HARV1" "HARV2"
+
+$SPEC$label
+[1] "" "" "" "" "" ""
+
+$SPEC$format
+[1] "" "" "" "" "" ""
+
+$SPEC$sexptype
+[1] 16 14 14 14 14 14
+
+$SPEC$tailpad
+[1] 0
+
+$SPEC$length
+[1] 40
+
+
+> Alfalfa <- read.xport("Alfalfa.xpt")
+> summary(Alfalfa)
+ POP SAMPLE REP SEEDWT HARV1
+ MAX:20 Min. :0.0 Min. :1.00 Min. :35.00 Min. :120.6
+ min:20 1st Qu.:2.0 1st Qu.:1.75 1st Qu.:47.75 1st Qu.:148.3
+ Median :4.5 Median :2.50 Median :59.00 Median :165.8
+ Mean :4.5 Mean :2.50 Mean :56.08 Mean :163.0
+ 3rd Qu.:7.0 3rd Qu.:3.25 3rd Qu.:62.25 3rd Qu.:176.4
+ Max. :9.0 Max. :4.00 Max. :75.00 Max. :193.4
+ HARV2
+ Min. :129.1
+ 1st Qu.:150.6
+ Median :163.2
+ Mean :167.1
+ 3rd Qu.:179.6
+ Max. :235.3
+> ## test data provided by FRohde birchdavis com
+> lookup.xport("test.xpt")
+$TEST
+$TEST$headpad
+[1] 800
+
+$TEST$type
+[1] "numeric" "numeric"
+
+$TEST$width
+[1] 8 8
+
+$TEST$index
+[1] 1 2
+
+$TEST$position
+[1] 0 8
+
+$TEST$name
+[1] "I" "K"
+
+$TEST$label
+[1] "" ""
+
+$TEST$format
+[1] "" ""
+
+$TEST$sexptype
+[1] 14 14
+
+$TEST$tailpad
+[1] 48
+
+$TEST$length
+[1] 12
+
+
+> testdata <- read.xport("test.xpt")
+> summary(testdata)
+ I K
+ Min. :1.00 Min. :1
+ 1st Qu.:1.75 1st Qu.:1
+ Median :2.50 Median :2
+ Mean :2.50 Mean :2
+ 3rd Qu.:3.25 3rd Qu.:3
+ Max. :4.00 Max. :3
+> q()
diff --git a/win32/deps/library/grDevices/DESCRIPTION b/win32/deps/library/grDevices/DESCRIPTION
index 0aaf8d1..ee7afcb 100644
--- a/win32/deps/library/grDevices/DESCRIPTION
+++ b/win32/deps/library/grDevices/DESCRIPTION
@@ -1,9 +1,9 @@
Package: grDevices
-Version: 2.9.2
+Version: 2.15.2
Priority: base
Title: The R Graphics Devices and Support for Colours and Fonts
-Author: R Development Core Team and contributors worldwide
+Author: R Core Team and contributors worldwide
Maintainer: R Core Team <R-core r-project org>
Description: Graphics devices and support for base and grid graphics
-License: Part of R 2.9.2
-Built: R 2.9.2; i386-pc-mingw32; 2009-08-24 12:43:40 UTC; windows
+License: Part of R 2.15.2
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:05:46 UTC; windows
diff --git a/win32/deps/library/grDevices/INDEX b/win32/deps/library/grDevices/INDEX
index 1eaeefa..bcc610d 100644
--- a/win32/deps/library/grDevices/INDEX
+++ b/win32/deps/library/grDevices/INDEX
@@ -2,7 +2,11 @@ Devices List of Graphical Devices
Hershey Hershey Vector Fonts in R
Japanese Japanese characters in R
Type1Font Type 1 and CID Fonts
+adjustcolor Adjust Colors in One or More Directions
+ Conveniently.
as.graphicsAnnot Coerce an Object for Graphics Annotation
+as.raster Create a Raster Object
+axisTicks Compute Pretty Axis Tick Scales
boxplot.stats Box Plot Statistics
bringToTop Assign Focus to a Window
check.options Set Options with Consistency Checks
@@ -12,14 +16,19 @@ col2rgb Color to RGB Conversion
colorRamp Color interpolation
colors Color Names
contourLines Calculate Contour Lines
-convertColor Convert between colour spaces
+convertColor Convert between Colour Spaces
densCols Colors for Smooth Density Plots
+dev.capabilities Query Capabilities of the Current Graphics
+ Device
+dev.capture Capture device output as a raster image
dev.copy Copy Graphics Between Multiple Devices
dev.cur Control Multiple Devices
-dev.interactive Is the Current Graphics Device Interactive ?
+dev.flush Hold or Flush Output on an On-Screen Graphics
+ Device.
+dev.interactive Is the Current Graphics Device Interactive?
dev.size Find Size of Device Surface
dev2bitmap Graphics Device for Bitmap Files via
- GhostScript
+ Ghostscript
devAskNewPage Prompt before New Page
embedFonts Embed Fonts in PostScript and PDF
extendrange Extend a Numerical Range by a Small Percentage
@@ -44,16 +53,19 @@ plotmath Mathematical Annotation in R
png BMP, JPEG, PNG and TIFF graphics devices
postscript PostScript Graphics
postscriptFonts PostScript and PDF Font Families
+pretty.Date Pretty Breakpoints for Date-Time Classes
ps.options Auxiliary Function to Set/View Defaults for
Arguments of postscript
rainbow Color Palettes
-recordGraphics Record graphics operations
+recordGraphics Record Graphics Operations
recordPlot Record and Replay Plots
rgb RGB Color Specification
rgb2hsv RGB to HSV Conversion
savePlot Save Windows Plot to a File
+svg Cairo-based SVG, PDF and PostScript Graphics
+ Devices
trans3d 3D to 2D Transformation for Perspective Plots
-windows Windows graphics devices
+windows Windows Graphics Devices
windows.options Auxiliary Function to Set/View Defaults for
Arguments of windows()
windowsFonts Windows Fonts
diff --git a/win32/deps/library/grDevices/Meta/Rd.rds b/win32/deps/library/grDevices/Meta/Rd.rds
index 3f128e5..96579d4 100644
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diff --git a/win32/deps/library/grDevices/Meta/hsearch.rds b/win32/deps/library/grDevices/Meta/hsearch.rds
index e2f423c..357442d 100644
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diff --git a/win32/deps/library/grDevices/Meta/links.rds b/win32/deps/library/grDevices/Meta/links.rds
new file mode 100644
index 0000000..8033b9f
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diff --git a/win32/deps/library/grDevices/Meta/nsInfo.rds b/win32/deps/library/grDevices/Meta/nsInfo.rds
index a8d218f..cb66138 100644
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diff --git a/win32/deps/library/grDevices/Meta/package.rds b/win32/deps/library/grDevices/Meta/package.rds
index c5e334f..b8bf427 100644
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diff --git a/win32/deps/library/grDevices/NAMESPACE b/win32/deps/library/grDevices/NAMESPACE
index 314dd2f..cfc1de6 100644
--- a/win32/deps/library/grDevices/NAMESPACE
+++ b/win32/deps/library/grDevices/NAMESPACE
@@ -3,31 +3,35 @@
## conflict with functions on Windows, i.e. savePlot.
if(tools:::.OStype() == "windows") {
- useDynLib(grDevices, R_chull,
+ useDynLib(grDevices, R_chull, R_CreateAtVector, R_GAxisPars,
PicTeX, PostScript, XFig, PDF,
- Cdevga=devga, CsavePlot=savePlot,
+ Cdevga=devga, CsavePlot=savePlot, devCairo,
Type1FontInUse, CIDFontInUse, R_GD_nullDevice)
} else {
- useDynLib(grDevices, R_chull,
- PicTeX, PostScript, XFig, PDF, CQuartz = Quartz,
- Type1FontInUse, CIDFontInUse, R_GD_nullDevice)
+ useDynLib(grDevices, R_chull, R_CreateAtVector, R_GAxisPars,
+ PicTeX, PostScript, XFig, PDF, CQuartz = Quartz, devCairo,
+ Type1FontInUse, CIDFontInUse, R_GD_nullDevice,
+ cairoProps, makeQuartzDefault)
}
-export(Hershey, as.graphicsAnnot, blues9, boxplot.stats, check.options, chull,
- CIDFont, col2rgb, colors, colours, cm, colorRamp,
- colorRampPalette, contourLines, convertColor, colorConverter,
- colorspaces, cm.colors, densCols, devAskNewPage, dev.control,
- dev.copy, dev.copy2eps, dev.copy2pdf, dev.cur, dev.interactive,
- dev.list, dev.new, dev.next, dev.off, dev.prev, dev.print,
- dev.set, dev.size, dev2bitmap, deviceIsInteractive, embedFonts,
- extendrange, getGraphicsEvent, graphics.off, gray, grey,
- gray.colors, grey.colors, heat.colors, hsv, hcl, make.rgb,
+export(Hershey, adjustcolor, as.graphicsAnnot, as.raster, axisTicks, blues9,
+ boxplot.stats, check.options, chull, CIDFont, col2rgb, colors,
+ colours, cm, colorRamp, colorRampPalette, contourLines,
+ convertColor, colorConverter, colorspaces, cm.colors, densCols,
+ devAskNewPage, dev.capabilities, dev.capture, dev.control, dev.copy,
+ dev.copy2eps, dev.copy2pdf, dev.cur, dev.hold, dev.flush,
+ dev.interactive, dev.list, dev.new, dev.next, dev.off,
+ dev.prev, dev.print, dev.set, dev.size, dev2bitmap,
+ deviceIsInteractive, embedFonts, extendrange, getGraphicsEvent,
+ getGraphicsEventEnv, graphics.off, gray, grey, gray.colors,
+ grey.colors, heat.colors, hsv, hcl, is.raster, make.rgb,
n2mfrow, nclass.Sturges, nclass.FD, nclass.scott, palette, pdf,
pdf.options, pdfFonts, pictex, postscript, postscriptFont,
postscriptFonts, ps.options, rainbow, recordGraphics,
- recordPlot, replayPlot, rgb, rgb2hsv, savePlot, setEPS, setPS,
- terrain.colors, topo.colors, trans3d, Type1Font, xfig, xyTable,
- xy.coords, xyz.coords)
+ recordPlot, replayPlot, rgb, rgb2hsv, savePlot, setEPS,
+ setGraphicsEventEnv, setGraphicsEventHandlers, setPS,
+ terrain.colors, topo.colors, trans3d, Type1Font, .axisPars,
+ xfig, xyTable, xy.coords, xyz.coords)
## devices common to all platforms
export(X11, x11, bitmap, bmp, jpeg, png, tiff)
@@ -42,9 +46,29 @@ S3method("checkFont", "CIDFont")
S3method("matchEncoding", "Type1Font")
S3method("matchEncoding", "CIDFont")
+S3method("as.raster", "raster")
+S3method("as.raster", "logical")
+S3method("as.raster", "numeric")
+S3method("as.raster", "character")
+S3method("as.raster", "matrix")
+S3method("as.raster", "array")
+
+S3method("as.matrix", "raster")
+S3method("is.na", "raster")
+S3method("[", "raster")
+S3method("[<-", "raster")
+S3method("Ops", "raster")
+
+S3method("print", "raster")
+
+S3method(pretty, Date)
+S3method(pretty, POSIXt)
+
+
if(tools:::.OStype() == "windows") {
export(bringToTop, msgWindow, win.graph, win.metafile, win.print,
windows, windows.options, windowsFont, windowsFonts)
+ export(cairo_pdf, cairo_ps, svg)
S3method("[", SavedPlots)
S3method(print, SavedPlots)
diff --git a/win32/deps/library/grDevices/R/grDevices b/win32/deps/library/grDevices/R/grDevices
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/grDevices/R/grDevices
+++ b/win32/deps/library/grDevices/R/grDevices
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
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diff --git a/win32/deps/library/grDevices/afm/tir_____.afm.gz b/win32/deps/library/grDevices/afm/tir_____.afm.gz
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diff --git a/win32/deps/library/grDevices/help/AnIndex b/win32/deps/library/grDevices/help/AnIndex
index 7a55016..7b98f68 100644
--- a/win32/deps/library/grDevices/help/AnIndex
+++ b/win32/deps/library/grDevices/help/AnIndex
@@ -1,7 +1,16 @@
grDevices-package grDevices-package
+.axisPars axisTicks
.ps.prolog postscript
+adjustcolor adjustcolor
as.graphicsAnnot as.graphicsAnnot
+as.raster as.raster
+as.raster.array as.raster
+as.raster.character as.raster
+as.raster.logical as.raster
+as.raster.matrix as.raster
+as.raster.numeric as.raster
atop plotmath
+axisTicks axisTicks
bar plotmath
bgroup plotmath
bitmap dev2bitmap
@@ -11,6 +20,8 @@ bold plotmath
bolditalic plotmath
boxplot.stats boxplot.stats
bringToTop bringToTop
+cairo_pdf cairo
+cairo_ps cairo
check.options check.options
chull chull
CIDFont Type1Font
@@ -26,11 +37,15 @@ colours colors
contourLines contourLines
convertColor convertColor
densCols densCols
+dev.capabilities dev.capabilities
+dev.capture dev.capture
dev.control dev2
dev.copy dev2
dev.copy2eps dev2
dev.copy2pdf dev2
dev.cur dev
+dev.flush dev.flush
+dev.hold dev.flush
dev.interactive dev.interactive
dev.list dev
dev.new dev
@@ -51,6 +66,7 @@ embedFonts embedFonts
extendrange extendrange
frac plotmath
getGraphicsEvent getGraphicsEvent
+getGraphicsEventEnv getGraphicsEvent
graphics.off dev
gray gray
gray.colors gray.colors
@@ -65,6 +81,7 @@ Hershey Hershey
hsv hsv
inf plotmath
integral plotmath
+is.raster as.raster
italic plotmath
Japanese Japanese
jpeg png
@@ -87,6 +104,8 @@ png png
postscript postscript
postscriptFont grDevices-defunct
postscriptFonts postscriptFonts
+pretty.Date pretty.Date
+pretty.POSIXt pretty.Date
print.recordedplot recordplot
print.SavedPlots windows
ps.options ps.options
@@ -101,9 +120,12 @@ savePlot savePlot
scriptscriptstyle plotmath
scriptstyle plotmath
setEPS ps.options
+setGraphicsEventEnv getGraphicsEvent
+setGraphicsEventHandlers getGraphicsEvent
setPS ps.options
stayOnTop bringToTop
sup plotmath
+svg cairo
symbol plotmath
terrain.colors palettes
textstyle plotmath
diff --git a/win32/deps/library/grDevices/help/aliases.rds b/win32/deps/library/grDevices/help/aliases.rds
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index 0000000..c680af4
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new file mode 100644
index 0000000..aa8d8e6
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diff --git a/win32/deps/library/grDevices/help/grDevices.rdx b/win32/deps/library/grDevices/help/grDevices.rdx
new file mode 100644
index 0000000..d5374ae
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diff --git a/win32/deps/library/grDevices/help/paths.rds b/win32/deps/library/grDevices/help/paths.rds
new file mode 100644
index 0000000..c5697c5
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diff --git a/win32/deps/library/grDevices/html/00Index.html b/win32/deps/library/grDevices/html/00Index.html
new file mode 100644
index 0000000..9e810cc
--- /dev/null
+++ b/win32/deps/library/grDevices/html/00Index.html
@@ -0,0 +1,455 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: The R Graphics Devices and Support for Colours and Fonts</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> The R Graphics Devices and Support for Colours and Fonts
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘grDevices’ version 2.15.2</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<p align="center">
+<a href="# "> </a>
+<a href="#A">A</a>
+<a href="#B">B</a>
+<a href="#C">C</a>
+<a href="#D">D</a>
+<a href="#E">E</a>
+<a href="#F">F</a>
+<a href="#G">G</a>
+<a href="#H">H</a>
+<a href="#I">I</a>
+<a href="#J">J</a>
+<a href="#M">M</a>
+<a href="#N">N</a>
+<a href="#O">O</a>
+<a href="#P">P</a>
+<a href="#R">R</a>
+<a href="#S">S</a>
+<a href="#T">T</a>
+<a href="#U">U</a>
+<a href="#W">W</a>
+<a href="#X">X</a>
+<a href="#misc">misc</a>
+</p>
+
+<table width="100%">
+<tr><td width="25%"><a href="grDevices-package.html">grDevices-package</a></td>
+<td>The R Graphics Devices and Support for Colours and Fonts</td></tr>
+</table>
+
+<h2><a name="A">-- A --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="adjustcolor.html">adjustcolor</a></td>
+<td>Adjust Colors in One or More Directions Conveniently.</td></tr>
+<tr><td width="25%"><a href="as.graphicsAnnot.html">as.graphicsAnnot</a></td>
+<td>Coerce an Object for Graphics Annotation</td></tr>
+<tr><td width="25%"><a href="as.raster.html">as.raster</a></td>
+<td>Create a Raster Object</td></tr>
+<tr><td width="25%"><a href="as.raster.html">as.raster.array</a></td>
+<td>Create a Raster Object</td></tr>
+<tr><td width="25%"><a href="as.raster.html">as.raster.character</a></td>
+<td>Create a Raster Object</td></tr>
+<tr><td width="25%"><a href="as.raster.html">as.raster.logical</a></td>
+<td>Create a Raster Object</td></tr>
+<tr><td width="25%"><a href="as.raster.html">as.raster.matrix</a></td>
+<td>Create a Raster Object</td></tr>
+<tr><td width="25%"><a href="as.raster.html">as.raster.numeric</a></td>
+<td>Create a Raster Object</td></tr>
+<tr><td width="25%"><a href="plotmath.html">atop</a></td>
+<td>Mathematical Annotation in R</td></tr>
+<tr><td width="25%"><a href="axisTicks.html">axisTicks</a></td>
+<td>Compute Pretty Axis Tick Scales</td></tr>
+</table>
+
+<h2><a name="B">-- B --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="plotmath.html">bar</a></td>
+<td>Mathematical Annotation in R</td></tr>
+<tr><td width="25%"><a href="plotmath.html">bgroup</a></td>
+<td>Mathematical Annotation in R</td></tr>
+<tr><td width="25%"><a href="dev2bitmap.html">bitmap</a></td>
+<td>Graphics Device for Bitmap Files via Ghostscript</td></tr>
+<tr><td width="25%"><a href="densCols.html">blues9</a></td>
+<td>Colors for Smooth Density Plots</td></tr>
+<tr><td width="25%"><a href="png.html">bmp</a></td>
+<td>BMP, JPEG, PNG and TIFF graphics devices</td></tr>
+<tr><td width="25%"><a href="plotmath.html">bold</a></td>
+<td>Mathematical Annotation in R</td></tr>
+<tr><td width="25%"><a href="plotmath.html">bolditalic</a></td>
+<td>Mathematical Annotation in R</td></tr>
+<tr><td width="25%"><a href="boxplot.stats.html">boxplot.stats</a></td>
+<td>Box Plot Statistics</td></tr>
+<tr><td width="25%"><a href="bringToTop.html">bringToTop</a></td>
+<td>Assign Focus to a Window</td></tr>
+</table>
+
+<h2><a name="C">-- C --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="cairo.html">cairo_pdf</a></td>
+<td>Cairo-based SVG, PDF and PostScript Graphics Devices</td></tr>
+<tr><td width="25%"><a href="cairo.html">cairo_ps</a></td>
+<td>Cairo-based SVG, PDF and PostScript Graphics Devices</td></tr>
+<tr><td width="25%"><a href="check.options.html">check.options</a></td>
+<td>Set Options with Consistency Checks</td></tr>
+<tr><td width="25%"><a href="chull.html">chull</a></td>
+<td>Compute Convex Hull of a Set of Points</td></tr>
+<tr><td width="25%"><a href="Type1Font.html">CIDFont</a></td>
+<td>Type 1 and CID Fonts</td></tr>
+<tr><td width="25%"><a href="cm.html">cm</a></td>
+<td>Unit Transformation</td></tr>
+<tr><td width="25%"><a href="palettes.html">cm.colors</a></td>
+<td>Color Palettes</td></tr>
+<tr><td width="25%"><a href="col2rgb.html">col2rgb</a></td>
+<td>Color to RGB Conversion</td></tr>
+<tr><td width="25%"><a href="make.rgb.html">colorConverter</a></td>
+<td>Create colour spaces</td></tr>
+<tr><td width="25%"><a href="colorRamp.html">colorRamp</a></td>
+<td>Color interpolation</td></tr>
+<tr><td width="25%"><a href="colorRamp.html">colorRampPalette</a></td>
+<td>Color interpolation</td></tr>
+<tr><td width="25%"><a href="colors.html">colors</a></td>
+<td>Color Names</td></tr>
+<tr><td width="25%"><a href="convertColor.html">colorspaces</a></td>
+<td>Convert between Colour Spaces</td></tr>
+<tr><td width="25%"><a href="colors.html">colours</a></td>
+<td>Color Names</td></tr>
+<tr><td width="25%"><a href="contourLines.html">contourLines</a></td>
+<td>Calculate Contour Lines</td></tr>
+<tr><td width="25%"><a href="convertColor.html">convertColor</a></td>
+<td>Convert between Colour Spaces</td></tr>
+</table>
+
+<h2><a name="D">-- D --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="densCols.html">densCols</a></td>
+<td>Colors for Smooth Density Plots</td></tr>
+<tr><td width="25%"><a href="dev.capabilities.html">dev.capabilities</a></td>
+<td>Query Capabilities of the Current Graphics Device</td></tr>
+<tr><td width="25%"><a href="dev.capture.html">dev.capture</a></td>
+<td>Capture device output as a raster image</td></tr>
+<tr><td width="25%"><a href="dev2.html">dev.control</a></td>
+<td>Copy Graphics Between Multiple Devices</td></tr>
+<tr><td width="25%"><a href="dev2.html">dev.copy</a></td>
+<td>Copy Graphics Between Multiple Devices</td></tr>
+<tr><td width="25%"><a href="dev2.html">dev.copy2eps</a></td>
+<td>Copy Graphics Between Multiple Devices</td></tr>
+<tr><td width="25%"><a href="dev2.html">dev.copy2pdf</a></td>
+<td>Copy Graphics Between Multiple Devices</td></tr>
+<tr><td width="25%"><a href="dev.html">dev.cur</a></td>
+<td>Control Multiple Devices</td></tr>
+<tr><td width="25%"><a href="dev.flush.html">dev.flush</a></td>
+<td>Hold or Flush Output on an On-Screen Graphics Device.</td></tr>
+<tr><td width="25%"><a href="dev.flush.html">dev.hold</a></td>
+<td>Hold or Flush Output on an On-Screen Graphics Device.</td></tr>
+<tr><td width="25%"><a href="dev.interactive.html">dev.interactive</a></td>
+<td>Is the Current Graphics Device Interactive?</td></tr>
+<tr><td width="25%"><a href="dev.html">dev.list</a></td>
+<td>Control Multiple Devices</td></tr>
+<tr><td width="25%"><a href="dev.html">dev.new</a></td>
+<td>Control Multiple Devices</td></tr>
+<tr><td width="25%"><a href="dev.html">dev.next</a></td>
+<td>Control Multiple Devices</td></tr>
+<tr><td width="25%"><a href="dev.html">dev.off</a></td>
+<td>Control Multiple Devices</td></tr>
+<tr><td width="25%"><a href="dev.html">dev.prev</a></td>
+<td>Control Multiple Devices</td></tr>
+<tr><td width="25%"><a href="dev2.html">dev.print</a></td>
+<td>Copy Graphics Between Multiple Devices</td></tr>
+<tr><td width="25%"><a href="dev.html">dev.set</a></td>
+<td>Control Multiple Devices</td></tr>
+<tr><td width="25%"><a href="dev.size.html">dev.size</a></td>
+<td>Find Size of Device Surface</td></tr>
+<tr><td width="25%"><a href="dev2bitmap.html">dev2bitmap</a></td>
+<td>Graphics Device for Bitmap Files via Ghostscript</td></tr>
+<tr><td width="25%"><a href="devAskNewPage.html">devAskNewPage</a></td>
+<td>Prompt before New Page</td></tr>
+<tr><td width="25%"><a href="Devices.html">device</a></td>
+<td>List of Graphical Devices</td></tr>
+<tr><td width="25%"><a href="dev.interactive.html">deviceIsInteractive</a></td>
+<td>Is the Current Graphics Device Interactive?</td></tr>
+<tr><td width="25%"><a href="Devices.html">Devices</a></td>
+<td>List of Graphical Devices</td></tr>
+<tr><td width="25%"><a href="plotmath.html">displaystyle</a></td>
+<td>Mathematical Annotation in R</td></tr>
+<tr><td width="25%"><a href="plotmath.html">dot</a></td>
+<td>Mathematical Annotation in R</td></tr>
+</table>
+
+<h2><a name="E">-- E --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="embedFonts.html">embedFonts</a></td>
+<td>Embed Fonts in PostScript and PDF</td></tr>
+<tr><td width="25%"><a href="extendrange.html">extendrange</a></td>
+<td>Extend a Numerical Range by a Small Percentage</td></tr>
+</table>
+
+<h2><a name="F">-- F --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="plotmath.html">frac</a></td>
+<td>Mathematical Annotation in R</td></tr>
+</table>
+
+<h2><a name="G">-- G --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="getGraphicsEvent.html">getGraphicsEvent</a></td>
+<td>Wait for a mouse or keyboard event from a graphics window</td></tr>
+<tr><td width="25%"><a href="getGraphicsEvent.html">getGraphicsEventEnv</a></td>
+<td>Wait for a mouse or keyboard event from a graphics window</td></tr>
+<tr><td width="25%"><a href="dev.html">graphics.off</a></td>
+<td>Control Multiple Devices</td></tr>
+<tr><td width="25%"><a href="gray.html">gray</a></td>
+<td>Gray Level Specification</td></tr>
+<tr><td width="25%"><a href="gray.colors.html">gray.colors</a></td>
+<td>Gray Color Palette</td></tr>
+<tr><td width="25%"><a href="grDevices-package.html">grDevices</a></td>
+<td>The R Graphics Devices and Support for Colours and Fonts</td></tr>
+<tr><td width="25%"><a href="gray.html">grey</a></td>
+<td>Gray Level Specification</td></tr>
+<tr><td width="25%"><a href="gray.colors.html">grey.colors</a></td>
+<td>Gray Color Palette</td></tr>
+<tr><td width="25%"><a href="plotmath.html">group</a></td>
+<td>Mathematical Annotation in R</td></tr>
+</table>
+
+<h2><a name="H">-- H --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="plotmath.html">hat</a></td>
+<td>Mathematical Annotation in R</td></tr>
+<tr><td width="25%"><a href="hcl.html">hcl</a></td>
+<td>HCL Color Specification</td></tr>
+<tr><td width="25%"><a href="palettes.html">heat.colors</a></td>
+<td>Color Palettes</td></tr>
+<tr><td width="25%"><a href="Hershey.html">Hershey</a></td>
+<td>Hershey Vector Fonts in R</td></tr>
+<tr><td width="25%"><a href="hsv.html">hsv</a></td>
+<td>HSV Color Specification</td></tr>
+</table>
+
+<h2><a name="I">-- I --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="plotmath.html">inf</a></td>
+<td>Mathematical Annotation in R</td></tr>
+<tr><td width="25%"><a href="plotmath.html">integral</a></td>
+<td>Mathematical Annotation in R</td></tr>
+<tr><td width="25%"><a href="as.raster.html">is.raster</a></td>
+<td>Create a Raster Object</td></tr>
+<tr><td width="25%"><a href="plotmath.html">italic</a></td>
+<td>Mathematical Annotation in R</td></tr>
+</table>
+
+<h2><a name="J">-- J --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Japanese.html">Japanese</a></td>
+<td>Japanese characters in R</td></tr>
+<tr><td width="25%"><a href="png.html">jpeg</a></td>
+<td>BMP, JPEG, PNG and TIFF graphics devices</td></tr>
+</table>
+
+<h2><a name="M">-- M --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="make.rgb.html">make.rgb</a></td>
+<td>Create colour spaces</td></tr>
+<tr><td width="25%"><a href="msgWindow.html">msgWindow</a></td>
+<td>Manipulate a Window</td></tr>
+</table>
+
+<h2><a name="N">-- N --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="n2mfrow.html">n2mfrow</a></td>
+<td>Compute Default mfrow From Number of Plots</td></tr>
+<tr><td width="25%"><a href="nclass.html">nclass.FD</a></td>
+<td>Compute the Number of Classes for a Histogram</td></tr>
+<tr><td width="25%"><a href="nclass.html">nclass.scott</a></td>
+<td>Compute the Number of Classes for a Histogram</td></tr>
+<tr><td width="25%"><a href="nclass.html">nclass.Sturges</a></td>
+<td>Compute the Number of Classes for a Histogram</td></tr>
+</table>
+
+<h2><a name="O">-- O --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="plotmath.html">over</a></td>
+<td>Mathematical Annotation in R</td></tr>
+</table>
+
+<h2><a name="P">-- P --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="palette.html">palette</a></td>
+<td>Set or View the Graphics Palette</td></tr>
+<tr><td width="25%"><a href="pdf.html">pdf</a></td>
+<td>PDF Graphics Device</td></tr>
+<tr><td width="25%"><a href="pdf.options.html">pdf.options</a></td>
+<td>Auxiliary Function to Set/View Defaults for Arguments of pdf</td></tr>
+<tr><td width="25%"><a href="postscriptFonts.html">pdfFonts</a></td>
+<td>PostScript and PDF Font Families</td></tr>
+<tr><td width="25%"><a href="plotmath.html">phantom</a></td>
+<td>Mathematical Annotation in R</td></tr>
+<tr><td width="25%"><a href="pictex.html">pictex</a></td>
+<td>A PicTeX Graphics Driver</td></tr>
+<tr><td width="25%"><a href="plotmath.html">plain</a></td>
+<td>Mathematical Annotation in R</td></tr>
+<tr><td width="25%"><a href="plotmath.html">plotmath</a></td>
+<td>Mathematical Annotation in R</td></tr>
+<tr><td width="25%"><a href="png.html">png</a></td>
+<td>BMP, JPEG, PNG and TIFF graphics devices</td></tr>
+<tr><td width="25%"><a href="postscript.html">postscript</a></td>
+<td>PostScript Graphics</td></tr>
+<tr><td width="25%"><a href="postscriptFonts.html">postscriptFonts</a></td>
+<td>PostScript and PDF Font Families</td></tr>
+<tr><td width="25%"><a href="pretty.Date.html">pretty.Date</a></td>
+<td>Pretty Breakpoints for Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="pretty.Date.html">pretty.POSIXt</a></td>
+<td>Pretty Breakpoints for Date-Time Classes</td></tr>
+<tr><td width="25%"><a href="recordplot.html">print.recordedplot</a></td>
+<td>Record and Replay Plots</td></tr>
+<tr><td width="25%"><a href="windows.html">print.SavedPlots</a></td>
+<td>Windows Graphics Devices</td></tr>
+<tr><td width="25%"><a href="ps.options.html">ps.options</a></td>
+<td>Auxiliary Function to Set/View Defaults for Arguments of postscript</td></tr>
+</table>
+
+<h2><a name="R">-- R --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="palettes.html">rainbow</a></td>
+<td>Color Palettes</td></tr>
+<tr><td width="25%"><a href="recordGraphics.html">recordGraphics</a></td>
+<td>Record Graphics Operations</td></tr>
+<tr><td width="25%"><a href="recordplot.html">recordPlot</a></td>
+<td>Record and Replay Plots</td></tr>
+<tr><td width="25%"><a href="recordplot.html">replayPlot</a></td>
+<td>Record and Replay Plots</td></tr>
+<tr><td width="25%"><a href="rgb.html">rgb</a></td>
+<td>RGB Color Specification</td></tr>
+<tr><td width="25%"><a href="rgb2hsv.html">rgb2hsv</a></td>
+<td>RGB to HSV Conversion</td></tr>
+<tr><td width="25%"><a href="plotmath.html">ring</a></td>
+<td>Mathematical Annotation in R</td></tr>
+</table>
+
+<h2><a name="S">-- S --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="savePlot.html">savePlot</a></td>
+<td>Save Windows Plot to a File</td></tr>
+<tr><td width="25%"><a href="plotmath.html">scriptscriptstyle</a></td>
+<td>Mathematical Annotation in R</td></tr>
+<tr><td width="25%"><a href="plotmath.html">scriptstyle</a></td>
+<td>Mathematical Annotation in R</td></tr>
+<tr><td width="25%"><a href="ps.options.html">setEPS</a></td>
+<td>Auxiliary Function to Set/View Defaults for Arguments of postscript</td></tr>
+<tr><td width="25%"><a href="getGraphicsEvent.html">setGraphicsEventEnv</a></td>
+<td>Wait for a mouse or keyboard event from a graphics window</td></tr>
+<tr><td width="25%"><a href="getGraphicsEvent.html">setGraphicsEventHandlers</a></td>
+<td>Wait for a mouse or keyboard event from a graphics window</td></tr>
+<tr><td width="25%"><a href="ps.options.html">setPS</a></td>
+<td>Auxiliary Function to Set/View Defaults for Arguments of postscript</td></tr>
+<tr><td width="25%"><a href="bringToTop.html">stayOnTop</a></td>
+<td>Assign Focus to a Window</td></tr>
+<tr><td width="25%"><a href="plotmath.html">sup</a></td>
+<td>Mathematical Annotation in R</td></tr>
+<tr><td width="25%"><a href="cairo.html">svg</a></td>
+<td>Cairo-based SVG, PDF and PostScript Graphics Devices</td></tr>
+<tr><td width="25%"><a href="plotmath.html">symbol</a></td>
+<td>Mathematical Annotation in R</td></tr>
+</table>
+
+<h2><a name="T">-- T --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="palettes.html">terrain.colors</a></td>
+<td>Color Palettes</td></tr>
+<tr><td width="25%"><a href="plotmath.html">textstyle</a></td>
+<td>Mathematical Annotation in R</td></tr>
+<tr><td width="25%"><a href="png.html">tiff</a></td>
+<td>BMP, JPEG, PNG and TIFF graphics devices</td></tr>
+<tr><td width="25%"><a href="palettes.html">topo.colors</a></td>
+<td>Color Palettes</td></tr>
+<tr><td width="25%"><a href="trans3d.html">trans3d</a></td>
+<td>3D to 2D Transformation for Perspective Plots</td></tr>
+<tr><td width="25%"><a href="Type1Font.html">Type1Font</a></td>
+<td>Type 1 and CID Fonts</td></tr>
+</table>
+
+<h2><a name="U">-- U --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="plotmath.html">underline</a></td>
+<td>Mathematical Annotation in R</td></tr>
+</table>
+
+<h2><a name="W">-- W --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="plotmath.html">widehat</a></td>
+<td>Mathematical Annotation in R</td></tr>
+<tr><td width="25%"><a href="plotmath.html">widetilde</a></td>
+<td>Mathematical Annotation in R</td></tr>
+<tr><td width="25%"><a href="windows.html">win.graph</a></td>
+<td>Windows Graphics Devices</td></tr>
+<tr><td width="25%"><a href="windows.html">win.metafile</a></td>
+<td>Windows Graphics Devices</td></tr>
+<tr><td width="25%"><a href="windows.html">win.print</a></td>
+<td>Windows Graphics Devices</td></tr>
+<tr><td width="25%"><a href="windows.html">windows</a></td>
+<td>Windows Graphics Devices</td></tr>
+<tr><td width="25%"><a href="windows.options.html">windows.options</a></td>
+<td>Auxiliary Function to Set/View Defaults for Arguments of windows()</td></tr>
+<tr><td width="25%"><a href="windowsFonts.html">windowsFont</a></td>
+<td>Windows Fonts</td></tr>
+<tr><td width="25%"><a href="windowsFonts.html">windowsFonts</a></td>
+<td>Windows Fonts</td></tr>
+</table>
+
+<h2><a name="X">-- X --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="windows.html">X11</a></td>
+<td>Windows Graphics Devices</td></tr>
+<tr><td width="25%"><a href="windows.html">x11</a></td>
+<td>Windows Graphics Devices</td></tr>
+<tr><td width="25%"><a href="xfig.html">xfig</a></td>
+<td>XFig Graphics Device</td></tr>
+<tr><td width="25%"><a href="xy.coords.html">xy.coords</a></td>
+<td>Extracting Plotting Structures</td></tr>
+<tr><td width="25%"><a href="xyTable.html">xyTable</a></td>
+<td>Multiplicities of (x,y) Points, e.g., for a Sunflower Plot</td></tr>
+<tr><td width="25%"><a href="xyz.coords.html">xyz.coords</a></td>
+<td>Extracting Plotting Structures</td></tr>
+</table>
+
+<h2><a name="misc">-- misc --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="axisTicks.html">.axisPars</a></td>
+<td>Compute Pretty Axis Tick Scales</td></tr>
+<tr><td width="25%"><a href="postscript.html">.ps.prolog</a></td>
+<td>PostScript Graphics</td></tr>
+<tr><td width="25%"><a href="windows.html">[.SavedPlots</a></td>
+<td>Windows Graphics Devices</td></tr>
+</table>
+</body></html>
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diff --git a/win32/deps/library/grDevices/po/zh_CN/LC_MESSAGES/R-grDevices.mo b/win32/deps/library/grDevices/po/zh_CN/LC_MESSAGES/R-grDevices.mo
new file mode 100644
index 0000000..b1365b8
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diff --git a/win32/deps/library/grDevices/po/zh_CN/LC_MESSAGES/grDevices.mo b/win32/deps/library/grDevices/po/zh_CN/LC_MESSAGES/grDevices.mo
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diff --git a/win32/deps/library/grDevices/tests/ps-tests.R b/win32/deps/library/grDevices/tests/ps-tests.R
new file mode 100644
index 0000000..e504010
--- /dev/null
+++ b/win32/deps/library/grDevices/tests/ps-tests.R
@@ -0,0 +1,39 @@
+## tests of the fonts in the postscript() device.
+
+testit <- function(family, encoding="default")
+{
+ postscript("ps-tests.ps", height=7, width=7, family=family,
+ encoding=encoding)
+ plot(1:10, type="n")
+ text(5, 9, "Some text")
+ text(5, 8 , expression(italic("italic")))
+ text(5, 7 , expression(bold("bold")))
+ text(5, 6 , expression(bolditalic("bold & italic")))
+ text(8, 3, expression(paste(frac(1, sigma*sqrt(2*pi)), " ",
+ plain(e)^{frac(-(x-mu)^2, 2*sigma^2)})))
+ dev.off()
+}
+
+testit("Helvetica")
+testit("AvantGarde")
+testit("Bookman")
+testit("Courier")
+testit("Helvetica-Narrow")
+testit("NewCenturySchoolbook")
+testit("Palatino")
+testit("Times")
+
+testit("URWGothic")
+testit("URWBookman")
+testit("NimbusMon")
+testit("NimbusSan")
+testit("NimbusSanCond")
+testit("CenturySch")
+testit("URWPalladio")
+testit("NimbusRom")
+testit("URWHelvetica")
+testit("URWTimes")
+
+testit("ComputerModern", "TeXtext.enc")
+
+unlink("ps-tests.ps")
diff --git a/win32/deps/library/grDevices/tests/ps-tests.Rout.save b/win32/deps/library/grDevices/tests/ps-tests.Rout.save
new file mode 100644
index 0000000..105f699
--- /dev/null
+++ b/win32/deps/library/grDevices/tests/ps-tests.Rout.save
@@ -0,0 +1,95 @@
+
+R : Copyright 2005, The R Foundation for Statistical Computing
+Version 2.3.0 Under development (unstable) (2005-11-06 r36200)
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for a HTML browser interface to help.
+Type 'q()' to quit R.
+
+> ## tests of the fonts in the postscript() device.
+>
+> testit <- function(family, encoding="default")
++ {
++ postscript("ps-tests.ps", height=7, width=7, family=family,
++ encoding=encoding)
++ plot(1:10, type="n")
++ text(5, 9, "Some text")
++ text(5, 8 , expression(italic("italic")))
++ text(5, 7 , expression(bold("bold")))
++ text(5, 6 , expression(bolditalic("bold & italic")))
++ text(8, 3, expression(paste(frac(1, sigma*sqrt(2*pi)), " ",
++ plain(e)^{frac(-(x-mu)^2, 2*sigma^2)})))
++ dev.off()
++ }
+>
+> testit("Helvetica")
+null device
+ 1
+> testit("AvantGarde")
+null device
+ 1
+> testit("Bookman")
+null device
+ 1
+> testit("Courier")
+null device
+ 1
+> testit("Helvetica-Narrow")
+null device
+ 1
+> testit("NewCenturySchoolbook")
+null device
+ 1
+> testit("Palatino")
+null device
+ 1
+> testit("Times")
+null device
+ 1
+>
+> testit("URWGothic")
+null device
+ 1
+> testit("URWBookman")
+null device
+ 1
+> testit("NimbusMon")
+null device
+ 1
+> testit("NimbusSan")
+null device
+ 1
+> testit("NimbusSanCond")
+null device
+ 1
+> testit("CenturySch")
+null device
+ 1
+> testit("URWPalladio")
+null device
+ 1
+> testit("NimbusRom")
+null device
+ 1
+> testit("URWHelvetica")
+null device
+ 1
+> testit("URWTimes")
+null device
+ 1
+>
+> testit("ComputerModern", "TeXtext.enc")
+null device
+ 1
+>
+> unlink("ps-tests.ps")
+>
diff --git a/win32/deps/library/grDevices/tests/xfig-tests.R b/win32/deps/library/grDevices/tests/xfig-tests.R
new file mode 100644
index 0000000..798ccad
--- /dev/null
+++ b/win32/deps/library/grDevices/tests/xfig-tests.R
@@ -0,0 +1,84 @@
+## tests for the xfig device
+
+
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=TRUE)
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=FALSE)
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=TRUE)
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=FALSE)
+
+unlink("xfig-tests.fig")
+
+## tests for the xfig device
+
+
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=TRUE)
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=FALSE)
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=TRUE)
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=FALSE)
+
+unlink("xfig-tests.fig")
+
+## tests for the xfig device
+
+
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=TRUE)
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=FALSE)
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=TRUE)
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=FALSE)
+
+unlink("xfig-tests.fig")
+
+## tests for the xfig device
+
+
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=TRUE)
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=FALSE)
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=TRUE)
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=FALSE)
+
+unlink("xfig-tests.fig")
+
+## tests for the xfig device
+
+
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=TRUE)
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=FALSE)
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=TRUE)
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=FALSE)
+
+unlink("xfig-tests.fig")
+
+## tests for the xfig device
+
+
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=TRUE)
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=FALSE)
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=TRUE)
+
+xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=FALSE)
+
+unlink("xfig-tests.fig")
+
diff --git a/win32/deps/library/grDevices/tests/xfig-tests.Rout.save b/win32/deps/library/grDevices/tests/xfig-tests.Rout.save
new file mode 100644
index 0000000..91af2f6
--- /dev/null
+++ b/win32/deps/library/grDevices/tests/xfig-tests.Rout.save
@@ -0,0 +1,102 @@
+
+R version 2.9.0 Under development (unstable) (2009-01-21 r47661)
+Copyright (C) 2009 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> ## tests for the xfig device
+>
+>
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=TRUE)
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=FALSE)
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=TRUE)
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=FALSE)
+>
+> unlink("xfig-tests.fig")
+>
+> ## tests for the xfig device
+>
+>
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=TRUE)
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=FALSE)
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=TRUE)
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=FALSE)
+>
+> unlink("xfig-tests.fig")
+>
+> ## tests for the xfig device
+>
+>
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=TRUE)
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=FALSE)
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=TRUE)
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=FALSE)
+>
+> unlink("xfig-tests.fig")
+>
+> ## tests for the xfig device
+>
+>
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=TRUE)
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=FALSE)
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=TRUE)
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=FALSE)
+>
+> unlink("xfig-tests.fig")
+>
+> ## tests for the xfig device
+>
+>
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=TRUE)
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=FALSE)
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=TRUE)
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=FALSE)
+>
+> unlink("xfig-tests.fig")
+>
+> ## tests for the xfig device
+>
+>
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=TRUE)
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=TRUE,textspecial=FALSE)
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=TRUE)
+>
+> xfig("xfig-tests.fig",onefile=TRUE,defaultfont=FALSE,textspecial=FALSE)
+>
+> unlink("xfig-tests.fig")
+>
+>
diff --git a/win32/deps/library/graphics/DESCRIPTION b/win32/deps/library/graphics/DESCRIPTION
index c0f8ce0..19c169a 100644
--- a/win32/deps/library/graphics/DESCRIPTION
+++ b/win32/deps/library/graphics/DESCRIPTION
@@ -1,10 +1,10 @@
Package: graphics
-Version: 2.9.2
+Version: 2.15.2
Priority: base
Title: The R Graphics Package
-Author: R Development Core Team and contributors worldwide
+Author: R Core Team and contributors worldwide
Maintainer: R Core Team <R-core r-project org>
Description: R functions for base graphics
Imports: grDevices
-License: Part of R 2.9.2
-Built: R 2.9.2; ; 2009-08-24 12:44:02 UTC; windows
+License: Part of R 2.15.2
+Built: R 2.15.2; ; 2012-10-27 03:05:59 UTC; windows
diff --git a/win32/deps/library/graphics/INDEX b/win32/deps/library/graphics/INDEX
index bae46f9..bcc52dc 100644
--- a/win32/deps/library/graphics/INDEX
+++ b/win32/deps/library/graphics/INDEX
@@ -1,4 +1,4 @@
-Axis Generic function to add an Axis to a Plot
+Axis Generic Function to Add an Axis to a Plot
abline Add Straight Lines to a Plot
arrows Add Arrows to a Plot
assocplot Association Plots
@@ -16,7 +16,7 @@ clip Set Clipping Region
contour Display Contours
coplot Conditioning Plots
curve Draw Function Plots
-dotchart Cleveland Dot Plots
+dotchart Cleveland's Dot Plots
filled.contour Level (Contour) Plots
fourfoldplot Fourfold Plots
frame Create / Start a New Plot Frame
@@ -42,7 +42,7 @@ pie Pie Charts
plot Generic X-Y Plotting
plot.data.frame Plot Method for Data Frames
plot.default The Default Scatterplot Function
-plot.design Plot Univariate Effects of a 'Design' or Model
+plot.design Plot Univariate Effects of a Design or Model
plot.factor Plotting Factor Variables
plot.formula Formula Notation for Scatterplots
plot.histogram Plot Histograms
@@ -51,6 +51,8 @@ plot.window Set up World Coordinates for Graphics Window
plot.xy Basic Internal Plot Function
points Add Points to a Plot
polygon Polygon Drawing
+polypath Path Drawing
+rasterImage Draw One or More Raster Images
rect Draw One or More Rectangles
rug Add a Rug to a Plot
screen Creating and Controlling Multiple Screens on a
@@ -66,7 +68,7 @@ strwidth Plotting Dimensions of Character Strings and
Math Expressions
sunflowerplot Produce a Sunflower Scatter Plot
symbols Draw Symbols (Circles, Squares, Stars,
- Thermometers, Boxplots) on a Plot
+ Thermometers, Boxplots)
text Add Text to a Plot
title Plot Annotation
xinch Graphical Units
diff --git a/win32/deps/library/graphics/Meta/Rd.rds b/win32/deps/library/graphics/Meta/Rd.rds
index 6997ecd..564f9cc 100644
Binary files a/win32/deps/library/graphics/Meta/Rd.rds and b/win32/deps/library/graphics/Meta/Rd.rds differ
diff --git a/win32/deps/library/graphics/Meta/demo.rds b/win32/deps/library/graphics/Meta/demo.rds
index afe1d71..16c136b 100644
Binary files a/win32/deps/library/graphics/Meta/demo.rds and b/win32/deps/library/graphics/Meta/demo.rds differ
diff --git a/win32/deps/library/graphics/Meta/hsearch.rds b/win32/deps/library/graphics/Meta/hsearch.rds
index 700f64a..0034a0e 100644
Binary files a/win32/deps/library/graphics/Meta/hsearch.rds and b/win32/deps/library/graphics/Meta/hsearch.rds differ
diff --git a/win32/deps/library/graphics/Meta/links.rds b/win32/deps/library/graphics/Meta/links.rds
new file mode 100644
index 0000000..dc8a3a6
Binary files /dev/null and b/win32/deps/library/graphics/Meta/links.rds differ
diff --git a/win32/deps/library/graphics/Meta/nsInfo.rds b/win32/deps/library/graphics/Meta/nsInfo.rds
index 4cf71e5..20fa967 100644
Binary files a/win32/deps/library/graphics/Meta/nsInfo.rds and b/win32/deps/library/graphics/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/graphics/Meta/package.rds b/win32/deps/library/graphics/Meta/package.rds
index d89fbe9..d3f7bc6 100644
Binary files a/win32/deps/library/graphics/Meta/package.rds and b/win32/deps/library/graphics/Meta/package.rds differ
diff --git a/win32/deps/library/graphics/NAMESPACE b/win32/deps/library/graphics/NAMESPACE
index 54f7343..e5b30f1 100644
--- a/win32/deps/library/graphics/NAMESPACE
+++ b/win32/deps/library/graphics/NAMESPACE
@@ -8,10 +8,11 @@ export(abline, arrows, assocplot, axTicks, Axis, axis, axis.Date,
image, layout, layout.show, lcm, legend, lines, lines.default,
locator, matlines, matplot, matpoints, mosaicplot, mtext,
pairs, panel.smooth, par, persp, pie, plot, plot.design,
- plot.new, plot.window, plot.xy, points, polygon, rect, rug,
- screen, segments, smoothScatter, spineplot, split.screen, stars, stem,
- strheight, stripchart, strwidth, sunflowerplot, symbols, text,
- title, xinch, xspline, xyinch, yinch)
+ plot.function, plot.new, plot.window, plot.xy, points, polygon,
+ polypath, rasterImage, rect, rug, screen, segments,
+ smoothScatter, spineplot, split.screen, stars, stem, strheight,
+ stripchart, strwidth, sunflowerplot, symbols, text, title,
+ xinch, xspline, xyinch, yinch, .filled.contour)
# leave most of the default methods visible as people seem to call them.
export(barplot.default, boxplot.default, boxplot.matrix,
@@ -23,8 +24,8 @@ export(piechart)
S3method(Axis, default)
S3method(Axis, Date)
-S3method(Axis, POSIXct)
-S3method(Axis, POSIXlt)
+S3method(Axis, POSIXt)
+S3method(Axis, table)
S3method(barplot, default)
S3method(boxplot, default)
S3method(boxplot, formula)
@@ -39,24 +40,27 @@ S3method(image, default)
S3method(lines, default)
S3method(lines, formula)
S3method(lines, histogram)
+S3method(lines, table)
S3method(mosaicplot, default)
S3method(mosaicplot, formula)
S3method(pairs, default)
S3method(pairs, formula)
S3method(persp, default)
S3method(plot, data.frame)
-S3method(plot, Date)
S3method(plot, default)
S3method(plot, factor)
S3method(plot, formula)
+S3method(plot, "function")
S3method(plot, histogram)
-S3method(plot, POSIXct)
-S3method(plot, POSIXlt)
S3method(plot, table)
S3method(points, default)
S3method(points, formula)
+S3method(points, table)
S3method(spineplot, default)
S3method(spineplot, formula)
S3method(stripchart, default)
S3method(stripchart, formula)
+S3method(sunflowerplot, default)
+S3method(sunflowerplot, formula)
S3method(text, default)
+S3method(text, formula)
diff --git a/win32/deps/library/graphics/R/graphics b/win32/deps/library/graphics/R/graphics
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/graphics/R/graphics
+++ b/win32/deps/library/graphics/R/graphics
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/graphics/R/graphics.rdb b/win32/deps/library/graphics/R/graphics.rdb
index c62aa12..9c68f1c 100644
Binary files a/win32/deps/library/graphics/R/graphics.rdb and b/win32/deps/library/graphics/R/graphics.rdb differ
diff --git a/win32/deps/library/graphics/R/graphics.rdx b/win32/deps/library/graphics/R/graphics.rdx
index 5fdbbe9..f1d415c 100644
Binary files a/win32/deps/library/graphics/R/graphics.rdx and b/win32/deps/library/graphics/R/graphics.rdx differ
diff --git a/win32/deps/library/graphics/demo/Hershey.R b/win32/deps/library/graphics/demo/Hershey.R
index 7abf001..4785069 100644
--- a/win32/deps/library/graphics/demo/Hershey.R
+++ b/win32/deps/library/graphics/demo/Hershey.R
@@ -1,3 +1,5 @@
+# Copyright (C) 2003-2009 The R Core Team
+
#### --- Hershey Vector Fonts ---
require(grDevices); require(graphics)
diff --git a/win32/deps/library/graphics/demo/Japanese.R b/win32/deps/library/graphics/demo/Japanese.R
index 9ff591e..8cbfc4c 100644
--- a/win32/deps/library/graphics/demo/Japanese.R
+++ b/win32/deps/library/graphics/demo/Japanese.R
@@ -1,3 +1,5 @@
+# Copyright (C) 2003-2009 The R Core Team
+
require(grDevices); require(graphics)
## --- Japanese characters in the Hershey Vector Fonts
diff --git a/win32/deps/library/graphics/demo/graphics.R b/win32/deps/library/graphics/demo/graphics.R
index 612e173..009a8ac 100644
--- a/win32/deps/library/graphics/demo/graphics.R
+++ b/win32/deps/library/graphics/demo/graphics.R
@@ -1,3 +1,5 @@
+# Copyright (C) 1997-2009 The R Core Team
+
require(datasets)
require(grDevices); require(graphics)
diff --git a/win32/deps/library/graphics/demo/image.R b/win32/deps/library/graphics/demo/image.R
index dc1aadd..4b23bd9 100644
--- a/win32/deps/library/graphics/demo/image.R
+++ b/win32/deps/library/graphics/demo/image.R
@@ -1,3 +1,5 @@
+# Copyright (C) 1997-2009 The R Core Team
+
require(datasets)
require(grDevices); require(graphics)
diff --git a/win32/deps/library/graphics/demo/persp.R b/win32/deps/library/graphics/demo/persp.R
index 5db28cb..0c7295e 100644
--- a/win32/deps/library/graphics/demo/persp.R
+++ b/win32/deps/library/graphics/demo/persp.R
@@ -7,7 +7,7 @@ require(grDevices); require(graphics)
## (1) The Obligatory Mathematical surface.
## Rotated sinc function.
-x <- seq(-10, 10, length = 50)
+x <- seq(-10, 10, length.out = 50)
y <- x
rotsinc <- function(x,y)
{
@@ -49,7 +49,7 @@ z <- rbind(z0, cbind(z0, z, z0), z0)
x <- c(min(x) - 1e-10, x, max(x) + 1e-10)
y <- c(min(y) - 1e-10, y, max(y) + 1e-10)
-fill <- matrix("green3", nr = nrow(z)-1, nc = ncol(z)-1)
+fill <- matrix("green3", nrow = nrow(z)-1, ncol = ncol(z)-1)
fill[ , i2 <- c(1,ncol(fill))] <- "gray"
fill[i1 <- c(1,nrow(fill)) , ] <- "gray"
@@ -75,7 +75,8 @@ fcol <- fill
zi <- volcano[ -1,-1] + volcano[ -1,-61] +
volcano[-87,-1] + volcano[-87,-61] ## / 4
fcol[-i1,-i2] <-
- terrain.colors(20)[cut(zi, stats::quantile(zi, seq(0,1, len = 21)),
+ terrain.colors(20)[cut(zi,
+ stats::quantile(zi, seq(0,1, length.out = 21)),
include.lowest = TRUE)]
persp(x, y, 2*z, theta = 110, phi = 40, col = fcol, scale = FALSE,
ltheta = -120, shade = 0.4, border = NA, box = FALSE)
diff --git a/win32/deps/library/graphics/demo/plotmath.R b/win32/deps/library/graphics/demo/plotmath.R
index a758667..b1be384 100644
--- a/win32/deps/library/graphics/demo/plotmath.R
+++ b/win32/deps/library/graphics/demo/plotmath.R
@@ -1,3 +1,5 @@
+# Copyright (C) 2002-2009 The R Core Team
+
require(datasets)
require(grDevices); require(graphics)
diff --git a/win32/deps/library/graphics/help/AnIndex b/win32/deps/library/graphics/help/AnIndex
index 2619489..b699f24 100644
--- a/win32/deps/library/graphics/help/AnIndex
+++ b/win32/deps/library/graphics/help/AnIndex
@@ -1,4 +1,5 @@
graphics-package graphics-package
+.filled.contour filled.contour
.Pars par
abline abline
arrows arrows
@@ -33,6 +34,8 @@ erase.screen screen
filled.contour filled.contour
fourfoldplot fourfoldplot
frame frame
+graphical parameter par
+graphical parameters par
graphics graphics-package
graphics-defunct graphics-defunct
grconvertX convertXY
@@ -52,8 +55,9 @@ lcm layout
legend legend
lines lines
lines.default lines
-lines.formula plotformula
+lines.formula plot.formula
lines.histogram plothistogram
+lines.table plot.table
locator locator
matlines matplot
matplot matplot
@@ -74,28 +78,28 @@ pie pie
piechart graphics-defunct
plot plot
plot.data.frame plot.dataframe
-plot.Date axis.POSIXct
-plot.default plotdefault
+plot.default plot.default
plot.design plot.design
-plot.factor plotfactor
-plot.formula plotformula
+plot.factor plot.factor
+plot.formula plot.formula
plot.function curve
plot.histogram plothistogram
plot.new frame
-plot.POSIXct axis.POSIXct
-plot.POSIXlt axis.POSIXct
plot.table plot.table
plot.window plot.window
plot.xy plot.xy
points points
points.default points
-points.formula plotformula
+points.formula plot.formula
+points.table plot.table
polygon polygon
+polypath polypath
+rasterImage rasterImage
rect rect
rug rug
screen screen
segments segments
-smoothScatter smoothscatter
+smoothScatter smoothScatter
spineplot spineplot
spineplot.default spineplot
spineplot.formula spineplot
@@ -109,9 +113,12 @@ stripchart.formula stripchart
stripplot graphics-defunct
strwidth strwidth
sunflowerplot sunflowerplot
+sunflowerplot.default sunflowerplot
+sunflowerplot.formula sunflowerplot
symbols symbols
text text
text.default text
+text.formula plot.formula
title title
xinch units
xlim plot.window
diff --git a/win32/deps/library/graphics/help/aliases.rds b/win32/deps/library/graphics/help/aliases.rds
new file mode 100644
index 0000000..53baa5f
Binary files /dev/null and b/win32/deps/library/graphics/help/aliases.rds differ
diff --git a/win32/deps/library/graphics/help/figures/mai.pdf b/win32/deps/library/graphics/help/figures/mai.pdf
new file mode 100644
index 0000000..eccb58a
Binary files /dev/null and b/win32/deps/library/graphics/help/figures/mai.pdf differ
diff --git a/win32/deps/library/graphics/help/figures/mai.png b/win32/deps/library/graphics/help/figures/mai.png
new file mode 100644
index 0000000..c0cbb9a
Binary files /dev/null and b/win32/deps/library/graphics/help/figures/mai.png differ
diff --git a/win32/deps/library/graphics/help/figures/oma.pdf b/win32/deps/library/graphics/help/figures/oma.pdf
new file mode 100644
index 0000000..6ad1d18
Binary files /dev/null and b/win32/deps/library/graphics/help/figures/oma.pdf differ
diff --git a/win32/deps/library/graphics/help/figures/oma.png b/win32/deps/library/graphics/help/figures/oma.png
new file mode 100644
index 0000000..f212cec
Binary files /dev/null and b/win32/deps/library/graphics/help/figures/oma.png differ
diff --git a/win32/deps/library/graphics/help/figures/pch.pdf b/win32/deps/library/graphics/help/figures/pch.pdf
new file mode 100644
index 0000000..ccbb92b
Binary files /dev/null and b/win32/deps/library/graphics/help/figures/pch.pdf differ
diff --git a/win32/deps/library/graphics/help/figures/pch.png b/win32/deps/library/graphics/help/figures/pch.png
new file mode 100644
index 0000000..9706e86
Binary files /dev/null and b/win32/deps/library/graphics/help/figures/pch.png differ
diff --git a/win32/deps/library/graphics/help/figures/pch.svg b/win32/deps/library/graphics/help/figures/pch.svg
new file mode 100644
index 0000000..5df8da5
--- /dev/null
+++ b/win32/deps/library/graphics/help/figures/pch.svg
@@ -0,0 +1,185 @@
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+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: The R Graphics Package</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> The R Graphics Package
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘graphics’ version 2.15.2</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+<li><a href="../demo">Code demos</a>. Use <a href="../../utils/help/demo">demo()</a> to run them.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<table width="100%">
+<tr><td width="25%"><a href="graphics-package.html">graphics-package</a></td>
+<td>The R Graphics Package</td></tr>
+<tr><td width="25%"><a href="filled.contour.html">.filled.contour</a></td>
+<td>Level (Contour) Plots</td></tr>
+<tr><td width="25%"><a href="par.html">.Pars</a></td>
+<td>Set or Query Graphical Parameters</td></tr>
+<tr><td width="25%"><a href="abline.html">abline</a></td>
+<td>Add Straight Lines to a Plot</td></tr>
+<tr><td width="25%"><a href="arrows.html">arrows</a></td>
+<td>Add Arrows to a Plot</td></tr>
+<tr><td width="25%"><a href="plot.window.html">asp</a></td>
+<td>Set up World Coordinates for Graphics Window</td></tr>
+<tr><td width="25%"><a href="assocplot.html">assocplot</a></td>
+<td>Association Plots</td></tr>
+<tr><td width="25%"><a href="zAxis.html">Axis</a></td>
+<td>Generic Function to Add an Axis to a Plot</td></tr>
+<tr><td width="25%"><a href="axis.html">axis</a></td>
+<td>Add an Axis to a Plot</td></tr>
+<tr><td width="25%"><a href="axis.POSIXct.html">axis.POSIXct</a></td>
+<td>Date and Date-time Plotting Functions</td></tr>
+<tr><td width="25%"><a href="axTicks.html">axTicks</a></td>
+<td>Compute Axis Tickmark Locations</td></tr>
+<tr><td width="25%"><a href="barplot.html">barplot</a></td>
+<td>Bar Plots</td></tr>
+<tr><td width="25%"><a href="box.html">box</a></td>
+<td>Draw a Box around a Plot</td></tr>
+<tr><td width="25%"><a href="boxplot.html">boxplot</a></td>
+<td>Box Plots</td></tr>
+<tr><td width="25%"><a href="boxplot.matrix.html">boxplot.matrix</a></td>
+<td>Draw a Boxplot for each Column (Row) of a Matrix</td></tr>
+<tr><td width="25%"><a href="bxp.html">bxp</a></td>
+<td>Draw Box Plots from Summaries</td></tr>
+<tr><td width="25%"><a href="cdplot.html">cdplot</a></td>
+<td>Conditional Density Plots</td></tr>
+<tr><td width="25%"><a href="clip.html">clip</a></td>
+<td>Set Clipping Region</td></tr>
+<tr><td width="25%"><a href="screen.html">close.screen</a></td>
+<td>Creating and Controlling Multiple Screens on a Single Device</td></tr>
+<tr><td width="25%"><a href="coplot.html">co.intervals</a></td>
+<td>Conditioning Plots</td></tr>
+<tr><td width="25%"><a href="contour.html">contour</a></td>
+<td>Display Contours</td></tr>
+<tr><td width="25%"><a href="coplot.html">coplot</a></td>
+<td>Conditioning Plots</td></tr>
+<tr><td width="25%"><a href="curve.html">curve</a></td>
+<td>Draw Function Plots</td></tr>
+<tr><td width="25%"><a href="dotchart.html">dotchart</a></td>
+<td>Cleveland's Dot Plots</td></tr>
+<tr><td width="25%"><a href="screen.html">erase.screen</a></td>
+<td>Creating and Controlling Multiple Screens on a Single Device</td></tr>
+<tr><td width="25%"><a href="filled.contour.html">filled.contour</a></td>
+<td>Level (Contour) Plots</td></tr>
+<tr><td width="25%"><a href="fourfoldplot.html">fourfoldplot</a></td>
+<td>Fourfold Plots</td></tr>
+<tr><td width="25%"><a href="frame.html">frame</a></td>
+<td>Create / Start a New Plot Frame</td></tr>
+<tr><td width="25%"><a href="par.html">graphical parameter</a></td>
+<td>Set or Query Graphical Parameters</td></tr>
+<tr><td width="25%"><a href="par.html">graphical parameters</a></td>
+<td>Set or Query Graphical Parameters</td></tr>
+<tr><td width="25%"><a href="graphics-package.html">graphics</a></td>
+<td>The R Graphics Package</td></tr>
+<tr><td width="25%"><a href="convertXY.html">grconvertX</a></td>
+<td>Convert between Graphics Coordinate Systems</td></tr>
+<tr><td width="25%"><a href="convertXY.html">grconvertY</a></td>
+<td>Convert between Graphics Coordinate Systems</td></tr>
+<tr><td width="25%"><a href="grid.html">grid</a></td>
+<td>Add Grid to a Plot</td></tr>
+<tr><td width="25%"><a href="hist.html">hist</a></td>
+<td>Histograms</td></tr>
+<tr><td width="25%"><a href="hist.POSIXt.html">hist.POSIXt</a></td>
+<td>Histogram of a Date or Date-Time Object</td></tr>
+<tr><td width="25%"><a href="identify.html">identify</a></td>
+<td>Identify Points in a Scatter Plot</td></tr>
+<tr><td width="25%"><a href="image.html">image</a></td>
+<td>Display a Color Image</td></tr>
+<tr><td width="25%"><a href="layout.html">layout</a></td>
+<td>Specifying Complex Plot Arrangements</td></tr>
+<tr><td width="25%"><a href="layout.html">lcm</a></td>
+<td>Specifying Complex Plot Arrangements</td></tr>
+<tr><td width="25%"><a href="legend.html">legend</a></td>
+<td>Add Legends to Plots</td></tr>
+<tr><td width="25%"><a href="lines.html">lines</a></td>
+<td>Add Connected Line Segments to a Plot</td></tr>
+<tr><td width="25%"><a href="plot.formula.html">lines.formula</a></td>
+<td>Formula Notation for Scatterplots</td></tr>
+<tr><td width="25%"><a href="plothistogram.html">lines.histogram</a></td>
+<td>Plot Histograms</td></tr>
+<tr><td width="25%"><a href="plot.table.html">lines.table</a></td>
+<td>Plot Methods for 'table' Objects</td></tr>
+<tr><td width="25%"><a href="locator.html">locator</a></td>
+<td>Graphical Input</td></tr>
+<tr><td width="25%"><a href="matplot.html">matlines</a></td>
+<td>Plot Columns of Matrices</td></tr>
+<tr><td width="25%"><a href="matplot.html">matplot</a></td>
+<td>Plot Columns of Matrices</td></tr>
+<tr><td width="25%"><a href="matplot.html">matpoints</a></td>
+<td>Plot Columns of Matrices</td></tr>
+<tr><td width="25%"><a href="mosaicplot.html">mosaicplot</a></td>
+<td>Mosaic Plots</td></tr>
+<tr><td width="25%"><a href="mtext.html">mtext</a></td>
+<td>Write Text into the Margins of a Plot</td></tr>
+<tr><td width="25%"><a href="pairs.html">pairs</a></td>
+<td>Scatterplot Matrices</td></tr>
+<tr><td width="25%"><a href="panel.smooth.html">panel.smooth</a></td>
+<td>Simple Panel Plot</td></tr>
+<tr><td width="25%"><a href="par.html">par</a></td>
+<td>Set or Query Graphical Parameters</td></tr>
+<tr><td width="25%"><a href="points.html">pch</a></td>
+<td>Add Points to a Plot</td></tr>
+<tr><td width="25%"><a href="persp.html">persp</a></td>
+<td>Perspective Plots</td></tr>
+<tr><td width="25%"><a href="pie.html">pie</a></td>
+<td>Pie Charts</td></tr>
+<tr><td width="25%"><a href="plot.html">plot</a></td>
+<td>Generic X-Y Plotting</td></tr>
+<tr><td width="25%"><a href="plot.dataframe.html">plot.data.frame</a></td>
+<td>Plot Method for Data Frames</td></tr>
+<tr><td width="25%"><a href="plot.default.html">plot.default</a></td>
+<td>The Default Scatterplot Function</td></tr>
+<tr><td width="25%"><a href="plot.design.html">plot.design</a></td>
+<td>Plot Univariate Effects of a Design or Model</td></tr>
+<tr><td width="25%"><a href="plot.factor.html">plot.factor</a></td>
+<td>Plotting Factor Variables</td></tr>
+<tr><td width="25%"><a href="plot.formula.html">plot.formula</a></td>
+<td>Formula Notation for Scatterplots</td></tr>
+<tr><td width="25%"><a href="curve.html">plot.function</a></td>
+<td>Draw Function Plots</td></tr>
+<tr><td width="25%"><a href="plothistogram.html">plot.histogram</a></td>
+<td>Plot Histograms</td></tr>
+<tr><td width="25%"><a href="frame.html">plot.new</a></td>
+<td>Create / Start a New Plot Frame</td></tr>
+<tr><td width="25%"><a href="plot.table.html">plot.table</a></td>
+<td>Plot Methods for 'table' Objects</td></tr>
+<tr><td width="25%"><a href="plot.window.html">plot.window</a></td>
+<td>Set up World Coordinates for Graphics Window</td></tr>
+<tr><td width="25%"><a href="plot.xy.html">plot.xy</a></td>
+<td>Basic Internal Plot Function</td></tr>
+<tr><td width="25%"><a href="points.html">points</a></td>
+<td>Add Points to a Plot</td></tr>
+<tr><td width="25%"><a href="plot.formula.html">points.formula</a></td>
+<td>Formula Notation for Scatterplots</td></tr>
+<tr><td width="25%"><a href="plot.table.html">points.table</a></td>
+<td>Plot Methods for 'table' Objects</td></tr>
+<tr><td width="25%"><a href="polygon.html">polygon</a></td>
+<td>Polygon Drawing</td></tr>
+<tr><td width="25%"><a href="polypath.html">polypath</a></td>
+<td>Path Drawing</td></tr>
+<tr><td width="25%"><a href="rasterImage.html">rasterImage</a></td>
+<td>Draw One or More Raster Images</td></tr>
+<tr><td width="25%"><a href="rect.html">rect</a></td>
+<td>Draw One or More Rectangles</td></tr>
+<tr><td width="25%"><a href="rug.html">rug</a></td>
+<td>Add a Rug to a Plot</td></tr>
+<tr><td width="25%"><a href="screen.html">screen</a></td>
+<td>Creating and Controlling Multiple Screens on a Single Device</td></tr>
+<tr><td width="25%"><a href="segments.html">segments</a></td>
+<td>Add Line Segments to a Plot</td></tr>
+<tr><td width="25%"><a href="smoothScatter.html">smoothScatter</a></td>
+<td>Scatterplots with Smoothed Densities Color Representation</td></tr>
+<tr><td width="25%"><a href="spineplot.html">spineplot</a></td>
+<td>Spine Plots and Spinograms</td></tr>
+<tr><td width="25%"><a href="screen.html">split.screen</a></td>
+<td>Creating and Controlling Multiple Screens on a Single Device</td></tr>
+<tr><td width="25%"><a href="stars.html">stars</a></td>
+<td>Star (Spider/Radar) Plots and Segment Diagrams</td></tr>
+<tr><td width="25%"><a href="stem.html">stem</a></td>
+<td>Stem-and-Leaf Plots</td></tr>
+<tr><td width="25%"><a href="strwidth.html">strheight</a></td>
+<td>Plotting Dimensions of Character Strings and Math Expressions</td></tr>
+<tr><td width="25%"><a href="stripchart.html">stripchart</a></td>
+<td>1-D Scatter Plots</td></tr>
+<tr><td width="25%"><a href="strwidth.html">strwidth</a></td>
+<td>Plotting Dimensions of Character Strings and Math Expressions</td></tr>
+<tr><td width="25%"><a href="sunflowerplot.html">sunflowerplot</a></td>
+<td>Produce a Sunflower Scatter Plot</td></tr>
+<tr><td width="25%"><a href="symbols.html">symbols</a></td>
+<td>Draw Symbols (Circles, Squares, Stars, Thermometers, Boxplots)</td></tr>
+<tr><td width="25%"><a href="text.html">text</a></td>
+<td>Add Text to a Plot</td></tr>
+<tr><td width="25%"><a href="plot.formula.html">text.formula</a></td>
+<td>Formula Notation for Scatterplots</td></tr>
+<tr><td width="25%"><a href="title.html">title</a></td>
+<td>Plot Annotation</td></tr>
+<tr><td width="25%"><a href="units.html">xinch</a></td>
+<td>Graphical Units</td></tr>
+<tr><td width="25%"><a href="plot.window.html">xlim</a></td>
+<td>Set up World Coordinates for Graphics Window</td></tr>
+<tr><td width="25%"><a href="xspline.html">xspline</a></td>
+<td>Draw an X-spline</td></tr>
+<tr><td width="25%"><a href="units.html">xyinch</a></td>
+<td>Graphical Units</td></tr>
+<tr><td width="25%"><a href="units.html">yinch</a></td>
+<td>Graphical Units</td></tr>
+<tr><td width="25%"><a href="plot.window.html">ylim</a></td>
+<td>Set up World Coordinates for Graphics Window</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/graphics/html/R.css b/win32/deps/library/graphics/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/graphics/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/graphics/po/da/LC_MESSAGES/R-graphics.mo b/win32/deps/library/graphics/po/da/LC_MESSAGES/R-graphics.mo
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diff --git a/win32/deps/library/graphics/po/ja/LC_MESSAGES/R-graphics.mo b/win32/deps/library/graphics/po/ja/LC_MESSAGES/R-graphics.mo
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diff --git a/win32/deps/library/graphics/po/pl/LC_MESSAGES/R-graphics.mo b/win32/deps/library/graphics/po/pl/LC_MESSAGES/R-graphics.mo
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diff --git a/win32/deps/library/graphics/po/pt_BR/LC_MESSAGES/R-graphics.mo b/win32/deps/library/graphics/po/pt_BR/LC_MESSAGES/R-graphics.mo
new file mode 100644
index 0000000..d30c05f
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diff --git a/win32/deps/library/graphics/po/ru/LC_MESSAGES/R-graphics.mo b/win32/deps/library/graphics/po/ru/LC_MESSAGES/R-graphics.mo
new file mode 100644
index 0000000..936d7d5
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diff --git a/win32/deps/library/graphics/po/zh_CN/LC_MESSAGES/R-graphics.mo b/win32/deps/library/graphics/po/zh_CN/LC_MESSAGES/R-graphics.mo
new file mode 100644
index 0000000..b1f0db2
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diff --git a/win32/deps/library/grid/DESCRIPTION b/win32/deps/library/grid/DESCRIPTION
index 72f995e..ffd5dbc 100644
--- a/win32/deps/library/grid/DESCRIPTION
+++ b/win32/deps/library/grid/DESCRIPTION
@@ -1,12 +1,12 @@
Package: grid
-Version: 2.9.2
+Version: 2.15.2
Priority: base
Title: The Grid Graphics Package
Author: Paul Murrell <paul stat auckland ac nz>
Maintainer: R Core Team <R-core r-project org>
Description: A rewrite of the graphics layout capabilities, plus some
- support for interaction
+ support for interaction
Imports: grDevices
Suggests: lattice
-License: Part of R 2.9.2
-Built: R 2.9.2; i386-pc-mingw32; 2009-08-24 12:45:46 UTC; windows
+License: Part of R 2.15.2
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:07:42 UTC; windows
diff --git a/win32/deps/library/grid/INDEX b/win32/deps/library/grid/INDEX
index 892afc7..1bcc664 100644
--- a/win32/deps/library/grid/INDEX
+++ b/win32/deps/library/grid/INDEX
@@ -1,6 +1,7 @@
Grid Grid Graphics
absolute.size Absolute Size of a Grob
arrow Describe arrows to add to a line.
+calcStringMetric Calculate Metric Information for Text
convertNative Convert a Unit Object to Native units
current.viewport Get the Current Grid Viewport (Tree)
dataViewport Create a Viewport with Scales based on Data
@@ -11,8 +12,11 @@ gPath Concatenate Grob Names
getNames List the names of grobs on the display list
gpar Handling Grid Graphical Parameters
grid-package The Grid Graphics Package
+grid.DLapply Modify the Grid Display List
grid.add Add a Grid Graphical Object
grid.arrows Draw Arrows
+grid.bezier Draw a Bezier Curve
+grid.cap Capture a raster image
grid.circle Draw a Circle
grid.clip Set the Clipping Region
grid.collection Create a Coherent Group of Grid Graphical
@@ -25,6 +29,7 @@ grid.display.list Control the Grid Display List
grid.draw Draw a grid grob
grid.edit Edit the Description of a Grid Graphical Object
grid.frame Create a Frame for Packing Objects
+grid.function Draw a curve representing a function
grid.get Get a Grid Graphical Object
grid.grab Grab the current grid output
grid.grill Draw a Grill
@@ -37,12 +42,14 @@ grid.move.to Move or Draw to a Specified Position
grid.newpage Move to a New Page on a Grid Device
grid.null Null Graphical Object
grid.pack Pack an Object within a Frame
+grid.path Draw a Path
grid.place Place an Object within a Frame
grid.plot.and.legend A Simple Plot and Legend Demo
grid.points Draw Data Symbols
grid.polygon Draw a Polygon
grid.pretty Generate a Sensible Set of Breakpoints
grid.prompt Prompt before New Page
+grid.raster Render a raster object
grid.record Encapsulate calculations and drawing
grid.rect Draw rectangles
grid.refresh Refresh the current grid scene
@@ -65,7 +72,10 @@ push.viewport Push a Viewport onto the Grid Viewport Stack
pushViewport Maintaining and Navigating the Grid Viewport
Tree
roundrect Draw a rectangle with rounded corners
-stringWidth Create a Unit Describing the Width of a String
+showGrob Label grid grobs.
+showViewport Display grid viewports.
+stringWidth Create a Unit Describing the Width and Height
+ of a String or Math Expression
unit Function to Create a Unit Object
unit.c Combine Unit Objects
unit.length Length of a Unit Object
@@ -77,3 +87,5 @@ viewport Create a Grid Viewport
vpPath Concatenate Viewport Names
widthDetails Width and Height of a grid grob
xDetails Boundary of a grid grob
+xsplinePoints Return the points that would be used to draw an
+ Xspline (or a Bezier curve).
diff --git a/win32/deps/library/grid/Meta/Rd.rds b/win32/deps/library/grid/Meta/Rd.rds
index bbf9d18..c22fa0f 100644
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index 9419bd2..c194acf 100644
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diff --git a/win32/deps/library/grid/Meta/links.rds b/win32/deps/library/grid/Meta/links.rds
new file mode 100644
index 0000000..54eed6d
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diff --git a/win32/deps/library/grid/Meta/nsInfo.rds b/win32/deps/library/grid/Meta/nsInfo.rds
index 60d2249..96b8297 100644
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diff --git a/win32/deps/library/grid/Meta/package.rds b/win32/deps/library/grid/Meta/package.rds
index a13f7c8..8c99f28 100644
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diff --git a/win32/deps/library/grid/Meta/vignette.rds b/win32/deps/library/grid/Meta/vignette.rds
index 53850ed..4bd332c 100644
Binary files a/win32/deps/library/grid/Meta/vignette.rds and b/win32/deps/library/grid/Meta/vignette.rds differ
diff --git a/win32/deps/library/grid/NAMESPACE b/win32/deps/library/grid/NAMESPACE
index b9740d5..4e3f4cb 100644
--- a/win32/deps/library/grid/NAMESPACE
+++ b/win32/deps/library/grid/NAMESPACE
@@ -7,6 +7,7 @@ export(
# Conversion of units
"convertUnit", "convertX", "convertY",
"convertWidth", "convertHeight",
+ "calcStringMetric",
# Deprecated conversion functions
"convertNative",
"grid.convertWidth", "grid.convertX", "grid.convertY",
@@ -18,7 +19,7 @@ export(
"gpar", "get.gpar",
"grid.collection",
"grid.copy", "grid.display.list", "grid.draw",
- "grid.record",
+ "grid.record", "grid.DLapply",
"grid.grill",
"grid.layout", "grid.locator",
"grid.newpage",
@@ -31,8 +32,9 @@ export(
"unit",
"is.unit",
"unit.c", "unit.length", "unit.pmax", "unit.pmin", "unit.rep",
- "stringWidth", "stringHeight",
+ "stringWidth", "stringHeight", "stringAscent", "stringDescent",
"grobX", "grobY", "grobWidth", "grobHeight",
+ "grobAscent", "grobDescent",
"absolute.size",
"valid.just",
@@ -42,12 +44,14 @@ export(
"popViewport", "pushViewport",
"dataViewport", "plotViewport",
"downViewport", "upViewport", "seekViewport",
+ "showViewport",
"drawDetails", "preDrawDetails", "postDrawDetails",
"editDetails",
"validDetails",
"heightDetails", "widthDetails",
"xDetails", "yDetails",
+ "ascentDetails", "descentDetails",
# "height", "heightDetails",
# "width", "widthDetails",
@@ -62,8 +66,10 @@ export(
"getGrob", "setGrob", "addGrob", "removeGrob", "editGrob",
"gEdit", "gEditList", "applyEdit", "applyEdits",
"grid.grab", "grid.grabExpr",
+ "grid.cap",
"setChildren",
-
+ "showGrob",
+
# Listing grobs and viewports
"grid.ls",
"nestedListing", "pathListing", "grobPathListing",
@@ -71,16 +77,20 @@ export(
"getNames", "childNames",
# Creating and drawing predefined grobs and gTrees
+ "grid.abline",
"grid.arrows", "grid.circle", "grid.clip", "grid.curve",
+ "grid.function",
"grid.line.to", "grid.lines", "grid.move.to", "grid.null",
- "grid.points", "grid.polygon", "grid.polyline",
- "grid.rect", "grid.roundrect",
- "grid.segments", "grid.text", "grid.xspline",
+ "grid.points", "grid.path", "grid.polygon", "grid.polyline",
+ "grid.raster", "grid.rect", "grid.roundrect",
+ "grid.segments", "grid.text", "grid.xspline", "grid.bezier",
"arrowsGrob", "circleGrob", "clipGrob", "curveGrob",
+ "functionGrob",
"linesGrob", "lineToGrob", "moveToGrob", "nullGrob",
- "pointsGrob", "polygonGrob", "polylineGrob",
- "rectGrob", "roundrectGrob",
- "segmentsGrob", "textGrob", "xsplineGrob",
+ "pointsGrob", "pathGrob", "polygonGrob", "polylineGrob",
+ "rasterGrob", "rectGrob", "roundrectGrob",
+ "segmentsGrob", "textGrob", "xsplineGrob", "bezierGrob",
+ "xsplinePoints", "bezierPoints",
"grid.xaxis", "grid.yaxis",
"xaxisGrob", "yaxisGrob",
@@ -114,6 +124,7 @@ S3method("[", "gpar")
S3method("[", "unit")
S3method("[", "unit.arithmetic")
S3method("[", "unit.list")
+S3method("[", "vpPath")
S3method("Ops", "unit")
S3method("Summary", "unit")
S3method("as.character", "grob")
@@ -141,14 +152,17 @@ S3method("downViewport", "vpPath")
S3method("drawDetails", "arrows")
S3method("drawDetails", "circle")
S3method("drawDetails", "curve")
+S3method("drawDetails", "functiongrob")
S3method("drawDetails", "grob")
S3method("drawDetails", "line.to")
S3method("drawDetails", "lines")
S3method("drawDetails", "move.to")
S3method("drawDetails", "points")
+S3method("drawDetails", "pathgrob")
S3method("drawDetails", "polygon")
S3method("drawDetails", "polyline")
S3method("drawDetails", "xspline")
+S3method("drawDetails", "beziergrob")
S3method("drawDetails", "rect")
S3method("drawDetails", "roundrect")
S3method("drawDetails", "segments")
@@ -200,9 +214,19 @@ S3method("grobY", "gList")
S3method("grobY", "gPath")
S3method("grobY", "default")
+S3method("grobAscent", "grob")
+S3method("grobAscent", "gList")
+S3method("grobAscent", "gPath")
+S3method("grobAscent", "default")
+S3method("grobDescent", "grob")
+S3method("grobDescent", "gList")
+S3method("grobDescent", "gPath")
+S3method("grobDescent", "default")
+
S3method("heightDetails", "arrows")
S3method("heightDetails", "circle")
S3method("heightDetails", "curve")
+S3method("heightDetails", "functiongrob")
S3method("heightDetails", "default")
S3method("heightDetails", "frame")
S3method("heightDetails", "lines")
@@ -214,6 +238,7 @@ S3method("heightDetails", "roundrect")
S3method("heightDetails", "segments")
S3method("heightDetails", "text")
S3method("heightDetails", "xspline")
+S3method("heightDetails", "beziergrob")
#S3method("height.details", "viewport")
S3method("postDraw", "grob")
@@ -235,6 +260,7 @@ S3method("validDetails", "arrows")
S3method("validDetails", "circle")
S3method("validDetails", "clip")
S3method("validDetails", "curve")
+S3method("validDetails", "functiongrob")
S3method("validDetails", "grob")
S3method("validDetails", "lines")
S3method("validDetails", "line.to")
@@ -250,6 +276,7 @@ S3method("validDetails", "text")
S3method("widthDetails", "arrows")
S3method("widthDetails", "circle")
S3method("widthDetails", "curve")
+S3method("widthDetails", "functiongrob")
S3method("widthDetails", "default")
S3method("widthDetails", "frame")
S3method("widthDetails", "lines")
@@ -261,10 +288,12 @@ S3method("widthDetails", "roundrect")
S3method("widthDetails", "segments")
S3method("widthDetails", "text")
S3method("widthDetails", "xspline")
+S3method("widthDetails", "beziergrob")
#S3method("width.details", "viewport")
S3method("xDetails", "circle")
S3method("xDetails", "curve")
+S3method("xDetails", "functiongrob")
S3method("xDetails", "lines")
S3method("xDetails", "points")
S3method("xDetails", "polygon")
@@ -274,9 +303,11 @@ S3method("xDetails", "roundrect")
S3method("xDetails", "segments")
S3method("xDetails", "text")
S3method("xDetails", "xspline")
+S3method("xDetails", "beziergrob")
S3method("yDetails", "circle")
S3method("yDetails", "curve")
+S3method("yDetails", "functiongrob")
S3method("yDetails", "lines")
S3method("yDetails", "points")
S3method("yDetails", "polygon")
@@ -286,6 +317,14 @@ S3method("yDetails", "roundrect")
S3method("yDetails", "segments")
S3method("yDetails", "text")
S3method("yDetails", "xspline")
+S3method("yDetails", "beziergrob")
+
+S3method("ascentDetails", "default")
+S3method("ascentDetails", "grob")
+S3method("ascentDetails", "text")
+
+S3method("descentDetails", "default")
+S3method("descentDetails", "text")
# S3 methods for internal generics that are used in calls to external fns
S3method("depth", "viewport")
@@ -293,6 +332,16 @@ S3method("depth", "vpList")
S3method("depth", "vpStack")
S3method("depth", "vpTree")
S3method("depth", "path")
+S3method("drawVP", "viewport")
+S3method("drawVP", "vpList")
+S3method("drawVP", "vpStack")
+S3method("drawVP", "vpTree")
+S3method("labelGrob", "grob")
+S3method("labelGrob", "gTree")
+S3method("leafPaths", "viewport")
+S3method("leafPaths", "vpList")
+S3method("leafPaths", "vpStack")
+S3method("leafPaths", "vpTree")
S3method("pushgrobvp", "viewport")
S3method("pushgrobvp", "vpPath")
S3method("popgrobvp", "viewport")
@@ -312,8 +361,6 @@ S3method("dim", "layout")
# S3 method for generic rep (in base)
S3method("rep", "unit")
-S3method("rep", "unit.arithmetic")
-S3method("rep", "unit.list")
# S3 method for generic length (in base)
S3method("length", "unit")
diff --git a/win32/deps/library/grid/R/grid b/win32/deps/library/grid/R/grid
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/grid/R/grid
+++ b/win32/deps/library/grid/R/grid
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/grid/R/grid.rdb b/win32/deps/library/grid/R/grid.rdb
index 6a8293d..0297bdc 100644
Binary files a/win32/deps/library/grid/R/grid.rdb and b/win32/deps/library/grid/R/grid.rdb differ
diff --git a/win32/deps/library/grid/R/grid.rdx b/win32/deps/library/grid/R/grid.rdx
index 0149dcf..6e1e3e4 100644
Binary files a/win32/deps/library/grid/R/grid.rdx and b/win32/deps/library/grid/R/grid.rdx differ
diff --git a/win32/deps/library/grid/doc/changes.txt b/win32/deps/library/grid/doc/changes.txt
new file mode 100644
index 0000000..19f3ec4
--- /dev/null
+++ b/win32/deps/library/grid/doc/changes.txt
@@ -0,0 +1,1374 @@
+Changes from grid_2.14.0 to grid_2.15.0:
+--------------------------------------
+
+1. Added calcStringMetric() function.
+
+2. Added "strascent" and "strdescent" units, plus
+ stringAscent() and stringDescent() convenience functions.
+
+3. Added "grobascent" and "grobdescent" units, plus
+ grobAscent() and grobDescent() convenience functions.
+
+ The "ascent" of a grob is equivalent to its height by default,
+ but ascentDetails() methods can be written
+ (e.g., text grobs are different).
+
+ The "descent" of a grob is zero by default,
+ but descentDetails() methods can be written
+ (e.g., text grobs are different).
+
+4. Fix for xsplinePoints() so that it copes with xspline grob
+ with non-NULL 'id' AND so that it takes the 'vp' and 'gp'
+ settings into account.
+
+5. Added grid.bezier() function to draw Bezier curve
+ (using an X-spline approximation).
+
+ Also added bezierPoints() function.
+
+6. Added grid.DLapply() function.
+
+
+Changes from grid_2.12.0 to grid_2.13.0:
+--------------------------------------
+
+1. Added grid.function() for drawing lines to represent functions.
+
+2. Fixed bug in calculation of x, y, width, and height of segments
+ grobs.
+
+3. Fixed bug in grid.grab(wrap=TRUE) when the scene includes
+ downViewport()s.
+
+4. Added showGrob() function.
+
+
+Changes from grid_2.11.0 to grid_2.12.0:
+--------------------------------------
+
+1. Neither width nor height need to be specified in
+ grid.raster(). The image aspect ratio will be used
+ to calculate an appropriate image size for the
+ current viewport.
+
+2. Added [x|y|width|height]Details() methods for "rastergrob"s
+
+3. "roundrect" grobs now obey their 'just' setting
+ (bug reported by Beau Benjamin Bruce)
+
+4. Added grid.path() for rendering paths with holes.
+
+
+Changes from grid_2.10.0 to grid_2.11.0:
+--------------------------------------
+
+1. Added xsplinePoints() function to return the (x, y)
+ locations that an Xspline would be drawn through.
+ Useful for, e.g., clipping an Xspline against a
+ boundary.
+
+2. Added grid.raster() function for rendering raster images.
+
+3. Added grid.cap() function for capturing output on
+ current graphics device as a raster image.
+
+4. Fixed PROTECT() bug in grid.rect() PR#14199
+ Thanks to Andrew Runnalls for the bug report.
+
+5. Fixed multiple problems in rep.unit() and unit subsetting.
+ Motivated by PR#14170. Thanks to Bert Gunter.
+
+
+Changes from grid_2.9.0 to grid_2.10.0:
+--------------------------------------
+
+1. Added showViewport() function for displaying viewport trees
+ graphically.
+
+2. Fixed bug in unit() indexing; negative integer indices now work.
+
+3. Modified behaviour of editGrob() and addGrob() so that they
+ return the original grob if the specified gPath does not exist,
+ and issue a warning (if new argument 'warn' is TRUE).
+
+
+Changes from grid_2.8.0 to grid_2.9.0:
+------------------------------------
+
+1. Copied grid.roundRect() from 'RGraphics' package into 'grid'.
+
+ Renamed to grid.roundrect() and also used roundrectGrob()
+ rather than roundRect(), partly for more consistent naming,
+ partly to avoid namespace collision until original functions
+ get removed from 'RGraphics' package.
+
+2. Fixed bug in grid.curve() when curve is horizontal or vertical
+ straight line.
+
+3. Exposed is.grob() and valid.just() via the NAMESPACE.
+
+4. Fixed bug in downViewport(), which meant that unsuccessful
+ downViewport()s were still being recorded on the graphics
+ engine display list. This could cause interesting results
+ when a window is resized (i.e., when the display list is
+ replayed).
+
+ Bug reported by Felix Andrews.
+
+5. Added some pseudonyms for come units. For example, it is now
+ possible to specify just "in" instead of "inches".
+
+
+Changes from grid_2.7.0 to grid_2.8.0:
+------------------------------------
+
+1. Added grid.null() and nullGrob(); grob that is guaranteed
+ to have zero-width, zero-height, and draw nothing.
+
+ Useful as zero-size placeholder AND as invisible reference
+ point for other grobs to draw relative to.
+
+2. Fixed bug in listing, via grid.ls(), of frame grobs. If the frame
+ had a vpPath in its 'vp' component, you got an error from vpStack().
+
+ Problem reported by Hadley Wickham.
+
+3. Fixed a bug in grid.ls() when attempting to list the display list
+ following the removal of a grob (i.e., so that there were NULLs
+ in the display list).
+
+ Problem reported by Felix Andrews.
+
+
+Changes from grid_2.6.0 to grid_2.7.0:
+------------------------------------
+
+1. Grid will no longer complain about clipping to a rotated
+ viewport if the rotation is a multiple of 90 degrees.
+
+ Prompted by report from Gustaf Rydevik.
+
+2. Open Xsplines must have zero shape for first and last
+ control point, but this was not being enforced correctly
+ for the case where there were multiple Xsplines in a
+ single grid.xspline() call (i.e., with use of 'id' or
+ 'id.length'). The problem can be seen with this code
+ (most curves do not connect to the first control point
+ [there are also subtle errors in the curve shapes]):
+
+ grid.newpage()
+ pushViewport(viewport(w=.5, h=.5))
+ grid.xspline(x=outer(c(0, .5, 1, .5), 5:1/5),
+ s=1,
+ y=outer(c(.5, 1, .5, 0), 5:1/5),
+ id.lengths=rep(4, 5),
+ gp=gpar(col=1:5, lwd=3))
+ grid.rect()
+
+3. Frame grobs have been improved so that all of the viewports
+ that are generated during the drawing of a frame (and its
+ cells) are left on the display list (previously, they were
+ popped).
+
+ This has implications particularly for ggplot[2] because
+ it means that it is now possible to downViewport() to
+ viewports created during the drawing of a ggplot[2] plot
+ to, for example, add further annotations to the plot.
+
+4. Small fixes to grid.ls():
+
+ - viewports pushed by cellGrobs within frames are now
+ shown by grid.ls()
+
+ - fixed warning (bug really) when display list contains
+ only one grob (and padPrefix() is called).
+
+
+Changes from grid_2.5.0 to grid_2.6.0:
+------------------------------------
+
+1. Added grid.gedit() as convenience wrapper for grid.edit()
+ based on usage patterns of Hadley Wickham when working with
+ 'ggplot' package.
+
+ Ditto, grid.gget() and grid.gremove().
+
+2. Improved implementation of 'id' and 'id.lengths' arguments
+ for drawing multiple polygons/polylines/xsplines to gain
+ order 2 speed improvement.
+
+ Problem independently reported by Luke Tierney, Deepayan Sarkar and
+ Vilmos Prokaj.
+
+3. Bug fixes for grid.remove(), especially for grep=TRUE and global=TRUE
+ (i.e., removing all grobs from DL where the name matches a pattern).
+
+ Also some fixes to grid.remove() error messages when no match found.
+
+ Bug reports from Hadley Wickham.
+
+4. New function grid.ls() for listing grob trees and viewport trees
+ (including both grob trees and viewport trees interlaced).
+
+ Useful for exploring current grob/viewport tree, explaining
+ grob/viewport trees, and programming on or debugging
+ grob/viewport trees.
+
+
+Changes from grid_2.4.0 to grid_2.5.0:
+------------------------------------
+
+1. Added 'open' argument to grid.curve(). This allows, for example,
+ filling the segment of a circle.
+
+2. Fixed bug in arrow() function: segfault produced if either
+ 'ends' or 'type' argument are given as NULL. Thanks to
+ Sebastien Luque for the report.
+
+
+Changes from grid_2.3.0 to grid_2.4.0:
+------------------------------------
+
+1. Bug fix for colour used when drawing a rectangle in a
+ rotated viewport (reported by Olaf Burger).
+
+2. Removed 'units.per.obs' argument from grid.lines() and
+ grid.segments()
+
+ (This is a bug fix; should have been removed long ago).
+
+3. Added extra check on 'data' argument of unit(), which means
+ that if you supply a non-NULL value where the 'unit' is
+ not "str[width|height]" or "grob[x|y|width|height]", you
+ get an error. This may impact on existing code.
+
+4. Radii in grid.circle() are now silently converted to their
+ absolute value (negative values used to trigger an error).
+
+5. New function grobName() for generating unique (within-session)
+ grob names (based on class of grob).
+
+ Also, modified default naming of grobs to be based on class
+ of grob. This should not impact on existing code because
+ noone should be depending on the default names generated by grid.
+
+
+Changes from grid_2.2.0 to grid_2.3.0:
+------------------------------------
+
+1. Bug fix for stringWidth() and stringHeight() with mathematical
+ annotation.
+
+ These used to always convert the argument to "character".
+ Now they let language objects (e.g., expressions) pass through.
+
+2. New grid.xspline() function to draw X-splines (a general curve
+ approximated or interpolated relative to control points).
+
+3. New 'arrow' argument to grid.line.to(), grid.lines(), and
+ grid.segments(). This provides a new way to specify arrow
+ heads on either end of a line.
+
+ grid.arrows() has been deprecated.
+
+ NOTE: that the new 'arrow' arguments have been added BEFORE
+ the name, gp and vp arguments so existing code that specifies
+ any of these arguments *by position* (not by name) will fail.
+
+4. Added "[" (subset) methods for "gpar" objects.
+
+5. New grobX() and grobY() functions for producing units
+ describing a location on the boundary of a grob.
+
+6. Units produced by grobX() and grobY() make use of new
+ xDetails() and yDetails() generic functions to calculate the
+ boundary of a grob. Methods for these functions are provided
+ for all grid graphical primitives.
+
+7. Bug fix for grid.polygon() when 'x' is not just a simple unit
+ (e.g., it is unit arithmetic); 'index' was being calculated
+ incorrectly so not all of polygon would be drawn or, if
+ 'id' or 'id.length' were used, only a single polygon would
+ be drawn (with unexpected shape).
+
+8. New grid.curve() primitive for drawing a curve between two
+ locations.
+
+ Together with new grobX() and grobY() provides support for
+ drawing simple node-and-edge graphs and flow diagrams.
+
+9. New grid.clip() primitive for setting the clipping region
+ (more accurately, the clipping rectangle). Has effect until
+ the next grid.clip() or when the current viewport is popped.
+
+10. New dim.layout() method for layout objects. Allows easy
+ access to dimensions of layout via nrow() and ncol().
+
+11. unit.rep() deprecated in favour of unit method(s) for rep() function.
+
+12. unit.length() deprecated in favour of unit method(s) for length() function.
+
+13. New grid.polyline() primitive. Just like grid.lines() except has
+ 'id' and 'id.lengths' arguments.
+
+ These work like the corresponding arguments in grid.polygon() and
+ grid.xspline(), allowing multiple polylines to be drawn from a
+ single grid.polyline() call.
+
+14. Fixed drawing of top-level gList objects so that they
+ (actually the grobs in the gList) are recorded on the
+ grid display list.
+
+ Allowed a gList to be component of a gList
+ (the gList constructor merges sub-gList into resulting gList).
+
+ Added subset method for gList objects
+ (so that result is still a gList).
+
+15. Bug fix for grid.rect() and grid.circle() with gpar(lty="blank").
+ (problem was actually in the graphics engine).
+
+ Reported by John Braun (private correspondence).
+
+
+Changes from grid_2.1.0 to grid_2.2.0:
+------------------------------------
+
+1. current.vpPath() now exported.
+
+2. Grid now uses the 'fg' and 'bg' settings (if any) for
+ graphics devices to set the initial graphical parameter
+ settings of the top-level viewport (i.e., the 'gp' arg
+ of viewport[ROOT]).
+
+3. Fixed bug in evaluation of grobWidth(polygonGrob()).
+ The C function L_locnBounds was not exported AND
+ the widthDetails.polygon method was not exposed properly
+ via the NAMESPACE.
+
+ Reported in private correspondence by Deepayan Sarkar.
+
+ Also corrected export of heightDetails, validDetails, and
+ widthDetails for arrows, circle, polygon, points, rect, and
+ segments primitives.
+
+
+Changes from grid_2.0.1 to grid_2.1.0:
+------------------------------------
+
+1. preDrawDetails(), drawDetails(), and postDrawDetails()
+ methods are now recorded on the graphics engine
+ display list. This means that calculations within these
+ methods are now run when a device is resized or
+ when output is copied from one device to another. A simple
+ example (the rectangle remains 1inch wide when resizing the
+ device -- it does not in previous versions) ...
+
+ testgrob <- grob(cl="test")
+ drawDetails.test <- function(x, recording) {
+ w <- convertWidth(unit(1, "inches"), "npc")
+ grid.rect(width=w)
+ }
+ grid.draw(testgrob)
+
+2. Fixed bug in grid.text() when "rot" argument has length 0.
+ (privately reported by Emmanuel Paradis)
+
+3. New getNames() function to return just the names of all top-level
+ grobs on the display list.
+
+4. Recording on the grid display list is turned off within
+ preDrawDetails(), drawDetails(), and postDrawDetails() methods.
+
+ This means that you do not need to worry about specifying
+ recording=FALSE within these methods.
+
+5. Grid should recover better from errors or user-interrupts
+ during drawing (i.e., not leave you in a strange viewport
+ or with strange graphical parameter settings).
+
+6. New function grid.refresh() to redraw the grid display list.
+
+7. New function grid.record() to capture calculations
+ with grid graphics output. For example ...
+
+ grid.record({
+ w <- convertWidth(unit(1, "inches"), "npc")
+ grid.rect(width=w)
+ },
+ list())
+
+8. grobWidth and grobHeight ("grobwidth" and "grobheight" units)
+ for primitives (text, rects, etc, ...) are now
+ calculated based on a bounding box for the relevant grob.
+
+ These used to be calculated assuming a grob was scalar
+ rather than vector. For example, the following now behaves
+ much more sensibly ...
+
+ txt <- textGrob(c("This is a repeat", "This is a repeat"),
+ y=1:2/3, rot=45)
+ grid.draw(txt)
+ grid.rect(width=grobWidth(txt), height=grobHeight(txt))
+
+ NOTE: this has changed the calculation of the size of a scalar
+ rect (or circle or lines) so that, for example, something like ...
+
+ grid.pack(frame, rectGrob())
+
+ ... needs to become ...
+
+ grid.pack(frame, rectGrob(),
+ width=unit(1, "null"), height=unit(1, "null"))
+
+ ... if you just want a rectangle that fills the space available.
+
+9. New arguments "warn" and "wrap" for function grid.grab()
+
+ If warn>0 will warn if know (or, if warn>1, if even suspect)
+ that the grab has not faithfully captured the output.
+
+ If wrap=TRUE, will capture output by wrapping all non-grobs
+ on the display list in grobs. Resulting gTree is less
+ elegant and harder to work with, but should always faithfully
+ capture output.
+
+10. New function grid.grabExpr() which captures the output from
+ an expression (i.e., not from the current scene) without
+ doing any drawing (i.e., no impact on the current scene).
+
+11. upViewport() now (invisibly) returns the path that it goes up
+ (suggested by Ross Ihaka).
+
+ This makes it possible to do things like ...
+
+ upPath <- upViewport(n)
+ ...
+ downViewport(upPath)
+
+ ... (i.e., navigate up and then back down to where you came from).
+
+12. The "gamma" gpar has been deprecated (this is a device property
+ not a property of graphical objects; suggested by Ross Ihaka).
+
+13. New "lex" gpar; a line width multiplier.
+ The final line width is calculated as ...
+
+ gpar("lex")*gpar("lwd")
+
+ ... and the multiplier is cumulative (like cex) ...
+
+ grid.rect(height=0.5, width=0.5,
+ gp=gpar(lwd=16)) # lex = 1
+ pushViewport(viewport(gp=gpar(lex=0.5)))
+ grid.rect(height=0.5, width=0.5,
+ gp=gpar(lwd=16, col="red")) # lex = 0.5
+ pushViewport(viewport(gp=gpar(lex=0.5)))
+ grid.rect(height=0.5, width=0.5,
+ gp=gpar(lwd=16, col="green")) # lex = 0.25!
+
+ This (along with cex) provides support for "zooming" a grid scene.
+
+14. grid.text() now handles any language object as mathematical
+ annotation (instead of just expressions). For example ...
+
+ grid.text(call("sin", pi))
+
+15. plotViewport() has default value for "margins" argument (that match
+ the default value for par(mar)).
+
+16. The "extension" argument to dataViewport() can now be vector,
+ in which case the first value is used to extend the xscale and
+ the second value is used to extend the y scale.
+ (suggested by Ross Ihaka).
+
+17. All "just" arguments (for viewports, layouts, rectangles, text)
+ can now be numeric values (typically between 0 [left] and 1 [right])
+ as well as character values ("left", "right", ...).
+
+ For rectangles and text, there are additional "hjust" and "vjust"
+ arguments which allow numeric vectors of justification in
+ each direction (e.g., so that several pieces of text can have
+ different justifications). If these are specified, they
+ override the "just" argument.
+ (suggested by Ross Ihaka)
+
+18. New "edits" argument for grid.xaxis() and grid.yaxis() to
+ allow specification of on-the-fly edits to axis children
+ (when at == NULL, so children are generated on-the-fly).
+
+19. applyEdit(x, edit) returns x if target of edit (i.e., child
+ specified by a gPath) cannot be found.
+
+20. Fix for calculation of length of max/min/sum unit. Length is
+ now (correctly) reported as 1 (was reported as length of first arg).
+
+21. Viewport names can now be any string (they used to have to be a
+ valid R symbol).
+
+ The documentation now says that grob names can be any string
+ (they always could be, but the documentation said they had to
+ be a valid R symbol)
+
+22. The "label" argument for grid.xaxis() and grid.yaxis() can now
+ also be a language object or string vector, in which case it
+ specifies custom labels for the tick marks.
+
+
+Changes from grid_2.0.0 to grid_2.0.1:
+------------------------------------
+
+1. Fixed bug in grid.newpage(); it was not starting new page
+ on first grid call if there was already traditional graphics
+ output on the device (i.e., the device was "dirty" but not
+ "grid dirty").
+
+2. Fixed bug in grid.grab() when no viewports have been pushed.
+
+
+Changes from grid_1.9.0 to grid_2.0.0:
+------------------------------------
+
+1. Calculation of number of circles to draw in circleGrob now
+ looks at length of y and r as well as length of x.
+
+2. Calculation of number of rectangles to draw in rectGrob now
+ looks at length of y, w, and h as well as length of x.
+
+3. All primitives (rectangles, lines, text, ...) now handle
+ non-finite values (NA, Inf, -Inf, NaN) for locations and
+ sizes.
+
+ Non-finite values for locations, sizes, and scales of
+ viewports result in error messages.
+
+ There is a new vignette("nonfinite") which describes this
+ new behaviour.
+
+4. Fixed (unreported) bug in drawing circles. Now checks that
+ radius is non-negative.
+
+5. downViewport() now reports the depth it went down to find a
+ viewport. Handy for "going back" to where you started, e.g., ...
+
+ depth <- downViewport("vpname")
+ <draw stuff>
+ upViewport(depth)
+
+6. The "alpha" gpar() is now combined with the alpha channel of
+ colours when creating a gcontext as follows:
+
+ finalAlpha = gpar("alpha")*(R_ALPHA(col)/255)
+
+ This means that gpar(alpha=) settings now affect internal
+ colours so grid alpha transparency settings now are sent to
+ graphics devices.
+
+ The alpha setting is also cumulative. For example, ...
+
+ grid.rect(width=0.5, height=0.5,
+ gp=gpar(fill="blue")) # alpha = 1
+ pushViewport(viewport(gp=gpar(alpha=0.5)))
+ grid.rect(height=0.25, gp=gpar(fill="red")) # alpha = 0.5
+ pushViewport(viewport(gp=gpar(alpha=0.5)))
+ grid.rect(width=0.25, gp=gpar(fill="red")) # alpha = 0.25 !
+
+7. Editing a gp slot in a grob is now incremental. For example ...
+
+ grid.lines(name="line")
+ grid.edit("line", gp=gpar(col="red")) # line turns red
+ grid.edit("line", gp=gpar(lwd=3)) # line becomes thick AND STAYS red
+
+8. The "cex" gpar is now cumulative. For example ...
+
+ grid.rect(height=unit(4, "char")) # cex = 1
+ pushViewport(viewport(gp=gpar(cex=0.5)))
+ grid.rect(height=unit(4, "char")) # cex = 0.5
+ pushViewport(viewport(gp=gpar(cex=0.5)))
+ grid.rect(height=unit(4, "char")) # cex = 0.125 !!!
+
+9. New childNames() function to list the names of children
+ of a gTree.
+
+10. The "grep" and "global" arguments have been implemented for
+ grid.[add|edit|get|remove]Grob() functions.
+
+ The "grep" argument has also been implemented for the
+ grid.set() and setGrob().
+
+11. New function grid.grab() which creates a gTree from the
+ current display list (i.e., the current page of output can
+ be converted into a single gTree object with all grobs
+ on the current page as children of the gTree and all the
+ viewports used in drawing the current page in the childrenvp
+ slot of the gTree).
+
+12. New "lineend", "linejoin", and "linemitre" gpar()s:
+
+ line end can be "round", "butt", or "square".
+ line join can be "round", "mitre", or "bevel".
+ line mitre can be any number larger than 1
+ (controls when a mitre join gets turned into a bevel join;
+ proportional to angle between lines at join;
+ very big number means that conversion only happens for lines
+ that are almost parallel at join).
+
+13. New grid.prompt() function for controlling whether the user is
+ prompted before starting a new page of output.
+
+ Grid no longer responds to the par(ask) setting in the "graphics"
+ package.
+
+
+Changes from grid_1.9.0 to grid_1.9.1:
+------------------------------------
+
+1. Fixed (unreported) bug in internal calculation of unitArithmetic
+ object when op = * and numeric operand longer than unit operand
+
+2. Fixed (unreported) bug in creation of unitArithmetic objects
+ when numeric operand is integer. All numeric operands are now
+ coerced to real.
+
+
+Changes from grid_1.8.0 to grid_1.9.0:
+------------------------------------
+
+1. Renamed push/pop.viewport() to push/popViewport().
+
+2. Added upViewport(), downViewport(), and seekViewport() to
+ allow creation and navigation of viewport tree
+ (rather than just viewport stack).
+
+3. Added id and id.lengths arguments to grid.polygon() to allow
+ multiple polygons within single grid.polygon() call.
+
+4. Added vpList(), vpStack(), vpTree(), and current.vpTree()
+ to allow creation of viewport "bundles" that may be pushed
+ at once (lists are pushed in parallel, stacks in series).
+
+ current.vpTree() returns the current viewport tree.
+
+5. Added vpPath() to allow specification of viewport path
+ in downViewport() and seekViewport().
+
+ See ?viewports for an example of its use.
+
+ NOTE: it is also possible to specify a path directly,
+ e.g., something like "vp1::vp2", but this is only
+ advised for interactive use (in case I decide to change the
+ separator :: in later versions).
+
+6. Added "just" argument to grid.layout() to allow justification
+ of layout relative to parent viewport *IF* the layout is not
+ the same size as the viewport. There's an example in
+ help(grid.layout).
+
+7. Allowed the "vp" slot in a grob to be a viewport name or a
+ vpPath. The interpretation of these new alternatives is to
+ call downViewport() with the name or vpPath before drawing the
+ grob and upViewport() the appropriate amount after drawing the
+ grob. Here's an example of the possible usage:
+
+ pushViewport(viewport(w=.5, h=.5, name="A"))
+ grid.rect()
+ pushViewport(viewport(w=.5, h=.5, name="B"))
+ grid.rect(gp=gpar(col="grey"))
+ upViewport(2)
+ grid.rect(vp="A", gp=gpar(fill="red"))
+ grid.rect(vp=vpPath("A", "B"), gp=gpar(fill="blue"))
+
+8. Added engine.display.list() function. This allows the user to
+ tell grid NOT to use the graphics engine display list and to handle
+ ALL redraws using its own display list (including redraws after
+ device resizes and copies).
+
+ This provides a way to avoid some of the problems with resizing
+ a device when you have used grid.convert(), or the gridBase package,
+ or even base functions such as legend().
+
+ There is a document discussing the use of display lists in grid
+ on the grid web site
+ (http://www.stat.auckland.ac.nz/~paul/grid/grid.html)
+
+9. Changed the implementation of grob objects. They are no longer
+ implemented as external references. They are now regular R objects
+ which copy-by-value. This means that they can be saved/loaded
+ like normal R objects. In order to retain some existing grob
+ behaviour, the following changes were necessary:
+
+ - grobs all now have a "name" slot. The grob name is used to
+ uniquely identify a "drawn" grob (i.e., a grob on the display
+ list).
+ - grid.edit() and grid.pack() now take a grob name as the first
+ argument instead of a grob. (Actually, they take a gPath -
+ see below)
+ - the "grobwidth" and "grobheight" units take either a grob
+ OR a grob name (actually a gPath - see below). Only in the
+ latter case will the unit be updated if the grob "pointed to"
+ is modified.
+
+ In addition, the following features are now possible with grobs:
+
+ - grobs now save()/load() like any normal R object.
+ - many grid.*() functions now have a *Grob() counterpart. The
+ grid.*() version is used for its side-effect of drawing
+ something or modifying something which has been drawn; the
+ *Grob() version is used for its return value, which is a grob.
+ This makes it more convenient to just work with grob objects without
+ producing any graphical output (by using the *Grob() functions).
+ - there is a gTree object (derived from grob), which is a grob
+ which can have children. A gTree also has a "childrenvp" slot
+ which is a viewport which is pushed and then "up"ed before the
+ children are drawn; this allows the children of a gTree to
+ place themselves somewhere in the viewports specified in the
+ childrenvp by having a vpPath in their vp slot.
+ - there is a gPath object, which is essentially a concatenation
+ of grob names. This is used to specify the child of (a child of ...)
+ a gTree.
+ - there is a new API for creating/accessing/modifying grob objects:
+ grid.add(), grid.remove(), grid.edit(), grid.get() (and their
+ *Grob() counterparts can be used to add, remove, edit, or extract
+ a grob or the child of a gTree. NOTE: the new grid.edit() API
+ is incompatible with the previous version.
+
+10. Added stringWidth(), stringHeight(), grobWidth(), and grobHeight()
+ convenience functions (they produce "strwidth", "strheight",
+ "grobwidth", and "grobheight" unit objects, respectively).
+
+11. Allowed viewports to turn off clipping altogether. Possible settings
+ for viewport clip arg are now:
+
+ "on" = clip to the viewport (was TRUE)
+ "inherit" = clip to whatever parent says (was FALSE)
+ "off" = turn off clipping
+
+ Still accept logical values (and NA maps to "off")
+
+
+Changes from grid_1.8.0 to grid_1.8.1:
+------------------------------------
+
+1. I have effectively disabled the "mystrwidth", "mystrheight",
+ "mychars", and "mylines" units. These are now identical in
+ behaviour to the equivalent units without the "my".
+
+ Another way to look at it is that I have modified the behaviour
+ of "lines", "chars", "strwidth", and "strheight" so that they
+ ALWAYS obey the latest gpar settings (including any gpar
+ settings in a grob).
+
+ Some examples ...
+
+ This text is sized AND positioned in terms of a fontsize of 6:
+
+ grid.text("small text and small lines", y=unit(2, "lines"),
+ gp=gpar(fontsize=6))
+
+ This text is 6 pt in size, but is positioned in terms of the
+ (default on X11) fontsize 12:
+
+ push.viewport(viewport(y=unit(2, "lines")))
+ grid.text("small test and big lines", gp=gpar(fontsize=6))
+ pop.viewport()
+
+2. Fixed a bug in the calculation of "grobwidth" and "grobheight"
+ units. The following code demonstrates the problem (the black
+ rectangle should snugly bound the grey rectangles):
+
+ grid.newpage()
+ # Create a frame with fontsize=6
+ gf <- grid.frame(layout=grid.layout(10, 10,
+ widths=unit(rep(1, 10), "strwidth",
+ as.list(rep("o", 10))),
+ heights=unit(rep(1, 10), "strheight",
+ as.list(rep("o", 10)))),
+ gp=gpar(fontsize=6))
+ # Add a rect to the frame
+ for (i in 1:10)
+ grid.place(gf, grid.rect(gp=gpar(col="grey"), draw=FALSE),
+ col=i, row=i)
+ grid.draw(gf)
+ # Now draw a rect around the frame
+ grid.rect(width=unit(1, "grobwidth", gf),
+ height=unit(1, "grobheight", gf))
+
+3. Fixed a bug in the implementation of the "cex" gpar. This is now
+ used correctly in the transformation code in unit.c
+
+ The bug was demonstrated by the following simple example
+ (the second set of points should be twice the radius of the
+ first set of points):
+
+ grid.newpage()
+ push.viewport(viewport())
+ grid.points()
+ grid.points(gp = gpar(cex = 2))
+
+ Another demonstration from the original bug report from David Hinds:
+
+ xyplot(1:4~1:4, cex=1:4, pch=1)
+
+4. Fixed a bug in multiplication of scalar by unit object, when the
+ scalar has length > 1. The following example demonstrates
+ the problem:
+
+ grid.segments(x0=1:3/4, y0=0.1, x1=1:3/4,
+ y1=1:3/4*unit(1, "npc"))
+
+ This should behave the same as:
+
+ grid.segments(x0=1:3/4, y0=0.1, x1=1:3/4,
+ y1=unit(1:3/4, "npc"))
+
+
+Changes from grid_0.7-4 to grid_1.8.0:
+------------------------------------
+
+1. grid.text() now checks that the rot argument is numeric and finite.
+
+2. dataViewport() checks for is.null(<arg>) rather than missing(<arg>)
+ and has renamed arguments x and y to xData and yData.
+
+ All to avoid confusion with specifying x= and y= in the ... argument.
+
+ This also fortuitously fixed a bug in dataViewport where the
+ calculation of the x-range was partially dependent on the y-range(!)
+
+ Thanks to Russell Norvell for spotting and reporting the bug.
+
+3. unit() checks that units argument is character mode.
+
+ Fix for bug (first reported by Achim Zeileis) produced by,
+ for example ...
+
+ unit(1, 2)
+
+4. The function absolute.units() was recursive and now uses a loop.
+
+ Fixes the following problem (from Deepayan Sarkar):
+
+ gf <- grid.frame(layout = grid.layout(nrow=1, ncol=1), draw = FALSE)
+ grob.rect <- grid.rect(x = 1:99/100, y = 1:99/100,
+ h = rep(.01, 100), w = rep(.05, 100),
+ gp = gpar(col = terrain.colors(100)),
+ draw = FALSE)
+ grid.pack(frame = gf, row = 1, col = 1,
+ grob = grob.rect,
+ draw = FALSE)
+ grid.draw(gf) # Fails with stack overflow
+
+5. There is now a grid.locator() function for interactively selecting
+ locations within the current grid viewport with a mouse.
+
+6. There is a new grid.convert() function for converting between
+ different coordinate systems.
+
+ The convertNative() function has been deprecated.
+
+7. The default "top-level" viewport that is generated by grid
+ now has its "native" coordinate system set to the "native"
+ coordinate system of the device. For example, "native"
+ units at the top-level correspond to points on a PostScript
+ device, pixels on an X11 device, and so on.
+
+ For example, try the following:
+
+ library(grid)
+ x11()
+ grid.rect(x=10, y=10, width=10, height=10,
+ default.units="native")
+
+ This may cause consternation if you ever plot grid.points()
+ at the top-level because the default units for grid.points()
+ are "native" ... I consider this an unlikely occurrence.
+
+8. Added a new gpar called "alpha" for specifying transparency.
+ This is supposed to be a number from 1 (opaque) to 0 (transparent).
+ No R devices will take any notice of this whatsoever as yet.
+
+9. Modified "xaxis" and "yaxis" grobs so that they extend the
+ "collection" class. This means that, when a new generic function
+ is created, it may be possible to write methods just for the
+ collection class and not also separate xaxis and yaxis methods.
+
+10. Modified unit subsetting so that logical indices work.
+ For example ...
+
+ unit(1:4, "npc")[1:4 == 3]
+
+11. Fixed detaching/reloading of grid package (was causing an error).
+
+12. There is a new grid.arrows() primitive.
+
+ See the help file for example usage.
+
+13. Grid is now a base package (hence version number leap!)
+
+
+Changes from grid_0.7-3 to grid_0.7-4:
+------------------------------------
+
+1. Fixed the bug in the bug-fix in item 7. below.
+
+
+Changes from grid_0.7-2 to grid_0.7-3:
+------------------------------------
+
+1. Properly removed "origin" settings from viewports.
+
+2. Modified grid.pretty() slightly so that it would respond
+ sensibly/usefully to things like ...
+
+ grid.pretty(c(10, 0))
+
+ A side-effect of this is that the following sort of viewport
+ scale specifications become sensible/useful ...
+
+ push.viewport(viewport(layout=grid.layout(1, 2)))
+ push.viewport(viewport(layout.pos.col=1))
+ push.viewport(viewport(w=.8, h=.8,
+ xscale=c(10,0)))
+ grid.points(1:10, 1:10/11)
+ grid.xaxis()
+ grid.yaxis()
+ pop.viewport(2)
+ push.viewport(viewport(layout.pos.col=2))
+ push.viewport(viewport(w=.8, h=.8,
+ yscale=c(10,0)))
+ grid.points(1:10/11, 1:10)
+ grid.xaxis()
+ grid.yaxis()
+ pop.viewport(3)
+
+3. Fixed the calculation of number of "vertices" in grid.lines so that
+ it is the maximum of length(x) and length(y).
+
+ Used to be calculated solely on length(x).
+
+4. Grid now throws an error if you try to create a unit of length 0.
+
+ This to fix a bug reported by Bud Gibson, the essence of which was ...
+
+ grid.points(size=unit(numeric(0), "mm"))
+
+5. The default value of the "at" argument for grid.xaxis() and
+ grid.yaxis() is NULL (was NA; NA was inconsistent with other
+ default argument settings and basically a dumb idea)
+
+6. Grid now throws an error if you try to create a gpar object with
+ an element of length 0.
+
+ This is to fix a bug reported by Michael Friendly (and diagnosed by
+ Brian Ripley), the essence of which was ...
+
+ grid.lines(gpar(fontsize=numeric(0)))
+
+7. grid.text() now converts its label argument to a string.
+
+ This is to fix a bug where "grobwidth" or "grobheight" would
+ segfault if given a text grob for which the label was not a string.
+ (The fix involved including a check for "mystrwidth" and "mystrheight"
+ units in valid.data).
+
+ The bug could be produced by ...
+
+ grid.rect(w=unit(1, "grobwidth", data=grid.text(5)))
+
+
+Changes from grid_0.7-1 to grid_0.7-2:
+-------------------------------------
+
+1. Fixed some generic/method incompatibilities (pointed out by Kurt).
+
+
+Changes from grid_0.7 to grid_0.7-1:
+------------------------------------
+
+1. Fixed a bug where layout matrix respect was not being applied to
+ the correct cell. For example, the following caused the cell
+ 1,3 to be respected rather than 1,2 ...
+
+ lt.resp <- matrix(0, 2, 3)
+ lt.resp[1,2] <- 1
+ grid.show.layout(grid.layout(2, 3, respect = lt.resp))
+
+ Reported by Deepayan Sarkar.
+
+
+Changes from grid_0.6 to grid_0.7:
+------------------------------------
+
+1. The web pages for grid have moved to ...
+
+ http://www.stat.auckland.ac.nz/~paul/grid/grid.html
+
+2. Mathematical annotation is now available in grid.
+
+ Wherever grid expects a string, an expression may be used instead.
+ This covers not only producing mathematical annotation output,
+ but also correctly calculating width and height of expressions,
+ and checking for overlapping expressions.
+
+3. If you try to save/load a grid grob, it will now fail gracefully
+ rather than seg faulting.
+
+4. If you save a display list containing grid output, then detach
+ grid, then try to run the display list again, it will now fail
+ gracefully rather than seg faulting.
+
+5. All gpar() settings can now be vectors. Well, they could always
+ be vectors, but now values other than the first one will have an
+ effect. This will not happen in all contexts, for example,
+ viewports will only take notice of the first value in each setting,
+ but for graphics functions where multiple items can be output,
+ multiple settings may be sensibly given. Some examples are:
+
+ # multiple points with different colours
+ grid.points(1:10/11, 1:10/11, gp=gpar(col=1:10))
+
+ # multiple segments with different colours
+ grid.segments(1:10/11, 0, 1:10/11, 1, gp=gpar(col=1:10))
+
+ # multiple points with different sizes
+ grid.points(1:10/11, 1:10/11, size=unit(1:10, "mm"))
+
+ # multiple pieces of text with different font sizes
+ grid.text(1:10, x=1:10/11, gp=gpar(fontsize=10:20))
+
+ # multiple rects with different lineheights (and height is in "lines")
+ grid.rect(width=.05, x=1:10/11,
+ height=unit(1, "mylines"),
+ gp=gpar(lineheight=1:10))
+
+6. (Because of a fix to R/src/main/engine.c ...)
+ Multiple-line text (i.e., text with "\n"s in it) is now correctly
+ spaced vertically (i.e., takes notice of the current value of
+ "fontsize").
+
+ NOTE, however, that multiple-line text still takes no notice of the
+ current value of "lineheight".
+
+7. Fixed a bug in grid.layout(). It was the case that, if you
+ entered widths or heights which were not unit objects, they
+ were not converted properly to unit objects.
+
+8. Modified the defaulting of "just" arguments when a single value
+ is provided. See the new example in grid.text.
+
+9. Fixed a bug where grid.points(pch=NULL) would cause a crash.
+ This now defaults pch to the value 1.
+
+10. Added "fontfamily" and "fontface" gpar() settings. The fontfamily
+ setting will mostly be ignored until devices are modified to take
+ notice of the extra information, BUT this can be used NOW to
+ specify a Hershey Font family (on all devices). The fontface
+ setting is designed to take over from the old "face" setting,
+ but the latter is retained for backward compatibility.
+
+
+Changes from grid_0.5-1 to grid_0.6:
+------------------------------------
+
+1. Some internal changes to speed up creation of unit objects.
+ This may have a noticeable effect on drawing legends and anything
+ that relies on grid frames (e.g., "key"s in lattice).
+
+2. A couple of bug fixes for "grobwidth" and "grobheight" units.
+ Symptoms were legends not being allocated the correct amount of
+ space.
+
+ Thanks to Deepayan Sarkar and Peter Kleiweg for help diagnosing
+ the bug and testing the fix.
+
+3. Added plotViewport() and dataViewport()
+ convenience function for creating a
+ viewport that has the typical layout of an R plot.
+
+4. Altered viewport() function so that layout.pos.row and layout.pos.col
+ can be specified as a sequence and only the range() of that
+ sequence is used.
+
+5. Removed most documentation from the package to reduce the download
+ size. The user's guide and changes file are included with the
+ tar ball, but the other documents are only available via
+ http://www.stat.auckland.ac.nz/PEOPLE/paul/grid/grid.html
+
+ Also changed the format of the user's guide from postscript to pdf.
+
+6. Fixed bug in unit.length where the length of a unit.arithmetic object
+ was calculated incorrectly if the length() of the scalar multiplier
+ was longer than the unit.length() of the unit object being multiplied.
+
+7. Allowed character settings for pch in grid.points()
+
+8. The crash on Windows platforms when plot history is turned on
+ has been fixed in R version 1.5.
+
+ This fix means that grid_0.6 will only run on R version >= 1.5.0
+
+9. Added handling of NULL values for gpar elements. Except for col
+ and fill, this now means the same as specifying no setting at all
+ for the element -- previous behaviour was a segfault.
+
+
+Changes from grid_0.5 to grid_0.5-1:
+------------------------------------
+
+1. Fix for some grid bugs.
+
+ The problems were:
+ (i) grid output could not be saved in metafile format
+ (ii) non-grid output could not be saved in metafile format when
+ grid was loaded
+ (iii) empty page at start of grid postscript output
+ (iv) empty page at start of non-grid postscript output when
+ grid was loaded
+ (v) copying grid output from x11 to postscript (dev.copy)
+ produced blank pages in postscript
+
+ These problems were due to two things in grid:
+ (i) grid created a new page whenever a new device was started.
+ (ii) grid created a new page whenever the display list was
+ replayed (e.g., when a device was resized or the output
+ was copied from one device to another)
+
+ Grid now only creates a new page the first time grid output is
+ produced on a device AND only creates a new page for replaying
+ the display list IF there has already been grid output on the device.
+
+
+Changes from grid_0.2 to grid_0.5:
+----------------------------------
+
+1. R has a new device API and a new graphics engine. Grid uses these.
+
+ This means that this version will NOT work on R versions before 1.4.0
+
+ Another known "bug" is that this version of grid will crash R if
+ used in Windows with plot history recording turned on (although
+ "add"ing individual grid "plots" to the plot history should still
+ work).
+
+2. Added "mystrwidth" and "mystrheight" units; basically these just
+ complete the set of units which depend on font, fontsize, and/or
+ lineheight and therefore may refer to the current viewport settings
+ of these parameters OR to the current settings of the grob being
+ drawn.
+
+3. Added unit.rep function (the base rep() function is not generic
+ so I could not simply write a rep.unit method).
+
+4. Added new gpar, "gamma", for gamma-correction of colours
+ (defaults to 1). NOTE that only windows devices will currently
+ respond to on-the-fly changes in gamma.
+
+5. Added "clip" flag to viewports. If "clip" is TRUE, then output
+ is clipped to the viewport.
+
+ Clipping obeys only the most recent viewport clip setting.
+ For example, if you clip to viewport1, then clip to viewport2,
+ the clipping region is determined wholly by viewport2, the
+ size and shape of viewport1 is irrelevant (until viewport2
+ is popped of course).
+
+ If a viewport is rotated (because of its own "angle" setting
+ or because it is within another viewport which is rotated) then
+ the "clip" flag is ignored.
+
+6. The functions grid.start() and grid.stop() have been removed.
+ grid automatically "registers" with devices.
+
+7. Grid no longer automatically opens a device when it is loaded.
+ Instead, a device is created, if there are none open, when the
+ first drawing occurs or when the first viewport is pushed.
+
+8. Added new functions unit.pmin() and unit.pmax() which are unit
+ versions of pmax() and pmin()
+
+9. Added new function grid.place() which provides a simpler
+ interface to grid.pack() and is useful for using grid "frame"s
+ as just a convenient way of defining a layout and sticking
+ things in it.
+
+
+Changes from grid_0.1 to grid_0.2:
+----------------------------------
+
+1. Fixed bug in rotating viewports; this should be more reliable now.
+
+2. Added grid.line.to() and grid.move.to(). These allow drawing BETWEEN
+ different coordinate systems. See example in inst/doc/demo3.ps.
+
+3. Added some more demonstrations to the doc directory.
+
+4. Added more test code to the tests directory.
+
+5. Added "grobwidth" and "grobheight" units. See the document
+ grid/inst/doc/advanced/parentchild.ps
+
+6. Added more detailed documentation to grid/inst/doc/advanced. This
+ stuff is not as friendly for the reader, but may be useful if you're
+ tearing your hair out wondering why some strange effect is occurring.
+
+7. Changed frames and packing to use the new "grobwidth" and "grobheight"
+ units. This fixes some problems with frames and packing.
+
+8. Fixed a bug where the gpar settings for "fontsize" and "lineheight"
+ _within a grob_ would not affect the location or size of the grob
+ if they were specified in "lines" or "char" units.
+
+ This required adding new "mylines" and "mychar" units (alternative
+ suggestions for names welcome !) so that you can specify whether
+ a grob's a location/size is in terms of the current viewport's
+ fontsize and lineheight ("lines" and "char") or in terms of its own
+ fontsize and lineheight ("mylines" and "mychar").
+
+9. Added grid.polygon() and grid.circle() primitives
+
+10. Added newpage=TRUE argument to grid.start() so that you can restart
+ grid graphics mode without having to move to a new page.
+
+ For example, try ...
+
+ postscript()
+ grid.start()
+ grid.polygon()
+ grid.stop()
+ grid.start() # moves to new page
+ grid.circle()
+ grid.stop()
+ grid.start(newpage=FALSE) # does NOT move to new page
+ grid.rect()
+ grid.stop()
+ dev.off()
+
+11. Changed interface for pop.viewport(). This now just takes a
+ number of viewports to pop, which defaults to 1.
+ For example ...
+
+ push.viewport(viewport())
+ pop.viewport(current.viewport())
+
+ ... becomes ...
+
+ push.viewport(viewport())
+ pop.viewport()
+
+ ... and ...
+
+ vp1 <- viewport()
+ vp2 <- viewport()
+ push.viewport(vp1, vp2)
+ pop.viewport(vp2, vp1)
+
+ ... becomes ...
+
+ vp1 <- viewport()
+ vp2 <- viewport()
+ push.viewport(vp1, vp2)
+ pop.viewport(2)
+
+12. Speed-up of pushing and popping viewports. This will probably not
+ be noticeable in normal usage, but makes a big difference for
+ frames and packing.
+
+Changes from lattice_0.2 to grid_0.1:
+-------------------------------------
+
+0. Change of package name from "lattice" to "grid" (!!!!)
+
+ This means that most user functions have changed from l<something>
+ to grid.<something>
+
+1. Slight speed up of grid.push.viewport and grid.pop.viewport.
+
+2. Added sum() method for units.
+
+ For example, try ...
+
+ grid.rect(w=sum(unit(c(.25,.25), "npc")))
+ grid.rect(w=sum(unit(c(.25,.25), "npc"), unit(1, "cm")), border="red")
+
+3. Changed the usage of grid.edit() slightly. If you want to specify
+ several new values at once, you must use grid.prop.list() rather
+ than just list(). For example, for a single new value use ...
+
+ grid.edit(<grob>, col="red")
+
+ ... as before, but for multiple new values use ...
+
+ grid.edit(<grob>, grid.prop.list(col="red", lty="dashed"))
+
+ ... rather than ...
+
+ grid.edit(<grob>, list(col="red", lty="dashed"))
+
+4. Added a new grid.frame() grob. This acts a bit like a simple
+ grid.collection() BUT controls the placement of its children.
+ You add children using the grid.pack() function.
+
+5. All viewports and grobs now have a "gp" slot which contains a
+ "gpar" object. This is a list of graphical parameters, which
+ replaces the specification of individual graphical parameters
+ for each different type of grob.
+
+ For example, instead of the old ...
+
+ grid.rect(w=.8, h=.8, border="red")
+
+ ... we have the new ...
+
+ grid.rect(w=.8, h=.8, gp=gpar(border="red"))
+
+ This may seem like a loss (because you have to type more stuff),
+ and it is a loss, but the (hopefully greater) win is that (i) you only
+ have one parameter for all graphical settings, for example, ...
+
+ grid.rect(w=.8, h=.8, gp=gpar(border="red", lwd=3))
+
+ ... and (ii) this applies for all grobs, for example, ...
+
+ grid.text("hi", gp=gpar(col="red", fontsize=10))
+
+ ... and (iii) you can add more graphical parameters with minimal fuss,
+ for example, ...
+
+ grid.text("hi", gp=gpar(col="red", fontsize=10, new.par=whatever))
+
+ ... and (iv) its easier to automate things (see below).
+
+ Graphical parameter settings are "permanent" so, for example, if
+ an axis sets the colour to "red" then all of its children are
+ drawn in "red" unless they set colour to something else.
+
+ For example, try ...
+
+ grid.multipanel(vp = grid.viewport(0.5, 0.5, 0.8, 0.8,
+ gp=gpar(fontsize=20)))
+
+ ... and notice that all of the components of the multipanel take
+ notice of the fontsize setting of the parent viewport (except the
+ axis labels because they explicitly set the fontsize to 20 themselves).
+
+ The setting of graphical parameters is automated;
+ if you have a slot called "gp" in your grob, Lattice will
+ set the graphical parameters in that slot before calling
+ draw.details() and unset the parameters afterwards.
+
+6. The pushing and popping of "local" viewports has been automated.
+ If you have a slot called "vp" in your grob, Lattice will call
+ grid.push.viewport() on that slot before calling draw.details()
+ and grid.pop.viewport() afterwards.
+
+7. "collection" grobs and "[x|y]axis" grobs no longer pass editing
+ operations down to their children.
+
+ This was mainly (only ?) for sharing graphical parameter settings
+ and that duty is now performed by the gpar stuff in point 5 above.
+
+ This is a good thing because there are some cases where passing
+ down editing operations could cause serious damage. For example,
+ consider what would have happened if you had edited the "vp" slot
+ of a collection grob (!)
+
diff --git a/win32/deps/library/grid/doc/displaylist.R b/win32/deps/library/grid/doc/displaylist.R
new file mode 100644
index 0000000..45ac75a
--- /dev/null
+++ b/win32/deps/library/grid/doc/displaylist.R
@@ -0,0 +1,130 @@
+### R code from vignette source 'displaylist.Rnw'
+
+###################################################
+### code chunk number 1: displaylist.Rnw:25-31
+###################################################
+library(grDevices)
+library(graphics) # for plot()
+library(stats) # for runif()
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+
+
+###################################################
+### code chunk number 2: guts1 (eval = FALSE)
+###################################################
+## plot(1:10)
+## par(new = TRUE)
+## grid.rect(width = 0.5, height = 0.5, gp = gpar(lwd = 3), name = "gr")
+##
+
+
+###################################################
+### code chunk number 3: ex1
+###################################################
+plot(1:10)
+par(new = TRUE)
+grid.rect(width = 0.5, height = 0.5, gp = gpar(lwd = 3), name = "gr")
+
+grid.rect(width = 0.99, height = 0.99, gp = gpar(lty = "dashed"))
+
+
+###################################################
+### code chunk number 4: ex2
+###################################################
+grid.rect(width = 0.5, height = 0.5, gp = gpar(col = "red", lwd = 3))
+grid.rect(width = 0.99, height = 0.99, gp = gpar(lty = "dashed"))
+
+
+
+###################################################
+### code chunk number 5: displaylist.Rnw:101-102 (eval = FALSE)
+###################################################
+## grid.edit("gr", gp = gpar(col = "red", lwd = 3))
+
+
+###################################################
+### code chunk number 6: displaylist.Rnw:132-133
+###################################################
+grid.rect(width = convertWidth(unit(1, "inches"), "npc"))
+
+
+###################################################
+### code chunk number 7: displaylist.Rnw:141-146
+###################################################
+drawDetails.myrect <- function(x, recording) {
+ gr <- rectGrob(width = convertWidth(unit(1, "inches"), "npc"))
+ grid.draw(gr)
+}
+grid.draw(grob(cl = "myrect"))
+
+
+###################################################
+### code chunk number 8: displaylist.Rnw:160-176
+###################################################
+x <- c(0.88, 1.00, 0.67, 0.34)
+y <- c(0.87, 0.43, 0.04, 0.94)
+z <- matrix(runif(4*2), ncol = 2)
+
+maxpiesize <- unit(1, "inches")
+totals <- apply(z, 1, sum)
+sizemult <- totals/max(totals)
+
+gs <- segmentsGrob(x0 = unit(c(rep(0, 4), x),
+ rep(c("npc", "native"), each = 4)),
+ x1 = unit(c(x, x), rep("native", 8)),
+ y0 = unit(c(y, rep(0, 4)),
+ rep(c("native", "npc"), each = 4)),
+ y1 = unit(c(y, y), rep("native", 8)),
+ gp = gpar(lty = "dashed", col = "grey"))
+gr <- rectGrob(gp = gpar(col = "grey", fill = "white", lty = "dashed"))
+
+
+###################################################
+### code chunk number 9: displaylist.Rnw:183-201
+###################################################
+drawDetails.pieplot <- function(x, recording) {
+ plot(x$x, x$y, xlim = c(-0.2, 1.2), ylim = c(-0.2, 1.2), type = "n")
+ vps <- baseViewports()
+ pushViewport(vps$inner, vps$figure, vps$plot, recording = FALSE)
+ grid.draw(x$gs, recording = FALSE)
+ for (i in 1:4) {
+ pushViewport(viewport(x = unit(x$x[i], "native"),
+ y = unit(x$y[i], "native"),
+ width = x$sizemult[i]*x$maxpiesize,
+ height = x$sizemult[i]*x$maxpiesize),
+ recording = FALSE)
+ grid.draw(x$gr, recording = FALSE)
+ par(plt = gridPLT(), new = TRUE)
+ pie(x$z[i, ], radius = 1, labels = rep("", 2))
+ popViewport(recording = FALSE)
+ }
+ popViewport(3, recording = FALSE)
+}
+
+
+###################################################
+### code chunk number 10: displaylist.Rnw:210-215
+###################################################
+if (suppressWarnings(require("gridBase", quietly = TRUE))) {
+grid.draw(grob(x = x, y = y, z = z,
+ maxpiesize = maxpiesize, sizemult = sizemult,
+ gs = gs, gr = gr, cl = "pieplot"))
+}
+
+
+###################################################
+### code chunk number 11: displaylist.Rnw:231-240
+###################################################
+drawDetails.mylegend <- function(x, recording) {
+ x <- 0:64/64
+ y <- sin(3*pi*x)
+ plot(x, y, type = "l", col = "blue",
+ main = "points with bg & legend(*, pt.bg)")
+ points(x, y, pch = 21, bg = "white")
+ legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, col = "blue")
+}
+grid.draw(grob(cl = "mylegend"))
+
+
diff --git a/win32/deps/library/grid/doc/displaylist.Rnw b/win32/deps/library/grid/doc/displaylist.Rnw
new file mode 100644
index 0000000..c9ff658
--- /dev/null
+++ b/win32/deps/library/grid/doc/displaylist.Rnw
@@ -0,0 +1,243 @@
+\documentclass[a4paper]{article}
+
+\usepackage{Rd}
+
+% \VignetteIndexEntry{Display Lists in grid}
+% \VignettePackage{grid}
+% \VignetteDepends{graphics}
+% \VignetteDepends{gridBase}
+
+\newcommand{\grid}{\pkg{grid}}
+\newcommand{\gridBase}{\CRANpkg{gridBase}}
+\newcommand{\lattice}{\CRANpkg{lattice}}
+
+\setlength{\parindent}{0in}
+\setlength{\parskip}{.1in}
+\setlength{\textwidth}{140mm}
+\setlength{\oddsidemargin}{10mm}
+
+\title{Display Lists in \grid{}}
+\author{Paul Murrell}
+
+\begin{document}
+\maketitle
+
+<<echo=FALSE, results=hide>>=
+library(grDevices)
+library(graphics) # for plot()
+library(stats) # for runif()
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+@
+A display list is a record of drawing operations. It is used
+to redraw graphics output when a graphics window is resized,
+when graphics output is copied from one device to another, and
+when graphics output is edited (via \code{grid.edit}).
+
+There are two display lists that can be used when working with
+\grid{}. \R{}'s graphics engine maintains a display list and
+\grid{} maintains its own display list. The former is maintained at
+the C code level and records both base graphics output and
+\grid{} graphics output. The latter is maintained at the
+R code level and only records \grid{} output.
+
+In standard usage,
+the graphics engine's display list is used to redraw when a window
+is resized and when copying between devices. \grid{}'s display list
+is used for redrawing when editing \grid{} output.
+
+There are two main problems with this standard usage:
+\begin{enumerate}
+\item The graphics engine display list only records graphics output;
+none of the calculations leading up to producing the output are
+recorded. This particularly impacts on plots which perform calculations
+based on the physical dimensions of the device -- an example is
+the legend function which performs calculations in order to
+arrange the elements of the legend. The effect can be seen from
+any example which uses the legend function. Try running
+\code{example(legend)} then resize the device (make it quite
+tall and thin or quite wide and fat); the legend will start
+to look pretty sick.
+
+{\bf NOTE:} that this is a problem with the graphics engine display
+list -- it is not specific to \grid{}. In fact, much of \grid{}'s
+behaviour is protected from this problem because things like \grid{}
+units are ``declarative'' and will be re-evaluated on each redraw.
+However, there are situations where \grid{} output can be afflicted,
+in particular, whenever the \code{convertUnit()} function (or one of
+its variants) is used (the help file for \code{convertUnit()} gives an
+example).
+
+A situation where this problem becomes very relevant for
+\grid{} output is when the \gridBase{} package is used.
+This is a situation where lots of calculations are performed
+in order to align base and grid output, but these calculations
+are not recorded on the graphics engine display list, so
+if the device is resized the output will become very yukky.
+
+\item \grid{}'s display list does not record base graphics
+output\footnote{This is not quite true; it is possible
+to include base graphics output on the \grid{} display list
+as we will see later.} so if both base and \grid{} output appear
+on the same device then the result of editing will not redraw the
+base output. The following code provides a simple example:
+
+<<guts1, eval=FALSE>>=
+plot(1:10)
+par(new = TRUE)
+grid.rect(width = 0.5, height = 0.5, gp = gpar(lwd = 3), name = "gr")
+
+<<ex1, echo=FALSE, fig=TRUE, width=4, height=3, include=FALSE>>=
+<<guts1>>
+grid.rect(width = 0.99, height = 0.99, gp = gpar(lty = "dashed"))
+@
+\includegraphics[width=4in, height=3in]{displaylist-ex1}
+
+<<ex2, echo=FALSE, fig=TRUE, width=4, height=3, include=FALSE>>=
+grid.rect(width = 0.5, height = 0.5, gp = gpar(col = "red", lwd = 3))
+grid.rect(width = 0.99, height = 0.99, gp = gpar(lty = "dashed"))
+
+<<eval=FALSE>>=
+grid.edit("gr", gp = gpar(col = "red", lwd = 3))
+@
+\includegraphics[width=4in, height=3in]{displaylist-ex2}
+
+After the \code{grid.edit}, the rectangle has been redrawn, but the
+base plot has not.
+\end{enumerate}
+
+\section*{Saving calculations on the graphics engine display list\\
+and saving base graphics on the \grid{} display list}
+
+Both of the problems described in the previous section can be
+avoided by using a \code{drawDetails()} method in \grid{}.
+When a \grid{} grob is drawn, the \code{drawDetails} method
+for that grob is called; if calculations are put within
+a \code{drawDetails} method, then the calculations will be
+performed every time the grob is drawn.
+
+This means that it is possible, for example, to use \code{convertUnit()}
+and have the result consistent across device resizes or
+copies\footnote{In
+each of the examples that follow, you should execute the example
+code, resize the device to see any inconsistency, then close the
+device before trying the next example.}.
+This next piece of code is an example where the output becomes
+inconsistent when the device is resized. We specify a width for
+the rectangle in inches, but convert it (gratuitously) to
+NPC coordinates -- when the device is resized, the NPC coordinates
+will no longer correspond to 1''.
+
+<<results=hide>>=
+grid.rect(width = convertWidth(unit(1, "inches"), "npc"))
+@
+
+The next piece of code demonstrates that, if we
+place the calculations within a \code{drawDetails} method, then
+the output remains consistent across device resizes and
+copies.
+
+<<results=hide>>=
+drawDetails.myrect <- function(x, recording) {
+ gr <- rectGrob(width = convertWidth(unit(1, "inches"), "npc"))
+ grid.draw(gr)
+}
+grid.draw(grob(cl = "myrect"))
+@
+
+The next example shows that a \code{drawDetails()} method can also be
+used to save base graphics output on the \grid{} display list. This
+example uses \gridBase{} to combine base and \grid{} graphics output.
+Here I replicate the last example from the \gridBase{} vignette -- a
+set of base pie charts within \grid{} viewports within a base plot.
+In this case, I can produce all of the grobs required in the normal
+manner -- their locations and sizes are not based on special
+calculations\footnote{The example is wrapped inside a check for
+ whether the \CRANpkg{gridBase} package is installed so that the code
+ will still ``run'' on systems without \CRANpkg{gridBase}.}.
+
+<<results=hide>>=
+x <- c(0.88, 1.00, 0.67, 0.34)
+y <- c(0.87, 0.43, 0.04, 0.94)
+z <- matrix(runif(4*2), ncol = 2)
+
+maxpiesize <- unit(1, "inches")
+totals <- apply(z, 1, sum)
+sizemult <- totals/max(totals)
+
+gs <- segmentsGrob(x0 = unit(c(rep(0, 4), x),
+ rep(c("npc", "native"), each = 4)),
+ x1 = unit(c(x, x), rep("native", 8)),
+ y0 = unit(c(y, rep(0, 4)),
+ rep(c("native", "npc"), each = 4)),
+ y1 = unit(c(y, y), rep("native", 8)),
+ gp = gpar(lty = "dashed", col = "grey"))
+gr <- rectGrob(gp = gpar(col = "grey", fill = "white", lty = "dashed"))
+@
+What is important is that I place the calls to the \gridBase{} functions
+within the \code{drawDetails} method so that they are performed
+every time the grob is drawn {\em and} the calls to the base graphics
+functions are in here too so that they are called for every redraw.
+
+<<results=hide>>=
+drawDetails.pieplot <- function(x, recording) {
+ plot(x$x, x$y, xlim = c(-0.2, 1.2), ylim = c(-0.2, 1.2), type = "n")
+ vps <- baseViewports()
+ pushViewport(vps$inner, vps$figure, vps$plot, recording = FALSE)
+ grid.draw(x$gs, recording = FALSE)
+ for (i in 1:4) {
+ pushViewport(viewport(x = unit(x$x[i], "native"),
+ y = unit(x$y[i], "native"),
+ width = x$sizemult[i]*x$maxpiesize,
+ height = x$sizemult[i]*x$maxpiesize),
+ recording = FALSE)
+ grid.draw(x$gr, recording = FALSE)
+ par(plt = gridPLT(), new = TRUE)
+ pie(x$z[i, ], radius = 1, labels = rep("", 2))
+ popViewport(recording = FALSE)
+ }
+ popViewport(3, recording = FALSE)
+}
+@
+The ``pieplot'' is created by assembling the component grobs
+into a collective grob of the appropriate class; the \code{drawDetails}
+method takes care of actually producing the output.
+
+% produce figure, but don't include
+% (to avoid par setting contamination between code segments)
+
+<<results=hide, fig=TRUE, width=6, height=6, include=FALSE>>=
+if (suppressWarnings(require("gridBase", quietly = TRUE))) {
+grid.draw(grob(x = x, y = y, z = z,
+ maxpiesize = maxpiesize, sizemult = sizemult,
+ gs = gs, gr = gr, cl = "pieplot"))
+}
+@
+
+The output from this example can be resized safely; \grid{} handles
+all of the redrawing, and performs all of the actions within the
+\code{drawDetails} method for each redraw, including redrawing the
+base graphics output!
+
+As a final example, we will harness the \grid{} display list purely to
+achieve consistency in base graphics output. The following reproduces
+the last example from the \code{legend()} help page, but produces
+output which can be resized without the legend going crazy.
+
+% produce figure, but don't include
+% (to avoid par setting contamination between code segments)
+
+<<results=hide, fig=TRUE, include=FALSE>>=
+drawDetails.mylegend <- function(x, recording) {
+ x <- 0:64/64
+ y <- sin(3*pi*x)
+ plot(x, y, type = "l", col = "blue",
+ main = "points with bg & legend(*, pt.bg)")
+ points(x, y, pch = 21, bg = "white")
+ legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, col = "blue")
+}
+grid.draw(grob(cl = "mylegend"))
+@
+\end{document}
+
diff --git a/win32/deps/library/grid/doc/displaylist.pdf b/win32/deps/library/grid/doc/displaylist.pdf
new file mode 100644
index 0000000..ede2d8f
Binary files /dev/null and b/win32/deps/library/grid/doc/displaylist.pdf differ
diff --git a/win32/deps/library/grid/doc/frame.R b/win32/deps/library/grid/doc/frame.R
new file mode 100644
index 0000000..4895325
--- /dev/null
+++ b/win32/deps/library/grid/doc/frame.R
@@ -0,0 +1,148 @@
+### R code from vignette source 'frame.Rnw'
+
+###################################################
+### code chunk number 1: frame.Rnw:19-24
+###################################################
+library(grDevices)
+library(stats) # for runif
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+
+
+###################################################
+### code chunk number 2: frame.Rnw:50-51
+###################################################
+gf <- frameGrob()
+
+
+###################################################
+### code chunk number 3: frame.Rnw:96-97
+###################################################
+gf <- packGrob(gf, textGrob("Hello frame!"))
+
+
+###################################################
+### code chunk number 4: frame1
+###################################################
+st <- grid.text("some text")
+grid.rect(width = unit(1, "grobwidth", st),
+ height = unit(1, "grobheight", st))
+
+
+###################################################
+### code chunk number 5: frame1
+###################################################
+grid.text("some text", name = "st")
+grid.rect(width = unit(1, "grobwidth", "st"),
+ height = unit(1, "grobheight", "st"))
+
+
+###################################################
+### code chunk number 6: frame.Rnw:136-138 (eval = FALSE)
+###################################################
+## grid.edit("st", gp = gpar(fontsize = 20))
+##
+
+
+###################################################
+### code chunk number 7: frame2
+###################################################
+my.text <- textGrob("some text")
+my.text <- editGrob(my.text, gp = gpar(fontsize = 20))
+my.rect <- rectGrob(width = unit(1, "grobwidth", my.text),
+ height = unit(1, "grobheight", my.text))
+grid.draw(my.text)
+grid.draw(my.rect)
+
+
+###################################################
+### code chunk number 8: frame.Rnw:153-155 (eval = FALSE)
+###################################################
+## grid.edit("st", label="some different text")
+##
+
+
+###################################################
+### code chunk number 9: frame3
+###################################################
+my.text <- textGrob("some text")
+my.text <- editGrob(my.text, gp = gpar(fontsize = 20))
+my.text <- editGrob(my.text, label = "some different text")
+my.rect <- rectGrob(width = unit(1, "grobwidth", my.text),
+ height = unit(1, "grobheight", my.text))
+grid.draw(my.text)
+grid.draw(my.rect)
+
+
+###################################################
+### code chunk number 10: frame.Rnw:247-281
+###################################################
+legendGrob <- function(pch, labels, frame = TRUE,
+ hgap = unit(1, "lines"), vgap = unit(1, "lines"),
+ default.units = "lines",
+ vp = NULL) {
+ nkeys <- length(labels)
+ gf <- frameGrob(vp = vp)
+ for (i in 1:nkeys) {
+ if (i == 1) {
+ symbol.border <- unit.c(vgap, hgap, vgap, hgap)
+ text.border <- unit.c(vgap, unit(0, "npc"), vgap,
+ hgap)
+ } else {
+ symbol.border <- unit.c(vgap, hgap, unit(0, "npc"), hgap)
+ text.border <- unit.c(vgap, unit(0, "npc"), unit(0, "npc"), hgap)
+ }
+ gf <- packGrob(gf, pointsGrob(0.5, 0.5, pch = pch[i]),
+ col = 1, row = i, border = symbol.border,
+ width = unit(1, "lines"),
+ height = unit(1, "lines"), force.width = TRUE)
+ gf <- packGrob(gf, textGrob(labels[i], x = 0, y = 0.5,
+ just = c("left", "centre")),
+ col = 2, row = i, border = text.border)
+ }
+ gf
+}
+
+grid.legend <- function(pch, labels, frame = TRUE,
+ hgap = unit(1, "lines"), vgap = unit(1, "lines"),
+ default.units = "lines", draw = TRUE,
+ vp = NULL) {
+ gf <- legendGrob(pch, labels, frame, hgap, vgap, default.units, vp)
+ if (draw) grid.draw(gf)
+ gf
+}
+
+
+###################################################
+### code chunk number 11: legend
+###################################################
+grid.legend(1:3, c("one line", "two\nlines", "three\nlines\nof text"))
+
+
+
+###################################################
+### code chunk number 12: plot
+###################################################
+top.vp <- viewport(width = 0.8, height = 0.8)
+pushViewport(top.vp)
+x <- runif(10)
+y1 <- runif(10)
+y2 <- runif(10)
+pch <- 1:3
+labels <- c("Girls", "Boys", "Other")
+gf <- frameGrob()
+plt <- gTree(children = gList(rectGrob(),
+ pointsGrob(x, y1, pch = 1),
+ pointsGrob(x, y2, pch = 2),
+ xaxisGrob(),
+ yaxisGrob()))
+gf <- packGrob(gf, plt)
+gf <- packGrob(gf, legendGrob(pch, labels),
+ height = unit(1, "null"), side = "right")
+grid.rect(gp = gpar(col = "grey"))
+grid.draw(gf)
+popViewport()
+grid.rect(gp = gpar(lty = "dashed"), width = .99, height = .99)
+
+
diff --git a/win32/deps/library/grid/doc/frame.Rnw b/win32/deps/library/grid/doc/frame.Rnw
new file mode 100644
index 0000000..3c44b10
--- /dev/null
+++ b/win32/deps/library/grid/doc/frame.Rnw
@@ -0,0 +1,384 @@
+\documentclass[a4paper]{article}
+%\VignetteIndexEntry{Frames and packing grobs}
+%\VignettePackage{grid}
+\newcommand{\code}[1]{\texttt{#1}}
+\newcommand{\pkg}[1]{{\normalfont\fontseries{b}\selectfont #1}}
+\newcommand{\grid}{\pkg{grid}}
+\newcommand{\R}{{\sffamily R}}
+\setlength{\parindent}{0in}
+\setlength{\parskip}{.1in}
+\setlength{\textwidth}{140mm}
+\setlength{\oddsidemargin}{10mm}
+
+\title{A GUI-Builder Approach to \grid{} Graphics}
+\author{Paul Murrell}
+
+\begin{document}
+\maketitle
+
+<<echo=FALSE, results=hide>>=
+library(grDevices)
+library(stats) # for runif
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+@
+Grid contains a lot of support for locating, sizing, and arranging
+graphical components on a device and with respect to each other.
+However, most of this support relies on \emph{either} the parent
+object dictating both location and size (layouts) \emph{or} the child
+dictating both location and size.
+
+Some sorts of arrangements are more conveniently handled by having the
+parent dictate the location, but letting the child dictate the size.
+This is the situation for GUI-builders (software which forms
+arrangements of GUI components or widgets). The approach taken by
+(many ?) GUI-builders is to allow the user to create a parent
+\emph{frame} and then \emph{pack} widgets into this frame. The frame
+locates and arranges the children with the help of hints such as
+``place this widget at the bottom of the frame'', and the children
+dictate what size they would like to be.
+
+This document describes a first attempt at such an interface for
+arranging Grid graphical objects.
+
+\section*{The \code{"frame"} grob}
+You can create a \code{"frame"} graphical object using the function
+\code{frameGrob()}. You must assign the result to a variable in order
+to pack grobs into it.
+
+<<results=hide>>=
+gf <- frameGrob()
+@
+\section*{The \code{packGrob()} function}
+Having created a frame, you can then pack other graphical objects into
+it using the \code{packGrob()} function. This function has a complex
+interface which allows for a variety of methods of packing graphical
+objects. The required arguments are:
+\begin{description}
+\item[\code{frame}] is a \code{"frame"} object created by \code{grid.frame}.
+\item[\code{grob}] is the grob to pack into the frame.
+\end{description}
+The remaining arguments specify where the grob is located in the frame
+and possibly how much space the grob should occupy. The frame is effectively
+just a layout; you can add grobs to existing rows and columns
+or you can append the grob in a new row and/or column. If the
+grob is added to an existing row then the height of
+that row becomes the maximum of the new height and
+the previous height. If the row is new then it just
+gets the specified height. Similar rules apply for column widths.
+\begin{description}
+\item[\code{col}] is the column to put the grob in. This can be 1 greater than
+the existing number of columns (in which case a new column is added).
+\item[\code{row}] is like \code{col} but for rows.
+\item[\code{col.after}] specifies that the grob should be put in a
+new column inserted between \code{col.after} and \code{col.after + 1}.
+\item[\code{col.before}] specifies that the grob should be put in a
+new column inserted between \code{col.before} and \code{col.before + 1}.
+\item[\code{row.after} and \code{row.before}] do what you would expect.
+\item[\code{side}] specifies which side to append the new grob to.
+The valid values are \code{"left"}, \code{"right"}, \code{"bottom"},
+and \code{"top"}.
+\item[\code{width}] is the width of the row that the grob is being packed
+into. If this is not given then the grob supplies the width.
+\item[\code{height}] is like \code{width} but for rows.
+\end{description}
+It is possible to modify this default behaviour. For example, it is possible
+to add a grob to a row and force that row to have the specified height
+by setting \code{force.height=TRUE} (and similarly for column widths).
+It is also possible to pack a graphical object into several rows or
+columns at once (although you cannot simultaneously affect the heights or
+widths of those rows and columns).
+
+The result of this function is the modified frame, so you must
+assign the result to a variable.
+
+<<results=hide>>=
+gf <- packGrob(gf, textGrob("Hello frame!"))
+@
+\section*{\code{"grobwidth"} and \code{"grobheight"} units}
+
+A \code{"frame"} object allows a grob to specify its size by making
+use of \code{"grobwidth"} and \code{"grobheight"} units.
+These units may, of course, be used outside of frames too so
+their use is described here.
+
+Consider a simple example where I want to draw a rectangle around
+a piece of text. I can get the size of the piece of text from the
+\code{"text"} grob as follows:
+
+<<frame1, include=FALSE, width=4, height=2, fig=TRUE, results=hide>>=
+st <- grid.text("some text")
+grid.rect(width = unit(1, "grobwidth", st),
+ height = unit(1, "grobheight", st))
+@
+\begin{center}
+\includegraphics[height=1in, width=2in]{frame-frame1}
+\end{center}
+@
+You could do the same thing with simple \code{"strwidth"}
+and \code{"strheight"} units, but \code{"grobwidth"} and \code{"grobheight"}
+give you a lot more power. The biggest gain is that you
+can get the size of other objects besides pieces of text (more on that
+soon). Another thing you can do is provide a ``reference'' to a grob
+rather than the grob itself; you do this by giving the name of a grob.
+What this does is make the unit ``dynamic'' so that changes in the
+grob affect the unit. The following is a dynamic version of the
+previous example.
+
+<<frame1, include=FALSE, width=4, height=2, fig=TRUE, results=hide>>=
+grid.text("some text", name = "st")
+grid.rect(width = unit(1, "grobwidth", "st"),
+ height = unit(1, "grobheight", "st"))
+@
+Now watch what happens if I modify the text grob named \code{"st"}:
+
+<<results=hide, eval=FALSE>>=
+grid.edit("st", gp = gpar(fontsize = 20))
+
+<<frame2, echo=FALSE, include=FALSE, width=4, height=2, fig=TRUE, results=hide>>=
+my.text <- textGrob("some text")
+my.text <- editGrob(my.text, gp = gpar(fontsize = 20))
+my.rect <- rectGrob(width = unit(1, "grobwidth", my.text),
+ height = unit(1, "grobheight", my.text))
+grid.draw(my.text)
+grid.draw(my.rect)
+@
+\begin{center}
+\includegraphics[height=1in, width=2in]{frame-frame2}
+\end{center}
+@
+Similarly, I can change the text itself:
+
+<<results=hide, eval=FALSE>>=
+grid.edit("st", label="some different text")
+
+<<frame3, echo=FALSE, include=FALSE, width=4, height=2, fig=TRUE, results=hide>>=
+my.text <- textGrob("some text")
+my.text <- editGrob(my.text, gp = gpar(fontsize = 20))
+my.text <- editGrob(my.text, label = "some different text")
+my.rect <- rectGrob(width = unit(1, "grobwidth", my.text),
+ height = unit(1, "grobheight", my.text))
+grid.draw(my.text)
+grid.draw(my.rect)
+@
+\begin{center}
+\includegraphics[height=1in, width=2in]{frame-frame3}
+\end{center}
+@
+\section*{The \code{widthDetails} and \code{heightDetails} generic functions}
+
+The calculation of \code{"grobwidth"} and \code{"grobheight"} units
+is a bit complicated, but fortunately most of it is automated.
+The simple part is that a grob provides a normal \code{"unit"} object
+to express its width or height. The complication comes because that
+\code{"unit"} object has to be evaluated in the correct context; in
+particular, if the grob has a non-\code{NULL} \code{vp} argument then
+those viewports have to be pushed so that the size of the grob is
+the size it would be when it is drawn. This is achieved by calling the
+\code{preDrawDetails()} function for the grob and in most cases what
+happens by default will be correct. The thing to avoid is having
+any viewport operations in a \code{drawDetails()} method for your
+grob; they should go in a \code{preDrawDetails()} method.
+
+All that needs to be written (usually) are the functions that
+provide the \code{"unit"} objects. These functions need to be
+\code{widthDetails} and \code{heightDetails} methods.
+
+The default methods return \code{unit(1, "null")}
+so your grob will be of this size unless you write your own methods.
+
+The classic example methods are those for \code{"text"} grobs; these
+return \code{unit(1, "mystrwidth", <text grob label>)} and
+\code{unit(1, "mystrheight", <text grob label>)} respectively.
+
+The other very important examples of these methods are those for
+\code{"frame"} grobs. These return the \code{sum} of the
+widths (heights) of the columns (rows) of the layout that has been
+built up by packing grobs into the frame. This means that
+when a \code{"frame"} grob is packed within another \code{"frame"} grob
+the parent automatically leaves enough room for the child.
+
+Another useful pair of examples are those for \code{"rect"} grobs.
+These methods make use of the \code{absolute.size} function.
+When a grob is asked to specify its size, it makes sense to respond
+with the grob's width and height if the grob has an ``absolute'' size
+(e.g., \code{"inches"}, \code{"cm"}, \code{"lines"}, etc;
+ i.e., the grob knows exactly how big itself is).
+On the other hand, it does not make sense to respond with the grob's
+width and height if the grob has a ``relative'' size (e.g., \code{"npc"} or
+\code{"native"}; i.e.,
+the grob needs to know about it's parent's size before it can figure
+out its own). The \code{absolute.size} function leaves absolute
+units alone, but converts relative units to \code{"null"} units
+(i.e., the child says to the parent, ``you decide how big I should be''), so
+you can return something like \code{absolute.size(width(<grob>))} in order
+to always give a sensible answer.
+
+@
+\section*{Examples}
+The original motivating example for this GUI-builder approach was
+to be able to produce a quite general-purpose legend grob.
+
+A legend consists of data symbols and associated textual descriptions.
+In order to be quite general, it would be nice to allow, for example,
+multiple lines of text per data symbol. Rather than having to look at
+the text supplied for the legend in order to determine the arrangement
+of the legend, it would be nice to be able to simply specify the
+composition of the legend and let it figure out the arrangement for
+us. The code below defines just such a legend grob, using the new
+\code{"frame"} grob and \code{packGrob()} function. Some points to
+note are:
+
+\begin{itemize}
+\item The use of \code{border}s to create space around the legend
+components.
+\item The size of the data symbol component is specified, but the
+size of the text components are taken from the \code{"text"} grobs.
+
+\item The heights of the rows in the legend will be the maximum of
+$\code{vgap} + \code{unit(1, "lines")}$ and $\code{vgap} +
+\code{unit(1, "grobheight", <text grob>)}$.
+
+\item We have two functions, one for generating a grob and one
+for producing output.
+\end{itemize}
+
+<<>>=
+legendGrob <- function(pch, labels, frame = TRUE,
+ hgap = unit(1, "lines"), vgap = unit(1, "lines"),
+ default.units = "lines",
+ vp = NULL) {
+ nkeys <- length(labels)
+ gf <- frameGrob(vp = vp)
+ for (i in 1:nkeys) {
+ if (i == 1) {
+ symbol.border <- unit.c(vgap, hgap, vgap, hgap)
+ text.border <- unit.c(vgap, unit(0, "npc"), vgap,
+ hgap)
+ } else {
+ symbol.border <- unit.c(vgap, hgap, unit(0, "npc"), hgap)
+ text.border <- unit.c(vgap, unit(0, "npc"), unit(0, "npc"), hgap)
+ }
+ gf <- packGrob(gf, pointsGrob(0.5, 0.5, pch = pch[i]),
+ col = 1, row = i, border = symbol.border,
+ width = unit(1, "lines"),
+ height = unit(1, "lines"), force.width = TRUE)
+ gf <- packGrob(gf, textGrob(labels[i], x = 0, y = 0.5,
+ just = c("left", "centre")),
+ col = 2, row = i, border = text.border)
+ }
+ gf
+}
+
+grid.legend <- function(pch, labels, frame = TRUE,
+ hgap = unit(1, "lines"), vgap = unit(1, "lines"),
+ default.units = "lines", draw = TRUE,
+ vp = NULL) {
+ gf <- legendGrob(pch, labels, frame, hgap, vgap, default.units, vp)
+ if (draw) grid.draw(gf)
+ gf
+}
+@
+The next piece of code shows the \code{grid.legend()} function being
+used procedurally; the output is shown below the code.
+
+<<legend, include=FALSE, width=4, height=2, fig=TRUE, results=hide>>=
+grid.legend(1:3, c("one line", "two\nlines", "three\nlines\nof text"))
+
+@
+\begin{center}
+\includegraphics[height=2in, width=4in]{frame-legend}
+\end{center}
+
+@
+The legend example might not seem too difficult to do by hand rather
+than using frames and packing, but the next example shows how
+useful it can be.
+
+Suppose you want to arrange a legend next to a plot. This requires
+leaving enough space for the legend and then filling the remaining
+space with the plot. This requires figuring out how much space the
+legend needs, and that is a task that is neither trivial nor
+easy to cater for in the general case. Ideally, we want to know
+as little as possible about the legend.
+
+With the GUI-builder
+approach this becomes extremely simple. The code below
+shows how the construction of such a scene might be performed; the
+output from the code is again shown below.
+
+The following points are noteworthy:
+
+\begin{itemize}
+\item We don't need to know anything about how the legend was
+constructed; it could be any sort of grob.
+\item We specify the height of the legend to be \code{unit(1, "null")}
+so that it will occupy the full height of the plot. If we
+did not do this then the plot would be forced to be the height of
+the legend (because of the way that \code{"null"} units interact
+with other units).
+\item The width of the legend is calculated from the contents of the
+legend because the legend is a \code{"frame"} grob.
+\item The dimensions of the ``plot'' default to \code{unit(1, "null")}
+because \code{"collection"} grobs have no width or height methods, which
+means that the plot fills up whatever space remains once the
+legend has been accommodated.
+\end{itemize}
+
+<<plot, echo=FALSE, include=FALSE, fig=TRUE, results=hide>>=
+top.vp <- viewport(width = 0.8, height = 0.8)
+pushViewport(top.vp)
+x <- runif(10)
+y1 <- runif(10)
+y2 <- runif(10)
+pch <- 1:3
+labels <- c("Girls", "Boys", "Other")
+gf <- frameGrob()
+plt <- gTree(children = gList(rectGrob(),
+ pointsGrob(x, y1, pch = 1),
+ pointsGrob(x, y2, pch = 2),
+ xaxisGrob(),
+ yaxisGrob()))
+gf <- packGrob(gf, plt)
+gf <- packGrob(gf, legendGrob(pch, labels),
+ height = unit(1, "null"), side = "right")
+grid.rect(gp = gpar(col = "grey"))
+grid.draw(gf)
+popViewport()
+grid.rect(gp = gpar(lty = "dashed"), width = .99, height = .99)
+@
+\begin{center}
+\includegraphics{frame-plot}
+\end{center}
+@
+\section*{Notes}
+\begin{enumerate}
+\item There are \code{grid.frame()} and \code{grid.pack()} equivalents
+for these functions, but these are really only useful to see the
+changes in the frame as each packing operation takes place.
+
+\item This frame-and-packing stuff is easier to use, \emph{but}
+(in almost all cases) it is less efficient than specifying the
+arrangement by hand. There is consequently a penalty to pay in
+terms of memory (inconsequential I think) and in terms of speed
+(noticeably slower).
+
+Perhaps one sensible use of these functions is to
+build an image interactively using the simple arguments,
+which will be slow, then attempt to speed up the drawing
+by exploring some of the more advanced arguments.
+
+One way to speed things up a bit is to specify the layout when
+the frame is initially created and then use the \code{placeGrob()} function
+to put grobs into existing rows and columns.
+
+The speed penalty in the cases I have seen are mostly due to the time
+taken to generate the (sometimes very) complicated unit objects that
+express the heights and widths of the rows and columns of the frame
+layout. Future effort will be put into speeding up the creation of
+unit objects.
+\end{enumerate}
+\end{document}
+
+
diff --git a/win32/deps/library/grid/doc/frame.pdf b/win32/deps/library/grid/doc/frame.pdf
new file mode 100644
index 0000000..9558a6e
Binary files /dev/null and b/win32/deps/library/grid/doc/frame.pdf differ
diff --git a/win32/deps/library/grid/doc/grid.R b/win32/deps/library/grid/doc/grid.R
new file mode 100644
index 0000000..97a1da9
--- /dev/null
+++ b/win32/deps/library/grid/doc/grid.R
@@ -0,0 +1,329 @@
+### R code from vignette source 'grid.Rnw'
+
+###################################################
+### code chunk number 1: grid.Rnw:27-33
+###################################################
+library(grDevices)
+library(graphics) # for par
+library(stats) # for rnorm
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+
+
+###################################################
+### code chunk number 2: grid.Rnw:75-76 (eval = FALSE)
+###################################################
+## viewport(x = 0.5, y = 0.5, width = 0.5, height = 0.25, angle=45)
+
+
+###################################################
+### code chunk number 3: viewport
+###################################################
+grid.show.viewport(viewport(x = 0.5, y = 0.5, width = 0.5, height = 0.25,
+ angle = 45))
+
+
+###################################################
+### code chunk number 4: pushviewports
+###################################################
+grid.rect(gp = gpar(lty = "dashed"))
+vp1 <- viewport(x = 0, y = 0.5, w = 0.5, h = 0.5,
+ just = c("left", "bottom"), name = "vp1")
+vp2 <- viewport(x = 0.5, y = 0, w = 0.5, h = 0.5,
+ just = c("left", "bottom"))
+pushViewport(vp1)
+grid.rect(gp = gpar(col = "grey"))
+grid.text("Some drawing in graphics region 1", y = 0.8)
+upViewport()
+pushViewport(vp2)
+grid.rect(gp = gpar(col = "grey"))
+grid.text("Some drawing in graphics region 2", y = 0.8)
+upViewport()
+downViewport("vp1")
+grid.text("MORE drawing in graphics region 1", y = 0.2)
+popViewport()
+
+
+###################################################
+### code chunk number 5: vpstack
+###################################################
+grid.rect(gp = gpar(lty = "dashed"))
+vp <- viewport(width = 0.5, height = 0.5)
+pushViewport(vp)
+grid.rect(gp = gpar(col = "grey"))
+grid.text("quarter of the page", y = 0.85)
+pushViewport(vp)
+grid.rect()
+grid.text("quarter of the\nprevious viewport")
+popViewport(2)
+
+
+###################################################
+### code chunk number 6: units
+###################################################
+unit(1, "npc")
+unit(1:3/4, "npc")
+unit(1:3/4, "npc")[2]
+unit(1:3/4, "npc") + unit(1, "inches")
+min(unit(0.5, "npc"), unit(1, "inches"))
+unit.c(unit(0.5, "npc"), unit(2, "inches") + unit(1:3/4, "npc"),
+ unit(1, "strwidth", "hi there"))
+
+
+###################################################
+### code chunk number 7: vpcoords
+###################################################
+pushViewport(viewport(y = unit(3, "lines"), width = 0.9, height = 0.8,
+ just = "bottom", xscale = c(0, 100)))
+grid.rect(gp = gpar(col = "grey"))
+grid.xaxis()
+pushViewport(viewport(x = unit(60, "native"), y = unit(0.5, "npc"),
+ width = unit(1, "strwidth", "coordinates for everyone"),
+ height = unit(3, "inches")))
+grid.rect()
+grid.text("coordinates for everyone")
+popViewport(2)
+
+
+###################################################
+### code chunk number 8: vplayout
+###################################################
+pushViewport(viewport(layout = grid.layout(4, 5)))
+grid.rect(gp = gpar(col = "grey"))
+grid.segments(c(1:4/5, rep(0, 3)), c(rep(0, 4), 1:3/4),
+ c(1:4/5, rep(1, 3)), c(rep(1, 4), 1:3/4),
+ gp = gpar(col = "grey"))
+pushViewport(viewport(layout.pos.col = 2:3, layout.pos.row = 3))
+grid.rect(gp = gpar(lwd = 3))
+popViewport(2)
+
+
+###################################################
+### code chunk number 9: layoutcomplex
+###################################################
+grid.show.layout(grid.layout(4, 4, widths = unit(c(3, 1, 1, 1),
+ c("lines", "null", "null", "cm")),
+ heights = c(1, 1, 2, 3),
+ c("cm", "null", "null", "lines")))
+
+
+###################################################
+### code chunk number 10: gpar
+###################################################
+pushViewport(viewport(gp = gpar(fill = "grey", fontface = "italic")))
+grid.rect()
+grid.rect(width = 0.8, height = 0.6, gp = gpar(fill = "white"))
+grid.text(paste("This text and the inner rectangle",
+ "have specified their own gpar settings", sep = "\n"),
+ y = 0.75, gp = gpar(fontface = "plain"))
+grid.text(paste("This text and the outer rectangle",
+ "accept the gpar settings of the viewport", sep = "\n"),
+ y = 0.25)
+popViewport()
+
+
+###################################################
+### code chunk number 11: simpleplot
+###################################################
+grid.rect(gp = gpar(lty = "dashed"))
+x <- y <- 1:10
+pushViewport(plotViewport(c(5.1, 4.1, 4.1, 2.1)))
+pushViewport(dataViewport(x, y))
+grid.rect()
+grid.xaxis()
+grid.yaxis()
+grid.points(x, y)
+grid.text("1:10", x = unit(-3, "lines"), rot = 90)
+popViewport(2)
+
+
+###################################################
+### code chunk number 12: bpdata
+###################################################
+barData <- matrix(sample(1:4, 16, replace = TRUE), ncol = 4)
+
+
+###################################################
+### code chunk number 13: barconstraint
+###################################################
+boxColours <- 1:4
+
+
+###################################################
+### code chunk number 14: bpfun
+###################################################
+bp <- function(barData) {
+ nbars <- dim(barData)[2]
+ nmeasures <- dim(barData)[1]
+ barTotals <- rbind(rep(0, nbars), apply(barData, 2, cumsum))
+ barYscale <- c(0, max(barTotals)*1.05)
+ pushViewport(plotViewport(c(5, 4, 4, 1),
+ yscale = barYscale,
+ layout = grid.layout(1, nbars)))
+ grid.rect()
+ grid.yaxis()
+ for (i in 1:nbars) {
+ pushViewport(viewport(layout.pos.col = i, yscale = barYscale))
+ grid.rect(x = rep(0.5, nmeasures),
+ y = unit(barTotals[1:nmeasures, i], "native"),
+ height = unit(diff(barTotals[,i]), "native"),
+ width = 0.8, just = "bottom", gp = gpar(fill = boxColours))
+ popViewport()
+ }
+ popViewport()
+}
+
+
+###################################################
+### code chunk number 15: legendlabels
+###################################################
+legLabels <- c("Group A", "Group B", "Group C", "Something Longer")
+boxSize <- unit(0.5, "inches")
+
+
+###################################################
+### code chunk number 16: legfun
+###################################################
+leg <- function(legLabels) {
+ nlabels <- length(legLabels)
+ pushViewport(viewport(layout = grid.layout(nlabels, 1)))
+ for (i in 1:nlabels) {
+ pushViewport(viewport(layout.pos.row = i))
+ grid.rect(width = boxSize, height = boxSize, just = "bottom",
+ gp = gpar(fill = boxColours[i]))
+ grid.text(legLabels[i], y = unit(0.5, "npc") - unit(1, "lines"))
+ popViewport()
+ }
+ popViewport()
+}
+
+
+###################################################
+### code chunk number 17: barplot
+###################################################
+grid.rect(gp = gpar(lty = "dashed"))
+legend.width <- max(unit(rep(1, length(legLabels)),
+ "strwidth", as.list(legLabels)) +
+ unit(2, "lines"),
+ unit(0.5, "inches") + unit(2, "lines"))
+pushViewport(viewport(layout = grid.layout(1, 2,
+ widths = unit.c(unit(1,"null"), legend.width))))
+pushViewport(viewport(layout.pos.col = 1))
+bp(barData)
+popViewport()
+pushViewport(viewport(layout.pos.col = 2))
+pushViewport(plotViewport(c(5, 0, 4, 0)))
+leg(legLabels)
+popViewport(3)
+
+
+###################################################
+### code chunk number 18: grid.Rnw:649-650
+###################################################
+library(lattice)
+
+
+###################################################
+### code chunk number 19: trellisdata (eval = FALSE)
+###################################################
+## x <- rnorm(100)
+## y <- rnorm(100)
+## g <- sample(1:8, 100, replace = TRUE)
+
+
+###################################################
+### code chunk number 20: trellispanelplot (eval = FALSE)
+###################################################
+## xyplot(y ~ x | g, panel = function(x, y) {
+## panel.xyplot(x, y);
+## grid.lines(unit(c(0, 1), "npc"), unit(0, "native"),
+## gp = gpar(col = "grey"))
+## })
+
+
+###################################################
+### code chunk number 21: trellispanel
+###################################################
+x <- rnorm(100)
+y <- rnorm(100)
+g <- sample(1:8, 100, replace = TRUE)
+xyplot(y ~ x | g, panel = function(x, y) {
+ panel.xyplot(x, y);
+ grid.lines(unit(c(0, 1), "npc"), unit(0, "native"),
+ gp = gpar(col = "grey"))
+})
+
+
+###################################################
+### code chunk number 22: trellisstripplot (eval = FALSE)
+###################################################
+## xyplot(y ~ x | g, strip = function(which.given, which.panel, ...) {
+## grid.text(paste("Variable ", which.given, ": Level ",
+## which.panel[which.given], sep = ""),
+## unit(1, "mm"), .5, just = "left")
+## })
+
+
+###################################################
+### code chunk number 23: trellisstrip
+###################################################
+x <- rnorm(100)
+y <- rnorm(100)
+g <- sample(1:8, 100, replace = TRUE)
+xyplot(y ~ x | g, strip = function(which.given, which.panel, ...) {
+ grid.text(paste("Variable ", which.given, ": Level ",
+ which.panel[which.given], sep = ""),
+ unit(1, "mm"), .5, just = "left")
+})
+
+
+###################################################
+### code chunk number 24: trellisgridplot (eval = FALSE)
+###################################################
+## someText <- paste("A panel of text", "produced using", "raw grid code",
+## "that could be used", "to describe",
+## "the plot", "to the right.", sep = "\n")
+## latticePlot <- xyplot(y ~ x | g, layout = c(2, 4))
+## grid.rect(gp = gpar(lty = "dashed"))
+## pushViewport(viewport(layout = grid.layout(1, 2,
+## widths = unit.c(unit(1, "strwidth", someText) +
+## unit(2, "cm"),
+## unit(1, "null")))))
+## pushViewport(viewport(layout.pos.col = 1))
+## grid.rect(gp = gpar(fill = "light grey"))
+## grid.text(someText,
+## x = unit(1, "cm"), y = unit(1, "npc") - unit(1, "inches"),
+## just = c("left", "top"))
+## popViewport()
+## pushViewport(viewport(layout.pos.col = 2))
+## print(latticePlot, newpage = FALSE)
+## popViewport(2)
+
+
+###################################################
+### code chunk number 25: trellisgrid
+###################################################
+x <- rnorm(100)
+y <- rnorm(100)
+g <- sample(1:8, 100, replace = TRUE)
+someText <- paste("A panel of text", "produced using", "raw grid code",
+ "that could be used", "to describe",
+ "the plot", "to the right.", sep = "\n")
+latticePlot <- xyplot(y ~ x | g, layout = c(2, 4))
+grid.rect(gp = gpar(lty = "dashed"))
+pushViewport(viewport(layout = grid.layout(1, 2,
+ widths = unit.c(unit(1, "strwidth", someText) +
+ unit(2, "cm"),
+ unit(1, "null")))))
+pushViewport(viewport(layout.pos.col = 1))
+grid.rect(gp = gpar(fill = "light grey"))
+grid.text(someText,
+ x = unit(1, "cm"), y = unit(1, "npc") - unit(1, "inches"),
+ just = c("left", "top"))
+popViewport()
+pushViewport(viewport(layout.pos.col = 2))
+print(latticePlot, newpage = FALSE)
+popViewport(2)
+
+
diff --git a/win32/deps/library/grid/doc/grid.Rnw b/win32/deps/library/grid/doc/grid.Rnw
new file mode 100644
index 0000000..b2b00c1
--- /dev/null
+++ b/win32/deps/library/grid/doc/grid.Rnw
@@ -0,0 +1,751 @@
+\documentclass[a4paper]{article}
+
+\usepackage{Rd}
+
+% \VignetteIndexEntry{Introduction to grid}
+% \VignettePackage{grid}
+% \VignetteDepends{lattice}
+
+% Definitions
+\newcommand{\slan}{{\sffamily S}}
+\newcommand{\rlan}{{\sffamily R}}
+\newcommand{\grid}{\pkg{grid}}
+\newcommand{\lattice}{\CRANpkg{lattice}}
+
+\setlength{\parindent}{0in}
+\setlength{\parskip}{.1in}
+\setlength{\textwidth}{140mm}
+\setlength{\oddsidemargin}{10mm}
+
+\title{\grid{} Graphics}
+\author{Paul Murrell}
+
+\begin{document}
+
+\maketitle
+
+<<echo=FALSE, results=hide>>=
+library(grDevices)
+library(graphics) # for par
+library(stats) # for rnorm
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+@
+\grid{} is a low-level graphics system which provides a great deal
+of control and flexibility in the appearance and arrangement of
+graphical output. \grid{} does not provide high-level functions which
+create complete plots. What it does provide is a basis for developing
+such high-level functions (e.g., the \lattice{} and \CRANpkg{ggplot2}
+packages), the facilities for customising and manipulating \lattice{}
+output, the ability to produce high-level plots or non-statistical
+images from scratch, and the ability to add sophisticated annotations
+to the output from base graphics functions (see the \CRANpkg{gridBase}
+package).
+
+This document provides an introduction to the fundamental concepts
+underlying the \grid{} package: {\bf viewports}, {\bf units}, and
+{\bf graphical parameters}. There are also several examples to
+demonstrate what can be achieved and how to achieve it.
+
+The description of the fundamental \grid{} concepts is predicated on the
+following approach to constructing a statistical graphic
+(plot). You must be able to:
+\begin{enumerate}
+\item create and control different graphical regions
+and coordinate systems.
+\item control which graphical region and
+coordinate system graphical output goes into.
+\item produce graphical output (lines, points, text, \ldots{})
+including controlling its appearance (colour, line type, line width, \ldots{}).
+\end{enumerate}
+
+\section{Creating and Controlling Graphics Regions and Coordinate Systems}
+
+In \grid{} there can be any number of graphics regions. A graphics
+region is referred to as a \emph{viewport} and is created using the
+\code{viewport()} function. A viewport can be positioned anywhere on
+a graphics device (page, window, \ldots{}), it can be rotated, and it can
+be clipped to. The following code describes a viewport which is
+centred within the page, and is half
+the width of the page, one quarter of the height of the page,
+and rotated $45^{\circ}$; Figure \ref{figure:viewport}
+shows a diagram of this viewport.
+
+<<eval=FALSE>>=
+viewport(x = 0.5, y = 0.5, width = 0.5, height = 0.25, angle=45)
+<<viewport, echo=FALSE, results=hide, fig=TRUE, width=6, height=6, include=FALSE>>=
+grid.show.viewport(viewport(x = 0.5, y = 0.5, width = 0.5, height = 0.25,
+ angle = 45))
+@
+\begin{figure}[p]
+\begin{center}
+{
+\includegraphics[width=3.5in, height=3.5in]{grid-viewport}
+}
+\end{center}
+\caption{
+ \label{figure:viewport}
+ A diagram of a simple \grid{} viewport (produced using the
+ \code{grid.show.viewport()} function.}
+\end{figure}
+
+The object returned by the \code{viewport()} function is only a
+\emph{description} of a graphics region. A graphics region is only
+created on a graphics device when a viewport is ``pushed'' onto that
+device. This is achieved using the \code{pushViewport()} function.
+Each device has only one ``current viewport'' (by default this is the
+entire device surface), but it maintains a ``tree'' of viewports that
+have been pushed. The current viewport is a node on the viewport
+tree. The \code{pushViewport()} function adds a viewport as a leaf of
+the tree -- the previous ``current viewport'' becomes the parent of
+this leaf and the new leaf becomes the current viewport. The
+\code{popViewport()} function prunes the current viewport (and all its
+children) from the tree -- the parent of the pruned leaf becomes the
+current viewport. The function \code{upViewport()} acts like
+\code{popViewport()} in terms of setting the current viewport, but
+does not prune the previous ``current viewport''. The
+\code{downViewport()} function navigates down the tree to a viewport
+which has been specified by name (it adds no new viewports to the
+tree). This means that there is always only one graphics region
+selected to draw into, but it is possible to return to a previous
+graphics region through the appropriate set of push/pop/up/down
+operations.
+
+As an example, the following code creates a graphics
+region in the top-left corner of the page using \code{pushViewport()}.
+This viewport is given the name \code{"vp1"}.
+It then does some drawing and calls \code{upViewport()} to return
+to the root of the viewport tree. Next, it
+creates another region in the bottom-right corner of the page
+(again using \code{pushViewport()}) and does
+some drawing there. Finally, it performs an \code{upViewport()}
+to the root of the tree and a \code{downViewport()} to
+return to the first graphics region and
+does some more drawing there (see Figure \ref{figure:viewports}).
+
+<<pushviewports, results=hide, fig=TRUE, width=6, height=6, include=FALSE>>=
+grid.rect(gp = gpar(lty = "dashed"))
+vp1 <- viewport(x = 0, y = 0.5, w = 0.5, h = 0.5,
+ just = c("left", "bottom"), name = "vp1")
+vp2 <- viewport(x = 0.5, y = 0, w = 0.5, h = 0.5,
+ just = c("left", "bottom"))
+pushViewport(vp1)
+grid.rect(gp = gpar(col = "grey"))
+grid.text("Some drawing in graphics region 1", y = 0.8)
+upViewport()
+pushViewport(vp2)
+grid.rect(gp = gpar(col = "grey"))
+grid.text("Some drawing in graphics region 2", y = 0.8)
+upViewport()
+downViewport("vp1")
+grid.text("MORE drawing in graphics region 1", y = 0.2)
+popViewport()
+@
+\begin{figure}[p]
+\begin{center}
+{
+\includegraphics[width=3.5in, height=3.5in]{grid-pushviewports}
+}
+\end{center}
+\caption{\label{figure:viewports}
+ Defining and drawing in multiple graphics regions.}
+\end{figure}
+@
+When several viewports are pushed onto the viewport tree, leaf
+viewports are located and sized within the context of their parent
+viewports. The following code gives an example; a viewport is defined
+which is one-quarter the size of its parent (half the width and half the
+height), and this viewport is pushed twice. The first time it
+gets pushed the parent is the root of the viewport tree (which is the
+entire device) so it is quarter of the size of the page.
+The second time the viewport is pushed,
+it is quarter of the size of \emph{its parent viewport}.
+Figure \ref{figure:vpstack} shows the output of these
+commands.
+
+<<vpstack, results=hide, fig=TRUE, width=6, height=6, include=FALSE>>=
+grid.rect(gp = gpar(lty = "dashed"))
+vp <- viewport(width = 0.5, height = 0.5)
+pushViewport(vp)
+grid.rect(gp = gpar(col = "grey"))
+grid.text("quarter of the page", y = 0.85)
+pushViewport(vp)
+grid.rect()
+grid.text("quarter of the\nprevious viewport")
+popViewport(2)
+@
+\begin{figure}[p]
+\begin{center}
+{
+\includegraphics[width=3.5in, height=3.5in]{grid-vpstack}
+}
+\end{center}
+\caption{\label{figure:vpstack}
+ The result of pushing the same viewport onto the viewport
+stack twice.}
+\end{figure}
+@
+
+Each viewport has a number of coordinate systems available. The full
+set is described in Table \ref{table:coords}, but there are four main
+types: absolute coordinates (e.g., \code{"inches"}, \code{"cm"}) allow
+locations and sizes in terms of physical coordinates -- there is no
+dependence on the size of the page; normalised coordinates (e.g.,
+\code{"npc"}) allow locations and sizes as a proportion of the page
+size (or the current viewport); relative coordinates (i.e.,
+\code{"native"}) allow locations and sizes relative to a user-defined
+set of x- and y-ranges; referential coordinates (e.g.,
+\code{"strwidth"}) where locations and sizes are based on the size of
+some other graphical object.
+
+It is possible to specify the coordinate system
+for relative coordinates, but all other coordinate systems
+are implicitly defined based on the location and size of the viewport
+and/or the size of other graphical objects.
+
+\begin{table}[p]
+\begin{center}
+\begin{tabular}{l l} \hline
+{\bf Coordinate} & \\
+{\bf System Name} & {\bf Description} \\ \hline
+\code{"npc"} & \parbox[t]{3in}{Normalised Parent Coordinates. Treats
+the bottom-left corner of the current
+viewport as the location $(0, 0)$ and the top-right corner
+as $(1,1)$. } \\
+\code{"native"} & \parbox[t]{3in}{Locations and sizes are relative
+to the x- and y-scales for the current viewport.} \\
+\code{"inches"} & \parbox[t]{3in}{Locations and sizes are in terms
+of physical inches. For locations, $(0,0)$ is at the bottom-left
+of the viewport.} \\
+\code{"cm"} & \parbox[t]{3in}{Same as \code{"inches"}, except in
+centimetres.} \\
+\code{"mm"} & \parbox[t]{3in}{Millimetres.} \\
+\code{"points"} & \parbox[t]{3in}{Points. There are 72.27 points per inch.} \\
+\code{"bigpts"} & \parbox[t]{3in}{Big points. There are 72 big points per inch.} \\
+\code{"picas"} & \parbox[t]{3in}{Picas. There are 12 points per pica.} \\
+\code{"dida"} & \parbox[t]{3in}{Dida. 1157 dida equals 1238 points. } \\
+\code{"cicero"} & \parbox[t]{3in}{Cicero. There are 12 dida per cicero. } \\
+\code{"scaledpts"} & \parbox[t]{3in}{Scaled points. There are 65536 scaled
+points per point. } \\
+\code{"char"} & \parbox[t]{3in}{Locations and sizes are specified in
+terms of multiples of the current nominal \code{fontheight}.} \\
+\code{"lines"} & \parbox[t]{3in}{Locations and sizes are specified in
+terms of multiples of the height of a line of text
+ (dependent on both the current \code{fontsize} and
+the current \code{lineheight}).} \\
+\code{"snpc"} & \parbox[t]{3in}{Square Normalised Parent Coordinates.
+Locations and size are expressed as a proportion of the \emph{smaller}
+of the
+width and height of the current viewport.} \\
+\code{"strwidth"} & \parbox[t]{3in}{Locations and sizes are
+expressed as multiples of the width of a given string (dependent
+on the string and the current \code{fontsize}).} \\
+\code{"strheight"} & \parbox[t]{3in}{Locations and sizes are
+expressed as multiples of the height of a given string (dependent
+on the string and the current \code{fontsize}).} \\
+\code{"grobwidth"} & \parbox[t]{3in}{Locations and sizes are
+expressed as multiples of the width of a given graphical object
+(dependent on the current state of the graphical object). } \\
+\code{"grobheight"} & \parbox[t]{3in}{Locations and sizes are
+expressed as multiples of the height of a given graphical object
+(dependent on the current state of the graphical object). } \\
+\hline
+\end{tabular}
+\end{center}
+\caption{\label{table:coords}
+ The full set of coordinate systems available in \grid{}
+viewports.}
+\end{table}
+
+
+\section{Directing Graphics Output into Different \\Graphics Regions
+and Coordinate Systems}
+
+Graphics output is always relative to the current viewport (on the
+current device). Selecting which region you want is a matter of
+push/pop/up/downing the appropriate viewports. However, that is not
+all; every viewport has a number of coordinate systems associated with
+it, so it is also necessary to select the coordinate system that you
+want to work with.
+
+The selection of which coordinate system to use within the current
+viewport is made using the \code{unit()} function. The
+\code{unit()} function creates an object which is a combination
+of a value and a coordinate system (plus some extra
+information for certain coordinate systems). Here are some examples
+from the \code{help(unit)} page:
+
+<<units>>=
+unit(1, "npc")
+unit(1:3/4, "npc")
+unit(1:3/4, "npc")[2]
+unit(1:3/4, "npc") + unit(1, "inches")
+min(unit(0.5, "npc"), unit(1, "inches"))
+unit.c(unit(0.5, "npc"), unit(2, "inches") + unit(1:3/4, "npc"),
+ unit(1, "strwidth", "hi there"))
+@
+Notice that unit objects are treated much like numeric vectors. You
+can index a unit object, it is possible to do simple arithmetic
+(including \code{min} and \code{max}), and there are several
+unit-versions of common functions (e.g., \code{unit.c},
+\code{unit.rep}, and \code{unit.length}; \code{unit.pmin}, and
+\code{unit.pmax})).
+
+\grid{} functions that have arguments specifying locations and sizes
+typically assume a default coordinate system is being used. Most
+often this default is \code{"npc"}. In other words, if a raw numeric
+value, \code{x}, is specified this is implicitly taken to mean
+\code{unit(x, "npc")}. The \code{viewport()} function is one that
+assumes \code{"npc"} coordinates, so in all of the viewport examples
+to this point, we have only used \code{"npc"} coordinates to position
+viewports within the page or within each other. It is also possible
+to position viewports using any of the coordinate systems described in
+Table \ref{table:coords}.
+
+As an example, the following code makes use of \code{"npc"},
+\code{"native"}, \code{"inches"}, and \code{"strwidth"}
+coordinates. It first pushes a viewport with a user-defined
+x-scale, then pushes another viewport which is centred at the x-value
+60 and half-way up the first viewport, and
+is 3 inches high\footnote{If you want to check the figure, the scaling
+factor is $3.5/6$ (i.e., the rectangle in the figure should be 1.75\code{"} or
+3.94cm high).} and as wide as the text ``coordinates for everyone''.
+Figure \ref{figure:vpcoords} shows the resulting output.
+
+<<vpcoords, results=hide, fig=TRUE, width=6, height=6, include=FALSE>>=
+pushViewport(viewport(y = unit(3, "lines"), width = 0.9, height = 0.8,
+ just = "bottom", xscale = c(0, 100)))
+grid.rect(gp = gpar(col = "grey"))
+grid.xaxis()
+pushViewport(viewport(x = unit(60, "native"), y = unit(0.5, "npc"),
+ width = unit(1, "strwidth", "coordinates for everyone"),
+ height = unit(3, "inches")))
+grid.rect()
+grid.text("coordinates for everyone")
+popViewport(2)
+@
+\begin{figure}[p]
+\begin{center}
+{
+\includegraphics[width=3.5in, height=3.5in]{grid-vpcoords}
+}
+\end{center}
+\caption{\label{figure:vpcoords}
+ A viewport positioned using a variety of coordinate systems.}
+\end{figure}
+
+\clearpage
+\subsection{Layouts}
+
+\grid{} provides an alternative method for positioning viewports
+within each other based on \emph{layouts}\footnote{The primary reference
+for layouts is \cite{murrell:1999}. Layouts in \grid{} represent
+an extension of the idea to allow a greater range of units for
+specifying row heights and column widths. \grid{} also differs in the
+way that children of the layout specify their location within the layout.}.
+A layout may be specified
+for any viewport. Any viewport pushed immediately after a viewport
+containing a layout may specify its location with respect to that
+layout. In the following simple example, a viewport is pushed
+with a layout
+with 4 rows and 5 columns, then another viewport is pushed which
+occupies the second and third columns of the third row of the layout.
+
+<<vplayout, results=hide, fig=TRUE, width=6, height=6, include=FALSE>>=
+pushViewport(viewport(layout = grid.layout(4, 5)))
+grid.rect(gp = gpar(col = "grey"))
+grid.segments(c(1:4/5, rep(0, 3)), c(rep(0, 4), 1:3/4),
+ c(1:4/5, rep(1, 3)), c(rep(1, 4), 1:3/4),
+ gp = gpar(col = "grey"))
+pushViewport(viewport(layout.pos.col = 2:3, layout.pos.row = 3))
+grid.rect(gp = gpar(lwd = 3))
+popViewport(2)
+@
+\begin{figure}[tbp]
+\begin{center}
+{
+\includegraphics[width=3.5in, height=3.5in]{grid-vplayout}
+}
+\end{center}
+\caption{\label{figure:vplayout}
+ A viewport positioned using a layout.}
+\end{figure}
+
+Layouts introduce a special sort of unit called \code{"null"}. These
+can be used in layouts to specify relative column-widths or
+row-heights. In the following, slightly more complex, example, the
+layout specifies something similar to a standard plot arrangement;
+there are bottom and left margins 3 lines of text wide, top and right
+margins 1cm wide, and two rows and columns within these margins where
+the bottom row is twice the height of the top row (see Figure
+\ref{figure:vplayoutcomplex}).
+
+<<layoutcomplex, results=hide, fig=TRUE, width=6, height=6, include=FALSE>>=
+grid.show.layout(grid.layout(4, 4, widths = unit(c(3, 1, 1, 1),
+ c("lines", "null", "null", "cm")),
+ heights = c(1, 1, 2, 3),
+ c("cm", "null", "null", "lines")))
+@
+\begin{figure}[tbp]
+\begin{center}
+{
+\includegraphics[width=3.5in, height=3.5in]{grid-layoutcomplex}
+}
+\end{center}
+\caption{\label{figure:vplayoutcomplex}
+ A more complex layout.}
+\end{figure}
+
+\clearpage
+\section{Producing Graphics Output}
+
+\grid{} provides a standard set of graphical primitives: lines,
+text, points, rectangles, polygons, and circles. There are also
+two higher level components: x- and y-axes. Table \ref{table:primitives}
+lists the \grid{} functions that produce these primitives.
+
+{\bf NOTE:} all of these graphical primitives are available in
+all graphical regions and coordinate systems.
+
+There used to be (prior to R 2.3.0) a separate \code{grid.arrows()}
+function, but this has been superseded by an \code{arrow} argument
+to the line-drawing primitives (lines, segments, line-to).
+
+\begin{table}[h!]
+\begin{center}
+\begin{tabular}{l l} \hline
+\code{grid.text} & Can specify angle of rotation. \\
+\code{grid.rect} & \\
+\code{grid.circle} & \\
+\code{grid.polygon} & \\
+\code{grid.points} & Can specify type of plotting symbol. \\
+\code{grid.lines} & \\
+\code{grid.segments} & \\
+\code{grid.grill} & Convenience function for drawing grid lines \\
+\code{grid.move.to} & \\
+\code{grid.line.to} & \\
+& \\
+\code{grid.xaxis} & Top or bottom axis \\
+\code{grid.yaxis} & Left or right axis \\
+\hline
+\end{tabular}
+\end{center}
+\caption{\label{table:primitives}
+ \grid{} graphical primitives.}
+\end{table}
+
+
+\subsection{Controlling the Appearance of Graphics Output}
+
+\grid{} recognises a fixed set of graphical parameters for modifying
+the appearance of graphical output (see Table \ref{table:gpars}).
+
+\begin{table}[h!]
+\begin{center}
+\begin{tabular}{l l} \hline
+\code{col} & colour of lines, text, \ldots{} \\
+\code{fill} & colour for filling rectangles, circles, polygons, \ldots{} \\
+\code{lwd} & line width \\
+\code{lty} & line type \\
+\code{fontsize} & The size of text (in points) \\
+\code{fontface} & The font face (bold, italic, \ldots{}) \\
+\code{fontfamily} & The font family \\
+\hline
+\end{tabular}
+\end{center}
+\caption{\label{table:gpars}
+ \grid{} graphical parameters.}
+\end{table}
+
+Graphical parameter settings may be specified for both viewports
+and graphical objects. A graphical parameter setting for a viewport
+will hold for all graphical output within that viewport {\em and} for
+all viewports subsequently pushed onto the viewport stack, {\em unless}
+the graphical object or viewport specifies a different parameter
+setting.
+
+A description of graphical parameter settings is created using
+the \code{gpar()} function, and this description is associated with a
+viewport or a graphical object via the \code{gp} argument.
+The following code demonstrates the effect of graphical parameter
+settings (see Figure \ref{figure:gpar}).
+
+<<gpar, results=hide, fig=TRUE, width=6, height=6, include=FALSE>>=
+pushViewport(viewport(gp = gpar(fill = "grey", fontface = "italic")))
+grid.rect()
+grid.rect(width = 0.8, height = 0.6, gp = gpar(fill = "white"))
+grid.text(paste("This text and the inner rectangle",
+ "have specified their own gpar settings", sep = "\n"),
+ y = 0.75, gp = gpar(fontface = "plain"))
+grid.text(paste("This text and the outer rectangle",
+ "accept the gpar settings of the viewport", sep = "\n"),
+ y = 0.25)
+popViewport()
+@
+\begin{figure}[tbp]
+\begin{center}
+{
+\includegraphics[width=3.5in, height=3.5in]{grid-gpar}
+}
+\end{center}
+\caption{\label{figure:gpar}
+ The effect of different graphical parameter settings.}
+\end{figure}
+
+\clearpage
+\section{Examples}
+
+The remaining sections provide some code examples of the use
+of \grid{}.
+
+The first example constructs a simple scatterplot from first
+principles.
+Just like in base graphics, it is quite straightforward
+to create a simple plot by hand. The following code produces the equivalent
+of a standard \code{plot(1:10)} (see Figure \ref{figure:simpleplot}).
+
+<<simpleplot, results=hide, fig=TRUE, width=6, height=6, include=FALSE>>=
+grid.rect(gp = gpar(lty = "dashed"))
+x <- y <- 1:10
+pushViewport(plotViewport(c(5.1, 4.1, 4.1, 2.1)))
+pushViewport(dataViewport(x, y))
+grid.rect()
+grid.xaxis()
+grid.yaxis()
+grid.points(x, y)
+grid.text("1:10", x = unit(-3, "lines"), rot = 90)
+popViewport(2)
+@
+\begin{figure}[p]
+\begin{center}
+{
+\includegraphics[width=3.5in, height=3.5in]{grid-simpleplot}
+}
+\end{center}
+\caption{\label{figure:simpleplot}
+ The grid equivalent of \code{plot(1:10)}.}
+\end{figure}
+
+Now consider a more complex example, where we create a barplot
+with a legend (see Figure \ref{figure:barplot}).
+There are two main parts to this because
+grid has no predefined barplot function; the construction of the
+barplot will itself be instructive, so we will start with just that.
+
+The data to be plotted are as follows: we have four measures to
+represent at four levels; the data are in a matrix with the measures
+for each level in a column.
+
+<<bpdata>>=
+barData <- matrix(sample(1:4, 16, replace = TRUE), ncol = 4)
+@
+We will use colours to differentiate
+the measures.
+
+<<barconstraint>>=
+boxColours <- 1:4
+@
+We create the barplot within a function so that we can easily
+reproduce it when we combine it with the legend.
+
+<<bpfun>>=
+bp <- function(barData) {
+ nbars <- dim(barData)[2]
+ nmeasures <- dim(barData)[1]
+ barTotals <- rbind(rep(0, nbars), apply(barData, 2, cumsum))
+ barYscale <- c(0, max(barTotals)*1.05)
+ pushViewport(plotViewport(c(5, 4, 4, 1),
+ yscale = barYscale,
+ layout = grid.layout(1, nbars)))
+ grid.rect()
+ grid.yaxis()
+ for (i in 1:nbars) {
+ pushViewport(viewport(layout.pos.col = i, yscale = barYscale))
+ grid.rect(x = rep(0.5, nmeasures),
+ y = unit(barTotals[1:nmeasures, i], "native"),
+ height = unit(diff(barTotals[,i]), "native"),
+ width = 0.8, just = "bottom", gp = gpar(fill = boxColours))
+ popViewport()
+ }
+ popViewport()
+}
+@
+
+Now we turn our attention to the legend. We need some labels
+and we will enforce the constraint that the boxes in the legend should
+be 0.5\code{"} square:
+
+<<legendlabels>>=
+legLabels <- c("Group A", "Group B", "Group C", "Something Longer")
+boxSize <- unit(0.5, "inches")
+@
+
+The following draws the legend elements in a column, with each
+element consisting of a box with a label beneath.
+
+<<legfun>>=
+leg <- function(legLabels) {
+ nlabels <- length(legLabels)
+ pushViewport(viewport(layout = grid.layout(nlabels, 1)))
+ for (i in 1:nlabels) {
+ pushViewport(viewport(layout.pos.row = i))
+ grid.rect(width = boxSize, height = boxSize, just = "bottom",
+ gp = gpar(fill = boxColours[i]))
+ grid.text(legLabels[i], y = unit(0.5, "npc") - unit(1, "lines"))
+ popViewport()
+ }
+ popViewport()
+}
+@
+
+Now that we have the two components, we can arrange them together to
+form a complete image. Notice that we can perform some calculations
+to make sure that we leave enough room for the legend, including
+1 line of text as left and right margins. We also impose top and bottom
+margins on the legend to match the plot margins.
+
+<<barplot, results=hide, fig=TRUE, width=6, height=6, include=FALSE>>=
+grid.rect(gp = gpar(lty = "dashed"))
+legend.width <- max(unit(rep(1, length(legLabels)),
+ "strwidth", as.list(legLabels)) +
+ unit(2, "lines"),
+ unit(0.5, "inches") + unit(2, "lines"))
+pushViewport(viewport(layout = grid.layout(1, 2,
+ widths = unit.c(unit(1,"null"), legend.width))))
+pushViewport(viewport(layout.pos.col = 1))
+bp(barData)
+popViewport()
+pushViewport(viewport(layout.pos.col = 2))
+pushViewport(plotViewport(c(5, 0, 4, 0)))
+leg(legLabels)
+popViewport(3)
+@
+\begin{figure}[p]
+\begin{center}
+{
+\includegraphics[width=3.5in, height=3.5in]{grid-barplot}
+}
+\end{center}
+\caption{\label{figure:barplot}
+ A barplot plus legend from first principles using \grid{}.}
+\end{figure}
+
+
+\section{\grid{} and \lattice{}}
+
+The \lattice{} package is built on top of \grid{} and provides a
+quite sophisticated example of writing high-level plotting functions
+using \grid{}. Because \lattice{} consists of \grid{} calls, it is
+possible to both add \grid{} output to \lattice{} output, and
+\lattice{} output to \grid{} output.
+
+\subsection*{Adding \grid{} to \lattice{}}
+
+Panel functions in \lattice{} can include \grid{} calls.
+The following example adds a horizontal line at 0 to a standard
+\code{xyplot} (see Figure \ref{figure:trellispanel}):
+
+<<echo=FALSE, results=hide>>=
+library(lattice)
+<<trellisdata, echo=FALSE, eval=FALSE>>=
+x <- rnorm(100)
+y <- rnorm(100)
+g <- sample(1:8, 100, replace = TRUE)
+@
+% This is the code the reader sees
+% This WILL get run by checking code, but by then lattice will be
+% installed so it will be ok
+<<trellispanelplot, eval=FALSE>>=
+xyplot(y ~ x | g, panel = function(x, y) {
+ panel.xyplot(x, y);
+ grid.lines(unit(c(0, 1), "npc"), unit(0, "native"),
+ gp = gpar(col = "grey"))
+})
+@
+% This generates the actual plot
+<<trellispanel, echo=FALSE, results=hide, fig=TRUE, width=6, height=6, include=FALSE>>=
+<<trellisdata>>
+<<trellispanelplot>>
+@
+\begin{figure}[p]
+\begin{center}
+{
+\includegraphics[width=3.5in, height=3.5in]{grid-trellispanel}
+}
+\end{center}
+\caption{\label{figure:trellispanel}
+ A \lattice{} panel function using \grid{}.}
+\end{figure}
+@
+The following example writes a left-justified label in each strip
+(see Figure \ref{figure:trellisstrip}):
+
+<<trellisstripplot, eval=FALSE>>=
+xyplot(y ~ x | g, strip = function(which.given, which.panel, ...) {
+ grid.text(paste("Variable ", which.given, ": Level ",
+ which.panel[which.given], sep = ""),
+ unit(1, "mm"), .5, just = "left")
+})
+<<trellisstrip, echo=FALSE, results=hide, fig=TRUE, width=6, height=6, include=FALSE>>=
+<<trellisdata>>
+<<trellisstripplot>>
+@
+\begin{figure}[p]
+\begin{center}
+{
+\includegraphics[width=3.5in, height=3.5in]{grid-trellisstrip}
+}
+\end{center}
+\caption{\label{figure:trellisstrip}
+ A \lattice{} strip function using \grid{}.}
+\end{figure}
+
+\subsection*{Adding \lattice{} to \grid{}}
+
+It is also possible to use a \lattice{} plot as an element of
+a \grid{} image. The following example splits up the page
+so that there is an \code{xyplot} beside a panel of text
+(see Figure \ref{figure:trellisgrid}). First of all, the
+lattice plot is created, but
+not drawn. \grid{} is used to create some regions and the lattice
+plot is drawn into one of those regions.
+
+<<trellisgridplot, eval=FALSE>>=
+someText <- paste("A panel of text", "produced using", "raw grid code",
+ "that could be used", "to describe",
+ "the plot", "to the right.", sep = "\n")
+latticePlot <- xyplot(y ~ x | g, layout = c(2, 4))
+grid.rect(gp = gpar(lty = "dashed"))
+pushViewport(viewport(layout = grid.layout(1, 2,
+ widths = unit.c(unit(1, "strwidth", someText) +
+ unit(2, "cm"),
+ unit(1, "null")))))
+pushViewport(viewport(layout.pos.col = 1))
+grid.rect(gp = gpar(fill = "light grey"))
+grid.text(someText,
+ x = unit(1, "cm"), y = unit(1, "npc") - unit(1, "inches"),
+ just = c("left", "top"))
+popViewport()
+pushViewport(viewport(layout.pos.col = 2))
+print(latticePlot, newpage = FALSE)
+popViewport(2)
+<<trellisgrid, echo=FALSE, results=hide, fig=TRUE, width=6, height=6, include=FALSE>>=
+<<trellisdata>>
+<<trellisgridplot>>
+@
+\begin{figure}[tbp]
+\begin{center}
+{
+\includegraphics[width=3.5in, height=3.5in]{grid-trellisgrid}
+}
+\end{center}
+\caption{\label{figure:trellisgrid}
+ A \lattice{} plot used as a component of a larger \grid{} image.}
+\end{figure}
+
+
+\bibliographystyle{plain}
+\bibliography{grid}
+
+\end{document}
diff --git a/win32/deps/library/grid/doc/grid.pdf b/win32/deps/library/grid/doc/grid.pdf
new file mode 100644
index 0000000..048403f
Binary files /dev/null and b/win32/deps/library/grid/doc/grid.pdf differ
diff --git a/win32/deps/library/grid/doc/grobs.R b/win32/deps/library/grid/doc/grobs.R
new file mode 100644
index 0000000..e3827cd
--- /dev/null
+++ b/win32/deps/library/grid/doc/grobs.R
@@ -0,0 +1,313 @@
+### R code from vignette source 'grobs.Rnw'
+
+###################################################
+### code chunk number 1: grobs.Rnw:25-29
+###################################################
+library(grDevices)
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+
+
+###################################################
+### code chunk number 2: grobs.Rnw:43-45
+###################################################
+gl <- linesGrob()
+gl <- editGrob(gl, gp = gpar(col = "green"))
+
+
+###################################################
+### code chunk number 3: grobs.Rnw:59-63
+###################################################
+grid.newpage()
+grid.lines(name = "lines")
+grid.edit(gPath("lines"), gp = gpar(col = "pink"))
+grid.edit("lines", gp = gpar(col = "red"))
+
+
+###################################################
+### code chunk number 4: grobs.Rnw:79-86
+###################################################
+grid.newpage()
+pushViewport(viewport(w = .5, h = .5))
+grid.rect(gp = gpar(col = "grey"))
+grid.xaxis(name = "myxaxis")
+grid.edit("myxaxis", at = 1:4/5)
+grid.edit(gPath("myxaxis", "labels"), y = unit(-1, "lines"))
+
+
+
+###################################################
+### code chunk number 5: grobs.Rnw:98-108
+###################################################
+grid.newpage()
+pushViewport(viewport(w = .5, h = .5))
+myplot <-
+ gTree(name = "myplot",
+ children = gList(rectGrob(name = "box", gp = gpar(col = "grey")),
+ xaxisGrob(name = "xaxis")))
+grid.draw(myplot)
+grid.edit("myplot::xaxis", at = 1:10/11)
+grid.edit("myplot::xaxis::labels", label = round(1:10/11, 2))
+grid.edit("myplot::xaxis::labels", y = unit(-1, "lines"))
+
+
+###################################################
+### code chunk number 6: grobs.Rnw:116-119
+###################################################
+grid.newpage()
+gt <- grid.text("Hi there")
+grid.rect(width = unit(1, "grobwidth", gt))
+
+
+###################################################
+### code chunk number 7: grobs.Rnw:128-132
+###################################################
+grid.newpage()
+gt <- grid.text("Hi there", name = "sometext")
+grid.rect(width = unit(1, "grobwidth", "sometext"))
+grid.edit("sometext", label = "Something different")
+
+
+###################################################
+### code chunk number 8: grobs.Rnw:157-171
+###################################################
+grid.newpage()
+mygrob <- grob(name = "mygrob", cl = "mygrob")
+preDrawDetails.mygrob <- function(x)
+ pushViewport(viewport(gp = gpar(fontsize = 20)))
+
+drawDetails.mygrob <- function(x, recording = TRUE)
+ grid.draw(textGrob("hi there"), recording = FALSE)
+
+postDrawDetails.mygrob <- function(x) popViewport()
+
+widthDetails.mygrob <- function(x) unit(1, "strwidth", "hi there")
+
+grid.draw(mygrob)
+grid.rect(width = unit(1, "grobwidth", mygrob))
+
+
+###################################################
+### code chunk number 9: grobs.Rnw:189-201
+###################################################
+grid.newpage()
+mygtree <- gTree(name = "mygrob",
+ childrenvp = viewport(name = "labelvp",
+ gp = gpar(fontsize = 20)),
+ children = gList(textGrob("hi there", name = "label",
+ vp = "labelvp")),
+ cl = "mygtree")
+widthDetails.mygtree <- function(x)
+ unit(1, "grobwidth", getGrob(x, "label"))
+
+grid.draw(mygtree)
+grid.rect(width = unit(1, "grobwidth", mygtree))
+
+
+###################################################
+### code chunk number 10: grobs.Rnw:209-214
+###################################################
+grid.newpage()
+fg <- frameGrob(layout = grid.layout(1, 2))
+fg <- placeGrob(fg, textGrob("Hi there"), col = 1)
+fg <- placeGrob(fg, rectGrob(), col = 2)
+grid.draw(fg)
+
+
+###################################################
+### code chunk number 11: grobs.Rnw:219-235
+###################################################
+grid.newpage()
+pushViewport(viewport(layout = grid.layout(2, 2)))
+drawIt <- function(row, col) {
+ pushViewport(viewport(layout.pos.col = col, layout.pos.row = row))
+ grid.rect(gp = gpar(col = "grey"))
+ grid.draw(fg)
+ upViewport()
+}
+fg <- frameGrob()
+fg <- packGrob(fg, textGrob("Hi there"))
+fg <- placeGrob(fg, rectGrob())
+drawIt(1, 1)
+fg <- packGrob(fg, textGrob("Hello again"), side = "right")
+drawIt(1, 2)
+fg <- packGrob(fg, rectGrob(), side = "right", width = unit(1, "null"))
+drawIt(2, 2)
+
+
+###################################################
+### code chunk number 12: grobs.Rnw:247-256
+###################################################
+grid.newpage()
+fg <- frameGrob()
+fg <- packGrob(fg, textGrob("Hi there"))
+fg <- placeGrob(fg, rectGrob())
+fg <- packGrob(fg, textGrob("Hello again", name = "midtext"),
+ side = "right", dynamic = TRUE)
+fg <- packGrob(fg, rectGrob(), side = "right", width = unit(1, "null"))
+grid.draw(fg)
+grid.edit("midtext", label = "something much longer")
+
+
+###################################################
+### code chunk number 13: grobs.Rnw:280-304
+###################################################
+grid.newpage()
+pushViewport(viewport(layout = grid.layout(2, 2)))
+drawIt <- function(row, col) {
+ pushViewport(viewport(layout.pos.col = col, layout.pos.row = row))
+ grid.rect(gp = gpar(col = "grey"))
+ grid.draw(gplot)
+ upViewport()
+}
+gplot <- gTree(x = NULL, y = NULL,
+ childrenvp = vpTree(
+ plotViewport(c(5, 4, 4, 2), name = "plotRegion"),
+ vpList(viewport(name = "dataRegion"))),
+ children = gList(
+ xaxisGrob(vp = "plotRegion::dataRegion"),
+ yaxisGrob(vp = "plotRegion::dataRegion"),
+ rectGrob(vp = "plotRegion")))
+drawIt(1, 1)
+gplot <- addGrob(gplot, pointsGrob(vp = "plotRegion::dataRegion"))
+drawIt(1, 2)
+gplot <- addGrob(gplot, pointsGrob(name = "data1", pch = 2,
+ vp = "plotRegion::dataRegion"))
+drawIt(2, 1)
+gplot <- removeGrob(gplot, "data1")
+drawIt(2, 2)
+
+
+###################################################
+### code chunk number 14: grobs.Rnw:311-332
+###################################################
+gplot <- gTree(x = NULL, y = NULL,
+ childrenvp = vpTree(
+ plotViewport(c(5, 4, 4, 2), name = "plotRegion"),
+ vpList(viewport(name = "dataRegion"))),
+ children = gList(
+ xaxisGrob(vp = "plotRegion::dataRegion"),
+ yaxisGrob(vp = "plotRegion::dataRegion"),
+ rectGrob(vp = "plotRegion")))
+save(gplot, file = "gplot1")
+gplot <- addGrob(gplot, pointsGrob(vp = "plotRegion::dataRegion"))
+save(gplot, file = "gplot2")
+grid.newpage()
+pushViewport(viewport(layout = grid.layout(1, 2)))
+pushViewport(viewport(layout.pos.col = 1))
+load("gplot1")
+grid.draw(gplot)
+popViewport()
+pushViewport(viewport(layout.pos.col = 2))
+load("gplot2")
+grid.draw(gplot)
+popViewport()
+
+
+###################################################
+### code chunk number 15: grobs.Rnw:343-354
+###################################################
+myplot <- gTree(name = "myplot",
+ children = gList(
+ rectGrob(name = "box", gp = gpar(col = "grey")),
+ xaxisGrob(name = "xaxis")))
+myplot <- editGrob(myplot, gPath = "xaxis", at = 1:10/11)
+myplot <- editGrob(myplot, gPath = "xaxis::labels", label = round(1:10/11, 2))
+myplot <- editGrob(myplot, gPath = "xaxis::labels", y = unit(-1, "lines"))
+grid.newpage()
+pushViewport(viewport(w = .5, h = .5))
+grid.draw(myplot)
+
+
+
+###################################################
+### code chunk number 16: grobs.Rnw:360-373
+###################################################
+myplot <- gTree(name = "myplot",
+ children = gList(
+ rectGrob(name = "box", gp = gpar(col = "grey")),
+ xaxisGrob(name = "xaxis")))
+getGrob(myplot, "xaxis")
+myplot <- editGrob(myplot, gPath="xaxis", at=1:10/11)
+getGrob(myplot, "xaxis::labels")
+grid.newpage()
+pushViewport(viewport(w=.5, h=.5))
+grid.draw(myplot)
+grid.get("myplot")
+grid.get("myplot::xaxis")
+grid.get("myplot::xaxis::labels")
+
+
+###################################################
+### code chunk number 17: grobs.Rnw:394-410
+###################################################
+myplot <- gTree(name = "myplot",
+ children = gList(rectGrob(name = "box", gp = gpar(col = "grey")),
+ xaxisGrob(name = "xaxis")))
+myplot <- setGrob(myplot, "xaxis", rectGrob(name = "xaxis"))
+grid.newpage()
+pushViewport(viewport(w = .5, h = .5))
+grid.draw(myplot)
+grid.set("myplot::xaxis", xaxisGrob(name = "xaxis", at = 1:3/4))
+grid.set("myplot::xaxis::labels",
+ textGrob(name = "labels", x = unit(1:3/4, "native"),
+ y = unit(-1, "lines"), label = letters[1:3]))
+myplot <- setGrob(grid.get("myplot"), "xaxis::labels",
+ circleGrob(name = "labels"))
+grid.newpage()
+pushViewport(viewport(w = .5, h = .5))
+grid.draw(myplot)
+
+
+###################################################
+### code chunk number 18: grobs.Rnw:428-459
+###################################################
+drawIt <- function(row, col) {
+ pushViewport(viewport(layout.pos.col = col, layout.pos.row = row))
+ grid.rect(gp = gpar(col = "grey"))
+ grid.draw(gplot)
+ upViewport()
+}
+gplot <- gTree(name = "plot1",
+ childrenvp = vpTree(
+ plotViewport(c(5, 4, 4, 2), name = "plotRegion"),
+ vpList(viewport(name = "dataRegion"))),
+ children = gList(
+ xaxisGrob(name = "xaxis", vp = "plotRegion::dataRegion"),
+ yaxisGrob(name = "yaxis", vp = "plotRegion::dataRegion"),
+ rectGrob(name = "box", vp = "plotRegion")))
+grid.newpage()
+pushViewport(viewport(layout = grid.layout(2, 2)))
+drawIt(1, 1)
+grid.add("plot1", pointsGrob(0.5, 0.5, name = "data1",
+ vp = "plotRegion::dataRegion"))
+grid.add("plot1::xaxis",
+ textGrob("X Axis", y = unit(-2, "lines"), name = "xlab"))
+grid.edit("plot1::xaxis::xlab", y = unit(-3, "lines"))
+gplot <- grid.get("plot1")
+gplot <- addGrob(gplot, gPath = "yaxis",
+ textGrob("Y Axis", x = unit(-3, "lines"), rot = 90,
+ name = "ylab"))
+drawIt(1, 2)
+gplot <- removeGrob(gplot, "xaxis::xlab")
+drawIt(2, 1)
+grid.remove("plot1::data1")
+grid.remove("plot1")
+
+
+###################################################
+### code chunk number 19: grobs.Rnw:467-477
+###################################################
+grid.newpage()
+grid.frame(name = "myframe", layout = grid.layout(1, 2))
+grid.place("myframe", textGrob("Hi there"), col = 1)
+grid.place("myframe", rectGrob(), col = 2)
+grid.newpage()
+grid.frame(name = "frame2")
+grid.pack("frame2", textGrob("Hi there"))
+grid.place("frame2", rectGrob())
+grid.pack("frame2", textGrob("Hello again"), side = "right")
+grid.pack("frame2", rectGrob(), side = "right", width = unit(1, "null"))
+
+
diff --git a/win32/deps/library/grid/doc/grobs.Rnw b/win32/deps/library/grid/doc/grobs.Rnw
new file mode 100644
index 0000000..0c9b952
--- /dev/null
+++ b/win32/deps/library/grid/doc/grobs.Rnw
@@ -0,0 +1,482 @@
+\documentclass[a4paper]{article}
+
+\usepackage{Rd}
+
+% \VignetteIndexEntry{Working with grid grobs}
+% \VignettePackage{grid}
+
+\newcommand{\grid}{\pkg{grid}}
+\newcommand{\grob}{\code{grob}}
+\newcommand{\gTree}{\code{gTree}}
+\newcommand{\gPath}{\code{gPath}}
+\newcommand{\lattice}{\CRANpkg{lattice}}
+
+\setlength{\parindent}{0in}
+\setlength{\parskip}{.1in}
+\setlength{\textwidth}{140mm}
+\setlength{\oddsidemargin}{10mm}
+
+\title{Modifying \grid{} \code{grob}s}
+\author{Paul Murrell}
+
+\begin{document}
+\maketitle
+
+<<echo=FALSE, results=hide>>=
+library(grDevices)
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+@
+There is a distinction between \grob{}s which are just stored
+in user-level \R{} objects and \grob{}s which represent
+drawn output (i.e., \grob{}s on the \grid{} display list).
+There is a naming convention that \code{grid.*()} functions are
+(mainly) used for their side-effect of producing output or
+modifying existing output (they create/affect \grob{}s on the display list).
+Functions of the form \code{*Grob()} are used for their return value;
+the \grob{} that they create/modify.
+For example, the following creates a \grob{} and then modifies it, but
+performs absolutely no drawing; this is purely manipulating a
+description of a graphical object.
+
+<<>>=
+gl <- linesGrob()
+gl <- editGrob(gl, gp = gpar(col = "green"))
+@
+
+The next example produces output. A \grob{} is returned,
+but that \grob{} is just a description of the output that was drawn
+and has no direct link to the output. It is possible to access the
+grob representing the output by
+using the \grob{}'s \code{name}. In order to access a \grob{}
+which represents drawn output (i.e., a \grob{} on the display list),
+you must specify a \gPath{}. The \gPath{} should be created using the
+\code{gPath()} function for writing scripts, but in interactive use, it
+is possible to specify the \gPath{} directly as a string. The code below
+shows both approaches.
+
+<<results=hide>>=
+grid.newpage()
+grid.lines(name = "lines")
+grid.edit(gPath("lines"), gp = gpar(col = "pink"))
+grid.edit("lines", gp = gpar(col = "red"))
+@
+
+Complex graphical objects are provided by the \gTree{} class. A
+\gTree{} is a \grob{} which may have other \grob{}s as children. The
+\code{xaxis} and \code{yaxis} \grob{}s provided by \grid{} are
+examples of \gTree{}s; the children of an axis include a lines \grob{}
+for the tick-marks and a text \grob{} for the tick-mark labels. The
+function \code{childNames()} can be used to list the names of the
+children of a \gTree{}. When dealing with these hierarchical objects,
+more complex \gPath{}s can be used to access children of a \gTree{}.
+In the following example, an x-axis is drawn, then the xaxis itself is
+edited to modify the locations of the tick-marks, then the xaxis's
+text child is edited to modify the location of the labels on the
+tick-marks.
+
+<<results=hide>>=
+grid.newpage()
+pushViewport(viewport(w = .5, h = .5))
+grid.rect(gp = gpar(col = "grey"))
+grid.xaxis(name = "myxaxis")
+grid.edit("myxaxis", at = 1:4/5)
+grid.edit(gPath("myxaxis", "labels"), y = unit(-1, "lines"))
+
+@
+
+This next example extends the idea a step further to edit the child of
+a child of a \gTree{}. It also shows the use of the \gTree{} function
+to construct a simple \gTree{} (this is just creating an instance of
+the \gTree{} class -- it is also possible to extend the \gTree{} class
+in order to provide specialised behaviour for drawing and other
+things; more on this later). Finally, the example demonstrates how
+\gPath{}s of depth greater than 1 can be specified directly as a
+string.
+
+<<results=hide>>=
+grid.newpage()
+pushViewport(viewport(w = .5, h = .5))
+myplot <-
+ gTree(name = "myplot",
+ children = gList(rectGrob(name = "box", gp = gpar(col = "grey")),
+ xaxisGrob(name = "xaxis")))
+grid.draw(myplot)
+grid.edit("myplot::xaxis", at = 1:10/11)
+grid.edit("myplot::xaxis::labels", label = round(1:10/11, 2))
+grid.edit("myplot::xaxis::labels", y = unit(-1, "lines"))
+@
+\code{"grobwidth"} units require a \grob{} to give the width of.
+There are two ways to specify the \grob{}. The following example
+shows the most obvious method of simply supplying a \grob{}. Notice
+that if you modify \code{gt} it will have no effect on the width of
+the drawn rectangle.
+
+<<results=hide>>=
+grid.newpage()
+gt <- grid.text("Hi there")
+grid.rect(width = unit(1, "grobwidth", gt))
+@
+In order to allow a \code{"grobwidth"} unit to track changes in the
+\grob{}, it is possible to specify a \gPath{} rather than a \grob{} as
+the data for a \code{"grobwidth"} unit. The following example
+modifies the previous example to use a \gPath{}. Now, the width of
+the rectangle changes when the width of the underlying \grob{}
+changes.
+
+<<results=hide>>=
+grid.newpage()
+gt <- grid.text("Hi there", name = "sometext")
+grid.rect(width = unit(1, "grobwidth", "sometext"))
+grid.edit("sometext", label = "Something different")
+@
+
+One issue in the evaluation of \code{"grobwidth"} units involves
+establishing the correct ``context'' for a \grob{} when determining its width
+(if a \grob{} has a viewport in its \code{vp} slot then that viewport gets
+pushed before the \grob{} is drawn; that viewport should also be pushed
+when determining the width
+of the \grob{}).
+To achieve this there are
+\code{preDrawDetails()}, \code{drawDetails()}, and \code{postDrawDetails()}
+generic functions.
+(suggestions for better names welcome!). The idea is that
+pushing and popping of viewports should occur in the \code{pre} and
+\code{post} generics, and any actual drawing happens in the main
+\code{drawDetails()} generic. This allows the code that calculates a
+\grob{} width to call the \code{preDrawDetails()} in order to establish
+the context in which the \grob{} would be drawn before calculating its
+width. The following example shows a test case; a \grob{} is created
+(extending to a new class to allow specific methods to be written),
+and methods are provided which establish a particular context
+for drawing the \grob{}. These methods are used both in the drawing
+of the \grob{} and in the calculation of the \grob{}'s width (when
+drawing a bounding rectangle).
+
+<<results=hide>>=
+grid.newpage()
+mygrob <- grob(name = "mygrob", cl = "mygrob")
+preDrawDetails.mygrob <- function(x)
+ pushViewport(viewport(gp = gpar(fontsize = 20)))
+
+drawDetails.mygrob <- function(x, recording = TRUE)
+ grid.draw(textGrob("hi there"), recording = FALSE)
+
+postDrawDetails.mygrob <- function(x) popViewport()
+
+widthDetails.mygrob <- function(x) unit(1, "strwidth", "hi there")
+
+grid.draw(mygrob)
+grid.rect(width = unit(1, "grobwidth", mygrob))
+@
+
+This next example shows a slightly different test case where the
+standard \code{preDrawDetails()} and \code{postDrawDetails()} methods
+are used, but the \grob{} does have a \code{vp} slot so these methods
+do something. Another interesting feature of this example is the
+slightly more complex \gTree{} that is created. The \gTree{} has a
+\code{childrenvp} specified. When the \gTree{} is drawn, this
+viewport is pushed and then ``up''ed before the children of the
+\gTree{} are drawn. This means that the children of the \gTree{} can
+specify a \code{vpPath} to the viewport they should be in. This
+allows the parent \gTree{} to create a suite of viewports and then
+children of the \gTree{} select which one they want -- this can be
+more efficient than having each child push and pop the viewports it
+needs, especially if several children are drawn within the same
+viewport. Another, more realistic example of this is given later.
+
+<<results=hide>>=
+grid.newpage()
+mygtree <- gTree(name = "mygrob",
+ childrenvp = viewport(name = "labelvp",
+ gp = gpar(fontsize = 20)),
+ children = gList(textGrob("hi there", name = "label",
+ vp = "labelvp")),
+ cl = "mygtree")
+widthDetails.mygtree <- function(x)
+ unit(1, "grobwidth", getGrob(x, "label"))
+
+grid.draw(mygtree)
+grid.rect(width = unit(1, "grobwidth", mygtree))
+@
+
+Constructing a description of a \code{frame} \grob{} must be
+done via \code{packGrob()} and \code{placeGrob()}. The following example
+shows the construction of a simple frame consisting of two
+equal-size columns.
+
+<<results = hide>>=
+grid.newpage()
+fg <- frameGrob(layout = grid.layout(1, 2))
+fg <- placeGrob(fg, textGrob("Hi there"), col = 1)
+fg <- placeGrob(fg, rectGrob(), col = 2)
+grid.draw(fg)
+@
+
+This next example constructs a slightly fancier frame using packing.
+
+<<results=hide>>=
+grid.newpage()
+pushViewport(viewport(layout = grid.layout(2, 2)))
+drawIt <- function(row, col) {
+ pushViewport(viewport(layout.pos.col = col, layout.pos.row = row))
+ grid.rect(gp = gpar(col = "grey"))
+ grid.draw(fg)
+ upViewport()
+}
+fg <- frameGrob()
+fg <- packGrob(fg, textGrob("Hi there"))
+fg <- placeGrob(fg, rectGrob())
+drawIt(1, 1)
+fg <- packGrob(fg, textGrob("Hello again"), side = "right")
+drawIt(1, 2)
+fg <- packGrob(fg, rectGrob(), side = "right", width = unit(1, "null"))
+drawIt(2, 2)
+@
+
+In order to allow frames to update when the objects packed within them
+are modified, there is a \code{dynamic} argument to \code{packGrob()}
+(and \code{grid.pack()}). The following extends the previous example
+to show how this might be used. Another feature of this example is
+the demonstration of ``non-strict'' searching that occurs in the
+\code{grid.edit()} call; the \grob{} called \code{"midtext"} is not at
+the top-level, but is still found. Something like
+\code{grid.get("midtext", strict = TRUE)} would fail.
+
+<<results=hide>>=
+grid.newpage()
+fg <- frameGrob()
+fg <- packGrob(fg, textGrob("Hi there"))
+fg <- placeGrob(fg, rectGrob())
+fg <- packGrob(fg, textGrob("Hello again", name = "midtext"),
+ side = "right", dynamic = TRUE)
+fg <- packGrob(fg, rectGrob(), side = "right", width = unit(1, "null"))
+grid.draw(fg)
+grid.edit("midtext", label = "something much longer")
+@
+
+There have been a few examples already which have involved creating a
+\gTree{}. This next example explicitly demonstrates this technique.
+A \gTree{} is created with two important components. The
+\code{childrenvp} is a \code{vpTree} consisting of a
+\code{"plotRegion"} viewport to provide margins around a plot and a
+\code{"dataRegion"} viewport to provide x- and y-scales. The
+\code{"dataRegion"} gets pushed within the \code{"plotRegion"} and
+both are pushed and then ``up''ed before the children are drawn. The
+\code{children} of the \gTree{} are an \code{xaxis} and a \code{yaxis}
+both drawn within the \code{"dataRegion"}, and a \code{rect} drawn
+around the border of the \code{"plotRegion"}. A further feature of
+this example is the use of the \code{addGrob()} and
+\code{removeGrob()} functions to modify the \gTree{}. The first
+modification involves adding a new child to the \gTree{} which is a
+set of points drawn within the \code{"dataRegion"}. The second
+modification involves adding another set of points with a different
+symbol (NOTE that this second set of points is given a name so that it
+is easy to identify this set amongst the children of the \gTree{}).
+The final modification is to remove the second set of points from the
+\gTree{}.
+
+<<results=hide>>=
+grid.newpage()
+pushViewport(viewport(layout = grid.layout(2, 2)))
+drawIt <- function(row, col) {
+ pushViewport(viewport(layout.pos.col = col, layout.pos.row = row))
+ grid.rect(gp = gpar(col = "grey"))
+ grid.draw(gplot)
+ upViewport()
+}
+gplot <- gTree(x = NULL, y = NULL,
+ childrenvp = vpTree(
+ plotViewport(c(5, 4, 4, 2), name = "plotRegion"),
+ vpList(viewport(name = "dataRegion"))),
+ children = gList(
+ xaxisGrob(vp = "plotRegion::dataRegion"),
+ yaxisGrob(vp = "plotRegion::dataRegion"),
+ rectGrob(vp = "plotRegion")))
+drawIt(1, 1)
+gplot <- addGrob(gplot, pointsGrob(vp = "plotRegion::dataRegion"))
+drawIt(1, 2)
+gplot <- addGrob(gplot, pointsGrob(name = "data1", pch = 2,
+ vp = "plotRegion::dataRegion"))
+drawIt(2, 1)
+gplot <- removeGrob(gplot, "data1")
+drawIt(2, 2)
+@
+
+This next example provides a simple demonstration of saving and
+loading \grid{} \grob{}s. It is also a nice demonstration that
+\grob{}s copy like normal \R{} objects.
+
+<<results=hide>>=
+gplot <- gTree(x = NULL, y = NULL,
+ childrenvp = vpTree(
+ plotViewport(c(5, 4, 4, 2), name = "plotRegion"),
+ vpList(viewport(name = "dataRegion"))),
+ children = gList(
+ xaxisGrob(vp = "plotRegion::dataRegion"),
+ yaxisGrob(vp = "plotRegion::dataRegion"),
+ rectGrob(vp = "plotRegion")))
+save(gplot, file = "gplot1")
+gplot <- addGrob(gplot, pointsGrob(vp = "plotRegion::dataRegion"))
+save(gplot, file = "gplot2")
+grid.newpage()
+pushViewport(viewport(layout = grid.layout(1, 2)))
+pushViewport(viewport(layout.pos.col = 1))
+load("gplot1")
+grid.draw(gplot)
+popViewport()
+pushViewport(viewport(layout.pos.col = 2))
+load("gplot2")
+grid.draw(gplot)
+popViewport()
+@
+
+This next example just demonstrates that it is possible to use a
+\gPath{} to access the children of a \gTree{} when editing. This is
+the \code{editGrob()} equivalent of an earlier example that used
+\code{grid.edit()}. One useful application of this API is the ability
+to modify the appearance of quite precise elements of a large, complex
+graphical object by editing the \code{gp} slot of a child (of a child
+\ldots{}) of a \gTree{}.
+
+<<results = hide>>=
+myplot <- gTree(name = "myplot",
+ children = gList(
+ rectGrob(name = "box", gp = gpar(col = "grey")),
+ xaxisGrob(name = "xaxis")))
+myplot <- editGrob(myplot, gPath = "xaxis", at = 1:10/11)
+myplot <- editGrob(myplot, gPath = "xaxis::labels", label = round(1:10/11, 2))
+myplot <- editGrob(myplot, gPath = "xaxis::labels", y = unit(-1, "lines"))
+grid.newpage()
+pushViewport(viewport(w = .5, h = .5))
+grid.draw(myplot)
+
+@
+The following example demonstrates
+the use of the \code{getGrob()} and \code{grid.get()} (along with
+\gPath{}s) to access \grob{}s.
+
+<<results = hide>>=
+myplot <- gTree(name = "myplot",
+ children = gList(
+ rectGrob(name = "box", gp = gpar(col = "grey")),
+ xaxisGrob(name = "xaxis")))
+getGrob(myplot, "xaxis")
+myplot <- editGrob(myplot, gPath="xaxis", at=1:10/11)
+getGrob(myplot, "xaxis::labels")
+grid.newpage()
+pushViewport(viewport(w=.5, h=.5))
+grid.draw(myplot)
+grid.get("myplot")
+grid.get("myplot::xaxis")
+grid.get("myplot::xaxis::labels")
+@
+
+There is also an API for (re)setting children of a \gTree{}
+or any drawn \grob{}. This is not intended for general user use,
+but provides a simple way for developers to perform modifications
+to the structure of a \gTree{} by doing something like \ldots{}
+
+\begin{verbatim}
+grob <- getGrob(<spec>)
+<modify grob>
+setGrob(<spec>, grob)
+\end{verbatim}
+
+This approach is used in the implementation of packing and placing grobs.
+The following example shows some simple usage of the
+\code{setGrob()} and \code{grid.set()} functions to replace
+children of a \gTree{} with different \grob{}s. NOTE that currently
+such replacement can only occur if the name of the new \grob{}
+is the same as the name of the old \grob{}.
+
+<<results=hide>>=
+myplot <- gTree(name = "myplot",
+ children = gList(rectGrob(name = "box", gp = gpar(col = "grey")),
+ xaxisGrob(name = "xaxis")))
+myplot <- setGrob(myplot, "xaxis", rectGrob(name = "xaxis"))
+grid.newpage()
+pushViewport(viewport(w = .5, h = .5))
+grid.draw(myplot)
+grid.set("myplot::xaxis", xaxisGrob(name = "xaxis", at = 1:3/4))
+grid.set("myplot::xaxis::labels",
+ textGrob(name = "labels", x = unit(1:3/4, "native"),
+ y = unit(-1, "lines"), label = letters[1:3]))
+myplot <- setGrob(grid.get("myplot"), "xaxis::labels",
+ circleGrob(name = "labels"))
+grid.newpage()
+pushViewport(viewport(w = .5, h = .5))
+grid.draw(myplot)
+@
+
+This next example just shows more complex use of the add/remove
+facilities for modifying \grob{}s. Again, \code{addGrob()} and
+\code{removeGrob()} are for constructing descriptions of graphical
+objects and \code{grid.add()} and \code{grid.remove()} are for
+modifying drawn output. Of particular note are the last two lines
+involving \code{grid.remove()}. The first point is that there are
+multiple \grob{}s on the display list with the same name. The example
+only affects the first one it finds; this could easily be extended to
+affect the display list ``globally'' (for children of \gTree{}s, there
+cannot be multiple children with the same name so the issue does not
+arise). The last line is interesting because it actually erases the
+\grob{} named \code{"plot1"} from the display list altogether (well,
+the first instance on the display list of a \grob{} called
+\code{"plot1"} anyway).
+
+<<results=hide>>=
+drawIt <- function(row, col) {
+ pushViewport(viewport(layout.pos.col = col, layout.pos.row = row))
+ grid.rect(gp = gpar(col = "grey"))
+ grid.draw(gplot)
+ upViewport()
+}
+gplot <- gTree(name = "plot1",
+ childrenvp = vpTree(
+ plotViewport(c(5, 4, 4, 2), name = "plotRegion"),
+ vpList(viewport(name = "dataRegion"))),
+ children = gList(
+ xaxisGrob(name = "xaxis", vp = "plotRegion::dataRegion"),
+ yaxisGrob(name = "yaxis", vp = "plotRegion::dataRegion"),
+ rectGrob(name = "box", vp = "plotRegion")))
+grid.newpage()
+pushViewport(viewport(layout = grid.layout(2, 2)))
+drawIt(1, 1)
+grid.add("plot1", pointsGrob(0.5, 0.5, name = "data1",
+ vp = "plotRegion::dataRegion"))
+grid.add("plot1::xaxis",
+ textGrob("X Axis", y = unit(-2, "lines"), name = "xlab"))
+grid.edit("plot1::xaxis::xlab", y = unit(-3, "lines"))
+gplot <- grid.get("plot1")
+gplot <- addGrob(gplot, gPath = "yaxis",
+ textGrob("Y Axis", x = unit(-3, "lines"), rot = 90,
+ name = "ylab"))
+drawIt(1, 2)
+gplot <- removeGrob(gplot, "xaxis::xlab")
+drawIt(2, 1)
+grid.remove("plot1::data1")
+grid.remove("plot1")
+@
+
+The next example is just a \code{grid.place()} and \code{grid.pack()}
+equivalent of an earlier example involving
+\code{placeGrob()} and \code{packGrob()}. The interesting feature is
+that each action is reflected in the output as it occurs.
+
+<<results=hide>>=
+grid.newpage()
+grid.frame(name = "myframe", layout = grid.layout(1, 2))
+grid.place("myframe", textGrob("Hi there"), col = 1)
+grid.place("myframe", rectGrob(), col = 2)
+grid.newpage()
+grid.frame(name = "frame2")
+grid.pack("frame2", textGrob("Hi there"))
+grid.place("frame2", rectGrob())
+grid.pack("frame2", textGrob("Hello again"), side = "right")
+grid.pack("frame2", rectGrob(), side = "right", width = unit(1, "null"))
+@
+\end{document}
+
+
+
diff --git a/win32/deps/library/grid/doc/grobs.pdf b/win32/deps/library/grid/doc/grobs.pdf
new file mode 100644
index 0000000..70ab90b
Binary files /dev/null and b/win32/deps/library/grid/doc/grobs.pdf differ
diff --git a/win32/deps/library/grid/doc/index.html b/win32/deps/library/grid/doc/index.html
new file mode 100644
index 0000000..753cd9e
--- /dev/null
+++ b/win32/deps/library/grid/doc/index.html
@@ -0,0 +1,87 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Vignettes</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="/doc/html/R.css">
+</head><body>
+<h1> Vignettes
+<img class="toplogo" src="/doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="/doc/html/index.html"><img src="/doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div>
+<h2>Vignettes from package 'grid'</h2>
+<table width="100%">
+<col width="22%">
+<col width="2%">
+<col width="50%">
+<col width="8%">
+<col width="8%">
+<col width="8%">
+<tr><td align="right" valign="top"><a href="../../../library/grid/doc/displaylist.pdf">grid::displaylist</a></td>
+<td></td><td valign="top">Display Lists in grid</td>
+<td valign="top"><a href="../../../library/grid/doc/displaylist.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/grid/doc/displaylist.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/grid/doc/displaylist.R">R code</a></td></tr>
+<tr><td align="right" valign="top"><a href="../../../library/grid/doc/frame.pdf">grid::frame</a></td>
+<td></td><td valign="top">Frames and packing grobs</td>
+<td valign="top"><a href="../../../library/grid/doc/frame.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/grid/doc/frame.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/grid/doc/frame.R">R code</a></td></tr>
+<tr><td align="right" valign="top"><a href="../../../library/grid/doc/grid.pdf">grid::grid</a></td>
+<td></td><td valign="top">Introduction to grid</td>
+<td valign="top"><a href="../../../library/grid/doc/grid.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/grid/doc/grid.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/grid/doc/grid.R">R code</a></td></tr>
+<tr><td align="right" valign="top"><a href="../../../library/grid/doc/grobs.pdf">grid::grobs</a></td>
+<td></td><td valign="top">Working with grid grobs</td>
+<td valign="top"><a href="../../../library/grid/doc/grobs.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/grid/doc/grobs.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/grid/doc/grobs.R">R code</a></td></tr>
+<tr><td align="right" valign="top"><a href="../../../library/grid/doc/interactive.pdf">grid::interactive</a></td>
+<td></td><td valign="top">Editing grid Graphics</td>
+<td valign="top"><a href="../../../library/grid/doc/interactive.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/grid/doc/interactive.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/grid/doc/interactive.R">R code</a></td></tr>
+<tr><td align="right" valign="top"><a href="../../../library/grid/doc/locndimn.pdf">grid::locndimn</a></td>
+<td></td><td valign="top">Locations versus Dimensions</td>
+<td valign="top"><a href="../../../library/grid/doc/locndimn.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/grid/doc/locndimn.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/grid/doc/locndimn.R">R code</a></td></tr>
+<tr><td align="right" valign="top"><a href="../../../library/grid/doc/moveline.pdf">grid::moveline</a></td>
+<td></td><td valign="top">Demonstrating move-to and line-to</td>
+<td valign="top"><a href="../../../library/grid/doc/moveline.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/grid/doc/moveline.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/grid/doc/moveline.R">R code</a></td></tr>
+<tr><td align="right" valign="top"><a href="../../../library/grid/doc/nonfinite.pdf">grid::nonfinite</a></td>
+<td></td><td valign="top">Non-finite values</td>
+<td valign="top"><a href="../../../library/grid/doc/nonfinite.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/grid/doc/nonfinite.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/grid/doc/nonfinite.R">R code</a></td></tr>
+<tr><td align="right" valign="top"><a href="../../../library/grid/doc/plotexample.pdf">grid::plotexample</a></td>
+<td></td><td valign="top">Writing grid Code</td>
+<td valign="top"><a href="../../../library/grid/doc/plotexample.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/grid/doc/plotexample.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/grid/doc/plotexample.R">R code</a></td></tr>
+<tr><td align="right" valign="top"><a href="../../../library/grid/doc/rotated.pdf">grid::rotated</a></td>
+<td></td><td valign="top">Rotated Viewports</td>
+<td valign="top"><a href="../../../library/grid/doc/rotated.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/grid/doc/rotated.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/grid/doc/rotated.R">R code</a></td></tr>
+<tr><td align="right" valign="top"><a href="../../../library/grid/doc/saveload.pdf">grid::saveload</a></td>
+<td></td><td valign="top">Persistent representations</td>
+<td valign="top"><a href="../../../library/grid/doc/saveload.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/grid/doc/saveload.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/grid/doc/saveload.R">R code</a></td></tr>
+<tr><td align="right" valign="top"><a href="../../../library/grid/doc/sharing.pdf">grid::sharing</a></td>
+<td></td><td valign="top">Modifying multiple grobs simultaneously</td>
+<td valign="top"><a href="../../../library/grid/doc/sharing.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/grid/doc/sharing.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/grid/doc/sharing.R">R code</a></td></tr>
+<tr><td align="right" valign="top"><a href="../../../library/grid/doc/viewports.pdf">grid::viewports</a></td>
+<td></td><td valign="top">Working with viewports</td>
+<td valign="top"><a href="../../../library/grid/doc/viewports.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/grid/doc/viewports.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/grid/doc/viewports.R">R code</a></td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/grid/doc/interactive.R b/win32/deps/library/grid/doc/interactive.R
new file mode 100644
index 0000000..e0547a7
--- /dev/null
+++ b/win32/deps/library/grid/doc/interactive.R
@@ -0,0 +1,90 @@
+### R code from vignette source 'interactive.Rnw'
+
+###################################################
+### code chunk number 1: interactive.Rnw:18-22
+###################################################
+library(grDevices)
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+
+
+###################################################
+### code chunk number 2: fig1
+###################################################
+grid.xaxis(at = 1:4/5, vp = viewport(w = .5, h = 0.01), name = "gxa")
+
+
+###################################################
+### code chunk number 3: edit1 (eval = FALSE)
+###################################################
+## grid.edit("gxa", gp = gpar(col = "red"))
+
+
+###################################################
+### code chunk number 4: fig2
+###################################################
+gxa <- xaxisGrob(at = 1:4/5, vp = viewport(w = .5, h = .01))
+gxa <- editGrob(gxa, gp = gpar(col = "red"))
+grid.draw(gxa)
+
+
+###################################################
+### code chunk number 5: edit2 (eval = FALSE)
+###################################################
+## grid.edit(gPath("gxa", "labels"), gp = gpar(col = "green"))
+
+
+###################################################
+### code chunk number 6: fig3
+###################################################
+gxa <- xaxisGrob(at = 1:4/5, vp = viewport(w = .5, h = .01))
+gxa <- editGrob(gxa, gp = gpar(col = "red"))
+gxa <- editGrob(gxa, gPath = "labels", gp = gpar(col = "green"))
+grid.draw(gxa)
+
+
+###################################################
+### code chunk number 7: edit3 (eval = FALSE)
+###################################################
+## grid.edit("gxa", at = c(0.0, 0.5, 1.0))
+
+
+###################################################
+### code chunk number 8: fig4
+###################################################
+gxa <- xaxisGrob(at = 1:4/5, vp = viewport(w = .5, h = .01))
+gxa <- editGrob(gxa, gp = gpar(col = "red"))
+gxa <- editGrob(gxa, gPath = "labels", gp = gpar(col = "green"))
+gxa <- editGrob(gxa, at = c(0.0, 0.5, 1.0))
+grid.draw(gxa)
+
+
+###################################################
+### code chunk number 9: edit4 (eval = FALSE)
+###################################################
+## grid.edit("gxa::labels", gp = gpar(col = "black"), rot = 30)
+
+
+###################################################
+### code chunk number 10: fig5
+###################################################
+gxa <- xaxisGrob(at = 1:4/5, vp = viewport(w = .5, h = .01))
+gxa <- editGrob(gxa, gp = gpar(col = "red"))
+gxa <- editGrob(gxa, gPath = "labels", gp = gpar(col = "green"))
+gxa <- editGrob(gxa, at = c(0.0, 0.5, 1.0))
+gxa <- editGrob(gxa, gPath = "labels", gp = gpar(col = "black"), rot = 30)
+grid.draw(gxa)
+
+
+###################################################
+### code chunk number 11: interactive.Rnw:123-129
+###################################################
+gxa <- xaxisGrob(at = 1:4/5, vp = viewport(w = .5, h = .01))
+gxa <- editGrob(gxa, gp = gpar(col = "red"))
+gxa <- editGrob(gxa, gPath = "labels", gp = gpar(col = "green"))
+gxa <- editGrob(gxa, at = c(0.0, 0.5, 1.0))
+gxa <- editGrob(gxa, gPath = "labels", gp = gpar(col = "black"), rot = 30)
+grid.draw(gxa)
+
+
diff --git a/win32/deps/library/grid/doc/interactive.Rnw b/win32/deps/library/grid/doc/interactive.Rnw
new file mode 100644
index 0000000..a4362eb
--- /dev/null
+++ b/win32/deps/library/grid/doc/interactive.Rnw
@@ -0,0 +1,132 @@
+\documentclass[a4paper]{article}
+%\VignetteIndexEntry{Editing grid Graphics}
+%\VignettePackage{grid}
+\newcommand{\code}[1]{\texttt{#1}}
+\newcommand{\pkg}[1]{{\normalfont\fontseries{b}\selectfont #1}}
+\newcommand{\grid}{\pkg{grid}}
+\newcommand{\R}{{\sffamily R}}
+\setlength{\parindent}{0in}
+\setlength{\parskip}{.1in}
+\setlength{\textwidth}{140mm}
+\setlength{\oddsidemargin}{10mm}
+\title{An Example of Interactive Graphics Editing in \grid}
+\author{Paul Murrell}
+
+\begin{document}
+\maketitle
+
+<<echo=FALSE, results=hide>>=
+library(grDevices)
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+@
+First of all, we create an x-axis and draw it on the device.
+It is very important that we specify a \code{name} for the object
+so that we can refer to it later.
+
+<<fig1, results=hide, fig=TRUE, width=6, height=2, include=FALSE>>=
+grid.xaxis(at = 1:4/5, vp = viewport(w = .5, h = 0.01), name = "gxa")
+@
+\begin{center}
+{
+\includegraphics[width=3in, height=1in]{interactive-fig1}
+}
+\end{center}
+@
+
+Now we edit the axis, changing the colour of the entire axis to red.
+Notice that we refer to the x-axis by its name.
+
+<<edit1, eval=FALSE>>=
+grid.edit("gxa", gp = gpar(col = "red"))
+<<fig2, echo=FALSE, results=hide, fig=TRUE, width=6, height=2, include=FALSE>>=
+gxa <- xaxisGrob(at = 1:4/5, vp = viewport(w = .5, h = .01))
+gxa <- editGrob(gxa, gp = gpar(col = "red"))
+grid.draw(gxa)
+@
+\begin{center}
+{
+\includegraphics[width=3in, height=1in]{interactive-fig2}
+}
+\end{center}
+
+@
+
+Now we change just the labels of the x-axis to green. We use the
+\code{gPath()} function to concatenate the grob names (we could have used
+\code{"gxa::labels"} here, but \code{gPath()} is recommended for
+writing code that will be reused).
+
+<<edit2, eval=FALSE>>=
+grid.edit(gPath("gxa", "labels"), gp = gpar(col = "green"))
+<<fig3, echo=FALSE, results=hide, fig=TRUE, width=6, height=2, include=FALSE>>=
+gxa <- xaxisGrob(at = 1:4/5, vp = viewport(w = .5, h = .01))
+gxa <- editGrob(gxa, gp = gpar(col = "red"))
+gxa <- editGrob(gxa, gPath = "labels", gp = gpar(col = "green"))
+grid.draw(gxa)
+@
+\begin{center}
+{
+\includegraphics[width=3in, height=1in]{interactive-fig3}
+}
+\end{center}
+@
+
+It is also possible to change the number of tick marks.
+Notice that the labels all change back to red; this happens
+because new labels are created by the axis and these ``inherit''
+the colour of the axis by default. In other words, the
+colour specification of the old labels was specific to the old labels
+and was discarded when the old labels were discarded.
+
+<<edit3, eval=FALSE>>=
+grid.edit("gxa", at = c(0.0, 0.5, 1.0))
+<<fig4, echo=FALSE, results=hide, fig=TRUE, width=6, height=2, include=FALSE>>=
+gxa <- xaxisGrob(at = 1:4/5, vp = viewport(w = .5, h = .01))
+gxa <- editGrob(gxa, gp = gpar(col = "red"))
+gxa <- editGrob(gxa, gPath = "labels", gp = gpar(col = "green"))
+gxa <- editGrob(gxa, at = c(0.0, 0.5, 1.0))
+grid.draw(gxa)
+@
+\begin{center}
+{
+\includegraphics[width=3in, height=1in]{interactive-fig4}
+}
+\end{center}
+@
+
+Finally, we change the labels back to black and rotate them all $30\deg$.
+
+<<edit4, eval=FALSE>>=
+grid.edit("gxa::labels", gp = gpar(col = "black"), rot = 30)
+<<fig5, echo=FALSE, results=hide, fig=TRUE, width=6, height=2, include=FALSE>>=
+gxa <- xaxisGrob(at = 1:4/5, vp = viewport(w = .5, h = .01))
+gxa <- editGrob(gxa, gp = gpar(col = "red"))
+gxa <- editGrob(gxa, gPath = "labels", gp = gpar(col = "green"))
+gxa <- editGrob(gxa, at = c(0.0, 0.5, 1.0))
+gxa <- editGrob(gxa, gPath = "labels", gp = gpar(col = "black"), rot = 30)
+grid.draw(gxa)
+@
+\begin{center}
+{
+\includegraphics[width=3in, height=1in]{interactive-fig5}
+}
+\end{center}
+@
+
+The above examples describe how to perform editing on a grid object
+and have the changes updated on screen. The equivalent can be done
+entirely ``off-screen'', by just working with the grid object.
+The off-screen equivalent in this case would look like:
+
+<<results=hide>>=
+gxa <- xaxisGrob(at = 1:4/5, vp = viewport(w = .5, h = .01))
+gxa <- editGrob(gxa, gp = gpar(col = "red"))
+gxa <- editGrob(gxa, gPath = "labels", gp = gpar(col = "green"))
+gxa <- editGrob(gxa, at = c(0.0, 0.5, 1.0))
+gxa <- editGrob(gxa, gPath = "labels", gp = gpar(col = "black"), rot = 30)
+grid.draw(gxa)
+@
+\end{document}
+
diff --git a/win32/deps/library/grid/doc/interactive.pdf b/win32/deps/library/grid/doc/interactive.pdf
new file mode 100644
index 0000000..f753d7c
Binary files /dev/null and b/win32/deps/library/grid/doc/interactive.pdf differ
diff --git a/win32/deps/library/grid/doc/locndimn.R b/win32/deps/library/grid/doc/locndimn.R
new file mode 100644
index 0000000..7512860
--- /dev/null
+++ b/win32/deps/library/grid/doc/locndimn.R
@@ -0,0 +1,72 @@
+### R code from vignette source 'locndimn.Rnw'
+
+###################################################
+### code chunk number 1: locndimn.Rnw:20-24
+###################################################
+library(grDevices)
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+
+
+###################################################
+### code chunk number 2: locndimn.Rnw:52-91
+###################################################
+diagram.locn <- function(i, n, locn) {
+ x <- i/(n+1)
+ grid.lines(x = unit(rep(x, 2), "npc"),
+ y = unit.c(unit(0, "npc"), locn))
+ grid.lines(x = unit(x, "npc") + unit(c(-2, 0, 2), "mm"),
+ y = locn + unit(c(-2, 0, -2), "mm"))
+ grid.text(paste(as.character(locn), "as a location"),
+ x = unit(x, "npc") - unit(1, "mm"),
+ y = locn - unit(3, "mm"),
+ just = c("right", "bottom"),
+ rot = 90)
+}
+diagram.dimn <- function(i, n, dimn) {
+ x <- i/(n+1)
+ pushViewport(viewport(x = unit(x, "npc"), y = unit(0, "native"),
+ h = dimn, w = unit(1, "lines"), just = c("centre", "bottom")))
+ grid.rect()
+ grid.text(paste(as.character(dimn), "as a dimension"),
+ rot = 90)
+ popViewport()
+}
+pushViewport(viewport(w = 0.8, y=unit(1.7, "inches"),
+ h = unit(4, "inches"),
+ just = c("centre", "bottom"),
+ yscale = c(-0.6, 1.3)))
+grid.grill(v = c(0, 1), h = seq(-0.5, 1, 0.5), default.units = "native")
+grid.rect()
+grid.yaxis()
+n <- 10
+diagram.locn(1, n, unit(1, "native"))
+diagram.locn(2, n, unit(-0.4, "native"))
+diagram.locn(3, n, unit(0.4, "native"))
+diagram.locn(4, n, unit(1, "native") + unit(-0.4, "native"))
+diagram.locn(5, n, unit(1, "native") - unit(0.4, "native"))
+diagram.dimn(6, n, unit(1, "native"))
+diagram.dimn(7, n, unit(-0.4, "native"))
+diagram.dimn(8, n, unit(0.4, "native"))
+diagram.dimn(9, n, unit(1, "native") + unit(-0.4, "native"))
+diagram.dimn(10, n, unit(1, "native") - unit(0.4, "native"))
+
+
+###################################################
+### code chunk number 3: locndimn.Rnw:102-114
+###################################################
+pushViewport(viewport(yscale = c(-0.6, 1.3)))
+# Unexpected results?
+convertY(unit(1,'native'), "native")
+convertY(unit(-.4,'native'), "native")
+convertY(unit(1,'native')+unit(-.4,'native'), "native")
+convertY(unit(1,'native')-unit(.4,'native'), "native")
+# Expected results
+convertHeight(unit(1,'native'), "native")
+convertHeight(unit(-.4,'native'), "native")
+convertHeight(unit(1,'native')+unit(-.4,'native'), "native")
+convertHeight(unit(1,'native')-unit(.4,'native'), "native")
+popViewport()
+
+
diff --git a/win32/deps/library/grid/doc/locndimn.Rnw b/win32/deps/library/grid/doc/locndimn.Rnw
new file mode 100644
index 0000000..826f447
--- /dev/null
+++ b/win32/deps/library/grid/doc/locndimn.Rnw
@@ -0,0 +1,117 @@
+\documentclass[a4paper]{article}
+%\VignetteIndexEntry{Locations versus Dimensions}
+%\VignettePackage{grid}
+\setlength{\parindent}{0in}
+\setlength{\parskip}{.1in}
+\setlength{\textwidth}{140mm}
+\setlength{\oddsidemargin}{10mm}
+
+\newcommand{\code}[1]{\texttt{#1}}
+\newcommand{\pkg}[1]{{\normalfont\fontseries{b}\selectfont #1}}
+\newcommand{\grid}{\pkg{grid}}
+
+\title{The difference between Locations and Dimensions in \grid{}}
+\author{Paul Murrell}
+
+\begin{document}
+
+\maketitle
+
+<<echo=FALSE, results=hide>>=
+library(grDevices)
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+@
+\grid{} makes use of unit objects to express both the locations and
+dimensions of graphical components. For example, the \code{grid.rect()}
+function treats its x- and y-arguments as locations within the current
+viewport, and its width- and height-arguments as dimensions within the
+current viewport.
+
+These different interpretations of units are usually implicit like this;
+if its an x- or y-value then its a location, if its a width- or height-value
+then its a dimension.
+
+The distinction is made at all because, in some coordinate systems, notably
+\code{"native"} coordinates, the location $x$ can have a very different
+meaning
+from the dimension $x$ -- basically, whenever the minimum value of the
+coordinate system is not zero.
+
+In the specification of simple units, the difference between locations
+and dimensions is often not noticeable. However, there are a couple
+of tricky areas:
+
+\begin{enumerate}
+\item When adding (or performing any arithmetic operation on) units,
+it is important to keep in mind that locations are added like vectors
+and dimensions are added like lengths. The following
+diagram demonstrates the difference:
+
+<<fig=TRUE, echo=FALSE, results=hide>>=
+diagram.locn <- function(i, n, locn) {
+ x <- i/(n+1)
+ grid.lines(x = unit(rep(x, 2), "npc"),
+ y = unit.c(unit(0, "npc"), locn))
+ grid.lines(x = unit(x, "npc") + unit(c(-2, 0, 2), "mm"),
+ y = locn + unit(c(-2, 0, -2), "mm"))
+ grid.text(paste(as.character(locn), "as a location"),
+ x = unit(x, "npc") - unit(1, "mm"),
+ y = locn - unit(3, "mm"),
+ just = c("right", "bottom"),
+ rot = 90)
+}
+diagram.dimn <- function(i, n, dimn) {
+ x <- i/(n+1)
+ pushViewport(viewport(x = unit(x, "npc"), y = unit(0, "native"),
+ h = dimn, w = unit(1, "lines"), just = c("centre", "bottom")))
+ grid.rect()
+ grid.text(paste(as.character(dimn), "as a dimension"),
+ rot = 90)
+ popViewport()
+}
+pushViewport(viewport(w = 0.8, y=unit(1.7, "inches"),
+ h = unit(4, "inches"),
+ just = c("centre", "bottom"),
+ yscale = c(-0.6, 1.3)))
+grid.grill(v = c(0, 1), h = seq(-0.5, 1, 0.5), default.units = "native")
+grid.rect()
+grid.yaxis()
+n <- 10
+diagram.locn(1, n, unit(1, "native"))
+diagram.locn(2, n, unit(-0.4, "native"))
+diagram.locn(3, n, unit(0.4, "native"))
+diagram.locn(4, n, unit(1, "native") + unit(-0.4, "native"))
+diagram.locn(5, n, unit(1, "native") - unit(0.4, "native"))
+diagram.dimn(6, n, unit(1, "native"))
+diagram.dimn(7, n, unit(-0.4, "native"))
+diagram.dimn(8, n, unit(0.4, "native"))
+diagram.dimn(9, n, unit(1, "native") + unit(-0.4, "native"))
+diagram.dimn(10, n, unit(1, "native") - unit(0.4, "native"))
+@
+\item The functions \code{convertX},
+\code{convertY}, \code{convertWidth}, \code{convertHeight}
+ are used to convert from one coordinate system to another.
+Again, it is important whether the conversion is for a location or
+for a dimension.
+The following code
+demonstrates some results from these functions based on a similar
+situation to that in the preceding diagram:
+
+<<fig=FALSE>>=
+pushViewport(viewport(yscale = c(-0.6, 1.3)))
+# Unexpected results?
+convertY(unit(1,'native'), "native")
+convertY(unit(-.4,'native'), "native")
+convertY(unit(1,'native')+unit(-.4,'native'), "native")
+convertY(unit(1,'native')-unit(.4,'native'), "native")
+# Expected results
+convertHeight(unit(1,'native'), "native")
+convertHeight(unit(-.4,'native'), "native")
+convertHeight(unit(1,'native')+unit(-.4,'native'), "native")
+convertHeight(unit(1,'native')-unit(.4,'native'), "native")
+popViewport()
+@
+\end{enumerate}
+\end{document}
diff --git a/win32/deps/library/grid/doc/locndimn.pdf b/win32/deps/library/grid/doc/locndimn.pdf
new file mode 100644
index 0000000..3cc24b7
Binary files /dev/null and b/win32/deps/library/grid/doc/locndimn.pdf differ
diff --git a/win32/deps/library/grid/doc/moveline.R b/win32/deps/library/grid/doc/moveline.R
new file mode 100644
index 0000000..e342a08
--- /dev/null
+++ b/win32/deps/library/grid/doc/moveline.R
@@ -0,0 +1,30 @@
+### R code from vignette source 'moveline.Rnw'
+
+###################################################
+### code chunk number 1: moveline.Rnw:19-23
+###################################################
+library(grDevices)
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+
+
+###################################################
+### code chunk number 2: fig
+###################################################
+pushViewport(
+ viewport(w = 0.8, h = 0.8,
+ layout = grid.layout(1, 3,
+ widths = unit(rep(1, 3),
+ c("null", "inches", "null")))))
+pushViewport(viewport(layout.pos.col = 1, yscale = c(0, 4)))
+grid.grill(); grid.yaxis(); grid.xaxis()
+grid.points(0.5, unit(2, "native"))
+grid.move.to(0.5, unit(2,"native"))
+popViewport()
+pushViewport(viewport(layout.pos.col = 3, yscale = c(0, 2)))
+grid.grill(); grid.yaxis(); grid.xaxis()
+grid.points(0.5, unit(2, "native"))
+grid.line.to(0.5, unit(2,"native"))
+
+
diff --git a/win32/deps/library/grid/doc/moveline.Rnw b/win32/deps/library/grid/doc/moveline.Rnw
new file mode 100644
index 0000000..76f3abf
--- /dev/null
+++ b/win32/deps/library/grid/doc/moveline.Rnw
@@ -0,0 +1,64 @@
+\documentclass[a4paper]{article}
+%\VignetteIndexEntry{Demonstrating move-to and line-to}
+%\VignettePackage{grid}
+\newcommand{\code}[1]{\texttt{#1}}
+\newcommand{\pkg}[1]{{\normalfont\fontseries{b}\selectfont #1}}
+\newcommand{\grid}{\pkg{grid}}
+\newcommand{\R}{{\sffamily R}}
+\setlength{\parindent}{0in}
+\setlength{\parskip}{.1in}
+\setlength{\textwidth}{140mm}
+\setlength{\oddsidemargin}{10mm}
+\title{Drawing Lines Between Viewports: \\
+\code{grid.move.to} and \code{grid.line.to}}
+\author{Paul Murrell}
+
+\begin{document}
+\maketitle
+
+<<echo=FALSE, results=hide>>=
+library(grDevices)
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+@
+
+Many graphics systems have the notion of a current drawing location.
+This has been added to Grid, with the additional benefit that the
+drawing location can be specified relative to an arbitrary viewport.
+This allows drawing across coordinate
+systems\footnote{There was a request on R-help for exactly this
+sort of thing - I will try to find the exact reference - and there has
+since been another (From: Ross Darnell; Subject: Problems with
+segments and multiple graphs). }.
+
+The following code demonstrates a simple example (the output is
+given after the code).
+
+<<fig, results=hide, fig=TRUE, width=5, height=4, include=FALSE>>=
+pushViewport(
+ viewport(w = 0.8, h = 0.8,
+ layout = grid.layout(1, 3,
+ widths = unit(rep(1, 3),
+ c("null", "inches", "null")))))
+pushViewport(viewport(layout.pos.col = 1, yscale = c(0, 4)))
+grid.grill(); grid.yaxis(); grid.xaxis()
+grid.points(0.5, unit(2, "native"))
+grid.move.to(0.5, unit(2,"native"))
+popViewport()
+pushViewport(viewport(layout.pos.col = 3, yscale = c(0, 2)))
+grid.grill(); grid.yaxis(); grid.xaxis()
+grid.points(0.5, unit(2, "native"))
+grid.line.to(0.5, unit(2,"native"))
+@
+\begin{center}
+{
+\includegraphics[width=5in, height=4in]{moveline-fig}
+}
+\end{center}
+
+@
+\end{document}
+
+
+
diff --git a/win32/deps/library/grid/doc/moveline.pdf b/win32/deps/library/grid/doc/moveline.pdf
new file mode 100644
index 0000000..7505f0a
Binary files /dev/null and b/win32/deps/library/grid/doc/moveline.pdf differ
diff --git a/win32/deps/library/grid/doc/nonfinite.R b/win32/deps/library/grid/doc/nonfinite.R
new file mode 100644
index 0000000..776ed57
--- /dev/null
+++ b/win32/deps/library/grid/doc/nonfinite.R
@@ -0,0 +1,73 @@
+### R code from vignette source 'nonfinite.Rnw'
+
+###################################################
+### code chunk number 1: nonfinite.Rnw:16-20
+###################################################
+library(grDevices)
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+
+
+###################################################
+### code chunk number 2: prim1
+###################################################
+pushViewport(viewport(layout = grid.layout(1, 2,
+ widths = unit(c(1, 1), c("inches", "null")))))
+grid.rect(gp = gpar(col = "grey"))
+pushViewport(viewport(layout.pos.col = 1))
+grid.text(c("segments", "text", "lines", "rectangles", "circles", "points"),
+ x = 1, just = "right", y = c(0.75, 6:2/10), gp = gpar(col = "grey"))
+popViewport()
+pushViewport(viewport(layout.pos.col = 2))
+x <- 1:7/8
+x[4] <- NA
+grid.lines(x, 0.5)
+grid.text(letters[1:5], x, 0.6)
+grid.segments(x, 0.7, x, 0.8)
+grid.points(x, rep(0.2, 7))
+grid.rect(x, 0.4, 0.02, 0.02)
+grid.circle(x, 0.3, 0.02)
+grid.text("NA", 0.5, 2:8/10, gp = gpar(col = "grey"))
+popViewport(2)
+
+
+###################################################
+### code chunk number 3: prim2
+###################################################
+n <- 7
+primtest2 <- function(nas, na) {
+ t <- seq(0, 2*pi, length = n+1)[-(n+1)]
+ y <- 0.5 + 0.4*sin(t)
+ x <- 0.5 + 0.4*cos(t)
+ if (any(nas))
+ grid.text(paste("NA", (1:n)[nas], sep = ""),
+ x[nas], y[nas], gp = gpar(col = "grey"))
+ x[nas] <- na
+ y[nas] <- na
+ grid.move.to(x[1], y[1])
+ for (i in 2:n)
+ grid.line.to(x[i], y[i], gp = gpar(lty = "dashed", lwd = 5))
+ grid.polygon(x, y, gp = gpar(fill = "grey", col = NULL))
+ grid.lines(x, y, arrow = arrow())
+}
+celltest <- function(r, c, nas, na) {
+ pushViewport(viewport(layout.pos.col = c, layout.pos.row = r))
+ primtest2(nas, na)
+ grid.rect(gp = gpar(col = "grey"))
+ popViewport()
+}
+cellnas <- function(i) {
+ temp <- rep(FALSE, n)
+ temp[i] <- TRUE
+ temp[n - 3 + i] <- TRUE
+ temp
+}
+pushViewport(viewport(layout = grid.layout(2, 2)))
+celltest(1, 1, rep(FALSE, n), NA)
+celltest(1, 2, cellnas(1), NA)
+celltest(2, 1, cellnas(2), NA)
+celltest(2, 2, cellnas(3), NA)
+popViewport()
+
+
diff --git a/win32/deps/library/grid/doc/nonfinite.Rnw b/win32/deps/library/grid/doc/nonfinite.Rnw
new file mode 100644
index 0000000..1b47c64
--- /dev/null
+++ b/win32/deps/library/grid/doc/nonfinite.Rnw
@@ -0,0 +1,135 @@
+\documentclass[a4paper]{article}
+%\VignetteIndexEntry{Non-finite values}
+%\VignettePackage{grid}
+\newcommand{\pkg}[1]{{\normalfont\fontseries{b}\selectfont #1}}
+\newcommand{\grid}{\pkg{grid}}
+\setlength{\parindent}{0in}
+\setlength{\parskip}{.1in}
+\setlength{\textwidth}{140mm}
+\setlength{\oddsidemargin}{10mm}
+\title{How \grid{} Responds to Non-Finite Values}
+\author{Paul Murrell}
+
+\begin{document}
+\maketitle
+
+<<echo=FALSE, results=hide>>=
+library(grDevices)
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+@
+
+It is possible to include non-finite values, \texttt{NA}, \texttt{NaN}, {\tt
+ Inf}, and \texttt{-Inf}, in specifications of locations and sizes in
+\grid{} functions. This document describes how \grid{} responds to
+non-finite values in different cases.
+
+\textbf{viewports} {~} \\
+Non-finite values are not permitted in the location, size, or
+scales of a viewport. Viewport scales are checked
+when a viewport is created. It is very hard to be certain that
+locations and sizes are not non-finite when the viewport is created
+so this is only checked
+when the viewport is pushed.
+Non-finite values result in error messages.
+
+\textbf{lines},
+\textbf{segments},
+\textbf{rectangles},
+\textbf{text},
+\textbf{points},
+\textbf{circles} {~} \\
+For all of these primitives, non-finite values for locations or
+sizes result in the corresponding primitive not being drawn.
+The following image provides a simple demonstration. Each primitive
+is drawn at seven x-locations, with the fourth location made non-finite
+ (as indicated by a grey \texttt{"NA"}).
+
+<<prim1, echo=FALSE, fig=TRUE, results=hide, width=4, height=2, include=FALSE>>=
+pushViewport(viewport(layout = grid.layout(1, 2,
+ widths = unit(c(1, 1), c("inches", "null")))))
+grid.rect(gp = gpar(col = "grey"))
+pushViewport(viewport(layout.pos.col = 1))
+grid.text(c("segments", "text", "lines", "rectangles", "circles", "points"),
+ x = 1, just = "right", y = c(0.75, 6:2/10), gp = gpar(col = "grey"))
+popViewport()
+pushViewport(viewport(layout.pos.col = 2))
+x <- 1:7/8
+x[4] <- NA
+grid.lines(x, 0.5)
+grid.text(letters[1:5], x, 0.6)
+grid.segments(x, 0.7, x, 0.8)
+grid.points(x, rep(0.2, 7))
+grid.rect(x, 0.4, 0.02, 0.02)
+grid.circle(x, 0.3, 0.02)
+grid.text("NA", 0.5, 2:8/10, gp = gpar(col = "grey"))
+popViewport(2)
+@
+
+\vspace{.5in}
+\includegraphics{nonfinite-prim1}
+
+\newpage
+
+\textbf{lineTo} {~} \\
+A line segment is only drawn if the previous location and the
+new location are both not non-finite.
+
+\textbf{polygon} {~} \\
+A non-finite value breaks the polygon into two separate polygons.
+NOTE that this break happens within the current polygon as specified
+by the \texttt{id} argument. All polygons with the same \texttt{id}
+receive the same \texttt{gp} settings.
+
+\textbf{arrows} {~} \\
+An arrow head is only drawn if the first or last line segment is
+drawn.
+
+The following image demonstrates the behaviour of these primitives
+where x- and y-locations are seven equally-spaced locations around
+the perimeter of a circle. In the top-left figure, all locations
+are not non-finite. In each of the other figures, two locations have
+been made non-finite (indicated in each case by grey text).
+
+<<prim2, echo=FALSE, fig=TRUE, results=hide, include=FALSE>>=
+n <- 7
+primtest2 <- function(nas, na) {
+ t <- seq(0, 2*pi, length = n+1)[-(n+1)]
+ y <- 0.5 + 0.4*sin(t)
+ x <- 0.5 + 0.4*cos(t)
+ if (any(nas))
+ grid.text(paste("NA", (1:n)[nas], sep = ""),
+ x[nas], y[nas], gp = gpar(col = "grey"))
+ x[nas] <- na
+ y[nas] <- na
+ grid.move.to(x[1], y[1])
+ for (i in 2:n)
+ grid.line.to(x[i], y[i], gp = gpar(lty = "dashed", lwd = 5))
+ grid.polygon(x, y, gp = gpar(fill = "grey", col = NULL))
+ grid.lines(x, y, arrow = arrow())
+}
+celltest <- function(r, c, nas, na) {
+ pushViewport(viewport(layout.pos.col = c, layout.pos.row = r))
+ primtest2(nas, na)
+ grid.rect(gp = gpar(col = "grey"))
+ popViewport()
+}
+cellnas <- function(i) {
+ temp <- rep(FALSE, n)
+ temp[i] <- TRUE
+ temp[n - 3 + i] <- TRUE
+ temp
+}
+pushViewport(viewport(layout = grid.layout(2, 2)))
+celltest(1, 1, rep(FALSE, n), NA)
+celltest(1, 2, cellnas(1), NA)
+celltest(2, 1, cellnas(2), NA)
+celltest(2, 2, cellnas(3), NA)
+popViewport()
+@
+
+\vspace{.5in}
+\includegraphics{nonfinite-prim2}
+\end{document}
+
diff --git a/win32/deps/library/grid/doc/nonfinite.pdf b/win32/deps/library/grid/doc/nonfinite.pdf
new file mode 100644
index 0000000..13d67e0
Binary files /dev/null and b/win32/deps/library/grid/doc/nonfinite.pdf differ
diff --git a/win32/deps/library/grid/doc/plotexample.R b/win32/deps/library/grid/doc/plotexample.R
new file mode 100644
index 0000000..2e7defd
--- /dev/null
+++ b/win32/deps/library/grid/doc/plotexample.R
@@ -0,0 +1,465 @@
+### R code from vignette source 'plotexample.Rnw'
+
+###################################################
+### code chunk number 1: plotexample.Rnw:28-33
+###################################################
+library(grDevices)
+library(stats) # for runif()
+library(grid)
+ps.options(pointsize=12)
+options(width=60)
+
+
+###################################################
+### code chunk number 2: plotexample.Rnw:88-90
+###################################################
+x <- runif(10)
+y <- runif(10)
+
+
+###################################################
+### code chunk number 3: datavp
+###################################################
+data.vp <- viewport(x = unit(5, "lines"),
+ y = unit(4, "lines"),
+ width = unit(1, "npc") - unit(7, "lines"),
+ height = unit(1, "npc") - unit(7, "lines"),
+ just = c("left", "bottom"),
+ xscale = range(x) + c(-0.05, 0.05)*diff(range(x)),
+ yscale = range(y) + c(-0.05, 0.05)*diff(range(y)))
+
+
+###################################################
+### code chunk number 4: procplot
+###################################################
+pushViewport(data.vp)
+grid.points(x, y)
+grid.rect()
+grid.xaxis()
+grid.yaxis()
+grid.text("x axis", y = unit(-3, "lines"),
+ gp = gpar(fontsize = 14))
+grid.text("y axis", x = unit(-4, "lines"),
+ gp = gpar(fontsize = 14), rot = 90)
+grid.text("A Simple Plot",
+ y = unit(1, "npc") + unit(1.5, "lines"),
+ gp = gpar(fontsize = 16))
+popViewport()
+
+
+###################################################
+### code chunk number 5: plotexample.Rnw:125-126
+###################################################
+pushViewport(data.vp)
+grid.points(x, y)
+grid.rect()
+grid.xaxis()
+grid.yaxis()
+grid.text("x axis", y = unit(-3, "lines"),
+ gp = gpar(fontsize = 14))
+grid.text("y axis", x = unit(-4, "lines"),
+ gp = gpar(fontsize = 14), rot = 90)
+grid.text("A Simple Plot",
+ y = unit(1, "npc") + unit(1.5, "lines"),
+ gp = gpar(fontsize = 16))
+popViewport()
+
+
+###################################################
+### code chunk number 6: ann1
+###################################################
+pushViewport(data.vp)
+grid.text(date(), x = unit(1, "npc"), y = 0,
+ just = c("right", "bottom"), gp = gpar(col="grey"))
+popViewport()
+
+
+###################################################
+### code chunk number 7: plotexample.Rnw:142-144
+###################################################
+pushViewport(data.vp)
+grid.points(x, y)
+grid.rect()
+grid.xaxis()
+grid.yaxis()
+grid.text("x axis", y = unit(-3, "lines"),
+ gp = gpar(fontsize = 14))
+grid.text("y axis", x = unit(-4, "lines"),
+ gp = gpar(fontsize = 14), rot = 90)
+grid.text("A Simple Plot",
+ y = unit(1, "npc") + unit(1.5, "lines"),
+ gp = gpar(fontsize = 16))
+popViewport()
+pushViewport(data.vp)
+grid.text(date(), x = unit(1, "npc"), y = 0,
+ just = c("right", "bottom"), gp = gpar(col="grey"))
+popViewport()
+
+
+###################################################
+### code chunk number 8: plotexample.Rnw:159-180
+###################################################
+data.vp <- viewport(name = "dataregion",
+ x = unit(5, "lines"),
+ y = unit(4, "lines"),
+ width = unit(1, "npc") - unit(7, "lines"),
+ height = unit(1, "npc") - unit(7, "lines"),
+ just = c("left", "bottom"),
+ xscale = range(x) + c(-0.05, 0.05)*diff(range(x)),
+ yscale = range(y) + c(-0.05, 0.05)*diff(range(y)))
+pushViewport(data.vp)
+grid.points(x, y)
+grid.rect()
+grid.xaxis()
+grid.yaxis()
+grid.text("x axis", y = unit(-3, "lines"),
+ gp = gpar(fontsize = 14))
+grid.text("y axis", x = unit(-4, "lines"),
+ gp = gpar(fontsize = 14), rot = 90)
+grid.text("A Simple Plot",
+ y = unit(1, "npc") + unit(1.5, "lines"),
+ gp = gpar(fontsize = 16))
+upViewport()
+
+
+###################################################
+### code chunk number 9: plotexample.Rnw:186-190
+###################################################
+downViewport("dataregion")
+grid.text(date(), x = unit(1, "npc"), y = 0,
+ just = c("right", "bottom"), gp = gpar(col = "grey"))
+upViewport()
+
+
+###################################################
+### code chunk number 10: funcplot
+###################################################
+splot <- function(x = runif(10), y = runif(10), title = "A Simple Plot") {
+ data.vp <- viewport(name = "dataregion",
+ x = unit(5, "lines"),
+ y = unit(4, "lines"),
+ width = unit(1, "npc") - unit(7, "lines"),
+ height = unit(1, "npc") - unit(7, "lines"),
+ just = c("left", "bottom"),
+ xscale = range(x) + c(-.05, .05)*diff(range(x)),
+ yscale = range(y) + c(-.05, .05)*diff(range(y)))
+ pushViewport(data.vp)
+ grid.points(x, y)
+ grid.rect()
+ grid.xaxis()
+ grid.yaxis()
+ grid.text("y axis", x = unit(-4, "lines"),
+ gp = gpar(fontsize = 14), rot = 90)
+ grid.text(title, y = unit(1, "npc") + unit(1.5, "lines"),
+ gp = gpar(fontsize = 16))
+ upViewport()
+}
+
+
+###################################################
+### code chunk number 11: embed
+###################################################
+grid.rect(gp = gpar(fill = "grey"))
+message <-
+ paste("I could draw all sorts",
+ "of stuff over here",
+ "then create a viewport",
+ "over there and stick",
+ "a scatterplot in it.", sep = "\n")
+grid.text(message, x = 0.25)
+grid.lines(x = unit.c(unit(0.25, "npc") + 0.5*stringWidth(message) +
+ unit(2, "mm"),
+ unit(0.5, "npc") - unit(2, "mm")),
+ y = 0.5,
+ arrow = arrow(angle = 15, type = "closed"),
+ gp = gpar(lwd = 3, fill = "black"))
+pushViewport(viewport(x = 0.5, height = 0.5, width = 0.45, just = "left",
+ gp = gpar(cex = 0.5)))
+grid.rect(gp = gpar(fill = "white"))
+splot(1:10, 1:10, title = "An Embedded Plot")
+upViewport()
+
+
+###################################################
+### code chunk number 12: ann2 (eval = FALSE)
+###################################################
+## downViewport("dataregion")
+## grid.text(date(), x = unit(1, "npc"), y = 0,
+## just = c("right", "bottom"), gp = gpar(col = "grey"))
+## upViewport(0)
+
+
+###################################################
+### code chunk number 13: plotexample.Rnw:266-268
+###################################################
+grid.rect(gp = gpar(fill = "grey"))
+message <-
+ paste("I could draw all sorts",
+ "of stuff over here",
+ "then create a viewport",
+ "over there and stick",
+ "a scatterplot in it.", sep = "\n")
+grid.text(message, x = 0.25)
+grid.lines(x = unit.c(unit(0.25, "npc") + 0.5*stringWidth(message) +
+ unit(2, "mm"),
+ unit(0.5, "npc") - unit(2, "mm")),
+ y = 0.5,
+ arrow = arrow(angle = 15, type = "closed"),
+ gp = gpar(lwd = 3, fill = "black"))
+pushViewport(viewport(x = 0.5, height = 0.5, width = 0.45, just = "left",
+ gp = gpar(cex = 0.5)))
+grid.rect(gp = gpar(fill = "white"))
+splot(1:10, 1:10, title = "An Embedded Plot")
+upViewport()
+downViewport("dataregion")
+grid.text(date(), x = unit(1, "npc"), y = 0,
+ just = c("right", "bottom"), gp = gpar(col = "grey"))
+upViewport(0)
+
+
+###################################################
+### code chunk number 14: plotexample.Rnw:295-331
+###################################################
+splot.data.vp <- function(x, y) {
+ viewport(name = "dataregion",
+ x = unit(5, "lines"),
+ y = unit(4, "lines"),
+ width = unit(1, "npc") - unit(7, "lines"),
+ height = unit(1, "npc") - unit(7, "lines"),
+ just = c("left", "bottom"),
+ xscale = range(x) + c(-.05, .05)*diff(range(x)),
+ yscale = range(y) + c(-.05, .05)*diff(range(y)))
+}
+
+splot.title <- function(title) {
+ textGrob(title, name = "title",
+ y = unit(1, "npc") + unit(1.5, "lines"),
+ gp = gpar(fontsize = 16), vp = "dataregion")
+}
+
+splot <- function(x, y, title, name=NULL, draw=TRUE, gp=gpar(), vp=NULL) {
+ spg <- gTree(x = x, y = y, title = title, name = name,
+ childrenvp = splot.data.vp(x, y),
+ children = gList(rectGrob(name = "border",
+ vp = "dataregion"),
+ xaxisGrob(name = "xaxis", vp = "dataregion"),
+ yaxisGrob(name = "yaxis", vp = "dataregion"),
+ pointsGrob(x, y, name = "points", vp = "dataregion"),
+ textGrob("x axis", y = unit(-3, "lines"), name = "xlab",
+ gp = gpar(fontsize = 14), vp = "dataregion"),
+ textGrob("y axis", x = unit(-4, "lines"), name = "ylab",
+ gp = gpar(fontsize = 14), rot = 90,
+ vp = "dataregion"),
+ splot.title(title)),
+ gp = gp, vp = vp,
+ cl = "splot")
+ if (draw) grid.draw(spg)
+ spg
+}
+
+
+###################################################
+### code chunk number 15: splotgrob (eval = FALSE)
+###################################################
+## sg <- splot(1:10, 1:10, "Same as Before", name = "splot", draw = FALSE)
+
+
+###################################################
+### code chunk number 16: plotexample.Rnw:348-353
+###################################################
+splot(1:10, 1:10, "Same as Before", name = "splot")
+downViewport("dataregion")
+grid.text(date(), x = unit(1, "npc"), y = 0,
+ just = c("right", "bottom"), gp = gpar(col = "grey"))
+upViewport(0)
+
+
+###################################################
+### code chunk number 17: plotexample.Rnw:401-403
+###################################################
+splot(1:10, 1:10, "Same as Before", name = "splot")
+grid.edit("splot", gp = gpar(cex=0.5))
+
+
+###################################################
+### code chunk number 18: plotexample.Rnw:404-407
+###################################################
+sg <- splot(1:10, 1:10, "Same as Before", name = "splot", draw = FALSE)
+sg <- editGrob(sg, gp = gpar(cex = 0.5))
+grid.draw(sg)
+
+
+###################################################
+### code chunk number 19: plotexample.Rnw:413-415
+###################################################
+splot(1:10, 1:10, "Same as Before", name = "splot")
+grid.edit(gPath("splot", "points"), gp = gpar(col = 1:10))
+
+
+###################################################
+### code chunk number 20: plotexample.Rnw:416-420
+###################################################
+sg <- splot(1:10, 1:10, "Same as Before", name = "splot", draw = FALSE)
+sg <- editGrob(sg, gPath = "points", gp = gpar(col = 1:10))
+grid.draw(sg)
+
+
+
+###################################################
+### code chunk number 21: plotexample.Rnw:428-440
+###################################################
+editDetails.splot <- function(x, specs) {
+ if (any(c("x", "y") %in% names(specs))) {
+ if (is.null(specs$x)) xx <- x$x else xx <- specs$x
+ if (is.null(specs$y)) yy <- x$y else yy <- specs$y
+ x$childrenvp <- splot.data.vp(xx, yy)
+ x <- addGrob(x, pointsGrob(xx, yy, name = "points",
+ vp = "dataregion"))
+ }
+ x
+}
+splot(1:10, 1:10, "Same as Before", name = "splot")
+grid.edit("splot", x = 1:100, y = (1:100)^2)
+
+
+###################################################
+### code chunk number 22: plotexample.Rnw:441-444
+###################################################
+sg <- splot(1:10, 1:10, "Same as Before", name = "splot", draw = FALSE)
+sg <- editGrob(sg, x = 1:100, y = (1:100)^2)
+grid.draw(sg)
+
+
+###################################################
+### code chunk number 23: plotexample.Rnw:455-496
+###################################################
+cellname <- function(i, j) paste("cell", i, j, sep = "")
+
+splom.vpTree <- function(n) {
+ vplist <- vector("list", n^2)
+ for (i in 1:n)
+ for (j in 1:n)
+ vplist[[(i - 1)*n + j]] <-
+ viewport(layout.pos.row = i, layout.pos.col = j,
+ name = cellname(i, j))
+ vpTree(viewport(layout = grid.layout(n, n), name = "cellgrid"),
+ do.call("vpList", vplist))
+}
+
+cellpath <- function(i, j) vpPath("cellgrid", cellname(i, j))
+
+splom <- function(df, name = NULL, draw = TRUE) {
+ n <- dim(df)[2]
+ glist <- vector("list", n*n)
+ for (i in 1:n)
+ for (j in 1:n) {
+ glist[[(i - 1)*n + j]] <-if (i == j)
+ textGrob(paste("diag", i, sep = ""),
+ gp = gpar(col = "grey"), vp = cellpath(i, j))
+ else if (j > i)
+ textGrob(cellname(i, j),
+ name = cellname(i, j),
+ gp = gpar(col = "grey"), vp = cellpath(i, j))
+ else
+ splot(df[,j], df[,i], "",
+ name = paste("plot", i, j, sep = ""),
+ vp = cellpath(i, j),
+ gp = gpar(cex = 0.5), draw = FALSE)
+ }
+ smg <- gTree(name = name, childrenvp = splom.vpTree(n),
+ children = do.call("gList", glist))
+ if (draw) grid.draw(smg)
+ smg
+}
+
+df <- data.frame(x = rnorm(10), y = rnorm(10), z = rnorm(10))
+splom(df)
+
+
+###################################################
+### code chunk number 24: plotexample.Rnw:501-506
+###################################################
+splom(df)
+grid.edit("plot21::xlab", label = "", redraw = FALSE)
+grid.edit("plot32::ylab", label = "", redraw = FALSE)
+grid.edit("plot21::xaxis", label = FALSE, redraw = FALSE)
+grid.edit("plot32::yaxis", label = FALSE)
+
+
+###################################################
+### code chunk number 25: splomgrob (eval = FALSE)
+###################################################
+## smg <- splom(df, draw = FALSE)
+
+
+###################################################
+### code chunk number 26: plotexample.Rnw:509-515
+###################################################
+smg <- splom(df, draw = FALSE)
+smg <- editGrob(smg, gPath = "plot21::xaxis", label = FALSE)
+smg <- editGrob(smg, gPath = "plot21::xlab", label = "")
+smg <- editGrob(smg, gPath = "plot32::yaxis", label = FALSE)
+smg <- editGrob(smg, gPath = "plot32::ylab", label = "")
+grid.draw(smg)
+
+
+###################################################
+### code chunk number 27: plotexample.Rnw:525-530
+###################################################
+splom(df, name = "splom")
+grid.remove("cell12")
+grid.add("splom", textGrob(date(), name = "date",
+ gp = gpar(fontface = "italic"),
+ vp = "cellgrid::cell12"))
+
+
+###################################################
+### code chunk number 28: plotexample.Rnw:531-537
+###################################################
+smg <- splom(df, draw = FALSE)
+smg <- removeGrob(smg, "cell12")
+smg <- addGrob(smg, textGrob(date(), name = "date",
+ gp = gpar(fontface = "italic"),
+ vp = "cellgrid::cell12"))
+grid.draw(smg)
+
+
+###################################################
+### code chunk number 29: plotexample.Rnw:545-561
+###################################################
+splom(df, name = "splom")
+grid.remove("cell12")
+grid.add("splom", textGrob(date(), name = "date",
+ gp = gpar(fontface = "italic"),
+ vp = "cellgrid::cell12"))
+smg <- grid.get("splom")
+save(smg, file = "splom.RData")
+load("splom.RData")
+plot <- getGrob(smg, "plot31")
+date <- getGrob(smg, "date")
+plot <- editGrob(plot, vp = NULL, gp = gpar(cex = 1))
+date <- editGrob(date, y = unit(1, "npc") - unit(1, "lines"), vp = NULL)
+grid.newpage()
+grid.draw(plot)
+grid.draw(date)
+
+
+
+###################################################
+### code chunk number 30: plotexample.Rnw:562-575
+###################################################
+smg <- splom(df, draw = FALSE)
+smg <- removeGrob(smg, "cell12")
+smg <- addGrob(smg, textGrob(date(), name = "date",
+ gp = gpar(fontface = "italic"),
+ vp = "cellgrid::cell12"))
+save(smg, file = "splom.RData")
+load("splom.RData")
+plot <- getGrob(smg, "plot31")
+date <- getGrob(smg, "date")
+plot <- editGrob(plot, vp = NULL, gp = gpar(cex = 1))
+date <- editGrob(date, y = unit(1, "npc") - unit(1, "lines"), vp = NULL)
+grid.draw(plot)
+grid.draw(date)
+
+
diff --git a/win32/deps/library/grid/doc/plotexample.Rnw b/win32/deps/library/grid/doc/plotexample.Rnw
new file mode 100644
index 0000000..8f489e1
--- /dev/null
+++ b/win32/deps/library/grid/doc/plotexample.Rnw
@@ -0,0 +1,582 @@
+\documentclass[a4paper]{article}
+%\VignetteIndexEntry{Writing grid Code}
+%\VignettePackage{grid}
+\newcommand{\code}[1]{\texttt{#1}}
+\newcommand{\pkg}[1]{{\normalfont\fontseries{b}\selectfont #1}}
+\newcommand{\grid}{\pkg{grid}}
+\newcommand{\grob}{\code{grob}}
+\newcommand{\gTree}{\code{gTree}}
+\newcommand{\R}{{\sffamily R}}
+\setlength{\parindent}{0in}
+\setlength{\parskip}{.1in}
+\setlength{\textwidth}{140mm}
+\setlength{\oddsidemargin}{10mm}
+
+\newcommand{\aside}[1]{\begin{list}{}
+ {\setlength{\leftmargin}{1in}
+ \setlength{\rightmargin}{1in}
+ \setlength{\itemindent}{0in}}
+ \item \textsc{Aside:} \emph{#1}
+ \end{list}}
+
+\title{Writing \grid{} Code}
+\author{Paul Murrell}
+
+\begin{document}
+\maketitle
+
+<<echo=FALSE, results=hide>>=
+library(grDevices)
+library(stats) # for runif()
+library(grid)
+ps.options(pointsize=12)
+options(width=60)
+@
+
+The \grid{} system contains a degree of complexity in order
+to allow things like editing graphical objects, ``packing'' graphical
+objects, and so on. This means that many of the
+predefined Grid graphics functions are
+relatively complicated\footnote{Although there are exceptions; some
+functions, such as \code{grid.show.viewport}, are purely for producing
+illustrative diagrams and remain simple and procedural.}.
+
+One design aim of \grid{} is to allow users to create simple graphics
+simply and not to force them to use complicated concepts or write
+complicated code unless they actually need to. Along similar lines,
+it is intended that people should be able to prototype even complex
+graphics very simply and then refine the implementation into a more
+sophisticated form if necessary.
+
+With the predefined graphics functions being fully-developed and
+complicated implementations, there is a lack of examples of simple,
+prototype code. Furthermore, given that the aim is to allow a range
+of ways to produce the same graphical output, there is a need for
+examples which demonstrate the various stages, from simple to complex,
+that a piece of \grid{} code can go through.
+
+This document describes the construction of a scatterplot object, like
+that shown below, going from the simplest, prototype implementation to
+the most complex and sophisticated. It demonstrates that if you only
+want simple graphics output then you can do it pretty simply and
+quickly. It also demonstrates how to write functions that allow your
+graphics to be used by other people. Finally, it demonstrates how to
+make your graphics fully interactive (or at least as interactive as
+Grid will let you make it).
+
+@
+This document should be read {\em after} the \grid{} Users'
+Guide. Here we are assuming that the reader has an understanding
+of viewports, layouts, and units. For the later sections of the
+document, it will also be helpful to have an understanding of
+\R{}'s \code{S3} object system.
+
+\section*{Procedural \grid{}}
+
+The simplest way to produce graphical output in Grid is just like
+producing standard R graphical output. You simply issue a series of
+graphics commands and each command adds more ink to the plot. The
+purpose of the commands is simply to produce graphics output; in
+particular, we are not concerned with any values returned by the
+plotting functions. I will call this \emph{procedural graphics}.
+
+In order to draw a simple scatterplot, we can issue a series
+of commands which draw the various components of the plot.
+
+Here are some random data to plot.
+
+<<>>=
+x <- runif(10)
+y <- runif(10)
+@
+\noindent
+The first step in creating the plot involves defining a ``data'' region.
+This is a region which has sensible scales on the axes for plotting the
+data and margins around the outside
+for the axes to fit in, with a space for a title at the top.
+
+<<datavp>>=
+data.vp <- viewport(x = unit(5, "lines"),
+ y = unit(4, "lines"),
+ width = unit(1, "npc") - unit(7, "lines"),
+ height = unit(1, "npc") - unit(7, "lines"),
+ just = c("left", "bottom"),
+ xscale = range(x) + c(-0.05, 0.05)*diff(range(x)),
+ yscale = range(y) + c(-0.05, 0.05)*diff(range(y)))
+@
+\noindent
+Now we create the data region and draw the components of the plot
+relative to it: points, axes, labels, and a title.
+
+<<procplot>>=
+pushViewport(data.vp)
+grid.points(x, y)
+grid.rect()
+grid.xaxis()
+grid.yaxis()
+grid.text("x axis", y = unit(-3, "lines"),
+ gp = gpar(fontsize = 14))
+grid.text("y axis", x = unit(-4, "lines"),
+ gp = gpar(fontsize = 14), rot = 90)
+grid.text("A Simple Plot",
+ y = unit(1, "npc") + unit(1.5, "lines"),
+ gp = gpar(fontsize = 16))
+popViewport()
+<<fig=TRUE, echo=FALSE, results=hide>>=
+<<procplot>>
+@
+\section*{Facilitating Annotation}
+
+Issuing a series of commands to produce a plot, like in the previous
+section, allows the user to have a great deal of flexibility.
+It is always possible to recreate viewports in order to add
+further annotations. For example, the following code
+recreates the data region in order to place the date
+at the bottom right corner.
+
+<<ann1>>=
+pushViewport(data.vp)
+grid.text(date(), x = unit(1, "npc"), y = 0,
+ just = c("right", "bottom"), gp = gpar(col="grey"))
+popViewport()
+<<fig=TRUE, echo=FALSE, results=hide>>=
+<<procplot>>
+<<ann1>>
+@
+
+When more complex arrangements of viewports are involved, there may be
+a bewildering array of viewports created, which may make it difficult
+for other users to revisit a particular region of a plot. A
+\code{lattice} plot is a good example. In such cases, it will be more
+cooperative to use \code{upViewport()} rather than
+\code{popViewport()} and leave the viewports that were created during
+the drawing of the plot. Other users can then use \code{vpPath}s to
+navigate to the desired region. For example, here is a slight
+modification of the original series of commands, where the original
+data viewport is given a name and \code{upViewport()} is used at the
+end.
+
+<<results=hide>>=
+data.vp <- viewport(name = "dataregion",
+ x = unit(5, "lines"),
+ y = unit(4, "lines"),
+ width = unit(1, "npc") - unit(7, "lines"),
+ height = unit(1, "npc") - unit(7, "lines"),
+ just = c("left", "bottom"),
+ xscale = range(x) + c(-0.05, 0.05)*diff(range(x)),
+ yscale = range(y) + c(-0.05, 0.05)*diff(range(y)))
+pushViewport(data.vp)
+grid.points(x, y)
+grid.rect()
+grid.xaxis()
+grid.yaxis()
+grid.text("x axis", y = unit(-3, "lines"),
+ gp = gpar(fontsize = 14))
+grid.text("y axis", x = unit(-4, "lines"),
+ gp = gpar(fontsize = 14), rot = 90)
+grid.text("A Simple Plot",
+ y = unit(1, "npc") + unit(1.5, "lines"),
+ gp = gpar(fontsize = 16))
+upViewport()
+@
+
+The date is now added using \code{downViewport()} to get to the data
+region.
+
+<<results=hide>>=
+downViewport("dataregion")
+grid.text(date(), x = unit(1, "npc"), y = 0,
+ just = c("right", "bottom"), gp = gpar(col = "grey"))
+upViewport()
+@
+\section*{Writing a \grid{} Function}
+
+Here is the scatterplot code wrapped up as a simple function.
+
+<<funcplot>>=
+splot <- function(x = runif(10), y = runif(10), title = "A Simple Plot") {
+ data.vp <- viewport(name = "dataregion",
+ x = unit(5, "lines"),
+ y = unit(4, "lines"),
+ width = unit(1, "npc") - unit(7, "lines"),
+ height = unit(1, "npc") - unit(7, "lines"),
+ just = c("left", "bottom"),
+ xscale = range(x) + c(-.05, .05)*diff(range(x)),
+ yscale = range(y) + c(-.05, .05)*diff(range(y)))
+ pushViewport(data.vp)
+ grid.points(x, y)
+ grid.rect()
+ grid.xaxis()
+ grid.yaxis()
+ grid.text("y axis", x = unit(-4, "lines"),
+ gp = gpar(fontsize = 14), rot = 90)
+ grid.text(title, y = unit(1, "npc") + unit(1.5, "lines"),
+ gp = gpar(fontsize = 16))
+ upViewport()
+}
+@
+There are several advantages to creating a
+function:
+\begin{enumerate}
+\item We get the standard advantages of a function:
+we can reuse and maintain the plot code more easily.
+\item We can slightly generalise the plot. In this case, we can use it for
+different data and have a different title. We could
+add more arguments to allow different margins, control over
+the axis scales, and so on.
+\item The plot can be embedded in other graphics output.
+\end{enumerate}
+Here is an example which uses the \code{splot()} function to
+create a slightly modified scatterplot, embedded within
+other \grid{} output.
+
+<<embed, fig=TRUE, results=hide>>=
+grid.rect(gp = gpar(fill = "grey"))
+message <-
+ paste("I could draw all sorts",
+ "of stuff over here",
+ "then create a viewport",
+ "over there and stick",
+ "a scatterplot in it.", sep = "\n")
+grid.text(message, x = 0.25)
+grid.lines(x = unit.c(unit(0.25, "npc") + 0.5*stringWidth(message) +
+ unit(2, "mm"),
+ unit(0.5, "npc") - unit(2, "mm")),
+ y = 0.5,
+ arrow = arrow(angle = 15, type = "closed"),
+ gp = gpar(lwd = 3, fill = "black"))
+pushViewport(viewport(x = 0.5, height = 0.5, width = 0.45, just = "left",
+ gp = gpar(cex = 0.5)))
+grid.rect(gp = gpar(fill = "white"))
+splot(1:10, 1:10, title = "An Embedded Plot")
+upViewport()
+@
+
+It is still straightforward to annotate the scatterplot as long as
+we have enough information about the viewports. In this case,
+a non-strict \code{downViewport()} will still work (though note
+that \code{upViewport({\bf 0})} is required to get right back to the
+top level).
+
+<<ann2, echo = FALSE, eval=FALSE>>=
+downViewport("dataregion")
+grid.text(date(), x = unit(1, "npc"), y = 0,
+ just = c("right", "bottom"), gp = gpar(col = "grey"))
+upViewport(0)
+<<echo=FALSE, results=hide>>=
+<<embed>>
+<<ann2>>
+@
+\section*{Creating \grid{} Graphical Objects}
+
+A \grid{} function like the one in the previous section provides
+output which is very flexible and can be annotated in arbitrary ways
+and can be embedded within other output. This is likely
+to satisfy most uses.
+
+However, there are some things that cannot be done (or at least would
+be extremely hard to do) with such a function. The output produced by
+the function cannot be addressed as a coherent whole. It is not
+possible, for example, to to change the \code{x} and \code{y} data
+used in the plot and have the points and axes update automatically.
+There is no scatterplot object to save; the individual components
+exist, but they are not bound together as a whole. If/when these
+sorts of issues become important, it becomes necessary to create a
+\grid{} graphical object (a \grob{}) to represent the plot.
+
+The first step is to write a function which will create a \grob{}
+-- a \emph{constructor} function. In most cases, this will involve
+creating a special sort of \grob{} called a \gTree{}; this is just
+a \grob{} that can have other \grob{}s as children. Here's an example
+for creating an \code{splot} \grob{}. I have put bits of the
+construction into separate functions, for reasons which will become
+apparent later.
+
+<<>>=
+splot.data.vp <- function(x, y) {
+ viewport(name = "dataregion",
+ x = unit(5, "lines"),
+ y = unit(4, "lines"),
+ width = unit(1, "npc") - unit(7, "lines"),
+ height = unit(1, "npc") - unit(7, "lines"),
+ just = c("left", "bottom"),
+ xscale = range(x) + c(-.05, .05)*diff(range(x)),
+ yscale = range(y) + c(-.05, .05)*diff(range(y)))
+}
+
+splot.title <- function(title) {
+ textGrob(title, name = "title",
+ y = unit(1, "npc") + unit(1.5, "lines"),
+ gp = gpar(fontsize = 16), vp = "dataregion")
+}
+
+splot <- function(x, y, title, name=NULL, draw=TRUE, gp=gpar(), vp=NULL) {
+ spg <- gTree(x = x, y = y, title = title, name = name,
+ childrenvp = splot.data.vp(x, y),
+ children = gList(rectGrob(name = "border",
+ vp = "dataregion"),
+ xaxisGrob(name = "xaxis", vp = "dataregion"),
+ yaxisGrob(name = "yaxis", vp = "dataregion"),
+ pointsGrob(x, y, name = "points", vp = "dataregion"),
+ textGrob("x axis", y = unit(-3, "lines"), name = "xlab",
+ gp = gpar(fontsize = 14), vp = "dataregion"),
+ textGrob("y axis", x = unit(-4, "lines"), name = "ylab",
+ gp = gpar(fontsize = 14), rot = 90,
+ vp = "dataregion"),
+ splot.title(title)),
+ gp = gp, vp = vp,
+ cl = "splot")
+ if (draw) grid.draw(spg)
+ spg
+}
+@
+
+There are four important additions to the argument list compared
+to the original \code{splot()} function:
+\begin{enumerate}
+\item The \code{name} argument allows a string identifier to be
+ associated with the scatterplot object we create. This is important
+ for being able to specify the scatterplot when we try to edit it
+ after drawing it and/or when it is part of a larger \grob{} (see
+ later examples).
+
+\item The \code{draw} argument makes it possible to use the function
+ in a procedural manner as before:
+
+<<splotgrob, eval=FALSE, echo=FALSE>>=
+sg <- splot(1:10, 1:10, "Same as Before", name = "splot", draw = FALSE)
+<<>>=
+splot(1:10, 1:10, "Same as Before", name = "splot")
+downViewport("dataregion")
+grid.text(date(), x = unit(1, "npc"), y = 0,
+ just = c("right", "bottom"), gp = gpar(col = "grey"))
+upViewport(0)
+@
+\item The \code{gp} argument allows the user to supply \code{gpar()}
+ settings for the scatterplot as a whole.
+
+\item The \code{vp} argument allows the user to supply a viewport for
+ the \code{splot} \grob{} to be drawn in. This is especially useful
+ for specifying a \code{vpPath} when the \code{splot} is used as a
+ component of another \grob{} (see scatterplot matrix example below).
+\end{enumerate}
+
+The important parts of the \gTree{} definition are:
+\begin{enumerate}
+\item The \code{children} argument provides a list of \grob{}s which
+ are part of the scatterplot. When the scatterplot is drawn, all
+ children will be drawn. Notice that instead of the procedural
+ \code{grid.*()} functions we use \code{*Grob()} functions which just
+ produce \grob{}s and do not perform any drawing. Also notice that I
+ have given each of the children a name; this will make it possible
+ to access the components of the scatterplot (see later examples).
+\item The \code{childrenvp} argument provides a viewport (or
+ \code{vpStack}, \code{vpList}, or \code{vpTree}) which will be
+ pushed before the children are drawn. The difference between this
+ argument and the \code{vp} argument common to all \grob{}s is that
+ the \code{vp} is pushed before drawing the children and then popped
+ after, whereas the \code{childrenvp} gets pushed \emph{and} then a
+ call to \code{upViewport()} is made before the children are drawn.
+ This allows the children to simply specify the viewport they should
+ be drawn in by way of a \code{vpPath} in their \code{vp} argument.
+ In this way, viewports remain available for further annotation such
+ as we have already seen in procedural code.
+\item The \code{gp} and \code{vp} arguments are automatically handled
+ by the \gTree{} drawing methods so that \code{gpar()} settings will
+ be enforced and the viewport will be pushed when the \code{splot} is
+ drawn.
+\item The \code{cl} argument means that the \grob{} created is a
+ special sort of \grob{} called \code{splot}. This will allow us to
+ write methods specifically for our scatterplot (see later examples).
+\end{enumerate}
+
+
+@
+
+Now that we have a \grob{}, there are some more interesting things
+that we can do with it. First of all, the \code{splot} \grob{}
+provides a container for the \grob{}s which make up the scatterplot.
+If we modify the \code{splot} \grob{}, it affects all of the children.
+
+<<results=hide>>=
+splot(1:10, 1:10, "Same as Before", name = "splot")
+grid.edit("splot", gp = gpar(cex=0.5))
+<<fig=TRUE, echo=FALSE, results=hide>>=
+<<splotgrob>>
+sg <- editGrob(sg, gp = gpar(cex = 0.5))
+grid.draw(sg)
+@
+
+We can access elements of the \code{splot} \grob{} to edit them
+individually.
+
+<<results=hide>>=
+splot(1:10, 1:10, "Same as Before", name = "splot")
+grid.edit(gPath("splot", "points"), gp = gpar(col = 1:10))
+<<fig=TRUE, echo=FALSE, results=hide>>=
+<<splotgrob>>
+sg <- editGrob(sg, gPath = "points", gp = gpar(col = 1:10))
+grid.draw(sg)
+
+@
+
+With a little more work we can make the scatterplot a bit more dynamic.
+The following describes a \code{editDetails()} method for the
+\code{splot} \grob{}. This will be called whenever a scatterplot
+is edited and will update the components of the scatterplot.
+
+<<>>=
+editDetails.splot <- function(x, specs) {
+ if (any(c("x", "y") %in% names(specs))) {
+ if (is.null(specs$x)) xx <- x$x else xx <- specs$x
+ if (is.null(specs$y)) yy <- x$y else yy <- specs$y
+ x$childrenvp <- splot.data.vp(xx, yy)
+ x <- addGrob(x, pointsGrob(xx, yy, name = "points",
+ vp = "dataregion"))
+ }
+ x
+}
+splot(1:10, 1:10, "Same as Before", name = "splot")
+grid.edit("splot", x = 1:100, y = (1:100)^2)
+<<fig=TRUE, echo=FALSE, results=hide>>=
+<<splotgrob>>
+sg <- editGrob(sg, x = 1:100, y = (1:100)^2)
+grid.draw(sg)
+@
+
+The \code{splot} \grob{} can also be used in the construction of other
+\grob{}s. Here's a simple scatterplot matrix \grob{}\footnote{{\bf
+ Warning:} As the number of \grob{}s in a \gTree{} gets larger the
+ construction of the \gTree{} will get slow. If this happens, the
+ best solution is to just use a \grid{} function rather than a
+ \gTree{}, and wait for me to implement some ideas for speeding
+ things up!}.
+
+<<fig=TRUE>>=
+cellname <- function(i, j) paste("cell", i, j, sep = "")
+
+splom.vpTree <- function(n) {
+ vplist <- vector("list", n^2)
+ for (i in 1:n)
+ for (j in 1:n)
+ vplist[[(i - 1)*n + j]] <-
+ viewport(layout.pos.row = i, layout.pos.col = j,
+ name = cellname(i, j))
+ vpTree(viewport(layout = grid.layout(n, n), name = "cellgrid"),
+ do.call("vpList", vplist))
+}
+
+cellpath <- function(i, j) vpPath("cellgrid", cellname(i, j))
+
+splom <- function(df, name = NULL, draw = TRUE) {
+ n <- dim(df)[2]
+ glist <- vector("list", n*n)
+ for (i in 1:n)
+ for (j in 1:n) {
+ glist[[(i - 1)*n + j]] <-if (i == j)
+ textGrob(paste("diag", i, sep = ""),
+ gp = gpar(col = "grey"), vp = cellpath(i, j))
+ else if (j > i)
+ textGrob(cellname(i, j),
+ name = cellname(i, j),
+ gp = gpar(col = "grey"), vp = cellpath(i, j))
+ else
+ splot(df[,j], df[,i], "",
+ name = paste("plot", i, j, sep = ""),
+ vp = cellpath(i, j),
+ gp = gpar(cex = 0.5), draw = FALSE)
+ }
+ smg <- gTree(name = name, childrenvp = splom.vpTree(n),
+ children = do.call("gList", glist))
+ if (draw) grid.draw(smg)
+ smg
+}
+
+df <- data.frame(x = rnorm(10), y = rnorm(10), z = rnorm(10))
+splom(df)
+@
+
+This \grob{} can be edited as usual:
+
+<<>>=
+splom(df)
+grid.edit("plot21::xlab", label = "", redraw = FALSE)
+grid.edit("plot32::ylab", label = "", redraw = FALSE)
+grid.edit("plot21::xaxis", label = FALSE, redraw = FALSE)
+grid.edit("plot32::yaxis", label = FALSE)
+<<splomgrob, eval=FALSE, echo=FALSE>>=
+smg <- splom(df, draw = FALSE)
+<<fig=TRUE, echo=FALSE, results=hide>>=
+<<splomgrob>>
+smg <- editGrob(smg, gPath = "plot21::xaxis", label = FALSE)
+smg <- editGrob(smg, gPath = "plot21::xlab", label = "")
+smg <- editGrob(smg, gPath = "plot32::yaxis", label = FALSE)
+smg <- editGrob(smg, gPath = "plot32::ylab", label = "")
+grid.draw(smg)
+@
+
+But of more interest, because this is a \grob{}, is the
+\emph{programmatic} interface. With a \grob{} (as opposed to a
+function) it is possible to modify the description of what is being
+drawn via an API (as opposed to having to edit the original code). In
+the following, we remove one of the ``spare'' cell labels and put in
+its place the current date.
+
+<<>>=
+splom(df, name = "splom")
+grid.remove("cell12")
+grid.add("splom", textGrob(date(), name = "date",
+ gp = gpar(fontface = "italic"),
+ vp = "cellgrid::cell12"))
+<<fig=TRUE, echo=FALSE, results=hide>>=
+<<splomgrob>>
+smg <- removeGrob(smg, "cell12")
+smg <- addGrob(smg, textGrob(date(), name = "date",
+ gp = gpar(fontface = "italic"),
+ vp = "cellgrid::cell12"))
+grid.draw(smg)
+@
+
+With the date added as a component of the scatterplot matrix, it is
+saved as part of the matrix. The next sequence saves the scatterplot
+matrix, loads it again, extracts the bottom-left plot and the date
+and just draws those two objects together.
+
+<<>>=
+splom(df, name = "splom")
+grid.remove("cell12")
+grid.add("splom", textGrob(date(), name = "date",
+ gp = gpar(fontface = "italic"),
+ vp = "cellgrid::cell12"))
+smg <- grid.get("splom")
+save(smg, file = "splom.RData")
+load("splom.RData")
+plot <- getGrob(smg, "plot31")
+date <- getGrob(smg, "date")
+plot <- editGrob(plot, vp = NULL, gp = gpar(cex = 1))
+date <- editGrob(date, y = unit(1, "npc") - unit(1, "lines"), vp = NULL)
+grid.newpage()
+grid.draw(plot)
+grid.draw(date)
+
+<<fig=TRUE, echo=FALSE, results=hide>>=
+<<splomgrob>>
+smg <- removeGrob(smg, "cell12")
+smg <- addGrob(smg, textGrob(date(), name = "date",
+ gp = gpar(fontface = "italic"),
+ vp = "cellgrid::cell12"))
+save(smg, file = "splom.RData")
+load("splom.RData")
+plot <- getGrob(smg, "plot31")
+date <- getGrob(smg, "date")
+plot <- editGrob(plot, vp = NULL, gp = gpar(cex = 1))
+date <- editGrob(date, y = unit(1, "npc") - unit(1, "lines"), vp = NULL)
+grid.draw(plot)
+grid.draw(date)
+@
+
+All of this may seem a bit irrelevant to interactive use, but it does
+provide a basis for creating an editable plot interface as used in
+M.~Kondrin's \pkg{Rgrace} package (available on CRAN 2005--7).
+
+\end{document}
diff --git a/win32/deps/library/grid/doc/plotexample.pdf b/win32/deps/library/grid/doc/plotexample.pdf
new file mode 100644
index 0000000..382b636
Binary files /dev/null and b/win32/deps/library/grid/doc/plotexample.pdf differ
diff --git a/win32/deps/library/grid/doc/rotated.R b/win32/deps/library/grid/doc/rotated.R
new file mode 100644
index 0000000..a93f292
--- /dev/null
+++ b/win32/deps/library/grid/doc/rotated.R
@@ -0,0 +1,188 @@
+### R code from vignette source 'rotated.Rnw'
+
+###################################################
+### code chunk number 1: rotated.Rnw:18-24
+###################################################
+library(grDevices)
+library(graphics) # for boxplot
+library(stats) # for rnorm
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+
+
+###################################################
+### code chunk number 2: rotated.Rnw:30-33
+###################################################
+pushViewport(viewport(h = .8, w = .8, angle = 15))
+grid.multipanel(newpage = FALSE)
+popViewport()
+
+
+###################################################
+### code chunk number 3: complex1
+###################################################
+x <- rnorm(50)
+y <- x + rnorm(50, 1, 2)
+
+
+###################################################
+### code chunk number 4: complex2
+###################################################
+# We will extend the axes over the entire region so
+# extrapolate scale from main data region
+scale <- extendrange(r = range(x,y))
+extscale <- c(min(scale), max(scale)+diff(scale)*1/3)
+
+
+###################################################
+### code chunk number 5: complex3
+###################################################
+lay <- grid.layout(2, 2,
+ widths = unit(c(3, 1), "inches"),
+ heights = unit(c(1, 3), "inches"))
+vp1 <- viewport(width = unit(4, "inches"), height = unit(4, "inches"),
+ layout = lay, xscale = extscale, yscale = extscale)
+
+
+###################################################
+### code chunk number 6: complex4
+###################################################
+grid.newpage()
+pushViewport(vp1)
+grid.rect()
+grid.xaxis()
+grid.text("Test", y = unit(-3, "lines"))
+grid.yaxis()
+grid.text("Retest", x = unit(-3, "lines"), rot = 90)
+
+
+###################################################
+### code chunk number 7: complex5
+###################################################
+vp2 <- viewport(layout.pos.row = 2, layout.pos.col = 1,
+ xscale = scale, yscale = scale)
+pushViewport(vp2)
+grid.lines()
+grid.points(x, y, gp = gpar(col = "blue"))
+popViewport()
+
+
+###################################################
+### code chunk number 8: complex6
+###################################################
+diffs <- (y - x)
+rdiffs <- range(diffs)
+ddiffs <- diff(rdiffs)
+bxp <- boxplot(diffs, plot = FALSE)
+vp3 <- viewport(x = unit(3, "inches"),
+ y = unit(3, "inches"),
+ width = unit(.5, "inches"),
+ # NOTE that the axis on the boxplot represents
+ # actual (y - x) values BUT to make
+ # the bits of the boxplot line
+ # up with the data points we have to plot
+ # (y - x)/sqrt(2)
+ # Hence the sin(pi/4) below
+ height = unit(ddiffs*sin(pi/4)/diff(scale)*3, "inches"),
+ just = c("centre", "center"),
+ angle = 45,
+ gp = gpar(col = "red"),
+ yscale = c(-ddiffs/2, ddiffs/2))
+pushViewport(vp3)
+left <- -.3
+width <- .8
+middle <- left + width/2
+grid.rect(x = left, y = unit(bxp$conf[1,1], "native"),
+ width = width, height = unit(diff(bxp$conf[,1]), "native"),
+ just = c("left", "bottom"),
+ gp = gpar(col = NULL, fill = "orange"))
+grid.rect(x = left, y = unit(bxp$stats[4,1], "native"),
+ width = width, height = unit(diff(bxp$stats[4:3,1]), "native"),
+ just = c("left", "bottom"))
+grid.rect(x = left, y = unit(bxp$stats[3,1], "native"),
+ width = width, height = unit(diff(bxp$stats[3:2,1]), "native"),
+ just = c("left", "bottom"))
+grid.lines(x = c(middle, middle), y = unit(bxp$stats[1:2,1], "native"))
+grid.lines(x = c(middle, middle), y = unit(bxp$stats[4:5,1], "native"))
+grid.lines(x = c(middle-.1, middle+.1), y = unit(bxp$stats[1,1], "native"))
+grid.lines(x = c(middle-.1, middle+.1), y = unit(bxp$stats[5,1], "native"))
+np <- length(bxp$out)
+if (np > 0)
+ grid.points(x = rep(middle, np), y = unit(bxp$out, "native"))
+grid.yaxis(main = FALSE)
+popViewport(2)
+
+
+
+###################################################
+### code chunk number 9: rotated.Rnw:139-145
+###################################################
+x <- rnorm(50)
+y <- x + rnorm(50, 1, 2)
+# We will extend the axes over the entire region so
+# extrapolate scale from main data region
+scale <- extendrange(r = range(x,y))
+extscale <- c(min(scale), max(scale)+diff(scale)*1/3)
+lay <- grid.layout(2, 2,
+ widths = unit(c(3, 1), "inches"),
+ heights = unit(c(1, 3), "inches"))
+vp1 <- viewport(width = unit(4, "inches"), height = unit(4, "inches"),
+ layout = lay, xscale = extscale, yscale = extscale)
+grid.newpage()
+pushViewport(vp1)
+grid.rect()
+grid.xaxis()
+grid.text("Test", y = unit(-3, "lines"))
+grid.yaxis()
+grid.text("Retest", x = unit(-3, "lines"), rot = 90)
+vp2 <- viewport(layout.pos.row = 2, layout.pos.col = 1,
+ xscale = scale, yscale = scale)
+pushViewport(vp2)
+grid.lines()
+grid.points(x, y, gp = gpar(col = "blue"))
+popViewport()
+diffs <- (y - x)
+rdiffs <- range(diffs)
+ddiffs <- diff(rdiffs)
+bxp <- boxplot(diffs, plot = FALSE)
+vp3 <- viewport(x = unit(3, "inches"),
+ y = unit(3, "inches"),
+ width = unit(.5, "inches"),
+ # NOTE that the axis on the boxplot represents
+ # actual (y - x) values BUT to make
+ # the bits of the boxplot line
+ # up with the data points we have to plot
+ # (y - x)/sqrt(2)
+ # Hence the sin(pi/4) below
+ height = unit(ddiffs*sin(pi/4)/diff(scale)*3, "inches"),
+ just = c("centre", "center"),
+ angle = 45,
+ gp = gpar(col = "red"),
+ yscale = c(-ddiffs/2, ddiffs/2))
+pushViewport(vp3)
+left <- -.3
+width <- .8
+middle <- left + width/2
+grid.rect(x = left, y = unit(bxp$conf[1,1], "native"),
+ width = width, height = unit(diff(bxp$conf[,1]), "native"),
+ just = c("left", "bottom"),
+ gp = gpar(col = NULL, fill = "orange"))
+grid.rect(x = left, y = unit(bxp$stats[4,1], "native"),
+ width = width, height = unit(diff(bxp$stats[4:3,1]), "native"),
+ just = c("left", "bottom"))
+grid.rect(x = left, y = unit(bxp$stats[3,1], "native"),
+ width = width, height = unit(diff(bxp$stats[3:2,1]), "native"),
+ just = c("left", "bottom"))
+grid.lines(x = c(middle, middle), y = unit(bxp$stats[1:2,1], "native"))
+grid.lines(x = c(middle, middle), y = unit(bxp$stats[4:5,1], "native"))
+grid.lines(x = c(middle-.1, middle+.1), y = unit(bxp$stats[1,1], "native"))
+grid.lines(x = c(middle-.1, middle+.1), y = unit(bxp$stats[5,1], "native"))
+np <- length(bxp$out)
+if (np > 0)
+ grid.points(x = rep(middle, np), y = unit(bxp$out, "native"))
+grid.yaxis(main = FALSE)
+popViewport(2)
+
+
+
diff --git a/win32/deps/library/grid/doc/rotated.Rnw b/win32/deps/library/grid/doc/rotated.Rnw
new file mode 100644
index 0000000..68ad412
--- /dev/null
+++ b/win32/deps/library/grid/doc/rotated.Rnw
@@ -0,0 +1,156 @@
+\documentclass[a4paper]{article}
+%\VignetteIndexEntry{Rotated Viewports}
+%\VignettePackage{grid}
+\newcommand{\code}[1]{\texttt{#1}}
+\newcommand{\pkg}[1]{{\normalfont\fontseries{b}\selectfont #1}}
+\newcommand{\grid}{\pkg{grid}}
+\newcommand{\R}{{\sffamily R}}
+\setlength{\parindent}{0in}
+\setlength{\parskip}{.1in}
+\setlength{\textwidth}{140mm}
+\setlength{\oddsidemargin}{10mm}
+\title{Rotated Viewports}
+\author{Paul Murrell}
+
+\begin{document}
+\maketitle
+
+<<echo=FALSE, results=hide>>=
+library(grDevices)
+library(graphics) # for boxplot
+library(stats) # for rnorm
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+@
+It is possible to specify an angle of rotation for a Grid viewport.
+For example, the following code draws the example multipanel plot
+at an angle of $15^\circ$.
+
+<<fig=TRUE, results=hide>>=
+pushViewport(viewport(h = .8, w = .8, angle = 15))
+grid.multipanel(newpage = FALSE)
+popViewport()
+@
+
+\vspace{.5in}
+A more complicated example is now developed. First of all we
+generate some data to plot; an $x$ and a $y$ with an obvious correlation.
+
+<<complex1, results=hide>>=
+x <- rnorm(50)
+y <- x + rnorm(50, 1, 2)
+@
+\noindent
+Next we generate some statistics from the data.
+
+<<complex2, results=hide>>=
+# We will extend the axes over the entire region so
+# extrapolate scale from main data region
+scale <- extendrange(r = range(x,y))
+extscale <- c(min(scale), max(scale)+diff(scale)*1/3)
+@
+\noindent
+Now generate a layout of regions: a 3" by 3" region for a
+scatterplot, inside a 4" by 4" region.
+
+<<complex3, results=hide>>=
+lay <- grid.layout(2, 2,
+ widths = unit(c(3, 1), "inches"),
+ heights = unit(c(1, 3), "inches"))
+vp1 <- viewport(width = unit(4, "inches"), height = unit(4, "inches"),
+ layout = lay, xscale = extscale, yscale = extscale)
+@
+\noindent
+We draw a box around the outside and axes on the entire region.
+
+<<complex4, results=hide>>=
+grid.newpage()
+pushViewport(vp1)
+grid.rect()
+grid.xaxis()
+grid.text("Test", y = unit(-3, "lines"))
+grid.yaxis()
+grid.text("Retest", x = unit(-3, "lines"), rot = 90)
+@
+\noindent
+We draw points within the interior region.
+
+<<complex5, results=hide>>=
+vp2 <- viewport(layout.pos.row = 2, layout.pos.col = 1,
+ xscale = scale, yscale = scale)
+pushViewport(vp2)
+grid.lines()
+grid.points(x, y, gp = gpar(col = "blue"))
+popViewport()
+@
+\noindent
+Now we use a rotated viewport to draw a boxplot which indicates
+the distribution of the distances between the points in the scatterplot
+and the line $y = x$\footnote{This may look like a large amount of
+code, but that's mostly because its doing a boxplot by hand
+rather than using a predefined high-level function.}.
+
+The final output is shown on the last page.
+
+<<complex6, results=hide>>=
+diffs <- (y - x)
+rdiffs <- range(diffs)
+ddiffs <- diff(rdiffs)
+bxp <- boxplot(diffs, plot = FALSE)
+vp3 <- viewport(x = unit(3, "inches"),
+ y = unit(3, "inches"),
+ width = unit(.5, "inches"),
+ # NOTE that the axis on the boxplot represents
+ # actual (y - x) values BUT to make
+ # the bits of the boxplot line
+ # up with the data points we have to plot
+ # (y - x)/sqrt(2)
+ # Hence the sin(pi/4) below
+ height = unit(ddiffs*sin(pi/4)/diff(scale)*3, "inches"),
+ just = c("centre", "center"),
+ angle = 45,
+ gp = gpar(col = "red"),
+ yscale = c(-ddiffs/2, ddiffs/2))
+pushViewport(vp3)
+left <- -.3
+width <- .8
+middle <- left + width/2
+grid.rect(x = left, y = unit(bxp$conf[1,1], "native"),
+ width = width, height = unit(diff(bxp$conf[,1]), "native"),
+ just = c("left", "bottom"),
+ gp = gpar(col = NULL, fill = "orange"))
+grid.rect(x = left, y = unit(bxp$stats[4,1], "native"),
+ width = width, height = unit(diff(bxp$stats[4:3,1]), "native"),
+ just = c("left", "bottom"))
+grid.rect(x = left, y = unit(bxp$stats[3,1], "native"),
+ width = width, height = unit(diff(bxp$stats[3:2,1]), "native"),
+ just = c("left", "bottom"))
+grid.lines(x = c(middle, middle), y = unit(bxp$stats[1:2,1], "native"))
+grid.lines(x = c(middle, middle), y = unit(bxp$stats[4:5,1], "native"))
+grid.lines(x = c(middle-.1, middle+.1), y = unit(bxp$stats[1,1], "native"))
+grid.lines(x = c(middle-.1, middle+.1), y = unit(bxp$stats[5,1], "native"))
+np <- length(bxp$out)
+if (np > 0)
+ grid.points(x = rep(middle, np), y = unit(bxp$out, "native"))
+grid.yaxis(main = FALSE)
+popViewport(2)
+
+<<echo=FALSE, fig=TRUE, results=hide>>=
+<<complex1>>
+<<complex2>>
+<<complex3>>
+<<complex4>>
+<<complex5>>
+<<complex6>>
+@
+\section*{Problems}
+
+\begin{enumerate}
+\item Data symbols will not be affected by the angle of rotation. For
+ round data symbols this does not matter, but it will make just about
+ everything else look pretty odd.
+\end{enumerate}
+
+@
+\end{document}
diff --git a/win32/deps/library/grid/doc/rotated.pdf b/win32/deps/library/grid/doc/rotated.pdf
new file mode 100644
index 0000000..4e406a9
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diff --git a/win32/deps/library/grid/doc/saveload.R b/win32/deps/library/grid/doc/saveload.R
new file mode 100644
index 0000000..695d8ad
--- /dev/null
+++ b/win32/deps/library/grid/doc/saveload.R
@@ -0,0 +1,40 @@
+### R code from vignette source 'saveload.Rnw'
+
+###################################################
+### code chunk number 1: saveload.Rnw:18-22
+###################################################
+library(grDevices)
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+
+
+###################################################
+### code chunk number 2: saveload.Rnw:49-51
+###################################################
+gt <- textGrob("hi")
+save(gt, file = "mygridplot")
+
+
+###################################################
+### code chunk number 3: saveload.Rnw:55-57
+###################################################
+load("mygridplot")
+grid.draw(gt)
+
+
+###################################################
+### code chunk number 4: saveload.Rnw:90-93
+###################################################
+grid.grill()
+temp <- recordPlot()
+save(temp, file = "mygridplot")
+
+
+###################################################
+### code chunk number 5: saveload.Rnw:100-102
+###################################################
+load("mygridplot")
+temp
+
+
diff --git a/win32/deps/library/grid/doc/saveload.Rnw b/win32/deps/library/grid/doc/saveload.Rnw
new file mode 100644
index 0000000..513588c
--- /dev/null
+++ b/win32/deps/library/grid/doc/saveload.Rnw
@@ -0,0 +1,110 @@
+\documentclass[a4paper]{article}
+%\VignetteIndexEntry{Persistent representations}
+%\VignettePackage{grid}
+\newcommand{\code}[1]{\texttt{#1}}
+\newcommand{\pkg}[1]{{\normalfont\fontseries{b}\selectfont #1}}
+\newcommand{\grid}{\pkg{grid}}
+\newcommand{\R}{{\sffamily R}}
+\setlength{\parindent}{0in}
+\setlength{\parskip}{.1in}
+\setlength{\textwidth}{140mm}
+\setlength{\oddsidemargin}{10mm}
+\title{Saving and Loading \grid{} Graphics}
+\author{Paul Murrell}
+
+\begin{document}
+\maketitle
+
+<<echo=FALSE, results=hide>>=
+library(grDevices)
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+@
+This is a general discussion concerning how you might go about
+creating (and reusing) persistent representations of \grid{}
+graphics, and some of the pitfalls in the various options.
+
+\subsection*{\R{} code}
+
+The way I usually work with graphics is to write \R{} code in a text file
+and copy-and-paste or \code{source()} it into R. In this case,
+the persistent
+representation of the graphics is the raw \R{} code.
+
+The representation is fully editable.
+
+The representation is persistent across \R{} sessions, but may not be
+persistent across \R{} versions because the names, argument lists,
+and/or behaviour of the \grid{} functions may
+change. The representation can be reloaded into R.
+Incompatibilities between versions should be handled gracefully by
+\R{}'s argument-matching, type-checking, and/or version-checking.
+
+\subsection*{\grid{} \code{grob}s}
+
+The next most flexible way of creating a persistent version of \grid{}
+graphics is to \code{save()} a \grid{} \code{grob} \ldots
+
+<<>>=
+gt <- textGrob("hi")
+save(gt, file = "mygridplot")
+@
+The representation is reloadable so you can reproduce an image \ldots{}
+
+<<results=hide>>=
+load("mygridplot")
+grid.draw(gt)
+@
+And the representation is editable; there is an API for interacting
+with \grid{} \code{grobs}, including adding new elements, removing
+elements, editing features of a \code{grob} and so on. See
+\code{getGrob()}, \code{addGrob()}, \code{removeGrob()},
+and \code{editGrob()}.
+
+The representation is persistent across \R{} sessions, but is
+vulnerable to changes in the internal representation of \grid{}
+\code{grob}s. The advantage of this representation is that it is
+possible to share and edit graphics produced by someone else,
+without seeing the code they used to produce it.
+
+\subsection*{Device output}
+
+A third way of creating a persistent version of \grid{} graphics is to
+``save'' it to a persistent device format (e.g., PostScript, PDF, \ldots).
+
+It is possible to edit these representations, but hardly convenient.
+In particular, none of the coordinate systems used in the
+construction of plots (e.g., axis scales) are available for editing.
+
+The representation is persistent regardless of \R{} sessions or versions,
+but it cannot be reloaded into \R{}.
+
+\subsection*{Display lists}
+
+This final option is \emph{not} recommended, but it is possible to do
+so its downsides need to be explained.
+
+What you can do is ``save'' an \R{} display list using, for example, \ldots
+
+<<>>=
+grid.grill()
+temp <- recordPlot()
+save(temp, file = "mygridplot")
+@
+This representation is not editable\footnote{Well, there's nothing stopping
+you editing it, but you should take out life insurance first.}, but it can be
+reloaded
+and rerun to reproduce the output \ldots
+
+<<>>=
+load("mygridplot")
+temp
+@
+The representation is persistent across \R{} sessions, but the saved
+information involves non-public interfaces and structures which may
+change between \R{} versions. You also have to make sure that \grid{}
+has been reloaded. Differences between \grid{} and/or \R{} versions
+may lead to segmentation faults.
+\end{document}
+
diff --git a/win32/deps/library/grid/doc/saveload.pdf b/win32/deps/library/grid/doc/saveload.pdf
new file mode 100644
index 0000000..fee31b0
Binary files /dev/null and b/win32/deps/library/grid/doc/saveload.pdf differ
diff --git a/win32/deps/library/grid/doc/sharing.R b/win32/deps/library/grid/doc/sharing.R
new file mode 100644
index 0000000..c42446d
--- /dev/null
+++ b/win32/deps/library/grid/doc/sharing.R
@@ -0,0 +1,140 @@
+### R code from vignette source 'sharing.Rnw'
+
+###################################################
+### code chunk number 1: sharing.Rnw:15-21
+###################################################
+library(grDevices)
+library(graphics)
+library(stats) # for rnorm
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+
+
+###################################################
+### code chunk number 2: axes1 (eval = FALSE)
+###################################################
+## pushViewport(viewport(layout = grid.layout(1, 2, respect = TRUE)))
+
+
+###################################################
+### code chunk number 3: axes2 (eval = FALSE)
+###################################################
+## x <- 1:10
+## y1 <- rnorm(10)
+## vp1a <- viewport(layout.pos.col = 1)
+## vp1b <- viewport(width = 0.6, height = 0.6,
+## xscale = c(0, 11), yscale = c(-4, 4))
+## pushViewport(vp1a, vp1b)
+## grid.xaxis(name = "xaxis")
+## grid.yaxis(name = "yaxis")
+## grid.points(x, y1)
+## popViewport(2)
+
+
+###################################################
+### code chunk number 4: axes3 (eval = FALSE)
+###################################################
+## y2 <- rnorm(10)
+## vp2a <- viewport(layout.pos.col = 2)
+## vp2b <- viewport(width = 0.6, height = 0.6,
+## xscale = c(0, 11), yscale = c(-4, 4))
+## pushViewport(vp2a, vp2b)
+## grid.xaxis
+## grid.xaxis(name = "xaxis")
+## grid.yaxis(name = "yaxis")
+## grid.points(x, y2)
+## popViewport(2)
+
+
+###################################################
+### code chunk number 5: shared
+###################################################
+pushViewport(viewport(layout = grid.layout(1, 2, respect = TRUE)))
+x <- 1:10
+y1 <- rnorm(10)
+vp1a <- viewport(layout.pos.col = 1)
+vp1b <- viewport(width = 0.6, height = 0.6,
+ xscale = c(0, 11), yscale = c(-4, 4))
+pushViewport(vp1a, vp1b)
+grid.xaxis(name = "xaxis")
+grid.yaxis(name = "yaxis")
+grid.points(x, y1)
+popViewport(2)
+y2 <- rnorm(10)
+vp2a <- viewport(layout.pos.col = 2)
+vp2b <- viewport(width = 0.6, height = 0.6,
+ xscale = c(0, 11), yscale = c(-4, 4))
+pushViewport(vp2a, vp2b)
+grid.xaxis
+grid.xaxis(name = "xaxis")
+grid.yaxis(name = "yaxis")
+grid.points(x, y2)
+popViewport(2)
+
+
+
+###################################################
+### code chunk number 6: axesedit (eval = FALSE)
+###################################################
+## grid.edit("xaxis", at = c(1, 5, 9), global = TRUE)
+##
+
+
+###################################################
+### code chunk number 7: shared2
+###################################################
+postscript("shared2-%02d.eps", onefile = FALSE, paper = "special",
+ width = 4, height = 2)
+pushViewport(viewport(layout = grid.layout(1, 2, respect = TRUE)))
+x <- 1:10
+y1 <- rnorm(10)
+vp1a <- viewport(layout.pos.col = 1)
+vp1b <- viewport(width = 0.6, height = 0.6,
+ xscale = c(0, 11), yscale = c(-4, 4))
+pushViewport(vp1a, vp1b)
+grid.xaxis(name = "xaxis")
+grid.yaxis(name = "yaxis")
+grid.points(x, y1)
+popViewport(2)
+y2 <- rnorm(10)
+vp2a <- viewport(layout.pos.col = 2)
+vp2b <- viewport(width = 0.6, height = 0.6,
+ xscale = c(0, 11), yscale = c(-4, 4))
+pushViewport(vp2a, vp2b)
+grid.xaxis
+grid.xaxis(name = "xaxis")
+grid.yaxis(name = "yaxis")
+grid.points(x, y2)
+popViewport(2)
+grid.edit("xaxis", at = c(1, 5, 9), global = TRUE)
+
+dev.off()
+
+pdf("shared2-%02d.pdf", onefile = FALSE, width = 4, height = 2)
+pushViewport(viewport(layout = grid.layout(1, 2, respect = TRUE)))
+x <- 1:10
+y1 <- rnorm(10)
+vp1a <- viewport(layout.pos.col = 1)
+vp1b <- viewport(width = 0.6, height = 0.6,
+ xscale = c(0, 11), yscale = c(-4, 4))
+pushViewport(vp1a, vp1b)
+grid.xaxis(name = "xaxis")
+grid.yaxis(name = "yaxis")
+grid.points(x, y1)
+popViewport(2)
+y2 <- rnorm(10)
+vp2a <- viewport(layout.pos.col = 2)
+vp2b <- viewport(width = 0.6, height = 0.6,
+ xscale = c(0, 11), yscale = c(-4, 4))
+pushViewport(vp2a, vp2b)
+grid.xaxis
+grid.xaxis(name = "xaxis")
+grid.yaxis(name = "yaxis")
+grid.points(x, y2)
+popViewport(2)
+grid.edit("xaxis", at = c(1, 5, 9), global = TRUE)
+
+dev.off()
+
+
diff --git a/win32/deps/library/grid/doc/sharing.Rnw b/win32/deps/library/grid/doc/sharing.Rnw
new file mode 100644
index 0000000..0509be5
--- /dev/null
+++ b/win32/deps/library/grid/doc/sharing.Rnw
@@ -0,0 +1,110 @@
+\documentclass[a4paper]{article}
+%\VignetteIndexEntry{Modifying multiple grobs simultaneously}
+\newcommand{\code}[1]{\texttt{#1}}
+\newcommand{\pkg}[1]{{\normalfont\fontseries{b}\selectfont #1}}
+\newcommand{\grid}{\pkg{grid}}
+\newcommand{\R}{{\sffamily R}}
+\setlength{\parindent}{0in}
+\setlength{\parskip}{.1in}
+\title{An Example of ``Linking'' Graphical Objects in \grid{}}
+\author{Paul Murrell}
+
+\begin{document}
+\maketitle
+
+<<echo=FALSE, results=hide>>=
+library(grDevices)
+library(graphics)
+library(stats) # for rnorm
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+@
+Suppose that I am drawing two graphs on a page, which are the results
+from two subjects in an experiment. I want the graphs to have the same
+axes to aid in comparison of the subjects.
+
+First of all, I will split the page up into two bits for the two graphs.
+
+<<axes1, eval=FALSE, results=hide>>=
+pushViewport(viewport(layout = grid.layout(1, 2, respect = TRUE)))
+@
+Now I generate some data and draw the first plot.
+
+<<axes2, eval=FALSE, results=hide>>=
+x <- 1:10
+y1 <- rnorm(10)
+vp1a <- viewport(layout.pos.col = 1)
+vp1b <- viewport(width = 0.6, height = 0.6,
+ xscale = c(0, 11), yscale = c(-4, 4))
+pushViewport(vp1a, vp1b)
+grid.xaxis(name = "xaxis")
+grid.yaxis(name = "yaxis")
+grid.points(x, y1)
+popViewport(2)
+@
+Notice that I have named the graphical objects for the axes.
+When I draw the second plot I will use the same names for the
+axis objects.
+
+<<axes3, eval=FALSE, results=hide>>=
+y2 <- rnorm(10)
+vp2a <- viewport(layout.pos.col = 2)
+vp2b <- viewport(width = 0.6, height = 0.6,
+ xscale = c(0, 11), yscale = c(-4, 4))
+pushViewport(vp2a, vp2b)
+grid.xaxis
+grid.xaxis(name = "xaxis")
+grid.yaxis(name = "yaxis")
+grid.points(x, y2)
+popViewport(2)
+@
+The output looks like the figure below.
+
+<<shared, results=hide, fig=TRUE, echo=FALSE, width=4, height=2, include=FALSE>>=
+<<axes1>>
+<<axes2>>
+<<axes3>>
+
+@
+\begin{center}
+\includegraphics[width=4in, height=2in]{sharing-shared}
+\end{center}
+@
+
+Because I have used the same name for the axis objects in both plots,
+ I can edit the axes for both plots
+simultaneously rather than having to edit each one in turn.
+For example ...
+
+<<axesedit, eval=FALSE, results=hide>>=
+grid.edit("xaxis", at = c(1, 5, 9), global = TRUE)
+
+@
+The output now looks like the figure below.
+
+<<shared2, results=hide, echo=FALSE>>=
+postscript("shared2-%02d.eps", onefile = FALSE, paper = "special",
+ width = 4, height = 2)
+<<axes1>>
+<<axes2>>
+<<axes3>>
+<<axesedit>>
+dev.off()
+
+pdf("shared2-%02d.pdf", onefile = FALSE, width = 4, height = 2)
+<<axes1>>
+<<axes2>>
+<<axes3>>
+<<axesedit>>
+dev.off()
+@
+\begin{center}
+\includegraphics[width=4in, height=2in]{shared2-02}
+\end{center}
+@
+
+This might seem a very small gain in this example, but it is
+potentially of great use in, for example, the implementation of a scatterplot
+matrix.
+\end{document}
diff --git a/win32/deps/library/grid/doc/sharing.pdf b/win32/deps/library/grid/doc/sharing.pdf
new file mode 100644
index 0000000..1e25bfd
Binary files /dev/null and b/win32/deps/library/grid/doc/sharing.pdf differ
diff --git a/win32/deps/library/grid/doc/viewports.R b/win32/deps/library/grid/doc/viewports.R
new file mode 100644
index 0000000..add9952
--- /dev/null
+++ b/win32/deps/library/grid/doc/viewports.R
@@ -0,0 +1,288 @@
+### R code from vignette source 'viewports.Rnw'
+
+###################################################
+### code chunk number 1: viewports.Rnw:21-26
+###################################################
+library(grDevices)
+library(stats) # for runif()
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+
+
+###################################################
+### code chunk number 2: viewports.Rnw:45-48
+###################################################
+pushViewport(viewport())
+upViewport()
+pushViewport(viewport())
+
+
+###################################################
+### code chunk number 3: viewports.Rnw:63-65
+###################################################
+grid.newpage()
+
+
+
+###################################################
+### code chunk number 4: viewports.Rnw:66-71
+###################################################
+pushViewport(viewport(name = "A"))
+upViewport()
+pushViewport(viewport(name = "B"))
+upViewport()
+downViewport("A")
+
+
+###################################################
+### code chunk number 5: viewports.Rnw:80-81
+###################################################
+seekViewport("B")
+
+
+###################################################
+### code chunk number 6: viewports.Rnw:86-88
+###################################################
+current.vpTree()
+
+
+
+###################################################
+### code chunk number 7: vpstackguts
+###################################################
+vp <- viewport(width = 0.5, height = 0.5)
+grid.rect(vp = vpStack(vp, vp))
+
+
+###################################################
+### code chunk number 8: viewports.Rnw:109-111
+###################################################
+grid.rect(gp = gpar(col = "grey"))
+vp <- viewport(width = 0.5, height = 0.5)
+grid.rect(vp = vpStack(vp, vp))
+
+
+###################################################
+### code chunk number 9: viewports.Rnw:135-137
+###################################################
+grid.newpage()
+
+
+
+###################################################
+### code chunk number 10: viewports.Rnw:138-141
+###################################################
+pushViewport(viewport(name = "A"))
+pushViewport(viewport(name = "B"))
+pushViewport(viewport(name = "A"))
+
+
+###################################################
+### code chunk number 11: viewports.Rnw:147-149
+###################################################
+seekViewport("A")
+current.vpTree(FALSE)
+
+
+###################################################
+### code chunk number 12: viewports.Rnw:154-156
+###################################################
+seekViewport(vpPath("B", "A"))
+current.vpTree(FALSE)
+
+
+###################################################
+### code chunk number 13: viewports.Rnw:161-162
+###################################################
+vpPath("A", "B")
+
+
+###################################################
+### code chunk number 14: viewports.Rnw:169-171 (eval = FALSE)
+###################################################
+## seekViewport(vpPath("A", "B"))
+## seekViewport("A::B")
+
+
+###################################################
+### code chunk number 15: viewports.Rnw:180-182
+###################################################
+x <- runif(10)
+y <- runif(10)
+
+
+###################################################
+### code chunk number 16: viewports.Rnw:187-189
+###################################################
+xscale <- extendrange(x)
+yscale <- extendrange(y)
+
+
+###################################################
+### code chunk number 17: viewports.Rnw:198-203
+###################################################
+top.vp <-
+ viewport(layout=grid.layout(3, 3,
+ widths=unit(c(5, 1, 2), c("lines", "null", "lines")),
+ heights=unit(c(5, 1, 4), c("lines", "null", "lines"))))
+
+
+
+###################################################
+### code chunk number 18: viewports.Rnw:204-205
+###################################################
+grid.show.layout(viewport.layout(top.vp))
+
+
+###################################################
+### code chunk number 19: viewports.Rnw:212-222
+###################################################
+margin1 <- viewport(layout.pos.col = 2, layout.pos.row = 3,
+ name = "margin1")
+margin2 <- viewport(layout.pos.col = 1, layout.pos.row = 2,
+ name = "margin2")
+margin3 <- viewport(layout.pos.col = 2, layout.pos.row = 1,
+ name = "margin3")
+margin4 <- viewport(layout.pos.col = 3, layout.pos.row = 2,
+ name = "margin4")
+plot <- viewport(layout.pos.col = 2, layout.pos.row = 2,
+ name = "plot", xscale = xscale, yscale = yscale)
+
+
+###################################################
+### code chunk number 20: viewports.Rnw:229-230
+###################################################
+splot <- vpTree(top.vp, vpList(margin1, margin2, margin3, margin4, plot))
+
+
+###################################################
+### code chunk number 21: viewports
+###################################################
+pushViewport(splot)
+
+
+###################################################
+### code chunk number 22: grid (eval = FALSE)
+###################################################
+## labelvp <- function(name) {
+## seekViewport(name)
+## grid.rect(gp = gpar(col = "grey", lwd = 5))
+## grid.rect(x = 0, y = 1, width = unit(1, "strwidth", name) + unit(2, "mm"),
+## height = unit(1, "lines"), just = c("left", "top"),
+## gp = gpar(fill = "grey", col = NULL))
+## grid.text(name, x = unit(1, "mm"), y = unit(1, "npc") - unit(1, "mm"),
+## just = c("left", "top"), gp = gpar(col = "white"))
+## }
+## labelvp("plot")
+## labelvp("margin1")
+## labelvp("margin2")
+## labelvp("margin3")
+## labelvp("margin4")
+
+
+###################################################
+### code chunk number 23: plot (eval = FALSE)
+###################################################
+## seekViewport("plot")
+## grid.points(x, y)
+## grid.xaxis()
+## grid.yaxis()
+## grid.rect()
+
+
+###################################################
+### code chunk number 24: margin1 (eval = FALSE)
+###################################################
+## seekViewport("margin1")
+## grid.text("Random X", y = unit(1, "lines"))
+
+
+###################################################
+### code chunk number 25: margin2 (eval = FALSE)
+###################################################
+## seekViewport("margin2")
+## grid.text("Random Y", x = unit(1, "lines"), rot = 90)
+##
+
+
+###################################################
+### code chunk number 26: viewports.Rnw:282-288
+###################################################
+pushViewport(viewport(w = 0.9, h = 0.9))
+pushViewport(splot)
+labelvp <- function(name) {
+ seekViewport(name)
+ grid.rect(gp = gpar(col = "grey", lwd = 5))
+ grid.rect(x = 0, y = 1, width = unit(1, "strwidth", name) + unit(2, "mm"),
+ height = unit(1, "lines"), just = c("left", "top"),
+ gp = gpar(fill = "grey", col = NULL))
+ grid.text(name, x = unit(1, "mm"), y = unit(1, "npc") - unit(1, "mm"),
+ just = c("left", "top"), gp = gpar(col = "white"))
+}
+labelvp("plot")
+labelvp("margin1")
+labelvp("margin2")
+labelvp("margin3")
+labelvp("margin4")
+seekViewport("plot")
+grid.points(x, y)
+grid.xaxis()
+grid.yaxis()
+grid.rect()
+seekViewport("margin1")
+grid.text("Random X", y = unit(1, "lines"))
+seekViewport("margin2")
+grid.text("Random Y", x = unit(1, "lines"), rot = 90)
+
+
+
+###################################################
+### code chunk number 27: viewports.Rnw:302-303
+###################################################
+upViewport(0)
+
+
+###################################################
+### code chunk number 28: annguts (eval = FALSE)
+###################################################
+## seekViewport("margin3")
+## grid.text("The user adds a title!", gp = gpar(fontsize = 20))
+##
+
+
+###################################################
+### code chunk number 29: viewports.Rnw:320-328
+###################################################
+pushViewport(viewport(w = 0.9, h = 0.9))
+pushViewport(splot)
+labelvp <- function(name) {
+ seekViewport(name)
+ grid.rect(gp = gpar(col = "grey", lwd = 5))
+ grid.rect(x = 0, y = 1, width = unit(1, "strwidth", name) + unit(2, "mm"),
+ height = unit(1, "lines"), just = c("left", "top"),
+ gp = gpar(fill = "grey", col = NULL))
+ grid.text(name, x = unit(1, "mm"), y = unit(1, "npc") - unit(1, "mm"),
+ just = c("left", "top"), gp = gpar(col = "white"))
+}
+labelvp("plot")
+labelvp("margin1")
+labelvp("margin2")
+labelvp("margin3")
+labelvp("margin4")
+seekViewport("plot")
+grid.points(x, y)
+grid.xaxis()
+grid.yaxis()
+grid.rect()
+seekViewport("margin1")
+grid.text("Random X", y = unit(1, "lines"))
+seekViewport("margin2")
+grid.text("Random Y", x = unit(1, "lines"), rot = 90)
+
+seekViewport("margin3")
+grid.text("The user adds a title!", gp = gpar(fontsize = 20))
+
+popViewport(0)
+
+
diff --git a/win32/deps/library/grid/doc/viewports.Rnw b/win32/deps/library/grid/doc/viewports.Rnw
new file mode 100644
index 0000000..c693448
--- /dev/null
+++ b/win32/deps/library/grid/doc/viewports.Rnw
@@ -0,0 +1,332 @@
+\documentclass[a4paper]{article}
+
+\usepackage{Rd}
+
+% \VignetteIndexEntry{Working with viewports}
+
+\newcommand{\grid}{\pkg{grid}}
+\newcommand{\lattice}{\CRANpkg{lattice}}
+
+\setlength{\parindent}{0in}
+\setlength{\parskip}{.1in}
+\setlength{\textwidth}{140mm}
+\setlength{\oddsidemargin}{10mm}
+
+\title{Working with \grid{} Viewports}
+\author{Paul Murrell}
+
+\begin{document}
+\maketitle
+
+<<echo=FALSE, results=hide>>=
+library(grDevices)
+library(stats) # for runif()
+library(grid)
+ps.options(pointsize = 12)
+options(width = 60)
+@
+This document describes some features of \grid{} viewports which
+make it easy to travel back and forth between multiple regions
+on a device (without having to recreate those regions), and provides a
+mechanism for a complex plotting function to provide users with access
+to all of the regions created during plotting.
+
+\section*{The viewport tree}
+
+\grid{} maintains a
+tree of pushed viewports on each device.
+When the \code{upViewport()}
+function is called it works like \code{popViewport()} except that
+it does not remove viewports from the viewport tree.
+For example, the following code pushes a viewport, then navigates
+back up to the top level viewport and pushes another viewport,
+without removing the first viewport.
+
+<<>>=
+pushViewport(viewport())
+upViewport()
+pushViewport(viewport())
+@
+There are now two viewports pushed directly beneath the top-level
+viewport. This immediately creates an ambiguity; if I navigate
+back up to the top-level and attempt to revisit one of the
+viewports, how can I specify which one I want? The answer is that
+viewports have a \code{name} argument\footnote{The print method
+for viewports shows the viewport name within square brackets. Try
+typing \code{current.viewport()}.}. This name, combined with
+the \code{downViewport()} function, makes it possible to
+navigate back down to viewports in the viewport tree. Consider the
+following example, which pushes two viewports called \code{"A"} and
+\code{"B"}, then navigates to viewport \code{"A"} from the
+top level.
+
+<<echo=FALSE, results=hide>>=
+grid.newpage()
+
+<<>>=
+pushViewport(viewport(name = "A"))
+upViewport()
+pushViewport(viewport(name = "B"))
+upViewport()
+downViewport("A")
+@
+The \code{downViewport()} function searches down the tree from the
+current position in the tree. The \code{seekViewport()}
+function is similar, but it always starts searching from the top-level
+viewport. In the previous example we ended up in viewport
+\code{"A"}; the following command navigates from \code{"A"} to \code{"B"}
+in a single step.
+
+<<>>=
+seekViewport("B")
+@
+The function \code{current.vpTree()} provides a
+(textual) view of the current viewport tree.
+
+<<>>=
+current.vpTree()
+
+@
+\section*{Viewport stacks, lists, and trees}
+
+It is possible to create multiple viewport descriptions
+\emph{and their relationships}. The functions
+\code{vpStack()}, \code{vpList()}, and
+\code{vpTree()} can be used to create a stack, a list, or a tree
+of viewport descriptions, respectively. It is then possible to
+push these multiple descriptions at once; viewports in a stack
+are pushed in series, viewports in a list are pushed in parallel,
+and for a tree of viewports, the parent is pushed then the children
+are pushed in parallel. The following simple
+example demonstrates one usage of this feature; a \grid{} rectangle
+is drawn \emph{two} viewports below the current level by
+specifying a stack of viewports in its \code{vp} argument.
+
+
+<<vpstackguts>>=
+vp <- viewport(width = 0.5, height = 0.5)
+grid.rect(vp = vpStack(vp, vp))
+<<echo=FALSE, fig=TRUE>>=
+grid.rect(gp = gpar(col = "grey"))
+<<vpstackguts>>
+@
+\section*{Viewport paths}
+The previous example demonstrates a subtle feature of \grid{}'s viewport
+tree. The same viewport, \emph{with the same name}, was pushed
+twice (in series). This demonstrates that viewport names only
+have to be unique for viewports which share the same parent.
+This makes it possible, especially in repetitive plot arrangements,
+to reuse convenient viewport names. For example, in a \lattice{}
+style plot, each panel could have a viewport called \code{"strip"}
+to represent the strip region.
+
+This design creates a further ambiguity because there may be
+more than one viewport with the same name within the viewport
+tree\footnote{\code{downViewport()} and \code{seekViewport()} will stop at the
+first match they find (the search is currently depth-first).}.
+This ambiguity can be resolved by using the \code{vpPath()}
+function to generate a specification of a stack of viewports
+that must be matched by name. This path can be passed to
+either \code{downViewport()} or \code{seekViewport()} as in the
+following example; notice that we are calling
+\code{current.vpTree(FALSE)} in order to see the current viewport
+tree \emph{only from the current viewport down}.
+
+<<echo=FALSE, results=hide>>=
+grid.newpage()
+
+<<>>=
+pushViewport(viewport(name = "A"))
+pushViewport(viewport(name = "B"))
+pushViewport(viewport(name = "A"))
+@
+
+When we do a seek on just \code{"A"}, we find the first \code{"A"}
+(just below the top-level viewport).
+
+<<>>=
+seekViewport("A")
+current.vpTree(FALSE)
+@
+By specifying a \code{vpPath}, we can get the \code{"A"} directly
+below viewport \code{"B"}.
+
+<<>>=
+seekViewport(vpPath("B", "A"))
+current.vpTree(FALSE)
+@
+A viewport path is conceptually just a concatenation of several
+names using a path separator (currently \code{::}).
+
+<<>>=
+vpPath("A", "B")
+@
+For interactive use, it is possible to specify the path as a simple
+string, but this is not recommended otherwise in case the path
+separator changes in future versions of \grid{}. As an example, the
+following two commands are currently equivalent.
+
+<<eval=FALSE>>=
+seekViewport(vpPath("A", "B"))
+seekViewport("A::B")
+@
+\section*{An example}
+
+In this section, we consider a simple example to demonstrate
+how these new viewport features might be used together.
+The goal is to produce a simple scatterplot. We will work
+with some random data.
+
+<<>>=
+x <- runif(10)
+y <- runif(10)
+@
+We will be establishing some scales appropriate for these data,
+so we calculate sensible ranges now.
+
+<<>>=
+xscale <- extendrange(x)
+yscale <- extendrange(y)
+@
+We now produce a set of viewports that will be useful in creating the
+plot. The first viewport contains a layout to divide the drawing region
+into several rows and columns. The left and right columns and top and
+bottom rows provide room for axes and labels, while the central cell provides
+a region for plotting the data. The diagram below the code shows
+the layout that we create.
+
+<<>>=
+top.vp <-
+ viewport(layout=grid.layout(3, 3,
+ widths=unit(c(5, 1, 2), c("lines", "null", "lines")),
+ heights=unit(c(5, 1, 4), c("lines", "null", "lines"))))
+
+<<echo=FALSE, fig=TRUE>>=
+grid.show.layout(viewport.layout(top.vp))
+@
+
+Next we create a set of viewports which will occupy different areas within the
+layout, corresponding to the margins for axes and labels, and the plotting
+region.
+
+<<>>=
+margin1 <- viewport(layout.pos.col = 2, layout.pos.row = 3,
+ name = "margin1")
+margin2 <- viewport(layout.pos.col = 1, layout.pos.row = 2,
+ name = "margin2")
+margin3 <- viewport(layout.pos.col = 2, layout.pos.row = 1,
+ name = "margin3")
+margin4 <- viewport(layout.pos.col = 3, layout.pos.row = 2,
+ name = "margin4")
+plot <- viewport(layout.pos.col = 2, layout.pos.row = 2,
+ name = "plot", xscale = xscale, yscale = yscale)
+@
+Notice that we have not pushed any of these viewports yet so no regions
+exist on the output device. We first of all arrange the viewports into
+a tree structure, with the \code{top.vp} as the parent node and
+all of the other viewports as its children.
+
+<<>>=
+splot <- vpTree(top.vp, vpList(margin1, margin2, margin3, margin4, plot))
+@
+Now we can push this entire tree of viewports in order to create all of the
+different areas within the drawing region that we need to draw the
+scatterplot.
+The result of this push is that we are left in the \code{plot} viewport.
+
+<<viewports>>=
+pushViewport(splot)
+@
+Now we can navigate to whichever viewport we require and draw the
+different elements of the plot\footnote{The named viewports that we created
+are drawn as grey rectangles as a guide.}.
+
+<<grid, echo=FALSE, eval=FALSE>>=
+labelvp <- function(name) {
+ seekViewport(name)
+ grid.rect(gp = gpar(col = "grey", lwd = 5))
+ grid.rect(x = 0, y = 1, width = unit(1, "strwidth", name) + unit(2, "mm"),
+ height = unit(1, "lines"), just = c("left", "top"),
+ gp = gpar(fill = "grey", col = NULL))
+ grid.text(name, x = unit(1, "mm"), y = unit(1, "npc") - unit(1, "mm"),
+ just = c("left", "top"), gp = gpar(col = "white"))
+}
+labelvp("plot")
+labelvp("margin1")
+labelvp("margin2")
+labelvp("margin3")
+labelvp("margin4")
+@
+The data symbols and axes are drawn relative to the plot region \ldots{}
+
+<<plot, eval=FALSE>>=
+seekViewport("plot")
+grid.points(x, y)
+grid.xaxis()
+grid.yaxis()
+grid.rect()
+@
+\ldots{} the x-axis label is drawn in margin 1 \ldots{}
+
+<<margin1, eval=FALSE>>=
+seekViewport("margin1")
+grid.text("Random X", y = unit(1, "lines"))
+@
+\ldots{} and the y-axis label is drawn in margin 2 (the final output
+is shown on the next page).
+
+<<margin2, eval=FALSE>>=
+seekViewport("margin2")
+grid.text("Random Y", x = unit(1, "lines"), rot = 90)
+
+<<echo=FALSE, results=hide, fig=TRUE>>=
+pushViewport(viewport(w = 0.9, h = 0.9))
+<<viewports>>
+<<grid>>
+<<plot>>
+<<margin1>>
+<<margin2>>
+@
+
+As a final step, we navigate back to the top-level viewport (i.e.,
+back to the viewport we started in)\footnote{Here we have used
+ \code{0} to indicate ``navigate to the top-level viewport''. When
+ writing code that could be used by others (i.e., a graphical
+ component that could be embedded within something else), it would be
+ necessary to specify a precise number of viewports to navigate back
+ up. In this case, the number would be {\tt} 2. The
+ \code{downViewport()} function returns the number of viewports it
+ went down, so a general solution is of the form: \code{depth <-
+ downViewport("avp"); upViewport(depth)}.}.
+
+<<>>=
+upViewport(0)
+@
+So far this example has just shown
+an alternative way of constructing this sort of plot. The output we have
+generated so far could have been done using \code{pushViewport()}
+and \code{popViewport()}. The difference is that we still have
+all of the viewports in the \grid{} viewport tree (and they are addressable
+by name). This means that a user can seek any of the viewports
+we used to construct the plot (by name) and add annotations or
+use \code{grid.locator()} or whatever. For example, a user could
+use the following commands
+to add a title.
+
+<<annguts, eval=FALSE>>=
+seekViewport("margin3")
+grid.text("The user adds a title!", gp = gpar(fontsize = 20))
+
+<<echo=FALSE, results=hide, fig=TRUE>>=
+pushViewport(viewport(w = 0.9, h = 0.9))
+<<viewports>>
+<<grid>>
+<<plot>>
+<<margin1>>
+<<margin2>>
+<<annguts>>
+popViewport(0)
+@
+
+\end{document}
+
diff --git a/win32/deps/library/grid/doc/viewports.pdf b/win32/deps/library/grid/doc/viewports.pdf
new file mode 100644
index 0000000..9d94768
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diff --git a/win32/deps/library/grid/help/AnIndex b/win32/deps/library/grid/help/AnIndex
index b0d9b5d..d8cbcde 100644
--- a/win32/deps/library/grid/help/AnIndex
+++ b/win32/deps/library/grid/help/AnIndex
@@ -6,6 +6,10 @@ applyEdits gEdit
arcCurvature grid.curve
arrow arrow
arrowsGrob grid.arrows
+ascentDetails widthDetails
+bezierGrob grid.bezier
+bezierPoints xsplinePoints
+calcStringMetric calcStringMetric
childNames grid.grob
circleGrob grid.circle
clipGrob grid.clip
@@ -21,6 +25,7 @@ current.vpPath current.viewport
current.vpTree current.viewport
curveGrob grid.curve
dataViewport dataViewport
+descentDetails widthDetails
downViewport viewports
draw.details drawDetails
drawDetails drawDetails
@@ -28,6 +33,7 @@ editDetails editDetails
editGrob grid.edit
engine.display.list grid.display.list
frameGrob grid.frame
+functionGrob grid.function
gEdit gEdit
gEditList gEdit
get.gpar gpar
@@ -37,8 +43,11 @@ gList grid.grob
gpar gpar
gPath gPath
Grid Grid
+grid.abline grid.function
grid.add grid.add
grid.arrows grid.arrows
+grid.bezier grid.bezier
+grid.cap grid.cap
grid.circle grid.circle
grid.clip grid.clip
grid.collection grid.collection
@@ -50,9 +59,11 @@ grid.convertY grid.convert
grid.copy grid.copy
grid.curve grid.curve
grid.display.list grid.display.list
+grid.DLapply grid.DLapply
grid.draw grid.draw
grid.edit grid.edit
grid.frame grid.frame
+grid.function grid.function
grid.gedit grid.edit
grid.get grid.get
grid.gget grid.get
@@ -73,6 +84,7 @@ grid.newpage grid.newpage
grid.null grid.null
grid.pack grid.pack
grid.panel grid-internal
+grid.path grid.path
grid.place grid.place
grid.plot.and.legend grid.plot.and.legend
grid.points grid.points
@@ -80,6 +92,7 @@ grid.polygon grid.polygon
grid.polyline grid.lines
grid.pretty grid.pretty
grid.prompt grid.prompt
+grid.raster grid.raster
grid.record grid.record
grid.rect grid.rect
grid.refresh grid.refresh
@@ -95,6 +108,8 @@ grid.xaxis grid.xaxis
grid.xspline grid.xspline
grid.yaxis grid.yaxis
grob grid.grob
+grobAscent grobWidth
+grobDescent grobWidth
grobHeight grobWidth
grobName grobName
grobPathListing grid.ls
@@ -116,6 +131,7 @@ moveToGrob grid.move.to
nestedListing grid.ls
nullGrob grid.null
packGrob grid.pack
+pathGrob grid.path
pathListing grid.ls
placeGrob grid.place
plotViewport plotViewport
@@ -128,6 +144,7 @@ postDrawDetails drawDetails
preDrawDetails drawDetails
push.viewport push.viewport
pushViewport viewports
+rasterGrob grid.raster
recordGrob grid.record
rectGrob grid.rect
removeGrob grid.remove
@@ -137,6 +154,10 @@ seekViewport viewports
segmentsGrob grid.segments
setChildren grid.add
setGrob grid.set
+showGrob showGrob
+showViewport showViewport
+stringAscent stringWidth
+stringDescent stringWidth
stringHeight stringWidth
stringWidth stringWidth
textGrob grid.text
@@ -160,5 +181,6 @@ widthDetails widthDetails
xaxisGrob grid.xaxis
xDetails xDetails
xsplineGrob grid.xspline
+xsplinePoints xsplinePoints
yaxisGrob grid.yaxis
yDetails xDetails
diff --git a/win32/deps/library/grid/help/aliases.rds b/win32/deps/library/grid/help/aliases.rds
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diff --git a/win32/deps/library/grid/help/paths.rds b/win32/deps/library/grid/help/paths.rds
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diff --git a/win32/deps/library/grid/html/00Index.html b/win32/deps/library/grid/html/00Index.html
new file mode 100644
index 0000000..6f9b7a0
--- /dev/null
+++ b/win32/deps/library/grid/html/00Index.html
@@ -0,0 +1,504 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: The Grid Graphics Package</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> The Grid Graphics Package
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘grid’ version 2.15.2</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+<li><a href="../doc/index.html">Overview of user guides and package vignettes</a>; browse <a href="../doc">directory</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<p align="center">
+<a href="# "> </a>
+<a href="#A">A</a>
+<a href="#B">B</a>
+<a href="#C">C</a>
+<a href="#D">D</a>
+<a href="#E">E</a>
+<a href="#F">F</a>
+<a href="#G">G</a>
+<a href="#H">H</a>
+<a href="#I">I</a>
+<a href="#L">L</a>
+<a href="#M">M</a>
+<a href="#N">N</a>
+<a href="#P">P</a>
+<a href="#R">R</a>
+<a href="#S">S</a>
+<a href="#T">T</a>
+<a href="#U">U</a>
+<a href="#V">V</a>
+<a href="#W">W</a>
+<a href="#X">X</a>
+<a href="#Y">Y</a>
+</p>
+
+<table width="100%">
+<tr><td width="25%"><a href="grid-package.html">grid-package</a></td>
+<td>The Grid Graphics Package</td></tr>
+</table>
+
+<h2><a name="A">-- A --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="absolute.size.html">absolute.size</a></td>
+<td>Absolute Size of a Grob</td></tr>
+<tr><td width="25%"><a href="grid.add.html">addGrob</a></td>
+<td>Add a Grid Graphical Object</td></tr>
+<tr><td width="25%"><a href="gEdit.html">applyEdit</a></td>
+<td>Create and Apply Edit Objects</td></tr>
+<tr><td width="25%"><a href="gEdit.html">applyEdits</a></td>
+<td>Create and Apply Edit Objects</td></tr>
+<tr><td width="25%"><a href="grid.curve.html">arcCurvature</a></td>
+<td>Draw a Curve Between Locations</td></tr>
+<tr><td width="25%"><a href="arrow.html">arrow</a></td>
+<td>Describe arrows to add to a line.</td></tr>
+<tr><td width="25%"><a href="grid.arrows.html">arrowsGrob</a></td>
+<td>Draw Arrows</td></tr>
+<tr><td width="25%"><a href="widthDetails.html">ascentDetails</a></td>
+<td>Width and Height of a grid grob</td></tr>
+</table>
+
+<h2><a name="B">-- B --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="grid.bezier.html">bezierGrob</a></td>
+<td>Draw a Bezier Curve</td></tr>
+<tr><td width="25%"><a href="xsplinePoints.html">bezierPoints</a></td>
+<td>Return the points that would be used to draw an Xspline (or a Bezier curve).</td></tr>
+</table>
+
+<h2><a name="C">-- C --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="calcStringMetric.html">calcStringMetric</a></td>
+<td>Calculate Metric Information for Text</td></tr>
+<tr><td width="25%"><a href="grid.grob.html">childNames</a></td>
+<td>Create a Grid Graphical Object</td></tr>
+<tr><td width="25%"><a href="grid.circle.html">circleGrob</a></td>
+<td>Draw a Circle</td></tr>
+<tr><td width="25%"><a href="grid.clip.html">clipGrob</a></td>
+<td>Set the Clipping Region</td></tr>
+<tr><td width="25%"><a href="grid.convert.html">convertHeight</a></td>
+<td>Convert Between Different grid Coordinate Systems</td></tr>
+<tr><td width="25%"><a href="convertNative.html">convertNative</a></td>
+<td>Convert a Unit Object to Native units</td></tr>
+<tr><td width="25%"><a href="grid.convert.html">convertUnit</a></td>
+<td>Convert Between Different grid Coordinate Systems</td></tr>
+<tr><td width="25%"><a href="grid.convert.html">convertWidth</a></td>
+<td>Convert Between Different grid Coordinate Systems</td></tr>
+<tr><td width="25%"><a href="grid.convert.html">convertX</a></td>
+<td>Convert Between Different grid Coordinate Systems</td></tr>
+<tr><td width="25%"><a href="grid.convert.html">convertY</a></td>
+<td>Convert Between Different grid Coordinate Systems</td></tr>
+<tr><td width="25%"><a href="current.viewport.html">current.transform</a></td>
+<td>Get the Current Grid Viewport (Tree)</td></tr>
+<tr><td width="25%"><a href="current.viewport.html">current.viewport</a></td>
+<td>Get the Current Grid Viewport (Tree)</td></tr>
+<tr><td width="25%"><a href="current.viewport.html">current.vpPath</a></td>
+<td>Get the Current Grid Viewport (Tree)</td></tr>
+<tr><td width="25%"><a href="current.viewport.html">current.vpTree</a></td>
+<td>Get the Current Grid Viewport (Tree)</td></tr>
+<tr><td width="25%"><a href="grid.curve.html">curveGrob</a></td>
+<td>Draw a Curve Between Locations</td></tr>
+</table>
+
+<h2><a name="D">-- D --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="dataViewport.html">dataViewport</a></td>
+<td>Create a Viewport with Scales based on Data</td></tr>
+<tr><td width="25%"><a href="widthDetails.html">descentDetails</a></td>
+<td>Width and Height of a grid grob</td></tr>
+<tr><td width="25%"><a href="viewports.html">downViewport</a></td>
+<td>Maintaining and Navigating the Grid Viewport Tree</td></tr>
+<tr><td width="25%"><a href="drawDetails.html">draw.details</a></td>
+<td>Customising grid Drawing</td></tr>
+<tr><td width="25%"><a href="drawDetails.html">drawDetails</a></td>
+<td>Customising grid Drawing</td></tr>
+</table>
+
+<h2><a name="E">-- E --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="editDetails.html">editDetails</a></td>
+<td>Customising grid Editing</td></tr>
+<tr><td width="25%"><a href="grid.edit.html">editGrob</a></td>
+<td>Edit the Description of a Grid Graphical Object</td></tr>
+<tr><td width="25%"><a href="grid.display.list.html">engine.display.list</a></td>
+<td>Control the Grid Display List</td></tr>
+</table>
+
+<h2><a name="F">-- F --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="grid.frame.html">frameGrob</a></td>
+<td>Create a Frame for Packing Objects</td></tr>
+<tr><td width="25%"><a href="grid.function.html">functionGrob</a></td>
+<td>Draw a curve representing a function</td></tr>
+</table>
+
+<h2><a name="G">-- G --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="gEdit.html">gEdit</a></td>
+<td>Create and Apply Edit Objects</td></tr>
+<tr><td width="25%"><a href="gEdit.html">gEditList</a></td>
+<td>Create and Apply Edit Objects</td></tr>
+<tr><td width="25%"><a href="gpar.html">get.gpar</a></td>
+<td>Handling Grid Graphical Parameters</td></tr>
+<tr><td width="25%"><a href="grid.get.html">getGrob</a></td>
+<td>Get a Grid Graphical Object</td></tr>
+<tr><td width="25%"><a href="getNames.html">getNames</a></td>
+<td>List the names of grobs on the display list</td></tr>
+<tr><td width="25%"><a href="grid.grob.html">gList</a></td>
+<td>Create a Grid Graphical Object</td></tr>
+<tr><td width="25%"><a href="gpar.html">gpar</a></td>
+<td>Handling Grid Graphical Parameters</td></tr>
+<tr><td width="25%"><a href="gPath.html">gPath</a></td>
+<td>Concatenate Grob Names</td></tr>
+<tr><td width="25%"><a href="Grid.html">Grid</a></td>
+<td>Grid Graphics</td></tr>
+<tr><td width="25%"><a href="grid.function.html">grid.abline</a></td>
+<td>Draw a curve representing a function</td></tr>
+<tr><td width="25%"><a href="grid.add.html">grid.add</a></td>
+<td>Add a Grid Graphical Object</td></tr>
+<tr><td width="25%"><a href="grid.arrows.html">grid.arrows</a></td>
+<td>Draw Arrows</td></tr>
+<tr><td width="25%"><a href="grid.bezier.html">grid.bezier</a></td>
+<td>Draw a Bezier Curve</td></tr>
+<tr><td width="25%"><a href="grid.cap.html">grid.cap</a></td>
+<td>Capture a raster image</td></tr>
+<tr><td width="25%"><a href="grid.circle.html">grid.circle</a></td>
+<td>Draw a Circle</td></tr>
+<tr><td width="25%"><a href="grid.clip.html">grid.clip</a></td>
+<td>Set the Clipping Region</td></tr>
+<tr><td width="25%"><a href="grid.collection.html">grid.collection</a></td>
+<td>Create a Coherent Group of Grid Graphical Objects</td></tr>
+<tr><td width="25%"><a href="grid.convert.html">grid.convert</a></td>
+<td>Convert Between Different grid Coordinate Systems</td></tr>
+<tr><td width="25%"><a href="grid.convert.html">grid.convertHeight</a></td>
+<td>Convert Between Different grid Coordinate Systems</td></tr>
+<tr><td width="25%"><a href="grid.convert.html">grid.convertWidth</a></td>
+<td>Convert Between Different grid Coordinate Systems</td></tr>
+<tr><td width="25%"><a href="grid.convert.html">grid.convertX</a></td>
+<td>Convert Between Different grid Coordinate Systems</td></tr>
+<tr><td width="25%"><a href="grid.convert.html">grid.convertY</a></td>
+<td>Convert Between Different grid Coordinate Systems</td></tr>
+<tr><td width="25%"><a href="grid.copy.html">grid.copy</a></td>
+<td>Make a Copy of a Grid Graphical Object</td></tr>
+<tr><td width="25%"><a href="grid.curve.html">grid.curve</a></td>
+<td>Draw a Curve Between Locations</td></tr>
+<tr><td width="25%"><a href="grid.display.list.html">grid.display.list</a></td>
+<td>Control the Grid Display List</td></tr>
+<tr><td width="25%"><a href="grid.DLapply.html">grid.DLapply</a></td>
+<td>Modify the Grid Display List</td></tr>
+<tr><td width="25%"><a href="grid.draw.html">grid.draw</a></td>
+<td>Draw a grid grob</td></tr>
+<tr><td width="25%"><a href="grid.edit.html">grid.edit</a></td>
+<td>Edit the Description of a Grid Graphical Object</td></tr>
+<tr><td width="25%"><a href="grid.frame.html">grid.frame</a></td>
+<td>Create a Frame for Packing Objects</td></tr>
+<tr><td width="25%"><a href="grid.function.html">grid.function</a></td>
+<td>Draw a curve representing a function</td></tr>
+<tr><td width="25%"><a href="grid.edit.html">grid.gedit</a></td>
+<td>Edit the Description of a Grid Graphical Object</td></tr>
+<tr><td width="25%"><a href="grid.get.html">grid.get</a></td>
+<td>Get a Grid Graphical Object</td></tr>
+<tr><td width="25%"><a href="grid.get.html">grid.gget</a></td>
+<td>Get a Grid Graphical Object</td></tr>
+<tr><td width="25%"><a href="grid.grab.html">grid.grab</a></td>
+<td>Grab the current grid output</td></tr>
+<tr><td width="25%"><a href="grid.grab.html">grid.grabExpr</a></td>
+<td>Grab the current grid output</td></tr>
+<tr><td width="25%"><a href="grid.remove.html">grid.gremove</a></td>
+<td>Remove a Grid Graphical Object</td></tr>
+<tr><td width="25%"><a href="grid.grill.html">grid.grill</a></td>
+<td>Draw a Grill</td></tr>
+<tr><td width="25%"><a href="grid.grob.html">grid.grob</a></td>
+<td>Create a Grid Graphical Object</td></tr>
+<tr><td width="25%"><a href="grid.layout.html">grid.layout</a></td>
+<td>Create a Grid Layout</td></tr>
+<tr><td width="25%"><a href="grid.move.to.html">grid.line.to</a></td>
+<td>Move or Draw to a Specified Position</td></tr>
+<tr><td width="25%"><a href="grid.lines.html">grid.lines</a></td>
+<td>Draw Lines in a Grid Viewport</td></tr>
+<tr><td width="25%"><a href="grid.locator.html">grid.locator</a></td>
+<td>Capture a Mouse Click</td></tr>
+<tr><td width="25%"><a href="grid.ls.html">grid.ls</a></td>
+<td>List the names of grobs or viewports</td></tr>
+<tr><td width="25%"><a href="grid.move.to.html">grid.move.to</a></td>
+<td>Move or Draw to a Specified Position</td></tr>
+<tr><td width="25%"><a href="grid.newpage.html">grid.newpage</a></td>
+<td>Move to a New Page on a Grid Device</td></tr>
+<tr><td width="25%"><a href="grid.null.html">grid.null</a></td>
+<td>Null Graphical Object</td></tr>
+<tr><td width="25%"><a href="grid.pack.html">grid.pack</a></td>
+<td>Pack an Object within a Frame</td></tr>
+<tr><td width="25%"><a href="grid.path.html">grid.path</a></td>
+<td>Draw a Path</td></tr>
+<tr><td width="25%"><a href="grid.place.html">grid.place</a></td>
+<td>Place an Object within a Frame</td></tr>
+<tr><td width="25%"><a href="grid.plot.and.legend.html">grid.plot.and.legend</a></td>
+<td>A Simple Plot and Legend Demo</td></tr>
+<tr><td width="25%"><a href="grid.points.html">grid.points</a></td>
+<td>Draw Data Symbols</td></tr>
+<tr><td width="25%"><a href="grid.polygon.html">grid.polygon</a></td>
+<td>Draw a Polygon</td></tr>
+<tr><td width="25%"><a href="grid.lines.html">grid.polyline</a></td>
+<td>Draw Lines in a Grid Viewport</td></tr>
+<tr><td width="25%"><a href="grid.pretty.html">grid.pretty</a></td>
+<td>Generate a Sensible Set of Breakpoints</td></tr>
+<tr><td width="25%"><a href="grid.prompt.html">grid.prompt</a></td>
+<td>Prompt before New Page</td></tr>
+<tr><td width="25%"><a href="grid.raster.html">grid.raster</a></td>
+<td>Render a raster object</td></tr>
+<tr><td width="25%"><a href="grid.record.html">grid.record</a></td>
+<td>Encapsulate calculations and drawing</td></tr>
+<tr><td width="25%"><a href="grid.rect.html">grid.rect</a></td>
+<td>Draw rectangles</td></tr>
+<tr><td width="25%"><a href="grid.refresh.html">grid.refresh</a></td>
+<td>Refresh the current grid scene</td></tr>
+<tr><td width="25%"><a href="grid.remove.html">grid.remove</a></td>
+<td>Remove a Grid Graphical Object</td></tr>
+<tr><td width="25%"><a href="grid.roundrect.html">grid.roundrect</a></td>
+<td>Draw a rectangle with rounded corners</td></tr>
+<tr><td width="25%"><a href="grid.segments.html">grid.segments</a></td>
+<td>Draw Line Segments</td></tr>
+<tr><td width="25%"><a href="grid.set.html">grid.set</a></td>
+<td>Set a Grid Graphical Object</td></tr>
+<tr><td width="25%"><a href="grid.show.layout.html">grid.show.layout</a></td>
+<td>Draw a Diagram of a Grid Layout</td></tr>
+<tr><td width="25%"><a href="grid.show.viewport.html">grid.show.viewport</a></td>
+<td>Draw a Diagram of a Grid Viewport</td></tr>
+<tr><td width="25%"><a href="grid.text.html">grid.text</a></td>
+<td>Draw Text</td></tr>
+<tr><td width="25%"><a href="grid.xaxis.html">grid.xaxis</a></td>
+<td>Draw an X-Axis</td></tr>
+<tr><td width="25%"><a href="grid.xspline.html">grid.xspline</a></td>
+<td>Draw an Xspline</td></tr>
+<tr><td width="25%"><a href="grid.yaxis.html">grid.yaxis</a></td>
+<td>Draw a Y-Axis</td></tr>
+<tr><td width="25%"><a href="grid.grob.html">grob</a></td>
+<td>Create a Grid Graphical Object</td></tr>
+<tr><td width="25%"><a href="grobWidth.html">grobAscent</a></td>
+<td>Create a Unit Describing the Width of a Grob</td></tr>
+<tr><td width="25%"><a href="grobWidth.html">grobDescent</a></td>
+<td>Create a Unit Describing the Width of a Grob</td></tr>
+<tr><td width="25%"><a href="grobWidth.html">grobHeight</a></td>
+<td>Create a Unit Describing the Width of a Grob</td></tr>
+<tr><td width="25%"><a href="grobName.html">grobName</a></td>
+<td>Generate a Name for a Grob</td></tr>
+<tr><td width="25%"><a href="grid.ls.html">grobPathListing</a></td>
+<td>List the names of grobs or viewports</td></tr>
+<tr><td width="25%"><a href="grid.grob.html">grobTree</a></td>
+<td>Create a Grid Graphical Object</td></tr>
+<tr><td width="25%"><a href="grobWidth.html">grobWidth</a></td>
+<td>Create a Unit Describing the Width of a Grob</td></tr>
+<tr><td width="25%"><a href="grobX.html">grobX</a></td>
+<td>Create a Unit Describing a Grob Boundary Location</td></tr>
+<tr><td width="25%"><a href="grobX.html">grobY</a></td>
+<td>Create a Unit Describing a Grob Boundary Location</td></tr>
+<tr><td width="25%"><a href="grid.grob.html">gTree</a></td>
+<td>Create a Grid Graphical Object</td></tr>
+</table>
+
+<h2><a name="H">-- H --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="widthDetails.html">heightDetails</a></td>
+<td>Width and Height of a grid grob</td></tr>
+</table>
+
+<h2><a name="I">-- I --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="grid.grob.html">is.grob</a></td>
+<td>Create a Grid Graphical Object</td></tr>
+</table>
+
+<h2><a name="L">-- L --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="grid.lines.html">linesGrob</a></td>
+<td>Draw Lines in a Grid Viewport</td></tr>
+<tr><td width="25%"><a href="grid.move.to.html">lineToGrob</a></td>
+<td>Move or Draw to a Specified Position</td></tr>
+</table>
+
+<h2><a name="M">-- M --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="grid.move.to.html">moveToGrob</a></td>
+<td>Move or Draw to a Specified Position</td></tr>
+</table>
+
+<h2><a name="N">-- N --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="grid.ls.html">nestedListing</a></td>
+<td>List the names of grobs or viewports</td></tr>
+<tr><td width="25%"><a href="grid.null.html">nullGrob</a></td>
+<td>Null Graphical Object</td></tr>
+</table>
+
+<h2><a name="P">-- P --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="grid.pack.html">packGrob</a></td>
+<td>Pack an Object within a Frame</td></tr>
+<tr><td width="25%"><a href="grid.path.html">pathGrob</a></td>
+<td>Draw a Path</td></tr>
+<tr><td width="25%"><a href="grid.ls.html">pathListing</a></td>
+<td>List the names of grobs or viewports</td></tr>
+<tr><td width="25%"><a href="grid.place.html">placeGrob</a></td>
+<td>Place an Object within a Frame</td></tr>
+<tr><td width="25%"><a href="plotViewport.html">plotViewport</a></td>
+<td>Create a Viewport with a Standard Plot Layout</td></tr>
+<tr><td width="25%"><a href="grid.points.html">pointsGrob</a></td>
+<td>Draw Data Symbols</td></tr>
+<tr><td width="25%"><a href="grid.polygon.html">polygonGrob</a></td>
+<td>Draw a Polygon</td></tr>
+<tr><td width="25%"><a href="grid.lines.html">polylineGrob</a></td>
+<td>Draw Lines in a Grid Viewport</td></tr>
+<tr><td width="25%"><a href="pop.viewport.html">pop.viewport</a></td>
+<td>Pop a Viewport off the Grid Viewport Stack</td></tr>
+<tr><td width="25%"><a href="viewports.html">popViewport</a></td>
+<td>Maintaining and Navigating the Grid Viewport Tree</td></tr>
+<tr><td width="25%"><a href="drawDetails.html">postDrawDetails</a></td>
+<td>Customising grid Drawing</td></tr>
+<tr><td width="25%"><a href="drawDetails.html">preDrawDetails</a></td>
+<td>Customising grid Drawing</td></tr>
+<tr><td width="25%"><a href="push.viewport.html">push.viewport</a></td>
+<td>Push a Viewport onto the Grid Viewport Stack</td></tr>
+<tr><td width="25%"><a href="viewports.html">pushViewport</a></td>
+<td>Maintaining and Navigating the Grid Viewport Tree</td></tr>
+</table>
+
+<h2><a name="R">-- R --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="grid.raster.html">rasterGrob</a></td>
+<td>Render a raster object</td></tr>
+<tr><td width="25%"><a href="grid.record.html">recordGrob</a></td>
+<td>Encapsulate calculations and drawing</td></tr>
+<tr><td width="25%"><a href="grid.rect.html">rectGrob</a></td>
+<td>Draw rectangles</td></tr>
+<tr><td width="25%"><a href="grid.remove.html">removeGrob</a></td>
+<td>Remove a Grid Graphical Object</td></tr>
+<tr><td width="25%"><a href="grid.roundrect.html">roundrect</a></td>
+<td>Draw a rectangle with rounded corners</td></tr>
+<tr><td width="25%"><a href="grid.roundrect.html">roundrectGrob</a></td>
+<td>Draw a rectangle with rounded corners</td></tr>
+</table>
+
+<h2><a name="S">-- S --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="viewports.html">seekViewport</a></td>
+<td>Maintaining and Navigating the Grid Viewport Tree</td></tr>
+<tr><td width="25%"><a href="grid.segments.html">segmentsGrob</a></td>
+<td>Draw Line Segments</td></tr>
+<tr><td width="25%"><a href="grid.add.html">setChildren</a></td>
+<td>Add a Grid Graphical Object</td></tr>
+<tr><td width="25%"><a href="grid.set.html">setGrob</a></td>
+<td>Set a Grid Graphical Object</td></tr>
+<tr><td width="25%"><a href="showGrob.html">showGrob</a></td>
+<td>Label grid grobs.</td></tr>
+<tr><td width="25%"><a href="showViewport.html">showViewport</a></td>
+<td>Display grid viewports.</td></tr>
+<tr><td width="25%"><a href="stringWidth.html">stringAscent</a></td>
+<td>Create a Unit Describing the Width and Height of a String or Math Expression</td></tr>
+<tr><td width="25%"><a href="stringWidth.html">stringDescent</a></td>
+<td>Create a Unit Describing the Width and Height of a String or Math Expression</td></tr>
+<tr><td width="25%"><a href="stringWidth.html">stringHeight</a></td>
+<td>Create a Unit Describing the Width and Height of a String or Math Expression</td></tr>
+<tr><td width="25%"><a href="stringWidth.html">stringWidth</a></td>
+<td>Create a Unit Describing the Width and Height of a String or Math Expression</td></tr>
+</table>
+
+<h2><a name="T">-- T --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="grid.text.html">textGrob</a></td>
+<td>Draw Text</td></tr>
+</table>
+
+<h2><a name="U">-- U --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="unit.html">unit</a></td>
+<td>Function to Create a Unit Object</td></tr>
+<tr><td width="25%"><a href="unit.c.html">unit.c</a></td>
+<td>Combine Unit Objects</td></tr>
+<tr><td width="25%"><a href="unit.length.html">unit.length</a></td>
+<td>Length of a Unit Object</td></tr>
+<tr><td width="25%"><a href="unit.pmin.html">unit.pmax</a></td>
+<td>Parallel Unit Minima and Maxima</td></tr>
+<tr><td width="25%"><a href="unit.pmin.html">unit.pmin</a></td>
+<td>Parallel Unit Minima and Maxima</td></tr>
+<tr><td width="25%"><a href="unit.rep.html">unit.rep</a></td>
+<td>Replicate Elements of Unit Objects</td></tr>
+<tr><td width="25%"><a href="viewports.html">upViewport</a></td>
+<td>Maintaining and Navigating the Grid Viewport Tree</td></tr>
+</table>
+
+<h2><a name="V">-- V --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="valid.just.html">valid.just</a></td>
+<td>Validate a Justification</td></tr>
+<tr><td width="25%"><a href="validDetails.html">validDetails</a></td>
+<td>Customising grid grob Validation</td></tr>
+<tr><td width="25%"><a href="viewport.html">viewport</a></td>
+<td>Create a Grid Viewport</td></tr>
+<tr><td width="25%"><a href="viewport.html">vpList</a></td>
+<td>Create a Grid Viewport</td></tr>
+<tr><td width="25%"><a href="vpPath.html">vpPath</a></td>
+<td>Concatenate Viewport Names</td></tr>
+<tr><td width="25%"><a href="viewport.html">vpStack</a></td>
+<td>Create a Grid Viewport</td></tr>
+<tr><td width="25%"><a href="viewport.html">vpTree</a></td>
+<td>Create a Grid Viewport</td></tr>
+</table>
+
+<h2><a name="W">-- W --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="widthDetails.html">widthDetails</a></td>
+<td>Width and Height of a grid grob</td></tr>
+</table>
+
+<h2><a name="X">-- X --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="grid.xaxis.html">xaxisGrob</a></td>
+<td>Draw an X-Axis</td></tr>
+<tr><td width="25%"><a href="xDetails.html">xDetails</a></td>
+<td>Boundary of a grid grob</td></tr>
+<tr><td width="25%"><a href="grid.xspline.html">xsplineGrob</a></td>
+<td>Draw an Xspline</td></tr>
+<tr><td width="25%"><a href="xsplinePoints.html">xsplinePoints</a></td>
+<td>Return the points that would be used to draw an Xspline (or a Bezier curve).</td></tr>
+</table>
+
+<h2><a name="Y">-- Y --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="grid.yaxis.html">yaxisGrob</a></td>
+<td>Draw a Y-Axis</td></tr>
+<tr><td width="25%"><a href="xDetails.html">yDetails</a></td>
+<td>Boundary of a grid grob</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/grid/html/R.css b/win32/deps/library/grid/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/grid/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/grid/libs/i386/grid.dll b/win32/deps/library/grid/libs/i386/grid.dll
new file mode 100644
index 0000000..f498e0a
Binary files /dev/null and b/win32/deps/library/grid/libs/i386/grid.dll differ
diff --git a/win32/deps/library/grid/po/da/LC_MESSAGES/R-grid.mo b/win32/deps/library/grid/po/da/LC_MESSAGES/R-grid.mo
new file mode 100644
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diff --git a/win32/deps/library/grid/tests/bugs.R b/win32/deps/library/grid/tests/bugs.R
new file mode 100644
index 0000000..d491c63
--- /dev/null
+++ b/win32/deps/library/grid/tests/bugs.R
@@ -0,0 +1,30 @@
+library(grid)
+
+# Physical units in viewport of height 0
+pushViewport(viewport(h=0))
+stopifnot(is.finite(convertHeight(unit(72, "bigpts"), "inches")))
+popViewport()
+
+# The gpar font settings for a grob should affect the grob itself
+stopifnot(round(convertHeight(grobHeight(rectGrob(height=unit(1, "lines"),
+ gp=gpar(lineheight=2))),
+ "inches", valueOnly=TRUE) -
+ convertHeight(grobHeight(rectGrob(height=unit(1, "lines"),
+ vp=viewport(
+ gp=gpar(lineheight=2)))),
+ "inches", valueOnly=TRUE),
+ digits=5) == 0)
+
+# Calculation of size of packed grob with gp which is non-empty
+gf1 <- frameGrob(gp=gpar(fontsize=20))
+gf1 <- packGrob(gf1, textGrob("howdy"))
+gf1 <- packGrob(gf1, rectGrob(), col=1, row=1)
+gf2 <- frameGrob()
+gf2 <- packGrob(gf2, gf1)
+gf2 <- packGrob(gf2, rectGrob(gp=gpar(col="red")), col=1, row=1)
+stopifnot(round(convertWidth(grobWidth(gf1),
+ "inches", valueOnly=TRUE) -
+ convertWidth(grobWidth(gf2),
+ "inches", valueOnly=TRUE),
+ digits=5) == 0)
+
diff --git a/win32/deps/library/grid/tests/reg.R b/win32/deps/library/grid/tests/reg.R
new file mode 100644
index 0000000..51ee57f
--- /dev/null
+++ b/win32/deps/library/grid/tests/reg.R
@@ -0,0 +1,433 @@
+library(grid)
+
+# Unit conversions
+stopifnot(round(convertX(unit(1, "inches"), "inches", valueOnly=TRUE) - 1,
+ digits=5) == 0)
+stopifnot(round(convertX(unit(2.54, "cm"), "inches", valueOnly=TRUE) - 1,
+ digits=5) == 0)
+stopifnot(round(convertX(unit(25.4, "mm"), "inches", valueOnly=TRUE) - 1,
+ digits=5) == 0)
+stopifnot(round(convertX(unit(72.27, "points"), "inches", valueOnly=TRUE) - 1,
+ digits=5) == 0)
+stopifnot(round(convertX(unit(1/12*72.27, "picas"), "inches",
+ valueOnly=TRUE) - 1, digits=5) == 0)
+stopifnot(round(convertX(unit(72, "bigpts"), "inches", valueOnly=TRUE) - 1,
+ digits=5) == 0)
+stopifnot(round(convertX(unit(1157/1238*72.27, "dida"), "inches",
+ valueOnly=TRUE) - 1, digits=5) == 0)
+stopifnot(round(convertX(unit(1/12*1157/1238*72.27, "cicero"), "inches",
+ valueOnly=TRUE) - 1, digits=5) == 0)
+stopifnot(round(convertX(unit(65536*72.27, "scaledpts"), "inches",
+ valueOnly=TRUE) - 1, digits=5) == 0)
+stopifnot(round(convertX(unit(1/2.54, "inches"), "cm", valueOnly=TRUE) - 1,
+ digits=5) == 0)
+stopifnot(round(convertX(unit(1/25.4, "inches"), "mm", valueOnly=TRUE) - 1,
+ digits=5) == 0)
+stopifnot(round(convertX(unit(1/72.27, "inches"), "points",
+ valueOnly=TRUE) - 1, digits=5) == 0)
+stopifnot(round(convertX(unit(1/(1/12*72.27), "inches"), "picas",
+ valueOnly=TRUE) - 1, digits=5) == 0)
+stopifnot(round(convertX(unit(1/72, "inches"), "bigpts", valueOnly=TRUE) - 1,
+ digits=5) == 0)
+stopifnot(round(convertX(unit(1/(1157/1238*72.27), "inches"), "dida",
+ valueOnly=TRUE) - 1, digits=5) == 0)
+stopifnot(round(convertX(unit(1/(1/12*1157/1238*72.27), "inches"), "cicero",
+ valueOnly=TRUE) - 1, digits=5) == 0)
+stopifnot(round(convertX(unit(1/(65536*72.27), "inches"), "scaledpts",
+ valueOnly=TRUE) - 1, digits=5) == 0)
+
+pushViewport(viewport(width=unit(1, "inches"),
+ height=unit(2, "inches"),
+ xscale=c(0, 1),
+ yscale=c(1, 3)))
+ ## Location versus dimension
+stopifnot(round(convertY(unit(2, "native"), "inches", valueOnly=TRUE) -
+ 1, digits=5) == 0)
+stopifnot(round(convertHeight(unit(2, "native"), "inches", valueOnly=TRUE) -
+ 2, digits=5) == 0)
+ ## From "x" to "y" (the conversion is via "inches")
+stopifnot(round(convertUnit(unit(1, "native"), "native",
+ axisFrom="x", axisTo="y", valueOnly=TRUE) -
+ 2, digits=5) == 0)
+ ## Convert several values at once
+stopifnot(all(round(convertX(unit(c(0.5, 2.54), c("npc", "cm")),
+ c("inches", "native"), valueOnly=TRUE) -
+ c(0.5, 1), digits=5) == 0))
+popViewport()
+
+# packing a frame inside a frame
+fg <- frameGrob()
+fg <- packGrob(fg, textGrob("Hi there"))
+
+fg2 <- frameGrob()
+fg2 <- packGrob(fg2, fg)
+fg2 <- packGrob(fg2, rectGrob(), side="bottom")
+fg2 <- packGrob(fg2, rectGrob(height=unit(1, "inches")), side="top")
+
+stopifnot(convertHeight(fg2$framevp$layout$heights, "inches",
+ valueOnly=TRUE)[2] < 1)
+
+# Regression tests for:
+
+# A: grob[X|Y|Width|Height]
+
+# B: grid.[circle|lines|segments|rect|polygon|text|xspline|points]
+
+# C: at angles seq(0, 360, 45)[-1]
+
+# D: single AND multiple output
+
+# In each casem, set up a situation where the answer is (easily) known,
+# then compare the numeric answer
+
+test <- function(x, y) {
+ on.exit(cat(paste("x =", x, " ; y =", y, "\n")))
+ stopifnot(isTRUE(all.equal(x, y)))
+}
+
+testX <- function(x1, x2) {
+ test(convertX(x1, "inches", valueOnly=TRUE),
+ convertX(x2, "inches", valueOnly=TRUE))
+}
+
+testY <- function(y1, y2) {
+ test(convertY(y1, "inches", valueOnly=TRUE),
+ convertY(y2, "inches", valueOnly=TRUE))
+}
+
+testWidth <- function(w1, w2) {
+ test(convertWidth(w1, "inches", valueOnly=TRUE),
+ convertWidth(w2, "inches", valueOnly=TRUE))
+}
+
+testHeight <- function(h1, h2) {
+ test(convertHeight(h1, "inches", valueOnly=TRUE),
+ convertHeight(h2, "inches", valueOnly=TRUE))
+}
+
+########
+# CIRCLE
+########
+# A = X; B = circle; C = ALL; D = BOTH
+for (theta in seq(0, 360, 45)[-1]) {
+ testX(grobX(circleGrob(r=unit(.5, "inches")), theta),
+ unit(.5, "npc") + cos(theta/180*pi)*unit(.5, "inches"))
+ # Bounding box is 1" by 1"
+ testX(grobX(circleGrob(x=unit(.5, "npc") + unit(c(-.25, .25), "inches"),
+ y=unit(.5, "npc") + unit(c(-.25, .25), "inches"),
+ r=unit(.25, "inches")),
+ theta),
+ switch(as.character(theta),
+ "360"=, "315"=,
+ "45"=unit(.5, "npc") + unit(.5, "inches"),
+ "180"=, "225"=,
+ "135"=unit(.5, "npc") - unit(.5, "inches"),
+ "90"=,
+ "270"=unit(.5, "npc")))
+}
+
+# A = Y; B = circle; C = ALL; D = BOTH
+for (theta in seq(0, 360, 45)[-1]) {
+ testY(grobY(circleGrob(r=unit(.5, "inches")), theta),
+ unit(.5, "npc") + sin(theta/180*pi)*unit(.5, "inches"))
+ # Bounding box is 1" by 1"
+ testY(grobY(circleGrob(x=unit(.5, "npc") + unit(c(-.25, .25), "inches"),
+ y=unit(.5, "npc") + unit(c(-.25, .25), "inches"),
+ r=unit(.25, "inches")),
+ theta),
+ switch(as.character(theta),
+ "90"=, "135"=,
+ "45"=unit(.5, "npc") + unit(.5, "inches"),
+ "270"=, "315"=,
+ "225"=unit(.5, "npc") - unit(.5, "inches"),
+ "180"=,
+ "360"=unit(.5, "npc")))
+}
+
+# A = Width; B = circle; C = ALL; D = BOTH
+testWidth(grobWidth(circleGrob(r=unit(.5, "inches"))),
+ unit(1, "inches"))
+testWidth(grobWidth(circleGrob(x=unit(.5, "npc") +
+ unit(c(-.25, .25), "inches"),
+ y=unit(.5, "npc") +
+ unit(c(-.25, .25), "inches"),
+ r=unit(.25, "inches"))),
+ unit(1, "inches"))
+
+# A = Height; B = circle; C = ALL; D = BOTH
+testHeight(grobHeight(circleGrob(r=unit(.5, "inches"))),
+ unit(1, "inches"))
+testHeight(grobHeight(circleGrob(x=unit(.5, "npc") +
+ unit(c(-.25, .25), "inches"),
+ y=unit(.5, "npc") +
+ unit(c(-.25, .25), "inches"),
+ r=unit(.25, "inches"))),
+ unit(1, "inches"))
+
+########
+# RECT
+########
+# A = X; B = rect; C = ALL; D = BOTH
+for (theta in seq(0, 360, 45)[-1]) {
+ testX(grobX(rectGrob(width=unit(1, "inches"),
+ height=unit(1, "inches")), theta),
+ switch(as.character(theta),
+ "360"=, "315"=,
+ "45"=unit(.5, "npc") + unit(.5, "inches"),
+ "180"=, "225"=,
+ "135"=unit(.5, "npc") - unit(.5, "inches"),
+ "90"=,
+ "270"=unit(.5, "npc")))
+ # Bounding box is 1" by 1"
+ testX(grobX(rectGrob(x=unit(.5, "npc") + unit(c(-.25, .25), "inches"),
+ y=unit(.5, "npc") + unit(c(-.25, .25), "inches"),
+ width=unit(.5, "inches"),
+ height=unit(.5, "inches")),
+ theta),
+ switch(as.character(theta),
+ "360"=, "315"=,
+ "45"=unit(.5, "npc") + unit(.5, "inches"),
+ "180"=, "225"=,
+ "135"=unit(.5, "npc") - unit(.5, "inches"),
+ "90"=,
+ "270"=unit(.5, "npc")))
+}
+
+# A = Y; B = rect; C = ALL; D = BOTH
+for (theta in seq(0, 360, 45)[-1]) {
+ testY(grobY(rectGrob(width=unit(1, "inches"),
+ height=unit(1, "inches")), theta),
+ switch(as.character(theta),
+ "90"=, "135"=,
+ "45"=unit(.5, "npc") + unit(.5, "inches"),
+ "270"=, "315"=,
+ "225"=unit(.5, "npc") - unit(.5, "inches"),
+ "180"=,
+ "360"=unit(.5, "npc")))
+ # Bounding box is 1" by 1"
+ testY(grobY(rectGrob(x=unit(.5, "npc") + unit(c(-.25, .25), "inches"),
+ y=unit(.5, "npc") + unit(c(-.25, .25), "inches"),
+ width=unit(.5, "inches"),
+ height=unit(.5, "inches")),
+ theta),
+ switch(as.character(theta),
+ "90"=, "135"=,
+ "45"=unit(.5, "npc") + unit(.5, "inches"),
+ "270"=, "315"=,
+ "225"=unit(.5, "npc") - unit(.5, "inches"),
+ "180"=,
+ "360"=unit(.5, "npc")))
+}
+
+# A = Width; B = rect; C = ALL; D = BOTH
+testWidth(grobWidth(rectGrob(width=unit(1, "inches"),
+ height=unit(1, "inches"))),
+ unit(1, "inches"))
+testWidth(grobWidth(rectGrob(x=unit(.5, "npc") +
+ unit(c(-.25, .25), "inches"),
+ y=unit(.5, "npc") +
+ unit(c(-.25, .25), "inches"),
+ width=unit(.5, "inches"),
+ height=unit(.5, "inches"))),
+ unit(1, "inches"))
+
+# A = Height; B = rect; C = ALL; D = BOTH
+testHeight(grobHeight(rectGrob(width=unit(1, "inches"),
+ height=unit(1, "inches"))),
+ unit(1, "inches"))
+testHeight(grobHeight(rectGrob(x=unit(.5, "npc") +
+ unit(c(-.25, .25), "inches"),
+ y=unit(.5, "npc") +
+ unit(c(-.25, .25), "inches"),
+ width=unit(.5, "inches"),
+ height=unit(.5, "inches"))),
+ unit(1, "inches"))
+
+########
+# polygon
+# Four locations in a diamond
+########
+# A = X; B = polygon; C = ALL; D = BOTH
+for (theta in seq(0, 360, 45)[-1]) {
+ testX(grobX(polygonGrob(x=unit(.5, "npc") +
+ unit(c(-.5, 0, .5, 0), "inches"),
+ y=unit(.5, "npc") +
+ unit(c(0, -.5, 0, .5), "inches")),
+ theta),
+ switch(as.character(theta),
+ "45"=,
+ "315"=unit(.5, "npc") + unit(.25, "inches"),
+ "90"=,
+ "270"=unit(.5, "npc"),
+ "135"=,
+ "225"=unit(.5, "npc") - unit(.25, "inches"),
+ "180"=unit(.5, "npc") - unit(.5, "inches"),
+ "360"=unit(.5, "npc") + unit(.5, "inches")))
+ # NOTE: for polygons, even if there are multiple polygons,
+ # we still produce edge of hull for ALL points
+ testX(grobX(polygonGrob(x=unit(.5, "npc") +
+ unit(c(-.5, -.25, 0, -.25,
+ 0, .25, .5, .25), "inches"),
+ y=unit(.5, "npc") +
+ unit(c(-.25, -.5, -.25, 0,
+ .25, 0, .25, .5), "inches"),
+ id=rep(1:2, each=4)),
+ theta),
+ switch(as.character(theta),
+ "45"=unit(.5, "npc") + unit(.375, "inches"),
+ "90"=unit(.5, "npc"),
+ "135"=unit(.5, "npc") - unit(.125, "inches"),
+ "180"=unit(.5, "npc") - unit(.25, "inches"),
+ "225"=unit(.5, "npc") - unit(.375, "inches"),
+ "270"=unit(.5, "npc"),
+ "315"=unit(.5, "npc") + unit(.125, "inches"),
+ "360"=unit(.5, "npc") + unit(.25, "inches")))
+}
+
+# A = Y; B = polygon; C = ALL; D = BOTH
+for (theta in seq(0, 360, 45)[-1]) {
+ testY(grobY(polygonGrob(x=unit(.5, "npc") +
+ unit(c(-.5, 0, .5, 0), "inches"),
+ y=unit(.5, "npc") +
+ unit(c(0, -.5, 0, .5), "inches")),
+ theta),
+ switch(as.character(theta),
+ "45"=,
+ "135"=unit(.5, "npc") + unit(.25, "inches"),
+ "90"=unit(.5, "npc") + unit(.5, "inches"),
+ "180"=,
+ "360"=unit(.5, "npc"),
+ "225"=,
+ "315"=unit(.5, "npc") - unit(.25, "inches"),
+ "270"=unit(.5, "npc") - unit(.5, "inches")))
+ # NOTE: for polygons, even if there are multiple polygons,
+ # we still produce edge of hull for ALL points
+ testY(grobY(polygonGrob(x=unit(.5, "npc") +
+ unit(c(-.5, -.25, 0, -.25,
+ 0, .25, .5, .25), "inches"),
+ y=unit(.5, "npc") +
+ unit(c(-.25, -.5, -.25, 0,
+ .25, 0, .25, .5), "inches"),
+ id=rep(1:2, each=4)),
+ theta),
+ switch(as.character(theta),
+ "45"=unit(.5, "npc") + unit(.375, "inches"),
+ "90"=unit(.5, "npc") + unit(.25, "inches"),
+ "135"=unit(.5, "npc") + unit(.125, "inches"),
+ "180"=unit(.5, "npc"),
+ "225"=unit(.5, "npc") - unit(.375, "inches"),
+ "270"=unit(.5, "npc") - unit(.25, "inches"),
+ "315"=unit(.5, "npc") - unit(.125, "inches"),
+ "360"=unit(.5, "npc")))
+}
+
+# A = Width; B = polygon; C = ALL; D = BOTH
+testWidth(grobWidth(polygonGrob(x=unit(.5, "npc") +
+ unit(c(-.5, 0, .5, 0), "inches"),
+ y=unit(.5, "npc") +
+ unit(c(0, -.5, 0, .5), "inches"))),
+ unit(1, "inches"))
+testWidth(grobWidth(polygonGrob(x=unit(.5, "npc") +
+ unit(c(-.5, -.25, 0, -.25,
+ 0, .25, .5, .25), "inches"),
+ y=unit(.5, "npc") +
+ unit(c(-.25, -.5, -.25, 0,
+ .25, 0, .25, .5), "inches"),
+ id=rep(1:2, each=4))),
+ unit(1, "inches"))
+
+# A = Height; B = polygon; C = ALL; D = BOTH
+testHeight(grobHeight(polygonGrob(x=unit(.5, "npc") +
+ unit(c(-.5, 0, .5, 0), "inches"),
+ y=unit(.5, "npc") +
+ unit(c(0, -.5, 0, .5), "inches"))),
+ unit(1, "inches"))
+testHeight(grobHeight(polygonGrob(x=unit(.5, "npc") +
+ unit(c(-.5, -.25, 0, -.25,
+ 0, .25, .5, .25), "inches"),
+ y=unit(.5, "npc") +
+ unit(c(-.25, -.5, -.25, 0,
+ .25, 0, .25, .5), "inches"),
+ id=rep(1:2, each=4))),
+ unit(1, "inches"))
+
+########
+# TEXT
+########
+# A = X; B = text; C = ALL; D = BOTH
+str <- "testcase"
+strw <- stringWidth(str)
+strh <- stringHeight(str)
+for (theta in seq(0, 360, 45)[-1]) {
+ testX(grobX(textGrob(str), theta),
+ switch(as.character(theta),
+ "360"=unit(.5, "npc") + 0.5*strw,
+ "135"=,
+ "45"=unit(.5, "npc") + 1/tan(theta/180*pi)*0.5*strh,
+ "315"=,
+ "225"=unit(.5, "npc") - 1/tan(theta/180*pi)*0.5*strh,
+ "180"=unit(.5, "npc") - 0.5*strw,
+ "90"=,
+ "270"=unit(.5, "npc")))
+ # Bounding box is 1" by 1"
+ testX(grobX(textGrob(str,
+ x=unit(.5, "npc") + unit(c(-.5, .5), "inches"),
+ y=unit(.5, "npc") + unit(c(-.5, .5), "inches"),
+ hjust=c(0, 1), vjust=c(0, 1)),
+ theta),
+ switch(as.character(theta),
+ "360"=, "315"=,
+ "45"=unit(.5, "npc") + unit(.5, "inches"),
+ "180"=, "225"=,
+ "135"=unit(.5, "npc") - unit(.5, "inches"),
+ "90"=,
+ "270"=unit(.5, "npc")))
+}
+
+# A = Y; B = text; C = ALL; D = BOTH
+for (theta in seq(0, 360, 45)[-1]) {
+ testY(grobY(textGrob(str), theta),
+ switch(as.character(theta),
+ "90"=, "135"=,
+ "45"=unit(.5, "npc") + 0.5*strh,
+ "270"=, "315"=,
+ "225"=unit(.5, "npc") - 0.5*strh,
+ "180"=,
+ "360"=unit(.5, "npc")))
+ # Bounding box is 1" by 1"
+ testY(grobY(textGrob(str,
+ x=unit(.5, "npc") + unit(c(-.5, .5), "inches"),
+ y=unit(.5, "npc") + unit(c(-.5, .5), "inches"),
+ hjust=c(0, 1), vjust=c(0, 1)),
+ theta),
+ switch(as.character(theta),
+ "90"=, "135"=,
+ "45"=unit(.5, "npc") + unit(.5, "inches"),
+ "270"=, "315"=,
+ "225"=unit(.5, "npc") - unit(.5, "inches"),
+ "180"=,
+ "360"=unit(.5, "npc")))
+}
+
+# A = Width; B = text; C = ALL; D = BOTH
+testWidth(grobWidth(textGrob(str)),
+ strw)
+testWidth(grobWidth(textGrob(str,
+ x=unit(.5, "npc") + unit(c(-.5, .5), "inches"),
+ y=unit(.5, "npc") + unit(c(-.5, .5), "inches"),
+ hjust=c(0, 1), vjust=c(0, 1))),
+ unit(1, "inches"))
+
+# A = Height; B = text; C = ALL; D = BOTH
+testHeight(grobHeight(textGrob(str)),
+ strh)
+testHeight(grobHeight(textGrob(str,
+ x=unit(.5, "npc") + unit(c(-.5, .5), "inches"),
+ y=unit(.5, "npc") + unit(c(-.5, .5), "inches"),
+ hjust=c(0, 1), vjust=c(0, 1))),
+ unit(1, "inches"))
+
+# Determining unit lengths
+stopifnot(length(unit.c(unit(1, "npc") + unit(1, "cm"), unit(2, "cm"))) == 2)
+stopifnot(length(unit.c(unit(1, "npc") + unit(1, "cm"), unit(2:4, "cm"))) == 4)
+stopifnot(length(unit.c(unit(1:3, "npc") + unit(1, "cm"), unit(2:4, "cm"))) == 6)
diff --git a/win32/deps/library/grid/tests/testls.R b/win32/deps/library/grid/tests/testls.R
new file mode 100644
index 0000000..f651ef4
--- /dev/null
+++ b/win32/deps/library/grid/tests/testls.R
@@ -0,0 +1,158 @@
+library(grid)
+
+# Test hole in DL (deleted grob)
+grid.lines(name="foo")
+grid.lines(x=1:0, name="foo2")
+grid.ls()
+grid.remove("foo")
+grid.ls()
+# New blank page
+grid.newpage()
+
+
+#######
+# GROBS
+#######
+# Plain grob
+grid.ls(grob(name="g1"))
+# gList
+grid.ls(gList(grob(name="gl1"), grob(name="gl2")))
+# gTree
+grid.ls(gTree(children=gList(grob(name="child")),
+ name="parent"))
+grid.ls(gTree(children=gList(grob(name="child1"), grob(name="child1")),
+ name="parent"))
+
+###########
+# VIEWPORTS
+###########
+# Plain viewport
+grid.ls(viewport(name="vp1"),
+ view=TRUE)
+# vpList
+grid.ls(vpList(viewport(name="vpl1")),
+ view=TRUE)
+grid.ls(vpList(viewport(name="vpl1"), viewport(name="vpl2")),
+ view=TRUE)
+grid.ls(vpList(viewport(name="vpl1"), viewport(name="vpl2"),
+ viewport(name="vpl3")),
+ view=TRUE)
+# vpStack
+grid.ls(vpStack(viewport(name="vps1"), viewport(name="vps2")),
+ view=TRUE)
+grid.ls(vpStack(viewport(name="vps1"), viewport(name="vps2"),
+ viewport(name="vps3")),
+ view=TRUE)
+# vpTrees
+grid.ls(vpTree(viewport(name="parentvp"), vpList(viewport(name="childvp"))),
+ view=TRUE)
+grid.ls(vpTree(viewport(name="parentvp"),
+ vpList(viewport(name="cvp1"), viewport(name="cvp2"))),
+ view=TRUE)
+# vpPaths
+grid.ls(vpPath("A"),
+ view=TRUE)
+grid.ls(vpPath("A", "B"),
+ view=TRUE)
+grid.ls(vpPath("A", "B", "C"),
+ view=TRUE)
+
+##########
+# MIXTURES
+##########
+# grob with vp viewport
+g1 <- grob(vp=viewport(name="gvp"), name="g1")
+grid.ls(g1, view=TRUE, full=TRUE)
+grid.ls(g1, view=TRUE, full=TRUE, grob=FALSE)
+# grob with vp vpList
+grid.ls(grob(vp=vpList(viewport(name="vpl")), name="g1"),
+ view=TRUE, full=TRUE)
+grid.ls(grob(vp=vpList(viewport(name="vpl1"), viewport(name="vpl2")),
+ name="g1"),
+ view=TRUE, full=TRUE)
+# grob with vp vpStack
+grid.ls(grob(vp=vpStack(viewport(name="vps1"), viewport(name="vps2")),
+ name="g1"),
+ view=TRUE, full=TRUE)
+grid.ls(grob(vp=vpStack(viewport(name="vps1"), viewport(name="vps2"),
+ viewport(name="vps3")),
+ name="g1"),
+ view=TRUE)
+# grob with vp vpTree
+grid.ls(grob(vp=vpTree(viewport(name="parentvp"),
+ vpList(viewport(name="cvp"))),
+ name="g1"),
+ view=TRUE, full=TRUE)
+grid.ls(grob(vp=vpTree(viewport(name="parentvp"),
+ vpList(viewport(name="cvp1"), viewport(name="cvp2"))),
+ name="g1"),
+ view=TRUE, full=TRUE)
+# gTree with vp viewport
+# and child grob with vp viewport
+grid.ls(gTree(children=gList(grob(vp=viewport(name="childvp"), name="cg1"),
+ grob(name="cg2")),
+ name="parent",
+ vp=viewport(name="parentvp")),
+ view=TRUE)
+# gTree with childrenvp viewport
+grid.ls(gTree(childrenvp=viewport(name="vp"), name="gtree"),
+ view=TRUE, full=TRUE)
+grid.ls(gTree(childrenvp=viewport(name="vp"), name="gtree"),
+ view=TRUE, full=TRUE, grob=FALSE)
+grid.ls(gTree(children=gList(grob(name="child")),
+ name="parent",
+ childrenvp=viewport(name="vp")),
+ view=TRUE, full=TRUE)
+grid.ls(gTree(children=gList(grob(name="child1"), grob(name="child2")),
+ name="parent",
+ childrenvp=viewport(name="vp")),
+ view=TRUE, full=TRUE)
+grid.ls(gTree(children=gList(grob(name="child")),
+ childrenvp=viewport(name="vp"),
+ name="parent"),
+ view=TRUE, full=TRUE)
+grid.ls(gTree(children=gList(grob(name="child1"), grob(name="child2")),
+ name="parent",
+ childrenvp=viewport(name="vp")),
+ view=TRUE, full=TRUE, grob=FALSE)
+# gTree with childrenvp vpTree
+grid.ls(gTree(childrenvp=vpTree(parent=viewport(name="vp1"),
+ children=vpList(viewport(name="vp2"))),
+ name="gtree"),
+ view=TRUE, full=TRUE)
+grid.ls(gTree(children=gList(grob(name="child")),
+ name="parent",
+ childrenvp=vpTree(parent=viewport(name="vp1"),
+ children=vpList(viewport(name="vp2")))),
+ view=TRUE, full=TRUE)
+# gTree with childrenvp vpTree
+# and child grob with vp vpPath
+# A gTree, called "parent", with childrenvp vpTree (vp2 within vp1)
+# and child grob, called "child", with vp vpPath (down to vp2)
+sampleGTree <- gTree(name="parent",
+ children=gList(grob(name="child", vp="vp1::vp2")),
+ childrenvp=vpTree(parent=viewport(name="vp1"),
+ children=vpList(viewport(name="vp2"))))
+grid.ls(sampleGTree)
+# Show viewports too
+grid.ls(sampleGTree, view=TRUE)
+# Only show viewports
+grid.ls(sampleGTree, view=TRUE, grob=FALSE)
+# Alternate displays
+# nested listing, custom indent
+grid.ls(sampleGTree, view=TRUE, print=nestedListing, gindent="--")
+# path listing
+grid.ls(sampleGTree, view=TRUE, print=pathListing)
+# path listing, without grobs aligned
+grid.ls(sampleGTree, view=TRUE, print=pathListing, gAlign=FALSE)
+# grob path listing
+grid.ls(sampleGTree, view=TRUE, print=grobPathListing)
+# path listing, grobs only
+grid.ls(sampleGTree, print=pathListing)
+# path listing, viewports only
+grid.ls(sampleGTree, view=TRUE, grob=FALSE, print=pathListing)
+# raw flat listing
+str(grid.ls(sampleGTree, view=TRUE, print=FALSE))
+
+
+
diff --git a/win32/deps/library/grid/tests/testls.Rout.save b/win32/deps/library/grid/tests/testls.Rout.save
new file mode 100644
index 0000000..df8e0ed
--- /dev/null
+++ b/win32/deps/library/grid/tests/testls.Rout.save
@@ -0,0 +1,340 @@
+
+R version 2.8.0 Under development (unstable) (2008-07-28 r46138)
+Copyright (C) 2008 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(grid)
+>
+> # Test hole in DL (deleted grob)
+> grid.lines(name="foo")
+> grid.lines(x=1:0, name="foo2")
+> grid.ls()
+foo
+foo2
+> grid.remove("foo")
+> grid.ls()
+foo2
+> # New blank page
+> grid.newpage()
+>
+>
+> #######
+> # GROBS
+> #######
+> # Plain grob
+> grid.ls(grob(name="g1"))
+g1
+> # gList
+> grid.ls(gList(grob(name="gl1"), grob(name="gl2")))
+gl1
+gl2
+> # gTree
+> grid.ls(gTree(children=gList(grob(name="child")),
++ name="parent"))
+parent
+ child
+> grid.ls(gTree(children=gList(grob(name="child1"), grob(name="child1")),
++ name="parent"))
+parent
+ child1
+ child1
+>
+> ###########
+> # VIEWPORTS
+> ###########
+> # Plain viewport
+> grid.ls(viewport(name="vp1"),
++ view=TRUE)
+vp1
+> # vpList
+> grid.ls(vpList(viewport(name="vpl1")),
++ view=TRUE)
+vpl1
+> grid.ls(vpList(viewport(name="vpl1"), viewport(name="vpl2")),
++ view=TRUE)
+vpl1
+ 1
+vpl2
+> grid.ls(vpList(viewport(name="vpl1"), viewport(name="vpl2"),
++ viewport(name="vpl3")),
++ view=TRUE)
+vpl1
+ 1
+vpl2
+ 1
+vpl3
+> # vpStack
+> grid.ls(vpStack(viewport(name="vps1"), viewport(name="vps2")),
++ view=TRUE)
+vps1
+ vps2
+> grid.ls(vpStack(viewport(name="vps1"), viewport(name="vps2"),
++ viewport(name="vps3")),
++ view=TRUE)
+vps1
+ vps2
+ vps3
+> # vpTrees
+> grid.ls(vpTree(viewport(name="parentvp"), vpList(viewport(name="childvp"))),
++ view=TRUE)
+parentvp
+ childvp
+> grid.ls(vpTree(viewport(name="parentvp"),
++ vpList(viewport(name="cvp1"), viewport(name="cvp2"))),
++ view=TRUE)
+parentvp
+ cvp1
+ 1
+ cvp2
+> # vpPaths
+> grid.ls(vpPath("A"),
++ view=TRUE)
+A
+> grid.ls(vpPath("A", "B"),
++ view=TRUE)
+A
+ B
+> grid.ls(vpPath("A", "B", "C"),
++ view=TRUE)
+A
+ B
+ C
+>
+> ##########
+> # MIXTURES
+> ##########
+> # grob with vp viewport
+> g1 <- grob(vp=viewport(name="gvp"), name="g1")
+> grid.ls(g1, view=TRUE, full=TRUE)
+viewport[gvp]
+ grob[g1]
+ upViewport[1]
+> grid.ls(g1, view=TRUE, full=TRUE, grob=FALSE)
+viewport[gvp]
+ upViewport[1]
+> # grob with vp vpList
+> grid.ls(grob(vp=vpList(viewport(name="vpl")), name="g1"),
++ view=TRUE, full=TRUE)
+viewport[vpl]
+ grob[g1]
+ upViewport[1]
+> grid.ls(grob(vp=vpList(viewport(name="vpl1"), viewport(name="vpl2")),
++ name="g1"),
++ view=TRUE, full=TRUE)
+viewport[vpl1]
+ upViewport[1]
+viewport[vpl2]
+ grob[g1]
+ upViewport[1]
+> # grob with vp vpStack
+> grid.ls(grob(vp=vpStack(viewport(name="vps1"), viewport(name="vps2")),
++ name="g1"),
++ view=TRUE, full=TRUE)
+viewport[vps1]
+ viewport[vps2]
+ grob[g1]
+ upViewport[2]
+> grid.ls(grob(vp=vpStack(viewport(name="vps1"), viewport(name="vps2"),
++ viewport(name="vps3")),
++ name="g1"),
++ view=TRUE)
+vps1
+ vps2
+ vps3
+ g1
+ 3
+> # grob with vp vpTree
+> grid.ls(grob(vp=vpTree(viewport(name="parentvp"),
++ vpList(viewport(name="cvp"))),
++ name="g1"),
++ view=TRUE, full=TRUE)
+viewport[parentvp]
+ viewport[cvp]
+ grob[g1]
+ upViewport[2]
+> grid.ls(grob(vp=vpTree(viewport(name="parentvp"),
++ vpList(viewport(name="cvp1"), viewport(name="cvp2"))),
++ name="g1"),
++ view=TRUE, full=TRUE)
+viewport[parentvp]
+ viewport[cvp1]
+ upViewport[1]
+ viewport[cvp2]
+ grob[g1]
+ upViewport[2]
+> # gTree with vp viewport
+> # and child grob with vp viewport
+> grid.ls(gTree(children=gList(grob(vp=viewport(name="childvp"), name="cg1"),
++ grob(name="cg2")),
++ name="parent",
++ vp=viewport(name="parentvp")),
++ view=TRUE)
+parentvp
+ parent
+ childvp
+ cg1
+ 1
+ cg2
+ 1
+> # gTree with childrenvp viewport
+> grid.ls(gTree(childrenvp=viewport(name="vp"), name="gtree"),
++ view=TRUE, full=TRUE)
+gTree[gtree]
+ viewport[vp]
+ upViewport[1]
+> grid.ls(gTree(childrenvp=viewport(name="vp"), name="gtree"),
++ view=TRUE, full=TRUE, grob=FALSE)
+viewport[vp]
+ upViewport[1]
+> grid.ls(gTree(children=gList(grob(name="child")),
++ name="parent",
++ childrenvp=viewport(name="vp")),
++ view=TRUE, full=TRUE)
+gTree[parent]
+ viewport[vp]
+ upViewport[1]
+ grob[child]
+> grid.ls(gTree(children=gList(grob(name="child1"), grob(name="child2")),
++ name="parent",
++ childrenvp=viewport(name="vp")),
++ view=TRUE, full=TRUE)
+gTree[parent]
+ viewport[vp]
+ upViewport[1]
+ grob[child1]
+ grob[child2]
+> grid.ls(gTree(children=gList(grob(name="child")),
++ childrenvp=viewport(name="vp"),
++ name="parent"),
++ view=TRUE, full=TRUE)
+gTree[parent]
+ viewport[vp]
+ upViewport[1]
+ grob[child]
+> grid.ls(gTree(children=gList(grob(name="child1"), grob(name="child2")),
++ name="parent",
++ childrenvp=viewport(name="vp")),
++ view=TRUE, full=TRUE, grob=FALSE)
+viewport[vp]
+ upViewport[1]
+> # gTree with childrenvp vpTree
+> grid.ls(gTree(childrenvp=vpTree(parent=viewport(name="vp1"),
++ children=vpList(viewport(name="vp2"))),
++ name="gtree"),
++ view=TRUE, full=TRUE)
+gTree[gtree]
+ viewport[vp1]
+ viewport[vp2]
+ upViewport[2]
+> grid.ls(gTree(children=gList(grob(name="child")),
++ name="parent",
++ childrenvp=vpTree(parent=viewport(name="vp1"),
++ children=vpList(viewport(name="vp2")))),
++ view=TRUE, full=TRUE)
+gTree[parent]
+ viewport[vp1]
+ viewport[vp2]
+ upViewport[2]
+ grob[child]
+> # gTree with childrenvp vpTree
+> # and child grob with vp vpPath
+> # A gTree, called "parent", with childrenvp vpTree (vp2 within vp1)
+> # and child grob, called "child", with vp vpPath (down to vp2)
+> sampleGTree <- gTree(name="parent",
++ children=gList(grob(name="child", vp="vp1::vp2")),
++ childrenvp=vpTree(parent=viewport(name="vp1"),
++ children=vpList(viewport(name="vp2"))))
+> grid.ls(sampleGTree)
+parent
+ child
+> # Show viewports too
+> grid.ls(sampleGTree, view=TRUE)
+parent
+ vp1
+ vp2
+ 2
+ vp1
+ vp2
+ child
+ 2
+> # Only show viewports
+> grid.ls(sampleGTree, view=TRUE, grob=FALSE)
+vp1
+ vp2
+ 2
+vp1
+ vp2
+ 2
+> # Alternate displays
+> # nested listing, custom indent
+> grid.ls(sampleGTree, view=TRUE, print=nestedListing, gindent="--")
+parent
+--vp1
+----vp2
+------2
+--vp1
+----vp2
+------child
+------2
+> # path listing
+> grid.ls(sampleGTree, view=TRUE, print=pathListing)
+ | parent
+vp1
+vp1::vp2
+vp1::vp2::2
+vp1
+vp1::vp2
+vp1::vp2 | parent::child
+vp1::vp2::2
+> # path listing, without grobs aligned
+> grid.ls(sampleGTree, view=TRUE, print=pathListing, gAlign=FALSE)
+ | parent
+vp1
+vp1::vp2
+vp1::vp2::2
+vp1
+vp1::vp2
+vp1::vp2 | parent::child
+vp1::vp2::2
+> # grob path listing
+> grid.ls(sampleGTree, view=TRUE, print=grobPathListing)
+ | parent
+vp1::vp2 | parent::child
+> # path listing, grobs only
+> grid.ls(sampleGTree, print=pathListing)
+ | parent
+ | parent::child
+> # path listing, viewports only
+> grid.ls(sampleGTree, view=TRUE, grob=FALSE, print=pathListing)
+vp1
+vp1::vp2
+vp1::vp2::2
+vp1
+vp1::vp2
+vp1::vp2::2
+> # raw flat listing
+> str(grid.ls(sampleGTree, view=TRUE, print=FALSE))
+List of 6
+ $ name : chr [1:8] "parent" "vp1" "vp2" "2" ...
+ $ gDepth : num [1:8] 0 1 1 1 1 1 1 1
+ $ vpDepth: num [1:8] 0 0 1 2 0 1 2 2
+ $ gPath : chr [1:8] "" "parent" "parent" "parent" ...
+ $ vpPath : chr [1:8] "" "" "vp1" "vp1::vp2" ...
+ $ type : chr [1:8] "gTreeListing" "vpTreeListing" "vpListing" "vpUpListing" ...
+ - attr(*, "class")= chr "flatGridListing"
+>
+>
+>
+>
diff --git a/win32/deps/library/grid/tests/units.R b/win32/deps/library/grid/tests/units.R
new file mode 100644
index 0000000..a81cec5
--- /dev/null
+++ b/win32/deps/library/grid/tests/units.R
@@ -0,0 +1,135 @@
+
+library(grid)
+
+unitCheck <- function(u1, u2) {
+ stopifnot(identical(as.character(u1), as.character(u2)))
+}
+
+# Mixture of rep() arguments based on example(rep) examples
+
+# simple tests
+simpleUnit <- unit(1:4, "npc")
+
+unitCheck(rep(simpleUnit, 2),
+ unit(rep(1:4, 2), "npc"))
+unitCheck(rep(simpleUnit, each=2),
+ unit(rep(1:4, each=2), "npc"))
+unitCheck(rep(simpleUnit, c(2, 1, 2, 1)),
+ unit(rep(1:4, c(2, 1, 2, 1)), "npc"))
+unitCheck(rep(simpleUnit, each=2, len=4),
+ unit(rep(1:4, each=2, len=4), "npc"))
+unitCheck(rep(simpleUnit, each=2, len=10),
+ unit(rep(1:4, each=2, len=10), "npc"))
+unitCheck(rep(simpleUnit, each=2, times=3),
+ unit(rep(1:4, each=2, times=3), "npc"))
+
+simpleUnitMixed <- unit(1:4, c("npc", "cm"))
+
+unitCheck(rep(simpleUnitMixed, 2),
+ unit(rep(1:4, 2), c("npc", "cm")))
+unitCheck(rep(simpleUnitMixed, each=2),
+ unit(rep(1:4, each=2),
+ rep(c("npc", "cm"), each=2)))
+unitCheck(rep(simpleUnitMixed, c(2, 1, 2, 1)),
+ unit(rep(1:4, c(2, 1, 2, 1)),
+ rep(c("npc", "cm"), c(2, 1))))
+unitCheck(rep(simpleUnitMixed, each=2, len=4),
+ unit(rep(1:4, each=2, len=4),
+ rep(c("npc", "cm"), each=2, len=4)))
+unitCheck(rep(simpleUnitMixed, each=2, len=10),
+ unit(rep(1:4, each=2, len=10),
+ rep(c("npc", "cm"), each=2, len=10)))
+unitCheck(rep(simpleUnitMixed, each=2, times=3),
+ unit(rep(1:4, each=2, times=3),
+ rep(c("npc", "cm"), each=2, times=3)))
+
+units <- c("npc", "inch", "strwidth", "cm")
+dataL <- list(NULL, NULL, "test", NULL)
+unitWithData <- unit(1:4, units, data=dataL)
+unitCheck(rep(unitWithData, 2),
+ unit(rep(1:4, 2),
+ rep(units, 2),
+ rep(dataL, 2)))
+unitCheck(rep(unitWithData, each=2),
+ unit(rep(1:4, each=2),
+ rep(units, each=2),
+ rep(dataL, each=2)))
+unitCheck(rep(unitWithData, c(2, 1, 2, 1)),
+ unit(rep(1:4, c(2, 1, 2, 1)),
+ rep(units, c(2, 1, 2, 1)),
+ rep(dataL, c(2, 1, 2, 1))))
+unitCheck(rep(unitWithData, each=2, len=4),
+ unit(rep(1:4, each=2, len=4),
+ rep(units, each=2, len=4),
+ rep(dataL, each=2, len=4)))
+unitCheck(rep(unitWithData, each=2, len=10),
+ unit(rep(1:4, each=2, len=10),
+ rep(units, each=2, len=10),
+ rep(dataL, each=2, len=10)))
+unitCheck(rep(unitWithData, each=2, times=3),
+ unit(rep(1:4, each=2, times=3),
+ rep(units, each=2, times=3),
+ rep(dataL, each=2, times=3)))
+
+# unit.arithmetic
+unitArith <- unit(1, "npc") + unit(1:2, "inch")
+
+unitCheck(rep(unitArith, 2),
+ unit(1, "npc") + unit(rep(1:2, 2), "inch"))
+unitCheck(rep(unitArith, each=2),
+ unit(1, "npc") + unit(rep(1:2, each=2), "inch"))
+unitCheck(rep(unitArith, c(2, 1)),
+ unit(1, "npc") + unit(rep(1:2, c(2 ,1)), "inch"))
+unitCheck(rep(unitArith, each=2, len=3),
+ unit(1, "npc") + unit(rep(1:2, each=2, len=3), "inch"))
+unitCheck(rep(unitArith, each=2, len=5),
+ unit(1, "npc") + unit(rep(1:2, each=2, len=5), "inch"))
+unitCheck(rep(unitArith, each=2, times=3),
+ unit(1, "npc") + unit(rep(1:2, each=2, times=3), "inch"))
+
+# unit.list
+arg1 <- unit(1, "npc") + unit(1:2, "inch")
+arg2 <- unit(3, "cm")
+unitList <- unit.c(arg1, arg2)
+
+unitCheck(rep(unitList, 2),
+ unit.c(arg1, arg2, arg1, arg2))
+unitCheck(rep(unitList, each=2),
+ unit.c(rep(arg1, each=2), rep(arg2, 2)))
+unitCheck(rep(unitList, c(2, 1, 2)),
+ unit.c(rep(arg1, c(2, 1)), rep(arg2, 2)))
+unitCheck(rep(unitList, each=2, len=4),
+ rep(arg1, each=2))
+unitCheck(rep(unitList, each=2, len=8),
+ unit.c(rep(arg1, each=2), rep(arg2, 2), rep(arg1, each=2, len=2)))
+unitCheck(rep(unitList, each=2, times=3),
+ unit.c(rep(arg1, each=2), rep(arg2, 2),
+ rep(arg1, each=2), rep(arg2, 2),
+ rep(arg1, each=2), rep(arg2, 2)))
+
+# Special test
+# rep() unit.arithmetic where operands have different lengths
+uaDiffLength <- unit(1:2, "npc") + unit(1:3, "npc")
+uaSameLength <- unit(c(1, 2, 1), "npc") + unit(1:3, "npc")
+unitCheck(rep(uaDiffLength, 2),
+ rep(uaSameLength, 2))
+
+
+# Bug report PR#14170 test
+
+x <- unit.c(unit(5,"mm"),unit(3,"npc"))
+rep(x, 2)
+rep(x, each=2)
+rep(x, c(2, 2))
+
+x <- x - unit(1,"mm")
+rep(x, 2)
+rep(x, each=2)
+rep(x, c(2, 2))
+
+
+## grid::unit.pmax, PR#14443
+x <- unit(1, "cm")
+stopifnot(length(unit.pmax(x)) == 1L, length(unit.pmin(x)) == 1L)
+## was 3 in R <= 2.12.0
+
diff --git a/win32/deps/library/lattice/CITATION b/win32/deps/library/lattice/CITATION
new file mode 100644
index 0000000..3219f8b
--- /dev/null
+++ b/win32/deps/library/lattice/CITATION
@@ -0,0 +1,17 @@
+citHeader("To cite the lattice package in publications use:")
+
+citEntry(entry="Book",
+ title = "Lattice: Multivariate Data Visualization with R",
+ author = personList(as.person("Deepayan Sarkar")),
+ publisher = "Springer",
+ ## edition = "First",
+ address = "New York",
+ year = 2008,
+ note = "ISBN 978-0-387-75968-5",
+ url = "http://lmdvr.r-forge.r-project.org";,
+
+ textVersion =
+ paste("Sarkar, Deepayan (2008)",
+ "Lattice: Multivariate Data Visualization with R.",
+ "Springer, New York. ISBN 978-0-387-75968-5"))
+
diff --git a/win32/deps/library/lattice/DESCRIPTION b/win32/deps/library/lattice/DESCRIPTION
index 4d3e1cf..5581de5 100644
--- a/win32/deps/library/lattice/DESCRIPTION
+++ b/win32/deps/library/lattice/DESCRIPTION
@@ -1,20 +1,25 @@
-Package: lattice
-Version: 0.17-25
-Date: 2009/05/14
-Priority: recommended
-Title: Lattice Graphics
-Author: Deepayan Sarkar <deepayan sarkar r-project org>
-Maintainer: Deepayan Sarkar <deepayan sarkar r-project org>
-Description: Implementation of Trellis Graphics. See ?Lattice for a
- brief introduction
-Depends: R (>= 2.5.0)
-Suggests: grid, KernSmooth
-Imports: grid, grDevices, graphics, stats, utils
-Enhances: chron
-LazyLoad: yes
-LazyData: yes
-License: GPL (>= 2)
-Packaged: Thu May 14 16:27:57 2009; dsarkar
-Repository: CRAN
-Date/Publication: 2009-05-15 11:26:16
-Built: R 2.9.2; i386-pc-mingw32; 2009-08-24 13:04:25 UTC; windows
+Package: lattice
+Version: 0.20-10
+Date: 2012/08/21
+Priority: recommended
+Title: Lattice Graphics
+Author: Deepayan Sarkar <deepayan sarkar r-project org>
+Maintainer: Deepayan Sarkar <deepayan sarkar r-project org>
+Description: Lattice is a powerful and elegant high-level data
+ visualization system, with an emphasis on multivariate data,
+ that is sufficient for typical graphics needs, and is also
+ flexible enough to handle most nonstandard requirements. See
+ ?Lattice for an introduction.
+Depends: R (>= 2.14.0)
+Suggests: grid, KernSmooth, MASS
+Imports: grid, grDevices, graphics, stats, utils, methods
+Enhances: chron
+LazyLoad: yes
+LazyData: yes
+License: GPL (>= 2)
+URL: http://lattice.r-forge.r-project.org/
+Packaged: 2012-08-21 11:22:23 UTC; deepayan
+Repository: CRAN
+Date/Publication: 2012-08-22 13:48:18
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:10:35 UTC; windows
+Archs: i386, x64
diff --git a/win32/deps/library/lattice/INDEX b/win32/deps/library/lattice/INDEX
index f4e928a..5a9a01f 100644
--- a/win32/deps/library/lattice/INDEX
+++ b/win32/deps/library/lattice/INDEX
@@ -1,68 +1,70 @@
-axis.default Default axis annotation utilities
-banking Banking
-barchart.table table methods for barchart and dotplot
-barley Yield data from a Minnesota barley trial
-cloud 3d Scatter Plot and Wireframe Surface Plot
-draw.colorkey Produce a Colorkey for levelplot
-draw.key Produce a Legend or Key
-environmental Atmospheric environmental conditions in New
- York City
-equal.count shingles
-ethanol Engine exhaust fumes from burning ethanol
-histogram Histograms and Kernel Density Plots
-Lattice Lattice Graphics
-lattice.options Low-level Options Controlling Behaviour of
- Lattice
-latticeParseFormula Parse Trellis formula
-level.colors A function to compute false colors representing
- a numeric or categorical variable
-levelplot Level plots and contour plots
-llines Replacements of traditional graphics functions
-lset Interface to modify Trellis Settings -
- Deprecated
-make.groups Grouped data from multiple vectors
-melanoma Melanoma skin cancer incidence
-oneway Fit One-way Model
-packet.panel.default Associating Packets with Panels
-panel.axis Panel Function for Drawing Axis Ticks and
- Labels
-panel.barchart Default Panel Function for barchart
-panel.bwplot Default Panel Function for bwplot
-panel.cloud Default Panel Function for cloud
-panel.densityplot Default Panel Function for densityplot
-panel.dotplot Default Panel Function for dotplot
-panel.functions Useful Panel Functions
-panel.histogram Default Panel Function for histogram
-panel.identify Functions to Interact with Lattice Plots
-panel.levelplot Default Panel Function for levelplot
-panel.number Accessing Auxiliary Information During Plotting
-panel.pairs Default Superpanel Function for splom
-panel.parallel Default Panel Function for parallel
-panel.qqmath Default Panel and Prepanel Function for qqmath
-panel.qqmathline Useful panel function with qqmath
-panel.smoothScatter Lattice panel function analogous to
- smoothScatter
-panel.stripplot Default Panel Function for stripplot
-panel.superpose Panel Function for Display Marked by groups
-panel.violin Panel Function to create Violin Plots
-panel.xyplot Default Panel Function for xyplot
-prepanel.default.bwplot
- Default Prepanel Functions
-prepanel.lmline Useful Prepanel Function for Lattice
-print.trellis Plot and Summarize Trellis Objects
-qq Quantile-Quantile Plots of Two Samples
-qqmath Q-Q Plot with Theoretical Distribution
-rfs Residual and Fit Spread Plots
-Rows Extract rows from a list
-simpleKey Function to generate a simple key
-simpleTheme Function to generate a simple theme
-singer Heights of New York Choral Society singers
-splom Scatter Plot Matrices
-strip.default Default Trellis Strip Function
-tmd Tukey Mean-Difference Plot
-trellis.device Initializing Trellis Displays
-trellis.object A Trellis Plot Object
-trellis.par.get Graphical Parameters for Trellis Displays
-update.trellis Retrieve and Update Trellis Object
-utilities.3d Utility functions for 3-D plots
-xyplot Common Bivariate Trellis Plots
+Lattice Lattice Graphics
+Rows Extract rows from a list
+axis.default Default axis annotation utilities
+banking Banking
+barchart.table table methods for barchart and dotplot
+barley Yield data from a Minnesota barley trial
+cloud 3d Scatter Plot and Wireframe Surface Plot
+current.row Accessing Auxiliary Information During Plotting
+draw.colorkey Produce a Colorkey for levelplot
+draw.key Produce a Legend or Key
+environmental Atmospheric environmental conditions in New
+ York City
+equal.count shingles
+ethanol Engine exhaust fumes from burning ethanol
+histogram Histograms and Kernel Density Plots
+lattice.options Low-level Options Controlling Behaviour of
+ Lattice
+latticeParseFormula Parse Trellis formula
+level.colors A function to compute false colors representing
+ a numeric or categorical variable
+levelplot Level plots and contour plots
+llines Replacements of traditional graphics functions
+lset Interface to modify Trellis Settings - Defunct
+make.groups Grouped data from multiple vectors
+melanoma Melanoma skin cancer incidence
+oneway Fit One-way Model
+packet.panel.default Associating Packets with Panels
+panel.axis Panel Function for Drawing Axis Ticks and
+ Labels
+panel.barchart Default Panel Function for barchart
+panel.bwplot Default Panel Function for bwplot
+panel.cloud Default Panel Function for cloud
+panel.densityplot Default Panel Function for densityplot
+panel.dotplot Default Panel Function for dotplot
+panel.functions Useful Panel Function Components
+panel.histogram Default Panel Function for histogram
+panel.identify Functions to Interact with Lattice Plots
+panel.levelplot Panel Functions for levelplot and contourplot
+panel.loess Panel Function to Add a LOESS Smooth
+panel.pairs Default Superpanel Function for splom
+panel.parallel Default Panel Function for parallel
+panel.qqmath Default Panel Function for qqmath
+panel.qqmathline Useful panel function with qqmath
+panel.smoothScatter Lattice panel function analogous to
+ smoothScatter
+panel.spline Panel Function to Add a Spline Smooth
+panel.stripplot Default Panel Function for stripplot
+panel.superpose Panel Function for Display Marked by groups
+panel.violin Panel Function to create Violin Plots
+panel.xyplot Default Panel Function for xyplot
+prepanel.default.bwplot
+ Default Prepanel Functions
+prepanel.lmline Useful Prepanel Function for Lattice
+print.trellis Plot and Summarize Trellis Objects
+qq Quantile-Quantile Plots of Two Samples
+qqmath Q-Q Plot with Theoretical Distribution
+rfs Residual and Fit Spread Plots
+simpleKey Function to generate a simple key
+simpleTheme Function to generate a simple theme
+singer Heights of New York Choral Society singers
+splom Scatter Plot Matrices
+strip.default Default Trellis Strip Function
+tmd Tukey Mean-Difference Plot
+trellis.device Initializing Trellis Displays
+trellis.object A Trellis Plot Object
+trellis.par.get Graphical Parameters for Trellis Displays
+update.trellis Retrieve and Update Trellis Object
+utilities.3d Utility functions for 3-D plots
+xyplot Common Bivariate Trellis Plots
+xyplot.ts Time series plotting methods
diff --git a/win32/deps/library/lattice/LICENSE b/win32/deps/library/lattice/LICENSE
new file mode 100644
index 0000000..2e33dd5
--- /dev/null
+++ b/win32/deps/library/lattice/LICENSE
@@ -0,0 +1,16 @@
+
+This software is distributed under the terms of the GNU General Public
+License as published by the Free Software Foundation; either version 2
+of the License, or (at your option) any later version.
+
+As of writing, this essentially boils down to two possible licenses,
+GPL version 2 and version 3. Copies of these licenses are available
+in files GPL-2 and GPL-3 in the sources of this package, as well as at
+
+http://www.r-project.org/Licenses/
+
+They can also be viewed from within R using
+
+RShowDoc("GPL-2")
+RShowDoc("GPL-3")
+
diff --git a/win32/deps/library/lattice/Meta/Rd.rds b/win32/deps/library/lattice/Meta/Rd.rds
index 7a1dd63..56abff0 100644
Binary files a/win32/deps/library/lattice/Meta/Rd.rds and b/win32/deps/library/lattice/Meta/Rd.rds differ
diff --git a/win32/deps/library/lattice/Meta/data.rds b/win32/deps/library/lattice/Meta/data.rds
index 0054219..7f643bb 100644
Binary files a/win32/deps/library/lattice/Meta/data.rds and b/win32/deps/library/lattice/Meta/data.rds differ
diff --git a/win32/deps/library/lattice/Meta/demo.rds b/win32/deps/library/lattice/Meta/demo.rds
index b42b138..a827611 100644
Binary files a/win32/deps/library/lattice/Meta/demo.rds and b/win32/deps/library/lattice/Meta/demo.rds differ
diff --git a/win32/deps/library/lattice/Meta/hsearch.rds b/win32/deps/library/lattice/Meta/hsearch.rds
index e663335..ee2758e 100644
Binary files a/win32/deps/library/lattice/Meta/hsearch.rds and b/win32/deps/library/lattice/Meta/hsearch.rds differ
diff --git a/win32/deps/library/lattice/Meta/links.rds b/win32/deps/library/lattice/Meta/links.rds
new file mode 100644
index 0000000..73a41ac
Binary files /dev/null and b/win32/deps/library/lattice/Meta/links.rds differ
diff --git a/win32/deps/library/lattice/Meta/nsInfo.rds b/win32/deps/library/lattice/Meta/nsInfo.rds
index a815a4a..3806a85 100644
Binary files a/win32/deps/library/lattice/Meta/nsInfo.rds and b/win32/deps/library/lattice/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/lattice/Meta/package.rds b/win32/deps/library/lattice/Meta/package.rds
index 23511be..e99b233 100644
Binary files a/win32/deps/library/lattice/Meta/package.rds and b/win32/deps/library/lattice/Meta/package.rds differ
diff --git a/win32/deps/library/lattice/NAMESPACE b/win32/deps/library/lattice/NAMESPACE
index df109b8..216fbc1 100644
--- a/win32/deps/library/lattice/NAMESPACE
+++ b/win32/deps/library/lattice/NAMESPACE
@@ -3,16 +3,14 @@ useDynLib(lattice, .registration = TRUE)
import(grid)
-
-## ## can I do this?
-## export(grid.prompt)
-
+importFrom(methods, hasArg)
importFrom(grDevices,
- dev.list, cm.colors, gray, col2rgb,
+ dev.hold, dev.flush,
+ dev.list, cm.colors, gray, col2rgb, rgb,
heat.colors, grey, hsv, xy.coords,
- boxplot.stats, contourLines)
+ boxplot.stats, contourLines, colorRampPalette, as.raster)
importFrom(graphics, par, plot, co.intervals, hist)
@@ -23,7 +21,7 @@ importFrom(stats,
as.formula, density, fitted.values, loess.smooth, median,
ppoints, qnorm, residuals, update, var, coef, quantile, lm,
- dnorm, qunif)
+ dnorm, qunif, uniroot, smooth.spline)
export(
@@ -44,7 +42,8 @@ export(
cloud,
wireframe,
splom,
- parallel,
+ parallel, # deprecated
+ parallelplot,
tmd,
rfs,
@@ -62,7 +61,7 @@ export(
panel.stripplot,
panel.xyplot,
panel.contourplot,
- panel.levelplot,
+ panel.levelplot, panel.levelplot.raster,
panel.cloud, panel.3dscatter,
panel.wireframe, panel.3dwire,
panel.pairs,
@@ -78,6 +77,7 @@ export(
panel.superpose,
panel.superpose.2,
+ panel.superpose.plain,
## data-driven (usually summary of some sort)
@@ -88,6 +88,7 @@ export(
panel.linejoin,
panel.lmline,
panel.loess,
+ panel.spline,
panel.qqmathline,
## decorative / adds reference
@@ -126,6 +127,7 @@ export(
prepanel.tmd.default, prepanel.tmd.qqmath,
prepanel.lmline,
prepanel.loess,
+ prepanel.spline,
prepanel.qqmathline,
@@ -240,60 +242,66 @@ S3method(print, summary.trellis)
## methods for high level functions
-S3method(barchart, formula)
-S3method(barchart, array)
-S3method(barchart, default)
-S3method(barchart, matrix)
-S3method(barchart, numeric)
-S3method(barchart, table)
-
-S3method(bwplot, formula)
-S3method(bwplot, numeric)
-S3method(densityplot, formula)
-S3method(densityplot, numeric)
-S3method(dotplot, formula)
-S3method(dotplot, array)
-S3method(dotplot, default)
-S3method(dotplot, matrix)
-S3method(dotplot, numeric)
-S3method(dotplot, table)
-S3method(histogram, formula)
-S3method(histogram, factor)
-S3method(histogram, numeric)
-S3method(qqmath, formula)
-S3method(qqmath, numeric)
-S3method(stripplot, formula)
-S3method(stripplot, numeric)
-S3method(qq, formula)
-S3method(xyplot, formula)
-S3method(levelplot, formula)
-S3method(levelplot, table)
-S3method(levelplot, array)
-S3method(levelplot, matrix)
-S3method(contourplot, formula)
-S3method(contourplot, table)
-S3method(contourplot, array)
-S3method(contourplot, matrix)
-S3method(cloud, formula)
-S3method(cloud, matrix)
-S3method(cloud, table)
-S3method(wireframe, formula)
-S3method(wireframe, matrix)
-S3method(splom, formula)
-S3method(splom, matrix)
-S3method(splom, data.frame)
-S3method(parallel, formula)
-S3method(parallel, matrix)
-S3method(parallel, data.frame)
-
-S3method(tmd, formula)
-S3method(tmd, trellis)
-
-
-S3method(llines, default)
-S3method(ltext, default)
-S3method(lpoints, default)
-
+S3method(barchart, formula)
+S3method(barchart, array)
+S3method(barchart, default)
+S3method(barchart, matrix)
+S3method(barchart, numeric)
+S3method(barchart, table)
+
+S3method(bwplot, formula)
+S3method(bwplot, numeric)
+S3method(densityplot, formula)
+S3method(densityplot, numeric)
+S3method(dotplot, formula)
+S3method(dotplot, array)
+S3method(dotplot, default)
+S3method(dotplot, matrix)
+S3method(dotplot, numeric)
+S3method(dotplot, table)
+S3method(histogram, formula)
+S3method(histogram, factor)
+S3method(histogram, numeric)
+S3method(qqmath, formula)
+S3method(qqmath, numeric)
+S3method(stripplot, formula)
+S3method(stripplot, numeric)
+S3method(qq, formula)
+S3method(xyplot, formula)
+S3method(xyplot, ts)
+S3method(levelplot, formula)
+S3method(levelplot, table)
+S3method(levelplot, array)
+S3method(levelplot, matrix)
+S3method(contourplot, formula)
+S3method(contourplot, table)
+S3method(contourplot, array)
+S3method(contourplot, matrix)
+S3method(cloud, formula)
+S3method(cloud, matrix)
+S3method(cloud, table)
+S3method(wireframe, formula)
+S3method(wireframe, matrix)
+S3method(splom, formula)
+S3method(splom, matrix)
+S3method(splom, data.frame)
+
+S3method(parallelplot, formula)
+S3method(parallelplot, matrix)
+S3method(parallelplot, data.frame)
+
+# deprecated
+S3method(parallel, formula)
+S3method(parallel, matrix)
+S3method(parallel, data.frame)
+
+S3method(tmd, formula)
+S3method(tmd, trellis)
+
+
+S3method(llines, default)
+S3method(ltext, default)
+S3method(lpoints, default)
### Local variables:
diff --git a/win32/deps/library/lattice/NEWS b/win32/deps/library/lattice/NEWS
index b446364..48499d1 100644
--- a/win32/deps/library/lattice/NEWS
+++ b/win32/deps/library/lattice/NEWS
@@ -1,5 +1,126 @@
+Changes in lattice 0.20
+=======================
+
+ o The primary goal of the 0.20 series is to further improve
+ documentation, building up to an eventual 1.0 release. Specific
+ major changes are given below.
+
+ o Use dev.hold()/dev.flush() introduced in R 2.14.0 for smoother
+ displays and transition.
+
+ o It is now easier to use raster images in levelplot() by specifying
+ top-level argument 'useRaster=TRUE'.
+
+ o 'pos' can now be a vector in ltext(), just as it can in text().
+
+ o Explicit components in 'colorkey' (for levelplot()) to specify
+ graphical parameters of boundary and tick marks/labels.
+
+ o "spline" added as a possibly 'type' in panel.xyplot(), following a
+ suggestion from Patrick Breheny.
+
+ o Support for traditional graphics-like log scale annotation, using
+ 'scales=list(equispaced.log = FALSE)'.
+
+ o parallel() deprecated in favour of parallelplot(), to avoid
+ potential confusion with the parallel package.
+
+
+Changes in lattice 0.19
+=======================
+
+ o The primary goal of the 0.19 series is to improve documentation and
+ fix some obscure but long-standing bugs, building up to an eventual
+ 1.0 release. Specific major changes are given below.
+
+ o Added new arguments 'grid' and 'abline' in panel.xyplot().
+
+ o Added a "panel.background" setting.
+
+ o Restructured storage of plot-specific information, fixing bug
+ reported in
+ https://stat.ethz.ch/pipermail/r-help/2007-October/143567.html
+
+ o Added a CITATION file.
+
+ o Added a new "axis.text" setting.
+
+ o Added the option to scale data inside panel.3dscatter() and
+ panel.3dwire() rather than assuming ther are already scaled. This
+ may be helpful for use in user-written panel functions, with
+ (additional) data specified in the original scale.
+
+ o 'varnames' can now be expressions in splom()/parallel().
+
+ o Added support for 'xlab.top' and 'ylab.right' arguments.
+
+ o Improved axis labelling in splom(), including support for date-time
+ data.
+
+ o panel.pairs() now passes arguments i and j to (sub)panel and
+ diag.panel functions.
+
+ o Default prepanel functions are now user-settable through
+ lattice.options()
+
+ o par.[main|sub|xlab|ylab].text parameter settings are more powerful.
+
+ o Added support for 'just' component in draw.key() to allow
+ justification of legend placement.
+
+ o Graphical arguments in panel.superpose can now be lists.
+
+ o Added support for raster colorkeys.
+
+ o Added new 'height' component for keys.
+
+ o Improved vectorization of graphical parameters in panel.bwplot.
+
+ o Expanded trellis.grobname() and used it to provide a name for all grobs.
+
+ o New panel.spline() function.
+
+bug fixes
+---------
+
+ o More realistic check for equispaced grid in
+ panel.levelplot.raster().
+
+ o Improved partial matching of component names in 'key' and 'scales'.
+
+ o xyplot.ts() now allows graphical parameters to be given as vectors
+ (inside a list) for each series. Passes lists to panel.superpose.
+
+ o panel.axis() now does NOT draw tick marks if 'ticks = FALSE'.
+
+
+Changes in lattice 0.18
+=======================
+
+ o Hosting of the upstream sources has moved to R-forge. This allows,
+ among other things, the use of the R-forge issue tracker.
+
+ o New xyplot.ts method, merging versions previously available
+ in latticeExtra and zoo (thanks to the efforts of Felix Andrews)
+
+ o An argument 'group.value', containing the level of the group, is now
+ passed by panel.superpose to the 'panel.groups' function
+
+ o Specifying 'auto.key' as a list now produces a legend even in the
+ absence of 'groups', provided a 'text' component has been included
+
+ o The 'layout' argument now accepts NA for number of columns or rows.
+
+ o Scale limits 'xlim' & 'ylim' can have one NA to fix only one side.
+
+ o Date and POSIXt scales now use new methods to calculate axis ticks,
+ and now respond to the 'tick.number' component of 'scales'.
+
+ o 'panel.qqmath' gains an argument 'tails.n' for exact data on tails.
+
+
Changes in lattice 0.17
=======================
@@ -37,6 +158,8 @@ new features
o Added German translations (contributed by Chris Leick)
+ o reordered documentation to make PDF manual more readable
+
bug fixes
---------
@@ -76,7 +199,7 @@ changes in behaviour
their list form, they support more graphical parameters as well as
finer positioning (justification, rotation, etc.)
- o 'strip.left' gets called with 'horizontal = FALSE', so
+ o 'strip.left' gets called with 'horizontal = FALSE', so
'strip.left = strip.default' now works as expected
@@ -110,7 +233,7 @@ new features
panel.brush.splom()
o There is now an error handling mechanism for panel functions. By
- default, errors in panel functions no longer stop execution. See
+ default, errors in panel functions no longer stop execution. See
?print.trellis for details.
@@ -119,7 +242,7 @@ changes in behaviour
o non-numeric data no longer cause warnings in bwplot
- o the default padding between components has been changed to
+ o the default padding between components has been changed to
0.5 "chars"
@@ -207,7 +330,7 @@ new features
by calling 'panel.superpose'. Consequently, the default of 'panel'
in 'xyplot' etc does not need to be conditional on 'groups'.
- o added 'lineheight' as a graphical parameter where appropriate.
+ o added 'lineheight' as a graphical parameter where appropriate.
o added a 'grid.pars' setting for arbitrary grid parameters to be
set initially via gpar().
@@ -286,8 +409,8 @@ Changes in lattice 0.12
improvements
------------
- o panel.bwplot has a new 'stats' argument, which is a function used to
- calculate the statistics in the box and whisker plot. Defaults
+ o panel.bwplot has a new 'stats' argument, which is a function used to
+ calculate the statistics in the box and whisker plot. Defaults
to boxplot.stats, which was the hard-coded value earlier.
o panel.bwplot has been re-implemented. Faster, avoids direct grid
@@ -478,7 +601,7 @@ new features
o type="H" in lplot.xy (for horizontal line). New argument
'horizontal' for panel.xyplot, which affects what happens for
various 'type'-s.
-
+
o type="g" in panel.xyplot, which draws a reference grid
o the print method now (optionally) saves the (last) object printed
@@ -508,7 +631,7 @@ changes in behaviour
o choice of color for grouped barcharts now taken from a new setting
parameter 'superpose.fill' and not 'regions' as previously
- o arguments to panel.levelplot has changed (this is related to how
+ o arguments to panel.levelplot has changed (this is related to how
default colors are obtained, as described above).
@@ -576,8 +699,8 @@ new features
multiple legends and the use of arbitrary grid objects as keys
o option to NOT drop unused factor levels when subsetting, by setting
- drop.unused.levels = FALSE or
- drop.unused.levels = list(cond = FALSE, data = FALSE)
+ drop.unused.levels = FALSE or
+ drop.unused.levels = list(cond = FALSE, data = FALSE)
in high-level functions like xyplot.
o Ability to attach settings to a trellis object (rather than
@@ -612,7 +735,7 @@ bug fixes
o Fixed important bug concerning interaction of subscripts and
subsets
-
+
o lots of other fixes, mostly obscure
@@ -639,7 +762,7 @@ Changes in lattice 0.8
o Clipping can now be turned off in panels and strips via the
trellis.par.get("clip") setting.
-See the Changelog for other minor changes.
+See the Changelog for other minor changes.
@@ -692,7 +815,7 @@ scales
Changes in lattice 0.6
======================
-API change:
+API change:
----------
o panel functions: In earlier versions, panel functions and prepanel
@@ -747,7 +870,7 @@ New Features and Fixes:
routine currently used is a hack of axis.POSIXt (without the format
option), but will hopefully improve in future.
- o 3-D functions:
+ o 3-D functions:
The 3-D functions cloud and wireframe have been greatly improved in
terms of extensibility. The code is much cleaner, and writing new
@@ -778,7 +901,7 @@ New Features and Fixes:
-Known bugs:
+Known bugs:
==========
o Handling of NA values are often inconsistent and buggy. Some of
@@ -794,7 +917,7 @@ Known bugs:
Changes in lattice 0.5
======================
-Not many.
+Not many.
o Biggest change in the way settings are handled. Settings are now
stored in a global list called lattice.theme, and is truly
@@ -821,7 +944,7 @@ Not many.
o Following changes in grid, calls to base R graphics and lattice
functions can now be mixed.
-
+
Changes in lattice 0.4
======================
@@ -859,7 +982,7 @@ bugfixes (notably in levelplot). The important changes are:
the left, top or bottom as well
o new ``lines'' component in the par.strip.text argument that can be
- used to change the height of strips
+ used to change the height of strips
o xlab, main etc can be double height strings (containing "\n"-s),
the spaces allocated for these would be automatically adjusted
@@ -883,7 +1006,7 @@ bugfixes (notably in levelplot). The important changes are:
-
+
Changes in lattice 0.3
======================
@@ -905,13 +1028,13 @@ New Features:
o levelplot (but no contourplot. In particular, the contour = T option
in levelplot does not work)
- o tmd now works on the output from qq
+ o tmd now works on the output from qq
o panel function names can now be quoted strings
o scales and its x and y components can now be just a character
string like "free" or "sliced", i.e., the relation tag can be
- omitted.
+ omitted.
o extension to the `type' argument in panel.xyplot and
panel.superpose to allow stair-like and histogram-like plots
@@ -926,7 +1049,7 @@ New Features:
functions to help port existing S-Plus Trellis code. See below for
details.
- o changes in print.trellis to allow mixing of Lattice and usual R
+ o changes in print.trellis to allow mixing of Lattice and usual R
graphics. See below for details.
@@ -965,7 +1088,7 @@ Still Missing [OBSOLETE, except for the parts about piechart and scale]
o Some components of scale (I haven't found a full list, so
can't say exactly which are missing)
- o Fonts
+ o Fonts
o axis labels badly implemented, no checking for overlaps.
diff --git a/win32/deps/library/lattice/R/lattice b/win32/deps/library/lattice/R/lattice
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/lattice/R/lattice
+++ b/win32/deps/library/lattice/R/lattice
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/lattice/R/lattice.rdb b/win32/deps/library/lattice/R/lattice.rdb
index 42d9aaa..d857b91 100644
Binary files a/win32/deps/library/lattice/R/lattice.rdb and b/win32/deps/library/lattice/R/lattice.rdb differ
diff --git a/win32/deps/library/lattice/R/lattice.rdx b/win32/deps/library/lattice/R/lattice.rdx
index 7f21296..fc4fe4c 100644
Binary files a/win32/deps/library/lattice/R/lattice.rdx and b/win32/deps/library/lattice/R/lattice.rdx differ
diff --git a/win32/deps/library/lattice/data/Rdata.rdb b/win32/deps/library/lattice/data/Rdata.rdb
index bcce736..5af8262 100644
Binary files a/win32/deps/library/lattice/data/Rdata.rdb and b/win32/deps/library/lattice/data/Rdata.rdb differ
diff --git a/win32/deps/library/lattice/data/Rdata.rds b/win32/deps/library/lattice/data/Rdata.rds
index 64ed4a3..e4eb0a6 100644
Binary files a/win32/deps/library/lattice/data/Rdata.rds and b/win32/deps/library/lattice/data/Rdata.rds differ
diff --git a/win32/deps/library/lattice/data/Rdata.rdx b/win32/deps/library/lattice/data/Rdata.rdx
index ac4064f..a327b5e 100644
Binary files a/win32/deps/library/lattice/data/Rdata.rdx and b/win32/deps/library/lattice/data/Rdata.rdx differ
diff --git a/win32/deps/library/lattice/demo/lattice.R b/win32/deps/library/lattice/demo/lattice.R
index 3ec5b4f..f20b9c9 100644
--- a/win32/deps/library/lattice/demo/lattice.R
+++ b/win32/deps/library/lattice/demo/lattice.R
@@ -1,21 +1,7 @@
require(grid)
-
-## branch for compatibility with older R
-
-old.prompt <-
- if (exists("devAskNewPage", mode = "function",
- where = getNamespace("grDevices"),
- inherits = FALSE)) {
- devAskNewPage(TRUE)
- } else {
- grid.prompt(TRUE)
- }
-
-
-
+old.prompt <- devAskNewPage(TRUE)
## store current settings, to be restored later
-
old.settings <- trellis.par.get()
## changing settings to new 'theme'
@@ -52,7 +38,7 @@ states <- data.frame(state.x77,
xyplot(Murder ~ Population | state.region, data = states,
groups = state.name,
panel = function(x, y, subscripts, groups)
- ltext(x = x, y = y, label = groups[subscripts],
+ ltext(x = x, y = y, labels = groups[subscripts],
cex=.9, fontfamily = "HersheySans", fontface = "italic"),
par.strip.text = list(cex = 1.3, font = 4, col = "brown"),
xlab = list("Estimated Population, July 1, 1975", font = 2),
@@ -70,7 +56,7 @@ levels(states$state.region) <-
xyplot(Murder ~ Population | state.region, data = states,
groups = as.character(state.name),
panel = function(x, y, subscripts, groups)
- ltext(x = x, y = y, label = groups[subscripts], srt = -50, col = "blue",
+ ltext(x = x, y = y, labels = groups[subscripts], srt = -50, col = "blue",
cex=.9, fontfamily = "HersheySans"),
par.strip.text = list(cex = 1.3, font = 4, col = "brown", lines = 2),
xlab = "Estimated Population\nJuly 1, 1975",
@@ -93,14 +79,14 @@ wireframe(volcano, shade = TRUE,
aspect = c(61/87, 0.4),
screen = list(z = -120, x = -45),
light.source = c(0,0,10), distance = .2,
- shade.colors = function(irr, ref, height, w = .5)
+ shade.colors.palette = function(irr, ref, height, w = .5)
grey(w * irr + (1 - w) * (1 - (1-ref)^.4)))
## 3-D surface parametrized on a 2-D grid
n <- 50
-tx <- matrix(seq(-pi, pi, len = 2*n), 2*n, n)
-ty <- matrix(seq(-pi, pi, len = n) / 2, 2*n, n, byrow = T)
+tx <- matrix(seq(-pi, pi, length.out = 2*n), 2*n, n)
+ty <- matrix(seq(-pi, pi, length.out = n) / 2, 2*n, n, byrow = T)
xx <- cos(tx) * cos(ty)
yy <- sin(tx) * cos(ty)
zz <- sin(ty)
@@ -141,23 +127,29 @@ barchart(variety ~ yield | year * site, barley, origin = 0,
bg = trellis.par.get("strip.background")$col[which.given],
...) {
axis.line <- trellis.par.get("axis.line")
- pushViewport(viewport(clip = trellis.par.get("clip")$strip))
+ pushViewport(viewport(clip = trellis.par.get("clip")$strip,
+ name = trellis.vpname("strip")))
if (which.given == 1)
{
grid.rect(x = .26, just = "right",
+ name = trellis.grobname("fill", type="strip"),
gp = gpar(fill = bg, col = "transparent"))
ltext(factor.levels[which.panel[which.given]],
- x = .24, y = .5, adj = 1)
+ x = .24, y = .5, adj = 1,
+ name.type = "strip")
}
if (which.given == 2)
{
grid.rect(x = .26, just = "left",
+ name = trellis.grobname("fill", type="strip"),
gp = gpar(fill = bg, col = "transparent"))
ltext(factor.levels[which.panel[which.given]],
- x = .28, y = .5, adj = 0)
+ x = .28, y = .5, adj = 0,
+ name.type = "strip")
}
upViewport()
- grid.rect(gp =
+ grid.rect(name = trellis.grobname("border", type="strip"),
+ gp =
gpar(col = axis.line$col,
lty = axis.line$lty,
lwd = axis.line$lwd,
@@ -166,14 +158,7 @@ barchart(variety ~ yield | year * site, barley, origin = 0,
}, par.strip.text = list(lines = 0.4))
-trellis.par.set(theme = old.settings)
-
-if (exists("devAskNewPage", mode = "function",
- where = getNamespace("grDevices"),
- inherits = FALSE)) {
- devAskNewPage(old.prompt)
-} else {
- grid.prompt(old.prompt)
-}
+trellis.par.set(theme = old.settings, strict = 2)
+devAskNewPage(old.prompt)
diff --git a/win32/deps/library/lattice/help/AnIndex b/win32/deps/library/lattice/help/AnIndex
index c6dd221..1eab752 100644
--- a/win32/deps/library/lattice/help/AnIndex
+++ b/win32/deps/library/lattice/help/AnIndex
@@ -108,11 +108,12 @@ panel.identify interaction
panel.identify.cloud interaction
panel.identify.qqmath interaction
panel.levelplot panel.levelplot
+panel.levelplot.raster panel.levelplot
panel.linejoin panel.functions
panel.lines llines
panel.link.splom interaction
panel.lmline panel.functions
-panel.loess panel.functions
+panel.loess panel.loess
panel.mathdensity panel.functions
panel.number panel.number
panel.pairs panel.pairs
@@ -127,10 +128,12 @@ panel.refline panel.functions
panel.rug panel.functions
panel.segments llines
panel.smoothScatter panel.smoothScatter
+panel.spline panel.spline
panel.splom panel.xyplot
panel.stripplot panel.stripplot
panel.superpose panel.superpose
panel.superpose.2 panel.superpose
+panel.superpose.plain panel.superpose
panel.text llines
panel.tmd.default tmd
panel.tmd.qqmath tmd
@@ -138,9 +141,10 @@ panel.violin panel.violin
panel.wireframe panel.cloud
panel.xyplot panel.xyplot
parallel splom
-parallel.data.frame splom
-parallel.formula splom
-parallel.matrix splom
+parallelplot splom
+parallelplot.data.frame splom
+parallelplot.formula splom
+parallelplot.matrix splom
plot.shingle shingles
plot.trellis print.trellis
prepanel.default.bwplot prepanel.default
@@ -156,6 +160,7 @@ prepanel.default.xyplot prepanel.default
prepanel.lmline prepanel.functions
prepanel.loess prepanel.functions
prepanel.qqmathline prepanel.functions
+prepanel.spline prepanel.functions
prepanel.tmd.default tmd
prepanel.tmd.qqmath tmd
print.shingle shingles
@@ -210,6 +215,7 @@ wireframe.matrix cloud
xscale.components.default axis.default
xyplot xyplot
xyplot.formula xyplot
+xyplot.ts xyplot.ts
yscale.components.default axis.default
[.shingle shingles
[.trellis update.trellis
diff --git a/win32/deps/library/lattice/help/aliases.rds b/win32/deps/library/lattice/help/aliases.rds
new file mode 100644
index 0000000..aebed54
Binary files /dev/null and b/win32/deps/library/lattice/help/aliases.rds differ
diff --git a/win32/deps/library/lattice/help/lattice.rdb b/win32/deps/library/lattice/help/lattice.rdb
new file mode 100644
index 0000000..b8b45e2
Binary files /dev/null and b/win32/deps/library/lattice/help/lattice.rdb differ
diff --git a/win32/deps/library/lattice/help/lattice.rdx b/win32/deps/library/lattice/help/lattice.rdx
new file mode 100644
index 0000000..e177e0c
Binary files /dev/null and b/win32/deps/library/lattice/help/lattice.rdx differ
diff --git a/win32/deps/library/lattice/help/paths.rds b/win32/deps/library/lattice/help/paths.rds
new file mode 100644
index 0000000..951af64
Binary files /dev/null and b/win32/deps/library/lattice/help/paths.rds differ
diff --git a/win32/deps/library/lattice/html/00Index.html b/win32/deps/library/lattice/html/00Index.html
new file mode 100644
index 0000000..53f09d1
--- /dev/null
+++ b/win32/deps/library/lattice/html/00Index.html
@@ -0,0 +1,591 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Lattice Graphics</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Lattice Graphics
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘lattice’ version 0.20-10</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+<li><a href="../demo">Code demos</a>. Use <a href="../../utils/help/demo">demo()</a> to run them.</li>
+<li><a href="../NEWS">Package NEWS</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<p align="center">
+<a href="# "> </a>
+<a href="#A">A</a>
+<a href="#B">B</a>
+<a href="#C">C</a>
+<a href="#D">D</a>
+<a href="#E">E</a>
+<a href="#H">H</a>
+<a href="#I">I</a>
+<a href="#L">L</a>
+<a href="#M">M</a>
+<a href="#O">O</a>
+<a href="#P">P</a>
+<a href="#Q">Q</a>
+<a href="#R">R</a>
+<a href="#S">S</a>
+<a href="#T">T</a>
+<a href="#U">U</a>
+<a href="#W">W</a>
+<a href="#X">X</a>
+<a href="#Y">Y</a>
+<a href="#misc">misc</a>
+</p>
+
+<table width="100%">
+<tr><td width="25%"><a href="Lattice.html">lattice-package</a></td>
+<td>Lattice Graphics</td></tr>
+</table>
+
+<h2><a name="A">-- A --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="shingles.html">as.character.shingleLevel</a></td>
+<td>shingles</td></tr>
+<tr><td width="25%"><a href="shingles.html">as.data.frame.shingle</a></td>
+<td>shingles</td></tr>
+<tr><td width="25%"><a href="shingles.html">as.factorOrShingle</a></td>
+<td>shingles</td></tr>
+<tr><td width="25%"><a href="shingles.html">as.shingle</a></td>
+<td>shingles</td></tr>
+<tr><td width="25%"><a href="axis.default.html">axis.default</a></td>
+<td>Default axis annotation utilities</td></tr>
+</table>
+
+<h2><a name="B">-- B --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="banking.html">banking</a></td>
+<td>Banking</td></tr>
+<tr><td width="25%"><a href="xyplot.html">barchart</a></td>
+<td>Common Bivariate Trellis Plots</td></tr>
+<tr><td width="25%"><a href="barchart.table.html">barchart.array</a></td>
+<td>table methods for barchart and dotplot</td></tr>
+<tr><td width="25%"><a href="xyplot.html">barchart.default</a></td>
+<td>Common Bivariate Trellis Plots</td></tr>
+<tr><td width="25%"><a href="xyplot.html">barchart.formula</a></td>
+<td>Common Bivariate Trellis Plots</td></tr>
+<tr><td width="25%"><a href="barchart.table.html">barchart.matrix</a></td>
+<td>table methods for barchart and dotplot</td></tr>
+<tr><td width="25%"><a href="xyplot.html">barchart.numeric</a></td>
+<td>Common Bivariate Trellis Plots</td></tr>
+<tr><td width="25%"><a href="barchart.table.html">barchart.table</a></td>
+<td>table methods for barchart and dotplot</td></tr>
+<tr><td width="25%"><a href="barley.html">barley</a></td>
+<td>Yield data from a Minnesota barley trial</td></tr>
+<tr><td width="25%"><a href="xyplot.html">bwplot</a></td>
+<td>Common Bivariate Trellis Plots</td></tr>
+<tr><td width="25%"><a href="xyplot.html">bwplot.formula</a></td>
+<td>Common Bivariate Trellis Plots</td></tr>
+<tr><td width="25%"><a href="xyplot.html">bwplot.numeric</a></td>
+<td>Common Bivariate Trellis Plots</td></tr>
+</table>
+
+<h2><a name="C">-- C --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="trellis.device.html">canonical.theme</a></td>
+<td>Initializing Trellis Displays</td></tr>
+<tr><td width="25%"><a href="cloud.html">cloud</a></td>
+<td>3d Scatter Plot and Wireframe Surface Plot</td></tr>
+<tr><td width="25%"><a href="cloud.html">cloud.formula</a></td>
+<td>3d Scatter Plot and Wireframe Surface Plot</td></tr>
+<tr><td width="25%"><a href="cloud.html">cloud.matrix</a></td>
+<td>3d Scatter Plot and Wireframe Surface Plot</td></tr>
+<tr><td width="25%"><a href="cloud.html">cloud.table</a></td>
+<td>3d Scatter Plot and Wireframe Surface Plot</td></tr>
+<tr><td width="25%"><a href="trellis.device.html">col.whitebg</a></td>
+<td>Initializing Trellis Displays</td></tr>
+<tr><td width="25%"><a href="levelplot.html">contourplot</a></td>
+<td>Level plots and contour plots</td></tr>
+<tr><td width="25%"><a href="levelplot.html">contourplot.array</a></td>
+<td>Level plots and contour plots</td></tr>
+<tr><td width="25%"><a href="levelplot.html">contourplot.formula</a></td>
+<td>Level plots and contour plots</td></tr>
+<tr><td width="25%"><a href="levelplot.html">contourplot.matrix</a></td>
+<td>Level plots and contour plots</td></tr>
+<tr><td width="25%"><a href="levelplot.html">contourplot.table</a></td>
+<td>Level plots and contour plots</td></tr>
+<tr><td width="25%"><a href="panel.number.html">current.column</a></td>
+<td>Accessing Auxiliary Information During Plotting</td></tr>
+<tr><td width="25%"><a href="panel.axis.html">current.panel.limits</a></td>
+<td>Panel Function for Drawing Axis Ticks and Labels</td></tr>
+<tr><td width="25%"><a href="panel.number.html">current.row</a></td>
+<td>Accessing Auxiliary Information During Plotting</td></tr>
+</table>
+
+<h2><a name="D">-- D --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="histogram.html">densityplot</a></td>
+<td>Histograms and Kernel Density Plots</td></tr>
+<tr><td width="25%"><a href="histogram.html">densityplot.formula</a></td>
+<td>Histograms and Kernel Density Plots</td></tr>
+<tr><td width="25%"><a href="histogram.html">densityplot.numeric</a></td>
+<td>Histograms and Kernel Density Plots</td></tr>
+<tr><td width="25%"><a href="panel.pairs.html">diag.panel.splom</a></td>
+<td>Default Superpanel Function for splom</td></tr>
+<tr><td width="25%"><a href="print.trellis.html">dim.trellis</a></td>
+<td>Plot and Summarize Trellis Objects</td></tr>
+<tr><td width="25%"><a href="print.trellis.html">dimnames.trellis</a></td>
+<td>Plot and Summarize Trellis Objects</td></tr>
+<tr><td width="25%"><a href="histogram.html">do.breaks</a></td>
+<td>Histograms and Kernel Density Plots</td></tr>
+<tr><td width="25%"><a href="xyplot.html">dotplot</a></td>
+<td>Common Bivariate Trellis Plots</td></tr>
+<tr><td width="25%"><a href="barchart.table.html">dotplot.array</a></td>
+<td>table methods for barchart and dotplot</td></tr>
+<tr><td width="25%"><a href="xyplot.html">dotplot.default</a></td>
+<td>Common Bivariate Trellis Plots</td></tr>
+<tr><td width="25%"><a href="xyplot.html">dotplot.formula</a></td>
+<td>Common Bivariate Trellis Plots</td></tr>
+<tr><td width="25%"><a href="barchart.table.html">dotplot.matrix</a></td>
+<td>table methods for barchart and dotplot</td></tr>
+<tr><td width="25%"><a href="xyplot.html">dotplot.numeric</a></td>
+<td>Common Bivariate Trellis Plots</td></tr>
+<tr><td width="25%"><a href="barchart.table.html">dotplot.table</a></td>
+<td>table methods for barchart and dotplot</td></tr>
+<tr><td width="25%"><a href="draw.colorkey.html">draw.colorkey</a></td>
+<td>Produce a Colorkey for levelplot</td></tr>
+<tr><td width="25%"><a href="draw.key.html">draw.key</a></td>
+<td>Produce a Legend or Key</td></tr>
+</table>
+
+<h2><a name="E">-- E --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="environmental.html">environmental</a></td>
+<td>Atmospheric environmental conditions in New York City</td></tr>
+<tr><td width="25%"><a href="shingles.html">equal.count</a></td>
+<td>shingles</td></tr>
+<tr><td width="25%"><a href="ethanol.html">ethanol</a></td>
+<td>Engine exhaust fumes from burning ethanol</td></tr>
+</table>
+
+<h2><a name="H">-- H --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="histogram.html">histogram</a></td>
+<td>Histograms and Kernel Density Plots</td></tr>
+<tr><td width="25%"><a href="histogram.html">histogram.factor</a></td>
+<td>Histograms and Kernel Density Plots</td></tr>
+<tr><td width="25%"><a href="histogram.html">histogram.formula</a></td>
+<td>Histograms and Kernel Density Plots</td></tr>
+<tr><td width="25%"><a href="histogram.html">histogram.numeric</a></td>
+<td>Histograms and Kernel Density Plots</td></tr>
+</table>
+
+<h2><a name="I">-- I --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="shingles.html">is.shingle</a></td>
+<td>shingles</td></tr>
+</table>
+
+<h2><a name="L">-- L --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="llines.html">larrows</a></td>
+<td>Replacements of traditional graphics functions</td></tr>
+<tr><td width="25%"><a href="Lattice.html">Lattice</a></td>
+<td>Lattice Graphics</td></tr>
+<tr><td width="25%"><a href="Lattice.html">lattice</a></td>
+<td>Lattice Graphics</td></tr>
+<tr><td width="25%"><a href="lattice.options.html">lattice.getOption</a></td>
+<td>Low-level Options Controlling Behaviour of Lattice</td></tr>
+<tr><td width="25%"><a href="lattice.options.html">lattice.options</a></td>
+<td>Low-level Options Controlling Behaviour of Lattice</td></tr>
+<tr><td width="25%"><a href="latticeParseFormula.html">latticeParseFormula</a></td>
+<td>Parse Trellis formula</td></tr>
+<tr><td width="25%"><a href="level.colors.html">level.colors</a></td>
+<td>A function to compute false colors representing a numeric or categorical variable</td></tr>
+<tr><td width="25%"><a href="levelplot.html">levelplot</a></td>
+<td>Level plots and contour plots</td></tr>
+<tr><td width="25%"><a href="levelplot.html">levelplot.array</a></td>
+<td>Level plots and contour plots</td></tr>
+<tr><td width="25%"><a href="levelplot.html">levelplot.formula</a></td>
+<td>Level plots and contour plots</td></tr>
+<tr><td width="25%"><a href="levelplot.html">levelplot.matrix</a></td>
+<td>Level plots and contour plots</td></tr>
+<tr><td width="25%"><a href="levelplot.html">levelplot.table</a></td>
+<td>Level plots and contour plots</td></tr>
+<tr><td width="25%"><a href="llines.html">llines</a></td>
+<td>Replacements of traditional graphics functions</td></tr>
+<tr><td width="25%"><a href="llines.html">llines.default</a></td>
+<td>Replacements of traditional graphics functions</td></tr>
+<tr><td width="25%"><a href="llines.html">lplot.xy</a></td>
+<td>Replacements of traditional graphics functions</td></tr>
+<tr><td width="25%"><a href="llines.html">lpoints</a></td>
+<td>Replacements of traditional graphics functions</td></tr>
+<tr><td width="25%"><a href="llines.html">lpoints.default</a></td>
+<td>Replacements of traditional graphics functions</td></tr>
+<tr><td width="25%"><a href="llines.html">lpolygon</a></td>
+<td>Replacements of traditional graphics functions</td></tr>
+<tr><td width="25%"><a href="llines.html">lrect</a></td>
+<td>Replacements of traditional graphics functions</td></tr>
+<tr><td width="25%"><a href="llines.html">lsegments</a></td>
+<td>Replacements of traditional graphics functions</td></tr>
+<tr><td width="25%"><a href="lset.html">lset</a></td>
+<td>Interface to modify Trellis Settings - Defunct</td></tr>
+<tr><td width="25%"><a href="llines.html">ltext</a></td>
+<td>Replacements of traditional graphics functions</td></tr>
+<tr><td width="25%"><a href="llines.html">ltext.default</a></td>
+<td>Replacements of traditional graphics functions</td></tr>
+<tr><td width="25%"><a href="utilities.3d.html">ltransform3dMatrix</a></td>
+<td>Utility functions for 3-D plots</td></tr>
+<tr><td width="25%"><a href="utilities.3d.html">ltransform3dto3d</a></td>
+<td>Utility functions for 3-D plots</td></tr>
+</table>
+
+<h2><a name="M">-- M --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="make.groups.html">make.groups</a></td>
+<td>Grouped data from multiple vectors</td></tr>
+<tr><td width="25%"><a href="melanoma.html">melanoma</a></td>
+<td>Melanoma skin cancer incidence</td></tr>
+</table>
+
+<h2><a name="O">-- O --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="oneway.html">oneway</a></td>
+<td>Fit One-way Model</td></tr>
+</table>
+
+<h2><a name="P">-- P --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="panel.number.html">packet.number</a></td>
+<td>Accessing Auxiliary Information During Plotting</td></tr>
+<tr><td width="25%"><a href="packet.panel.default.html">packet.panel.default</a></td>
+<td>Associating Packets with Panels</td></tr>
+<tr><td width="25%"><a href="utilities.3d.html">palette.shade</a></td>
+<td>Utility functions for 3-D plots</td></tr>
+<tr><td width="25%"><a href="panel.cloud.html">panel.3dscatter</a></td>
+<td>Default Panel Function for cloud</td></tr>
+<tr><td width="25%"><a href="panel.cloud.html">panel.3dwire</a></td>
+<td>Default Panel Function for cloud</td></tr>
+<tr><td width="25%"><a href="panel.functions.html">panel.abline</a></td>
+<td>Useful Panel Function Components</td></tr>
+<tr><td width="25%"><a href="llines.html">panel.arrows</a></td>
+<td>Replacements of traditional graphics functions</td></tr>
+<tr><td width="25%"><a href="panel.functions.html">panel.average</a></td>
+<td>Useful Panel Function Components</td></tr>
+<tr><td width="25%"><a href="panel.axis.html">panel.axis</a></td>
+<td>Panel Function for Drawing Axis Ticks and Labels</td></tr>
+<tr><td width="25%"><a href="panel.barchart.html">panel.barchart</a></td>
+<td>Default Panel Function for barchart</td></tr>
+<tr><td width="25%"><a href="interaction.html">panel.brush.splom</a></td>
+<td>Functions to Interact with Lattice Plots</td></tr>
+<tr><td width="25%"><a href="panel.bwplot.html">panel.bwplot</a></td>
+<td>Default Panel Function for bwplot</td></tr>
+<tr><td width="25%"><a href="panel.cloud.html">panel.cloud</a></td>
+<td>Default Panel Function for cloud</td></tr>
+<tr><td width="25%"><a href="panel.levelplot.html">panel.contourplot</a></td>
+<td>Panel Functions for levelplot and contourplot</td></tr>
+<tr><td width="25%"><a href="panel.functions.html">panel.curve</a></td>
+<td>Useful Panel Function Components</td></tr>
+<tr><td width="25%"><a href="panel.densityplot.html">panel.densityplot</a></td>
+<td>Default Panel Function for densityplot</td></tr>
+<tr><td width="25%"><a href="panel.dotplot.html">panel.dotplot</a></td>
+<td>Default Panel Function for dotplot</td></tr>
+<tr><td width="25%"><a href="print.trellis.html">panel.error</a></td>
+<td>Plot and Summarize Trellis Objects</td></tr>
+<tr><td width="25%"><a href="panel.functions.html">panel.fill</a></td>
+<td>Useful Panel Function Components</td></tr>
+<tr><td width="25%"><a href="panel.functions.html">panel.functions</a></td>
+<td>Useful Panel Function Components</td></tr>
+<tr><td width="25%"><a href="panel.functions.html">panel.grid</a></td>
+<td>Useful Panel Function Components</td></tr>
+<tr><td width="25%"><a href="panel.histogram.html">panel.histogram</a></td>
+<td>Default Panel Function for histogram</td></tr>
+<tr><td width="25%"><a href="interaction.html">panel.identify</a></td>
+<td>Functions to Interact with Lattice Plots</td></tr>
+<tr><td width="25%"><a href="interaction.html">panel.identify.cloud</a></td>
+<td>Functions to Interact with Lattice Plots</td></tr>
+<tr><td width="25%"><a href="interaction.html">panel.identify.qqmath</a></td>
+<td>Functions to Interact with Lattice Plots</td></tr>
+<tr><td width="25%"><a href="panel.levelplot.html">panel.levelplot</a></td>
+<td>Panel Functions for levelplot and contourplot</td></tr>
+<tr><td width="25%"><a href="panel.levelplot.html">panel.levelplot.raster</a></td>
+<td>Panel Functions for levelplot and contourplot</td></tr>
+<tr><td width="25%"><a href="panel.functions.html">panel.linejoin</a></td>
+<td>Useful Panel Function Components</td></tr>
+<tr><td width="25%"><a href="llines.html">panel.lines</a></td>
+<td>Replacements of traditional graphics functions</td></tr>
+<tr><td width="25%"><a href="interaction.html">panel.link.splom</a></td>
+<td>Functions to Interact with Lattice Plots</td></tr>
+<tr><td width="25%"><a href="panel.functions.html">panel.lmline</a></td>
+<td>Useful Panel Function Components</td></tr>
+<tr><td width="25%"><a href="panel.loess.html">panel.loess</a></td>
+<td>Panel Function to Add a LOESS Smooth</td></tr>
+<tr><td width="25%"><a href="panel.functions.html">panel.mathdensity</a></td>
+<td>Useful Panel Function Components</td></tr>
+<tr><td width="25%"><a href="panel.number.html">panel.number</a></td>
+<td>Accessing Auxiliary Information During Plotting</td></tr>
+<tr><td width="25%"><a href="panel.pairs.html">panel.pairs</a></td>
+<td>Default Superpanel Function for splom</td></tr>
+<tr><td width="25%"><a href="panel.parallel.html">panel.parallel</a></td>
+<td>Default Panel Function for parallel</td></tr>
+<tr><td width="25%"><a href="llines.html">panel.points</a></td>
+<td>Replacements of traditional graphics functions</td></tr>
+<tr><td width="25%"><a href="llines.html">panel.polygon</a></td>
+<td>Replacements of traditional graphics functions</td></tr>
+<tr><td width="25%"><a href="panel.xyplot.html">panel.qq</a></td>
+<td>Default Panel Function for xyplot</td></tr>
+<tr><td width="25%"><a href="panel.qqmath.html">panel.qqmath</a></td>
+<td>Default Panel Function for qqmath</td></tr>
+<tr><td width="25%"><a href="panel.qqmathline.html">panel.qqmathline</a></td>
+<td>Useful panel function with qqmath</td></tr>
+<tr><td width="25%"><a href="llines.html">panel.rect</a></td>
+<td>Replacements of traditional graphics functions</td></tr>
+<tr><td width="25%"><a href="panel.functions.html">panel.refline</a></td>
+<td>Useful Panel Function Components</td></tr>
+<tr><td width="25%"><a href="panel.functions.html">panel.rug</a></td>
+<td>Useful Panel Function Components</td></tr>
+<tr><td width="25%"><a href="llines.html">panel.segments</a></td>
+<td>Replacements of traditional graphics functions</td></tr>
+<tr><td width="25%"><a href="panel.smoothScatter.html">panel.smoothScatter</a></td>
+<td>Lattice panel function analogous to smoothScatter</td></tr>
+<tr><td width="25%"><a href="panel.spline.html">panel.spline</a></td>
+<td>Panel Function to Add a Spline Smooth</td></tr>
+<tr><td width="25%"><a href="panel.xyplot.html">panel.splom</a></td>
+<td>Default Panel Function for xyplot</td></tr>
+<tr><td width="25%"><a href="panel.stripplot.html">panel.stripplot</a></td>
+<td>Default Panel Function for stripplot</td></tr>
+<tr><td width="25%"><a href="panel.superpose.html">panel.superpose</a></td>
+<td>Panel Function for Display Marked by groups</td></tr>
+<tr><td width="25%"><a href="panel.superpose.html">panel.superpose.2</a></td>
+<td>Panel Function for Display Marked by groups</td></tr>
+<tr><td width="25%"><a href="panel.superpose.html">panel.superpose.plain</a></td>
+<td>Panel Function for Display Marked by groups</td></tr>
+<tr><td width="25%"><a href="llines.html">panel.text</a></td>
+<td>Replacements of traditional graphics functions</td></tr>
+<tr><td width="25%"><a href="tmd.html">panel.tmd.default</a></td>
+<td>Tukey Mean-Difference Plot</td></tr>
+<tr><td width="25%"><a href="tmd.html">panel.tmd.qqmath</a></td>
+<td>Tukey Mean-Difference Plot</td></tr>
+<tr><td width="25%"><a href="panel.violin.html">panel.violin</a></td>
+<td>Panel Function to create Violin Plots</td></tr>
+<tr><td width="25%"><a href="panel.cloud.html">panel.wireframe</a></td>
+<td>Default Panel Function for cloud</td></tr>
+<tr><td width="25%"><a href="panel.xyplot.html">panel.xyplot</a></td>
+<td>Default Panel Function for xyplot</td></tr>
+<tr><td width="25%"><a href="splom.html">parallel</a></td>
+<td>Scatter Plot Matrices</td></tr>
+<tr><td width="25%"><a href="splom.html">parallelplot</a></td>
+<td>Scatter Plot Matrices</td></tr>
+<tr><td width="25%"><a href="splom.html">parallelplot.data.frame</a></td>
+<td>Scatter Plot Matrices</td></tr>
+<tr><td width="25%"><a href="splom.html">parallelplot.formula</a></td>
+<td>Scatter Plot Matrices</td></tr>
+<tr><td width="25%"><a href="splom.html">parallelplot.matrix</a></td>
+<td>Scatter Plot Matrices</td></tr>
+<tr><td width="25%"><a href="shingles.html">plot.shingle</a></td>
+<td>shingles</td></tr>
+<tr><td width="25%"><a href="print.trellis.html">plot.trellis</a></td>
+<td>Plot and Summarize Trellis Objects</td></tr>
+<tr><td width="25%"><a href="prepanel.default.html">prepanel.default.bwplot</a></td>
+<td>Default Prepanel Functions</td></tr>
+<tr><td width="25%"><a href="prepanel.default.html">prepanel.default.cloud</a></td>
+<td>Default Prepanel Functions</td></tr>
+<tr><td width="25%"><a href="prepanel.default.html">prepanel.default.densityplot</a></td>
+<td>Default Prepanel Functions</td></tr>
+<tr><td width="25%"><a href="prepanel.default.html">prepanel.default.histogram</a></td>
+<td>Default Prepanel Functions</td></tr>
+<tr><td width="25%"><a href="prepanel.default.html">prepanel.default.levelplot</a></td>
+<td>Default Prepanel Functions</td></tr>
+<tr><td width="25%"><a href="prepanel.default.html">prepanel.default.parallel</a></td>
+<td>Default Prepanel Functions</td></tr>
+<tr><td width="25%"><a href="prepanel.default.html">prepanel.default.qq</a></td>
+<td>Default Prepanel Functions</td></tr>
+<tr><td width="25%"><a href="prepanel.default.html">prepanel.default.qqmath</a></td>
+<td>Default Prepanel Functions</td></tr>
+<tr><td width="25%"><a href="prepanel.default.html">prepanel.default.splom</a></td>
+<td>Default Prepanel Functions</td></tr>
+<tr><td width="25%"><a href="prepanel.default.html">prepanel.default.xyplot</a></td>
+<td>Default Prepanel Functions</td></tr>
+<tr><td width="25%"><a href="prepanel.functions.html">prepanel.lmline</a></td>
+<td>Useful Prepanel Function for Lattice</td></tr>
+<tr><td width="25%"><a href="prepanel.functions.html">prepanel.loess</a></td>
+<td>Useful Prepanel Function for Lattice</td></tr>
+<tr><td width="25%"><a href="prepanel.functions.html">prepanel.qqmathline</a></td>
+<td>Useful Prepanel Function for Lattice</td></tr>
+<tr><td width="25%"><a href="prepanel.functions.html">prepanel.spline</a></td>
+<td>Useful Prepanel Function for Lattice</td></tr>
+<tr><td width="25%"><a href="tmd.html">prepanel.tmd.default</a></td>
+<td>Tukey Mean-Difference Plot</td></tr>
+<tr><td width="25%"><a href="tmd.html">prepanel.tmd.qqmath</a></td>
+<td>Tukey Mean-Difference Plot</td></tr>
+<tr><td width="25%"><a href="shingles.html">print.shingle</a></td>
+<td>shingles</td></tr>
+<tr><td width="25%"><a href="shingles.html">print.shingleLevel</a></td>
+<td>shingles</td></tr>
+<tr><td width="25%"><a href="print.trellis.html">print.trellis</a></td>
+<td>Plot and Summarize Trellis Objects</td></tr>
+</table>
+
+<h2><a name="Q">-- Q --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="qq.html">qq</a></td>
+<td>Quantile-Quantile Plots of Two Samples</td></tr>
+<tr><td width="25%"><a href="qq.html">qq.formula</a></td>
+<td>Quantile-Quantile Plots of Two Samples</td></tr>
+<tr><td width="25%"><a href="qqmath.html">qqmath</a></td>
+<td>Q-Q Plot with Theoretical Distribution</td></tr>
+<tr><td width="25%"><a href="qqmath.html">qqmath.formula</a></td>
+<td>Q-Q Plot with Theoretical Distribution</td></tr>
+<tr><td width="25%"><a href="qqmath.html">qqmath.numeric</a></td>
+<td>Q-Q Plot with Theoretical Distribution</td></tr>
+</table>
+
+<h2><a name="R">-- R --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="rfs.html">rfs</a></td>
+<td>Residual and Fit Spread Plots</td></tr>
+<tr><td width="25%"><a href="Rows.html">Rows</a></td>
+<td>Extract rows from a list</td></tr>
+</table>
+
+<h2><a name="S">-- S --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="shingles.html">shingle</a></td>
+<td>shingles</td></tr>
+<tr><td width="25%"><a href="trellis.par.get.html">show.settings</a></td>
+<td>Graphical Parameters for Trellis Displays</td></tr>
+<tr><td width="25%"><a href="simpleKey.html">simpleKey</a></td>
+<td>Function to generate a simple key</td></tr>
+<tr><td width="25%"><a href="simpleTheme.html">simpleTheme</a></td>
+<td>Function to generate a simple theme</td></tr>
+<tr><td width="25%"><a href="singer.html">singer</a></td>
+<td>Heights of New York Choral Society singers</td></tr>
+<tr><td width="25%"><a href="splom.html">splom</a></td>
+<td>Scatter Plot Matrices</td></tr>
+<tr><td width="25%"><a href="splom.html">splom.data.frame</a></td>
+<td>Scatter Plot Matrices</td></tr>
+<tr><td width="25%"><a href="splom.html">splom.formula</a></td>
+<td>Scatter Plot Matrices</td></tr>
+<tr><td width="25%"><a href="splom.html">splom.matrix</a></td>
+<td>Scatter Plot Matrices</td></tr>
+<tr><td width="25%"><a href="trellis.device.html">standard.theme</a></td>
+<td>Initializing Trellis Displays</td></tr>
+<tr><td width="25%"><a href="strip.default.html">strip.custom</a></td>
+<td>Default Trellis Strip Function</td></tr>
+<tr><td width="25%"><a href="strip.default.html">strip.default</a></td>
+<td>Default Trellis Strip Function</td></tr>
+<tr><td width="25%"><a href="xyplot.html">stripplot</a></td>
+<td>Common Bivariate Trellis Plots</td></tr>
+<tr><td width="25%"><a href="xyplot.html">stripplot.formula</a></td>
+<td>Common Bivariate Trellis Plots</td></tr>
+<tr><td width="25%"><a href="xyplot.html">stripplot.numeric</a></td>
+<td>Common Bivariate Trellis Plots</td></tr>
+<tr><td width="25%"><a href="shingles.html">summary.shingle</a></td>
+<td>shingles</td></tr>
+<tr><td width="25%"><a href="print.trellis.html">summary.trellis</a></td>
+<td>Plot and Summarize Trellis Objects</td></tr>
+</table>
+
+<h2><a name="T">-- T --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="update.trellis.html">t.trellis</a></td>
+<td>Retrieve and Update Trellis Object</td></tr>
+<tr><td width="25%"><a href="tmd.html">tmd</a></td>
+<td>Tukey Mean-Difference Plot</td></tr>
+<tr><td width="25%"><a href="tmd.html">tmd.formula</a></td>
+<td>Tukey Mean-Difference Plot</td></tr>
+<tr><td width="25%"><a href="tmd.html">tmd.trellis</a></td>
+<td>Tukey Mean-Difference Plot</td></tr>
+<tr><td width="25%"><a href="panel.number.html">trellis.currentLayout</a></td>
+<td>Accessing Auxiliary Information During Plotting</td></tr>
+<tr><td width="25%"><a href="trellis.device.html">trellis.device</a></td>
+<td>Initializing Trellis Displays</td></tr>
+<tr><td width="25%"><a href="interaction.html">trellis.focus</a></td>
+<td>Functions to Interact with Lattice Plots</td></tr>
+<tr><td width="25%"><a href="interaction.html">trellis.grobname</a></td>
+<td>Functions to Interact with Lattice Plots</td></tr>
+<tr><td width="25%"><a href="update.trellis.html">trellis.last.object</a></td>
+<td>Retrieve and Update Trellis Object</td></tr>
+<tr><td width="25%"><a href="trellis.object.html">trellis.object</a></td>
+<td>A Trellis Plot Object</td></tr>
+<tr><td width="25%"><a href="interaction.html">trellis.panelArgs</a></td>
+<td>Functions to Interact with Lattice Plots</td></tr>
+<tr><td width="25%"><a href="trellis.par.get.html">trellis.par.get</a></td>
+<td>Graphical Parameters for Trellis Displays</td></tr>
+<tr><td width="25%"><a href="trellis.par.get.html">trellis.par.set</a></td>
+<td>Graphical Parameters for Trellis Displays</td></tr>
+<tr><td width="25%"><a href="interaction.html">trellis.switchFocus</a></td>
+<td>Functions to Interact with Lattice Plots</td></tr>
+<tr><td width="25%"><a href="interaction.html">trellis.unfocus</a></td>
+<td>Functions to Interact with Lattice Plots</td></tr>
+<tr><td width="25%"><a href="interaction.html">trellis.vpname</a></td>
+<td>Functions to Interact with Lattice Plots</td></tr>
+</table>
+
+<h2><a name="U">-- U --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="update.trellis.html">update.trellis</a></td>
+<td>Retrieve and Update Trellis Object</td></tr>
+<tr><td width="25%"><a href="utilities.3d.html">utilities.3d</a></td>
+<td>Utility functions for 3-D plots</td></tr>
+</table>
+
+<h2><a name="W">-- W --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="panel.number.html">which.packet</a></td>
+<td>Accessing Auxiliary Information During Plotting</td></tr>
+<tr><td width="25%"><a href="cloud.html">wireframe</a></td>
+<td>3d Scatter Plot and Wireframe Surface Plot</td></tr>
+<tr><td width="25%"><a href="cloud.html">wireframe.formula</a></td>
+<td>3d Scatter Plot and Wireframe Surface Plot</td></tr>
+<tr><td width="25%"><a href="cloud.html">wireframe.matrix</a></td>
+<td>3d Scatter Plot and Wireframe Surface Plot</td></tr>
+</table>
+
+<h2><a name="X">-- X --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="axis.default.html">xscale.components.default</a></td>
+<td>Default axis annotation utilities</td></tr>
+<tr><td width="25%"><a href="xyplot.html">xyplot</a></td>
+<td>Common Bivariate Trellis Plots</td></tr>
+<tr><td width="25%"><a href="xyplot.html">xyplot.formula</a></td>
+<td>Common Bivariate Trellis Plots</td></tr>
+<tr><td width="25%"><a href="xyplot.ts.html">xyplot.ts</a></td>
+<td>Time series plotting methods</td></tr>
+</table>
+
+<h2><a name="Y">-- Y --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="axis.default.html">yscale.components.default</a></td>
+<td>Default axis annotation utilities</td></tr>
+</table>
+
+<h2><a name="misc">-- misc --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="shingles.html">[.shingle</a></td>
+<td>shingles</td></tr>
+<tr><td width="25%"><a href="update.trellis.html">[.trellis</a></td>
+<td>Retrieve and Update Trellis Object</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/lattice/html/R.css b/win32/deps/library/lattice/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/lattice/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/lattice/libs/i386/lattice.dll b/win32/deps/library/lattice/libs/i386/lattice.dll
new file mode 100644
index 0000000..47736a3
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diff --git a/win32/deps/library/lattice/po/de/LC_MESSAGES/R-lattice.mo b/win32/deps/library/lattice/po/de/LC_MESSAGES/R-lattice.mo
new file mode 100644
index 0000000..026ccdd
Binary files /dev/null and b/win32/deps/library/lattice/po/de/LC_MESSAGES/R-lattice.mo differ
diff --git a/win32/deps/library/lattice/po/en quot/LC_MESSAGES/R-lattice.mo b/win32/deps/library/lattice/po/en quot/LC_MESSAGES/R-lattice.mo
new file mode 100644
index 0000000..62ba516
Binary files /dev/null and b/win32/deps/library/lattice/po/en quot/LC_MESSAGES/R-lattice.mo differ
diff --git a/win32/deps/library/lattice/po/fr/LC_MESSAGES/R-lattice.mo b/win32/deps/library/lattice/po/fr/LC_MESSAGES/R-lattice.mo
new file mode 100644
index 0000000..06d9e4c
Binary files /dev/null and b/win32/deps/library/lattice/po/fr/LC_MESSAGES/R-lattice.mo differ
diff --git a/win32/deps/library/lattice/tests/MASSch04.R b/win32/deps/library/lattice/tests/MASSch04.R
new file mode 100644
index 0000000..5f74de8
--- /dev/null
+++ b/win32/deps/library/lattice/tests/MASSch04.R
@@ -0,0 +1,179 @@
+#-*- R -*-
+
+## Script from Fourth Edition of `Modern Applied Statistics with S'
+
+# Chapter 4 Graphical Output
+
+library(MASS)
+library(lattice)
+trellis.device(postscript, file="ch04.ps", width=8, height=6,
+ pointsize=9)
+options(echo=T, width=65, digits=5)
+
+
+# 4.2 Basic plotting functions
+
+topo.loess <- loess(z ~ x * y, topo, degree = 2, span = 0.25)
+topo.mar <- list(x = seq(0, 6.5, 0.2), y=seq(0, 6.5, 0.2))
+topo.lo <- predict(topo.loess, expand.grid(topo.mar))
+topo.lo1 <- cbind(expand.grid(x=topo.mar$x, y=topo.mar$y),
+ z=as.vector(topo.lo))
+contourplot(z ~ x * y, topo.lo1, aspect = 1,
+ at = seq(700, 1000, 25), xlab = "", ylab = "",
+ panel = function(x, y, subscripts, ...) {
+ panel.levelplot(x, y, subscripts, ...)
+ panel.xyplot(topo$x, topo$y, cex = 0.5)
+ }
+)
+
+
+
+
+
+
+
+# 4.5 Trellis graphics
+
+
+xyplot(time ~ dist, data = hills,
+ panel = function(x, y, ...) {
+ panel.xyplot(x, y, ...)
+ panel.lmline(x, y, type = "l")
+ panel.abline(lqs(y ~ x), lty = 3)
+# identify(x, y, row.names(hills))
+ }
+)
+
+bwplot(Expt ~ Speed, data = michelson, ylab = "Experiment No.",
+ main = "Speed of Light Data")
+
+
+data(swiss)
+splom(~ swiss, aspect = "fill",
+ panel = function(x, y, ...) {
+ panel.xyplot(x, y, ...); panel.loess(x, y, ...)
+ }
+)
+
+sps <- trellis.par.get("superpose.symbol")
+sps$pch <- 1:7
+trellis.par.set("superpose.symbol", sps)
+xyplot(Time ~ Viscosity, data = stormer, groups = Wt,
+ panel = panel.superpose, type = "b",
+ key = list(columns = 3,
+ text = list(paste(c("Weight: ", "", ""),
+ unique(stormer$Wt), "gms")),
+ points = Rows(sps, 1:3)
+ )
+)
+rm(sps)
+
+topo.plt <- expand.grid(topo.mar)
+topo.plt$pred <- as.vector(predict(topo.loess, topo.plt))
+levelplot(pred ~ x * y, topo.plt, aspect = 1,
+ at = seq(690, 960, 10), xlab = "", ylab = "",
+ panel = function(x, y, subscripts, ...) {
+ panel.levelplot(x, y, subscripts, ...)
+ panel.xyplot(topo$x,topo$y, cex = 0.5, col = 1)
+ }
+)
+
+## if (F) {
+wireframe(pred ~ x * y, topo.plt, aspect = c(1, 0.5),
+ drape = T, screen = list(z = -150, x = -60),
+ colorkey = list(space="right", height=0.6))
+## }
+
+lcrabs.pc <- predict(princomp(log(crabs[,4:8])))
+crabs.grp <- c("B", "b", "O", "o")[rep(1:4, each = 50)]
+splom(~ lcrabs.pc[, 1:3], groups = crabs.grp,
+ panel = panel.superpose,
+ key = list(text = list(c("Blue male", "Blue female",
+ "Orange Male", "Orange female")),
+ points = Rows(trellis.par.get("superpose.symbol"), 1:4),
+ columns = 4)
+ )
+
+sex <- crabs$sex
+levels(sex) <- c("Female", "Male")
+sp <- crabs$sp
+levels(sp) <- c("Blue", "Orange")
+splom(~ lcrabs.pc[, 1:3] | sp*sex, cex = 0.5, pscales = 0)
+
+Quine <- quine
+levels(Quine$Eth) <- c("Aboriginal", "Non-aboriginal")
+levels(Quine$Sex) <- c("Female", "Male")
+levels(Quine$Age) <- c("primary", "first form",
+ "second form", "third form")
+levels(Quine$Lrn) <- c("Average learner", "Slow learner")
+bwplot(Age ~ Days | Sex*Lrn*Eth, data = Quine)
+
+bwplot(Age ~ Days | Sex*Lrn*Eth, data = Quine, layout = c(4, 2),
+ strip = function(...) strip.default(..., style = 1))
+
+stripplot(Age ~ Days | Sex*Lrn*Eth, data = Quine,
+ jitter = TRUE, layout = c(4, 2))
+
+stripplot(Age ~ Days | Eth*Sex, data = Quine,
+ groups = Lrn, jitter = TRUE,
+ panel = function(x, y, subscripts, jitter.data = F, ...) {
+ if(jitter.data) y <- jitter(as.numeric(y))
+ panel.superpose(x, y, subscripts, ...)
+ },
+ xlab = "Days of absence",
+ between = list(y = 1), par.strip.text = list(cex = 0.7),
+ key = list(columns = 2, text = list(levels(Quine$Lrn)),
+ points = Rows(trellis.par.get("superpose.symbol"), 1:2)
+ ),
+ strip = function(...)
+ strip.default(..., strip.names = c(TRUE, TRUE), style = 1)
+)
+
+fgl0 <- fgl[ ,-10] # omit type.
+fgl.df <- data.frame(type = rep(fgl$type, 9),
+ y = as.vector(as.matrix(fgl0)),
+ meas = factor(rep(1:9, each = 214), labels = names(fgl0)))
+stripplot(type ~ y | meas, data = fgl.df,
+ scales = list(x = "free"), xlab = "", cex = 0.5,
+ strip = function(...) strip.default(style = 1, ...))
+
+if(F) { # no data supplied
+xyplot(ratio ~ scant | subject, data = A5,
+ xlab = "scan interval (years)",
+ ylab = "ventricle/brain volume normalized to 1 at start",
+ subscripts = TRUE, ID = A5$ID,
+ strip = function(factor, ...)
+ strip.default(..., factor.levels = labs, style = 1),
+ layout = c(8, 5, 1),
+ skip = c(rep(FALSE, 37), rep(TRUE, 1), rep(FALSE, 1)),
+ panel = function(x, y, subscripts, ID) {
+ panel.xyplot(x, y, type = "b", cex = 0.5)
+ which <- unique(ID[subscripts])
+ panel.xyplot(c(0, 1.5), pr3[names(pr3) == which],
+ type = "l", lty = 3)
+ if(which == 303 || which == 341) points(1.4, 1.3)
+ })
+}
+
+Cath <- equal.count(swiss$Catholic, number = 6, overlap = 0.25)
+xyplot(Fertility ~ Education | Cath, data = swiss,
+ span = 1, layout = c(6, 1), aspect = 1,
+ panel = function(x, y, span) {
+ panel.xyplot(x, y); panel.loess(x, y, span)
+ }
+)
+
+Cath2 <- equal.count(swiss$Catholic, number = 2, overlap = 0)
+Agr <- equal.count(swiss$Agric, number = 3, overlap = 0.25)
+xyplot(Fertility ~ Education | Agr * Cath2, data = swiss,
+ span = 1, aspect = "xy",
+ panel = function(x, y, span) {
+ panel.xyplot(x, y); panel.loess(x, y, span)
+ }
+)
+
+Cath
+levels(Cath)
+plot(Cath, aspect = 0.3)
+
+# End of ch04
diff --git a/win32/deps/library/lattice/tests/dates.R b/win32/deps/library/lattice/tests/dates.R
new file mode 100644
index 0000000..88c2f37
--- /dev/null
+++ b/win32/deps/library/lattice/tests/dates.R
@@ -0,0 +1,25 @@
+
+postscript("date.ps")
+library(lattice)
+
+## POSIXt handling
+
+y <- Sys.time() + 10000 * 1:100
+x <- rnorm(100)
+b <- gl(3,1,100)
+
+xyplot(y ~ x | b)
+xyplot(y ~ x | b, scales = list(relation = "free", rot = 0))
+xyplot(y ~ x | b, scales = "sliced")
+
+## Date handling
+
+dat <-
+ data.frame(a = 1:10,
+ b = seq(as.Date("2003/1/1"), as.Date("2003/1/10"), by="day"))
+xyplot(a~b, dat)
+xyplot(a~b, dat, scales=list(x=list(at=dat$b)))
+
+
+dev.off()
+
diff --git a/win32/deps/library/lattice/tests/dotplotscoping.R b/win32/deps/library/lattice/tests/dotplotscoping.R
new file mode 100644
index 0000000..07f4c79
--- /dev/null
+++ b/win32/deps/library/lattice/tests/dotplotscoping.R
@@ -0,0 +1,13 @@
+postscript("dotplotscoping.ps")
+library(lattice)
+
+fubar <- function() {
+ k <- 2
+ kkk <- 1:10
+ names(kkk) <- 1:10
+ data = list(x=kkk)
+ dotplot(~x^k + rnorm(10), data)
+}
+
+fubar()
+dev.off()
diff --git a/win32/deps/library/lattice/tests/levelplot.R b/win32/deps/library/lattice/tests/levelplot.R
new file mode 100644
index 0000000..40cffc6
--- /dev/null
+++ b/win32/deps/library/lattice/tests/levelplot.R
@@ -0,0 +1,115 @@
+
+postscript("levelplot.ps")
+library(lattice)
+
+data(volcano)
+
+foo <-
+ data.frame(z = as.vector(volcano),
+ x = rep(1:87, 61),
+ y = rep(1:61, each = 87))
+
+levelplot(z ~ x * y, subset(foo, z > 150), contour = T)
+levelplot(z ~ x * y, foo, subset = z > 150, contour = T)
+contourplot(z ~ x * y, foo, subset = z > 150, cuts = 10)
+
+## subset group interaction has problems (does it any longer):
+
+cloud(Sepal.Length ~ Petal.Length * Petal.Width,
+ data = iris, cex = 0.8, groups = Species, subpanel = panel.superpose,
+ main = "Stereo", screen = list(z = 20, x = -70, y = 0), subset = 30:60)
+
+cloud(Sepal.Length ~ Petal.Length * Petal.Width,
+ data = iris[30:60, ], cex = 0.8, groups = Species, subpanel = panel.superpose,
+ main = "Stereo", screen = list(z = 20, x = -70, y = 0))
+
+
+levelplot(Sepal.Length ~ Petal.Length * Petal.Width,
+ data = iris, groups = Species,
+ subset = 30:60)
+
+
+
+
+cloud(z ~ x * y, foo)
+cloud(z ~ x * y, foo, subset = z > 150)
+
+
+
+## long format: NA's clipped at the beginning (??)
+
+splom(~iris[,1:4], iris, groups = Species)
+splom(~iris[,1:4], iris, groups = Species, subset = 70:130, auto.key = T)
+
+parallel(~iris[,1:4] | Species, iris, subset = 30:130)
+
+## NA-s in matrix
+
+volna <- volcano
+volna[20:40, 20:40] <- NA
+levelplot(volna)
+cloud(volna)
+wireframe(volna)
+
+
+
+dev.off()
+
+
+
+
+# grid.newpage()
+# pushViewport(viewport())
+# grid.lines(x = c(1:5, NA, 7:10) / 10,
+# y = c(1:5, NA, 7:10) / 10)
+
+# grid.points(x = c(1:5, NA, 7:10) / 10,
+# y = c(1:5, 6, 7:10) / 10)
+
+
+
+
+# grid.points(x = .5, y = .1, pch = 16, gp = gpar(cex = 1))
+# grid.points(x = .5, y = .2, pch = 16, gp = gpar(cex = 3))
+
+# grid.points(x = .5, y = .3, pch = '+', gp = gpar(cex = 1))
+# grid.points(x = .5, y = .4, pch = '+', gp = gpar(cex = 3))
+
+
+
+
+# viewport[ROOT] ->
+
+# (viewport[GRIDVP1182]->
+
+# (viewport[GRIDVP1185],
+# viewport[GRIDVP1187],
+# viewport[GRIDVP1189],
+# viewport[GRIDVP1190],
+
+# viewport[panel.1]->
+
+# (viewport[GRIDVP1184]->
+
+# (viewport[subpanel.1.1],
+# viewport[subpanel.1.2], viewport[subpanel.1.3],
+# viewport[subpanel.2.1], viewport[subpanel.2.2],
+# viewport[subpanel.2.3], viewport[subpanel.3.1],
+# viewport[subpanel.3.2], viewport[subpanel.3.3])),
+
+# viewport[panel.2]->
+# (viewport[GRIDVP1186]->
+# (viewport[subpanel.1.1],
+# viewport[subpanel.1.2], viewport[subpanel.1.3],
+# viewport[subpanel.2.1], viewport[subpanel.2.2],
+# viewport[subpanel.2.3], viewport[subpanel.3.1],
+# viewport[subpanel.3.2], viewport[subpanel.3.3])),
+
+# viewport[panel.3]->
+# (viewport[GRIDVP1188]->
+# (viewport[subpanel.1.1],
+# viewport[subpanel.1.2], viewport[subpanel.1.3],
+# viewport[subpanel.2.1], viewport[subpanel.2.2],
+# viewport[subpanel.2.3], viewport[subpanel.3.1],
+# viewport[subpanel.3.2], viewport[subpanel.3.3]))))
+
diff --git a/win32/deps/library/lattice/tests/scales.R b/win32/deps/library/lattice/tests/scales.R
new file mode 100644
index 0000000..0103ae7
--- /dev/null
+++ b/win32/deps/library/lattice/tests/scales.R
@@ -0,0 +1,174 @@
+
+postscript("scales.ps")
+## Testing weird scales options
+
+library(lattice)
+
+
+
+## relation = "free" for factors
+
+dat <- data.frame(a=letters[1:5], b=c("A","A","A","B","B"), y=1:5)
+dotplot(y ~ a | b, data=dat, scales = "same")
+dotplot(y ~ a | b, data=dat, scales = "free")
+dotplot(y ~ a | b, data=dat, scales = "sliced")
+
+
+
+dat <-
+ data.frame(a = letters[1:10],
+ b = c("A","A","A","B","B","A","B","B", "A", "A"))
+
+dat <- dat[sample(1:10, 200, rep = TRUE), ]
+dat$y <- rnorm(200, mean = unclass(as.factor(dat$a)))
+
+bwplot(a ~ y | b, data=dat, scales = "same")
+bwplot(a ~ y | b, data=dat, scales = "free")
+bwplot(a ~ y | b, data=dat, scales = "sliced")
+
+
+
+
+
+
+## text axis colors
+
+xyplot(1:10 ~ 1:10,
+ scales =
+ list(y = list(font = 2,
+ cex = 1,
+ col = "green", col.line = "cyan", tck = 5)),
+ xlab = list("one to ten", fontfamily = "HersheySerif"),
+ par.settings =
+ list(axis.text = list(col = "red", font = 4, cex = 3),
+ axis.line = list(col = "yellow")))
+
+
+
+
+x <- rnorm(100)
+y <- 2 + 3 * runif(100)
+a <- gl(3, 1, 100)
+
+xyplot(y ~ x | a)
+
+xyplot(y ~ x | a, scales = list(axs = "i"))
+
+xyplot(y ~ x | a, xlim = c(-5, 5), scales = list(limits = c(-6, 6)))
+
+xyplot(y ~ x | a, xlim = c(-5, 5), ylim = letters[1:5])
+
+
+## Should produce an error
+cat(try(print(xyplot(y ~ x | a, scales = list(x = list( relation = "same", axs = "i", limits = list( c(-5, 5), c(-4, 4), c(-3, 3) ) )))), silent = TRUE))
+xyplot(y ~ x | a, scales = list(x = list( relation = "free", axs = "i", limits = list( c(-5, 5), c(-4, 4), c(-3, 3) ) )))
+xyplot(y ~ x | a, scales = list(x = list( relation = "sliced", axs = "i", limits = list( c(-5, 5), c(-4, 4), c(-3, 3) ) )))
+
+## Should produce an error
+cat(try(print(xyplot(y ~ x | a, xlim = list( c(-5, 5), c(-4, 4), c(-3, 3) ), scales = list(x = list( relation = "same", axs = "i")))), silent = TRUE))
+xyplot(y ~ x | a, xlim = list( c(-5, 5), c(-4, 4), c(-3, 3) ), scales = list(x = list( relation = "free", axs = "i")))
+xyplot(y ~ x | a, xlim = list( c(-5, 5), c(-4, 4), c(-3, 3) ), scales = list(x = list( relation = "sliced", axs = "i")))
+
+
+
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "free" )))
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "free", limits = c(-5, 5))))
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "free", axs = "i", limits = list( c(-5, 5), c(-4, 4), c(-3, 3) ) )))
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "free",
+ limits = list( c(-5, 5), c(-4, 4), c(-3, 3) ),
+ at = c(-3, 3, 0))))
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "free",
+ limits = list( c(-5, 5), c(-4, 4), c(-3, 3) ),
+ at = list( c(0, 5, -5) , c(-4, 0, 4), c(-3, 3, 0) ))))
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "free",
+ limits = list( c(-5, 5), c(-4, 4), c(-3, 3) ),
+ at = list( c(0, 5, -5) , c(-4, 0, 4), c(-3, 3, 0) ),
+ labels = list( as.character(c(0, 5, -5)) , letters[5:7], c(-3, 3, 0) ))))
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "free",
+ limits = list( c(-5, 5), c(-4, 4), letters[1:5] ),
+ at = list( c(0, 5, -5) , c(-4, 0, 4), c(-3, 3, 0) ),
+ labels = list( as.character(c(0, 5, -5)) , letters[5:7], c(-3, 3, 0) ))))
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "free",
+ limits = list( c(-5, 5), c(-4, 4), letters[1:5] ),
+ at = list( c(0, 5, -5) , c(-4, 0, 4), FALSE ),
+ labels = list( as.character(c(0, 5, -5)) , letters[5:7], FALSE ))))
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "free",
+ limits = list( c(-5, 5), c(-4, 4), letters[1:5] ),
+ at = list( c(0, 5, -5) , c(-4, 0, 4), 1:5 ),
+ labels = list( as.character(c(0, 5, -5)) , letters[5:7], FALSE ))))
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "free", rot = 45,
+ limits = list( c(-5, 5), c(-4, 4), letters[1:5] ),
+ at = list( c(0, 5, -5) , c(-4, 0, 4), 1:5 ),
+ labels = list( as.character(c(0, 5, -5)) , letters[5:7], month.name[1:5] ))))
+
+
+
+
+
+
+
+
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "sliced" )))
+xyplot(y ~ x | a, scales = list(x = list( relation = "sliced" , axs = "i" )))
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "sliced", limits = c(-5, 5))))
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "sliced", axs = "i", limits = list( c(-5, 5), c(-4, 4), c(-3, 3) ) )))
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "sliced",
+ limits = list( c(-5, 5), c(-4, 4), c(-3, 3) ),
+ at = c(-3, 3, 0))))
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "sliced",
+ limits = list( c(-5, 5), c(-4, 4), c(-3, 3) ),
+ at = list( c(0, 5, -5) , c(-4, 0, 4), c(-3, 3, 0) ))))
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "sliced",
+ limits = list( c(-5, 5), c(-4, 4), c(-3, 3) ),
+ at = list( c(0, 5, -5) , c(-4, 0, 4), c(-3, 3, 0) ),
+ labels = list( as.character(c(0, 5, -5)) , letters[5:7], c(-3, 3, 0) ))))
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "sliced",
+ limits = list( c(-5, 5), c(-4, 4), letters[1:5] ),
+ at = list( c(0, 5, -5) , c(-4, 0, 4), c(-3, 3, 0) ),
+ labels = list( as.character(c(0, 5, -5)) , letters[5:7], c(-3, 3, 0) ))))
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "sliced",
+ limits = list( c(-5, 5), c(-4, 4), letters[1:5] ),
+ at = list( c(0, 5, -5) , c(-4, 0, 4), FALSE ),
+ labels = list( as.character(c(0, 5, -5)) , letters[5:7], FALSE ))))
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "sliced",
+ limits = list( c(-5, 5), c(-4, 4), letters[1:5] ),
+ at = list( c(0, 5, -5) , c(-4, 0, 4), 1:5 ),
+ labels = list( as.character(c(0, 5, -5)) , letters[5:7], FALSE ))))
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "sliced", rot = 45,
+ limits = list( c(-5, 5), c(-4, 4), letters[1:5] ),
+ at = list( c(0, 5, -5) , c(-4, 0, 4), 1:5 ),
+ labels = list( as.character(c(0, 5, -5)) , letters[5:7], month.name[1:5] ))))
+
+
+
+
+xyplot(y ~ x | a, scales = list(x = list( relation = "free", at = list( c(0, 5, -5) , c(-4, 0, 4), 1:5 ))))
+xyplot(y ~ x | a, scales = list(x = list( relation = "sliced", at = list( c(0, 5, -5) , c(-4, 0, 4), 1:5 ))))
+
+## should produce an error
+cat(try(print(xyplot(y ~ x | a, scales = list(y = list( relation = "same", at = list( c(0, 5, -5) , c(-4, 0, 4), 1:5 ))))), silent = TRUE))
+
+
+## problem
+stripplot(rep(1:20, 5) ~ x | a, scales = list(relation = "free", col = "transparent"))
+dev.off()
diff --git a/win32/deps/library/lattice/tests/temp.R b/win32/deps/library/lattice/tests/temp.R
new file mode 100644
index 0000000..4807f5b
--- /dev/null
+++ b/win32/deps/library/lattice/tests/temp.R
@@ -0,0 +1,141 @@
+
+postscript("temp.ps")
+library(lattice)
+
+
+## dotplot labels problem
+
+xx <- 1:10
+names(xx) <- rep(letters[1:5], 2)
+dotplot(xx)
+
+
+
+
+
+
+## missing levels of factors
+## drop unused levels
+
+x <- 1:100
+y <- rnorm(100)
+g <- gl(4, 25, 100)
+
+xyplot(y ~ x | g)
+xyplot(y ~ x | g, subset = g != "2")
+xyplot(y ~ x | g, subset = g != "2",
+ panel = function(x, y, subscripts) {
+ print(subscripts)
+ ltext(x, y, lab = subscripts)
+ })
+
+
+
+## subset & subscript interaction
+
+x <- rnorm(50)
+y <- rnorm(50)
+subset <- 20:40
+
+xyplot(y ~ x,
+ panel = function(x, y, subscripts) {
+ print(subscripts)
+ ltext(x, y, lab = subscripts)
+ })
+
+## gives subscripts = 20:40
+xyplot(y ~ x, subset = subset,
+ panel = function(x, y, subscripts) {
+ print(subscripts)
+ ltext(x, y, lab = subscripts)
+ })
+
+g <- gl(2,1,50)
+
+xyplot(y ~ x, groups = g, panel = panel.superpose)
+xyplot(y ~ x, groups = g, panel = panel.superpose, subset = subset)
+
+
+
+
+
+
+
+
+## reordering tests
+
+data(iris)
+iris$foo <- equal.count(iris$Sepal.Length)
+
+foo <- xyplot(Petal.Length ~ Petal.Width | Species + foo, iris)
+
+foo
+
+foo$subset.cond <- list(1:3, 1:6)
+foo$perm.cond <- 1:2
+foo
+
+foo$perm.cond <- 2:1
+foo$subset.cond <- list(c(1,2,3,1), 2:4)
+foo
+
+
+
+bar <- xyplot(Petal.Length ~ Petal.Width | Species + foo, iris, skip = c(F, T))
+bar
+
+bar <- xyplot(Petal.Length ~ Petal.Width | Species + foo, iris, skip = c(F, T), scales = "free")
+bar
+
+
+
+
+
+## other stuff
+
+x <- numeric(0)
+y <- numeric(0)
+
+bwplot(y ~ x) # fails? FIXME
+
+
+x <- c(rnorm(10), rep(NA, 10))
+y <- gl(1, 20)
+a <- gl(2, 10)
+
+bwplot(x ~ y | a)
+
+
+## warning: why ?
+bwplot(x ~ y | a * a)
+
+
+
+
+## example from Wolfram Fischer
+
+
+my.barley <- subset( barley, ! ( site == "Grand Rapids" & year == "1932" ) )
+
+dotplot(variety ~ yield | year * site, my.barley,
+ layout=c(6,2), between=list(x=c(0,6)))
+
+
+
+dotplot(variety ~ yield | year * site, data = my.barley,
+ layout=c(6,2),
+ scales =
+ list(rot = 0,
+ y =
+ list(relation='sliced',
+ at = rep( list( FALSE, NULL ), 6 ))),
+ par.settings =
+ list(layout.widths = list(axis.panel = rep(c(1, 0), 3))))
+
+
+
+
+dev.off()
+
+
+
diff --git a/win32/deps/library/lattice/tests/test.R b/win32/deps/library/lattice/tests/test.R
new file mode 100644
index 0000000..b448f29
--- /dev/null
+++ b/win32/deps/library/lattice/tests/test.R
@@ -0,0 +1,137 @@
+postscript("test.ps")
+library(lattice)
+
+lattice.options(default.args =
+ list(page = function(n) {
+ grid::grid.text(label = paste(deparse(trellis.last.object()$call, width.cutoff = 150L), collapse = "\n"),
+ x = 0.01, y = 0.99, just = c("left", "top"))
+ }))
+
+densityplot(~ 5)
+densityplot(~ 1:5 | letters[1:5])
+
+x <- rnorm(200)
+y <- rnorm(200)
+z <- equal.count(rnorm(200))
+a <- factor(rep(1:3, len = 200))
+
+df.test <- list(xx = x+1-min(x), yy = y, zz = z, aa = a)
+
+xyplot(y ~ x | z * a, strip = function(...) strip.default(..., style = 4),
+ par.strip.text = list(cex = 2, col = "blue", font = 2),
+ ##scales = list(x = list(draw = FALSE), y = "sliced"))
+ scales = list(x = list(rot = 0), y = list(rot = 0)))
+
+xyplot(a ~ x | z,
+ main = "xyplot call with modified options",
+ lattice.options =
+ list(panel.xyplot = "panel.bwplot",
+ default.args = list(between = list(x = 1, y = 1))))
+
+
+
+
+bwplot(zz ~ xx | aa, df.test)
+
+bwplot(aa ~ xx | zz, df.test,
+ scales =
+ list(x = list(log = "e", tck = 5, rot = 90, cex = 2),
+ y = list(col = "red", tck = 3, alternating = TRUE, cex = 5, rot = 0),
+ tick.number = 20),
+ main = list("main", cex = 5),
+ sub = list("sub", cex = 5),
+ xlab = list("xlab", cex = 5),
+ ylab = list("ylab", cex = 5))
+
+
+bwplot(~zz , df.test)
+bwplot(~xx , df.test)
+
+dotplot(zz ~ xx | aa, df.test)
+dotplot(aa ~ xx | zz, df.test)
+
+dotplot(~zz , df.test)
+dotplot(~xx , df.test)
+
+stripplot(zz ~ xx | aa, df.test)
+stripplot(aa ~ xx | zz, df.test)
+stripplot(~zz , df.test)
+stripplot(~xx , df.test)
+
+
+
+xa <- 1:8
+xb <- rep( c( NA, 10 ), 4 )
+
+xc <- rep( c( 'C2', 'C1' ), 4 )
+xyplot( xa ~ xb | xc)
+xyplot( xa ~ xb | xc, scales = "free")
+
+xc <- rep( c( 'C1', 'C2' ), 4 )
+xyplot( xa ~ xb | xc)
+xyplot( xa ~ xb | xc, scales = "free")
+
+x = sample(1:3, 100, replace=TRUE)
+histogram( ~ x, breaks=c(0,1.5,2.5,3.5), type='count')
+
+
+
+## splom pscales
+
+data(iris)
+iris2 <- iris[,1:4]
+
+splom(iris2, groups = iris$Species,
+ pscales = 10)
+
+splom(iris2, groups = iris$Species,
+ pscales = list(list(at = 6, lab = "six"), list(at = 3), list(at = 4), list(at = 1)))
+
+splom(iris2, groups = iris$Species,
+ pscales = list(list(at = 6, lab = "six", limits = c(-10, 10)),
+ list(at = 3), list(at = 4), list(limits = c(-5, 5))))
+
+
+## factors in formula
+
+data(barley)
+levelplot(yield ~ year * variety | site, barley,
+ panel = function(x, y, ...) {
+ x <- as.numeric(x)
+ y <- as.numeric(y)
+ panel.levelplot(x, y, ...)
+ })
+
+
+data(volcano)
+levelplot(volcano, key = list(x = .5, y = .5, points = list(col = 1:3)),
+ legend = list(top = list(fun = grid::textGrob("This \nis \na \nstupid \nlegend"))))
+
+
+## demo of seekViewport
+
+library(grid)
+
+splom(~iris[1:3]|Species, data = iris,
+ layout=c(2,2), pscales = 0,
+ varnames = c("Sepal\nLength", "Sepal\nWidth", "Petal\nLength"),
+ page = function(...) {
+ ltext(x = seq(.6, .8, len = 4),
+ y = seq(.9, .6, len = 4),
+ lab = c("Three", "Varieties", "of", "Iris"),
+ cex = 2)
+ }, par.settings = list(clip = list(panel = FALSE)))
+
+seekViewport(vpPath(trellis.vpname("panel", 1, 1), "pairs", "subpanel.2.3"))
+grid.yaxis(main = TRUE)
+
+seekViewport(vpPath(trellis.vpname("panel", 2, 1), "pairs", "subpanel.2.1"))
+grid.yaxis(main = FALSE)
+
+seekViewport(vpPath(trellis.vpname("panel", 1, 2), "pairs", "subpanel.2.2"))
+grid.yaxis(main = FALSE)
+
+demo("lattice")
+dev.off()
+
+
diff --git a/win32/deps/library/lattice/tests/wireframe.R b/win32/deps/library/lattice/tests/wireframe.R
new file mode 100644
index 0000000..8d2f02c
--- /dev/null
+++ b/win32/deps/library/lattice/tests/wireframe.R
@@ -0,0 +1,113 @@
+
+library(lattice)
+data(volcano)
+
+foo <-
+ data.frame(z = as.vector(volcano),
+ x = rep(1:87, 61),
+ y = rep(1:61, each = 87))
+
+wireframe(z ~ x * y, foo)
+
+## this used to give an error, but seems fine now (?)
+wireframe(z ~ x * y, foo, subset = z > 150)
+
+
+## Example 1 (a). valgrind shows warnings, starting with
+
+
+## ==9058== Invalid read of size 8
+## ==9058== at 0xA450AFF: wireframePanelCalculations (threeDplot.c:291)
+
+## and subsequently in various other places in that function leading to
+
+## ==9058== Conditional jump or move depends on uninitialised value(s)
+## ==9058== at 0x3FFAA466CF: __printf_fp (in /lib64/libc-2.4.so)
+## ==9058== by 0x3FFAA423AE: vfprintf (in /lib64/libc-2.4.so)
+## ==9058== by 0x3FFAA4A477: fprintf (in /lib64/libc-2.4.so)
+## ==9058== by 0x94975BE: PostScriptRLineTo (devPS.c:2683)
+
+## A bit more tracing shows it is accessing element 4016 in an array of
+## length 2456, and the plot seems nonsense (and random) when viewed on
+## screen. (BDR, 2006/09/17)
+
+## DS's earlier comment: what's this supposed to do ? weird thing is,
+## result is random (probably indicator of memory access errors)
+
+if (FALSE)
+{
+
+ wireframe(z + I(z + 100) ~ x * y, foo,
+ subset = z > 150,
+ scales = list(arrows = FALSE))
+}
+
+## this works as expected
+
+wireframe(z + I(z + 100) ~ x * y, foo)
+
+## Example 1 (b). Another way of seeing the problem:
+
+## this is OK:
+
+bar <- foo
+bar$z[bar$z < 150] <- NA
+wireframe(z + I(z + 100) ~ x * y, bar,
+ scales = list(arrows = FALSE))
+
+## but this is not
+if (FALSE)
+{
+ wireframe(z + I(z + 100) ~ x * y,
+ subset(bar, !is.na(z)),
+ scales = list(arrows = FALSE))
+}
+
+
+## Example 2. Probably another example of the same "bug": see
+## https://stat.ethz.ch/pipermail/r-devel/2005-September/034544.html
+
+
+library(lattice)
+
+n <- 20
+psteps <- 50
+binomtable <- function(n, psteps)
+{
+ x <- (0:(10*n))/10
+ p <- (0:psteps)/psteps
+ dd <- expand.grid(x=x,p=p)
+ dd$F <- pbinom(dd$x,n,dd$p)
+ dd$x0 <-trunc(dd$x)
+ dd
+}
+
+bt <- binomtable(n = 5, psteps = 100)
+bt[bt$x - bt$x0 >= 0.9, ]$F <- NA
+
+if (FALSE)
+{
+ ## this is problematic
+ wireframe(F ~ x * p, bt,
+ groups = bt$x0, shade = TRUE,
+ scales = list(arrows = FALSE))
+}
+
+## this one OK
+wireframe(F ~ x * p, bt, shade = TRUE,
+ scales = list(arrows = FALSE))
+
+## this too
+wireframe(F ~ x * p | factor(x0), bt,
+ ## groups = bt$x0,
+ shade = TRUE,
+ scales = list(arrows = FALSE))
+
+
+## Working hypothesis: the problem crops up when there are groups
+## (specified either directly or through the formula interface) AND x
+## and y values for each group don't represent the full evaluation
+## grid. The second condition is a bit unclear. In example 2, each
+## group's support is disjoint from that of the others. In example 1,
+## both groups have the same support, they are just not the full grid.
+
diff --git a/win32/deps/library/methods/DESCRIPTION b/win32/deps/library/methods/DESCRIPTION
index 2ff072d..ce1f5a5 100644
--- a/win32/deps/library/methods/DESCRIPTION
+++ b/win32/deps/library/methods/DESCRIPTION
@@ -1,14 +1,13 @@
Package: methods
-Version: 2.9.2
+Version: 2.15.2
Priority: base
Imports: utils
Title: Formal Methods and Classes
-Author: R Development Core Team
+Author: R Core Team
Maintainer: R Core Team <R-core r-project org>
-Description: Formally defined methods and classes for R objects, plus
- other programming tools, as described in the reference
-References: ``Programming with Data'' (1998), John M. Chambers,
- Springer NY. http://www.omegahat.org/RSMethods/Intro.ps and
- .../Intro.pdf
-License: Part of R 2.9.2
-Built: R 2.9.2; i386-pc-mingw32; 2009-08-24 12:45:21 UTC; windows
+Description: Formally defined methods and classes for R objects,
+ plus other programming tools, as described in the reference
+References: John M. Chambers (2008) ``Software for Data Analysis:
+ Programming with R''; Springer NY.
+License: Part of R 2.15.2
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:07:06 UTC; windows
diff --git a/win32/deps/library/methods/INDEX b/win32/deps/library/methods/INDEX
index c41209c..8556951 100644
--- a/win32/deps/library/methods/INDEX
+++ b/win32/deps/library/methods/INDEX
@@ -9,13 +9,15 @@ MethodDefinition-class
Classes to Represent Method Definitions
MethodWithNext-class Class MethodWithNext
Methods General Information on Methods
-MethodsList-class Class MethodsList, Representation of Methods
- for a Generic Function
+MethodsList-class Class MethodsList, Deprecated Representation of
+ Methods
ObjectsWithPackage-class
A Vector of Object Names, with associated
Package Names
+ReferenceClasses Objects With Fields Treated by Reference
+ (OOP-style)
S3Part S3-style Objects and S4-class Objects
-S4groupGeneric Group Generic Functions
+S4groupGeneric S4 Group Generic Functions
SClassExtension-class Class to Represent Inheritance (Extension)
Relations
as Force an Object to Belong to a Class
@@ -24,14 +26,18 @@ callNextMethod Call an Inherited Method
canCoerce Can an Object be Coerced to a Certain S4 Class?
cbind2 Combine two Objects by Columns or Rows
character-class Classes Corresponding to Basic Data Types
+className Class names including the corresponding package
classRepresentation-class
Class Objects
classesToAM Compute an Adjacency Matrix for Superclasses of
- one or more Class Definitions
-dotsMethods The Use of "..." in Method Signatures
-environment-class Class "environment"
+ Class Definitions
+dotsMethods The Use of '...' in Method Signatures
+envRefClass-class Class '"envRefClass"'
+environment-class Class '"environment"'
+evalSource Use Function Definitions from a Source File
+ without Reinstalling a Package
findClass Computations with Classes
-findMethods Descriptions of the Methods Defined for a
+findMethods Description of the Methods Defined for a
Generic Function
fixPre1.8 Fix Objects Saved from R Versions Previous to
1.8
@@ -41,8 +47,9 @@ getMethod Get or Test for the Definition of a Method
getPackageName The Name associated with a Given Package
hasArg Look for an Argument in the Call
implicitGeneric Manage Implicit Versions of Generic Functions
+inheritedSlotNames Names of Slots Inherited From a Super Class
initialize-methods Methods to Initialize New Objects from a Class
-is Is an Object from a Class
+is Is an Object from a Class?
isSealedMethod Check for a Sealed Method or Class
language-class Classes to Represent Unevaluated Language
Objects
@@ -62,12 +69,13 @@ selectSuperClasses Super Classes (of Specific Kinds) of a Class
setClass Create a Class Definition
setClassUnion Classes Defined as the Union of Other Classes
setGeneric Define a New Generic Function
+setLoadActions Set Actions For Package Loading
setMethod Create and Save a Method
setOldClass Register Old-Style (S3) Classes and Inheritance
show Show an Object
showMethods Show all the methods for the specified
function(s)
-signature-class Class "signature" For Method Definitions
+signature-class Class '"signature"' For Method Definitions
slot The Slots in an Object from a Formal Class
structure-class Classes Corresponding to Basic Structures
testInheritedMethods Test for and Report about Selection of
diff --git a/win32/deps/library/methods/Meta/Rd.rds b/win32/deps/library/methods/Meta/Rd.rds
index 65f1967..e0dac62 100644
Binary files a/win32/deps/library/methods/Meta/Rd.rds and b/win32/deps/library/methods/Meta/Rd.rds differ
diff --git a/win32/deps/library/methods/Meta/hsearch.rds b/win32/deps/library/methods/Meta/hsearch.rds
index 086bae6..a73e2be 100644
Binary files a/win32/deps/library/methods/Meta/hsearch.rds and b/win32/deps/library/methods/Meta/hsearch.rds differ
diff --git a/win32/deps/library/methods/Meta/links.rds b/win32/deps/library/methods/Meta/links.rds
new file mode 100644
index 0000000..d007e45
Binary files /dev/null and b/win32/deps/library/methods/Meta/links.rds differ
diff --git a/win32/deps/library/methods/Meta/nsInfo.rds b/win32/deps/library/methods/Meta/nsInfo.rds
index dbae3fb..0ad24e0 100644
Binary files a/win32/deps/library/methods/Meta/nsInfo.rds and b/win32/deps/library/methods/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/methods/Meta/package.rds b/win32/deps/library/methods/Meta/package.rds
index e60bb97..c603a99 100644
Binary files a/win32/deps/library/methods/Meta/package.rds and b/win32/deps/library/methods/Meta/package.rds differ
diff --git a/win32/deps/library/methods/NAMESPACE b/win32/deps/library/methods/NAMESPACE
index b0b70ac..b37fb65 100644
--- a/win32/deps/library/methods/NAMESPACE
+++ b/win32/deps/library/methods/NAMESPACE
@@ -33,8 +33,7 @@ export(Summary)
export(addNextMethod)
export(allGenerics)
export(allNames)
-export(as)
-export("as<-")
+export(as, "as<-")
export(asMethodDefinition)
export(assignClassDef)
export(assignMethodsMetaData)
@@ -48,9 +47,10 @@ export(callNextMethod)
export(canCoerce)
export(checkSlotAssignment)
export(classMetaName)
+export(classLabel)
+export(className, .classEnv)
export(classesToAM)
-export(coerce)
-export("coerce<-")
+export(coerce, "coerce<-")
export(completeClassDefinition)
export(completeExtends)
export(completeSubclasses)
@@ -60,12 +60,13 @@ export(defaultPrototype)
export(doPrimitiveMethod)
export(dumpMethod)
export(dumpMethods)
-export(el)
-export("el<-")
-export(elNamed)
-export("elNamed<-")
+export(el, "el<-")
+export(elNamed, "elNamed<-")
export(empty.dump)
export(emptyMethodsList)
+export(evalOnLoad)
+export(evalqOnLoad)
+export(evalSource)
export(existsFunction)
export(existsMethod)
export(extends)
@@ -78,8 +79,7 @@ export(findMethodSignatures)
export(findUnique)
export(fixPre1.8)
export(formalArgs)
-export(functionBody)
-export("functionBody<-")
+export(functionBody, "functionBody<-")
export(generic.skeleton)
export(getAccess)
export(getAllMethods)
@@ -96,6 +96,7 @@ export(getGeneric)
export(getGenerics)
export(getGroup)
export(getGroupMembers)
+export(getLoadActions)
export(getMethod)
export(getMethods)
export(getMethodsForDispatch)
@@ -108,10 +109,14 @@ export(getSubclasses)
export(getValidity)
export(getVirtual)
export(hasArg)
+export(hasLoadAction)
export(hasMethod)
export(hasMethods)
+export(inheritedSlotNames)
export(initialize)
+export(insertClassMethods)
export(insertMethod)
+export(insertSource)
export(is)
export(isClass)
export(isClassDef)
@@ -143,6 +148,7 @@ export(methodsPackageMetaName)
export(method.skeleton)
export(missingArg)
export(mlistMetaName)
+export(multipleClasses)
export(new)
export(newBasic)
export(newClassRepresentation)
@@ -176,8 +182,10 @@ export(setDataPart)
export(setGeneric)
export(setGroupGeneric)
export(setIs)
+export(setLoadAction)
+export(setLoadActions)
export(setMethod)
-export(setOldClass)
+export(setOldClass, .OldClassesList)
export(setPackageName)
export(setPrimitiveMethods)
export(setReplaceMethod)
@@ -190,8 +198,7 @@ export(showMethods)
export(showMlist)
export(sigToEnv)
export(signature)
-export(slot)
-export("slot<-")
+export(slot, "slot<-", ".hasSlot")
export(slotNames, ".slotNames")
export(slotsFromS3)
export(substituteDirect)
@@ -214,6 +221,7 @@ export(.EmptyPrimitiveSkeletons)
## to allow "S4-cbind/rbind (./R/cbind-rbind.R)
export(cbind2)
export(rbind2)
+export(kronecker)
## implicit generic functionality
@@ -221,3 +229,9 @@ export(implicitGeneric)
export(setGenericImplicit)
export(prohibitGeneric)
export(registerImplicitGenerics)
+
+## reference classes
+export(setRefClass)
+export(getRefClass)
+export(initFieldArgs) # used in initialize methods--old version
+export(initRefFields) # used in initialize methods
diff --git a/win32/deps/library/methods/R/methods b/win32/deps/library/methods/R/methods
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/methods/R/methods
+++ b/win32/deps/library/methods/R/methods
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/methods/R/methods.rdb b/win32/deps/library/methods/R/methods.rdb
index 35bb81e..fa6da41 100644
Binary files a/win32/deps/library/methods/R/methods.rdb and b/win32/deps/library/methods/R/methods.rdb differ
diff --git a/win32/deps/library/methods/R/methods.rdx b/win32/deps/library/methods/R/methods.rdx
index cccc8aa..0c5e3c3 100644
Binary files a/win32/deps/library/methods/R/methods.rdx and b/win32/deps/library/methods/R/methods.rdx differ
diff --git a/win32/deps/library/methods/help/AnIndex b/win32/deps/library/methods/help/AnIndex
index 5dc5ade..2c87306 100644
--- a/win32/deps/library/methods/help/AnIndex
+++ b/win32/deps/library/methods/help/AnIndex
@@ -1,13 +1,16 @@
methods-package methods-package
+$,envRefClass-method stdRefClass
+$<-,envRefClass-method stdRefClass
(-class LanguageClasses
.BasicClasses RClassUtils
.BasicFunsList zBasicFunsList
.BasicVectorClasses RClassUtils
-.conflicts.OK MethodSupport
+.classEnv RClassUtils
.doTracePrint TraceClasses
.EmptyPrimitiveSkeletons RMethodUtils
.environment-class Classes
.externalptr-class Classes
+.hasSlot slot
.InitBasicClasses RClassUtils
.InitMethodsListClass RClassUtils
.InitTraceFunctions TraceClasses
@@ -26,6 +29,7 @@ methods-package methods-package
.valueClassTest RMethodUtils
<--class LanguageClasses
@<- slot
+activeBindingFunction-class refClass
addNextMethod RMethodUtils
addNextMethod,MethodDefinition-method RMethodUtils
addNextMethod,MethodWithNext-method RMethodUtils
@@ -46,6 +50,7 @@ assignMethodsMetaData RMethodUtils
balanceMethodsList RMethodUtils
body<-,MethodDefinition-method MethodsList-class
browseAll Session
+builtin-class BasicClasses
cacheGenericsMetaData RMethodUtils
cacheMetaData RMethodUtils
cacheMethod MethodSupport
@@ -61,7 +66,11 @@ character-class BasicClasses
checkSlotAssignment RClassUtils
Classes Classes
classesToAM classesToAM
+classGeneratorFunction-class setClass
+classLabel RClassUtils
classMetaName RClassUtils
+className className
+className-class className
classPrototypeDef-class RClassUtils
classRepresentation-class classRepresentation-class
ClassUnionRepresentation-class setClassUnion
@@ -99,6 +108,7 @@ conformMethod RMethodUtils
data.frame-class setOldClass
data.frameRowLabels-class setOldClass
Date-class setOldClass
+defaultBindingFunction-class refClass
defaultDumpName RMethodUtils
defaultPrototype RClassUtils
density-class setOldClass
@@ -121,6 +131,10 @@ empty.dump RClassUtils
emptyMethodsList MethodsList
EmptyMethodsList-class EmptyMethodsList-class
environment-class EnvironmentClass
+envRefClass-class stdRefClass
+evalOnLoad setLoadActions
+evalqOnLoad setLoadActions
+evalSource evalSource
existsFunction methodUtilities
existsMethod getMethod
expression-class BasicClasses
@@ -162,6 +176,7 @@ getGeneric RMethodUtils
getGenerics GenericFunctions
getGroup RMethodUtils
getGroupMembers RMethodUtils
+getLoadActions setLoadActions
getMethod getMethod
getMethods findMethods
getMethodsForDispatch MethodSupport
@@ -169,6 +184,7 @@ getMethodsMetaData RMethodUtils
getPackageName getPackageName
getProperties methods-defunct
getPrototype methods-defunct
+getRefClass refClass
getSlots slot
getSubclasses methods-defunct
getValidity validObject
@@ -179,18 +195,23 @@ groupGenericFunction-class genericFunction-class
GroupGenericFunctions S4groupGeneric
groupGenericFunctionWithTrace-class TraceClasses
hasArg hasArg
+hasLoadAction setLoadActions
hasMethod getMethod
hasMethods findMethods
hsearch-class setOldClass
if-class LanguageClasses
implicit generic implicitGeneric
implicitGeneric implicitGeneric
+inheritedSlotNames inheritedSlotNames
inheritedSubMethodLists MethodsList
+initFieldArgs refClass
initialize new
+initialize,.environment-method initialize-methods
initialize,ANY-method initialize-methods
initialize,array-method StructureClasses
initialize,data.frame-method setOldClass
initialize,environment-method initialize-methods
+initialize,envRefClass-method stdRefClass
initialize,factor-method setOldClass
initialize,matrix-method StructureClasses
initialize,mts-method StructureClasses
@@ -202,8 +223,11 @@ initialize,traceable-method initialize-methods
initialize,ts-method StructureClasses
initialize-methods initialize-methods
initMethodDispatch methodUtilities
+initRefFields refClass
+insertClassMethods RMethodUtils
insertMethod MethodsList
insertMethodInEmptyList MethodsList
+insertSource evalSource
integer-class BasicClasses
integrate-class setOldClass
is is
@@ -226,6 +250,7 @@ LinearMethodsList-class LinearMethodsList-class
list-class BasicClasses
listFromMethods MethodSupport
listFromMlist MethodsList
+listOfMethods-class findMethods
lm-class setOldClass
loadMethod MethodsList
loadMethod,ANY-method MethodsList
@@ -257,6 +282,7 @@ MethodDefinition-class MethodDefinition-class
MethodDefinitionWithTrace-class TraceClasses
Methods Methods
methods-defunct methods-defunct
+methods-deprecated methods-deprecated
MethodSelectionReport-class testInheritedMethods
methodSignatureMatrix methodUtilities
MethodsList MethodsList
@@ -271,7 +297,9 @@ mlistMetaName methods-defunct
mlm-class setOldClass
mtable-class setOldClass
mts-class setOldClass
+multipleClasses className
name-class LanguageClasses
+namedList-class BasicClasses
new new
newBasic RClassUtils
newClassRepresentation RClassUtils
@@ -297,6 +325,7 @@ Ops,structure,vector-method StructureClasses
Ops,vector,nonStructure-method nonStructure-class
Ops,vector,structure-method StructureClasses
OptionalFunction-class RMethodUtils
+optionalMethod-class RMethodUtils
ordered-class setOldClass
packageInfo-class setOldClass
packageIQR-class setOldClass
@@ -321,6 +350,13 @@ rbind2,ANY,missing-method cbind2
rbind2-methods cbind2
reconcilePropertiesAndPrototype RClassUtils
recordedplot-class setOldClass
+refClass-class refClass
+refClassRepresentation-class refClass
+ReferenceClasses refClass
+refMethodDef-class refClass
+refMethodDefWithTrace-class refClass
+refObject-class refClass
+refObjectGenerator-class refClass
registerImplicitGenerics implicitGeneric
rematchDefinition RMethodUtils
removeClass findClass
@@ -359,21 +395,31 @@ setGeneric setGeneric
setGenericImplicit implicitGeneric
setGroupGeneric setGeneric
setIs is
+setLoadAction setLoadActions
+setLoadActions setLoadActions
setMethod setMethod
setOldClass setOldClass
setPackageName getPackageName
setPrimitiveMethods RMethodUtils
+setRefClass refClass
setReplaceMethod GenericFunctions
setSubclassMetaData RClassUtils
setValidity validObject
show show
show,ANY-method show
show,classRepresentation-method show
+show,envRefClass-method refClass
show,genericFunction-method show
+show,genericFunctionWithTrace-method TraceClasses
show,MethodDefinition-method show
+show,MethodDefinitionWithTrace-method TraceClasses
show,MethodWithNext-method show
+show,MethodWithNextWithTrace-method TraceClasses
show,ObjectsWithPackage-method show
+show,refClassRepresentation-method refClass
+show,refMethodDef-method refClass
show,signature-method signature-class
+show,sourceEnvironment-method TraceClasses
show,traceable-method show
show,ts-method StructureClasses
show-methods show
@@ -392,6 +438,8 @@ slot<- slot
slotNames slot
slotsFromS3 S3Part
socket-class setOldClass
+sourceEnvironment-class evalSource
+special-class BasicClasses
standardGeneric-class RMethodUtils
standardGenericWithTrace-class RMethodUtils
structure-class StructureClasses
@@ -400,7 +448,9 @@ substituteDirect substituteDirect
substituteFunctionArgs RMethodUtils
Summary S4groupGeneric
summary.table-class setOldClass
+summaryDefault-class setOldClass
superClassDepth RClassUtils
+SuperClassMethod-class refClass
table-class setOldClass
testInheritedMethods testInheritedMethods
testVirtual RClassUtils
@@ -408,8 +458,9 @@ traceable-class TraceClasses
traceOff Session
traceOn Session
tryNew RClassUtils
-trySilent RClassUtils
+trySilent methods-defunct
ts-class StructureClasses
+uninitializedField-class refClass
unRematchDefinition RMethodUtils
validObject validObject
validSlotNames RClassUtils
diff --git a/win32/deps/library/methods/help/aliases.rds b/win32/deps/library/methods/help/aliases.rds
new file mode 100644
index 0000000..4bb6f09
Binary files /dev/null and b/win32/deps/library/methods/help/aliases.rds differ
diff --git a/win32/deps/library/methods/help/methods.rdb b/win32/deps/library/methods/help/methods.rdb
new file mode 100644
index 0000000..27a4a10
Binary files /dev/null and b/win32/deps/library/methods/help/methods.rdb differ
diff --git a/win32/deps/library/methods/help/methods.rdx b/win32/deps/library/methods/help/methods.rdx
new file mode 100644
index 0000000..fa5c5a6
Binary files /dev/null and b/win32/deps/library/methods/help/methods.rdx differ
diff --git a/win32/deps/library/methods/help/paths.rds b/win32/deps/library/methods/help/paths.rds
new file mode 100644
index 0000000..8077a14
Binary files /dev/null and b/win32/deps/library/methods/help/paths.rds differ
diff --git a/win32/deps/library/methods/html/00Index.html b/win32/deps/library/methods/html/00Index.html
new file mode 100644
index 0000000..82bf5d7
--- /dev/null
+++ b/win32/deps/library/methods/html/00Index.html
@@ -0,0 +1,703 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Formal Methods and Classes</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Formal Methods and Classes
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘methods’ version 2.15.2</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<p align="center">
+<a href="# "> </a>
+<a href="#A">A</a>
+<a href="#B">B</a>
+<a href="#C">C</a>
+<a href="#D">D</a>
+<a href="#E">E</a>
+<a href="#F">F</a>
+<a href="#G">G</a>
+<a href="#H">H</a>
+<a href="#I">I</a>
+<a href="#L">L</a>
+<a href="#M">M</a>
+<a href="#N">N</a>
+<a href="#O">O</a>
+<a href="#P">P</a>
+<a href="#R">R</a>
+<a href="#S">S</a>
+<a href="#T">T</a>
+<a href="#U">U</a>
+<a href="#V">V</a>
+<a href="#W">W</a>
+<a href="#misc">misc</a>
+</p>
+
+<table width="100%">
+<tr><td width="25%"><a href="methods-package.html">methods-package</a></td>
+<td>Formal Methods and Classes</td></tr>
+</table>
+
+<h2><a name="A">-- A --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="refClass.html">activeBindingFunction-class</a></td>
+<td>Objects With Fields Treated by Reference (OOP-style)</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">anova-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">anova.glm-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">anova.glm.null-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="BasicClasses.html">ANY-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">aov-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="S4groupGeneric.html">Arith</a></td>
+<td>S4 Group Generic Functions</td></tr>
+<tr><td width="25%"><a href="StructureClasses.html">array-class</a></td>
+<td>Classes Corresponding to Basic Structures</td></tr>
+<tr><td width="25%"><a href="as.html">as</a></td>
+<td>Force an Object to Belong to a Class</td></tr>
+<tr><td width="25%"><a href="as.html">as<-</a></td>
+<td>Force an Object to Belong to a Class</td></tr>
+</table>
+
+<h2><a name="B">-- B --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="MethodsList-class.html">body<--method</a></td>
+<td>Class MethodsList, Deprecated Representation of Methods</td></tr>
+<tr><td width="25%"><a href="BasicClasses.html">builtin-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+</table>
+
+<h2><a name="C">-- C --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="LanguageClasses.html">call-class</a></td>
+<td>Classes to Represent Unevaluated Language Objects</td></tr>
+<tr><td width="25%"><a href="callGeneric.html">callGeneric</a></td>
+<td>Call the Current Generic Function from a Method</td></tr>
+<tr><td width="25%"><a href="NextMethod.html">callNextMethod</a></td>
+<td>Call an Inherited Method</td></tr>
+<tr><td width="25%"><a href="canCoerce.html">canCoerce</a></td>
+<td>Can an Object be Coerced to a Certain S4 Class?</td></tr>
+<tr><td width="25%"><a href="cbind2.html">cbind2</a></td>
+<td>Combine two Objects by Columns or Rows</td></tr>
+<tr><td width="25%"><a href="cbind2.html">cbind2-method</a></td>
+<td>Combine two Objects by Columns or Rows</td></tr>
+<tr><td width="25%"><a href="cbind2.html">cbind2-methods</a></td>
+<td>Combine two Objects by Columns or Rows</td></tr>
+<tr><td width="25%"><a href="BasicClasses.html">character-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+<tr><td width="25%"><a href="Classes.html">Classes</a></td>
+<td>Class Definitions</td></tr>
+<tr><td width="25%"><a href="classesToAM.html">classesToAM</a></td>
+<td>Compute an Adjacency Matrix for Superclasses of Class Definitions</td></tr>
+<tr><td width="25%"><a href="setClass.html">classGeneratorFunction-class</a></td>
+<td>Create a Class Definition</td></tr>
+<tr><td width="25%"><a href="className.html">className</a></td>
+<td>Class names including the corresponding package</td></tr>
+<tr><td width="25%"><a href="className.html">className-class</a></td>
+<td>Class names including the corresponding package</td></tr>
+<tr><td width="25%"><a href="classRepresentation-class.html">classRepresentation-class</a></td>
+<td>Class Objects</td></tr>
+<tr><td width="25%"><a href="setClassUnion.html">ClassUnionRepresentation-class</a></td>
+<td>Classes Defined as the Union of Other Classes</td></tr>
+<tr><td width="25%"><a href="as.html">coerce</a></td>
+<td>Force an Object to Belong to a Class</td></tr>
+<tr><td width="25%"><a href="as.html">coerce-method</a></td>
+<td>Force an Object to Belong to a Class</td></tr>
+<tr><td width="25%"><a href="S3Part.html">coerce-method</a></td>
+<td>S3-style Objects and S4-class Objects</td></tr>
+<tr><td width="25%"><a href="as.html">coerce-methods</a></td>
+<td>Force an Object to Belong to a Class</td></tr>
+<tr><td width="25%"><a href="as.html">coerce<-</a></td>
+<td>Force an Object to Belong to a Class</td></tr>
+<tr><td width="25%"><a href="S4groupGeneric.html">Compare</a></td>
+<td>S4 Group Generic Functions</td></tr>
+<tr><td width="25%"><a href="S4groupGeneric.html">Complex</a></td>
+<td>S4 Group Generic Functions</td></tr>
+<tr><td width="25%"><a href="BasicClasses.html">complex-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+</table>
+
+<h2><a name="D">-- D --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="setOldClass.html">data.frame-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">data.frameRowLabels-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">Date-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="refClass.html">defaultBindingFunction-class</a></td>
+<td>Objects With Fields Treated by Reference (OOP-style)</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">density-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="TraceClasses.html">derivedDefaultMethodWithTrace-class</a></td>
+<td>Classes Used Internally to Control Tracing</td></tr>
+<tr><td width="25%"><a href="Documentation.html">Documentation</a></td>
+<td>Using and Creating On-line Documentation for Classes and Methods</td></tr>
+<tr><td width="25%"><a href="Documentation.html">Documentation-class</a></td>
+<td>Using and Creating On-line Documentation for Classes and Methods</td></tr>
+<tr><td width="25%"><a href="Documentation.html">Documentation-methods</a></td>
+<td>Using and Creating On-line Documentation for Classes and Methods</td></tr>
+<tr><td width="25%"><a href="dotsMethods.html">dotsMethods</a></td>
+<td>The Use of '...' in Method Signatures</td></tr>
+<tr><td width="25%"><a href="BasicClasses.html">double-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">dump.frames-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="GenericFunctions.html">dumpMethod</a></td>
+<td>Tools for Managing Generic Functions</td></tr>
+<tr><td width="25%"><a href="GenericFunctions.html">dumpMethods</a></td>
+<td>Tools for Managing Generic Functions</td></tr>
+</table>
+
+<h2><a name="E">-- E --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="EnvironmentClass.html">environment-class</a></td>
+<td>Class '"environment"'</td></tr>
+<tr><td width="25%"><a href="stdRefClass.html">envRefClass-class</a></td>
+<td>Class '"envRefClass"'</td></tr>
+<tr><td width="25%"><a href="setLoadActions.html">evalOnLoad</a></td>
+<td>Set Actions For Package Loading</td></tr>
+<tr><td width="25%"><a href="setLoadActions.html">evalqOnLoad</a></td>
+<td>Set Actions For Package Loading</td></tr>
+<tr><td width="25%"><a href="evalSource.html">evalSource</a></td>
+<td>Use Function Definitions from a Source File without Reinstalling a Package</td></tr>
+<tr><td width="25%"><a href="getMethod.html">existsMethod</a></td>
+<td>Get or Test for the Definition of a Method</td></tr>
+<tr><td width="25%"><a href="BasicClasses.html">expression-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+<tr><td width="25%"><a href="is.html">extends</a></td>
+<td>Is an Object from a Class?</td></tr>
+<tr><td width="25%"><a href="BasicClasses.html">externalptr-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+</table>
+
+<h2><a name="F">-- F --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="setOldClass.html">factor-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="findClass.html">findClass</a></td>
+<td>Computations with Classes</td></tr>
+<tr><td width="25%"><a href="GenericFunctions.html">findFunction</a></td>
+<td>Tools for Managing Generic Functions</td></tr>
+<tr><td width="25%"><a href="getMethod.html">findMethod</a></td>
+<td>Get or Test for the Definition of a Method</td></tr>
+<tr><td width="25%"><a href="findMethods.html">findMethods</a></td>
+<td>Description of the Methods Defined for a Generic Function</td></tr>
+<tr><td width="25%"><a href="findMethods.html">findMethodSignatures</a></td>
+<td>Description of the Methods Defined for a Generic Function</td></tr>
+<tr><td width="25%"><a href="fixPrevious.html">fixPre1.8</a></td>
+<td>Fix Objects Saved from R Versions Previous to 1.8</td></tr>
+<tr><td width="25%"><a href="LanguageClasses.html">for-class</a></td>
+<td>Classes to Represent Unevaluated Language Objects</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">formula-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="BasicClasses.html">function-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+<tr><td width="25%"><a href="TraceClasses.html">functionWithTrace-class</a></td>
+<td>Classes Used Internally to Control Tracing</td></tr>
+</table>
+
+<h2><a name="G">-- G --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="genericFunction-class.html">genericFunction-class</a></td>
+<td>Generic Function Objects</td></tr>
+<tr><td width="25%"><a href="GenericFunctions.html">GenericFunctions</a></td>
+<td>Tools for Managing Generic Functions</td></tr>
+<tr><td width="25%"><a href="TraceClasses.html">genericFunctionWithTrace-class</a></td>
+<td>Classes Used Internally to Control Tracing</td></tr>
+<tr><td width="25%"><a href="getClass.html">getClass</a></td>
+<td>Get Class Definition</td></tr>
+<tr><td width="25%"><a href="getClass.html">getClassDef</a></td>
+<td>Get Class Definition</td></tr>
+<tr><td width="25%"><a href="findClass.html">getClasses</a></td>
+<td>Computations with Classes</td></tr>
+<tr><td width="25%"><a href="GenericFunctions.html">getGenerics</a></td>
+<td>Tools for Managing Generic Functions</td></tr>
+<tr><td width="25%"><a href="setLoadActions.html">getLoadActions</a></td>
+<td>Set Actions For Package Loading</td></tr>
+<tr><td width="25%"><a href="getMethod.html">getMethod</a></td>
+<td>Get or Test for the Definition of a Method</td></tr>
+<tr><td width="25%"><a href="findMethods.html">getMethods</a></td>
+<td>Description of the Methods Defined for a Generic Function</td></tr>
+<tr><td width="25%"><a href="getPackageName.html">getPackageName</a></td>
+<td>The Name associated with a Given Package</td></tr>
+<tr><td width="25%"><a href="refClass.html">getRefClass</a></td>
+<td>Objects With Fields Treated by Reference (OOP-style)</td></tr>
+<tr><td width="25%"><a href="slot.html">getSlots</a></td>
+<td>The Slots in an Object from a Formal Class</td></tr>
+<tr><td width="25%"><a href="validObject.html">getValidity</a></td>
+<td>Test the Validity of an Object</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">glm-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">glm.null-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="genericFunction-class.html">groupGenericFunction-class</a></td>
+<td>Generic Function Objects</td></tr>
+<tr><td width="25%"><a href="S4groupGeneric.html">GroupGenericFunctions</a></td>
+<td>S4 Group Generic Functions</td></tr>
+<tr><td width="25%"><a href="TraceClasses.html">groupGenericFunctionWithTrace-class</a></td>
+<td>Classes Used Internally to Control Tracing</td></tr>
+</table>
+
+<h2><a name="H">-- H --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="hasArg.html">hasArg</a></td>
+<td>Look for an Argument in the Call</td></tr>
+<tr><td width="25%"><a href="setLoadActions.html">hasLoadAction</a></td>
+<td>Set Actions For Package Loading</td></tr>
+<tr><td width="25%"><a href="getMethod.html">hasMethod</a></td>
+<td>Get or Test for the Definition of a Method</td></tr>
+<tr><td width="25%"><a href="findMethods.html">hasMethods</a></td>
+<td>Description of the Methods Defined for a Generic Function</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">hsearch-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+</table>
+
+<h2><a name="I">-- I --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="LanguageClasses.html">if-class</a></td>
+<td>Classes to Represent Unevaluated Language Objects</td></tr>
+<tr><td width="25%"><a href="implicitGeneric.html">implicit generic</a></td>
+<td>Manage Implicit Versions of Generic Functions</td></tr>
+<tr><td width="25%"><a href="implicitGeneric.html">implicitGeneric</a></td>
+<td>Manage Implicit Versions of Generic Functions</td></tr>
+<tr><td width="25%"><a href="inheritedSlotNames.html">inheritedSlotNames</a></td>
+<td>Names of Slots Inherited From a Super Class</td></tr>
+<tr><td width="25%"><a href="refClass.html">initFieldArgs</a></td>
+<td>Objects With Fields Treated by Reference (OOP-style)</td></tr>
+<tr><td width="25%"><a href="new.html">initialize</a></td>
+<td>Generate an Object from a Class</td></tr>
+<tr><td width="25%"><a href="initialize-methods.html">initialize-method</a></td>
+<td>Methods to Initialize New Objects from a Class</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">initialize-method</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="stdRefClass.html">initialize-method</a></td>
+<td>Class '"envRefClass"'</td></tr>
+<tr><td width="25%"><a href="StructureClasses.html">initialize-method</a></td>
+<td>Classes Corresponding to Basic Structures</td></tr>
+<tr><td width="25%"><a href="initialize-methods.html">initialize-methods</a></td>
+<td>Methods to Initialize New Objects from a Class</td></tr>
+<tr><td width="25%"><a href="refClass.html">initRefFields</a></td>
+<td>Objects With Fields Treated by Reference (OOP-style)</td></tr>
+<tr><td width="25%"><a href="evalSource.html">insertSource</a></td>
+<td>Use Function Definitions from a Source File without Reinstalling a Package</td></tr>
+<tr><td width="25%"><a href="BasicClasses.html">integer-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">integrate-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="is.html">is</a></td>
+<td>Is an Object from a Class?</td></tr>
+<tr><td width="25%"><a href="findClass.html">isClass</a></td>
+<td>Computations with Classes</td></tr>
+<tr><td width="25%"><a href="setClassUnion.html">isClassUnion</a></td>
+<td>Classes Defined as the Union of Other Classes</td></tr>
+<tr><td width="25%"><a href="GenericFunctions.html">isGeneric</a></td>
+<td>Tools for Managing Generic Functions</td></tr>
+<tr><td width="25%"><a href="GenericFunctions.html">isGroup</a></td>
+<td>Tools for Managing Generic Functions</td></tr>
+<tr><td width="25%"><a href="isSealedMethod.html">isSealedClass</a></td>
+<td>Check for a Sealed Method or Class</td></tr>
+<tr><td width="25%"><a href="isSealedMethod.html">isSealedMethod</a></td>
+<td>Check for a Sealed Method or Class</td></tr>
+<tr><td width="25%"><a href="S3Part.html">isXS3Class</a></td>
+<td>S3-style Objects and S4-class Objects</td></tr>
+</table>
+
+<h2><a name="L">-- L --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="LanguageClasses.html">language-class</a></td>
+<td>Classes to Represent Unevaluated Language Objects</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">libraryIQR-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="LinearMethodsList-class.html">LinearMethodsList-class</a></td>
+<td>Class "LinearMethodsList"</td></tr>
+<tr><td width="25%"><a href="BasicClasses.html">list-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+<tr><td width="25%"><a href="findMethods.html">listOfMethods-class</a></td>
+<td>Description of the Methods Defined for a Generic Function</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">lm-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="S4groupGeneric.html">Logic</a></td>
+<td>S4 Group Generic Functions</td></tr>
+<tr><td width="25%"><a href="BasicClasses.html">logical-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">logLik-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+</table>
+
+<h2><a name="M">-- M --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="setSClass.html">makeClassRepresentation</a></td>
+<td>Create a Class Definition</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">maov-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="S4groupGeneric.html">Math</a></td>
+<td>S4 Group Generic Functions</td></tr>
+<tr><td width="25%"><a href="nonStructure-class.html">Math-method</a></td>
+<td>A non-structure S4 Class for basic types</td></tr>
+<tr><td width="25%"><a href="StructureClasses.html">Math-method</a></td>
+<td>Classes Corresponding to Basic Structures</td></tr>
+<tr><td width="25%"><a href="S4groupGeneric.html">Math2</a></td>
+<td>S4 Group Generic Functions</td></tr>
+<tr><td width="25%"><a href="nonStructure-class.html">Math2-method</a></td>
+<td>A non-structure S4 Class for basic types</td></tr>
+<tr><td width="25%"><a href="StructureClasses.html">matrix-class</a></td>
+<td>Classes Corresponding to Basic Structures</td></tr>
+<tr><td width="25%"><a href="method.skeleton.html">method.skeleton</a></td>
+<td>Create a Skeleton File for a New Method</td></tr>
+<tr><td width="25%"><a href="MethodDefinition-class.html">MethodDefinition-class</a></td>
+<td>Classes to Represent Method Definitions</td></tr>
+<tr><td width="25%"><a href="TraceClasses.html">MethodDefinitionWithTrace-class</a></td>
+<td>Classes Used Internally to Control Tracing</td></tr>
+<tr><td width="25%"><a href="Methods.html">Methods</a></td>
+<td>General Information on Methods</td></tr>
+<tr><td width="25%"><a href="testInheritedMethods.html">MethodSelectionReport-class</a></td>
+<td>Test for and Report about Selection of Inherited Methods</td></tr>
+<tr><td width="25%"><a href="MethodsList-class.html">MethodsList-class</a></td>
+<td>Class MethodsList, Deprecated Representation of Methods</td></tr>
+<tr><td width="25%"><a href="MethodWithNext-class.html">MethodWithNext-class</a></td>
+<td>Class MethodWithNext</td></tr>
+<tr><td width="25%"><a href="TraceClasses.html">MethodWithNextWithTrace-class</a></td>
+<td>Classes Used Internally to Control Tracing</td></tr>
+<tr><td width="25%"><a href="BasicClasses.html">missing-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">mlm-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">mtable-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">mts-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="className.html">multipleClasses</a></td>
+<td>Class names including the corresponding package</td></tr>
+</table>
+
+<h2><a name="N">-- N --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="LanguageClasses.html">name-class</a></td>
+<td>Classes to Represent Unevaluated Language Objects</td></tr>
+<tr><td width="25%"><a href="BasicClasses.html">namedList-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+<tr><td width="25%"><a href="new.html">new</a></td>
+<td>Generate an Object from a Class</td></tr>
+<tr><td width="25%"><a href="TraceClasses.html">nonstandardGenericWithTrace-class</a></td>
+<td>Classes Used Internally to Control Tracing</td></tr>
+<tr><td width="25%"><a href="nonStructure-class.html">nonStructure-class</a></td>
+<td>A non-structure S4 Class for basic types</td></tr>
+<tr><td width="25%"><a href="BasicClasses.html">NULL-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+<tr><td width="25%"><a href="BasicClasses.html">numeric-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+</table>
+
+<h2><a name="O">-- O --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="ObjectsWithPackage-class.html">ObjectsWithPackage-class</a></td>
+<td>A Vector of Object Names, with associated Package Names</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">oldClass-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="S4groupGeneric.html">Ops</a></td>
+<td>S4 Group Generic Functions</td></tr>
+<tr><td width="25%"><a href="nonStructure-class.html">Ops-method</a></td>
+<td>A non-structure S4 Class for basic types</td></tr>
+<tr><td width="25%"><a href="StructureClasses.html">Ops-method</a></td>
+<td>Classes Corresponding to Basic Structures</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">ordered-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+</table>
+
+<h2><a name="P">-- P --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="setOldClass.html">packageInfo-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">packageIQR-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="getPackageName.html">packageSlot</a></td>
+<td>The Name associated with a Given Package</td></tr>
+<tr><td width="25%"><a href="getPackageName.html">packageSlot<-</a></td>
+<td>The Name associated with a Given Package</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">POSIXct-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">POSIXlt-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">POSIXt-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="implicitGeneric.html">prohibitGeneric</a></td>
+<td>Manage Implicit Versions of Generic Functions</td></tr>
+<tr><td width="25%"><a href="promptClass.html">promptClass</a></td>
+<td>Generate a Shell for Documentation of a Formal Class</td></tr>
+<tr><td width="25%"><a href="promptMethods.html">promptMethods</a></td>
+<td>Generate a Shell for Documentation of Formal Methods</td></tr>
+<tr><td width="25%"><a href="representation.html">prototype</a></td>
+<td>Construct a Representation or a Prototype for a Class Definition</td></tr>
+</table>
+
+<h2><a name="R">-- R --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="BasicClasses.html">raw-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+<tr><td width="25%"><a href="cbind2.html">rbind2</a></td>
+<td>Combine two Objects by Columns or Rows</td></tr>
+<tr><td width="25%"><a href="cbind2.html">rbind2-method</a></td>
+<td>Combine two Objects by Columns or Rows</td></tr>
+<tr><td width="25%"><a href="cbind2.html">rbind2-methods</a></td>
+<td>Combine two Objects by Columns or Rows</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">recordedplot-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="refClass.html">refClass-class</a></td>
+<td>Objects With Fields Treated by Reference (OOP-style)</td></tr>
+<tr><td width="25%"><a href="refClass.html">refClassRepresentation-class</a></td>
+<td>Objects With Fields Treated by Reference (OOP-style)</td></tr>
+<tr><td width="25%"><a href="refClass.html">ReferenceClasses</a></td>
+<td>Objects With Fields Treated by Reference (OOP-style)</td></tr>
+<tr><td width="25%"><a href="refClass.html">refMethodDef-class</a></td>
+<td>Objects With Fields Treated by Reference (OOP-style)</td></tr>
+<tr><td width="25%"><a href="refClass.html">refMethodDefWithTrace-class</a></td>
+<td>Objects With Fields Treated by Reference (OOP-style)</td></tr>
+<tr><td width="25%"><a href="refClass.html">refObject-class</a></td>
+<td>Objects With Fields Treated by Reference (OOP-style)</td></tr>
+<tr><td width="25%"><a href="refClass.html">refObjectGenerator-class</a></td>
+<td>Objects With Fields Treated by Reference (OOP-style)</td></tr>
+<tr><td width="25%"><a href="implicitGeneric.html">registerImplicitGenerics</a></td>
+<td>Manage Implicit Versions of Generic Functions</td></tr>
+<tr><td width="25%"><a href="findClass.html">removeClass</a></td>
+<td>Computations with Classes</td></tr>
+<tr><td width="25%"><a href="GenericFunctions.html">removeGeneric</a></td>
+<td>Tools for Managing Generic Functions</td></tr>
+<tr><td width="25%"><a href="setMethod.html">removeMethod</a></td>
+<td>Create and Save a Method</td></tr>
+<tr><td width="25%"><a href="GenericFunctions.html">removeMethods</a></td>
+<td>Tools for Managing Generic Functions</td></tr>
+<tr><td width="25%"><a href="LanguageClasses.html">repeat-class</a></td>
+<td>Classes to Represent Unevaluated Language Objects</td></tr>
+<tr><td width="25%"><a href="representation.html">representation</a></td>
+<td>Construct a Representation or a Prototype for a Class Definition</td></tr>
+<tr><td width="25%"><a href="findClass.html">resetClass</a></td>
+<td>Computations with Classes</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">rle-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+</table>
+
+<h2><a name="S">-- S --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="S3Part.html">S3</a></td>
+<td>S3-style Objects and S4-class Objects</td></tr>
+<tr><td width="25%"><a href="S3Part.html">S3-class</a></td>
+<td>S3-style Objects and S4-class Objects</td></tr>
+<tr><td width="25%"><a href="S3Part.html">S3Class</a></td>
+<td>S3-style Objects and S4-class Objects</td></tr>
+<tr><td width="25%"><a href="S3Part.html">S3Class<-</a></td>
+<td>S3-style Objects and S4-class Objects</td></tr>
+<tr><td width="25%"><a href="S3Part.html">S3Part</a></td>
+<td>S3-style Objects and S4-class Objects</td></tr>
+<tr><td width="25%"><a href="S3Part.html">S3Part<-</a></td>
+<td>S3-style Objects and S4-class Objects</td></tr>
+<tr><td width="25%"><a href="S3Part.html">S4</a></td>
+<td>S3-style Objects and S4-class Objects</td></tr>
+<tr><td width="25%"><a href="BasicClasses.html">S4-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+<tr><td width="25%"><a href="S4groupGeneric.html">S4groupGeneric</a></td>
+<td>S4 Group Generic Functions</td></tr>
+<tr><td width="25%"><a href="SClassExtension-class.html">SClassExtension-class</a></td>
+<td>Class to Represent Inheritance (Extension) Relations</td></tr>
+<tr><td width="25%"><a href="findClass.html">sealClass</a></td>
+<td>Computations with Classes</td></tr>
+<tr><td width="25%"><a href="MethodDefinition-class.html">SealedMethodDefinition-class</a></td>
+<td>Classes to Represent Method Definitions</td></tr>
+<tr><td width="25%"><a href="getMethod.html">selectMethod</a></td>
+<td>Get or Test for the Definition of a Method</td></tr>
+<tr><td width="25%"><a href="selectSuperClasses.html">selectSuperClasses</a></td>
+<td>Super Classes (of Specific Kinds) of a Class</td></tr>
+<tr><td width="25%"><a href="as.html">setAs</a></td>
+<td>Force an Object to Belong to a Class</td></tr>
+<tr><td width="25%"><a href="setClass.html">setClass</a></td>
+<td>Create a Class Definition</td></tr>
+<tr><td width="25%"><a href="setClassUnion.html">setClassUnion</a></td>
+<td>Classes Defined as the Union of Other Classes</td></tr>
+<tr><td width="25%"><a href="setGeneric.html">setGeneric</a></td>
+<td>Define a New Generic Function</td></tr>
+<tr><td width="25%"><a href="implicitGeneric.html">setGenericImplicit</a></td>
+<td>Manage Implicit Versions of Generic Functions</td></tr>
+<tr><td width="25%"><a href="setGeneric.html">setGroupGeneric</a></td>
+<td>Define a New Generic Function</td></tr>
+<tr><td width="25%"><a href="is.html">setIs</a></td>
+<td>Is an Object from a Class?</td></tr>
+<tr><td width="25%"><a href="setLoadActions.html">setLoadAction</a></td>
+<td>Set Actions For Package Loading</td></tr>
+<tr><td width="25%"><a href="setLoadActions.html">setLoadActions</a></td>
+<td>Set Actions For Package Loading</td></tr>
+<tr><td width="25%"><a href="setMethod.html">setMethod</a></td>
+<td>Create and Save a Method</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">setOldClass</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="getPackageName.html">setPackageName</a></td>
+<td>The Name associated with a Given Package</td></tr>
+<tr><td width="25%"><a href="refClass.html">setRefClass</a></td>
+<td>Objects With Fields Treated by Reference (OOP-style)</td></tr>
+<tr><td width="25%"><a href="GenericFunctions.html">setReplaceMethod</a></td>
+<td>Tools for Managing Generic Functions</td></tr>
+<tr><td width="25%"><a href="validObject.html">setValidity</a></td>
+<td>Test the Validity of an Object</td></tr>
+<tr><td width="25%"><a href="show.html">show</a></td>
+<td>Show an Object</td></tr>
+<tr><td width="25%"><a href="refClass.html">show-method</a></td>
+<td>Objects With Fields Treated by Reference (OOP-style)</td></tr>
+<tr><td width="25%"><a href="show.html">show-method</a></td>
+<td>Show an Object</td></tr>
+<tr><td width="25%"><a href="signature-class.html">show-method</a></td>
+<td>Class '"signature"' For Method Definitions</td></tr>
+<tr><td width="25%"><a href="StructureClasses.html">show-method</a></td>
+<td>Classes Corresponding to Basic Structures</td></tr>
+<tr><td width="25%"><a href="TraceClasses.html">show-method</a></td>
+<td>Classes Used Internally to Control Tracing</td></tr>
+<tr><td width="25%"><a href="show.html">show-methods</a></td>
+<td>Show an Object</td></tr>
+<tr><td width="25%"><a href="showMethods.html">showMethods</a></td>
+<td>Show all the methods for the specified function(s)</td></tr>
+<tr><td width="25%"><a href="GenericFunctions.html">signature</a></td>
+<td>Tools for Managing Generic Functions</td></tr>
+<tr><td width="25%"><a href="signature-class.html">signature-class</a></td>
+<td>Class '"signature"' For Method Definitions</td></tr>
+<tr><td width="25%"><a href="BasicClasses.html">single-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+<tr><td width="25%"><a href="slot.html">slot</a></td>
+<td>The Slots in an Object from a Formal Class</td></tr>
+<tr><td width="25%"><a href="slot.html">slot<-</a></td>
+<td>The Slots in an Object from a Formal Class</td></tr>
+<tr><td width="25%"><a href="slot.html">slotNames</a></td>
+<td>The Slots in an Object from a Formal Class</td></tr>
+<tr><td width="25%"><a href="S3Part.html">slotsFromS3</a></td>
+<td>S3-style Objects and S4-class Objects</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">socket-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="evalSource.html">sourceEnvironment-class</a></td>
+<td>Use Function Definitions from a Source File without Reinstalling a Package</td></tr>
+<tr><td width="25%"><a href="BasicClasses.html">special-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+<tr><td width="25%"><a href="StructureClasses.html">structure-class</a></td>
+<td>Classes Corresponding to Basic Structures</td></tr>
+<tr><td width="25%"><a href="S4groupGeneric.html">Summary</a></td>
+<td>S4 Group Generic Functions</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">summary.table-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">summaryDefault-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="refClass.html">SuperClassMethod-class</a></td>
+<td>Objects With Fields Treated by Reference (OOP-style)</td></tr>
+</table>
+
+<h2><a name="T">-- T --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="setOldClass.html">table-class</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="testInheritedMethods.html">testInheritedMethods</a></td>
+<td>Test for and Report about Selection of Inherited Methods</td></tr>
+<tr><td width="25%"><a href="TraceClasses.html">traceable-class</a></td>
+<td>Classes Used Internally to Control Tracing</td></tr>
+<tr><td width="25%"><a href="StructureClasses.html">ts-class</a></td>
+<td>Classes Corresponding to Basic Structures</td></tr>
+</table>
+
+<h2><a name="U">-- U --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="refClass.html">uninitializedField-class</a></td>
+<td>Objects With Fields Treated by Reference (OOP-style)</td></tr>
+</table>
+
+<h2><a name="V">-- V --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="validObject.html">validObject</a></td>
+<td>Test the Validity of an Object</td></tr>
+<tr><td width="25%"><a href="BasicClasses.html">vector-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+<tr><td width="25%"><a href="BasicClasses.html">VIRTUAL-class</a></td>
+<td>Classes Corresponding to Basic Data Types</td></tr>
+</table>
+
+<h2><a name="W">-- W --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="LanguageClasses.html">while-class</a></td>
+<td>Classes to Represent Unevaluated Language Objects</td></tr>
+</table>
+
+<h2><a name="misc">-- misc --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="stdRefClass.html">$-method</a></td>
+<td>Class '"envRefClass"'</td></tr>
+<tr><td width="25%"><a href="stdRefClass.html">$<--method</a></td>
+<td>Class '"envRefClass"'</td></tr>
+<tr><td width="25%"><a href="LanguageClasses.html">(-class</a></td>
+<td>Classes to Represent Unevaluated Language Objects</td></tr>
+<tr><td width="25%"><a href="zBasicFunsList.html">.BasicFunsList</a></td>
+<td>List of Builtin and Special Functions</td></tr>
+<tr><td width="25%"><a href="TraceClasses.html">.doTracePrint</a></td>
+<td>Classes Used Internally to Control Tracing</td></tr>
+<tr><td width="25%"><a href="Classes.html">.environment-class</a></td>
+<td>Class Definitions</td></tr>
+<tr><td width="25%"><a href="Classes.html">.externalptr-class</a></td>
+<td>Class Definitions</td></tr>
+<tr><td width="25%"><a href="slot.html">.hasSlot</a></td>
+<td>The Slots in an Object from a Formal Class</td></tr>
+<tr><td width="25%"><a href="TraceClasses.html">.InitTraceFunctions</a></td>
+<td>Classes Used Internally to Control Tracing</td></tr>
+<tr><td width="25%"><a href="TraceClasses.html">.makeTracedFunction</a></td>
+<td>Classes Used Internally to Control Tracing</td></tr>
+<tr><td width="25%"><a href="Classes.html">.name-class</a></td>
+<td>Class Definitions</td></tr>
+<tr><td width="25%"><a href="Classes.html">.NULL-class</a></td>
+<td>Class Definitions</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">.OldClassesList</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="testInheritedMethods.html">.Other-class</a></td>
+<td>Test for and Report about Selection of Inherited Methods</td></tr>
+<tr><td width="25%"><a href="selectSuperClasses.html">.selectSuperClasses</a></td>
+<td>Super Classes (of Specific Kinds) of a Class</td></tr>
+<tr><td width="25%"><a href="setOldClass.html">.setOldIs</a></td>
+<td>Register Old-Style (S3) Classes and Inheritance</td></tr>
+<tr><td width="25%"><a href="slot.html">.slotNames</a></td>
+<td>The Slots in an Object from a Formal Class</td></tr>
+<tr><td width="25%"><a href="TraceClasses.html">.untracedFunction</a></td>
+<td>Classes Used Internally to Control Tracing</td></tr>
+<tr><td width="25%"><a href="LanguageClasses.html"><--class</a></td>
+<td>Classes to Represent Unevaluated Language Objects</td></tr>
+<tr><td width="25%"><a href="slot.html">@<-</a></td>
+<td>The Slots in an Object from a Formal Class</td></tr>
+<tr><td width="25%"><a href="Classes.html">__ClassMetaData</a></td>
+<td>Class Definitions</td></tr>
+<tr><td width="25%"><a href="LanguageClasses.html">{-class</a></td>
+<td>Classes to Represent Unevaluated Language Objects</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/methods/html/R.css b/win32/deps/library/methods/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/methods/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
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diff --git a/win32/deps/library/methods/tests/S3.R b/win32/deps/library/methods/tests/S3.R
new file mode 100644
index 0000000..331d336
--- /dev/null
+++ b/win32/deps/library/methods/tests/S3.R
@@ -0,0 +1,29 @@
+## accumulate here tests of the relation between S4 and S3 classes
+
+## $<-.data.frame did stupid things with the class attribute
+## that clobbered S4 classes extending "data.frame"
+## Test that the S4 method (R 2.13.0) works transparently
+
+set.seed(864)
+
+xx <- data.frame(a=rnorm(10),
+ b=as.factor(sample(c("T", "F"), 10, TRUE)),
+ row.names = paste("R",1:10,sep=":"))
+
+setClass("myData", representation(extra = "character"),
+ contains = "data.frame")
+
+mx <- new("myData", xx, extra = "testing")
+
+## three kinds of $<-: replace, add, delete (NULL value)
+
+mx$a <- mx$a * 2
+xx$a <- xx$a * 2
+
+mx$c <- 1:10
+xx$c <- 1:10
+
+mx$b <- NULL
+xx$b <- NULL
+
+stopifnot(identical(mx, new("myData", xx, extra = "testing")))
diff --git a/win32/deps/library/methods/tests/basicRefClass.R b/win32/deps/library/methods/tests/basicRefClass.R
new file mode 100644
index 0000000..4460efe
--- /dev/null
+++ b/win32/deps/library/methods/tests/basicRefClass.R
@@ -0,0 +1,502 @@
+## simple call, only field names
+fg <- setRefClass("foo", c("bar", "flag"))
+f1 <- new("foo")
+f1$bar
+f1 <- fg$new(flag = "testing")
+f1$bar <- 1
+stopifnot(identical(f1$bar, 1))
+fg$methods(showAll = function() c(bar, flag))
+stopifnot(all.equal(f1$showAll(), c(1, "testing")))
+str(f1)
+
+fg <- setRefClass("foo", list(bar = "numeric", flag = "character",
+ tag = "ANY"),
+ methods = list(addToBar = function(incr) {
+ b <- bar + incr
+ bar <<- b
+ b
+ } )
+ )
+fg$lock("flag")
+stopifnot(identical(fg$lock(), "flag"))
+
+ff <- new("foo", bar = 1.5)
+stopifnot(identical(ff$bar, 1.5))
+ff$bar <- pi
+stopifnot(identical(ff$bar, pi))
+## flag has not yet been set
+ff$flag <- "flag test"
+stopifnot(identical(ff$flag, "flag test"))
+## but no second assign
+stopifnot(is(tryCatch(ff$flag <- "new", error = function(e)e), "error"))
+
+## test against generator
+
+f2 <- fg$new(bar = pi, flag = "flag test")
+## identical does not return TRUE if *contents* of env are identical
+stopifnot(identical(ff$bar, f2$bar), identical(ff$flag, f2$flag))
+## but flag was now assigned once
+stopifnot(is(tryCatch(f2$flag <- "new", error = function(e)e), "error"))
+
+str(f2)
+
+
+## add some accessor methods
+fg$accessors("bar")
+
+ff$setBar(1:3)
+stopifnot(identical(ff$getBar(), 1:3))
+
+ff$getBar()
+stopifnot(all.equal(ff$addToBar(1), 2:4))
+
+
+## Add a method
+fg$methods(barTimes = function(x) {
+ "This method multiples field bar by argument x
+and this string is self-documentation"
+ setBar(getBar() * x)})
+
+ffbar <- ff$getBar()
+ff$barTimes(10)
+stopifnot(all.equal(ffbar * 10, ff$getBar()))
+ff$barTimes(.1)
+
+## inheritance. redefines flag so should fail:
+stopifnot(is(tryCatch(setRefClass("foo2", list(b2 = "numeric",
+ flag = "complex"),
+ contains = "foo",
+ refMethods = list(addBoth = function(incr) {
+ addToBar(incr) #uses inherited class method
+ setB2(getB2() + incr)
+ })),
+ error = function(e)e), "error"))
+## but with flag as a subclass of "characters", should work
+## Also subclasses "tag" which had class "ANY before
+setClass("ratedChar", contains = "character",
+ representation(score = "numeric"))
+foo2 <- setRefClass("foo2", list(b2 = "numeric", flag = "ratedChar",
+ tag = "numeric"),
+ contains = "foo",
+ methods = list(addBoth = function(incr) {
+ addToBar(incr) #uses inherited class method
+ b2 <<- b2 + incr
+ }))
+## now lock the flag field; should still allow one write
+foo2$lock("flag")
+f2 <- foo2$new(bar = -3, flag = as("ANY", "ratedChar"),
+ b2 = ff$bar, tag = 1.5)
+## but not a second one
+stopifnot(is(tryCatch(f2$flag <- "Try again",
+ error = function(e)e), "error"))
+str(f2)
+f22 <- foo2$new(bar = f2$bar)
+## same story if assignment follows the initialization
+f22$flag <- f2$flag
+stopifnot(is(tryCatch(f22$flag <- "Try again",
+ error = function(e)e), "error"))
+## Exporting superclass object
+f22 <- fg$new(bar = f2$bar, flag = f2$flag)
+f2e <- f2$export("foo")
+stopifnot(identical(f2e$bar, f22$bar), identical(f2e$flag, f22$flag),
+ identical(class(f2e), class(f22)))
+stopifnot(identical(f2$flag, as("ANY", "ratedChar")),
+ identical(f2$bar, -3),
+ all.equal(f2$b2, 2:4+0))
+f2$addBoth(-1)
+stopifnot(all.equal(f2$bar, -4), all.equal(f2$b2, 1:3+0))
+
+## test callSuper()
+foo3 <- setRefClass("foo3", fields = list(flag2 = "ratedChar"),
+ contains = "foo2",
+ methods = list(addBoth = function(incr) {
+ callSuper(incr)
+ flag2 <<- as(paste(flag, paste(incr, collapse = ", "),
+ sep = "; "),
+ "ratedChar")
+ incr
+ }))
+
+f2 <- foo2$new(bar = -3, flag = as("ANY", "ratedChar"), b2 = 1:3)
+f3 <- foo3$new()
+f3$import(f2)
+stopifnot(all.equal(f3$b2, f2$b2), all.equal(f3$bar, f2$bar),
+ all.equal(f3$flag, f2$flag))
+f3$addBoth(1)
+stopifnot(all.equal(f3$bar, -2), all.equal(f3$b2, 2:4+0),
+ all.equal(f3$flag2, as("ANY; 1", "ratedChar")))
+
+## but the import should have used up the one write for $flag
+stopifnot(is(tryCatch(f3$flag <- "Try again",
+ error = function(e)e), "error"))
+str(f3)
+
+## importing the same class (not very useful but documented to work)
+f3 <- foo3$new()
+f4 <- foo3$new(bar = -3, flag = as("More", "ratedChar"), b2 = 1:3, flag2 = f2$flag)
+f3$import(f4)
+stopifnot(identical(f3$bar, f4$bar),
+ identical(f3$flag, f4$flag),
+ identical(f3$b2, f4$b2),
+ identical(f3$flag2, f4$flag2))
+
+## similar to $import() but using superclass object in the $new() call
+## The explicitly supplied flag= should override and be allowed
+## by the default $initialize()
+f3b <- foo3$new(f2, flag = as("Other", "ratedChar"),
+ flag2 = as("More", "ratedChar"))
+## check that inherited and direct field assignments worked
+stopifnot(identical(f3b$tag, f2$tag),
+ identical(f3b$flag, as("Other", "ratedChar")),
+ identical(f3b$flag2, as("More", "ratedChar")))
+
+## a class with an initialize method, and an extra slot (legal, not a good idea)
+setOldClass(c("simple.list", "list"))
+fg4 <- setRefClass("foo4",
+ contains = "foo2",
+ methods = list(
+ initialize = function(...) {
+ .self$initFields(...)
+ self made <<- R.version
+ .self
+ }),
+ representation = list(made = "simple.list")
+ )
+
+f4 <- new("foo4", flag = as("another test", "ratedChar"), bar = 1:3)
+stopifnot(identical(f4 made, R.version))
+
+## a trivial class with no fields, using fields = list(), failed up to rev 56035
+foo5 <- setRefClass("foo5", fields = list(),
+ methods = list(bar = function(test)
+ paste("*",test,"*")))
+
+f5 <- foo5$new()
+stopifnot(identical( f5$bar("xxx"), paste("*","xxx", "*")))
+
+
+## simple active binding test
+abGen <- setRefClass("ab",
+ fields = list(a = "ANY",
+ b = function(x) if(missing(x)) a else {a <<- x; x}))
+
+ab1 <- abGen$new(a = 1)
+
+stopifnot(identical(ab1$a, 1), identical(ab1$b, 1))
+
+ab1$b <- 2
+
+stopifnot(identical(ab1$a, 2), identical(ab1$b, 2))
+
+## a simple editor for matrix objects. Method $edit() changes some
+## range of values; method $undo() undoes the last edit.
+mEditor <- setRefClass("matrixEditor",
+ fields = list(data = "matrix",
+ edits = "list"),
+ methods = list(
+ edit = function(i, j, value) {
+ ## the following string documents the edit method
+ 'Replaces the range [i, j] of the
+ object by value.
+ '
+ backup <-
+ list(i, j, data[i,j])
+ data[i,j] <<- value
+ edits <<- c(list(backup),
+ edits)
+ invisible(value)
+ },
+ undo = function() {
+ 'Undoes the last edit() operation
+ and update the edits field accordingly.
+ '
+ prev <- edits
+ if(length(prev)) prev <- prev[[1]]
+ else stop("No more edits to undo")
+ edit(prev[[1]], prev[[2]], prev[[3]])
+ ## trim the edits list
+ length(edits) <<- length(edits) - 2
+ invisible(prev)
+ }
+ ))
+xMat <- matrix(1:12,4,3)
+xx <- mEditor$new(data = xMat)
+xx$edit(2, 2, 0)
+xx$data
+xx$undo()
+mEditor$help("undo")
+stopifnot(all.equal(xx$data, xMat))
+
+## add a method to save the object
+mEditor$methods(
+ save = function(file) {
+ 'Save the current object on the file
+ in R external object format.
+'
+ base::save(.self, file = file)
+ },
+ counter = function(i) {
+ 'The number of items in the i-th edit.
+ (Used to test usingMethods())
+'
+ if(i > 0 && i <= length(edits))
+ length(edits[[i]][[3]])
+ else
+ 0L
+ }
+)
+
+tf <- tempfile()
+xx$save(tf) #$
+load(tf)
+unlink(tf)
+stopifnot(identical(xx$data, .self$data))
+
+markViewer <- ""
+setMarkViewer <- function(what)
+ markViewer <<- what
+
+## Inheriting a reference class: a matrix viewer
+mv <- setRefClass("matrixViewer",
+ fields = c("viewerDevice", "viewerFile"),
+ contains = "matrixEditor",
+ methods = list( view = function() {
+ dd <- dev.cur(); dev.set(viewerDevice)
+ devAskNewPage(FALSE)
+ matplot(data, main = paste("After",length(edits),"edits"))
+ dev.set(dd)},
+ edit = # invoke previous method, then replot
+ function(i, j, value) {
+ callSuper(i, j, value)
+ view()
+ }))
+
+## initialize and finalize methods
+mv$methods( initialize = function(file = "./matrixView.pdf", ...) {
+ viewerFile <<- file
+ pdf(viewerFile)
+ viewerDevice <<- dev.cur()
+ message("Plotting to ", viewerFile)
+ dev.set(dev.prev())
+ setMarkViewer("ON")
+ initFields(...)
+ },
+ finalize = function() {
+ dev.off(viewerDevice)
+ setMarkViewer("OFF")
+ })
+
+## a counts method to test usingMethods()
+mv$methods( counts = function() {
+ usingMethods("counter")
+ sapply(seq_along(edits), "counter")
+})
+
+
+ff <- mv$new( data = xMat)
+stopifnot(identical(markViewer, "ON")) # check initialize
+ff$edit(2,2,0)
+ff$data
+stopifnot(identical(ff$counts(), length(ff$edits[[1]][[3]])))
+ff$undo()
+stopifnot(all.equal(ff$data, xMat))
+rm(ff)
+gc()
+stopifnot(identical(markViewer, "OFF")) #check finalize
+
+## tests of copying
+viewerPlus <- setRefClass("viewerPlus",
+ fields = list( text = "character",
+ viewer = "matrixViewer"))
+ff <- mv$new( data = xMat)
+v1 <- viewerPlus$new(text = letters, viewer = ff)
+v2 <- v1$copy()
+v3 <- v1$copy(TRUE)
+v2$text <- "Hello, world"
+v2$viewer$data <- t(xMat) # change a field in v2$viewer
+v3$text <- LETTERS
+v3$viewer <- mv$new( data = matrix(nrow=1,ncol=1))
+## with a deep copy all is protected, with a shallow copy
+## the environment of a copied field remains the same,
+## but replacing the whole field should be local
+stopifnot(identical(v1$text, letters),
+ identical(v1$viewer, ff),
+ identical(v2$text, "Hello, world"))
+v3 <- v1$copy(TRUE)
+v3$viewer$data <- t(xMat) # should modify v1$viewer as well
+stopifnot(identical(v1$viewer$data, t(xMat)))
+
+## the field() method
+stopifnot(identical(v1$text, v1$field("text")))
+v1$field("text", "Now is the time")
+stopifnot(identical(v1$field("text"), "Now is the time"))
+
+## setting a non-existent field, or a method, should throw an error
+stopifnot(is(tryCatch(v1$field("foobar", 0), error = function(e)e), "error"),
+ is(tryCatch(v1$field("copy", 0), error = function(e)e), "error") )
+
+## the methods to extract class definition and generator
+stopifnot(identical(v3$getRefClass()$def, getRefClass("viewerPlus")$def),
+ identical(v3$getClass(), getClass("viewerPlus")))
+
+## deal correctly with inherited methods and overriding existing
+## methods from $methods(...)
+refClassA <- setRefClass("refClassA", methods=list(foo=function() "A"))
+refClassB <- setRefClass("refClassB", contains="refClassA")
+mnames <- objects(getClass("refClassB")@refMethods)
+refClassB$methods(foo=function() callSuper())
+stopifnot(identical(refClassB$new()$foo(), "A"))
+mnames2 <- objects(getClass("refClassB")@refMethods)
+stopifnot(identical(mnames2[is.na(match(mnames2,mnames))], "foo#refClassA"))
+refClassB$methods(foo=function() paste(callSuper(), "Version 2"))
+stopifnot(identical(refClassB$new()$foo(), "A Version 2"))
+stopifnot(identical(mnames2, objects(getClass("refClassB")@refMethods)))
+
+if(methods:::.hasCodeTools()) {
+ ## code warnings assigning locally to field names
+ stopifnot(is(tryCatch(mv$methods(test = function(x)
+ { data <- x[!is.na(x)]; mean(data)}),
+ warning = function(e)e), "warning"))
+
+ ## warnings for nonlocal assignment that is not a field
+ stopifnot(is(tryCatch(mv$methods(test2 = function(x) {something <<- data[!is.na(x)]}), warning = function(e)e), "warning"))
+
+ ## error for trying to assign to a method name
+ stopifnot(is(tryCatch(mv$methods(test3 = function(x) {edit <<- data[!is.na(x)]}), error = function(e)e), "error"))
+} else
+ warning("Can't run some tests: recommended package codetools is not available")
+
+## tests (fragmentary by necessity) of promptClass for reference class
+ccon <- textConnection("ctxt", "w")
+suppressMessages(promptClass("refClassB", filename = ccon))
+## look for a method, inheritance, inherited method
+stopifnot(length(c(grep("foo.*refClassA", ctxt),
+ grep("code{foo()}", ctxt, fixed = TRUE),
+ grep("linkS4class{refClassA", ctxt, fixed = TRUE))) >= 3)
+close(ccon)
+rm(ctxt)
+
+
+## tests related to subclassing environments. These really test code in the core, viz. builtin.c
+a <- refClassA$new()
+ev <- new.env(parent = a) # parent= arg
+stopifnot(is.environment(ev))
+foo <- function()"A"; environment(foo) <- a # environment of function
+stopifnot(identical(as.environment(a), environment(foo)))
+xx <- 1:10; environment(xx) <- a # environment attribute
+stopifnot(identical(as.environment(a), environment(xx)))
+
+
+## tests of [[<- and $<- for subclasses of environment. At one point
+## methods for these assignments were defined and caused
+## inf. recursion when the arguments to the [[<- case were changed in base.
+setClass("myEnv", contains = "environment")
+m <- new("myEnv", a="test")
+m2 <- new("myEnv"); m3 <- new("myEnv")
+## test that new.env() is called for each new object
+stopifnot(!identical(as.environment(m), as.environment(m2)),
+ !identical(as.environment(m3), as.environment(m2)))
+m[["x"]] <- 1; m$y <- 2
+stopifnot(identical(c(m[["x"]], m$y), c(1,2)), is(m, "myEnv"))
+rm(x, envir = m) # check rm() works, does not clobber class
+stopifnot(identical(sort(objects(m)), sort(c("a", "y"))),
+ is(m, "myEnv"))
+
+## tests of binding & environment tools with subclases of environment
+lockBinding("y", m)
+stopifnot(bindingIsLocked("y", m))
+unlockBinding("y", m)
+stopifnot(!bindingIsLocked("y", m))
+
+makeActiveBinding("z", function(value) {
+ if(missing(value))
+ "dummy"
+ else
+ "dummy assignment"
+}, m)
+stopifnot(identical(get("z", m),"dummy"))
+## assignment will return the value but do nothing
+stopifnot(identical(assign("z","other", m), "other"),
+ identical(get("z", m),"dummy"))
+
+
+## this has to be last--Seems no way to unlock an environment!
+lockEnvironment(m)
+stopifnot(environmentIsLocked(m))
+
+rm(m)
+m <- new("myEnv")
+stopifnot(length(ls(m)) == 0)
+## used to contain the previous content
+
+
+## test of callSuper() to a hidden default method for initialize() (== initFields)
+TestClass <- setRefClass ("TestClass",
+ fields = list (text = "character"),
+ methods = list(
+ print = function () {cat(text)},
+ initialize = function(text = "", ...) callSuper(text = paste(text, ":", sep=""),...)
+ ))
+tt <- TestClass$new("hello world")
+stopifnot(identical(tt$text, "hello world:"))
+## now a subclass with another field & another layer of callSuper()
+TestClass2 <- setRefClass("TestClass2",
+ contains = "TestClass",
+ fields = list( version = "integer"),
+ methods = list(
+ initialize = function(..., version = 0L)
+ callSuper(..., version = version+1L))
+ )
+tt <- TestClass2$new("test", version = 1L)
+stopifnot(identical(tt$text, "test:"), identical(tt$version, as.integer(2)))
+tt <- TestClass2$new(version=3L) # default text
+stopifnot(identical(tt$text, ":"), identical(tt$version, as.integer(4)))
+
+
+## test some capabilities but read-only for .self
+.changeAllFields <- function(replacement) {
+ fields <- names( refClassDef fieldClasses)
+ for(field in fields)
+ eval(substitute(.self$FIELD <- replacement$FIELD,
+ list(FIELD = field)))
+}
+
+mEditor$methods(change = .changeAllFields)
+xx <- mEditor$new(data = xMat)
+xx$edit(2, 2, 0)
+
+yy <- mEditor$new(data = xMat+1)
+yy$change(xx)
+stopifnot(identical(yy$data, xx$data), identical(yy$edits, xx$edits))
+
+## but don't allow assigment
+if(methods:::.hasCodeTools())
+ stopifnot(is(tryCatch(yy$.self$data <- xMat, error = function(e)e), "error"))
+
+## the locked binding of refObjectGenerator class should prevent modifying
+## methods, locking fields or setting accessor methods
+evr <- getRefClass("refObjectGenerator") # in methods
+stopifnot(is(tryCatch(evr$methods(foo = function()"..."), error = function(e)e), "error"),
+ is(tryCatch(evr$lock("def"), error = function(e)e), "error"),
+ is(tryCatch(evr$accessors("def"), error = function(e)e), "error"))
+
+##getRefClass() method and function should work with either
+## a class name or a class representation (bug report 14600)
+tg <- setRefClass("tg", fields = "a")
+t1 <- tg$new(a=1)
+tgg <- t1$getRefClass()
+tggg <- getRefClass("tg")
+stopifnot(identical(tgg$def, tggg$def),
+ identical(tg$def, tgg$def))
+## TODO: the className returned by setRefClass should have
+## a package attribute, which would allow:
+## identical(tg$className, tgg$className))
+
+## this used to fail in initFieldArgs() from partial matching "self"
+selfClass <- setRefClass("selfClass",
+ fields=list(
+ self="character", super="character", sub="character"
+ )
+ )
+
+stopifnot(identical(selfClass$new(self="B", super="A", sub="C")$self, "B"))
diff --git a/win32/deps/library/methods/tests/duplicateClass.R b/win32/deps/library/methods/tests/duplicateClass.R
new file mode 100644
index 0000000..e8f167c
--- /dev/null
+++ b/win32/deps/library/methods/tests/duplicateClass.R
@@ -0,0 +1,27 @@
+## Tests for handling classes with same name & different package slots
+## First: Can we define the classes and get the separate definitions
+## from the appropriate namespace or from the package slot in class(x)?
+stopifnot(require(Matrix))
+
+## from: example(chol)
+sy2 <- new("dsyMatrix", Dim = as.integer(c(2,2)), x = c(14, NA,32,77))
+c2 <- chol(sy2)
+
+clM <- getClass("Cholesky")
+
+setClass("Cholesky", contains = "numeric", representation(size = "integer"))
+
+clG <- getClass("Cholesky", where = .GlobalEnv)
+
+stopifnot(identical(getClass("Cholesky", where = asNamespace("Matrix")),
+ clM))
+
+stopifnot(identical(getClass(class(c2)), clM))
+
+stopifnot(identical(evalq(getClass("Cholesky"), asNamespace("Matrix")),
+ clM))
+stopifnot(identical(getClass("Cholesky"), clG))
+
+## Second: tests of methods defined for the same generic
+## (NOT YET!)
+
diff --git a/win32/deps/library/methods/tests/fieldAssignments.R b/win32/deps/library/methods/tests/fieldAssignments.R
new file mode 100644
index 0000000..c06987d
--- /dev/null
+++ b/win32/deps/library/methods/tests/fieldAssignments.R
@@ -0,0 +1,30 @@
+dt <- setRefClass("dt", fields = list(data = "environment", row.names = "character"))
+
+ev <- new.env()
+
+d1 <- dt$new(data = ev, row.names = letters)
+
+stopifnot(identical(d1$data, ev),
+ identical(d1$row.names, letters))
+
+# an invalid class should generate an error
+d2 <- tryCatch(dt$new(data = ev, row.names = 1:12), error = function(e)e)
+
+stopifnot(is(d2, "error"),
+ grepl("row.names", d2$message, fixed = TRUE),
+ grepl("character", d2$message, fixed = TRUE),
+ grepl("integer", d2$message, fixed = TRUE))
+
+# a simple subclass should be used, unchanged
+
+setClass("tagStrings", contains = "character",
+ representation(tag = "Date"))
+
+date1 <- as.Date("2010-01-15")
+
+t1 <- new("tagStrings", letters, tag = date1)
+
+d3 <- dt$new(data = ev, row.names = t1)
+
+stopifnot(identical(d3$row.names, t1))
+
diff --git a/win32/deps/library/methods/tests/mixinInitialize.R b/win32/deps/library/methods/tests/mixinInitialize.R
new file mode 100644
index 0000000..139724d
--- /dev/null
+++ b/win32/deps/library/methods/tests/mixinInitialize.R
@@ -0,0 +1,65 @@
+setClass("A", representation(a="numeric"))
+
+a1 <- new("A", a=1.5)
+m1 <- as.matrix(1)
+
+setClass("M", contains = "matrix", representation(fuzz = "numeric"))
+
+set.seed(113)
+f1 <- runif(3)
+
+stopifnot(identical(as(new("M", 1:12, nrow = 3, fuzz = f1), "matrix"),
+ matrix(1:12, nrow=3)),
+ identical(as(new("M", 1:12, 3, fuzz = f1), "matrix"),
+ matrix(1:12, 3)),
+ identical(as(new("M", 1:12, ncol = 3, fuzz = f1), "matrix"),
+ matrix(1:12, ncol=3)))
+
+setClass("B", contains = c("matrix", "A"))
+
+stopifnot(## a new "B" element mixing two superclass objects
+ identical(new("B", m1, a1)@a, a1 a),
+ ## or not
+ identical(as(new("B", m1),"matrix"), m1),
+ ## or supplying a slot to override
+ identical(new("B", matrix(m1, nrow = 2), a1, a=pi)@a, pi))
+
+## an extra level of inheritance
+setClass("C", contains = "B", representation(c = "character"))
+new("C", m1, c = "Testing")
+
+## verify that validity tests work (PR#14284)
+setValidity("B", function(object) {
+ if(all(is.na(object a) | (object a > 0)))
+ TRUE
+ else
+ "elements of slot \"a\" must be positive"
+})
+
+a2 <- new("A", a= c(NA,3, -1, 2))
+
+## from the SoDA package on CRAN
+muststop <- function(expr, silent = TRUE) {
+ tryExpr <- substitute(tryCatch(expr, error=function(cond)cond))
+ value <- eval.parent(tryExpr)
+ if(inherits(value, "error")) {
+ if(!silent)
+ message("muststop reports: ", value)
+ invisible(value)
+ }
+ else
+ stop(gettextf("The expression %s should have thrown an error, but instead returned an object of class \"%s\"",
+ deparse(substitute(expr))[[1]], class(value)))
+}
+
+muststop(new("B", m1, a2))
+
+removeClass("B")
+removeClass("C")
+removeClass("M")
+
+## TODO: make versions of above inheriting from "array" and "ts"
+
+removeClass("A")
+
+
diff --git a/win32/deps/library/methods/tests/namesAndSlots.R b/win32/deps/library/methods/tests/namesAndSlots.R
new file mode 100644
index 0000000..2091921
--- /dev/null
+++ b/win32/deps/library/methods/tests/namesAndSlots.R
@@ -0,0 +1,16 @@
+setClass("B", contains = "numeric")
+xx <- new("B", 1)
+stopifnot(is(tryCatch(names(xx) <- "A" , warning = function(e)e), "warning"))
+names(xx) <- "A" # after this should not warn
+stopifnot(is(tryCatch(names(xx) <- "B" , warning = function(e)e), "character"))
+setClass("A", representation(xx = "numeric"))
+a <- new("A", xx = 1)
+stopifnot(is(tryCatch(names(a) <- "A" , error = function(e)e), "error"))
+setClass("C", representation(xx = "numeric", names= "character"))
+c <- new("C", xx = 1, names = "A")
+c names <- "B"
+stopifnot(is(tryCatch(names(c) <- "A" , error = function(e)e), "error"))
+setClass("D", contains = "numeric", representation(names = "character"))
+d <- new("D", 1)
+names(d) <- "A"
+stopifnot(identical(d names, "A"))
diff --git a/win32/deps/library/methods/tests/nextWithDots.R b/win32/deps/library/methods/tests/nextWithDots.R
new file mode 100644
index 0000000..1a55f43
--- /dev/null
+++ b/win32/deps/library/methods/tests/nextWithDots.R
@@ -0,0 +1,20 @@
+setClass("A")
+setClass("B", contains = c("array", "A"))
+a = array(1:12, c(2,3,4))
+bb = new("B", a)
+a2 = array(8:1, rep(2,3))
+stopifnot(identical(initialize(bb, a2), new("B",a2)))
+
+withDots <- function(x, ...) names(list(...))
+
+setGeneric("withDots")
+
+setClass("C", representation(x="numeric", y="character"))
+
+setMethod("withDots", "C", function(x, ...)
+ callNextMethod()
+ )
+stopifnot(identical(withDots(1, a=1, b=2), withDots(new("C"), a=1, b=2)))
+removeClass("C"); removeClass("B"); removeClass("A")
+removeGeneric("withDots")
+rm(a, bb, a2)
diff --git a/win32/deps/library/methods/tests/refClassExample.R b/win32/deps/library/methods/tests/refClassExample.R
new file mode 100644
index 0000000..cb39354
--- /dev/null
+++ b/win32/deps/library/methods/tests/refClassExample.R
@@ -0,0 +1,51 @@
+mEditor <- setRefClass("matrixEditor",
+ fields = list( data = "matrix",
+ edits = "list"),
+ methods = list(
+ edit = function(i, j, value) {
+ ## the following string documents the edit method
+ 'Replaces the range [i, j] of the
+ object by value.
+ '
+ backup <-
+ list(i, j, data[i,j])
+ data[i,j] <<- value
+ edits <<- c(edits, list(backup))
+ invisible(value)
+ },
+ undo = function() {
+ 'Undoes the last edit() operation
+ and update the edits field accordingly.
+ '
+ prev <- edits
+ if(length(prev)) prev <- prev[[length(prev)]]
+ else stop("No more edits to undo")
+ edit(prev[[1]], prev[[2]], prev[[3]])
+ ## trim the edits list
+ length(edits) <<- length(edits) - 2
+ invisible(prev)
+ }
+ ))
+
+xMat <- xEdited <- matrix(as.double(1:12),4,3)
+xEdited[[2,2]] <- 0
+xx <- mEditor$new(data = xMat)
+xx$edit(2, 2, 0)
+stopifnot(identical(xx$data, xEdited))
+xEdited[[1,3]] <- -1
+xx$edit(1,3, -1)
+stopifnot(identical(xx$data, xEdited))
+xx$undo()
+xEdited[[1,3]] <- xMat[[1,3]]
+stopifnot(identical(xx$data, xEdited))
+xx$undo()
+stopifnot(identical(xx$data, xMat))
+
+## the tracing method
+xx$trace(edit, quote(value <- 0))
+xx$edit(2,2, -1) # traced should assign 0
+stopifnot(identical(xx$data, xEdited))
+xx$untrace(edit)
+xx$edit(1, 3, -1) # now it should use -1
+xEdited[[1,3]] <- -1
+stopifnot(identical(xx$data, xEdited))
diff --git a/win32/deps/library/methods/tests/testConditionalIs.R b/win32/deps/library/methods/tests/testConditionalIs.R
new file mode 100644
index 0000000..4e27f27
--- /dev/null
+++ b/win32/deps/library/methods/tests/testConditionalIs.R
@@ -0,0 +1,38 @@
+setClass("maybe")
+
+setClass("A", representation(x = "numeric"))
+
+setIs("A", "maybe",
+ test = function(object)length(object x) >= 1 && object x[[1]] > 0,
+ coerce = function(from)from,
+ replace = function(from, value)
+ stop("meaningless to replace the \"maybe\" part of an object"))
+
+aa <- new("A", x=1)
+
+setGeneric("ff", function(x)"default ff")
+## test that the setGeneric() call created the generic & default
+stopifnot(is(ff, "standardGeneric"),
+ identical(body(getMethod("ff","ANY")), "default ff"))
+
+ffMaybe <- function(x) "ff maybe method"
+setMethod("ff", "maybe", ffMaybe)
+
+aa2 <- new("A", x = -1) # condition not TRUE
+stopifnot(identical(ff(aa), "default ff"),
+ identical(ff(aa2), "default ff"))# failed in R 2.11.0
+
+## a method to test the condition
+setMethod("ff", "A",
+ function(x) {
+ if(is(x, "maybe"))
+ ffMaybe(x)
+ else
+ callNextMethod()
+ })
+stopifnot(identical(ff(aa), "ff maybe method"),
+ identical(ff(aa2), "default ff"))
+
+removeClass("A")
+removeClass("maybe")
+removeGeneric("ff")
diff --git a/win32/deps/library/methods/tests/testGroupGeneric.R b/win32/deps/library/methods/tests/testGroupGeneric.R
new file mode 100644
index 0000000..0baafc8
--- /dev/null
+++ b/win32/deps/library/methods/tests/testGroupGeneric.R
@@ -0,0 +1,23 @@
+## reset inherited methods of group members
+## (contributed by Martin Morgan, 2011-2-9)
+setClass("A", representation("numeric"))
+a <- new("A")
+
+setMethod("Logic", c("A", "A"), function(e1, e2) FALSE)
+res0 <- a & a # inherit &,A,A-method
+setMethod("Logic", c("A", "A"), function(e1, e2) TRUE)
+stopifnot(a & a)
+
+removeMethod("Logic", c("A", "A"))
+stopifnot(logical() == a & a)
+
+removeClass("A")
+
+### Find inherited group methods:
+stopifnot(require(Matrix))
+sm <- selectMethod("-", c("dgCMatrix", "numeric"))# direct match with "Arith"
+s2 <- selectMethod("-", c("dtCMatrix", "numeric"))# ambiguity match with "Arith"
+stopifnot(sm generic == "Arith",
+ s2 generic == "Arith")
+## was not ok in R 2.14.x
+
diff --git a/win32/deps/library/methods/tests/testIs.R b/win32/deps/library/methods/tests/testIs.R
new file mode 100644
index 0000000..912cf06
--- /dev/null
+++ b/win32/deps/library/methods/tests/testIs.R
@@ -0,0 +1,31 @@
+## test (non-conditional) explicit inheritance
+setClass("xy", representation(x="numeric", y="numeric"))
+
+setIs("xy", "complex",
+ coerce = function(from) complex(real = from x, imaginary = from y),
+ replace = function(from, value) {
+ from x <- Re(value)
+ from y <- Im(value)
+ from
+ })
+
+set.seed(124)
+x1 <- rnorm(10)
+y1 <- rnorm(10)
+cc <- complex(real = x1, imaginary=y1)
+xyc <- new("xy", x = x1, y = y1)
+stopifnot(identical(cc, as(xyc, "complex")))
+as(xyc, "complex") <- cc * 1i
+stopifnot(identical(xyc, new("xy", x = -y1, y = x1)))
+
+setGeneric("size", function(x)standardGeneric("size"))
+## check that generic for size() was created w/o a default method
+stopifnot(is(size, "standardGeneric"),
+ is.null(selectMethod("size", "ANY",optional=TRUE)))
+
+setMethod("size", "vector", function(x)length(x))
+
+## class "xy" should inherit the vector method through complex
+stopifnot(identical(size(xyc), length(x1)))
+removeClass("xy")
+removeGeneric("size")
diff --git a/win32/deps/library/mgcv/CITATION b/win32/deps/library/mgcv/CITATION
index 9693f74..fba8ae7 100644
--- a/win32/deps/library/mgcv/CITATION
+++ b/win32/deps/library/mgcv/CITATION
@@ -1,7 +1,21 @@
-citHeader("2004 for additive model method and basics of gamm; 2008 for
-generalized additive model method; 2006 for overview; 2003 for thin plate
-regression splines; 2000 is the original method, but no longer the default.")
+citHeader("2011 for generalized additive model method;
+2004 for strictly additive GCV based model method and basics of gamm;
+2006 for overview; 2003 for thin plate regression splines;
+2000 is the original method, but no longer the default.")
+citEntry(
+ entry="Article",
+ title="Fast stable restricted maximum likelihood and marginal
+likelihood estimation of semiparametric generalized linear models",
+ journal="Journal of the Royal Statistical Society (B)",
+ volume= "73",
+ number="1",
+ pages="3-36",
+ year="2011",
+ author="S. N. Wood",
+ textVersion="Wood, S.N. (2011) Fast stable restricted maximum likelihood
+and marginal likelihood estimation of semiparametric generalized linear
+models. Journal of the Royal Statistical Society (B) 73(1):3-36" )
citEntry(
entry="Article",
@@ -19,21 +33,6 @@ citEntry(
)
citEntry(
- entry="Article",
- title="Fast stable direct fitting and smoothness selection for generalized
- additive models",
- journal="Journal of the Royal Statistical Society (B)",
- volume= "70",
- number="3",
- pages="495-518",
- year="2008",
- author="S. N. Wood",
- textVersion="Wood, S.N. (2008) Fast stable direct fitting and smoothness
- selection for generalized additive models. Journal of the Royal
- Statistical Society (B) 70(3):495-518 " )
-
-
-citEntry(
entry="Book",
title="Generalized Additive Models: An Introduction with R",
year="2006",
diff --git a/win32/deps/library/mgcv/DESCRIPTION b/win32/deps/library/mgcv/DESCRIPTION
index a8aa83d..eecc15b 100644
--- a/win32/deps/library/mgcv/DESCRIPTION
+++ b/win32/deps/library/mgcv/DESCRIPTION
@@ -1,18 +1,19 @@
-Package: mgcv
-Version: 1.5-5
-Author: Simon Wood <simon wood r-project org>
-Maintainer: Simon Wood <simon wood r-project org>
-Title: GAMs with GCV/AIC/REML smoothness estimation and GAMMs by PQL
-Description: Routines for GAMs and other generalized ridge regression
- with multiple smoothing parameter selection by GCV, REML or
- UBRE/AIC. Also GAMMs by REML or PQL. Includes a gam() function.
-Priority: recommended
-Depends: R (>= 2.3.0)
-Imports: graphics, stats, nlme
-Suggests: nlme (>= 3.1-64), splines
-LazyLoad: yes
-License: GPL (>= 2)
-Packaged: 2009-05-13 15:40:09 UTC; simon
-Repository: CRAN
-Date/Publication: 2009-05-15 11:26:39
-Built: R 2.9.2; i386-pc-mingw32; 2009-08-24 13:09:13 UTC; windows
+Package: mgcv
+Version: 1.7-22
+Author: Simon Wood <simon wood r-project org>
+Maintainer: Simon Wood <simon wood r-project org>
+Title: Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness
+ estimation
+Description: Routines for GAMs and other generalized ridge regression
+ with multiple smoothing parameter selection by GCV, REML
+ or UBRE/AIC. Also GAMMs. Includes a gam() function.
+Priority: recommended
+Depends: R (>= 2.14.0), stats, graphics
+Imports: nlme, methods, Matrix
+Suggests: nlme (>= 3.1-64), splines, Matrix, parallel
+LazyLoad: yes
+ByteCompile: yes
+License: GPL (>=2)
+Packaged: 2012-10-14 19:28:35 UTC; sw283
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:15:26 UTC; windows
+Archs: i386, x64
diff --git a/win32/deps/library/mgcv/Meta/Rd.rds b/win32/deps/library/mgcv/Meta/Rd.rds
index 1f1e097..b29fbc3 100644
Binary files a/win32/deps/library/mgcv/Meta/Rd.rds and b/win32/deps/library/mgcv/Meta/Rd.rds differ
diff --git a/win32/deps/library/mgcv/Meta/data.rds b/win32/deps/library/mgcv/Meta/data.rds
new file mode 100644
index 0000000..529b451
Binary files /dev/null and b/win32/deps/library/mgcv/Meta/data.rds differ
diff --git a/win32/deps/library/mgcv/Meta/hsearch.rds b/win32/deps/library/mgcv/Meta/hsearch.rds
index c7b63ff..ba50822 100644
Binary files a/win32/deps/library/mgcv/Meta/hsearch.rds and b/win32/deps/library/mgcv/Meta/hsearch.rds differ
diff --git a/win32/deps/library/mgcv/Meta/links.rds b/win32/deps/library/mgcv/Meta/links.rds
new file mode 100644
index 0000000..c28e7f9
Binary files /dev/null and b/win32/deps/library/mgcv/Meta/links.rds differ
diff --git a/win32/deps/library/mgcv/Meta/nsInfo.rds b/win32/deps/library/mgcv/Meta/nsInfo.rds
index 2b4ddb8..e4f99fe 100644
Binary files a/win32/deps/library/mgcv/Meta/nsInfo.rds and b/win32/deps/library/mgcv/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/mgcv/Meta/package.rds b/win32/deps/library/mgcv/Meta/package.rds
index 5d5a6a5..f54e468 100644
Binary files a/win32/deps/library/mgcv/Meta/package.rds and b/win32/deps/library/mgcv/Meta/package.rds differ
diff --git a/win32/deps/library/mgcv/NAMESPACE b/win32/deps/library/mgcv/NAMESPACE
index 61a9661..2fb2839 100644
--- a/win32/deps/library/mgcv/NAMESPACE
+++ b/win32/deps/library/mgcv/NAMESPACE
@@ -1,54 +1,81 @@
useDynLib(mgcv, .registration = TRUE, .fixes = "C_")
-export(anova.gam, cSplineDes,
+export(anova.gam, bam, bam.update, concurvity, cSplineDes,
exclude.too.far,extract.lme.cov, extract.lme.cov2,
formXtViX, full.score, formula.gam,fixDependence,fix.family.link,
- fix.family.var, fix.family.ls, gam, gam2derivative,
+ fix.family.var, fix.family.ls, fix.family.qf,fix.family.rd,
+ fs.test,fs.boundary,gam, gam2derivative,
gam2objective,
gamm, gam.check, gam.control,gam.fit3,
- gam.fit, gam.outer, gamSim , influence.gam,
- interpret.gam,
+ gam.fit, gam.outer,gam.vcomp, gamSim , influence.gam,
+ in.out,inSide,interpret.gam,
gam.side,
get.var,ldTweedie,
- initial.sp,logLik.gam,
- magic, magic.post.proc, mgcv, mgcv.control, model.matrix.gam,
+ initial.sp,logLik.gam,ls.size,
+ magic, magic.post.proc, model.matrix.gam,
mono.con, mroot, negbin, new.name,
notExp,notExp2,notLog,notLog2,pcls,null.space.dimension,
- pdIdnot,pdTens,
- place.knots, plot.gam, print.anova.gam,
+ pen.edf,pdIdnot,pdTens,
+ place.knots, plot.gam, polys.plot,print.anova.gam,
print.gam,print.summary.gam,predict.gam,
PredictMat,Predict.matrix,Predict.matrix2,
Predict.matrix.cr.smooth,
+ Predict.matrix.duchon.spline,
Predict.matrix.cs.smooth,
Predict.matrix.cyclic.smooth,
Predict.matrix.tensor.smooth,
Predict.matrix.tprs.smooth,
Predict.matrix.ts.smooth,
+ Predict.matrix.sos.smooth,
+ Predict.matrix.soap.film,
+ Predict.matrix.sf,
+ Predict.matrix.sw,
+ Predict.matrix.mrf.smooth,
Predict.matrix.pspline.smooth,
- residuals.gam, s,
+ Predict.matrix.random.effect,
+ qq.gam,
+ residuals.gam,rig,rTweedie, s,
+ slanczos,
smoothCon,smooth.construct,smooth.construct2,
smooth.construct.cc.smooth.spec,
smooth.construct.cp.smooth.spec,
smooth.construct.cr.smooth.spec,
smooth.construct.cs.smooth.spec,
+ smooth.construct.ds.smooth.spec,
smooth.construct.tensor.smooth.spec,
smooth.construct.tp.smooth.spec,
smooth.construct.ts.smooth.spec,
smooth.construct.ps.smooth.spec,
+ smooth.construct.re.smooth.spec,
+ smooth.construct.mrf.smooth.spec,
+ smooth.construct.sos.smooth.spec,
+ smooth.construct.so.smooth.spec,
+ smooth.construct.sf.smooth.spec,
+ smooth.construct.sw.smooth.spec,
smooth.construct.ad.smooth.spec,
summary.gam,sp.vcov,
- te,tensor.prod.model.matrix,tensor.prod.penalties,
+ spasm.construct,spasm.sp,spasm.smooth,
+ t2,te,tensor.prod.model.matrix,tensor.prod.penalties,
Tweedie,uniquecombs, vcov.gam, vis.gam)
importFrom(grDevices,cm.colors,gray,heat.colors,terrain.colors,topo.colors)
-importFrom(graphics,axis,box,contour,hist,lines,mtext, par, persp,plot,points,polygon,strheight,strwidth,text)
-importFrom(stats,.checkMFClasses,.getXlevels, as.formula, anova,anova.glmlist,coef,cooks.distance,cor,
- delete.response,family,fitted,formula,
- gaussian,glm,influence,lm,logLik,median,model.frame,model.matrix,model.offset,na.pass,napredict,naresid,nlm,optim,
- pchisq,pf,pnorm,pt,
- predict,printCoefmat ,quantile,qqnorm, reformulate,residuals,rnorm,runif,termplot,terms,terms.formula, uniroot,
- var,vcov)
+importFrom(graphics,axis,box,contour,hist,lines,mtext, par, persp,plot,points,
+ polygon,strheight,strwidth,text)
+#importFrom(stats,.checkMFClasses,.getXlevels, as.formula, anova,anova.glmlist,
+# coef,cooks.distance,cor,delete.response,family,fitted,formula,
+# gaussian,glm,influence,lm,logLik,median,model.frame,model.matrix,
+# model.offset,na.pass,napredict,naresid,nlm,optim,pchisq,pf,pnorm,pt,
+# predict,printCoefmat ,quantile,qqnorm, reformulate,residuals,rnorm,
+# runif,termplot,terms,terms.formula, uniroot,
+# var,vcov)
+
+importFrom(stats,anova,influence,cooks.distance,logLik,vcov,residuals,predict,
+ model.matrix)
importFrom(nlme,Dim,corMatrix,logDet,pdConstruct,pdFactor,pdMatrix)
+#importFrom(Matrix,t,mean,colMeans,colSums,chol,solve,diag)
+import(Matrix)
+importFrom(methods,cbind2)
+
S3method(anova, gam)
S3method(influence, gam)
S3method(cooks.distance, gam)
@@ -80,8 +107,6 @@ S3method(pdMatrix,pdIdnot)
S3method(solve,pdIdnot)
S3method(summary,pdIdnot)
-
-
S3method(smooth.construct,ad.smooth.spec)
S3method(smooth.construct,ps.smooth.spec)
S3method(smooth.construct,cp.smooth.spec)
@@ -101,6 +126,11 @@ S3method(Predict.matrix,cyclic.smooth)
S3method(Predict.matrix,tensor.smooth)
S3method(Predict.matrix,tprs.smooth)
+S3method(spasm.construct,cus)
+S3method(spasm.sp,cus)
+S3method(spasm.smooth,cus)
-
-
+S3method(smooth2random,mgcv.smooth)
+S3method(smooth2random,fs.interaction)
+S3method(smooth2random,tensor.smooth)
+S3method(smooth2random,t2.smooth)
diff --git a/win32/deps/library/mgcv/R/mgcv b/win32/deps/library/mgcv/R/mgcv
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/mgcv/R/mgcv
+++ b/win32/deps/library/mgcv/R/mgcv
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/mgcv/R/mgcv.rdb b/win32/deps/library/mgcv/R/mgcv.rdb
index 64f4c8e..d6941c9 100644
Binary files a/win32/deps/library/mgcv/R/mgcv.rdb and b/win32/deps/library/mgcv/R/mgcv.rdb differ
diff --git a/win32/deps/library/mgcv/R/mgcv.rdx b/win32/deps/library/mgcv/R/mgcv.rdx
index 724efd2..f945ab8 100644
Binary files a/win32/deps/library/mgcv/R/mgcv.rdx and b/win32/deps/library/mgcv/R/mgcv.rdx differ
diff --git a/win32/deps/library/mgcv/data/columb.polys.rda b/win32/deps/library/mgcv/data/columb.polys.rda
new file mode 100644
index 0000000..e651c72
Binary files /dev/null and b/win32/deps/library/mgcv/data/columb.polys.rda differ
diff --git a/win32/deps/library/mgcv/data/columb.rda b/win32/deps/library/mgcv/data/columb.rda
new file mode 100644
index 0000000..cff102f
Binary files /dev/null and b/win32/deps/library/mgcv/data/columb.rda differ
diff --git a/win32/deps/library/mgcv/help/AnIndex b/win32/deps/library/mgcv/help/AnIndex
index 50f22e2..a38dbf3 100644
--- a/win32/deps/library/mgcv/help/AnIndex
+++ b/win32/deps/library/mgcv/help/AnIndex
@@ -1,24 +1,35 @@
mgcv-package mgcv-package
adaptive.smooth smooth.construct.ad.smooth.spec
anova.gam anova.gam
+bam bam
+bam.update bam.update
choose.k choose.k
coef.pdIdnot pdIdnot
coef.pdTens pdTens
+columb columb
+columb.polys columb
+concurvity concurvity
corMatrix.pdIdnot pdIdnot
cSplineDes cSplineDes
cubic.regression.spline smooth.construct.cr.smooth.spec
cyclic.cubic.spline smooth.construct.cr.smooth.spec
cyclic.p.spline smooth.construct.ps.smooth.spec
Dim.pdIdnot pdIdnot
+Duchon.spline smooth.construct.ds.smooth.spec
exclude.too.far exclude.too.far
extract.lme.cov extract.lme.cov
extract.lme.cov2 extract.lme.cov
+factor.smooth.interaction smooth.construct.fs.smooth.spec
fix.family.link fix.family.link
fix.family.ls fix.family.link
+fix.family.qf fix.family.link
+fix.family.rd fix.family.link
fix.family.var fix.family.link
fixDependence fixDependence
formula.gam formula.gam
formXtViX formXtViX
+fs.boundary fs.test
+fs.test fs.test
full.score full.score
function.predictors linear.functional.terms
gam gam
@@ -32,25 +43,30 @@ gam.outer gam.outer
gam.performance gam.convergence
gam.selection gam.selection
gam.side gam.side
+gam.vcomp gam.vcomp
gam2derivative gam2objective
gam2objective gam2objective
gamm gamm
gamObject gamObject
gamSim gamSim
get.var get.var
+in.out in.out
influence.gam influence.gam
initial.sp initial.sp
+inSide inSide
interpret.gam interpret.gam
ldTweedie ldTweedie
linear.functional.terms linear.functional.terms
logDet.pdIdnot pdIdnot
logLik.gam logLik.gam
+ls.size ls.size
magic magic
magic.post.proc magic.post.proc
-mgcv mgcv
-mgcv.control mgcv.control
+mgcv mgcv-package
+mgcv-FAQ mgcv-FAQ
model.matrix.gam model.matrix.gam
mono.con mono.con
+mrf smooth.construct.mrf.smooth.spec
mroot mroot
negbin negbin
new.name new.name
@@ -69,15 +85,26 @@ pdIdnot pdIdnot
pdMatrix.pdIdnot pdIdnot
pdMatrix.pdTens pdTens
pdTens pdTens
+pen.edf pen.edf
persp.gam vis.gam
place.knots place.knots
plot.gam plot.gam
+polys.plot polys.plot
+predict.bam predict.bam
predict.gam predict.gam
Predict.matrix Predict.matrix
Predict.matrix.cr.smooth Predict.matrix.cr.smooth
Predict.matrix.cs.smooth Predict.matrix.cr.smooth
Predict.matrix.cyclic.smooth Predict.matrix.cr.smooth
+Predict.matrix.duchon.spline smooth.construct.ds.smooth.spec
+Predict.matrix.fs.interaction smooth.construct.fs.smooth.spec
+Predict.matrix.mrf.smooth smooth.construct.mrf.smooth.spec
Predict.matrix.pspline.smooth Predict.matrix.cr.smooth
+Predict.matrix.random.effect smooth.construct.re.smooth.spec
+Predict.matrix.sf Predict.matrix.soap.film
+Predict.matrix.soap.film Predict.matrix.soap.film
+Predict.matrix.sos.smooth smooth.construct.sos.smooth.spec
+Predict.matrix.sw Predict.matrix.soap.film
Predict.matrix.tensor.smooth Predict.matrix.cr.smooth
Predict.matrix.tprs.smooth Predict.matrix.cr.smooth
Predict.matrix.ts.smooth Predict.matrix.cr.smooth
@@ -86,28 +113,47 @@ PredictMat smoothCon
print.anova.gam anova.gam
print.gam print.gam
print.summary.gam summary.gam
+qq.gam qq.gam
+random.effects random.effects
residuals.gam residuals.gam
+rig rig
+rTweedie rTweedie
s s
signal.regression linear.functional.terms
+slanczos slanczos
smooth.construct smooth.construct
smooth.construct.ad.smooth.spec smooth.construct.ad.smooth.spec
smooth.construct.cc.smooth.spec smooth.construct.cr.smooth.spec
smooth.construct.cp.smooth.spec smooth.construct.ps.smooth.spec
smooth.construct.cr.smooth.spec smooth.construct.cr.smooth.spec
smooth.construct.cs.smooth.spec smooth.construct.cr.smooth.spec
+smooth.construct.ds.smooth.spec smooth.construct.ds.smooth.spec
+smooth.construct.fs.smooth.spec smooth.construct.fs.smooth.spec
+smooth.construct.mrf.smooth.spec smooth.construct.mrf.smooth.spec
smooth.construct.ps.smooth.spec smooth.construct.ps.smooth.spec
+smooth.construct.re.smooth.spec smooth.construct.re.smooth.spec
+smooth.construct.sf.smooth.spec smooth.construct.so.smooth.spec
+smooth.construct.so.smooth.spec smooth.construct.so.smooth.spec
+smooth.construct.sos.smooth.spec smooth.construct.sos.smooth.spec
+smooth.construct.sw.smooth.spec smooth.construct.so.smooth.spec
smooth.construct.tensor.smooth.spec smooth.construct.tensor.smooth.spec
smooth.construct.tp.smooth.spec smooth.construct.tp.smooth.spec
smooth.construct.ts.smooth.spec smooth.construct.tp.smooth.spec
smooth.construct2 smooth.construct
smooth.terms smooth.terms
smoothCon smoothCon
+soap smooth.construct.so.smooth.spec
solve.pdIdnot pdIdnot
sp.vcov sp.vcov
+spasm.construct spasm.construct
+spasm.smooth spasm.construct
+spasm.sp spasm.construct
+Spherical.Spline smooth.construct.sos.smooth.spec
step.gam step.gam
summary.gam summary.gam
summary.pdIdnot pdIdnot
summary.pdTens pdTens
+t2 t2
te te
tensor.prod.model.matrix tensor.prod.model.matrix
tensor.prod.penalties tensor.prod.model.matrix
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@@ -0,0 +1,467 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness
+estimation</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness
+estimation
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘mgcv’ version 1.7-22</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<p align="center">
+<a href="# "> </a>
+<a href="#A">A</a>
+<a href="#B">B</a>
+<a href="#C">C</a>
+<a href="#D">D</a>
+<a href="#E">E</a>
+<a href="#F">F</a>
+<a href="#G">G</a>
+<a href="#I">I</a>
+<a href="#L">L</a>
+<a href="#M">M</a>
+<a href="#N">N</a>
+<a href="#P">P</a>
+<a href="#Q">Q</a>
+<a href="#R">R</a>
+<a href="#S">S</a>
+<a href="#T">T</a>
+<a href="#U">U</a>
+<a href="#V">V</a>
+</p>
+
+<table width="100%">
+<tr><td width="25%"><a href="mgcv-package.html">mgcv-package</a></td>
+<td>Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness estimation and GAMMs by REML/PQL</td></tr>
+</table>
+
+<h2><a name="A">-- A --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="smooth.construct.ad.smooth.spec.html">adaptive.smooth</a></td>
+<td>Adaptive smooths in GAMs</td></tr>
+<tr><td width="25%"><a href="anova.gam.html">anova.gam</a></td>
+<td>Approximate hypothesis tests related to GAM fits</td></tr>
+</table>
+
+<h2><a name="B">-- B --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="bam.html">bam</a></td>
+<td>Generalized additive models for very large datasets</td></tr>
+<tr><td width="25%"><a href="bam.update.html">bam.update</a></td>
+<td>Update a strictly additive bam model for new data.</td></tr>
+</table>
+
+<h2><a name="C">-- C --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="choose.k.html">choose.k</a></td>
+<td>Basis dimension choice for smooths</td></tr>
+<tr><td width="25%"><a href="pdIdnot.html">coef.pdIdnot</a></td>
+<td>Overflow proof pdMat class for multiples of the identity matrix</td></tr>
+<tr><td width="25%"><a href="pdTens.html">coef.pdTens</a></td>
+<td>Functions implementing a pdMat class for tensor product smooths</td></tr>
+<tr><td width="25%"><a href="columb.html">columb</a></td>
+<td>Reduced version of Columbus OH crime data</td></tr>
+<tr><td width="25%"><a href="columb.html">columb.polys</a></td>
+<td>Reduced version of Columbus OH crime data</td></tr>
+<tr><td width="25%"><a href="concurvity.html">concurvity</a></td>
+<td>GAM concurvity measures</td></tr>
+<tr><td width="25%"><a href="pdIdnot.html">corMatrix.pdIdnot</a></td>
+<td>Overflow proof pdMat class for multiples of the identity matrix</td></tr>
+<tr><td width="25%"><a href="cSplineDes.html">cSplineDes</a></td>
+<td>Evaluate cyclic B spline basis</td></tr>
+<tr><td width="25%"><a href="smooth.construct.cr.smooth.spec.html">cubic.regression.spline</a></td>
+<td>Penalized Cubic regression splines in GAMs</td></tr>
+<tr><td width="25%"><a href="smooth.construct.cr.smooth.spec.html">cyclic.cubic.spline</a></td>
+<td>Penalized Cubic regression splines in GAMs</td></tr>
+<tr><td width="25%"><a href="smooth.construct.ps.smooth.spec.html">cyclic.p.spline</a></td>
+<td>P-splines in GAMs</td></tr>
+</table>
+
+<h2><a name="D">-- D --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="pdIdnot.html">Dim.pdIdnot</a></td>
+<td>Overflow proof pdMat class for multiples of the identity matrix</td></tr>
+<tr><td width="25%"><a href="smooth.construct.ds.smooth.spec.html">Duchon.spline</a></td>
+<td>Low rank Duchon 1977 splines</td></tr>
+</table>
+
+<h2><a name="E">-- E --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="exclude.too.far.html">exclude.too.far</a></td>
+<td>Exclude prediction grid points too far from data</td></tr>
+<tr><td width="25%"><a href="extract.lme.cov.html">extract.lme.cov</a></td>
+<td>Extract the data covariance matrix from an lme object</td></tr>
+<tr><td width="25%"><a href="extract.lme.cov.html">extract.lme.cov2</a></td>
+<td>Extract the data covariance matrix from an lme object</td></tr>
+</table>
+
+<h2><a name="F">-- F --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="smooth.construct.fs.smooth.spec.html">factor.smooth.interaction</a></td>
+<td>Factor smooth interactions in GAMs</td></tr>
+<tr><td width="25%"><a href="fix.family.link.html">fix.family.link</a></td>
+<td>Modify families for use in GAM fitting and checking</td></tr>
+<tr><td width="25%"><a href="fix.family.link.html">fix.family.ls</a></td>
+<td>Modify families for use in GAM fitting and checking</td></tr>
+<tr><td width="25%"><a href="fix.family.link.html">fix.family.qf</a></td>
+<td>Modify families for use in GAM fitting and checking</td></tr>
+<tr><td width="25%"><a href="fix.family.link.html">fix.family.rd</a></td>
+<td>Modify families for use in GAM fitting and checking</td></tr>
+<tr><td width="25%"><a href="fix.family.link.html">fix.family.var</a></td>
+<td>Modify families for use in GAM fitting and checking</td></tr>
+<tr><td width="25%"><a href="fixDependence.html">fixDependence</a></td>
+<td>Detect linear dependencies of one matrix on another</td></tr>
+<tr><td width="25%"><a href="formula.gam.html">formula.gam</a></td>
+<td>GAM formula</td></tr>
+<tr><td width="25%"><a href="formXtViX.html">formXtViX</a></td>
+<td>Form component of GAMM covariance matrix</td></tr>
+<tr><td width="25%"><a href="fs.test.html">fs.boundary</a></td>
+<td>FELSPLINE test function</td></tr>
+<tr><td width="25%"><a href="fs.test.html">fs.test</a></td>
+<td>FELSPLINE test function</td></tr>
+<tr><td width="25%"><a href="full.score.html">full.score</a></td>
+<td>GCV/UBRE score for use within nlm</td></tr>
+<tr><td width="25%"><a href="linear.functional.terms.html">function.predictors</a></td>
+<td>Linear functionals of a smooth in GAMs</td></tr>
+</table>
+
+<h2><a name="G">-- G --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="gam.html">gam</a></td>
+<td>Generalized additive models with integrated smoothness estimation</td></tr>
+<tr><td width="25%"><a href="gam.check.html">gam.check</a></td>
+<td>Some diagnostics for a fitted gam model</td></tr>
+<tr><td width="25%"><a href="gam.control.html">gam.control</a></td>
+<td>Setting GAM fitting defaults</td></tr>
+<tr><td width="25%"><a href="gam.convergence.html">gam.convergence</a></td>
+<td>GAM convergence and performance issues</td></tr>
+<tr><td width="25%"><a href="gam.fit.html">gam.fit</a></td>
+<td>GAM P-IRLS estimation with GCV/UBRE smoothness estimation</td></tr>
+<tr><td width="25%"><a href="gam.fit3.html">gam.fit3</a></td>
+<td>P-IRLS GAM estimation with GCV & UBRE/AIC or RE/ML derivative calculation</td></tr>
+<tr><td width="25%"><a href="gam.models.html">gam.models</a></td>
+<td>Specifying generalized additive models</td></tr>
+<tr><td width="25%"><a href="gam.outer.html">gam.outer</a></td>
+<td>Minimize GCV or UBRE score of a GAM using 'outer' iteration</td></tr>
+<tr><td width="25%"><a href="gam.convergence.html">gam.performance</a></td>
+<td>GAM convergence and performance issues</td></tr>
+<tr><td width="25%"><a href="gam.selection.html">gam.selection</a></td>
+<td>Generalized Additive Model Selection</td></tr>
+<tr><td width="25%"><a href="gam.side.html">gam.side</a></td>
+<td>Identifiability side conditions for a GAM</td></tr>
+<tr><td width="25%"><a href="gam.vcomp.html">gam.vcomp</a></td>
+<td>Report gam smoothness estimates as variance components</td></tr>
+<tr><td width="25%"><a href="gam2objective.html">gam2derivative</a></td>
+<td>Objective functions for GAM smoothing parameter estimation</td></tr>
+<tr><td width="25%"><a href="gam2objective.html">gam2objective</a></td>
+<td>Objective functions for GAM smoothing parameter estimation</td></tr>
+<tr><td width="25%"><a href="gamm.html">gamm</a></td>
+<td>Generalized Additive Mixed Models</td></tr>
+<tr><td width="25%"><a href="gamObject.html">gamObject</a></td>
+<td>Fitted gam object</td></tr>
+<tr><td width="25%"><a href="gamSim.html">gamSim</a></td>
+<td>Simulate example data for GAMs</td></tr>
+<tr><td width="25%"><a href="get.var.html">get.var</a></td>
+<td>Get named variable or evaluate expression from list or data.frame</td></tr>
+</table>
+
+<h2><a name="I">-- I --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="in.out.html">in.out</a></td>
+<td>Which of a set of points lie within a polygon defined region</td></tr>
+<tr><td width="25%"><a href="influence.gam.html">influence.gam</a></td>
+<td>Extract the diagonal of the influence/hat matrix for a GAM</td></tr>
+<tr><td width="25%"><a href="initial.sp.html">initial.sp</a></td>
+<td>Starting values for multiple smoothing parameter estimation</td></tr>
+<tr><td width="25%"><a href="inSide.html">inSide</a></td>
+<td>Are points inside boundary?</td></tr>
+<tr><td width="25%"><a href="interpret.gam.html">interpret.gam</a></td>
+<td>Interpret a GAM formula</td></tr>
+</table>
+
+<h2><a name="L">-- L --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="ldTweedie.html">ldTweedie</a></td>
+<td>Log Tweedie density evaluation</td></tr>
+<tr><td width="25%"><a href="linear.functional.terms.html">linear.functional.terms</a></td>
+<td>Linear functionals of a smooth in GAMs</td></tr>
+<tr><td width="25%"><a href="pdIdnot.html">logDet.pdIdnot</a></td>
+<td>Overflow proof pdMat class for multiples of the identity matrix</td></tr>
+<tr><td width="25%"><a href="logLik.gam.html">logLik.gam</a></td>
+<td>Extract the log likelihood for a fitted GAM</td></tr>
+<tr><td width="25%"><a href="ls.size.html">ls.size</a></td>
+<td>Size of list elements</td></tr>
+</table>
+
+<h2><a name="M">-- M --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="magic.html">magic</a></td>
+<td>Stable Multiple Smoothing Parameter Estimation by GCV or UBRE</td></tr>
+<tr><td width="25%"><a href="magic.post.proc.html">magic.post.proc</a></td>
+<td>Auxilliary information from magic fit</td></tr>
+<tr><td width="25%"><a href="mgcv-package.html">mgcv</a></td>
+<td>Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness estimation and GAMMs by REML/PQL</td></tr>
+<tr><td width="25%"><a href="mgcv-FAQ.html">mgcv-FAQ</a></td>
+<td>Frequently Asked Questions for package mgcv</td></tr>
+<tr><td width="25%"><a href="model.matrix.gam.html">model.matrix.gam</a></td>
+<td>Extract model matrix from GAM fit</td></tr>
+<tr><td width="25%"><a href="mono.con.html">mono.con</a></td>
+<td>Monotonicity constraints for a cubic regression spline</td></tr>
+<tr><td width="25%"><a href="smooth.construct.mrf.smooth.spec.html">mrf</a></td>
+<td>Markov Random Field Smooths</td></tr>
+<tr><td width="25%"><a href="mroot.html">mroot</a></td>
+<td>Smallest square root of matrix</td></tr>
+</table>
+
+<h2><a name="N">-- N --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="negbin.html">negbin</a></td>
+<td>GAM negative binomial family</td></tr>
+<tr><td width="25%"><a href="new.name.html">new.name</a></td>
+<td>Obtain a name for a new variable that is not already in use</td></tr>
+<tr><td width="25%"><a href="notExp.html">notExp</a></td>
+<td>Functions for better-than-log positive parameterization</td></tr>
+<tr><td width="25%"><a href="notExp2.html">notExp2</a></td>
+<td>Alternative to log parameterization for variance components</td></tr>
+<tr><td width="25%"><a href="notExp.html">notLog</a></td>
+<td>Functions for better-than-log positive parameterization</td></tr>
+<tr><td width="25%"><a href="notExp2.html">notLog2</a></td>
+<td>Alternative to log parameterization for variance components</td></tr>
+<tr><td width="25%"><a href="null.space.dimension.html">null.space.dimension</a></td>
+<td>The basis of the space of un-penalized functions for a TPRS</td></tr>
+</table>
+
+<h2><a name="P">-- P --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="smooth.construct.ps.smooth.spec.html">p.spline</a></td>
+<td>P-splines in GAMs</td></tr>
+<tr><td width="25%"><a href="pcls.html">pcls</a></td>
+<td>Penalized Constrained Least Squares Fitting</td></tr>
+<tr><td width="25%"><a href="pdIdnot.html">pdConstruct.pdIdnot</a></td>
+<td>Overflow proof pdMat class for multiples of the identity matrix</td></tr>
+<tr><td width="25%"><a href="pdTens.html">pdConstruct.pdTens</a></td>
+<td>Functions implementing a pdMat class for tensor product smooths</td></tr>
+<tr><td width="25%"><a href="pdIdnot.html">pdFactor.pdIdnot</a></td>
+<td>Overflow proof pdMat class for multiples of the identity matrix</td></tr>
+<tr><td width="25%"><a href="pdTens.html">pdFactor.pdTens</a></td>
+<td>Functions implementing a pdMat class for tensor product smooths</td></tr>
+<tr><td width="25%"><a href="pdIdnot.html">pdIdnot</a></td>
+<td>Overflow proof pdMat class for multiples of the identity matrix</td></tr>
+<tr><td width="25%"><a href="pdIdnot.html">pdMatrix.pdIdnot</a></td>
+<td>Overflow proof pdMat class for multiples of the identity matrix</td></tr>
+<tr><td width="25%"><a href="pdTens.html">pdMatrix.pdTens</a></td>
+<td>Functions implementing a pdMat class for tensor product smooths</td></tr>
+<tr><td width="25%"><a href="pdTens.html">pdTens</a></td>
+<td>Functions implementing a pdMat class for tensor product smooths</td></tr>
+<tr><td width="25%"><a href="pen.edf.html">pen.edf</a></td>
+<td>Extract the effective degrees of freedom associated with each penalty in a gam fit</td></tr>
+<tr><td width="25%"><a href="vis.gam.html">persp.gam</a></td>
+<td>Visualization of GAM objects</td></tr>
+<tr><td width="25%"><a href="place.knots.html">place.knots</a></td>
+<td>Automatically place a set of knots evenly through covariate values</td></tr>
+<tr><td width="25%"><a href="plot.gam.html">plot.gam</a></td>
+<td>Default GAM plotting</td></tr>
+<tr><td width="25%"><a href="polys.plot.html">polys.plot</a></td>
+<td>Plot geographic regions defined as polygons</td></tr>
+<tr><td width="25%"><a href="predict.bam.html">predict.bam</a></td>
+<td>Prediction from fitted Big Additive Model model</td></tr>
+<tr><td width="25%"><a href="predict.gam.html">predict.gam</a></td>
+<td>Prediction from fitted GAM model</td></tr>
+<tr><td width="25%"><a href="Predict.matrix.html">Predict.matrix</a></td>
+<td>Prediction methods for smooth terms in a GAM</td></tr>
+<tr><td width="25%"><a href="Predict.matrix.cr.smooth.html">Predict.matrix.cr.smooth</a></td>
+<td>Predict matrix method functions</td></tr>
+<tr><td width="25%"><a href="Predict.matrix.cr.smooth.html">Predict.matrix.cs.smooth</a></td>
+<td>Predict matrix method functions</td></tr>
+<tr><td width="25%"><a href="Predict.matrix.cr.smooth.html">Predict.matrix.cyclic.smooth</a></td>
+<td>Predict matrix method functions</td></tr>
+<tr><td width="25%"><a href="smooth.construct.ds.smooth.spec.html">Predict.matrix.duchon.spline</a></td>
+<td>Low rank Duchon 1977 splines</td></tr>
+<tr><td width="25%"><a href="smooth.construct.fs.smooth.spec.html">Predict.matrix.fs.interaction</a></td>
+<td>Factor smooth interactions in GAMs</td></tr>
+<tr><td width="25%"><a href="smooth.construct.mrf.smooth.spec.html">Predict.matrix.mrf.smooth</a></td>
+<td>Markov Random Field Smooths</td></tr>
+<tr><td width="25%"><a href="Predict.matrix.cr.smooth.html">Predict.matrix.pspline.smooth</a></td>
+<td>Predict matrix method functions</td></tr>
+<tr><td width="25%"><a href="smooth.construct.re.smooth.spec.html">Predict.matrix.random.effect</a></td>
+<td>Simple random effects in GAMs</td></tr>
+<tr><td width="25%"><a href="Predict.matrix.soap.film.html">Predict.matrix.sf</a></td>
+<td>Prediction matrix for soap film smooth</td></tr>
+<tr><td width="25%"><a href="Predict.matrix.soap.film.html">Predict.matrix.soap.film</a></td>
+<td>Prediction matrix for soap film smooth</td></tr>
+<tr><td width="25%"><a href="smooth.construct.sos.smooth.spec.html">Predict.matrix.sos.smooth</a></td>
+<td>Splines on the sphere</td></tr>
+<tr><td width="25%"><a href="Predict.matrix.soap.film.html">Predict.matrix.sw</a></td>
+<td>Prediction matrix for soap film smooth</td></tr>
+<tr><td width="25%"><a href="Predict.matrix.cr.smooth.html">Predict.matrix.tensor.smooth</a></td>
+<td>Predict matrix method functions</td></tr>
+<tr><td width="25%"><a href="Predict.matrix.cr.smooth.html">Predict.matrix.tprs.smooth</a></td>
+<td>Predict matrix method functions</td></tr>
+<tr><td width="25%"><a href="Predict.matrix.cr.smooth.html">Predict.matrix.ts.smooth</a></td>
+<td>Predict matrix method functions</td></tr>
+<tr><td width="25%"><a href="Predict.matrix.html">Predict.matrix2</a></td>
+<td>Prediction methods for smooth terms in a GAM</td></tr>
+<tr><td width="25%"><a href="smoothCon.html">PredictMat</a></td>
+<td>Prediction/Construction wrapper functions for GAM smooth terms</td></tr>
+<tr><td width="25%"><a href="anova.gam.html">print.anova.gam</a></td>
+<td>Approximate hypothesis tests related to GAM fits</td></tr>
+<tr><td width="25%"><a href="print.gam.html">print.gam</a></td>
+<td>Print a Generalized Additive Model object.</td></tr>
+<tr><td width="25%"><a href="summary.gam.html">print.summary.gam</a></td>
+<td>Summary for a GAM fit</td></tr>
+</table>
+
+<h2><a name="Q">-- Q --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="qq.gam.html">qq.gam</a></td>
+<td>QQ plots for gam model residuals</td></tr>
+</table>
+
+<h2><a name="R">-- R --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="random.effects.html">random.effects</a></td>
+<td>Random effects in GAMs</td></tr>
+<tr><td width="25%"><a href="residuals.gam.html">residuals.gam</a></td>
+<td>Generalized Additive Model residuals</td></tr>
+<tr><td width="25%"><a href="rig.html">rig</a></td>
+<td>Generate inverse Gaussian random deviates</td></tr>
+<tr><td width="25%"><a href="rTweedie.html">rTweedie</a></td>
+<td>Generate Tweedie random deviates</td></tr>
+</table>
+
+<h2><a name="S">-- S --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="s.html">s</a></td>
+<td>Defining smooths in GAM formulae</td></tr>
+<tr><td width="25%"><a href="linear.functional.terms.html">signal.regression</a></td>
+<td>Linear functionals of a smooth in GAMs</td></tr>
+<tr><td width="25%"><a href="slanczos.html">slanczos</a></td>
+<td>Compute truncated eigen decomposition of a symmetric matrix</td></tr>
+<tr><td width="25%"><a href="smooth.construct.html">smooth.construct</a></td>
+<td>Constructor functions for smooth terms in a GAM</td></tr>
+<tr><td width="25%"><a href="smooth.construct.ad.smooth.spec.html">smooth.construct.ad.smooth.spec</a></td>
+<td>Adaptive smooths in GAMs</td></tr>
+<tr><td width="25%"><a href="smooth.construct.cr.smooth.spec.html">smooth.construct.cc.smooth.spec</a></td>
+<td>Penalized Cubic regression splines in GAMs</td></tr>
+<tr><td width="25%"><a href="smooth.construct.ps.smooth.spec.html">smooth.construct.cp.smooth.spec</a></td>
+<td>P-splines in GAMs</td></tr>
+<tr><td width="25%"><a href="smooth.construct.cr.smooth.spec.html">smooth.construct.cr.smooth.spec</a></td>
+<td>Penalized Cubic regression splines in GAMs</td></tr>
+<tr><td width="25%"><a href="smooth.construct.cr.smooth.spec.html">smooth.construct.cs.smooth.spec</a></td>
+<td>Penalized Cubic regression splines in GAMs</td></tr>
+<tr><td width="25%"><a href="smooth.construct.ds.smooth.spec.html">smooth.construct.ds.smooth.spec</a></td>
+<td>Low rank Duchon 1977 splines</td></tr>
+<tr><td width="25%"><a href="smooth.construct.fs.smooth.spec.html">smooth.construct.fs.smooth.spec</a></td>
+<td>Factor smooth interactions in GAMs</td></tr>
+<tr><td width="25%"><a href="smooth.construct.mrf.smooth.spec.html">smooth.construct.mrf.smooth.spec</a></td>
+<td>Markov Random Field Smooths</td></tr>
+<tr><td width="25%"><a href="smooth.construct.ps.smooth.spec.html">smooth.construct.ps.smooth.spec</a></td>
+<td>P-splines in GAMs</td></tr>
+<tr><td width="25%"><a href="smooth.construct.re.smooth.spec.html">smooth.construct.re.smooth.spec</a></td>
+<td>Simple random effects in GAMs</td></tr>
+<tr><td width="25%"><a href="smooth.construct.so.smooth.spec.html">smooth.construct.sf.smooth.spec</a></td>
+<td>Soap film smoother constructer</td></tr>
+<tr><td width="25%"><a href="smooth.construct.so.smooth.spec.html">smooth.construct.so.smooth.spec</a></td>
+<td>Soap film smoother constructer</td></tr>
+<tr><td width="25%"><a href="smooth.construct.sos.smooth.spec.html">smooth.construct.sos.smooth.spec</a></td>
+<td>Splines on the sphere</td></tr>
+<tr><td width="25%"><a href="smooth.construct.so.smooth.spec.html">smooth.construct.sw.smooth.spec</a></td>
+<td>Soap film smoother constructer</td></tr>
+<tr><td width="25%"><a href="smooth.construct.tensor.smooth.spec.html">smooth.construct.tensor.smooth.spec</a></td>
+<td>Tensor product smoothing constructor</td></tr>
+<tr><td width="25%"><a href="smooth.construct.tp.smooth.spec.html">smooth.construct.tp.smooth.spec</a></td>
+<td>Penalized thin plate regression splines in GAMs</td></tr>
+<tr><td width="25%"><a href="smooth.construct.tp.smooth.spec.html">smooth.construct.ts.smooth.spec</a></td>
+<td>Penalized thin plate regression splines in GAMs</td></tr>
+<tr><td width="25%"><a href="smooth.construct.html">smooth.construct2</a></td>
+<td>Constructor functions for smooth terms in a GAM</td></tr>
+<tr><td width="25%"><a href="smooth.terms.html">smooth.terms</a></td>
+<td>Smooth terms in GAM</td></tr>
+<tr><td width="25%"><a href="smoothCon.html">smoothCon</a></td>
+<td>Prediction/Construction wrapper functions for GAM smooth terms</td></tr>
+<tr><td width="25%"><a href="smooth.construct.so.smooth.spec.html">soap</a></td>
+<td>Soap film smoother constructer</td></tr>
+<tr><td width="25%"><a href="pdIdnot.html">solve.pdIdnot</a></td>
+<td>Overflow proof pdMat class for multiples of the identity matrix</td></tr>
+<tr><td width="25%"><a href="sp.vcov.html">sp.vcov</a></td>
+<td>Extract smoothing parameter estimator covariance matrix from (RE)ML GAM fit</td></tr>
+<tr><td width="25%"><a href="spasm.construct.html">spasm.construct</a></td>
+<td>Experimental sparse smoothers</td></tr>
+<tr><td width="25%"><a href="spasm.construct.html">spasm.smooth</a></td>
+<td>Experimental sparse smoothers</td></tr>
+<tr><td width="25%"><a href="spasm.construct.html">spasm.sp</a></td>
+<td>Experimental sparse smoothers</td></tr>
+<tr><td width="25%"><a href="smooth.construct.sos.smooth.spec.html">Spherical.Spline</a></td>
+<td>Splines on the sphere</td></tr>
+<tr><td width="25%"><a href="step.gam.html">step.gam</a></td>
+<td>Alternatives to step.gam</td></tr>
+<tr><td width="25%"><a href="summary.gam.html">summary.gam</a></td>
+<td>Summary for a GAM fit</td></tr>
+<tr><td width="25%"><a href="pdIdnot.html">summary.pdIdnot</a></td>
+<td>Overflow proof pdMat class for multiples of the identity matrix</td></tr>
+<tr><td width="25%"><a href="pdTens.html">summary.pdTens</a></td>
+<td>Functions implementing a pdMat class for tensor product smooths</td></tr>
+</table>
+
+<h2><a name="T">-- T --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="t2.html">t2</a></td>
+<td>Define alternative tensor product smooths in GAM formulae</td></tr>
+<tr><td width="25%"><a href="te.html">te</a></td>
+<td>Define tensor product smooths in GAM formulae</td></tr>
+<tr><td width="25%"><a href="tensor.prod.model.matrix.html">tensor.prod.model.matrix</a></td>
+<td>Utility functions for constructing tensor product smooths</td></tr>
+<tr><td width="25%"><a href="tensor.prod.model.matrix.html">tensor.prod.penalties</a></td>
+<td>Utility functions for constructing tensor product smooths</td></tr>
+<tr><td width="25%"><a href="smooth.construct.tp.smooth.spec.html">tprs</a></td>
+<td>Penalized thin plate regression splines in GAMs</td></tr>
+<tr><td width="25%"><a href="Tweedie.html">Tweedie</a></td>
+<td>GAM Tweedie family</td></tr>
+</table>
+
+<h2><a name="U">-- U --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="uniquecombs.html">uniquecombs</a></td>
+<td>find the unique rows in a matrix</td></tr>
+<tr><td width="25%"><a href="smooth.construct.html">user.defined.smooth</a></td>
+<td>Constructor functions for smooth terms in a GAM</td></tr>
+</table>
+
+<h2><a name="V">-- V --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="vcov.gam.html">vcov.gam</a></td>
+<td>Extract parameter (estimator) covariance matrix from GAM fit</td></tr>
+<tr><td width="25%"><a href="vis.gam.html">vis.gam</a></td>
+<td>Visualization of GAM objects</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/mgcv/html/R.css b/win32/deps/library/mgcv/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/mgcv/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/mgcv/libs/i386/mgcv.dll b/win32/deps/library/mgcv/libs/i386/mgcv.dll
new file mode 100644
index 0000000..a9745b1
Binary files /dev/null and b/win32/deps/library/mgcv/libs/i386/mgcv.dll differ
diff --git a/win32/deps/library/nlme/CITATION b/win32/deps/library/nlme/CITATION
index e1d0e01..1942dcc 100644
--- a/win32/deps/library/nlme/CITATION
+++ b/win32/deps/library/nlme/CITATION
@@ -1,8 +1,7 @@
citHeader("To cite package 'nlme' in publications use:")
-desc <- packageDescription("nlme")
-year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", desc$Date)
-vers <- paste("R package version", desc$Version)
+year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", meta$Date, perl = TRUE)
+vers <- paste("R package version", meta$Version)
citEntry(entry="Manual",
title = "nlme: Linear and Nonlinear Mixed Effects Models",
@@ -10,12 +9,12 @@ citEntry(entry="Manual",
as.person("Douglas Bates"),
as.person("Saikat DebRoy"),
as.person("Deepayan Sarkar"),
- as.person("the R Core team")),
+ person("R Core Team")),
year = year,
note = vers,
textVersion =
- paste("Jose Pinheiro, Douglas Bates, Saikat DebRoy, Deepayan Sarkar and the R Core team (",
+ paste("Jose Pinheiro, Douglas Bates, Saikat DebRoy, Deepayan Sarkar and the R Development Core Team (",
year,
"). nlme: Linear and Nonlinear Mixed Effects Models. ",
vers, ".", sep=""))
diff --git a/win32/deps/library/nlme/DESCRIPTION b/win32/deps/library/nlme/DESCRIPTION
index 309515a..e15a68f 100644
--- a/win32/deps/library/nlme/DESCRIPTION
+++ b/win32/deps/library/nlme/DESCRIPTION
@@ -1,21 +1,28 @@
-Package: nlme
-Version: 3.1-93
-Date: 2009-08-16
-Priority: recommended
-Title: Linear and Nonlinear Mixed Effects Models
-Author: Jose Pinheiro <Jose Pinheiro pharma novartis com>, Douglas
- Bates <bates stat wisc edu>, Saikat DebRoy
- <saikat stat wisc edu>, Deepayan Sarkar
- <Deepayan Sarkar R-project org>, the R Core team.
-Maintainer: R-core <R-core R-project org>
-Description: Fit and compare Gaussian linear and nonlinear
- mixed-effects models.
-Depends: graphics, stats, R (>= 2.4.0)
-Imports: lattice
-LazyLoad: yes
-LazyData: yes
-License: GPL (>= 2)
-Packaged: 2009-08-16 11:31:19 UTC; ripley
-Repository: CRAN
-Date/Publication: 2009-08-16 15:26:54
-Built: R 2.9.2; i386-pc-mingw32; 2009-08-24 13:06:01 UTC; windows
+Package: nlme
+Version: 3.1-105
+Date: 2012-09-24
+Priority: recommended
+Title: Linear and Nonlinear Mixed Effects Models
+Authors R: c(person("Jose", "Pinheiro", comment = "S version"),
+ person("Douglas", "Bates", comment = "up to 2007"),
+ person("Saikat", "DebRoy", comment = "up to 2002"),
+ person("Deepayan", "Sarkar", comment = "up to 2005"),
+ person("R-core", email = "R-core R-project org", role =
+ c("aut", "cre")))
+Author: Jose Pinheiro (S version),
+ Douglas Bates (up to 2007),
+ Saikat DebRoy (up to 2002),
+ Deepayan Sarkar (up to 2005),
+ the R Core team.
+Maintainer: R-core <R-core R-project org>
+Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
+Depends: graphics, stats, R (>= 2.13)
+Imports: lattice
+Suggests: Hmisc, MASS
+LazyLoad: yes
+LazyData: yes
+License: GPL (>= 2)
+BugReports: http://bugs.r-project.org
+Packaged: 2012-10-11 13:26:52 UTC; ripley
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:13:31 UTC; windows
+Archs: i386, x64
diff --git a/win32/deps/library/nlme/LICENCE b/win32/deps/library/nlme/LICENCE
index 1a9ecbd..95ec041 100644
--- a/win32/deps/library/nlme/LICENCE
+++ b/win32/deps/library/nlme/LICENCE
@@ -2,6 +2,6 @@ This software is distributed under the terms of the GNU General Public
License as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
-A copy of the GNU General Public License is in file COPYING in the
+A copy of the GNU General Public License version 2 is in file GPL-2 in the
sources of this package, and is also available at
http://www.r-project.org/Licenses/
diff --git a/win32/deps/library/nlme/Meta/Rd.rds b/win32/deps/library/nlme/Meta/Rd.rds
index d6fb367..f0936e7 100644
Binary files a/win32/deps/library/nlme/Meta/Rd.rds and b/win32/deps/library/nlme/Meta/Rd.rds differ
diff --git a/win32/deps/library/nlme/Meta/data.rds b/win32/deps/library/nlme/Meta/data.rds
index ca7455e..66c8a0d 100644
Binary files a/win32/deps/library/nlme/Meta/data.rds and b/win32/deps/library/nlme/Meta/data.rds differ
diff --git a/win32/deps/library/nlme/Meta/hsearch.rds b/win32/deps/library/nlme/Meta/hsearch.rds
index 04c0964..0eb482a 100644
Binary files a/win32/deps/library/nlme/Meta/hsearch.rds and b/win32/deps/library/nlme/Meta/hsearch.rds differ
diff --git a/win32/deps/library/nlme/Meta/links.rds b/win32/deps/library/nlme/Meta/links.rds
new file mode 100644
index 0000000..6e93c1d
Binary files /dev/null and b/win32/deps/library/nlme/Meta/links.rds differ
diff --git a/win32/deps/library/nlme/Meta/nsInfo.rds b/win32/deps/library/nlme/Meta/nsInfo.rds
index 22a0783..61ea4db 100644
Binary files a/win32/deps/library/nlme/Meta/nsInfo.rds and b/win32/deps/library/nlme/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/nlme/Meta/package.rds b/win32/deps/library/nlme/Meta/package.rds
index c01ccd6..bb24719 100644
Binary files a/win32/deps/library/nlme/Meta/package.rds and b/win32/deps/library/nlme/Meta/package.rds differ
diff --git a/win32/deps/library/nlme/NAMESPACE b/win32/deps/library/nlme/NAMESPACE
index f721a1e..2f6643c 100644
--- a/win32/deps/library/nlme/NAMESPACE
+++ b/win32/deps/library/nlme/NAMESPACE
@@ -4,7 +4,7 @@ import(stats)
importFrom(graphics, pairs, plot)
export(ACF, allCoef, asOneFormula, asTable, augPred, balancedGrouped,
- BIC, "coef<-", "coefficients<-", collapse, compareFits,
+ "coef<-", "coefficients<-", collapse, compareFits,
comparePred, corAR1, corARMA, corCAR1, corCompSymm,
corExp, corFactor, corGaus, corIdent, corLin, corMatrix,
corNatural, corRatio, corSpatial, corSpher, corSymm,
@@ -72,12 +72,6 @@ S3method(asTable, groupedData)
S3method(augPred, gls)
S3method(augPred, lme)
S3method(augPred, lmList)
-S3method(BIC, gls)
-S3method(BIC, lm)
-S3method(BIC, lme)
-S3method(BIC, lmList)
-S3method(BIC, logLik)
-S3method(BIC, nls)
S3method(coef, corAR1)
S3method(coef, corARMA)
S3method(coef, corCAR1)
@@ -295,6 +289,9 @@ S3method(nlme, formula)
S3method(nlme, nlsList)
S3method(nlsList, formula)
S3method(nlsList, selfStart)
+S3method(nobs, gls)
+S3method(nobs, gnls)
+S3method(nobs, lme)
S3method(pairs, compareFits)
S3method(pairs, lme)
S3method(pairs, lmList)
diff --git a/win32/deps/library/nlme/R/nlme b/win32/deps/library/nlme/R/nlme
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/nlme/R/nlme
+++ b/win32/deps/library/nlme/R/nlme
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/nlme/R/nlme.rdb b/win32/deps/library/nlme/R/nlme.rdb
index 605af94..c83be7a 100644
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diff --git a/win32/deps/library/nlme/R/nlme.rdx b/win32/deps/library/nlme/R/nlme.rdx
index ae6fb41..be04120 100644
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diff --git a/win32/deps/library/nlme/data/Rdata.rdb b/win32/deps/library/nlme/data/Rdata.rdb
index 3b2ebc5..56116a0 100644
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diff --git a/win32/deps/library/nlme/data/Rdata.rds b/win32/deps/library/nlme/data/Rdata.rds
index fe88293..2f9b167 100644
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diff --git a/win32/deps/library/nlme/data/Rdata.rdx b/win32/deps/library/nlme/data/Rdata.rdx
index 7972fb1..5a1ba18 100644
Binary files a/win32/deps/library/nlme/data/Rdata.rdx and b/win32/deps/library/nlme/data/Rdata.rdx differ
diff --git a/win32/deps/library/nlme/help/AnIndex b/win32/deps/library/nlme/help/AnIndex
index 0c00949..7694b07 100644
--- a/win32/deps/library/nlme/help/AnIndex
+++ b/win32/deps/library/nlme/help/AnIndex
@@ -19,15 +19,6 @@ augPred.lme augPred
augPred.lmList augPred
balancedGrouped balancedGrouped
bdf bdf
-BIC BIC
-BIC.gls BIC
-BIC.lm BIC
-BIC.lme BIC
-BIC.lmList BIC
-BIC.logLik BIC.logLik
-BIC.nlme BIC
-BIC.nls BIC
-BIC.nlsList BIC
BodyWeight BodyWeight
Cefamandole Cefamandole
coef.corAR1 coef.corStruct
diff --git a/win32/deps/library/nlme/help/aliases.rds b/win32/deps/library/nlme/help/aliases.rds
new file mode 100644
index 0000000..efe64b3
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diff --git a/win32/deps/library/nlme/help/nlme.rdb b/win32/deps/library/nlme/help/nlme.rdb
new file mode 100644
index 0000000..d4c4fce
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diff --git a/win32/deps/library/nlme/help/nlme.rdx b/win32/deps/library/nlme/help/nlme.rdx
new file mode 100644
index 0000000..b042983
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diff --git a/win32/deps/library/nlme/help/paths.rds b/win32/deps/library/nlme/help/paths.rds
new file mode 100644
index 0000000..7de0dee
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diff --git a/win32/deps/library/nlme/html/00Index.html b/win32/deps/library/nlme/html/00Index.html
new file mode 100644
index 0000000..6845091
--- /dev/null
+++ b/win32/deps/library/nlme/html/00Index.html
@@ -0,0 +1,1230 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Linear and Nonlinear Mixed Effects Models</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Linear and Nonlinear Mixed Effects Models
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘nlme’ version 3.1-105</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<p align="center">
+<a href="#A">A</a>
+<a href="#B">B</a>
+<a href="#C">C</a>
+<a href="#D">D</a>
+<a href="#E">E</a>
+<a href="#F">F</a>
+<a href="#G">G</a>
+<a href="#I">I</a>
+<a href="#L">L</a>
+<a href="#M">M</a>
+<a href="#N">N</a>
+<a href="#O">O</a>
+<a href="#P">P</a>
+<a href="#Q">Q</a>
+<a href="#R">R</a>
+<a href="#S">S</a>
+<a href="#T">T</a>
+<a href="#U">U</a>
+<a href="#V">V</a>
+<a href="#W">W</a>
+<a href="#misc">misc</a>
+</p>
+
+
+<h2><a name="A">-- A --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="ACF.html">ACF</a></td>
+<td>Autocorrelation Function</td></tr>
+<tr><td width="25%"><a href="ACF.gls.html">ACF.gls</a></td>
+<td>Autocorrelation Function for gls Residuals</td></tr>
+<tr><td width="25%"><a href="ACF.lme.html">ACF.lme</a></td>
+<td>Autocorrelation Function for lme Residuals</td></tr>
+<tr><td width="25%"><a href="Alfalfa.html">Alfalfa</a></td>
+<td>Split-Plot Experiment on Varieties of Alfalfa</td></tr>
+<tr><td width="25%"><a href="allCoef.html">allCoef</a></td>
+<td>Extract Coefficients from a Set of Objects</td></tr>
+<tr><td width="25%"><a href="anova.gls.html">anova.gls</a></td>
+<td>Compare Likelihoods of Fitted Objects</td></tr>
+<tr><td width="25%"><a href="anova.lme.html">anova.lme</a></td>
+<td>Compare Likelihoods of Fitted Objects</td></tr>
+<tr><td width="25%"><a href="groupedData.html">as.data.frame.groupedData</a></td>
+<td>Construct a groupedData Object</td></tr>
+<tr><td width="25%"><a href="as.matrix.corStruct.html">as.matrix.corStruct</a></td>
+<td>Matrix of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="as.matrix.pdMat.html">as.matrix.pdMat</a></td>
+<td>Matrix of a pdMat Object</td></tr>
+<tr><td width="25%"><a href="as.matrix.reStruct.html">as.matrix.reStruct</a></td>
+<td>Matrices of an reStruct Object</td></tr>
+<tr><td width="25%"><a href="asOneFormula.html">asOneFormula</a></td>
+<td>Combine Formulas of a Set of Objects</td></tr>
+<tr><td width="25%"><a href="Assay.html">Assay</a></td>
+<td>Bioassay on Cell Culture Plate</td></tr>
+<tr><td width="25%"><a href="asTable.html">asTable</a></td>
+<td>Convert groupedData to a matrix</td></tr>
+<tr><td width="25%"><a href="asTable.html">asTable.groupedData</a></td>
+<td>Convert groupedData to a matrix</td></tr>
+<tr><td width="25%"><a href="augPred.html">augPred</a></td>
+<td>Augmented Predictions</td></tr>
+<tr><td width="25%"><a href="augPred.html">augPred.gls</a></td>
+<td>Augmented Predictions</td></tr>
+<tr><td width="25%"><a href="augPred.html">augPred.lme</a></td>
+<td>Augmented Predictions</td></tr>
+<tr><td width="25%"><a href="augPred.html">augPred.lmList</a></td>
+<td>Augmented Predictions</td></tr>
+</table>
+
+<h2><a name="B">-- B --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="balancedGrouped.html">balancedGrouped</a></td>
+<td>Create a groupedData object from a matrix</td></tr>
+<tr><td width="25%"><a href="bdf.html">bdf</a></td>
+<td>Language scores</td></tr>
+<tr><td width="25%"><a href="BodyWeight.html">BodyWeight</a></td>
+<td>Rat weight over time for different diets</td></tr>
+</table>
+
+<h2><a name="C">-- C --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Cefamandole.html">Cefamandole</a></td>
+<td>Pharmacokinetics of Cefamandole</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef.corAR1</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="corARMA.html">coef.corARMA</a></td>
+<td>ARMA(p,q) Correlation Structure</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef.corARMAd</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef.corCAR1</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef.corCompSymm</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef.corHF</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef.corIdent</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef.corLin</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef.corNatural</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef.corSpatial</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef.corSpher</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef.corStruct</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef.corSymm</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.gnls.html">coef.gnls</a></td>
+<td>Extract gnls Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.lme.html">coef.lme</a></td>
+<td>Extract lme Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.lmList.html">coef.lmList</a></td>
+<td>Extract lmList Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.modelStruct.html">coef.modelStruct</a></td>
+<td>Extract modelStruct Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.pdMat.html">coef.pdBlocked</a></td>
+<td>pdMat Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.pdMat.html">coef.pdCompSymm</a></td>
+<td>pdMat Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.pdMat.html">coef.pdDiag</a></td>
+<td>pdMat Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.pdMat.html">coef.pdIdent</a></td>
+<td>pdMat Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.pdMat.html">coef.pdMat</a></td>
+<td>pdMat Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.pdMat.html">coef.pdNatural</a></td>
+<td>pdMat Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.pdMat.html">coef.pdSymm</a></td>
+<td>pdMat Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.reStruct.html">coef.reStruct</a></td>
+<td>reStruct Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef.summary.nlsList</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.varFunc.html">coef.varComb</a></td>
+<td>varFunc Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.varFunc.html">coef.varConstPower</a></td>
+<td>varFunc Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.varFunc.html">coef.varExp</a></td>
+<td>varFunc Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.varFunc.html">coef.varFixed</a></td>
+<td>varFunc Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.varFunc.html">coef.varFunc</a></td>
+<td>varFunc Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.varFunc.html">coef.varIdent</a></td>
+<td>varFunc Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.varFunc.html">coef.varPower</a></td>
+<td>varFunc Object Coefficients</td></tr>
+<tr><td width="25%"><a href="Coef.html">coef<-</a></td>
+<td>Assign Values to Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef<-.corAR1</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef<-.corARMA</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef<-.corCAR1</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef<-.corCompSymm</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef<-.corHF</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef<-.corIdent</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef<-.corLin</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef<-.corNatural</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef<-.corSpatial</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef<-.corSpher</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef<-.corStruct</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.corStruct.html">coef<-.corSymm</a></td>
+<td>Coefficients of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="coef.modelStruct.html">coef<-.modelStruct</a></td>
+<td>Extract modelStruct Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.pdMat.html">coef<-.pdBlocked</a></td>
+<td>pdMat Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.pdMat.html">coef<-.pdMat</a></td>
+<td>pdMat Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.reStruct.html">coef<-.reStruct</a></td>
+<td>reStruct Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.varFunc.html">coef<-.varComb</a></td>
+<td>varFunc Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.varFunc.html">coef<-.varConstPower</a></td>
+<td>varFunc Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.varFunc.html">coef<-.varExp</a></td>
+<td>varFunc Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.varFunc.html">coef<-.varFixed</a></td>
+<td>varFunc Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.varFunc.html">coef<-.varIdent</a></td>
+<td>varFunc Object Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.varFunc.html">coef<-.varPower</a></td>
+<td>varFunc Object Coefficients</td></tr>
+<tr><td width="25%"><a href="Coef.html">coefficients<-</a></td>
+<td>Assign Values to Coefficients</td></tr>
+<tr><td width="25%"><a href="collapse.html">collapse</a></td>
+<td>Collapse According to Groups</td></tr>
+<tr><td width="25%"><a href="collapse.groupedData.html">collapse.groupedData</a></td>
+<td>Collapse a groupedData Object</td></tr>
+<tr><td width="25%"><a href="compareFits.html">compareFits</a></td>
+<td>Compare Fitted Objects</td></tr>
+<tr><td width="25%"><a href="comparePred.html">comparePred</a></td>
+<td>Compare Predictions</td></tr>
+<tr><td width="25%"><a href="comparePred.html">comparePred.gls</a></td>
+<td>Compare Predictions</td></tr>
+<tr><td width="25%"><a href="comparePred.html">comparePred.lme</a></td>
+<td>Compare Predictions</td></tr>
+<tr><td width="25%"><a href="comparePred.html">comparePred.lmList</a></td>
+<td>Compare Predictions</td></tr>
+<tr><td width="25%"><a href="corAR1.html">corAR1</a></td>
+<td>AR(1) Correlation Structure</td></tr>
+<tr><td width="25%"><a href="corARMA.html">corARMA</a></td>
+<td>ARMA(p,q) Correlation Structure</td></tr>
+<tr><td width="25%"><a href="corCAR1.html">corCAR1</a></td>
+<td>Continuous AR(1) Correlation Structure</td></tr>
+<tr><td width="25%"><a href="corClasses.html">corClasses</a></td>
+<td>Correlation Structure Classes</td></tr>
+<tr><td width="25%"><a href="corCompSymm.html">corCompSymm</a></td>
+<td>Compound Symmetry Correlation Structure</td></tr>
+<tr><td width="25%"><a href="corExp.html">corExp</a></td>
+<td>Exponential Correlation Structure</td></tr>
+<tr><td width="25%"><a href="corFactor.html">corFactor</a></td>
+<td>Factor of a Correlation Matrix</td></tr>
+<tr><td width="25%"><a href="corFactor.corStruct.html">corFactor.compSymm</a></td>
+<td>Factor of a corStruct Object Matrix</td></tr>
+<tr><td width="25%"><a href="corFactor.corStruct.html">corFactor.corAR1</a></td>
+<td>Factor of a corStruct Object Matrix</td></tr>
+<tr><td width="25%"><a href="corFactor.corStruct.html">corFactor.corARMA</a></td>
+<td>Factor of a corStruct Object Matrix</td></tr>
+<tr><td width="25%"><a href="corFactor.corStruct.html">corFactor.corCAR1</a></td>
+<td>Factor of a corStruct Object Matrix</td></tr>
+<tr><td width="25%"><a href="corFactor.corStruct.html">corFactor.corNatural</a></td>
+<td>Factor of a corStruct Object Matrix</td></tr>
+<tr><td width="25%"><a href="corFactor.corStruct.html">corFactor.corSpatial</a></td>
+<td>Factor of a corStruct Object Matrix</td></tr>
+<tr><td width="25%"><a href="corFactor.corStruct.html">corFactor.corStruct</a></td>
+<td>Factor of a corStruct Object Matrix</td></tr>
+<tr><td width="25%"><a href="corFactor.corStruct.html">corFactor.corSymm</a></td>
+<td>Factor of a corStruct Object Matrix</td></tr>
+<tr><td width="25%"><a href="corGaus.html">corGaus</a></td>
+<td>Gaussian Correlation Structure</td></tr>
+<tr><td width="25%"><a href="corClasses.html">corIdent</a></td>
+<td>Correlation Structure Classes</td></tr>
+<tr><td width="25%"><a href="corLin.html">corLin</a></td>
+<td>Linear Correlation Structure</td></tr>
+<tr><td width="25%"><a href="corMatrix.html">corMatrix</a></td>
+<td>Extract Correlation Matrix</td></tr>
+<tr><td width="25%"><a href="corMatrix.corStruct.html">corMatrix.compSymm</a></td>
+<td>Matrix of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="corMatrix.corStruct.html">corMatrix.corAR1</a></td>
+<td>Matrix of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="corMatrix.corStruct.html">corMatrix.corARMA</a></td>
+<td>Matrix of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="corMatrix.corStruct.html">corMatrix.corCAR1</a></td>
+<td>Matrix of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="corMatrix.corStruct.html">corMatrix.corCompSymm</a></td>
+<td>Matrix of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="corMatrix.corStruct.html">corMatrix.corIdent</a></td>
+<td>Matrix of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="corMatrix.corStruct.html">corMatrix.corNatural</a></td>
+<td>Matrix of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="corMatrix.corStruct.html">corMatrix.corSpatial</a></td>
+<td>Matrix of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="corMatrix.corStruct.html">corMatrix.corStruct</a></td>
+<td>Matrix of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="corMatrix.corStruct.html">corMatrix.corSymm</a></td>
+<td>Matrix of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="corMatrix.pdMat.html">corMatrix.pdBlocked</a></td>
+<td>Extract Correlation Matrix from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="corMatrix.pdMat.html">corMatrix.pdCompSymm</a></td>
+<td>Extract Correlation Matrix from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="corMatrix.pdMat.html">corMatrix.pdDiag</a></td>
+<td>Extract Correlation Matrix from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="corMatrix.pdMat.html">corMatrix.pdIdent</a></td>
+<td>Extract Correlation Matrix from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="corMatrix.pdMat.html">corMatrix.pdMat</a></td>
+<td>Extract Correlation Matrix from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="corMatrix.pdMat.html">corMatrix.pdSymm</a></td>
+<td>Extract Correlation Matrix from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="corMatrix.reStruct.html">corMatrix.reStruct</a></td>
+<td>Extract Correlation Matrix from Components of an reStruct Object</td></tr>
+<tr><td width="25%"><a href="corNatural.html">corNatural</a></td>
+<td>General correlation in natural parameterization</td></tr>
+<tr><td width="25%"><a href="corRatio.html">corRatio</a></td>
+<td>Rational Quadratic Correlation Structure</td></tr>
+<tr><td width="25%"><a href="corSpatial.html">corSpatial</a></td>
+<td>Spatial Correlation Structure</td></tr>
+<tr><td width="25%"><a href="corSpher.html">corSpher</a></td>
+<td>Spherical Correlation Structure</td></tr>
+<tr><td width="25%"><a href="corSymm.html">corSymm</a></td>
+<td>General Correlation Structure</td></tr>
+<tr><td width="25%"><a href="Covariate.html">covariate<-</a></td>
+<td>Assign Covariate Values</td></tr>
+<tr><td width="25%"><a href="Covariate.varFunc.html">covariate<-.varFunc</a></td>
+<td>Assign varFunc Covariate</td></tr>
+</table>
+
+<h2><a name="D">-- D --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Dialyzer.html">Dialyzer</a></td>
+<td>High-Flux Hemodialyzer</td></tr>
+<tr><td width="25%"><a href="Dim.html">Dim</a></td>
+<td>Extract Dimensions from an Object</td></tr>
+<tr><td width="25%"><a href="Dim.corSpatial.html">Dim.corSpatial</a></td>
+<td>Dimensions of a corSpatial Object</td></tr>
+<tr><td width="25%"><a href="Dim.corStruct.html">Dim.corStruct</a></td>
+<td>Dimensions of a corStruct Object</td></tr>
+<tr><td width="25%"><a href="Dim.html">Dim.default</a></td>
+<td>Extract Dimensions from an Object</td></tr>
+<tr><td width="25%"><a href="Dim.pdMat.html">Dim.pdCompSymm</a></td>
+<td>Dimensions of a pdMat Object</td></tr>
+<tr><td width="25%"><a href="Dim.pdMat.html">Dim.pdDiag</a></td>
+<td>Dimensions of a pdMat Object</td></tr>
+<tr><td width="25%"><a href="Dim.pdMat.html">Dim.pdIdent</a></td>
+<td>Dimensions of a pdMat Object</td></tr>
+<tr><td width="25%"><a href="Dim.pdMat.html">Dim.pdMat</a></td>
+<td>Dimensions of a pdMat Object</td></tr>
+<tr><td width="25%"><a href="Dim.pdMat.html">Dim.pdNatural</a></td>
+<td>Dimensions of a pdMat Object</td></tr>
+<tr><td width="25%"><a href="Dim.pdMat.html">Dim.pdSymm</a></td>
+<td>Dimensions of a pdMat Object</td></tr>
+</table>
+
+<h2><a name="E">-- E --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Earthquake.html">Earthquake</a></td>
+<td>Earthquake Intensity</td></tr>
+<tr><td width="25%"><a href="ergoStool.html">ergoStool</a></td>
+<td>Ergometrics experiment with stool types</td></tr>
+</table>
+
+<h2><a name="F">-- F --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Fatigue.html">Fatigue</a></td>
+<td>Cracks caused by metal fatigue</td></tr>
+<tr><td width="25%"><a href="fdHess.html">fdHess</a></td>
+<td>Finite difference Hessian</td></tr>
+<tr><td width="25%"><a href="fitted.glsStruct.html">fitted.glsStruct</a></td>
+<td>Calculate glsStruct Fitted Values</td></tr>
+<tr><td width="25%"><a href="fitted.gnlsStruct.html">fitted.gnlsStruct</a></td>
+<td>Calculate gnlsStruct Fitted Values</td></tr>
+<tr><td width="25%"><a href="fitted.lme.html">fitted.lme</a></td>
+<td>Extract lme Fitted Values</td></tr>
+<tr><td width="25%"><a href="fitted.lmeStruct.html">fitted.lmeStruct</a></td>
+<td>Calculate lmeStruct Fitted Values</td></tr>
+<tr><td width="25%"><a href="fitted.lmList.html">fitted.lmList</a></td>
+<td>Extract lmList Fitted Values</td></tr>
+<tr><td width="25%"><a href="fitted.nlmeStruct.html">fitted.nlmeStruct</a></td>
+<td>Calculate nlmeStruct Fitted Values</td></tr>
+<tr><td width="25%"><a href="fixed.effects.html">fixed.effects</a></td>
+<td>Extract Fixed Effects</td></tr>
+<tr><td width="25%"><a href="fixef.lmList.html">fixed.effects.lmList</a></td>
+<td>Extract lmList Fixed Effects</td></tr>
+<tr><td width="25%"><a href="fixed.effects.html">fixef</a></td>
+<td>Extract Fixed Effects</td></tr>
+<tr><td width="25%"><a href="fixef.lmList.html">fixef.lmList</a></td>
+<td>Extract lmList Fixed Effects</td></tr>
+<tr><td width="25%"><a href="formula.pdBlocked.html">formula.pdBlocked</a></td>
+<td>Extract pdBlocked Formula</td></tr>
+<tr><td width="25%"><a href="formula.pdMat.html">formula.pdMat</a></td>
+<td>Extract pdMat Formula</td></tr>
+<tr><td width="25%"><a href="formula.reStruct.html">formula.reStruct</a></td>
+<td>Extract reStruct Object Formula</td></tr>
+</table>
+
+<h2><a name="G">-- G --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="gapply.html">gapply</a></td>
+<td>Apply a Function by Groups</td></tr>
+<tr><td width="25%"><a href="Gasoline.html">Gasoline</a></td>
+<td>Refinery yield of gasoline</td></tr>
+<tr><td width="25%"><a href="getCovariate.html">getCovariate</a></td>
+<td>Extract Covariate from an Object</td></tr>
+<tr><td width="25%"><a href="getCovariate.corStruct.html">getCovariate.corSpatial</a></td>
+<td>Extract corStruct Object Covariate</td></tr>
+<tr><td width="25%"><a href="getCovariate.corStruct.html">getCovariate.corStruct</a></td>
+<td>Extract corStruct Object Covariate</td></tr>
+<tr><td width="25%"><a href="getCovariate.data.frame.html">getCovariate.data.frame</a></td>
+<td>Extract Data Frame Covariate</td></tr>
+<tr><td width="25%"><a href="getCovariate.varFunc.html">getCovariate.varFunc</a></td>
+<td>Extract varFunc Covariate</td></tr>
+<tr><td width="25%"><a href="getCovariateFormula.html">getCovariateFormula</a></td>
+<td>Extract Covariates Formula</td></tr>
+<tr><td width="25%"><a href="getData.html">getData</a></td>
+<td>Extract Data from an Object</td></tr>
+<tr><td width="25%"><a href="getData.gls.html">getData.gls</a></td>
+<td>Extract gls Object Data</td></tr>
+<tr><td width="25%"><a href="getData.gls.html">getData.gnls</a></td>
+<td>Extract gls Object Data</td></tr>
+<tr><td width="25%"><a href="getData.lme.html">getData.lme</a></td>
+<td>Extract lme Object Data</td></tr>
+<tr><td width="25%"><a href="getData.lmList.html">getData.lmList</a></td>
+<td>Extract lmList Object Data</td></tr>
+<tr><td width="25%"><a href="getData.lme.html">getData.nlme</a></td>
+<td>Extract lme Object Data</td></tr>
+<tr><td width="25%"><a href="getData.lme.html">getData.nls</a></td>
+<td>Extract lme Object Data</td></tr>
+<tr><td width="25%"><a href="getGroups.html">getGroups</a></td>
+<td>Extract Grouping Factors from an Object</td></tr>
+<tr><td width="25%"><a href="getGroups.corStruct.html">getGroups.corStruct</a></td>
+<td>Extract corStruct Groups</td></tr>
+<tr><td width="25%"><a href="getGroups.data.frame.html">getGroups.data.frame</a></td>
+<td>Extract Groups from a Data Frame</td></tr>
+<tr><td width="25%"><a href="getGroups.gls.html">getGroups.gls</a></td>
+<td>Extract gls Object Groups</td></tr>
+<tr><td width="25%"><a href="getGroups.lme.html">getGroups.lme</a></td>
+<td>Extract lme Object Groups</td></tr>
+<tr><td width="25%"><a href="getGroups.lmList.html">getGroups.lmList</a></td>
+<td>Extract lmList Object Groups</td></tr>
+<tr><td width="25%"><a href="getGroups.varFunc.html">getGroups.varFunc</a></td>
+<td>Extract varFunc Groups</td></tr>
+<tr><td width="25%"><a href="getGroupsFormula.html">getGroupsFormula</a></td>
+<td>Extract Grouping Formula</td></tr>
+<tr><td width="25%"><a href="getGroupsFormula.html">getGroupsFormula.default</a></td>
+<td>Extract Grouping Formula</td></tr>
+<tr><td width="25%"><a href="getGroupsFormula.html">getGroupsFormula.gls</a></td>
+<td>Extract Grouping Formula</td></tr>
+<tr><td width="25%"><a href="getGroupsFormula.html">getGroupsFormula.lme</a></td>
+<td>Extract Grouping Formula</td></tr>
+<tr><td width="25%"><a href="getGroupsFormula.html">getGroupsFormula.lmList</a></td>
+<td>Extract Grouping Formula</td></tr>
+<tr><td width="25%"><a href="getGroupsFormula.html">getGroupsFormula.reStruct</a></td>
+<td>Extract Grouping Formula</td></tr>
+<tr><td width="25%"><a href="getResponse.html">getResponse</a></td>
+<td>Extract Response Variable from an Object</td></tr>
+<tr><td width="25%"><a href="getResponse.html">getResponse.data.frame</a></td>
+<td>Extract Response Variable from an Object</td></tr>
+<tr><td width="25%"><a href="getResponseFormula.html">getResponseFormula</a></td>
+<td>Extract Formula Specifying Response Variable</td></tr>
+<tr><td width="25%"><a href="getVarCov.html">getVarCov</a></td>
+<td>Extract variance-covariance matrix</td></tr>
+<tr><td width="25%"><a href="getVarCov.html">getVarCov.gls</a></td>
+<td>Extract variance-covariance matrix</td></tr>
+<tr><td width="25%"><a href="getVarCov.html">getVarCov.lme</a></td>
+<td>Extract variance-covariance matrix</td></tr>
+<tr><td width="25%"><a href="gls.html">gls</a></td>
+<td>Fit Linear Model Using Generalized Least Squares</td></tr>
+<tr><td width="25%"><a href="glsControl.html">glsControl</a></td>
+<td>Control Values for gls Fit</td></tr>
+<tr><td width="25%"><a href="glsObject.html">glsObject</a></td>
+<td>Fitted gls Object</td></tr>
+<tr><td width="25%"><a href="glsStruct.html">glsStruct</a></td>
+<td>Generalized Least Squares Structure</td></tr>
+<tr><td width="25%"><a href="Glucose.html">Glucose</a></td>
+<td>Glucose levels over time</td></tr>
+<tr><td width="25%"><a href="Glucose2.html">Glucose2</a></td>
+<td>Glucose Levels Following Alcohol Ingestion</td></tr>
+<tr><td width="25%"><a href="gnls.html">gnls</a></td>
+<td>Fit Nonlinear Model Using Generalized Least Squares</td></tr>
+<tr><td width="25%"><a href="gnlsControl.html">gnlsControl</a></td>
+<td>Control Values for gnls Fit</td></tr>
+<tr><td width="25%"><a href="gnlsObject.html">gnlsObject</a></td>
+<td>Fitted gnls Object</td></tr>
+<tr><td width="25%"><a href="gnlsStruct.html">gnlsStruct</a></td>
+<td>Generalized Nonlinear Least Squares Structure</td></tr>
+<tr><td width="25%"><a href="groupedData.html">groupedData</a></td>
+<td>Construct a groupedData Object</td></tr>
+<tr><td width="25%"><a href="gsummary.html">gsummary</a></td>
+<td>Summarize by Groups</td></tr>
+<tr><td width="25%"><a href="Gun.html">Gun</a></td>
+<td>Methods for firing naval guns</td></tr>
+</table>
+
+<h2><a name="I">-- I --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="IGF.html">IGF</a></td>
+<td>Radioimmunoassay of IGF-I Protein</td></tr>
+<tr><td width="25%"><a href="Initialize.html">Initialize</a></td>
+<td>Initialize Object</td></tr>
+<tr><td width="25%"><a href="Initialize.corStruct.html">Initialize.corAR1</a></td>
+<td>Initialize corStruct Object</td></tr>
+<tr><td width="25%"><a href="Initialize.corStruct.html">Initialize.corARMA</a></td>
+<td>Initialize corStruct Object</td></tr>
+<tr><td width="25%"><a href="Initialize.corStruct.html">Initialize.corCAR1</a></td>
+<td>Initialize corStruct Object</td></tr>
+<tr><td width="25%"><a href="Initialize.corStruct.html">Initialize.corCompSymm</a></td>
+<td>Initialize corStruct Object</td></tr>
+<tr><td width="25%"><a href="Initialize.corStruct.html">Initialize.corHF</a></td>
+<td>Initialize corStruct Object</td></tr>
+<tr><td width="25%"><a href="Initialize.corStruct.html">Initialize.corIdent</a></td>
+<td>Initialize corStruct Object</td></tr>
+<tr><td width="25%"><a href="Initialize.corStruct.html">Initialize.corLin</a></td>
+<td>Initialize corStruct Object</td></tr>
+<tr><td width="25%"><a href="Initialize.corStruct.html">Initialize.corNatural</a></td>
+<td>Initialize corStruct Object</td></tr>
+<tr><td width="25%"><a href="Initialize.corStruct.html">Initialize.corSpatial</a></td>
+<td>Initialize corStruct Object</td></tr>
+<tr><td width="25%"><a href="Initialize.corStruct.html">Initialize.corSpher</a></td>
+<td>Initialize corStruct Object</td></tr>
+<tr><td width="25%"><a href="Initialize.corStruct.html">Initialize.corStruct</a></td>
+<td>Initialize corStruct Object</td></tr>
+<tr><td width="25%"><a href="Initialize.corStruct.html">Initialize.corSymm</a></td>
+<td>Initialize corStruct Object</td></tr>
+<tr><td width="25%"><a href="Initialize.glsStruct.html">Initialize.glsStruct</a></td>
+<td>Initialize a glsStruct Object</td></tr>
+<tr><td width="25%"><a href="gnlsStruct.html">Initialize.gnlsStruct</a></td>
+<td>Generalized Nonlinear Least Squares Structure</td></tr>
+<tr><td width="25%"><a href="Initialize.lmeStruct.html">Initialize.lmeStruct</a></td>
+<td>Initialize an lmeStruct Object</td></tr>
+<tr><td width="25%"><a href="Initialize.reStruct.html">Initialize.reStruct</a></td>
+<td>Initialize reStruct Object</td></tr>
+<tr><td width="25%"><a href="Initialize.varFunc.html">Initialize.varComb</a></td>
+<td>Initialize varFunc Object</td></tr>
+<tr><td width="25%"><a href="Initialize.varFunc.html">Initialize.varConstPower</a></td>
+<td>Initialize varFunc Object</td></tr>
+<tr><td width="25%"><a href="Initialize.varFunc.html">Initialize.varExp</a></td>
+<td>Initialize varFunc Object</td></tr>
+<tr><td width="25%"><a href="Initialize.varFunc.html">Initialize.varFixed</a></td>
+<td>Initialize varFunc Object</td></tr>
+<tr><td width="25%"><a href="Initialize.varFunc.html">Initialize.varFunc</a></td>
+<td>Initialize varFunc Object</td></tr>
+<tr><td width="25%"><a href="Initialize.varFunc.html">Initialize.varIdent</a></td>
+<td>Initialize varFunc Object</td></tr>
+<tr><td width="25%"><a href="Initialize.varFunc.html">Initialize.varPower</a></td>
+<td>Initialize varFunc Object</td></tr>
+<tr><td width="25%"><a href="intervals.html">intervals</a></td>
+<td>Confidence Intervals on Coefficients</td></tr>
+<tr><td width="25%"><a href="intervals.gls.html">intervals.gls</a></td>
+<td>Confidence Intervals on gls Parameters</td></tr>
+<tr><td width="25%"><a href="intervals.lme.html">intervals.lme</a></td>
+<td>Confidence Intervals on lme Parameters</td></tr>
+<tr><td width="25%"><a href="intervals.lmList.html">intervals.lmList</a></td>
+<td>Confidence Intervals on lmList Coefficients</td></tr>
+<tr><td width="25%"><a href="isBalanced.html">isBalanced</a></td>
+<td>Check a Design for Balance</td></tr>
+<tr><td width="25%"><a href="isBalanced.html">isBalanced.groupedData</a></td>
+<td>Check a Design for Balance</td></tr>
+<tr><td width="25%"><a href="isInitialized.html">isInitialized</a></td>
+<td>Check if Object is Initialized</td></tr>
+<tr><td width="25%"><a href="isInitialized.html">isInitialized.pdBlocked</a></td>
+<td>Check if Object is Initialized</td></tr>
+<tr><td width="25%"><a href="isInitialized.html">isInitialized.pdMat</a></td>
+<td>Check if Object is Initialized</td></tr>
+</table>
+
+<h2><a name="L">-- L --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="LDEsysMat.html">LDEsysMat</a></td>
+<td>Generate system matrix for LDEs</td></tr>
+<tr><td width="25%"><a href="lme.html">lme</a></td>
+<td>Linear Mixed-Effects Models</td></tr>
+<tr><td width="25%"><a href="lme.html">lme.formula</a></td>
+<td>Linear Mixed-Effects Models</td></tr>
+<tr><td width="25%"><a href="lme.groupedData.html">lme.groupedData</a></td>
+<td>LME fit from groupedData Object</td></tr>
+<tr><td width="25%"><a href="lme.lmList.html">lme.lmList</a></td>
+<td>LME fit from lmList Object</td></tr>
+<tr><td width="25%"><a href="lmeControl.html">lmeControl</a></td>
+<td>Control Values for lme Fit</td></tr>
+<tr><td width="25%"><a href="lmeObject.html">lmeObject</a></td>
+<td>Fitted lme Object</td></tr>
+<tr><td width="25%"><a href="lmeScale.html">lmeScale</a></td>
+<td>Scale for lme Optimization</td></tr>
+<tr><td width="25%"><a href="lmeStruct.html">lmeStruct</a></td>
+<td>Linear Mixed-Effects Structure</td></tr>
+<tr><td width="25%"><a href="lmList.html">lmList</a></td>
+<td>List of lm Objects with a Common Model</td></tr>
+<tr><td width="25%"><a href="lmList.html">lmList.formula</a></td>
+<td>List of lm Objects with a Common Model</td></tr>
+<tr><td width="25%"><a href="lmList.groupedData.html">lmList.groupedData</a></td>
+<td>lmList Fit from a groupedData Object</td></tr>
+<tr><td width="25%"><a href="logDet.html">logDet</a></td>
+<td>Extract the Logarithm of the Determinant</td></tr>
+<tr><td width="25%"><a href="logDet.corStruct.html">logDet.corIdent</a></td>
+<td>Extract corStruct Log-Determinant</td></tr>
+<tr><td width="25%"><a href="logDet.corStruct.html">logDet.corStruct</a></td>
+<td>Extract corStruct Log-Determinant</td></tr>
+<tr><td width="25%"><a href="logDet.pdMat.html">logDet.pdBlocked</a></td>
+<td>Extract Log-Determinant from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="logDet.pdMat.html">logDet.pdCompSymm</a></td>
+<td>Extract Log-Determinant from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="logDet.pdMat.html">logDet.pdDiag</a></td>
+<td>Extract Log-Determinant from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="logDet.pdMat.html">logDet.pdIdent</a></td>
+<td>Extract Log-Determinant from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="logDet.pdMat.html">logDet.pdMat</a></td>
+<td>Extract Log-Determinant from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="logDet.pdMat.html">logDet.pdNatural</a></td>
+<td>Extract Log-Determinant from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="logDet.pdMat.html">logDet.pdSymm</a></td>
+<td>Extract Log-Determinant from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="logDet.reStruct.html">logDet.reStruct</a></td>
+<td>Extract reStruct Log-Determinants</td></tr>
+<tr><td width="25%"><a href="logLik.corStruct.html">logLik.corStruct</a></td>
+<td>Extract corStruct Log-Likelihood</td></tr>
+<tr><td width="25%"><a href="logLik.lme.html">logLik.gls</a></td>
+<td>Log-Likelihood of an lme Object</td></tr>
+<tr><td width="25%"><a href="logLik.glsStruct.html">logLik.glsStruct</a></td>
+<td>Log-Likelihood of a glsStruct Object</td></tr>
+<tr><td width="25%"><a href="logLik.gnls.html">logLik.gnls</a></td>
+<td>Log-Likelihood of a gnls Object</td></tr>
+<tr><td width="25%"><a href="logLik.gnlsStruct.html">logLik.gnlsStruct</a></td>
+<td>Log-Likelihood of a gnlsStruct Object</td></tr>
+<tr><td width="25%"><a href="logLik.lme.html">logLik.lme</a></td>
+<td>Log-Likelihood of an lme Object</td></tr>
+<tr><td width="25%"><a href="logLik.lmeStruct.html">logLik.lmeStruct</a></td>
+<td>Log-Likelihood of an lmeStruct Object</td></tr>
+<tr><td width="25%"><a href="logLik.lmeStruct.html">logLik.lmeStructInt</a></td>
+<td>Log-Likelihood of an lmeStruct Object</td></tr>
+<tr><td width="25%"><a href="logLik.lmList.html">logLik.lmList</a></td>
+<td>Log-Likelihood of an lmList Object</td></tr>
+<tr><td width="25%"><a href="logLik.reStruct.html">logLik.reStruct</a></td>
+<td>Calculate reStruct Log-Likelihood</td></tr>
+<tr><td width="25%"><a href="logLik.varFunc.html">logLik.varComb</a></td>
+<td>Extract varFunc logLik</td></tr>
+<tr><td width="25%"><a href="logLik.varFunc.html">logLik.varFunc</a></td>
+<td>Extract varFunc logLik</td></tr>
+</table>
+
+<h2><a name="M">-- M --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Machines.html">Machines</a></td>
+<td>Productivity Scores for Machines and Workers</td></tr>
+<tr><td width="25%"><a href="MathAchieve.html">MathAchieve</a></td>
+<td>Mathematics achievement scores</td></tr>
+<tr><td width="25%"><a href="MathAchSchool.html">MathAchSchool</a></td>
+<td>School demographic data for MathAchieve</td></tr>
+<tr><td width="25%"><a href="Matrix.html">matrix<-</a></td>
+<td>Assign Matrix Values</td></tr>
+<tr><td width="25%"><a href="Matrix.pdMat.html">matrix<-.pdBlocked</a></td>
+<td>Assign Matrix to a pdMat Object</td></tr>
+<tr><td width="25%"><a href="Matrix.pdMat.html">matrix<-.pdMat</a></td>
+<td>Assign Matrix to a pdMat Object</td></tr>
+<tr><td width="25%"><a href="Matrix.reStruct.html">matrix<-.reStruct</a></td>
+<td>Assign reStruct Matrices</td></tr>
+<tr><td width="25%"><a href="Meat.html">Meat</a></td>
+<td>Tenderness of meat</td></tr>
+<tr><td width="25%"><a href="Milk.html">Milk</a></td>
+<td>Protein content of cows' milk</td></tr>
+<tr><td width="25%"><a href="model.matrix.reStruct.html">model.matrix.reStruct</a></td>
+<td>reStruct Model Matrix</td></tr>
+<tr><td width="25%"><a href="Muscle.html">Muscle</a></td>
+<td>Contraction of heart muscle sections</td></tr>
+</table>
+
+<h2><a name="N">-- N --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Names.html">Names</a></td>
+<td>Names Associated with an Object</td></tr>
+<tr><td width="25%"><a href="Names.formula.html">Names.formula</a></td>
+<td>Extract Names from a formula</td></tr>
+<tr><td width="25%"><a href="Names.formula.html">Names.listForm</a></td>
+<td>Extract Names from a formula</td></tr>
+<tr><td width="25%"><a href="Names.pdBlocked.html">Names.pdBlocked</a></td>
+<td>Names of a pdBlocked Object</td></tr>
+<tr><td width="25%"><a href="Names.pdMat.html">Names.pdMat</a></td>
+<td>Names of a pdMat Object</td></tr>
+<tr><td width="25%"><a href="Names.reStruct.html">Names.reStruct</a></td>
+<td>Names of an reStruct Object</td></tr>
+<tr><td width="25%"><a href="Names.html">Names<-</a></td>
+<td>Names Associated with an Object</td></tr>
+<tr><td width="25%"><a href="Names.pdBlocked.html">Names<-.pdBlocked</a></td>
+<td>Names of a pdBlocked Object</td></tr>
+<tr><td width="25%"><a href="Names.pdMat.html">Names<-.pdMat</a></td>
+<td>Names of a pdMat Object</td></tr>
+<tr><td width="25%"><a href="Names.reStruct.html">Names<-.reStruct</a></td>
+<td>Names of an reStruct Object</td></tr>
+<tr><td width="25%"><a href="needUpdate.html">needUpdate</a></td>
+<td>Check if Update is Needed</td></tr>
+<tr><td width="25%"><a href="needUpdate.modelStruct.html">needUpdate.corStruct</a></td>
+<td>Check if a modelStruct Object Needs Updating</td></tr>
+<tr><td width="25%"><a href="needUpdate.html">needUpdate.default</a></td>
+<td>Check if Update is Needed</td></tr>
+<tr><td width="25%"><a href="needUpdate.modelStruct.html">needUpdate.modelStruct</a></td>
+<td>Check if a modelStruct Object Needs Updating</td></tr>
+<tr><td width="25%"><a href="needUpdate.modelStruct.html">needUpdate.reStruct</a></td>
+<td>Check if a modelStruct Object Needs Updating</td></tr>
+<tr><td width="25%"><a href="needUpdate.html">needUpdate.varComb</a></td>
+<td>Check if Update is Needed</td></tr>
+<tr><td width="25%"><a href="needUpdate.html">needUpdate.varIdent</a></td>
+<td>Check if Update is Needed</td></tr>
+<tr><td width="25%"><a href="groupedData.html">nfGroupedData</a></td>
+<td>Construct a groupedData Object</td></tr>
+<tr><td width="25%"><a href="Nitrendipene.html">Nitrendipene</a></td>
+<td>Assay of nitrendipene</td></tr>
+<tr><td width="25%"><a href="nlme.html">nlme</a></td>
+<td>Nonlinear Mixed-Effects Models</td></tr>
+<tr><td width="25%"><a href="nlme.html">nlme.formula</a></td>
+<td>Nonlinear Mixed-Effects Models</td></tr>
+<tr><td width="25%"><a href="nlme.nlsList.html">nlme.nlsList</a></td>
+<td>NLME fit from nlsList Object</td></tr>
+<tr><td width="25%"><a href="nlmeControl.html">nlmeControl</a></td>
+<td>Control Values for nlme Fit</td></tr>
+<tr><td width="25%"><a href="nlmeObject.html">nlmeObject</a></td>
+<td>Fitted nlme Object</td></tr>
+<tr><td width="25%"><a href="nlmeStruct.html">nlmeStruct</a></td>
+<td>Nonlinear Mixed-Effects Structure</td></tr>
+<tr><td width="25%"><a href="nlsList.html">nlsList</a></td>
+<td>List of nls Objects with a Common Model</td></tr>
+<tr><td width="25%"><a href="nlsList.html">nlsList.formula</a></td>
+<td>List of nls Objects with a Common Model</td></tr>
+<tr><td width="25%"><a href="nlsList.selfStart.html">nlsList.selfStart</a></td>
+<td>nlsList Fit from a selfStart Function</td></tr>
+<tr><td width="25%"><a href="groupedData.html">nmGroupedData</a></td>
+<td>Construct a groupedData Object</td></tr>
+</table>
+
+<h2><a name="O">-- O --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Oats.html">Oats</a></td>
+<td>Split-plot Experiment on Varieties of Oats</td></tr>
+<tr><td width="25%"><a href="Orthodont.html">Orthodont</a></td>
+<td>Growth curve data on an orthdontic measurement</td></tr>
+<tr><td width="25%"><a href="Ovary.html">Ovary</a></td>
+<td>Counts of Ovarian Follicles</td></tr>
+<tr><td width="25%"><a href="Oxboys.html">Oxboys</a></td>
+<td>Heights of Boys in Oxford</td></tr>
+<tr><td width="25%"><a href="Oxide.html">Oxide</a></td>
+<td>Variability in Semiconductor Manufacturing</td></tr>
+</table>
+
+<h2><a name="P">-- P --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="pairs.compareFits.html">pairs.compareFits</a></td>
+<td>Pairs Plot of compareFits Object</td></tr>
+<tr><td width="25%"><a href="pairs.lme.html">pairs.lme</a></td>
+<td>Pairs Plot of an lme Object</td></tr>
+<tr><td width="25%"><a href="pairs.lmList.html">pairs.lmList</a></td>
+<td>Pairs Plot of an lmList Object</td></tr>
+<tr><td width="25%"><a href="PBG.html">PBG</a></td>
+<td>Effect of Phenylbiguanide on Blood Pressure</td></tr>
+<tr><td width="25%"><a href="pdBlocked.html">pdBlocked</a></td>
+<td>Positive-Definite Block Diagonal Matrix</td></tr>
+<tr><td width="25%"><a href="pdClasses.html">pdClasses</a></td>
+<td>Positive-Definite Matrix Classes</td></tr>
+<tr><td width="25%"><a href="pdCompSymm.html">pdCompSymm</a></td>
+<td>Positive-Definite Matrix with Compound Symmetry Structure</td></tr>
+<tr><td width="25%"><a href="pdConstruct.html">pdConstruct</a></td>
+<td>Construct pdMat Objects</td></tr>
+<tr><td width="25%"><a href="pdConstruct.pdBlocked.html">pdConstruct.pdBlocked</a></td>
+<td>Construct pdBlocked Objects</td></tr>
+<tr><td width="25%"><a href="pdConstruct.html">pdConstruct.pdCompSymm</a></td>
+<td>Construct pdMat Objects</td></tr>
+<tr><td width="25%"><a href="pdConstruct.html">pdConstruct.pdDiag</a></td>
+<td>Construct pdMat Objects</td></tr>
+<tr><td width="25%"><a href="pdConstruct.html">pdConstruct.pdIdent</a></td>
+<td>Construct pdMat Objects</td></tr>
+<tr><td width="25%"><a href="pdConstruct.html">pdConstruct.pdLogChol</a></td>
+<td>Construct pdMat Objects</td></tr>
+<tr><td width="25%"><a href="pdConstruct.html">pdConstruct.pdMat</a></td>
+<td>Construct pdMat Objects</td></tr>
+<tr><td width="25%"><a href="pdConstruct.html">pdConstruct.pdNatural</a></td>
+<td>Construct pdMat Objects</td></tr>
+<tr><td width="25%"><a href="pdConstruct.html">pdConstruct.pdSymm</a></td>
+<td>Construct pdMat Objects</td></tr>
+<tr><td width="25%"><a href="pdDiag.html">pdDiag</a></td>
+<td>Diagonal Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="pdFactor.html">pdFactor</a></td>
+<td>Square-Root Factor of a Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="pdFactor.html">pdFactor.pdBlocked</a></td>
+<td>Square-Root Factor of a Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="pdFactor.html">pdFactor.pdCompSymm</a></td>
+<td>Square-Root Factor of a Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="pdFactor.html">pdFactor.pdDiag</a></td>
+<td>Square-Root Factor of a Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="pdFactor.html">pdFactor.pdIdent</a></td>
+<td>Square-Root Factor of a Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="pdFactor.html">pdFactor.pdLogChol</a></td>
+<td>Square-Root Factor of a Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="pdFactor.html">pdFactor.pdMat</a></td>
+<td>Square-Root Factor of a Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="pdFactor.html">pdFactor.pdNatural</a></td>
+<td>Square-Root Factor of a Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="pdFactor.html">pdFactor.pdSymm</a></td>
+<td>Square-Root Factor of a Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="pdFactor.reStruct.html">pdFactor.reStruct</a></td>
+<td>Extract Square-Root Factor from Components of an reStruct Object</td></tr>
+<tr><td width="25%"><a href="pdIdent.html">pdIdent</a></td>
+<td>Multiple of the Identity Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="pdLogChol.html">pdLogChol</a></td>
+<td>General Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="pdMat.html">pdMat</a></td>
+<td>Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="pdMatrix.html">pdMatrix</a></td>
+<td>Extract Matrix or Square-Root Factor from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="pdMatrix.html">pdMatrix.pdBlocked</a></td>
+<td>Extract Matrix or Square-Root Factor from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="pdMatrix.html">pdMatrix.pdCompSymm</a></td>
+<td>Extract Matrix or Square-Root Factor from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="pdMatrix.html">pdMatrix.pdDiag</a></td>
+<td>Extract Matrix or Square-Root Factor from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="pdMatrix.html">pdMatrix.pdIdent</a></td>
+<td>Extract Matrix or Square-Root Factor from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="pdMatrix.html">pdMatrix.pdMat</a></td>
+<td>Extract Matrix or Square-Root Factor from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="pdMatrix.html">pdMatrix.pdNatural</a></td>
+<td>Extract Matrix or Square-Root Factor from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="pdMatrix.html">pdMatrix.pdSymm</a></td>
+<td>Extract Matrix or Square-Root Factor from a pdMat Object</td></tr>
+<tr><td width="25%"><a href="pdMatrix.reStruct.html">pdMatrix.reStruct</a></td>
+<td>Extract Matrix or Square-Root Factor from Components of an reStruct Object</td></tr>
+<tr><td width="25%"><a href="pdNatural.html">pdNatural</a></td>
+<td>General Positive-Definite Matrix in Natural Parametrization</td></tr>
+<tr><td width="25%"><a href="pdSymm.html">pdSymm</a></td>
+<td>General Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="Phenobarb.html">Phenobarb</a></td>
+<td>Phenobarbitol Kinetics</td></tr>
+<tr><td width="25%"><a href="phenoModel.html">phenoModel</a></td>
+<td>Model function for the Phenobarb data</td></tr>
+<tr><td width="25%"><a href="Pixel.html">Pixel</a></td>
+<td>X-ray pixel intensities over time</td></tr>
+<tr><td width="25%"><a href="plot.ACF.html">plot.ACF</a></td>
+<td>Plot an ACF Object</td></tr>
+<tr><td width="25%"><a href="plot.augPred.html">plot.augPred</a></td>
+<td>Plot an augPred Object</td></tr>
+<tr><td width="25%"><a href="plot.compareFits.html">plot.compareFits</a></td>
+<td>Plot a compareFits Object</td></tr>
+<tr><td width="25%"><a href="plot.gls.html">plot.gls</a></td>
+<td>Plot a gls Object</td></tr>
+<tr><td width="25%"><a href="plot.intervals.lmList.html">plot.intervals.lmList</a></td>
+<td>Plot lmList Confidence Intervals</td></tr>
+<tr><td width="25%"><a href="plot.lme.html">plot.lme</a></td>
+<td>Plot an lme or nls object</td></tr>
+<tr><td width="25%"><a href="plot.lmList.html">plot.lmList</a></td>
+<td>Plot an lmList Object</td></tr>
+<tr><td width="25%"><a href="plot.nffGroupedData.html">plot.nffGroupedData</a></td>
+<td>Plot an nffGroupedData Object</td></tr>
+<tr><td width="25%"><a href="plot.nfnGroupedData.html">plot.nfnGroupedData</a></td>
+<td>Plot an nfnGroupedData Object</td></tr>
+<tr><td width="25%"><a href="plot.lme.html">plot.nls</a></td>
+<td>Plot an lme or nls object</td></tr>
+<tr><td width="25%"><a href="plot.nmGroupedData.html">plot.nmGroupedData</a></td>
+<td>Plot an nmGroupedData Object</td></tr>
+<tr><td width="25%"><a href="pdMat.html">plot.pdMat</a></td>
+<td>Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="plot.ranef.lme.html">plot.ranef.lme</a></td>
+<td>Plot a ranef.lme Object</td></tr>
+<tr><td width="25%"><a href="plot.ranef.lmList.html">plot.ranef.lmList</a></td>
+<td>Plot a ranef.lmList Object</td></tr>
+<tr><td width="25%"><a href="simulate.lme.html">plot.simulate.lme</a></td>
+<td>Simulate Results from 'lme' Models</td></tr>
+<tr><td width="25%"><a href="plot.Variogram.html">plot.Variogram</a></td>
+<td>Plot a Variogram Object</td></tr>
+<tr><td width="25%"><a href="pooledSD.html">pooledSD</a></td>
+<td>Extract Pooled Standard Deviation</td></tr>
+<tr><td width="25%"><a href="predict.gls.html">predict.gls</a></td>
+<td>Predictions from a gls Object</td></tr>
+<tr><td width="25%"><a href="predict.gnls.html">predict.gnls</a></td>
+<td>Predictions from a gnls Object</td></tr>
+<tr><td width="25%"><a href="predict.lme.html">predict.lme</a></td>
+<td>Predictions from an lme Object</td></tr>
+<tr><td width="25%"><a href="predict.lmList.html">predict.lmList</a></td>
+<td>Predictions from an lmList Object</td></tr>
+<tr><td width="25%"><a href="predict.nlme.html">predict.nlme</a></td>
+<td>Predictions from an nlme Object</td></tr>
+<tr><td width="25%"><a href="anova.lme.html">print.anova.lme</a></td>
+<td>Compare Likelihoods of Fitted Objects</td></tr>
+<tr><td width="25%"><a href="compareFits.html">print.compareFits</a></td>
+<td>Compare Fitted Objects</td></tr>
+<tr><td width="25%"><a href="corNatural.html">print.corNatural</a></td>
+<td>General correlation in natural parameterization</td></tr>
+<tr><td width="25%"><a href="intervals.gls.html">print.intervals.gls</a></td>
+<td>Confidence Intervals on gls Parameters</td></tr>
+<tr><td width="25%"><a href="intervals.lme.html">print.intervals.lme</a></td>
+<td>Confidence Intervals on lme Parameters</td></tr>
+<tr><td width="25%"><a href="intervals.lmList.html">print.intervals.lmList</a></td>
+<td>Confidence Intervals on lmList Coefficients</td></tr>
+<tr><td width="25%"><a href="lmList.html">print.lmList</a></td>
+<td>List of lm Objects with a Common Model</td></tr>
+<tr><td width="25%"><a href="random.effects.html">print.ranef</a></td>
+<td>Extract Random Effects</td></tr>
+<tr><td width="25%"><a href="ranef.lme.html">print.ranef.lme</a></td>
+<td>Extract lme Random Effects</td></tr>
+<tr><td width="25%"><a href="reStruct.html">print.reStruct</a></td>
+<td>Random Effects Structure</td></tr>
+<tr><td width="25%"><a href="simulate.lme.html">print.simulate.lme</a></td>
+<td>Simulate Results from 'lme' Models</td></tr>
+<tr><td width="25%"><a href="print.summary.pdMat.html">print.summary.pdMat</a></td>
+<td>Print a summary.pdMat Object</td></tr>
+<tr><td width="25%"><a href="print.varFunc.html">print.varComb</a></td>
+<td>Print a varFunc Object</td></tr>
+<tr><td width="25%"><a href="VarCorr.html">print.VarCorr.lme</a></td>
+<td>Extract variance and correlation components</td></tr>
+<tr><td width="25%"><a href="getVarCov.html">print.VarCov</a></td>
+<td>Extract variance-covariance matrix</td></tr>
+<tr><td width="25%"><a href="print.varFunc.html">print.varFunc</a></td>
+<td>Print a varFunc Object</td></tr>
+</table>
+
+<h2><a name="Q">-- Q --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="qqnorm.gls.html">qqnorm.gls</a></td>
+<td>Normal Plot of Residuals from a gls Object</td></tr>
+<tr><td width="25%"><a href="qqnorm.lme.html">qqnorm.lm</a></td>
+<td>Normal Plot of Residuals or Random Effects from an lme Object</td></tr>
+<tr><td width="25%"><a href="qqnorm.lme.html">qqnorm.lme</a></td>
+<td>Normal Plot of Residuals or Random Effects from an lme Object</td></tr>
+<tr><td width="25%"><a href="qqnorm.lme.html">qqnorm.lmList</a></td>
+<td>Normal Plot of Residuals or Random Effects from an lme Object</td></tr>
+<tr><td width="25%"><a href="qqnorm.lme.html">qqnorm.nls</a></td>
+<td>Normal Plot of Residuals or Random Effects from an lme Object</td></tr>
+<tr><td width="25%"><a href="Quinidine.html">Quinidine</a></td>
+<td>Quinidine Kinetics</td></tr>
+<tr><td width="25%"><a href="quinModel.html">quinModel</a></td>
+<td>Model function for the Quinidine data</td></tr>
+</table>
+
+<h2><a name="R">-- R --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Rail.html">Rail</a></td>
+<td>Evaluation of Stress in Railway Rails</td></tr>
+<tr><td width="25%"><a href="random.effects.html">random.effects</a></td>
+<td>Extract Random Effects</td></tr>
+<tr><td width="25%"><a href="ranef.lme.html">random.effects.lme</a></td>
+<td>Extract lme Random Effects</td></tr>
+<tr><td width="25%"><a href="ranef.lmList.html">random.effects.lmList</a></td>
+<td>Extract lmList Random Effects</td></tr>
+<tr><td width="25%"><a href="random.effects.html">ranef</a></td>
+<td>Extract Random Effects</td></tr>
+<tr><td width="25%"><a href="ranef.lme.html">ranef.lme</a></td>
+<td>Extract lme Random Effects</td></tr>
+<tr><td width="25%"><a href="ranef.lmList.html">ranef.lmList</a></td>
+<td>Extract lmList Random Effects</td></tr>
+<tr><td width="25%"><a href="RatPupWeight.html">RatPupWeight</a></td>
+<td>The weight of rat pups</td></tr>
+<tr><td width="25%"><a href="recalc.html">recalc</a></td>
+<td>Recalculate Condensed Linear Model Object</td></tr>
+<tr><td width="25%"><a href="recalc.corStruct.html">recalc.corAR1</a></td>
+<td>Recalculate for corStruct Object</td></tr>
+<tr><td width="25%"><a href="recalc.corStruct.html">recalc.corARMA</a></td>
+<td>Recalculate for corStruct Object</td></tr>
+<tr><td width="25%"><a href="recalc.corStruct.html">recalc.corCAR1</a></td>
+<td>Recalculate for corStruct Object</td></tr>
+<tr><td width="25%"><a href="recalc.corStruct.html">recalc.corCompSymm</a></td>
+<td>Recalculate for corStruct Object</td></tr>
+<tr><td width="25%"><a href="recalc.corStruct.html">recalc.corHF</a></td>
+<td>Recalculate for corStruct Object</td></tr>
+<tr><td width="25%"><a href="recalc.corStruct.html">recalc.corIdent</a></td>
+<td>Recalculate for corStruct Object</td></tr>
+<tr><td width="25%"><a href="recalc.corStruct.html">recalc.corNatural</a></td>
+<td>Recalculate for corStruct Object</td></tr>
+<tr><td width="25%"><a href="recalc.corStruct.html">recalc.corSpatial</a></td>
+<td>Recalculate for corStruct Object</td></tr>
+<tr><td width="25%"><a href="recalc.corStruct.html">recalc.corStruct</a></td>
+<td>Recalculate for corStruct Object</td></tr>
+<tr><td width="25%"><a href="recalc.corStruct.html">recalc.corSymm</a></td>
+<td>Recalculate for corStruct Object</td></tr>
+<tr><td width="25%"><a href="recalc.modelStruct.html">recalc.modelStruct</a></td>
+<td>Recalculate for a modelStruct Object</td></tr>
+<tr><td width="25%"><a href="recalc.reStruct.html">recalc.reStruct</a></td>
+<td>Recalculate for an reStruct Object</td></tr>
+<tr><td width="25%"><a href="recalc.varFunc.html">recalc.varFunc</a></td>
+<td>Recalculate for varFunc Object</td></tr>
+<tr><td width="25%"><a href="recalc.varFunc.html">recalc.varIdent</a></td>
+<td>Recalculate for varFunc Object</td></tr>
+<tr><td width="25%"><a href="Relaxin.html">Relaxin</a></td>
+<td>Assay for Relaxin</td></tr>
+<tr><td width="25%"><a href="Remifentanil.html">Remifentanil</a></td>
+<td>Pharmacokinetics of remifentanil</td></tr>
+<tr><td width="25%"><a href="residuals.gls.html">residuals.gls</a></td>
+<td>Extract gls Residuals</td></tr>
+<tr><td width="25%"><a href="residuals.glsStruct.html">residuals.glsStruct</a></td>
+<td>Calculate glsStruct Residuals</td></tr>
+<tr><td width="25%"><a href="residuals.gls.html">residuals.gnls</a></td>
+<td>Extract gls Residuals</td></tr>
+<tr><td width="25%"><a href="residuals.gnlsStruct.html">residuals.gnlsStruct</a></td>
+<td>Calculate gnlsStruct Residuals</td></tr>
+<tr><td width="25%"><a href="residuals.lme.html">residuals.lme</a></td>
+<td>Extract lme Residuals</td></tr>
+<tr><td width="25%"><a href="residuals.lmeStruct.html">residuals.lmeStruct</a></td>
+<td>Calculate lmeStruct Residuals</td></tr>
+<tr><td width="25%"><a href="residuals.lmList.html">residuals.lmList</a></td>
+<td>Extract lmList Residuals</td></tr>
+<tr><td width="25%"><a href="residuals.nlmeStruct.html">residuals.nlmeStruct</a></td>
+<td>Calculate nlmeStruct Residuals</td></tr>
+<tr><td width="25%"><a href="reStruct.html">reStruct</a></td>
+<td>Random Effects Structure</td></tr>
+</table>
+
+<h2><a name="S">-- S --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="simulate.lme.html">simulate.lme</a></td>
+<td>Simulate Results from 'lme' Models</td></tr>
+<tr><td width="25%"><a href="solve.pdMat.html">solve.pdBlocked</a></td>
+<td>Calculate Inverse of a Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="solve.pdMat.html">solve.pdDiag</a></td>
+<td>Calculate Inverse of a Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="solve.pdMat.html">solve.pdIdent</a></td>
+<td>Calculate Inverse of a Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="solve.pdMat.html">solve.pdLogChol</a></td>
+<td>Calculate Inverse of a Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="solve.pdMat.html">solve.pdMat</a></td>
+<td>Calculate Inverse of a Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="solve.pdMat.html">solve.pdNatural</a></td>
+<td>Calculate Inverse of a Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="solve.pdMat.html">solve.pdSymm</a></td>
+<td>Calculate Inverse of a Positive-Definite Matrix</td></tr>
+<tr><td width="25%"><a href="solve.reStruct.html">solve.reStruct</a></td>
+<td>Apply Solve to an reStruct Object</td></tr>
+<tr><td width="25%"><a href="Soybean.html">Soybean</a></td>
+<td>Growth of soybean plants</td></tr>
+<tr><td width="25%"><a href="splitFormula.html">splitFormula</a></td>
+<td>Split a Formula</td></tr>
+<tr><td width="25%"><a href="Spruce.html">Spruce</a></td>
+<td>Growth of Spruce Trees</td></tr>
+<tr><td width="25%"><a href="summary.corStruct.html">summary.corAR1</a></td>
+<td>Summarize a corStruct Object</td></tr>
+<tr><td width="25%"><a href="summary.corStruct.html">summary.corARMA</a></td>
+<td>Summarize a corStruct Object</td></tr>
+<tr><td width="25%"><a href="summary.corStruct.html">summary.corCAR1</a></td>
+<td>Summarize a corStruct Object</td></tr>
+<tr><td width="25%"><a href="summary.corStruct.html">summary.corCompSymm</a></td>
+<td>Summarize a corStruct Object</td></tr>
+<tr><td width="25%"><a href="summary.corStruct.html">summary.corExp</a></td>
+<td>Summarize a corStruct Object</td></tr>
+<tr><td width="25%"><a href="summary.corStruct.html">summary.corGaus</a></td>
+<td>Summarize a corStruct Object</td></tr>
+<tr><td width="25%"><a href="summary.corStruct.html">summary.corIdent</a></td>
+<td>Summarize a corStruct Object</td></tr>
+<tr><td width="25%"><a href="summary.corStruct.html">summary.corLin</a></td>
+<td>Summarize a corStruct Object</td></tr>
+<tr><td width="25%"><a href="summary.corStruct.html">summary.corNatural</a></td>
+<td>Summarize a corStruct Object</td></tr>
+<tr><td width="25%"><a href="summary.corStruct.html">summary.corRatio</a></td>
+<td>Summarize a corStruct Object</td></tr>
+<tr><td width="25%"><a href="summary.corStruct.html">summary.corSpher</a></td>
+<td>Summarize a corStruct Object</td></tr>
+<tr><td width="25%"><a href="summary.corStruct.html">summary.corStruct</a></td>
+<td>Summarize a corStruct Object</td></tr>
+<tr><td width="25%"><a href="summary.corStruct.html">summary.corSymm</a></td>
+<td>Summarize a corStruct Object</td></tr>
+<tr><td width="25%"><a href="summary.gls.html">summary.gls</a></td>
+<td>Summarize a gls Object</td></tr>
+<tr><td width="25%"><a href="summary.lme.html">summary.lme</a></td>
+<td>Summarize an lme Object</td></tr>
+<tr><td width="25%"><a href="summary.lmList.html">summary.lmList</a></td>
+<td>Summarize an lmList Object</td></tr>
+<tr><td width="25%"><a href="summary.modelStruct.html">summary.modelStruct</a></td>
+<td>Summarize a modelStruct Object</td></tr>
+<tr><td width="25%"><a href="summary.nlsList.html">summary.nlsList</a></td>
+<td>Summarize an nlsList Object</td></tr>
+<tr><td width="25%"><a href="summary.pdMat.html">summary.pdBlocked</a></td>
+<td>Summarize a pdMat Object</td></tr>
+<tr><td width="25%"><a href="summary.pdMat.html">summary.pdCompSymm</a></td>
+<td>Summarize a pdMat Object</td></tr>
+<tr><td width="25%"><a href="summary.pdMat.html">summary.pdDiag</a></td>
+<td>Summarize a pdMat Object</td></tr>
+<tr><td width="25%"><a href="summary.pdMat.html">summary.pdIdent</a></td>
+<td>Summarize a pdMat Object</td></tr>
+<tr><td width="25%"><a href="summary.pdMat.html">summary.pdLogChol</a></td>
+<td>Summarize a pdMat Object</td></tr>
+<tr><td width="25%"><a href="summary.pdMat.html">summary.pdMat</a></td>
+<td>Summarize a pdMat Object</td></tr>
+<tr><td width="25%"><a href="summary.pdMat.html">summary.pdNatural</a></td>
+<td>Summarize a pdMat Object</td></tr>
+<tr><td width="25%"><a href="summary.pdMat.html">summary.pdSymm</a></td>
+<td>Summarize a pdMat Object</td></tr>
+<tr><td width="25%"><a href="summary.modelStruct.html">summary.reStruct</a></td>
+<td>Summarize a modelStruct Object</td></tr>
+<tr><td width="25%"><a href="summary.varFunc.html">summary.varComb</a></td>
+<td>Summarize varFunc Object</td></tr>
+<tr><td width="25%"><a href="summary.varFunc.html">summary.varConstPower</a></td>
+<td>Summarize varFunc Object</td></tr>
+<tr><td width="25%"><a href="VarCorr.html">summary.VarCorr.lme</a></td>
+<td>Extract variance and correlation components</td></tr>
+<tr><td width="25%"><a href="summary.varFunc.html">summary.varExp</a></td>
+<td>Summarize varFunc Object</td></tr>
+<tr><td width="25%"><a href="summary.varFunc.html">summary.varFixed</a></td>
+<td>Summarize varFunc Object</td></tr>
+<tr><td width="25%"><a href="summary.varFunc.html">summary.varFunc</a></td>
+<td>Summarize varFunc Object</td></tr>
+<tr><td width="25%"><a href="summary.varFunc.html">summary.varIdent</a></td>
+<td>Summarize varFunc Object</td></tr>
+<tr><td width="25%"><a href="summary.varFunc.html">summary.varPower</a></td>
+<td>Summarize varFunc Object</td></tr>
+</table>
+
+<h2><a name="T">-- T --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Tetracycline1.html">Tetracycline1</a></td>
+<td>Pharmacokinetics of tetracycline</td></tr>
+<tr><td width="25%"><a href="Tetracycline2.html">Tetracycline2</a></td>
+<td>Pharmacokinetics of tetracycline</td></tr>
+</table>
+
+<h2><a name="U">-- U --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="update.modelStruct.html">update.corStruct</a></td>
+<td>Update a modelStruct Object</td></tr>
+<tr><td width="25%"><a href="gls.html">update.gls</a></td>
+<td>Fit Linear Model Using Generalized Least Squares</td></tr>
+<tr><td width="25%"><a href="groupedData.html">update.groupedData</a></td>
+<td>Construct a groupedData Object</td></tr>
+<tr><td width="25%"><a href="lme.html">update.lme</a></td>
+<td>Linear Mixed-Effects Models</td></tr>
+<tr><td width="25%"><a href="lmList.html">update.lmList</a></td>
+<td>List of lm Objects with a Common Model</td></tr>
+<tr><td width="25%"><a href="update.modelStruct.html">update.modelStruct</a></td>
+<td>Update a modelStruct Object</td></tr>
+<tr><td width="25%"><a href="nlsList.html">update.nlsList</a></td>
+<td>List of nls Objects with a Common Model</td></tr>
+<tr><td width="25%"><a href="update.modelStruct.html">update.reStruct</a></td>
+<td>Update a modelStruct Object</td></tr>
+<tr><td width="25%"><a href="update.varFunc.html">update.varComb</a></td>
+<td>Update varFunc Object</td></tr>
+<tr><td width="25%"><a href="update.varFunc.html">update.varConstPower</a></td>
+<td>Update varFunc Object</td></tr>
+<tr><td width="25%"><a href="update.varFunc.html">update.varExp</a></td>
+<td>Update varFunc Object</td></tr>
+<tr><td width="25%"><a href="update.varFunc.html">update.varExpon</a></td>
+<td>Update varFunc Object</td></tr>
+<tr><td width="25%"><a href="update.varFunc.html">update.varFunc</a></td>
+<td>Update varFunc Object</td></tr>
+<tr><td width="25%"><a href="update.varFunc.html">update.varPower</a></td>
+<td>Update varFunc Object</td></tr>
+</table>
+
+<h2><a name="V">-- V --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="varClasses.html">varClasses</a></td>
+<td>Variance Function Classes</td></tr>
+<tr><td width="25%"><a href="varComb.html">varComb</a></td>
+<td>Combination of Variance Functions</td></tr>
+<tr><td width="25%"><a href="varConstPower.html">varConstPower</a></td>
+<td>Constant Plus Power Variance Function</td></tr>
+<tr><td width="25%"><a href="VarCorr.html">VarCorr</a></td>
+<td>Extract variance and correlation components</td></tr>
+<tr><td width="25%"><a href="VarCorr.html">VarCorr.lme</a></td>
+<td>Extract variance and correlation components</td></tr>
+<tr><td width="25%"><a href="VarCorr.html">VarCorr.pdBlocked</a></td>
+<td>Extract variance and correlation components</td></tr>
+<tr><td width="25%"><a href="VarCorr.html">VarCorr.pdMat</a></td>
+<td>Extract variance and correlation components</td></tr>
+<tr><td width="25%"><a href="varExp.html">varExp</a></td>
+<td>Exponential Variance Function</td></tr>
+<tr><td width="25%"><a href="varFixed.html">varFixed</a></td>
+<td>Fixed Variance Function</td></tr>
+<tr><td width="25%"><a href="varFunc.html">varFunc</a></td>
+<td>Variance Function Structure</td></tr>
+<tr><td width="25%"><a href="varIdent.html">varIdent</a></td>
+<td>Constant Variance Function</td></tr>
+<tr><td width="25%"><a href="Variogram.html">Variogram</a></td>
+<td>Calculate Semi-variogram</td></tr>
+<tr><td width="25%"><a href="Variogram.corExp.html">Variogram.corExp</a></td>
+<td>Calculate Semi-variogram for a corExp Object</td></tr>
+<tr><td width="25%"><a href="Variogram.corGaus.html">Variogram.corGaus</a></td>
+<td>Calculate Semi-variogram for a corGaus Object</td></tr>
+<tr><td width="25%"><a href="Variogram.corLin.html">Variogram.corLin</a></td>
+<td>Calculate Semi-variogram for a corLin Object</td></tr>
+<tr><td width="25%"><a href="Variogram.corRatio.html">Variogram.corRatio</a></td>
+<td>Calculate Semi-variogram for a corRatio Object</td></tr>
+<tr><td width="25%"><a href="Variogram.corSpatial.html">Variogram.corSpatial</a></td>
+<td>Calculate Semi-variogram for a corSpatial Object</td></tr>
+<tr><td width="25%"><a href="Variogram.corSpher.html">Variogram.corSpher</a></td>
+<td>Calculate Semi-variogram for a corSpher Object</td></tr>
+<tr><td width="25%"><a href="Variogram.default.html">Variogram.default</a></td>
+<td>Calculate Semi-variogram</td></tr>
+<tr><td width="25%"><a href="Variogram.gls.html">Variogram.gls</a></td>
+<td>Calculate Semi-variogram for Residuals from a gls Object</td></tr>
+<tr><td width="25%"><a href="Variogram.lme.html">Variogram.lme</a></td>
+<td>Calculate Semi-variogram for Residuals from an lme Object</td></tr>
+<tr><td width="25%"><a href="varPower.html">varPower</a></td>
+<td>Power Variance Function</td></tr>
+<tr><td width="25%"><a href="varWeights.html">varWeights</a></td>
+<td>Extract Variance Function Weights</td></tr>
+<tr><td width="25%"><a href="varWeights.glsStruct.html">varWeights.glsStruct</a></td>
+<td>Variance Weights for glsStruct Object</td></tr>
+<tr><td width="25%"><a href="varWeights.lmeStruct.html">varWeights.lmeStruct</a></td>
+<td>Variance Weights for lmeStruct Object</td></tr>
+<tr><td width="25%"><a href="varWeights.html">varWeights.varComb</a></td>
+<td>Extract Variance Function Weights</td></tr>
+<tr><td width="25%"><a href="varWeights.html">varWeights.varFunc</a></td>
+<td>Extract Variance Function Weights</td></tr>
+</table>
+
+<h2><a name="W">-- W --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Wafer.html">Wafer</a></td>
+<td>Modeling of Analog MOS Circuits</td></tr>
+<tr><td width="25%"><a href="Wheat.html">Wheat</a></td>
+<td>Yields by growing conditions</td></tr>
+<tr><td width="25%"><a href="Wheat2.html">Wheat2</a></td>
+<td>Wheat Yield Trials</td></tr>
+</table>
+
+<h2><a name="misc">-- misc --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="groupedData.html">[.groupedData</a></td>
+<td>Construct a groupedData Object</td></tr>
+<tr><td width="25%"><a href="Extract.pdMat.html">[.pdBlocked</a></td>
+<td>Subscript a pdMat Object</td></tr>
+<tr><td width="25%"><a href="Extract.pdMat.html">[.pdMat</a></td>
+<td>Subscript a pdMat Object</td></tr>
+<tr><td width="25%"><a href="reStruct.html">[.reStruct</a></td>
+<td>Random Effects Structure</td></tr>
+<tr><td width="25%"><a href="Extract.pdMat.html">[<-.pdMat</a></td>
+<td>Subscript a pdMat Object</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/nlme/html/R.css b/win32/deps/library/nlme/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/nlme/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/nlme/libs/i386/nlme.dll b/win32/deps/library/nlme/libs/i386/nlme.dll
new file mode 100644
index 0000000..5d2cfba
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diff --git a/win32/deps/library/nlme/po/de/LC_MESSAGES/R-nlme.mo b/win32/deps/library/nlme/po/de/LC_MESSAGES/R-nlme.mo
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diff --git a/win32/deps/library/nlme/po/de/LC_MESSAGES/nlme.mo b/win32/deps/library/nlme/po/de/LC_MESSAGES/nlme.mo
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diff --git a/win32/deps/library/nlme/po/en quot/LC_MESSAGES/R-nlme.mo b/win32/deps/library/nlme/po/en quot/LC_MESSAGES/R-nlme.mo
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diff --git a/win32/deps/library/nlme/po/en quot/LC_MESSAGES/nlme.mo b/win32/deps/library/nlme/po/en quot/LC_MESSAGES/nlme.mo
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diff --git a/win32/deps/library/nlme/po/fr/LC_MESSAGES/R-nlme.mo b/win32/deps/library/nlme/po/fr/LC_MESSAGES/R-nlme.mo
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diff --git a/win32/deps/library/nlme/po/pl/LC_MESSAGES/R-nlme.mo b/win32/deps/library/nlme/po/pl/LC_MESSAGES/R-nlme.mo
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diff --git a/win32/deps/library/nlme/po/pl/LC_MESSAGES/nlme.mo b/win32/deps/library/nlme/po/pl/LC_MESSAGES/nlme.mo
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diff --git a/win32/deps/library/nlme/tests/anova.gls.R b/win32/deps/library/nlme/tests/anova.gls.R
new file mode 100644
index 0000000..b03c827
--- /dev/null
+++ b/win32/deps/library/nlme/tests/anova.gls.R
@@ -0,0 +1,22 @@
+## Example of scoping problem.
+## Originally from a report by Markus Jantti:
+## https://stat.ethz.ch/pipermail/r-help/2005-November/081382.html
+library(nlme)
+## stolen from example(anova.gls)
+# AR(1) errors within each Mare
+fm1 <- gls(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), Ovary,
+ correlation = corAR1(form = ~ 1 | Mare))
+# variance changes with a power of the absolute fitted values?
+fm2 <- update(fm1, weights = varPower())
+anova(fm1, fm2)
+
+## now define a little function
+dummy <- function(obj) anova(obj[[1]], obj[[2]])
+dummy(list(fm1, fm2))
+## last failed < 3.1-66
+
+## PR#13567
+fm1Orth.gls <- gls(distance ~ Sex * I(age - 11), Orthodont,
+ correlation = corSymm(form = ~ 1 | Subject),
+ weights = varIdent(form = ~ 1 | age))
+anova(fm1Orth.gls, Terms = "Sex")
diff --git a/win32/deps/library/nlme/tests/augPred_lab.R b/win32/deps/library/nlme/tests/augPred_lab.R
new file mode 100644
index 0000000..2cc07af
--- /dev/null
+++ b/win32/deps/library/nlme/tests/augPred_lab.R
@@ -0,0 +1,14 @@
+library(nlme)
+if(require("Hmisc")) {
+ T.aug <- Orthodont
+ label(T.aug$age) <- 'anyL'
+ foo <- augPred(lme(distance ~ age, random = ~1|Subject, data=T.aug))
+ ## failed in 3.1-72
+}
+
+## failed even if there is a variable with a class that is not being used.
+T.aug <- Orthodont
+T.aug$newage <- T.aug$age
+class(T.aug$newage) <- 'anyC'
+foo <- augPred(lme(distance ~ age, random = ~1|Subject, data=T.aug))
+## failed in 3.1-72
diff --git a/win32/deps/library/nlme/tests/augPredmissing.R b/win32/deps/library/nlme/tests/augPredmissing.R
new file mode 100644
index 0000000..9dbaeb0
--- /dev/null
+++ b/win32/deps/library/nlme/tests/augPredmissing.R
@@ -0,0 +1,7 @@
+library(nlme)
+data(Orthodont)
+# add a column with an NA that is not used in the fit
+Orthodont$Others = runif(nrow(Orthodont))
+is.na(Orthodont$Others[3]) = TRUE
+fm1 = lme(Orthodont, random = ~1)
+augPred(fm1, length.out = 2, level = c(0,1))
diff --git a/win32/deps/library/nlme/tests/coef.R b/win32/deps/library/nlme/tests/coef.R
new file mode 100644
index 0000000..19da9b6
--- /dev/null
+++ b/win32/deps/library/nlme/tests/coef.R
@@ -0,0 +1,14 @@
+## tests of fix for PR#9831
+library(nlme)
+val <- c("10"=1.10,"14"=1.14)
+vf <- varIdent(value=val, form=~1|age, fixed=c("12"=1.12))
+vfi <- Initialize(vf,Orthodont)
+str(vfi)
+coef(vfi)
+coef(vfi, unconstrained = FALSE, allCoef = TRUE)
+vfiCopy <- vfi # copy of an initialized object
+length(vfiCopy) # length is 2
+coef(vfiCopy) <- c(11,12) # error in 3.1-84
+
+## error in 3.1-84
+gls.error <- gls(distance ~ age, weights = vfi, data=Orthodont)
diff --git a/win32/deps/library/nlme/tests/contrMat.R b/win32/deps/library/nlme/tests/contrMat.R
new file mode 100644
index 0000000..42e8a3e
--- /dev/null
+++ b/win32/deps/library/nlme/tests/contrMat.R
@@ -0,0 +1,40 @@
+## problem reported by Christian Ritz on R-help, Tue, 20 Mar 2007 14:55:38
+
+## Dataset PestSci from package drc
+PestSci <-
+data.frame(CURVE = rep(1:5, each=21),
+ HERBICIDE = rep(c("bentazon", "diuron"), times=c(63, 42)),
+ DOSE = rep(c(0, 0.62, 1.85, 5.56, 16.67, 50, 150, 0, 0.62,
+ 1.85, 5.56, 16.67, 50, 150, 0, 0.15, 0.59, 2.34, 9.38, 37.5,
+ 150, 0, 0.01, 0.03, 0.1, 0.3, 1, 3, 0, 0.01, 0.03, 0.1, 0.3, 1, 3),
+ each = 3),
+ SLOPE = c(1.81295, 1.86704, 1.95606, 1.39073, 1.15721, 1.06126,
+ 0.99409, 0.83298, 0.8334, 0.72513, 0.69548, 0.65299, 0.49855,
+ 0.36873, 0.42617, 0.26666, 0.26896, 0.25989, 0.16074, 0.16404,
+ 0.1475, 1.02654, 0.91306, 0.89371, 0.59074, 0.669, 0.5965,
+ 0.37561, 0.44823, 0.42093, 0.31874, 0.27342, 0.2725, 0.27182,
+ 0.21752, 0.19981, 0.17332, 0.17949, 0.15623, 0.12855, 0.14524,
+ 0.11533, 1.03872, 1.0917, 1.10324, 0.94274, 0.91256, 1.02352,
+ 0.78689, 0.69706, 0.65989, 0.5372, 0.51324, 0.54981, 0.37401,
+ 0.34033, 0.32491, 0.30518, 0.24593, 0.289, 0.17414, 0.12275,
+ 0.14788, 2.20963, 2.27931, 2.14703, 2.18831, 2.08863, 2.06676,
+ 2.18827, 2.10748, 1.84474, 1.78805, 1.75547, 1.61381, 0.70295,
+ 0.6983, 0.74045, 0.20673, 0.20784, 0.22402, 0.05268, 0.06519,
+ 0.09258, 1.94033, 1.80193, 1.71586, 1.71586, 1.98471, 1.74905,
+ 1.87795, 1.64081, 1.53094, 1.50709, 1.41035, 1.35367, 0.64427,
+ 0.62185, 0.60337, 0.14073, 0.12928, 0.15016, 8e-05, 0.00262,
+ 0.00303))
+
+
+library(nlme)
+sv <- c(0.43355869, 2.49963220, 0.05861799, 1.73290589, 0.38153146, 0.24316978)
+
+nlme(SLOPE ~ c + (d-c)/(1+exp(b*(log(DOSE)-log(e)))),
+ fixed = list(b ~ factor(HERBICIDE)-1,
+ c ~ 1,
+ d ~ 1,
+ e ~ factor(HERBICIDE)-1),
+ random = d ~ 1 | CURVE,
+ start = sv, data = PestSci)
+
+## failed in contrMat in 3.1-78
diff --git a/win32/deps/library/nlme/tests/data.frame.R b/win32/deps/library/nlme/tests/data.frame.R
new file mode 100644
index 0000000..cef3fa9
--- /dev/null
+++ b/win32/deps/library/nlme/tests/data.frame.R
@@ -0,0 +1,4 @@
+library(nlme)
+subs<-rep(LETTERS[1:10],rep(3,10))
+resp<-rnorm(30)
+groupedData(resp~1|subs)
diff --git a/win32/deps/library/nlme/tests/deparse.R b/win32/deps/library/nlme/tests/deparse.R
new file mode 100644
index 0000000..3a01197
--- /dev/null
+++ b/win32/deps/library/nlme/tests/deparse.R
@@ -0,0 +1,171 @@
+# Tests to make sure that the deparse(as.vector(x)) construction is not
+# tripping us up again.
+
+library(nlme)
+data(Loblolly)
+fm1 <- nlme(height ~ SSasymp(age, Asym, R0, lrc),
+ data = Loblolly,
+ fixed = Asym + R0 + lrc ~ 1,
+ random = Asym ~ 1,
+ start = c(Asym = 103, R0 = -8.5, lrc = -3.3))
+fm1
+
+model <- height ~ SSasymp(age, Asym, R0, lrc)
+fixed <- Asym + R0 + lrc ~ 1
+random <- Asym ~ 1
+start <- c(Asym = 103, R0 = -8.5, lrc = -3.3)
+fm2 <- nlme(model,
+ data = Loblolly,
+ fixed = fixed,
+ random = random,
+ start = start)
+fm2
+
+## deparse can give multiple lines
+## example from https://stat.ethz.ch/pipermail/r-help/2006-February/086648.html
+"mydata2" <-
+structure(list(Tps = c(1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3,
+3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6,
+6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 9, 9, 9,
+9, 9, 9, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 14,
+14, 14, 14, 14, 17, 17, 17, 17, 17, 20, 20, 20, 20, 25, 28, 29,
+50, 50, 50, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136,
+1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 4,
+4, 4, 4, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7,
+7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10,
+10, 10, 11, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 17, 17, 17,
+17, 17, 20, 20, 20, 20, 25, 28, 29, 50, 50, 50, 136, 136, 136,
+136, 136, 136, 136, 136, 136, 136, 1, 1, 1, 1, 1, 1, 2, 2, 2,
+2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5,
+6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8,
+8, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11,
+11, 11, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 20, 20, 20, 20,
+25, 28, 29, 50, 50, 50, 136, 136, 136, 136, 136, 136, 136, 136,
+136, 136), Conc = c(0, 0, 0, 0, 0, 0, 0, 0.807852503274902,
+0.204371494701886,
+0.579222129993907, 0.989062273721619, 0, 1.11728297897571,
+1.41057428121324,
+0.888883702851307, 1.259907624008, 1.45753269675829, 1.07077516747401,
+0.843279379, 0, 0.763110069196737, 1.11297791434297, 1.10087763997637,
+0.946929594501016, 1.33112168, 0.654041755, 0.694167499, 1.289548703,
+1.117139864, 0.807196192, 0.720221376552025, 0.560082823, 0.476583438,
+2.590855204, 0.51510972, 1.072946887, 0.537999938614396, 0.886684225905255,
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+1.80365598487402, 1.13240352674377, 1.50086243061644, 2.06355364280445,
+0.439350890906039, 1.54692793444949, 1.78758216051046, 1.09043400023239,
+0.811328376840514, 0.459192443530981, 0.695333473157298, 0.387995007681174,
+0.784627063444921, 1.02282256375842, 0.382687104107726, 0.554290634950242,
+0.130420456296453, 0.324194753224919, 0.31106140274139, 0.513473505828888,
+0.878620320248701, 1.18404358659996, 0.136926837896477, 0, 0,
+0.835588760032974, 0.558617235576616, 1.21002805866839, 0.769381068031404,
+1.04514254228094, 0.373251847173678, 0.389005898972802, 0.183141006154896,
+0.223596336820146, 0.315526423315647, 0.0930349732768131,
+0.169959185212759,
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+0, 0.153175826795441, 0.0428171049833677, 0, 0, 0, 0, 0, 0, 0,
+0, 0, 0, 26.564295705327, 5.5893744508169, 7.22612934071834,
+36.6563989567777, 0, 28.8967184437329, 28.4030370337251, 28.0886043901352,
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+26.6249506083603, 31.3001451026823, 23.7339071829084, 23.3702284599355,
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+29.4259634309146, 45.6112405959009, 48.1231689836687, 55.0037961570027,
+32.9822316456421, 20.0382768189682, 26.0986380308655, 28.8915584506145,
+28.7949023823068, 30.0278417498425, 58.8089779973569, 20.3602570111197,
+29.6269605259023, 28.4404986724604, 30.2165182590977, 19.9204461889074,
+31.1019196559556, 30.3847467747055, 36.8726911479995, 51.0618036275519,
+23.5408013442579, 36.6948355347593, 27.4753860809429, 24.1341667099646,
+27.5411488989643, 35.9021799354022, 19.7417897046158, 31.1403887303244,
+46.1743622734049, 34.8235854891765, 22.1714704189293, 33.6805966894274,
+35.2814908686112, 42.9767437212852, 38.1264997164547, 5.3651357974451,
+42.8990434918385, 25.4908883698364, 25.99649502, 36.4958105490917,
+40.8004126550705, 5.36867162116895, 0.00898476265269363, 0,
+27.6810997945798,
+28.7918300045713, 45.7577183830352, 35.9276318604787, 34.9717618087238,
+29.620354272564, 24.6537513599869, 13.5363982464958, 25.8289073574818,
+12.0090406245759, 4.753436805, 11.849214652228, 8.41410147611612,
+0, 1.80855352862552, 1.1987530031681, 1.01148025243171, 0.495675369574172,
+1.62701127228732, 0, 16.6288242287241, 1.23656061354912, 0.323708776035328,
+0, 0.566916625204436, 0, 0, 0, 0, 0, 0, 0, 2.53578781871283,
+3.50083667130797, 0, 0.98049572179098, 0, 3.57129673217304,
+2.77298867949388,
+2.12302645642669, 4.11923869203499, 4.69069462193674, 2.8698666062651,
+2.05079837323067, 0.0602771574448942, 5.96454350250626, 2.26267114439802,
+3.06911285674854, 2.04233129537404, 2.62181873844029, 1.51813653072598,
+1.46193772981073, 2.69864635755833, 3.44016493913122, 2.50834832469627,
+3.48170744166168, 1.00637581555435, 1.67065398473081, 4.18855363095027,
+3.39649762611015, 1.72804613460423, 1.40053679329531, 2.37032387724109,
+3.19332545080983, 2.49474373894248, 2.17800931288708, 2.7601484443213,
+0.91266104095844, 1.93485048639199, 1.19692593420788, 1.79537330666258,
+2.14020930767983, 3.0122526724942, 2.81112226980754, 3.54890724398174,
+3.01022926452999, 2.38263226710738, 3.53569238341869, 3.47869329713911,
+0.679333339820719, 2.4764260756438, 3.82615100065366, 2.20449890383871,
+1.371303113329, 1.2427787019995, 1.73319133880954, 0.391268883238408,
+1.73610193837913, 2.68494324646718, 1.77065393606844, 1.45079980147062,
+0.763775702906329, 0.98566725668627, 0.37838763208699, 0.841811919286804,
+1.46436462204795, 1.98409602726, 0.507005887891038, 0.465515668274195,
+0, 1.873365675227, 1.69023864630648, 2.65530855919137, 2.34392199908302,
+1.61917643594837, 1.05165934333345, 0.564642823436471, 0.121621029620328,
+0.515007625737071, 0.524345809084086, 0.130898614090571, 0.332427740242623,
+0.110214989555118, 0, 0.128642193589, 0.119407067173878, 0.128926224027295,
+0.0622331866694357, 0.215645168287442, 0, 0.859343941945178,
+0.0500810300696456, 0, 0, 0.0628746592609754), Organ =
+structure(as.integer(c(1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3,
+3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
+3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
+3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
+3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
+3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
+2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
+2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
+2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
+2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
+2, 2, 2, 2, 2)), .Label = c("Carc", "TD", "Foie"), class = c("ordered",
+"factor"))), .Names = c("Tps", "Conc", "Organ"), row.names = c("1",
+"2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13",
+"14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24",
+"25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35",
+"36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46",
+"47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57",
+"58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68",
+"69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79",
+"80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90",
+"91", "92", "93", "94", "95", "96", "97", "98", "99", "100",
+"101", "102", "103", "104", "105", "106", "107", "108", "109",
+"110", "111", "112", "113", "114", "115", "116", "117", "118",
+"119", "120", "121", "122", "123", "124", "125", "126", "127",
+"128", "129", "130", "131", "132", "133", "134", "135", "136",
+"137", "138", "139", "140", "141", "142", "143", "144", "145",
+"146", "147", "148", "149", "150", "151", "152", "153", "154",
+"155", "156", "157", "158", "159", "160", "161", "162", "163",
+"164", "165", "166", "167", "168", "169", "170", "171", "172",
+"173", "174", "175", "176", "177", "178", "179", "180", "181",
+"182", "183", "184", "185", "186", "187", "188", "189", "190",
+"191", "192", "193", "194", "195", "196", "197", "198", "199",
+"200", "201", "202", "203", "204", "205", "206", "207", "208",
+"209", "210", "211", "212", "213", "214", "215", "216", "217",
+"218", "219", "220", "221", "222", "223", "224", "225", "226",
+"227", "228", "229", "230", "231", "232", "233", "234", "235",
+"236", "237", "238", "239", "240", "241", "242", "243", "244",
+"245", "246", "247", "248", "249", "250", "251", "252", "253",
+"254", "255", "256", "257", "258", "259", "260", "261", "262",
+"263", "264", "265", "266", "267", "268", "269", "270", "271",
+"272", "273", "274", "275", "276", "277", "278", "279", "280",
+"281", "282", "283", "284", "285", "286", "287", "288", "289",
+"290", "291", "292", "293", "294", "295", "296", "297", "298",
+"299", "300"), class = c("nfnGroupedData", "nfGroupedData", "groupedData",
+"data.frame"), formula = quote(Conc ~ Tps | Organ), FUN = function (x)
+max(x, na.rm = TRUE), order.groups = TRUE)
+
+mydata2$Dose <- 100
+mymod3 <- nlsList(Conc+1 ~ Dose * exp(lKe+lKa-lCl) *
+ (exp(-exp(lKe)*Tps)-exp(-exp(lKa)*Tps)) /(exp(lKa)-exp(lKe)) | Organ,
+ data=mydata2, start= c(lKe=-2.77, lKa=-1.41, lCl=-1.13))
+mymod3
diff --git a/win32/deps/library/nlme/tests/getData.R b/win32/deps/library/nlme/tests/getData.R
new file mode 100644
index 0000000..50b5583
--- /dev/null
+++ b/win32/deps/library/nlme/tests/getData.R
@@ -0,0 +1,8 @@
+library(nlme)
+fm1 <- lme(distance ~ age, Orthodont)
+str(o1 <- getData(fm1))
+
+df <- Orthodont # note that the name conflicts with df in the stats
+fm2 <- lme(distance ~ age, df)
+str(o2 <- getData(fm2))
+stopifnot(identical(o1, o2))
diff --git a/win32/deps/library/nlme/tests/gls.R b/win32/deps/library/nlme/tests/gls.R
new file mode 100644
index 0000000..1ae924c
--- /dev/null
+++ b/win32/deps/library/nlme/tests/gls.R
@@ -0,0 +1,24 @@
+## reported by simon bond <shug0131 yahoo co uk> to R-help 2007-03-16
+
+library(nlme)
+x <- rnorm(10, 0.1, 1)
+try(gls(x ~ 0)) # segfaulted in 3.1-79
+
+
+## PR#10364
+# copied verbatim from Pinheiro & Bates 8.3.3
+fm1Dial.gnls <-
+ gnls(rate ~ SSasympOff(pressure, Asym, lrc, c0),
+ data = Dialyzer, params = list(Asym + lrc ~ QB, c0 ~ 1),
+ start = c(53.6, 8.6, 0.51, -0.26, 0.225))
+(p1 <- predict(fm1Dial.gnls))
+(p2 <- predict(fm1Dial.gnls, newdata = Dialyzer))
+# failed, factor levels complaint
+# also, missed row names as names
+stopifnot(all.equal(as.vector(p1), as.vector(p2)), # 'label' differs
+ identical(names(p1), names(p2)))
+
+## PR#13418
+fm1 <- gls(weight ~ Time * Diet, BodyWeight)
+Variogram(fm1, form = ~ Time | Rat)[1:10,]
+## failed in 3.1-89
diff --git a/win32/deps/library/nlme/tests/lmList.R b/win32/deps/library/nlme/tests/lmList.R
new file mode 100644
index 0000000..fbb0c2a
--- /dev/null
+++ b/win32/deps/library/nlme/tests/lmList.R
@@ -0,0 +1,11 @@
+## PR#13788
+
+library(nlme)
+qm <- lmList(height ~ age | Subject, data = Oxboys)
+nd <- with(Oxboys,
+ expand.grid(age = seq(min(age),max(age),length=50),
+ Subject = levels(Subject))
+ )
+
+## failed in 3.1-92
+res <- predict(qm, nd, se=TRUE)
diff --git a/win32/deps/library/nlme/tests/lme.R b/win32/deps/library/nlme/tests/lme.R
new file mode 100644
index 0000000..d335692
--- /dev/null
+++ b/win32/deps/library/nlme/tests/lme.R
@@ -0,0 +1,37 @@
+library(nlme)
+fm1 <- lmList(Oxboys)
+fm1
+fm2 <- lme(fm1)
+fm2
+
+# bug report from Arne Mueller sanofi-aventis com
+mod <- distance ~ age + Sex
+fm3 <- lme(mod, Orthodont, random = ~ 1)
+predict(fm3, Orthodont)
+
+## bug report and fix from Dimitris Rizopoulos and Spencer Graves:
+## when 'returnObject = TRUE', do not stop() but give warning() on non-convergence:
+fm1 <- lme(distance ~ age, data = Orthodont,
+ control = lmeControl(msMaxIter = 1, returnObject = TRUE))
+
+## based on bug report on R-help
+predict(fm3, Orthodont[1,])
+# failed in 3.1-88
+
+## wrong results from getData:
+load("ss2.rda")
+m1 <- lme(PV1MATH ~ ESCS + Age +time ,
+ random = ~ time|SCHOOLID,
+ data = ss2,
+ weights = varIdent(form=~1|time),
+ corr = corCompSymm(form=~1|SCHOOLID/StIDStd),
+ na.action = na.omit)
+plot(m1, resid(.) ~ WEALTH)
+
+m2 <- lme(PV1MATH ~ ESCS + Age +time ,
+ random = ~ time|SCHOOLID,
+ data = ss2,
+ weights = varIdent(form=~1|time),
+ corr = corCompSymm(form=~1|SCHOOLID/StIDStd),
+ na.action = na.omit)
+plot(m2, resid(.) ~ WEALTH)
diff --git a/win32/deps/library/nlme/tests/lme.Rout.save b/win32/deps/library/nlme/tests/lme.Rout.save
new file mode 100644
index 0000000..edfb703
--- /dev/null
+++ b/win32/deps/library/nlme/tests/lme.Rout.save
@@ -0,0 +1,146 @@
+
+R Under development (unstable) (2011-07-19 r56420)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(nlme)
+> fm1 <- lmList(Oxboys)
+> fm1
+Call:
+ Model: height ~ age | Subject
+ Data: Oxboys
+
+Coefficients:
+ (Intercept) age
+10 130.2616 3.722915
+26 137.9927 5.588783
+25 139.2105 4.024081
+9 138.1369 6.009057
+2 142.8584 5.440176
+6 146.7908 3.963171
+7 146.1279 4.990050
+17 142.9777 8.611780
+16 147.5447 4.545196
+15 144.2759 7.124260
+8 148.2929 6.464712
+20 151.4707 4.374466
+1 148.1203 7.178151
+18 151.1804 5.957793
+5 151.4293 6.246128
+23 151.0645 7.185123
+11 150.0467 8.506082
+21 150.5210 7.497794
+3 155.6508 4.774669
+24 153.1404 6.764705
+22 154.5670 8.087514
+12 156.8106 7.015468
+13 156.0714 8.493806
+14 159.4738 8.670886
+19 164.5761 9.065620
+4 165.0724 9.360561
+
+Degrees of freedom: 234 total; 182 residual
+Residual standard error: 0.6598878
+> fm2 <- lme(fm1)
+> fm2
+Linear mixed-effects model fit by REML
+ Data: Oxboys
+ Log-restricted-likelihood: -362.0455
+ Fixed: height ~ age
+(Intercept) age
+ 149.371753 6.525469
+
+Random effects:
+ Formula: ~age | Subject
+ Structure: General positive-definite, Log-Cholesky parametrization
+ StdDev Corr
+(Intercept) 8.081077 (Intr)
+age 1.680717 0.641
+Residual 0.659889
+
+Number of Observations: 234
+Number of Groups: 26
+>
+> # bug report from Arne Mueller sanofi-aventis com
+> mod <- distance ~ age + Sex
+> fm3 <- lme(mod, Orthodont, random = ~ 1)
+> predict(fm3, Orthodont)
+ M01 M01 M01 M01 M02 M02 M02 M02
+25.39237 26.71274 28.03311 29.35348 21.61052 22.93089 24.25126 25.57163
+ M03 M03 M03 M03 M04 M04 M04 M04
+22.36689 23.68726 25.00763 26.32800 24.41990 25.74027 27.06064 28.38101
+ M05 M05 M05 M05 M06 M06 M06 M06
+21.28636 22.60673 23.92710 25.24747 24.20379 25.52416 26.84453 28.16490
+ M07 M07 M07 M07 M08 M08 M08 M08
+21.93468 23.25505 24.57542 25.89579 22.04273 23.36310 24.68347 26.00384
+ M09 M09 M09 M09 M10 M10 M10 M10
+23.12326 24.44363 25.76400 27.08437 26.90511 28.22548 29.54585 30.86622
+ M11 M11 M11 M11 M12 M12 M12 M12
+21.82663 23.14700 24.46737 25.78774 22.36689 23.68726 25.00763 26.32800
+ M13 M13 M13 M13 M14 M14 M14 M14
+22.36689 23.68726 25.00763 26.32800 22.90715 24.22753 25.54790 26.86827
+ M15 M15 M15 M15 M16 M16 M16 M16
+23.77158 25.09195 26.41232 27.73269 21.28636 22.60673 23.92710 25.24747
+ F01 F01 F01 F01 F02 F02 F02 F02
+19.56700 20.88737 22.20774 23.52811 20.97168 22.29205 23.61243 24.93280
+ F03 F03 F03 F03 F04 F04 F04 F04
+21.62000 22.94037 24.26074 25.58111 22.59248 23.91285 25.23322 26.55359
+ F05 F05 F05 F05 F06 F06 F06 F06
+20.64753 21.96790 23.28827 24.60864 19.35089 20.67126 21.99163 23.31200
+ F07 F07 F07 F07 F08 F08 F08 F08
+20.97168 22.29205 23.61243 24.93280 21.29584 22.61621 23.93658 25.25695
+ F09 F09 F09 F09 F10 F10 F10 F10
+19.35089 20.67126 21.99163 23.31200 17.08178 18.40215 19.72252 21.04289
+ F11 F11 F11 F11
+23.88911 25.20948 26.52985 27.85022
+attr(,"label")
+[1] "Predicted values (mm)"
+>
+> ## bug report and fix from Dimitris Rizopoulos and Spencer Graves:
+> ## when 'returnObject = TRUE', do not stop() but give warning() on non-convergence:
+> fm1 <- lme(distance ~ age, data = Orthodont,
++ control = lmeControl(msMaxIter = 1, returnObject = TRUE))
+Warning message:
+In lme.formula(distance ~ age, data = Orthodont, control = lmeControl(msMaxIter = 1, :
+ nlminb problem, convergence error code = 1
+ message = iteration limit reached without convergence (10)
+>
+> ## based on bug report on R-help
+> predict(fm3, Orthodont[1,])
+ M01
+25.39237
+attr(,"label")
+[1] "Predicted values (mm)"
+> # failed in 3.1-88
+>
+> ## wrong results from getData:
+> load("ss2.rda")
+> m1 <- lme(PV1MATH ~ ESCS + Age +time ,
++ random = ~ time|SCHOOLID,
++ data = ss2,
++ weights = varIdent(form=~1|time),
++ corr = corCompSymm(form=~1|SCHOOLID/StIDStd),
++ na.action = na.omit)
+> plot(m1, resid(.) ~ WEALTH)
+>
+> m2 <- lme(PV1MATH ~ ESCS + Age +time ,
++ random = ~ time|SCHOOLID,
++ data = ss2,
++ weights = varIdent(form=~1|time),
++ corr = corCompSymm(form=~1|SCHOOLID/StIDStd),
++ na.action = na.omit)
+> plot(m2, resid(.) ~ WEALTH)
+>
diff --git a/win32/deps/library/nlme/tests/missing.R b/win32/deps/library/nlme/tests/missing.R
new file mode 100644
index 0000000..a513cf7
--- /dev/null
+++ b/win32/deps/library/nlme/tests/missing.R
@@ -0,0 +1,26 @@
+library(nlme)
+
+options(digits=4) # avoid rounding differences
+
+Ovary[c(1,272), 2] <- NA
+fm1 <- gls(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), Ovary,
+ correlation = corAR1(form = ~ 1 | Mare), na.action=na.exclude)
+fitted(fm1)
+residuals(fm1)
+summary(fm1)
+
+Orthodont[100:102, 2] <- NA
+fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1,
+ na.action=na.exclude)
+fitted(fm2, 0:1)
+fitted(fm2)
+residuals(fm2, 0:1)
+round(residuals(fm2), 2)
+summary(fm2)
+
+Soybean[1:5, "Time"] <- NA
+fm3 <- gnls(weight ~ SSlogis(Time, Asym, xmid, scal), Soybean,
+ weights = varPower(), na.action=na.exclude)
+fitted(fm3)
+residuals(fm3)
+summary(fm3)
diff --git a/win32/deps/library/nlme/tests/missing.Rout.save b/win32/deps/library/nlme/tests/missing.Rout.save
new file mode 100644
index 0000000..1f0b47a
--- /dev/null
+++ b/win32/deps/library/nlme/tests/missing.Rout.save
@@ -0,0 +1,791 @@
+
+R version 2.6.0 Under development (unstable) (2007-06-13 r41937)
+Copyright (C) 2007 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(nlme)
+>
+> options(digits=4) # avoid rounding differences
+>
+> Ovary[c(1,272), 2] <- NA
+> fm1 <- gls(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), Ovary,
++ correlation = corAR1(form = ~ 1 | Mare), na.action=na.exclude)
+> fitted(fm1)
+ 1 2 3 4 5 6 7 8 9 10 11
+ NA 12.856 12.061 11.271 10.551 9.960 9.544 9.338 9.359 9.604 10.054
+ 12 13 14 15 16 17 18 19 20 21 22
+10.673 11.410 12.205 12.995 13.715 14.307 14.722 14.928 14.907 14.662 14.212
+ 23 24 25 26 27 28 29 30 31 32 33
+13.593 12.856 12.061 11.271 10.551 9.960 9.544 13.794 13.010 12.141 11.271
+ 34 35 36 37 38 39 40 41 42 43 44
+10.485 9.861 9.459 9.319 9.454 9.852 10.473 11.256 12.125 12.995 13.781
+ 45 46 47 48 49 50 51 52 53 54 55
+14.405 14.807 14.947 14.812 14.414 13.794 13.010 12.141 11.271 10.485 9.861
+ 56 57 58 59 60 61 62 63 64 65 66
+ 9.459 13.904 13.098 12.188 11.271 10.448 9.807 9.419 9.325 9.535 10.026
+ 67 68 69 70 71 72 73 74 75 76 77
+10.746 11.616 12.542 13.424 14.166 14.688 14.933 14.874 14.518 13.904 13.098
+ 78 79 80 81 82 83 84 85 86 87 88
+12.188 11.271 10.448 9.807 9.419 13.593 12.856 12.061 11.271 10.551 9.960
+ 89 90 91 92 93 94 95 96 97 98 99
+ 9.544 9.338 9.359 9.604 10.054 10.673 11.410 12.205 12.995 13.715 14.307
+ 100 101 102 103 104 105 106 107 108 109 110
+14.722 14.928 14.907 14.662 14.212 13.593 12.856 12.061 11.271 10.551 9.960
+ 111 112 113 114 115 116 117 118 119 120 121
+ 9.544 13.593 12.856 12.061 11.271 10.551 9.960 9.544 9.338 9.359 9.604
+ 122 123 124 125 126 127 128 129 130 131 132
+10.054 10.673 11.410 12.205 12.995 13.715 14.307 14.722 14.928 14.907 14.662
+ 133 134 135 136 137 138 139 140 141 142 143
+14.212 13.593 12.856 12.061 11.271 10.551 9.960 9.544 13.593 12.856 12.061
+ 144 145 146 147 148 149 150 151 152 153 154
+11.271 10.551 9.960 9.544 9.338 9.359 9.604 10.054 10.673 11.410 12.205
+ 155 156 157 158 159 160 161 162 163 164 165
+12.995 13.715 14.307 14.722 14.928 14.907 14.662 14.212 13.593 12.856 12.061
+ 166 167 168 169 170 171 172 173 174 175 176
+11.271 10.551 9.960 9.544 13.794 13.010 12.141 11.271 10.485 9.861 9.459
+ 177 178 179 180 181 182 183 184 185 186 187
+ 9.319 9.454 9.852 10.473 11.256 12.125 12.995 13.781 14.405 14.807 14.947
+ 188 189 190 191 192 193 194 195 196 197 198
+14.812 14.414 13.794 13.010 12.141 11.271 10.485 9.861 9.459 13.418 12.726
+ 199 200 201 202 203 204 205 206 207 208 209
+11.994 11.271 10.607 10.047 9.629 9.382 9.322 9.454 9.769 10.244 10.848
+ 210 211 212 213 214 215 216 217 218 219 220
+11.540 12.272 12.995 13.659 14.219 14.637 14.884 14.944 14.812 14.498 14.022
+ 221 222 223 224 225 226 227 228 229 230 231
+13.418 12.726 11.994 11.271 10.607 10.047 9.629 14.022 13.195 12.239 11.271
+ 232 233 234 235 236 237 238 239 240 241 242
+10.407 9.751 9.382 9.345 9.645 10.244 11.072 12.027 12.995 13.859 14.515
+ 243 244 245 246 247 248 249 250 251 252 253
+14.884 14.921 14.622 14.022 13.195 12.239 11.271 10.407 9.751 9.382 13.593
+ 254 255 256 257 258 259 260 261 262 263 264
+12.856 12.061 11.271 10.551 9.960 9.544 9.338 9.359 9.604 10.054 10.673
+ 265 266 267 268 269 270 271 272 273 274 275
+11.410 12.205 12.995 13.715 14.307 14.722 14.928 NA 14.662 14.212 13.593
+ 276 277 278 279 280 281 282 283 284 285 286
+12.856 12.061 11.271 10.551 9.960 9.544 13.794 13.010 12.141 11.271 10.485
+ 287 288 289 290 291 292 293 294 295 296 297
+ 9.861 9.459 9.319 9.454 9.852 10.473 11.256 12.125 12.995 13.781 14.405
+ 298 299 300 301 302 303 304 305 306 307 308
+14.807 14.947 14.812 14.414 13.794 13.010 12.141 11.271 10.485 9.861 9.459
+attr(,"label")
+[1] "Fitted values"
+> residuals(fm1)
+ 1 2 3 4 5 6 7 8
+ NA 2.14386 6.93937 4.72901 2.44882 0.04046 2.45603 4.66184
+ 9 10 11 12 13 14 15 16
+ 3.64122 10.39585 11.94560 4.32695 6.59002 4.79451 1.00487 4.28507
+ 17 18 19 20 21 22 23 24
+ -0.30658 1.27786 2.07205 3.09266 3.33803 2.78828 0.40693 -0.85614
+ 25 26 27 28 29 30 31 32
+ -0.06063 2.72901 -0.55118 1.04046 6.45603 -7.79359 -7.01022 -4.14099
+ 33 34 35 36 37 38 39 40
+ -4.27099 5.51463 0.13897 3.54090 -0.31891 -2.45420 -3.85170 -2.47253
+ 41 42 43 44 45 46 47 48
+ -3.25589 -6.12512 -4.99513 -6.78075 -5.40508 -8.80702 -10.94720 -9.81192
+ 49 50 51 52 53 54 55 56
+ -6.41441 -2.79359 -0.01022 -2.14099 -5.27099 -3.48537 -3.86103 -4.45910
+ 57 58 59 60 61 62 63 64
+ -0.90420 -2.09816 -2.18752 -5.27099 -2.44787 -3.80737 -0.41890 -0.32454
+ 65 66 67 68 69 70 71 72
+ 0.46546 -2.02612 3.25398 1.38377 1.45755 2.57570 5.83377 6.31217
+ 73 74 75 76 77 78 79 80
+ 10.06742 8.12604 4.48168 8.09580 2.90184 8.81248 7.72901 9.55213
+ 81 82 83 84 85 86 87 88
+ 7.19263 14.58110 -4.59307 -3.85614 -5.06063 -5.27099 -3.55118 -3.95954
+ 89 90 91 92 93 94 95 96
+ -8.54397 -8.33816 -8.35878 -4.60415 -4.05440 -7.67305 -6.40998 -9.20549
+ 97 98 99 100 101 102 103 104
+ -6.99513 -5.71493 -8.30658 -9.72214 -8.92795 -6.90734 -3.66197 -0.21172
+ 105 106 107 108 109 110 111 112
+ -5.59307 -3.85614 -2.06063 -4.27099 -3.55118 -3.95954 1.45603 -3.59307
+ 113 114 115 116 117 118 119 120
+ -0.85614 -0.06063 5.72901 -1.55118 0.04046 -6.54397 2.66184 3.64122
+ 121 122 123 124 125 126 127 128
+ -0.60415 -6.05440 -3.67305 -7.40998 -0.20549 1.00487 -1.71493 0.69342
+ 129 130 131 132 133 134 135 136
+ 2.27786 0.07205 -1.90734 3.33803 4.78828 -0.59307 -3.85614 -0.06063
+ 137 138 139 140 141 142 143 144
+ -3.27099 -0.55118 -4.95954 4.45603 2.40693 4.14386 0.93937 5.72901
+ 145 146 147 148 149 150 151 152
+ 4.44882 -0.95954 -1.54397 -4.33816 -0.35878 -1.60415 -2.05440 2.32695
+ 153 154 155 156 157 158 159 160
+ 2.59002 0.79451 1.00487 0.28507 -3.30658 2.27786 6.07205 6.09266
+ 161 162 163 164 165 166 167 168
+ 6.33803 5.78828 3.40693 5.14386 9.93937 -1.27099 0.44882 1.04046
+ 169 170 171 172 173 174 175 176
+ 2.45603 4.20641 -0.01022 1.85901 0.72901 0.51463 -1.86103 -4.45910
+ 177 178 179 180 181 182 183 184
+ -1.31891 0.54580 1.14830 -0.47253 0.74411 -2.12512 -3.99513 -1.78075
+ 185 186 187 188 189 190 191 192
+ -0.40508 1.19298 -1.94720 -3.81192 -1.41441 -0.79359 -2.01022 -1.14099
+ 193 194 195 196 197 198 199 200
+ -3.27099 3.51463 -5.86103 -2.45910 -0.41772 -3.72591 3.00630 3.72901
+ 201 202 203 204 205 206 207 208
+ 1.39298 -2.04705 0.37076 -3.38206 -0.32236 -1.45420 0.23140 -4.24413
+ 209 210 211 212 213 214 215 216
+ -2.84839 1.45980 -0.27241 -0.99513 1.34090 6.78094 10.36312 6.11594
+ 217 218 219 220 221 222 223 224
+ 6.05624 9.18808 5.50248 5.97801 4.58228 7.27409 8.00630 7.72901
+ 225 226 227 228 229 230 231 232
+ 1.39298 -3.04706 -1.62924 -4.02199 0.80539 -0.23920 -1.27099 -3.40675
+ 233 234 235 236 237 238 239 240
+ 2.24927 0.61794 -1.34520 0.35541 4.75587 3.92850 -0.02691 6.00487
+ 241 242 243 244 245 246 247 248
+ 1.14063 1.48462 0.11594 2.07908 -0.62153 1.97801 1.80539 -1.23920
+ 249 250 251 252 253 254 255 256
+ -1.27099 -3.40675 -5.75074 -1.38206 -2.59307 3.14386 2.93937 0.72901
+ 257 258 259 260 261 262 263 264
+ 0.44882 -3.95954 1.45603 2.66184 1.64122 6.39585 4.94560 0.32695
+ 265 266 267 268 269 270 271 272
+ -4.40998 1.79451 7.00487 8.28507 8.69342 6.27786 6.07205 NA
+ 273 274 275 276 277 278 279 280
+ 7.33803 7.78828 3.40693 4.14386 4.93937 5.72901 3.44882 2.04046
+ 281 282 283 284 285 286 287 288
+ 1.45603 -4.79359 -5.01022 -4.14099 -3.27099 -2.48537 -3.86103 -2.45910
+ 289 290 291 292 293 294 295 296
+ -1.31891 0.54580 0.14830 3.52747 1.74411 -4.12512 -4.99513 -5.78075
+ 297 298 299 300 301 302 303 304
+ -5.40508 1.19298 -2.94720 -4.81192 -2.41441 -1.79359 -4.01022 -6.14099
+ 305 306 307 308
+ -2.27099 -3.48537 -4.86103 -4.45910
+attr(,"std")
+ [1] NA 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+ [13] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+ [25] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+ [37] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+ [49] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+ [61] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+ [73] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+ [85] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+ [97] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+[109] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+[121] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+[133] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+[145] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+[157] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+[169] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+[181] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+[193] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+[205] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+[217] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+[229] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+[241] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+[253] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+[265] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 NA 4.581 4.581 4.581 4.581
+[277] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+[289] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+[301] 4.581 4.581 4.581 4.581 4.581 4.581 4.581 4.581
+attr(,"label")
+[1] "Residuals"
+> summary(fm1)
+Generalized least squares fit by REML
+ Model: follicles ~ sin(2 * pi * Time) + cos(2 * pi * Time)
+ Data: Ovary
+ AIC BIC logLik
+ 1560 1579 -775.1
+
+Correlation Structure: AR(1)
+ Formula: ~1 | Mare
+ Parameter estimate(s):
+ Phi
+0.7498
+
+Coefficients:
+ Value Std.Error t-value p-value
+(Intercept) 12.133 0.6574 18.456 0.0000
+sin(2 * pi * Time) -2.679 0.6436 -4.162 0.0000
+cos(2 * pi * Time) -0.862 0.6902 -1.249 0.2126
+
+ Correlation:
+ (Intr) s(*p*T
+sin(2 * pi * Time) -0.007
+cos(2 * pi * Time) -0.295 0.003
+
+Standardized residuals:
+ Min Q1 Med Q3 Max
+-2.38972 -0.75655 -0.01324 0.63960 3.18298
+
+Residual standard error: 4.581
+Degrees of freedom: 306 total; 303 residual
+>
+> Orthodont[100:102, 2] <- NA
+> fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1,
++ na.action=na.exclude)
+> fitted(fm2, 0:1)
+ fixed Subject
+1 22.95 25.35
+2 24.30 26.69
+3 25.64 28.04
+4 26.98 29.38
+5 22.95 21.58
+6 24.30 22.92
+7 25.64 24.27
+8 26.98 25.61
+9 22.95 22.34
+10 24.30 23.68
+11 25.64 25.02
+12 26.98 26.36
+13 22.95 24.38
+14 24.30 25.72
+15 25.64 27.07
+16 26.98 28.41
+17 22.95 21.26
+18 24.30 22.60
+19 25.64 23.94
+20 26.98 25.29
+21 22.95 24.17
+22 24.30 25.51
+23 25.64 26.85
+24 26.98 28.19
+25 22.95 21.90
+26 24.30 23.25
+27 25.64 24.59
+28 26.98 25.93
+29 22.95 22.01
+30 24.30 23.35
+31 25.64 24.70
+32 26.98 26.04
+33 22.95 23.09
+34 24.30 24.43
+35 25.64 25.77
+36 26.98 27.12
+37 22.95 26.86
+38 24.30 28.20
+39 25.64 29.55
+40 26.98 30.89
+41 22.95 21.80
+42 24.30 23.14
+43 25.64 24.48
+44 26.98 25.82
+45 22.95 22.34
+46 24.30 23.68
+47 25.64 25.02
+48 26.98 26.36
+49 22.95 22.34
+50 24.30 23.68
+51 25.64 25.02
+52 26.98 26.36
+53 22.95 22.87
+54 24.30 24.22
+55 25.64 25.56
+56 26.98 26.90
+57 22.95 23.74
+58 24.30 25.08
+59 25.64 26.42
+60 26.98 27.76
+61 22.95 21.26
+62 24.30 22.60
+63 25.64 23.94
+64 26.98 25.29
+65 20.69 19.54
+66 22.03 20.89
+67 23.37 22.23
+68 24.71 23.57
+69 20.69 20.94
+70 22.03 22.29
+71 23.37 23.63
+72 24.71 24.97
+73 20.69 21.59
+74 22.03 22.93
+75 23.37 24.28
+76 24.71 25.62
+77 20.69 22.56
+78 22.03 23.90
+79 23.37 25.25
+80 24.71 26.59
+81 20.69 20.62
+82 22.03 21.96
+83 23.37 23.31
+84 24.71 24.65
+85 20.69 19.33
+86 22.03 20.67
+87 23.37 22.01
+88 24.71 23.36
+89 20.69 20.94
+90 22.03 22.29
+91 23.37 23.63
+92 24.71 24.97
+93 20.69 21.27
+94 22.03 22.61
+95 23.37 23.95
+96 24.71 25.30
+97 20.69 19.84
+98 22.03 21.18
+99 23.37 22.52
+100 NA NA
+101 NA NA
+102 NA NA
+103 23.37 19.74
+104 24.71 21.08
+105 20.69 23.85
+106 22.03 25.20
+107 23.37 26.54
+108 24.71 27.88
+> fitted(fm2)
+ M01 M01 M01 M01 M02 M02 M02 M02 M03 M03 M03 M03 M04
+25.35 26.69 28.04 29.38 21.58 22.92 24.27 25.61 22.34 23.68 25.02 26.36 24.38
+ M04 M04 M04 M05 M05 M05 M05 M06 M06 M06 M06 M07 M07
+25.72 27.07 28.41 21.26 22.60 23.94 25.29 24.17 25.51 26.85 28.19 21.90 23.25
+ M07 M07 M08 M08 M08 M08 M09 M09 M09 M09 M10 M10 M10
+24.59 25.93 22.01 23.35 24.70 26.04 23.09 24.43 25.77 27.12 26.86 28.20 29.55
+ M10 M11 M11 M11 M11 M12 M12 M12 M12 M13 M13 M13 M13
+30.89 21.80 23.14 24.48 25.82 22.34 23.68 25.02 26.36 22.34 23.68 25.02 26.36
+ M14 M14 M14 M14 M15 M15 M15 M15 M16 M16 M16 M16 F01
+22.87 24.22 25.56 26.90 23.74 25.08 26.42 27.76 21.26 22.60 23.94 25.29 19.54
+ F01 F01 F01 F02 F02 F02 F02 F03 F03 F03 F03 F04 F04
+20.89 22.23 23.57 20.94 22.29 23.63 24.97 21.59 22.93 24.28 25.62 22.56 23.90
+ F04 F04 F05 F05 F05 F05 F06 F06 F06 F06 F07 F07 F07
+25.25 26.59 20.62 21.96 23.31 24.65 19.33 20.67 22.01 23.36 20.94 22.29 23.63
+ F07 F08 F08 F08 F08 F09 F09 F09 <NA> <NA> <NA> F10 F10
+24.97 21.27 22.61 23.95 25.30 19.84 21.18 22.52 NA NA NA 19.74 21.08
+ F11 F11 F11 F11
+23.85 25.20 26.54 27.88
+attr(,"label")
+[1] "Fitted values (mm)"
+> residuals(fm2, 0:1)
+ fixed Subject
+1 3.04531 0.648269
+2 0.70260 -1.694434
+3 3.35990 0.962862
+4 4.01719 1.620159
+5 -1.45469 -0.081112
+6 -1.79740 -0.423816
+7 -2.64010 -1.266519
+8 -0.48281 0.890777
+9 0.04531 0.664764
+10 -1.79740 -1.177940
+11 -1.64010 -1.020643
+12 0.51719 1.136654
+13 2.54531 1.117857
+14 3.20260 1.775153
+15 0.85990 -0.567550
+16 0.01719 -1.410254
+17 -2.95469 -1.257916
+18 -0.79740 0.899380
+19 -3.14010 -1.443323
+20 -0.98281 0.713973
+21 1.54531 0.333321
+22 1.20260 -0.009383
+23 1.35990 0.147914
+24 1.51719 0.305210
+25 -0.95469 0.095692
+26 -2.29740 -1.247012
+27 -1.14010 -0.089715
+28 -0.48281 0.567581
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+30 -2.79740 -1.854744
+31 -1.14010 -0.197447
+32 -1.48281 -0.540150
+33 0.04531 -0.089360
+34 -3.79740 -3.932063
+35 5.35990 5.225233
+36 -0.98281 -1.117470
+37 4.54531 0.640022
+38 3.70260 -0.202682
+39 5.35990 1.454615
+40 4.51719 0.611911
+41 0.04531 1.203424
+42 -1.29740 -0.139280
+43 -2.14010 -0.981983
+44 -1.98281 -0.824687
+45 -1.45469 -0.835236
+46 -0.79740 -0.177940
+47 -1.64010 -1.020643
+48 1.01719 1.636654
+49 -5.95469 -5.335236
+50 0.20260 0.822060
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+53 -0.45469 -0.373896
+54 1.20260 1.283401
+55 -0.14010 -0.059303
+56 -0.98281 -0.902006
+57 0.04531 -0.735752
+58 0.20260 -0.578455
+59 0.35990 -0.421158
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+61 -0.95469 0.742084
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+63 -2.14010 -0.443323
+64 -1.98281 -0.286027
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+67 -1.87187 -0.729465
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+73 -0.18647 -1.090965
+74 1.97083 1.066331
+75 1.12813 0.223628
+76 1.28542 0.380924
+77 2.81353 0.939447
+78 2.47083 0.596743
+79 1.62813 -0.245960
+80 1.78542 -0.088663
+81 0.81353 0.878622
+82 0.97083 1.035919
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+84 -1.21458 -1.149488
+85 -0.68647 0.671406
+86 -1.02917 0.328702
+87 -2.37187 -1.014001
+88 -2.21458 -0.856704
+89 0.81353 0.555426
+90 0.47083 0.212723
+91 -0.37187 -0.629980
+92 0.28542 0.027316
+93 2.31353 1.732230
+94 0.97083 0.389527
+95 0.12813 -0.453176
+96 -0.71458 -1.295880
+97 -0.68647 0.161483
+98 -1.02917 -0.181220
+99 -1.37187 -0.523924
+100 NA NA
+101 NA NA
+102 NA NA
+103 -4.37187 -0.742221
+104 -5.21458 -1.584924
+105 3.81353 0.646663
+106 2.97083 -0.196040
+107 4.62813 1.461257
+108 3.28542 0.118553
+> round(residuals(fm2), 2)
+ M01 M01 M01 M01 M02 M02 M02 M02 M03 M03 M03 M03 M04
+ 0.65 -1.69 0.96 1.62 -0.08 -0.42 -1.27 0.89 0.66 -1.18 -1.02 1.14 1.12
+ M04 M04 M04 M05 M05 M05 M05 M06 M06 M06 M06 M07 M07
+ 1.78 -0.57 -1.41 -1.26 0.90 -1.44 0.71 0.33 -0.01 0.15 0.31 0.10 -1.25
+ M07 M07 M08 M08 M08 M08 M09 M09 M09 M09 M10 M10 M10
+-0.09 0.57 1.99 -1.85 -0.20 -0.54 -0.09 -3.93 5.23 -1.12 0.64 -0.20 1.45
+ M10 M11 M11 M11 M11 M12 M12 M12 M12 M13 M13 M13 M13
+ 0.61 1.20 -0.14 -0.98 -0.82 -0.84 -0.18 -1.02 1.64 -5.34 0.82 0.98 3.14
+ M14 M14 M14 M14 M15 M15 M15 M15 M16 M16 M16 M16 F01
+-0.37 1.28 -0.06 -0.90 -0.74 -0.58 -0.42 2.24 0.74 -1.10 -0.44 -0.29 1.46
+ F01 F01 F01 F02 F02 F02 F02 F03 F03 F03 F03 F04 F04
+-0.89 -0.73 -0.57 0.06 -0.79 0.37 0.53 -1.09 1.07 0.22 0.38 0.94 0.60
+ F04 F04 F05 F05 F05 F05 F06 F06 F06 F06 F07 F07 F07
+-0.25 -0.09 0.88 1.04 -0.81 -1.15 0.67 0.33 -1.01 -0.86 0.56 0.21 -0.63
+ F07 F08 F08 F08 F08 F09 F09 F09 <NA> <NA> <NA> F10 F10
+ 0.03 1.73 0.39 -0.45 -1.30 0.16 -0.18 -0.52 NA NA NA -0.74 -1.58
+ F11 F11 F11 F11
+ 0.65 -0.20 1.46 0.12
+attr(,"label")
+[1] "Residuals (mm)"
+> summary(fm2)
+Linear mixed-effects model fit by REML
+ Data: Orthodont
+ AIC BIC logLik
+ 436.5 449.7 -213.3
+
+Random effects:
+ Formula: ~1 | Subject
+ (Intercept) Residual
+StdDev: 1.797 1.439
+
+Fixed effects: distance ~ age + Sex
+ Value Std.Error DF t-value p-value
+(Intercept) 17.584 0.8503 77 20.679 0.0000
+age 0.671 0.0636 77 10.562 0.0000
+SexFemale -2.268 0.7616 25 -2.978 0.0064
+ Correlation:
+ (Intr) age
+age -0.822
+SexFemale -0.357 -0.006
+
+Standardized Within-Group Residuals:
+ Min Q1 Med Q3 Max
+-3.70787 -0.54714 -0.05637 0.46661 3.63142
+
+Number of Observations: 105
+Number of Groups: 27
+>
+> Soybean[1:5, "Time"] <- NA
+> fm3 <- gnls(weight ~ SSlogis(Time, Asym, xmid, scal), Soybean,
++ weights = varPower(), na.action=na.exclude)
+> fitted(fm3)
+ 1 2 3 4 5 6 7 8 9 10
+ NA NA NA NA NA 7.0472 10.9577 14.0820 15.8940 16.7560
+ 11 12 13 14 15 16 17 18 19 20
+ 0.1203 0.2977 0.7259 1.7085 3.7237 7.0472 10.9577 15.8940 16.7560 0.1203
+ 21 22 23 24 25 26 27 28 29 30
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+ 31 32 33 34 35 36 37 38 39 40
+ 0.2977 0.7259 1.7085 3.7237 7.0472 10.9577 14.0820 15.8940 16.7560 0.1203
+ 41 42 43 44 45 46 47 48 49 50
+ 0.2977 0.7259 1.7085 3.7237 7.0472 10.9577 15.8940 0.1203 0.2977 0.7259
+ 51 52 53 54 55 56 57 58 59 60
+ 1.7085 3.7237 7.0472 10.9577 14.0820 15.8940 16.7560 0.1203 0.2977 0.7259
+ 61 62 63 64 65 66 67 68 69 70
+ 1.7085 3.7237 7.0472 10.9577 15.8940 16.7560 0.1203 0.2977 0.7259 1.7085
+ 71 72 73 74 75 76 77 78 79 80
+ 3.7237 7.0472 10.9577 14.0820 15.8940 16.7560 0.1203 0.2977 0.7259 1.7085
+ 81 82 83 84 85 86 87 88 89 90
+ 3.7237 7.0472 10.9577 14.0820 15.8940 16.7560 0.1203 0.2977 0.7259 1.7085
+ 91 92 93 94 95 96 97 98 99 100
+ 3.7237 7.0472 10.9577 14.0820 15.8940 16.7560 0.1203 0.2977 0.7259 1.7085
+ 101 102 103 104 105 106 107 108 109 110
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+ 281 282 283 284 285 286 287 288 289 290
+ 3.3548 10.4188 15.7056 17.1274 0.1370 0.3849 0.9316 2.1566 4.1212 8.1661
+ 291 292 293 294 295 296 297 298 299 300
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+ 301 302 303 304 305 306 307 308 309 310
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+ 311 312 313 314 315 316 317 318 319 320
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+ 321 322 323 324 325 326 327 328 329 330
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+ 331 332 333 334 335 336 337 338 339 340
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+ 341 342 343 344 345 346 347 348 349 350
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+ 351 352 353 354 355 356 357 358 359 360
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+ 361 362 363 364 365 366 367 368 369 370
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+ 371 372 373 374 375 376 377 378 379 380
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+ 381 382 383 384 385 386 387 388 389 390
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+ 391 392 393 394 395 396 397 398 399 400
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+ 401 402 403 404 405 406 407 408 409 410
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+ 411 412
+14.4182 16.8967
+attr(,"label")
+[1] "Fitted values (g)"
+> residuals(fm3)
+ 1 2 3 4 5 6 7 8
+ NA NA NA NA NA -0.817235 -2.247725 -0.732029
+ 9 10 11 12 13 14 15 16
+ 0.447744 0.994846 -0.016267 -0.028703 0.052087 0.411533 -0.793662 -1.757235
+ 17 18 19 20 21 22 23 24
+-1.457725 1.072744 0.990716 -0.012267 -0.006703 -0.058913 0.341533 0.086338
+ 25 26 27 28 29 30 31 32
+-0.917235 -0.677725 3.997971 4.288544 5.054816 -0.015267 0.001297 0.118087
+ 33 34 35 36 37 38 39 40
+-0.388467 -1.483662 -2.367235 -2.137725 1.007971 -1.233956 -2.751384 -0.019267
+ 41 42 43 44 45 46 47 48
+-0.024703 0.122087 0.241533 1.046338 -1.037235 -1.047725 3.368344 -0.014267
+ 49 50 51 52 53 54 55 56
+ 0.039297 -0.026913 -0.178467 0.146338 -1.447235 -1.527725 -0.352029 1.486844
+ 57 58 59 60 61 62 63 64
+ 3.176316 -0.018267 -0.022703 0.041087 -0.258467 0.226338 -2.107235 -1.317725
+ 65 66 67 68 69 70 71 72
+ 1.986044 0.968216 -0.017267 -0.024703 0.016087 -0.298467 -0.713662 -1.787235
+ 73 74 75 76 77 78 79 80
+-1.147725 -1.232029 2.320214 2.924016 0.010733 0.040297 -0.024913 -0.048467
+ 81 82 83 84 85 86 87 88
+ 0.526338 2.192765 1.192275 2.697971 0.031044 0.516316 0.007733 0.106297
+ 89 90 91 92 93 94 95 96
+ 0.171087 0.071533 0.186338 0.352765 -0.887725 4.777971 1.117744 10.614016
+ 97 98 99 100 101 102 103 104
+ 0.010733 0.081297 0.400087 0.731533 0.166338 -0.137235 1.532275 1.587971
+ 105 106 107 108 109 110 111 112
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+ 113 114 115 116 117 118 119 120
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+ 129 130 131 132 133 134 135 136
+ 0.368087 0.421533 0.316338 0.572765 1.522275 3.847971 -1.472256 13.515716
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+ 0.388834 -0.382788 3.700134 -0.949991 -0.026529 0.071132 0.438381 -0.011557
+ 401 402 403 404 405 406 407 408
+ 1.708834 0.637212 -2.183196 0.888339 0.009038 0.178799 0.546711 0.445110
+ 409 410 411 412
+ 2.222164 -2.034448 1.993504 0.050039
+attr(,"std")
+ [1] NA NA NA NA NA 2.05137 3.02284 3.76791 4.19054
+ [10] 4.38951 0.05745 0.12737 0.27864 0.59092 1.17142 2.05137 3.02284 4.19054
+ [19] 4.38951 0.05745 0.12737 0.27864 0.59092 1.17142 2.05137 3.02284 3.76791
+ [28] 4.19054 4.38951 0.05745 0.12737 0.27864 0.59092 1.17142 2.05137 3.02284
+ [37] 3.76791 4.19054 4.38951 0.05745 0.12737 0.27864 0.59092 1.17142 2.05137
+ [46] 3.02284 4.19054 0.05745 0.12737 0.27864 0.59092 1.17142 2.05137 3.02284
+ [55] 3.76791 4.19054 4.38951 0.05745 0.12737 0.27864 0.59092 1.17142 2.05137
+ [64] 3.02284 4.19054 4.38951 0.05745 0.12737 0.27864 0.59092 1.17142 2.05137
+ [73] 3.02284 3.76791 4.19054 4.38951 0.05745 0.12737 0.27864 0.59092 1.17142
+ [82] 2.05137 3.02284 3.76791 4.19054 4.38951 0.05745 0.12737 0.27864 0.59092
+ [91] 1.17142 2.05137 3.02284 3.76791 4.19054 4.38951 0.05745 0.12737 0.27864
+[100] 0.59092 1.17142 2.05137 3.02284 3.76791 4.19054 4.38951 0.05745 0.12737
+[109] 0.27864 0.59092 1.17142 2.05137 3.02284 3.76791 4.19054 4.38951 0.05745
+[118] 0.12737 0.27864 0.59092 1.17142 2.05137 3.02284 3.76791 4.19054 4.38951
+[127] 0.05745 0.12737 0.27864 0.59092 1.17142 2.05137 3.02284 3.76791 4.19054
+[136] 4.38951 0.05745 0.12737 0.27864 0.59092 1.17142 2.05137 3.02284 3.76791
+[145] 4.19054 4.38951 0.05745 0.12737 0.27864 0.59092 1.17142 2.05137 3.02284
+[154] 3.76791 4.19054 4.38951 0.05745 0.11374 0.24949 0.53236 1.06887 2.89187
+[163] 4.14689 4.47486 0.05745 0.11374 0.24949 0.53236 1.06887 2.89187 4.14689
+[172] 4.47486 0.05745 0.11374 0.24949 0.53236 1.06887 2.89187 4.14689 4.47486
+[181] 0.05745 0.11374 0.24949 0.53236 1.06887 2.89187 4.14689 4.47486 0.05745
+[190] 0.11374 0.24949 0.53236 1.06887 2.89187 4.14689 4.47486 0.05745 0.11374
+[199] 0.24949 0.53236 1.06887 2.89187 4.14689 4.47486 0.05745 0.11374 0.24949
+[208] 0.53236 1.06887 2.89187 4.14689 4.47486 0.05745 0.11374 0.24949 0.53236
+[217] 1.06887 2.89187 4.14689 4.47486 0.05745 0.11374 0.24949 0.53236 1.06887
+[226] 2.89187 4.14689 4.47486 0.05745 0.11374 0.24949 0.53236 1.06887 2.89187
+[235] 4.14689 4.47486 0.05745 0.11374 0.24949 0.53236 1.06887 2.89187 4.14689
+[244] 4.47486 0.05745 0.11374 0.24949 0.53236 1.06887 2.89187 4.14689 4.47486
+[253] 0.05745 0.11374 0.24949 0.53236 1.06887 2.89187 4.14689 4.47486 0.05745
+[262] 0.11374 0.24949 0.53236 1.06887 2.89187 4.14689 4.47486 0.05745 0.11374
+[271] 0.24949 0.53236 1.06887 2.89187 4.14689 4.47486 0.05745 0.11374 0.24949
+[280] 0.53236 1.06887 2.89187 4.14689 4.47486 0.06440 0.15959 0.34691 0.72506
+[289] 1.28057 2.33481 3.84680 4.42186 0.06440 0.15959 0.34691 0.72506 1.28057
+[298] 2.33481 3.84680 4.42186 0.06440 0.15959 0.34691 0.72506 1.28057 2.33481
+[307] 3.84680 4.42186 0.06440 0.15959 0.34691 0.72506 1.28057 2.33481 3.84680
+[316] 4.42186 0.06440 0.15959 0.34691 0.72506 1.28057 2.33481 3.84680 4.42186
+[325] 0.06440 0.15959 0.34691 0.72506 1.28057 2.33481 3.84680 4.42186 0.06440
+[334] 0.15959 0.34691 0.72506 1.28057 2.33481 3.84680 4.42186 0.06440 0.15959
+[343] 0.34691 0.72506 1.28057 2.33481 3.84680 4.42186 0.06440 0.15959 0.34691
+[352] 0.72506 1.28057 2.33481 3.84680 4.42186 0.06440 0.15959 0.34691 0.72506
+[361] 1.28057 2.33481 3.84680 4.42186 0.06440 0.15959 0.34691 0.72506 1.28057
+[370] 2.33481 3.84680 4.42186 0.06440 0.15959 0.34691 0.72506 1.28057 2.33481
+[379] 3.84680 4.42186 0.06440 0.15959 0.34691 0.72506 1.28057 2.33481 3.84680
+[388] 4.42186 0.06440 0.15959 0.34691 0.72506 1.28057 2.33481 3.84680 4.42186
+[397] 0.06440 0.15959 0.34691 0.72506 1.28057 2.33481 3.84680 4.42186 0.06440
+[406] 0.15959 0.34691 0.72506 1.28057 2.33481 3.84680 4.42186
+attr(,"label")
+[1] "Residuals (g)"
+> summary(fm3)
+Generalized nonlinear least squares fit
+ Model: weight ~ SSlogis(Time, Asym, xmid, scal)
+ Data: Soybean
+ AIC BIC logLik
+ 987.3 1007 -488.6
+
+Variance function:
+ Structure: Power of variance covariate
+ Formula: ~fitted(.)
+ Parameter estimates:
+ power
+0.8783
+
+Coefficients:
+ Value Std.Error t-value p-value
+Asym 17.38 0.5251 33.11 0
+xmid 51.93 0.5982 86.80 0
+scal 7.64 0.1415 53.96 0
+
+ Correlation:
+ Asym xmid
+xmid 0.788
+scal 0.488 0.842
+
+Standardized residuals:
+ Min Q1 Med Q3 Max
+-2.306636 -0.654470 -0.001905 0.501223 4.967561
+
+Residual standard error: 0.3692
+Degrees of freedom: 407 total; 404 residual
+>
diff --git a/win32/deps/library/nlme/tests/nlme.R b/win32/deps/library/nlme/tests/nlme.R
new file mode 100644
index 0000000..5c28a5b
--- /dev/null
+++ b/win32/deps/library/nlme/tests/nlme.R
@@ -0,0 +1,7 @@
+library(nlme)
+data(Loblolly)
+fm1 <- nlsList(SSasymp, Loblolly)
+fm1
+fm2 <- nlme(fm1, random = Asym ~ 1)
+fm2
+q()
diff --git a/win32/deps/library/nlme/tests/nlme.Rout.save b/win32/deps/library/nlme/tests/nlme.Rout.save
new file mode 100644
index 0000000..f388bad
--- /dev/null
+++ b/win32/deps/library/nlme/tests/nlme.Rout.save
@@ -0,0 +1,61 @@
+
+R : Copyright 2005, The R Foundation for Statistical Computing
+Version 2.2.0 Under development (unstable) (2005-05-11), ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for a HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(nlme)
+> data(Loblolly)
+> fm1 <- nlsList(SSasymp, Loblolly)
+> fm1
+Call:
+ Model: height ~ SSasymp(age, Asym, R0, lrc) | Seed
+ Data: Loblolly
+
+Coefficients:
+ Asym R0 lrc
+329 94.12820 -8.250753 -3.217578
+327 94.94058 -7.757495 -3.229325
+325 89.88487 -8.759017 -3.086219
+307 110.69919 -8.169431 -3.390345
+331 111.00287 -8.462608 -3.397574
+311 109.98575 -8.558543 -3.362518
+315 101.05622 -8.443628 -3.232825
+321 127.13400 -7.679356 -3.575331
+319 101.08748 -8.502343 -3.214021
+301 95.66688 -9.078241 -3.116381
+323 95.55627 -9.665035 -3.092266
+309 113.51390 -7.595622 -3.352815
+303 105.71792 -8.906081 -3.222957
+305 99.17191 -9.916654 -3.084841
+
+Degrees of freedom: 84 total; 42 residual
+Residual standard error: 0.7003965
+> fm2 <- nlme(fm1, random = Asym ~ 1)
+> fm2
+Nonlinear mixed-effects model fit by maximum likelihood
+ Model: height ~ SSasymp(age, Asym, R0, lrc)
+ Data: Loblolly
+ Log-likelihood: -114.743
+ Fixed: list(Asym ~ 1, R0 ~ 1, lrc ~ 1)
+ Asym R0 lrc
+101.448300 -8.627494 -3.233730
+
+Random effects:
+ Formula: Asym ~ 1 | Seed
+ Asym Residual
+StdDev: 3.650645 0.7188624
+
+Number of Observations: 84
+Number of Groups: 14
+> q()
diff --git a/win32/deps/library/nlme/tests/predict.lme.R b/win32/deps/library/nlme/tests/predict.lme.R
new file mode 100644
index 0000000..d799fab
--- /dev/null
+++ b/win32/deps/library/nlme/tests/predict.lme.R
@@ -0,0 +1,8 @@
+## from PR#8905
+library(nlme)
+fm <- lme(distance ~ poly(age, 3) + Sex, data = Orthodont, random = ~ 1)
+# data for predictions
+Newdata <- head(Orthodont)
+Newdata$Sex <- factor(Newdata$Sex, levels = levels(Orthodont$Sex))
+(pr <- predict(fm, Newdata))
+stopifnot(all.equal(c(pr), fitted(fm)[1:6]))
diff --git a/win32/deps/library/nlme/tests/ss2.rda b/win32/deps/library/nlme/tests/ss2.rda
new file mode 100644
index 0000000..46884b3
Binary files /dev/null and b/win32/deps/library/nlme/tests/ss2.rda differ
diff --git a/win32/deps/library/nlme/tests/update.R b/win32/deps/library/nlme/tests/update.R
new file mode 100644
index 0000000..0029736
--- /dev/null
+++ b/win32/deps/library/nlme/tests/update.R
@@ -0,0 +1,8 @@
+library(nlme)
+data(petrol, package = 'MASS')
+Petrol <- petrol
+Petrol[, 2:5] <- scale(Petrol[, 2:5], scale = F)
+pet3.lme <- lme(Y ~ SG + VP + V10 + EP,
+ random = ~ 1 | No, data = Petrol, method="ML")
+nform <- as.formula("Y ~ SG + VP + V10")
+update(pet3.lme, nform)
diff --git a/win32/deps/library/nlme/tests/updateLme.R b/win32/deps/library/nlme/tests/updateLme.R
new file mode 100644
index 0000000..cdec799
--- /dev/null
+++ b/win32/deps/library/nlme/tests/updateLme.R
@@ -0,0 +1,12 @@
+library(nlme)
+data(Assay)
+as1 <- lme(logDens~sample*dilut, data=Assay,
+ random=pdBlocked(list(
+ pdIdent(~1),
+ pdIdent(~sample-1),
+ pdIdent(~dilut-1))))
+
+update(as1,random=pdCompSymm(~sample-1))
+update(as1,random=pdCompSymm(~sample-1))
+update(as1,random=pdCompSymm(~sample-1))
+update(as1,random=pdCompSymm(~sample-1))
diff --git a/win32/deps/library/nlme/tests/varIdent.R b/win32/deps/library/nlme/tests/varIdent.R
new file mode 100644
index 0000000..ef5532a
--- /dev/null
+++ b/win32/deps/library/nlme/tests/varIdent.R
@@ -0,0 +1,7 @@
+## test for PR#9765
+library(nlme)
+Orth <- subset(Orthodont, Subject %in% c("M01","F01"))
+# Argument fixed in varIdent is ignored
+vf <- varIdent(form=~1|Sex,fixed=c(Female=0.5))
+vf <- Initialize(vf, data=Orth)
+stopifnot(varWeights(vf) == rep(c(1,2), each=4))
diff --git a/win32/deps/library/nnet/CITATION b/win32/deps/library/nnet/CITATION
index f6a6566..4fe884a 100644
--- a/win32/deps/library/nnet/CITATION
+++ b/win32/deps/library/nnet/CITATION
@@ -1,4 +1,4 @@
-citHeader("To cite the VR bundle (MASS, class, nnet, spatial) in publications use:")
+citHeader("To cite the nnet package in publications use:")
citEntry(entry="Book",
title = "Modern Applied Statistics with S",
diff --git a/win32/deps/library/nnet/DESCRIPTION b/win32/deps/library/nnet/DESCRIPTION
index f322cb8..674d16f 100644
--- a/win32/deps/library/nnet/DESCRIPTION
+++ b/win32/deps/library/nnet/DESCRIPTION
@@ -1,24 +1,19 @@
-Bundle: VR
-Contains: MASS class nnet spatial
-Priority: recommended
-Version: 7.2-48
-Date: 2009-07-29
-Depends: R (>= 2.5.0), grDevices, graphics, stats, utils
-Suggests: lattice, nlme, survival
-Author: S original by Venables & Ripley. R port by Brian Ripley
- <ripley stats ox ac uk>, following earlier work by Kurt Hornik
- and Albrecht Gebhardt.
-Maintainer: Brian Ripley <ripley stats ox ac uk>
-BundleDescription: Functions and datasets to support Venables and
- Ripley, 'Modern Applied Statistics with S' (4th edition).
-License: GPL-2 | GPL-3
-URL: http://www.stats.ox.ac.uk/pub/MASS4/
-Packaged: 2009-07-31 13:56:57 UTC; ripley
-Repository: CRAN
-Date/Publication: 2009-08-05 11:20:53
-Package: nnet
-Description: Software for feed-forward neural networks with a single
- hidden layer, and for multinomial log-linear models.
-Title: Feed-forward Neural Networks and Multinomial Log-Linear Models
-LazyLoad: yes
-Built: R 2.9.2; i386-pc-mingw32; 2009-08-24 13:01:08 UTC; windows
+Package: nnet
+Priority: recommended
+Version: 7.3-5
+Date: 2012-10-11
+Depends: R (>= 2.5.0), stats, utils
+Suggests: MASS
+Authors R: c(person("Brian", "Ripley", role = c("aut", "cre", "cph"),
+ email = "ripley stats ox ac uk"))
+Author: Brian Ripley <ripley stats ox ac uk>.
+Maintainer: Brian Ripley <ripley stats ox ac uk>
+Description: Software for feed-forward neural networks with a single
+ hidden layer, and for multinomial log-linear models.
+Title: Feed-forward Neural Networks and Multinomial Log-Linear Models
+License: GPL-2 | GPL-3
+URL: http://www.stats.ox.ac.uk/pub/MASS4/
+LazyLoad: yes
+Packaged: 2012-10-11 13:01:30 UTC; ripley
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:15:19 UTC; windows
+Archs: i386, x64
diff --git a/win32/deps/library/nnet/LICENCE b/win32/deps/library/nnet/LICENCE
index e694c08..14b4e51 100644
--- a/win32/deps/library/nnet/LICENCE
+++ b/win32/deps/library/nnet/LICENCE
@@ -15,16 +15,7 @@ possible individual files also carry brief copyright notices.
Copyrights
==========
-File MASS/R/profiles.R copyright (C) 1996 D. M. Bates and W. N. Venables.
- port to R by B. D. Ripley copyright (C) 1998
- corrections copyright (C) 2000,3,6 B. D. Ripley
-
-Our understanding is that the dataset files MASS/data/*.rda are not copyright.
-
-Files spatial/data/*.dat were generated or digitized by B. D. Ripley: no
-copyright is asserted.
-
-All other files are copyright (C) 1994-2007 W. N. Venables and
+All files are copyright (C) 1994-2009 W. N. Venables and
B. D. Ripley. Those parts which were distributed with the first
edition are also copyright (C) 1994 Springer-Verlag New York Inc, with
all rights assigned to W. N. Venables and B. D. Ripley.
diff --git a/win32/deps/library/nnet/Meta/Rd.rds b/win32/deps/library/nnet/Meta/Rd.rds
index e525bbf..20c6e94 100644
Binary files a/win32/deps/library/nnet/Meta/Rd.rds and b/win32/deps/library/nnet/Meta/Rd.rds differ
diff --git a/win32/deps/library/nnet/Meta/hsearch.rds b/win32/deps/library/nnet/Meta/hsearch.rds
index 950b0b3..e478146 100644
Binary files a/win32/deps/library/nnet/Meta/hsearch.rds and b/win32/deps/library/nnet/Meta/hsearch.rds differ
diff --git a/win32/deps/library/nnet/Meta/links.rds b/win32/deps/library/nnet/Meta/links.rds
new file mode 100644
index 0000000..78773e1
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diff --git a/win32/deps/library/nnet/Meta/nsInfo.rds b/win32/deps/library/nnet/Meta/nsInfo.rds
index dbcf1fb..20a951f 100644
Binary files a/win32/deps/library/nnet/Meta/nsInfo.rds and b/win32/deps/library/nnet/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/nnet/Meta/package.rds b/win32/deps/library/nnet/Meta/package.rds
index 8478121..eb1b37a 100644
Binary files a/win32/deps/library/nnet/Meta/package.rds and b/win32/deps/library/nnet/Meta/package.rds differ
diff --git a/win32/deps/library/nnet/NEWS b/win32/deps/library/nnet/NEWS
index f4af050..c4639e4 100644
--- a/win32/deps/library/nnet/NEWS
+++ b/win32/deps/library/nnet/NEWS
@@ -19,6 +19,8 @@ This file documents software changes since the third edition.
- added logLik() method for multinom.
- summary() for multinom now defaults to correlation=FALSE.
- nnet() reports on 'convergence'.
-- confint.multinom() works better with a non-default 'parm'
+- confint.multinom() works better with a non-default 'parm'.
- multinom() and nnet(softmax=TRUE) give an explicit error message for
one-category responses.
+- the loglik() method for multinom() returns an "nobs" attribute.
+
diff --git a/win32/deps/library/nnet/R/nnet b/win32/deps/library/nnet/R/nnet
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/nnet/R/nnet
+++ b/win32/deps/library/nnet/R/nnet
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/nnet/R/nnet.rdb b/win32/deps/library/nnet/R/nnet.rdb
index 4807eea..35148b1 100644
Binary files a/win32/deps/library/nnet/R/nnet.rdb and b/win32/deps/library/nnet/R/nnet.rdb differ
diff --git a/win32/deps/library/nnet/R/nnet.rdx b/win32/deps/library/nnet/R/nnet.rdx
index 82b4e09..5b47560 100644
Binary files a/win32/deps/library/nnet/R/nnet.rdx and b/win32/deps/library/nnet/R/nnet.rdx differ
diff --git a/win32/deps/library/nnet/help/aliases.rds b/win32/deps/library/nnet/help/aliases.rds
new file mode 100644
index 0000000..9f198e1
Binary files /dev/null and b/win32/deps/library/nnet/help/aliases.rds differ
diff --git a/win32/deps/library/nnet/help/nnet.rdb b/win32/deps/library/nnet/help/nnet.rdb
new file mode 100644
index 0000000..5555d18
Binary files /dev/null and b/win32/deps/library/nnet/help/nnet.rdb differ
diff --git a/win32/deps/library/nnet/help/nnet.rdx b/win32/deps/library/nnet/help/nnet.rdx
new file mode 100644
index 0000000..e96960c
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diff --git a/win32/deps/library/nnet/help/paths.rds b/win32/deps/library/nnet/help/paths.rds
new file mode 100644
index 0000000..2985a04
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diff --git a/win32/deps/library/nnet/html/00Index.html b/win32/deps/library/nnet/html/00Index.html
new file mode 100644
index 0000000..72b7dfd
--- /dev/null
+++ b/win32/deps/library/nnet/html/00Index.html
@@ -0,0 +1,78 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Feed-forward Neural Networks and Multinomial Log-Linear Models</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Feed-forward Neural Networks and Multinomial Log-Linear Models
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘nnet’ version 7.3-5</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+<li><a href="../NEWS">Package NEWS</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<table width="100%">
+<tr><td width="25%"><a href="nnet.html">add.net</a></td>
+<td>Fit Neural Networks</td></tr>
+<tr><td width="25%"><a href="multinom.html">add1.multinom</a></td>
+<td>Fit Multinomial Log-linear Models</td></tr>
+<tr><td width="25%"><a href="multinom.html">anova.multinom</a></td>
+<td>Fit Multinomial Log-linear Models</td></tr>
+<tr><td width="25%"><a href="class.ind.html">class.ind</a></td>
+<td>Generates Class Indicator Matrix from a Factor</td></tr>
+<tr><td width="25%"><a href="multinom.html">coef.multinom</a></td>
+<td>Fit Multinomial Log-linear Models</td></tr>
+<tr><td width="25%"><a href="nnet.html">coef.nnet</a></td>
+<td>Fit Neural Networks</td></tr>
+<tr><td width="25%"><a href="multinom.html">drop1.multinom</a></td>
+<td>Fit Multinomial Log-linear Models</td></tr>
+<tr><td width="25%"><a href="nnet.html">eval.nn</a></td>
+<td>Fit Neural Networks</td></tr>
+<tr><td width="25%"><a href="multinom.html">extractAIC.multinom</a></td>
+<td>Fit Multinomial Log-linear Models</td></tr>
+<tr><td width="25%"><a href="multinom.html">logLik.multinom</a></td>
+<td>Fit Multinomial Log-linear Models</td></tr>
+<tr><td width="25%"><a href="multinom.html">model.frame.multinom</a></td>
+<td>Fit Multinomial Log-linear Models</td></tr>
+<tr><td width="25%"><a href="multinom.html">multinom</a></td>
+<td>Fit Multinomial Log-linear Models</td></tr>
+<tr><td width="25%"><a href="nnet.html">nnet</a></td>
+<td>Fit Neural Networks</td></tr>
+<tr><td width="25%"><a href="nnet.html">nnet.default</a></td>
+<td>Fit Neural Networks</td></tr>
+<tr><td width="25%"><a href="nnet.html">nnet.formula</a></td>
+<td>Fit Neural Networks</td></tr>
+<tr><td width="25%"><a href="nnet.Hess.html">nnetHess</a></td>
+<td>Evaluates Hessian for a Neural Network</td></tr>
+<tr><td width="25%"><a href="nnet.html">norm.net</a></td>
+<td>Fit Neural Networks</td></tr>
+<tr><td width="25%"><a href="multinom.html">predict.multinom</a></td>
+<td>Fit Multinomial Log-linear Models</td></tr>
+<tr><td width="25%"><a href="predict.nnet.html">predict.nnet</a></td>
+<td>Predict New Examples by a Trained Neural Net</td></tr>
+<tr><td width="25%"><a href="multinom.html">print.multinom</a></td>
+<td>Fit Multinomial Log-linear Models</td></tr>
+<tr><td width="25%"><a href="nnet.html">print.nnet</a></td>
+<td>Fit Neural Networks</td></tr>
+<tr><td width="25%"><a href="multinom.html">print.summary.multinom</a></td>
+<td>Fit Multinomial Log-linear Models</td></tr>
+<tr><td width="25%"><a href="nnet.html">print.summary.nnet</a></td>
+<td>Fit Neural Networks</td></tr>
+<tr><td width="25%"><a href="multinom.html">summary.multinom</a></td>
+<td>Fit Multinomial Log-linear Models</td></tr>
+<tr><td width="25%"><a href="nnet.html">summary.nnet</a></td>
+<td>Fit Neural Networks</td></tr>
+<tr><td width="25%"><a href="multinom.html">vcov.multinom</a></td>
+<td>Fit Multinomial Log-linear Models</td></tr>
+<tr><td width="25%"><a href="which.is.max.html">which.is.max</a></td>
+<td>Find Maximum Position in Vector</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/nnet/html/R.css b/win32/deps/library/nnet/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/nnet/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/nnet/libs/i386/nnet.dll b/win32/deps/library/nnet/libs/i386/nnet.dll
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diff --git a/win32/deps/library/parallel/DESCRIPTION b/win32/deps/library/parallel/DESCRIPTION
new file mode 100644
index 0000000..8aa7624
--- /dev/null
+++ b/win32/deps/library/parallel/DESCRIPTION
@@ -0,0 +1,12 @@
+Package: parallel
+Version: 2.15.2
+Priority: base
+Title: Support for Parallel computation in R
+Author: R Core Team
+Maintainer: R Core Team <R-core r-project org>
+Description: Support for parallel computation, including by forking
+ (taken from package multicore), by sockets (taken from package snow)
+ and random-number generation.
+License: Part of R 2.15.2
+Enhances: snow
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:08:04 UTC; windows
diff --git a/win32/deps/library/parallel/INDEX b/win32/deps/library/parallel/INDEX
new file mode 100644
index 0000000..d9f5a7d
--- /dev/null
+++ b/win32/deps/library/parallel/INDEX
@@ -0,0 +1,8 @@
+clusterApply Apply Operations using Clusters
+detectCores Detect the Number of CPU Cores
+makeCluster Create a Parallel Socket Cluster
+mclapply Serial versions of 'mclapply', 'mcmapply' and
+ 'pvec'
+nextRNGStream Implementation of Pierre L'Ecuyer's RngStreams
+parallel-package Support for Parallel Computation
+splitIndices Divide Tasks for Distribution in a Cluster
diff --git a/win32/deps/library/parallel/Meta/Rd.rds b/win32/deps/library/parallel/Meta/Rd.rds
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diff --git a/win32/deps/library/parallel/Meta/vignette.rds b/win32/deps/library/parallel/Meta/vignette.rds
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diff --git a/win32/deps/library/parallel/NAMESPACE b/win32/deps/library/parallel/NAMESPACE
new file mode 100644
index 0000000..dc8806c
--- /dev/null
+++ b/win32/deps/library/parallel/NAMESPACE
@@ -0,0 +1,44 @@
+## Namespace for package 'parallel'
+useDynLib("parallel", .registration = TRUE, .fixes = "C_")
+
+export(nextRNGStream, nextRNGSubStream, clusterSetRNGStream)
+
+if(tools:::.OStype() == "unix") {
+ export(mccollect, mcparallel, mc.reset.stream)
+}
+
+export(clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
+ clusterExport, clusterMap, clusterSplit, detectCores,
+ makeCluster, makeForkCluster, makePSOCKcluster, mclapply,
+ mcmapply, parApply, parCapply, parLapply, parLapplyLB,
+ parRapply, parSapply, parSapplyLB, pvec, setDefaultCluster,
+ splitIndices, stopCluster)
+
+S3method(print, SOCKcluster)
+S3method(print, SOCKnode)
+S3method(print, SOCK0node)
+S3method("[", cluster)
+S3method(closeNode, SOCKnode)
+S3method(closeNode, SOCK0node)
+S3method(closeNode, default)
+S3method(recvData, SOCKnode)
+S3method(recvData, SOCK0node)
+S3method(recvOneData, SOCKcluster)
+S3method(sendData, SOCKnode)
+S3method(sendData, SOCK0node)
+S3method(stopCluster, default)
+
+## To support snow clusters
+S3method(closeNode, NWSnode)
+S3method(recvData, MPInode)
+S3method(recvData, NWSnode)
+S3method(recvData, PVMnode)
+S3method(recvOneData, MPIcluster)
+S3method(recvOneData, NWScluster)
+S3method(recvOneData, PVMcluster)
+S3method(sendData, MPInode)
+S3method(sendData, NWSnode)
+S3method(sendData, PVMnode)
+S3method(stopCluster, MPIcluster)
+S3method(stopCluster, NWScluster)
+S3method(stopCluster, spawnedMPIcluster)
diff --git a/win32/deps/library/parallel/R/parallel b/win32/deps/library/parallel/R/parallel
new file mode 100644
index 0000000..ac8cebe
--- /dev/null
+++ b/win32/deps/library/parallel/R/parallel
@@ -0,0 +1,9 @@
+local({
+ info <- loadingNamespaceInfo()
+ ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
+ if (is.null(ns))
+ stop("cannot find namespace environment");
+ barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
+ dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
+ lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
+})
diff --git a/win32/deps/library/parallel/R/parallel.rdb b/win32/deps/library/parallel/R/parallel.rdb
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diff --git a/win32/deps/library/parallel/R/parallel.rdx b/win32/deps/library/parallel/R/parallel.rdx
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diff --git a/win32/deps/library/parallel/doc/index.html b/win32/deps/library/parallel/doc/index.html
new file mode 100644
index 0000000..7e9613c
--- /dev/null
+++ b/win32/deps/library/parallel/doc/index.html
@@ -0,0 +1,27 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Vignettes</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="/doc/html/R.css">
+</head><body>
+<h1> Vignettes
+<img class="toplogo" src="/doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="/doc/html/index.html"><img src="/doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div>
+<h2>Vignettes from package 'parallel'</h2>
+<table width="100%">
+<col width="22%">
+<col width="2%">
+<col width="50%">
+<col width="8%">
+<col width="8%">
+<col width="8%">
+<tr><td align="right" valign="top"><a href="../../../library/parallel/doc/parallel.pdf">parallel::parallel</a></td>
+<td></td><td valign="top">Package 'parallel'</td>
+<td valign="top"><a href="../../../library/parallel/doc/parallel.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/parallel/doc/parallel.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/parallel/doc/parallel.R">R code</a></td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/parallel/doc/parallel.R b/win32/deps/library/parallel/doc/parallel.R
new file mode 100644
index 0000000..894e4bb
--- /dev/null
+++ b/win32/deps/library/parallel/doc/parallel.R
@@ -0,0 +1,224 @@
+### R code from vignette source 'parallel.Rnw'
+
+###################################################
+### code chunk number 1: parallel.Rnw:468-469 (eval = FALSE)
+###################################################
+## library(parallel)
+
+
+###################################################
+### code chunk number 2: parallel.Rnw:494-501 (eval = FALSE)
+###################################################
+## library(boot)
+## cd4.rg <- function(data, mle) MASS::mvrnorm(nrow(data), mle$m, mle$v)
+## cd4.mle <- list(m = colMeans(cd4), v = var(cd4))
+## cd4.boot <- boot(cd4, corr, R = 999, sim = "parametric",
+## ran.gen = cd4.rg, mle = cd4.mle)
+## boot.ci(cd4.boot, type = c("norm", "basic", "perc"),
+## conf = 0.9, h = atanh, hinv = tanh)
+
+
+###################################################
+### code chunk number 3: parallel.Rnw:506-516 (eval = FALSE)
+###################################################
+## cd4.rg <- function(data, mle) MASS::mvrnorm(nrow(data), mle$m, mle$v)
+## cd4.mle <- list(m = colMeans(cd4), v = var(cd4))
+## run1 <- function(...) boot(cd4, corr, R = 500, sim = "parametric",
+## ran.gen = cd4.rg, mle = cd4.mle)
+## mc <- 2 # set as appropriate for your hardware
+## ## To make this reproducible:
+## set.seed(123, "L'Ecuyer")
+## cd4.boot <- do.call(c, mclapply(seq_len(mc), run1) )
+## boot.ci(cd4.boot, type = c("norm", "basic", "perc"),
+## conf = 0.9, h = atanh, hinv = tanh)
+
+
+###################################################
+### code chunk number 4: parallel.Rnw:521-522 (eval = FALSE)
+###################################################
+## do.call(c, lapply(seq_len(mc), run1))
+
+
+###################################################
+### code chunk number 5: parallel.Rnw:526-541 (eval = FALSE)
+###################################################
+## run1 <- function(...) {
+## library(boot)
+## cd4.rg <- function(data, mle) MASS::mvrnorm(nrow(data), mle$m, mle$v)
+## cd4.mle <- list(m = colMeans(cd4), v = var(cd4))
+## boot(cd4, corr, R = 500, sim = "parametric",
+## ran.gen = cd4.rg, mle = cd4.mle)
+## }
+## cl <- makeCluster(mc)
+## ## make this reproducible
+## clusterSetRNGStream(cl, 123)
+## library(boot) # needed for c() method on master
+## cd4.boot <- do.call(c, parLapply(cl, seq_len(mc), run1) )
+## boot.ci(cd4.boot, type = c("norm", "basic", "perc"),
+## conf = 0.9, h = atanh, hinv = tanh)
+## stopCluster(cl)
+
+
+###################################################
+### code chunk number 6: parallel.Rnw:551-564 (eval = FALSE)
+###################################################
+## cl <- makeCluster(mc)
+## cd4.rg <- function(data, mle) MASS::mvrnorm(nrow(data), mle$m, mle$v)
+## cd4.mle <- list(m = colMeans(cd4), v = var(cd4))
+## clusterExport(cl, c("cd4.rg", "cd4.mle"))
+## junk <- clusterEvalQ(cl, library(boot)) # discard result
+## clusterSetRNGStream(cl, 123)
+## res <- clusterEvalQ(cl, boot(cd4, corr, R = 500,
+## sim = "parametric", ran.gen = cd4.rg, mle = cd4.mle))
+## library(boot) # needed for c() method on master
+## cd4.boot <- do.call(c, res)
+## boot.ci(cd4.boot, type = c("norm", "basic", "perc"),
+## conf = 0.9, h = atanh, hinv = tanh)
+## stopCluster(cl)
+
+
+###################################################
+### code chunk number 7: parallel.Rnw:569-583 (eval = FALSE)
+###################################################
+## R <- 999; M <- 999 ## we would like at least 999 each
+## cd4.nest <- boot(cd4, nested.corr, R=R, stype="w", t0=corr(cd4), M=M)
+## ## nested.corr is a function in package boot
+## op <- par(pty = "s", xaxs = "i", yaxs = "i")
+## qqplot((1:R)/(R+1), cd4.nest$t[, 2], pch = ".", asp = 1,
+## xlab = "nominal", ylab = "estimated")
+## abline(a = 0, b = 1, col = "grey")
+## abline(h = 0.05, col = "grey")
+## abline(h = 0.95, col = "grey")
+## par(op)
+##
+## nominal <- (1:R)/(R+1)
+## actual <- cd4.nest$t[, 2]
+## 100*nominal[c(sum(actual <= 0.05), sum(actual < 0.95))]
+
+
+###################################################
+### code chunk number 8: parallel.Rnw:588-596 (eval = FALSE)
+###################################################
+## mc <- 9
+## R <- 999; M <- 999; RR <- floor(R/mc)
+## run2 <- function(...)
+## cd4.nest <- boot(cd4, nested.corr, R=RR, stype="w", t0=corr(cd4), M=M)
+## cd4.nest <- do.call(c, mclapply(seq_len(mc), run2, mc.cores = mc) )
+## nominal <- (1:R)/(R+1)
+## actual <- cd4.nest$t[, 2]
+## 100*nominal[c(sum(actual <= 0.05), sum(actual < 0.95))]
+
+
+###################################################
+### code chunk number 9: parallel.Rnw:610-621 (eval = FALSE)
+###################################################
+## library(spatial)
+## towns <- ppinit("towns.dat")
+## tget <- function(x, r=3.5) sum(dist(cbind(x$x, x$y)) < r)
+## t0 <- tget(towns)
+## R <- 1000
+## c <- seq(0, 1, 0.1)
+## ## res[1] = 0
+## res <- c(0, sapply(c[-1], function(c)
+## mean(replicate(R, tget(Strauss(69, c=c, r=3.5))))))
+## plot(c, res, type="l", ylab="E t")
+## abline(h=t0, col="grey")
+
+
+###################################################
+### code chunk number 10: parallel.Rnw:625-634 (eval = FALSE)
+###################################################
+## run3 <- function(c) {
+## library(spatial)
+## towns <- ppinit("towns.dat") # has side effects
+## mean(replicate(R, tget(Strauss(69, c=c, r=3.5))))
+## }
+## cl <- makeCluster(10, methods = FALSE)
+## clusterExport(cl, c("R", "towns", "tget"))
+## res <- c(0, parSapply(cl, c[-1], run3)) # 10 tasks
+## stopCluster(cl)
+
+
+###################################################
+### code chunk number 11: parallel.Rnw:638-642 (eval = FALSE)
+###################################################
+## cl <- makeForkCluster(10) # fork after the variables have been set up
+## run4 <- function(c) mean(replicate(R, tget(Strauss(69, c=c, r=3.5))))
+## res <- c(0, parSapply(cl, c[-1], run4))
+## stopCluster(cl)
+
+
+###################################################
+### code chunk number 12: parallel.Rnw:645-647 (eval = FALSE)
+###################################################
+## run4 <- function(c) mean(replicate(R, tget(Strauss(69, c=c, r=3.5))))
+## res <- c(0, unlist(mclapply(c[-1], run4, mc.cores = 10)))
+
+
+###################################################
+### code chunk number 13: parallel.Rnw:678-712 (eval = FALSE)
+###################################################
+## pkgs <- "<names of packages to be installed>"
+## M <- 20 # number of parallel installs
+## M <- min(M, length(pkgs))
+## library(parallel)
+## unlink("install_log")
+## cl <- makeCluster(M, outfile = "install_log")
+## clusterExport(cl, c("tars", "fakes", "gcc")) # variables needed by do_one
+##
+## ## set up available via a call to available.packages() for
+## ## repositories containing all the packages involved and all their
+## ## dependencies.
+## DL <- utils:::.make_dependency_list(pkgs, available, recursive = TRUE)
+## DL <- lapply(DL, function(x) x[x %in% pkgs])
+## lens <- sapply(DL, length)
+## ready <- names(DL[lens == 0L])
+## done <- character() # packages already installed
+## n <- length(ready)
+## submit <- function(node, pkg)
+## parallel:::sendCall(cl[[node]], do_one, list(pkg), tag = pkg)
+## for (i in 1:min(n, M)) submit(i, ready[i])
+## DL <- DL[!names(DL) %in% ready[1:min(n, M)]]
+## av <- if(n < M) (n+1L):M else integer() # available workers
+## while(length(done) < length(pkgs)) {
+## d <- parallel:::recvOneResult(cl)
+## av <- c(av, d$node)
+## done <- c(done, d$tag)
+## OK <- unlist(lapply(DL, function(x) all(x %in% done) ))
+## if (!any(OK)) next
+## p <- names(DL)[OK]
+## m <- min(length(p), length(av)) # >= 1
+## for (i in 1:m) submit(av[i], p[i])
+## av <- av[-(1:m)]
+## DL <- DL[!names(DL) %in% p[1:m]]
+## }
+
+
+###################################################
+### code chunk number 14: parallel.Rnw:725-742 (eval = FALSE)
+###################################################
+## fn <- function(r) statistic(data, i[r, ], ...)
+## RR <- sum(R)
+## res <- if (ncpus > 1L && (have_mc || have_snow)) {
+## if (have_mc) {
+## parallel::mclapply(seq_len(RR), fn, mc.cores = ncpus)
+## } else if (have_snow) {
+## list(...) # evaluate any promises
+## if (is.null(cl)) {
+## cl <- parallel::makePSOCKcluster(rep("localhost", ncpus))
+## if(RNGkind()[1L] == "L'Ecuyer-CMRG")
+## parallel::clusterSetRNGStream(cl)
+## res <- parallel::parLapply(cl, seq_len(RR), fn)
+## parallel::stopCluster(cl)
+## res
+## } else parallel::parLapply(cl, seq_len(RR), fn)
+## }
+## } else lapply(seq_len(RR), fn)
+
+
+###################################################
+### code chunk number 15: parallel.Rnw:745-746 (eval = FALSE)
+###################################################
+## list(...) # evaluate any promises
+
+
diff --git a/win32/deps/library/parallel/doc/parallel.Rnw b/win32/deps/library/parallel/doc/parallel.Rnw
new file mode 100644
index 0000000..66a3edf
--- /dev/null
+++ b/win32/deps/library/parallel/doc/parallel.Rnw
@@ -0,0 +1,803 @@
+\documentclass[a4paper]{article}
+
+\usepackage{Rd, parskip, amsmath, enumerate}
+\usepackage[round]{natbib}
+\usepackage{hyperref}
+\usepackage{color}
+\definecolor{Blue}{rgb}{0,0,0.8}
+\hypersetup{%
+colorlinks,%
+plainpages=true,%
+linkcolor=black,%
+citecolor=black,%
+urlcolor=Blue,%
+pdfstartview={XYZ null null 1},% 100%
+pdfview={XYZ null null null},%
+pdfpagemode=UseNone,% for no outline
+pdfauthor={R Core},%
+pdftitle={Package `parallel'}% Could also have pdfusetitle
+}
+
+%\VignetteIndexEntry{Package 'parallel'}
+%\VignettePackage{parallel}
+
+
+\title{Package `parallel'}
+\author{R-core}
+
+
+\begin{document}
+
+\maketitle
+
+\section{Introduction}
+
+Package \pkg{parallel} was first included in \R{} 2.14.0. It builds
+on the work done for CRAN packages \CRANpkg{multicore} \citep{multicore}
+and \CRANpkg{snow} \citep{snow} and provides drop-in replacements for most
+of the functionality of those packages, with integrated handling of
+random-number generation.
+
+Parallelism can be done in computation at many different levels: this
+package is principally concerned with `coarse-grained
+parallelization'. At the lowest level, modern CPUs can do several
+basic operations simultaneously (e.g.{} integer and floating-point
+arithmetic), and several implementations of external BLAS libraries
+use multiple threads to do parts of basic vector/matrix operations in
+parallel. Several contributed \R{} packages use multiple threads at C
+level \emph{via} OpenMP or pthreads.
+
+This package handles running much larger chunks of computations in
+parallel. A typical example is to evaluate the same \R{} function on
+many different sets of data: often simulated data as in bootstrap
+computations (or with `data' being the random-number stream). The
+crucial point is that these chunks of computation are unrelated and do
+not need to communicate in any way. It is often the case that the
+chunks take approximately the same length of time. The basic
+computational model is
+\begin{enumerate}[(a)]
+\item Start up $M$ `worker' processes, and do any initialization
+ needed on the workers.
+\item Send any data required for each task to the workers.
+\item Split the task into $M$ roughly equally-sized chunks, and send
+ the chunks (including the \R{} code needed) to the workers.
+\item Wait for all the workers to complete their tasks, and ask them
+ for their results.
+\item Repeat steps (b--d) for any further tasks.
+\item Shut down the worker processes.
+\end{enumerate}
+Amongst the initializations which may be needed are to load packages
+and initialize the random-number stream.
+
+There are implementations of this model in the functions
+\code{mclapply} and \code{parLapply} as near-drop-in replacements for
+\code{lapply}.
+
+A slightly different model is to split the task into $M_1 > M$ chunks,
+send the first $M$ chunks to the workers, then repeatedly wait for any
+worker to complete and send it the next remaining task: see the
+section on `load balancing'.
+
+In principle the workers could be implemented by threads\footnote{only
+ `in principle' since the \R{} interpreter is not thread-safe.} or
+lightweight processes, but in the current implementation they are full
+processes. They can be created in one of three ways:
+\begin{enumerate}
+\item \emph{Via} \code{system("Rscript")} or similar to launch a new
+ process on the current machine or a similar machine with an identical
+ \R{} installation. This then needs a way to communicate between
+ master and worker processes, which is usually done \emph{via}
+ sockets.
+
+ This should be available on all \R{} platforms, although it is
+ conceivable that zealous security measures could block the
+ inter-process communication \emph{via} sockets. Users of Windows
+ and Mac OS X may expect pop-up dialog boxes from the firewall asking
+ if an \R{} process should accept incoming connections.
+
+ Following \CRANpkg{snow}, a pool of worker processes listening
+ \emph{via} sockets for commands from the master is called a
+ `cluster' of nodes.
+
+\item \emph{Via} forking. \emph{Fork} is a
+ concept\footnote{\url{http://en.wikipedia.org/wiki/Fork_(operating_system)}}
+ from POSIX operating systems, and should be available on all \R{}
+ platforms except Windows. This creates a new \R{} process by taking
+ a complete copy of the master process, including the workspace and
+ state of the random-number stream. However, the copy will (in any
+ reasonable OS) share memory pages with the master until modified so
+ forking is very fast.
+
+ The use of forking was pioneered by package \CRANpkg{multicore}.
+
+ Note that as it does share the complete process, it also shares any
+ GUI elements, for example an \R{} console and on-screen devices.
+ This can cause havoc.\footnote{Some precautions are taken on Mac OS
+ X: for example the event loops for \command{R.app} and the
+ \code{quartz} device are inhibited in the child. This information
+ is available at C level in the \code{Rboolean} variable
+ \code{R\_isForkedChild}.}
+
+ There needs to be a way to communicate between master and worker.
+ Once again there are several possibilities since master and workers
+ share memory. In \CRANpkg{multicore} the initial fork sends an \R{}
+ expression to be evaluated to the worker, and the master process
+ opens a pipe for reading that is used by the worker to return the
+ results. Both that and creating a cluster of nodes communicating
+ \emph{via} sockets are supported in package \pkg{parallel}.
+
+\item Using OS-level facilities to set up a means to send tasks to
+ other members of a group of machines. There are several ways to do
+ that, and for example package \CRANpkg{snow} can make use of MPI
+ (`message passing interface') using \R{} package \CRANpkg{Rmpi}.
+ Communication overheads can dominate computation times in this
+ approach, so it is most often used on tightly-coupled networks of
+ computers with high-speed interconnects.
+
+ CRAN packages following this approach include \CRANpkg{GridR} (using
+ Condor or Globus) and \CRANpkg{Rsge} (using SGE, currently called
+ `Oracle Grid Engine').
+
+ It will not be considered further in this vignette, but those parts
+ of \pkg{parallel} which provide \CRANpkg{snow}-like functions will
+ accept \CRANpkg{snow} clusters including MPI clusters.
+\end{enumerate}
+
+The landscape of parallel computing has changed with the advent of
+shared-memory computers with multiple (and often many) CPU cores.
+Until the late 2000's parallel computing was mainly done on clusters
+of large numbers of single- or dual-CPU computers: nowadays even
+laptops have two or four cores, and servers with 8 or more cores are
+commonplace. It is such hardware that package \pkg{parallel} is
+designed to exploit. It can also be used with several computers
+running the same version of \R{} connected by (reasonable-speed)
+ethernet: the computers need not be running the same OS.
+
+Note that all these methods of communication use
+\code{serialize}/\code{unserialize} to send \R{} objects between
+processes. This has limits (typically hundreds of millions of
+elements) which a well-designed parallelized algorithm should not
+approach.
+
+%<<>>=
+%library(parallel)
+%@
+
+\section{Numbers of CPUs/cores}
+
+In setting up parallel computations it can be helpful to have some
+idea of the number of CPUs or cores available, but this is a rather
+slippery concept. Nowadays almost all physical CPUs contain two or
+more cores that run more-or-less independently (they may share parts
+of the cache memory, and they do share access to RAM). However, on
+some processors these cores may themselves be able to run multiple
+tasks simultaneously, and some OSes (e.g.{} Windows) have the concept
+of \emph{logical} CPUs which may exceed the number of cores.
+
+Note that all a program can possibly determine is the total number of
+CPUs and/or cores available. This is not necessarily the same as the
+number of CPUs available \emph{to the current user} which may well be
+restricted by system policies on multi-user systems. Nor does it give
+much idea of a reasonable number of CPUs to use for the current task:
+the user may be running many \R{} processes simultaneously, and those
+processes may themselves be using multiple threads through a
+multi-threaded BLAS, compiled code using OpenMP or other low-level
+forms of parallelism. We have even seen instances of
+\CRANpkg{multicore}'s \code{mclapply} being called
+recursively,\footnote{\code{parallel::mclapply} detects this and runs
+ nested calls serially.} generating $2n + n^2$ processes on a machine
+estimated to have $n = 16$ cores.
+
+But in so far as it is a useful guideline, function
+\code{detectCores()} tries to determine the number of CPU cores in the
+machine on which \R{} is running: it has ways to do so on all known
+current \R{} platforms. What exactly it measures is OS-specific: we
+try where possible to report the number of physical cores available.
+
+On Windows the default is to report the number of logical CPUs. On
+modern hardware (e.g.{} Intel \emph{Core i7}) the latter may not be
+unreasonable as hyper-threading does give a significant extra
+throughput. What \code{detectCores(logical = FALSE)} reports is
+OS-version-dependent: on recent versions of Windows it reports the
+number of physical cores but on older versions it might report the
+number of physical CPU packages.
+
+\section{Analogues of apply functions}
+
+By far the most common direct applications of packages \CRANpkg{multicore}
+and \CRANpkg{snow} have been to provide parallelized replacements of
+\code{lapply}, \code{sapply}, \code{apply} and related functions.
+
+As analogues of \code{lapply} there are
+\begin{verbatim}
+parLapply(cl, x, FUN, ...)
+mclapply(X, FUN, ..., mc.cores)
+\end{verbatim}
+where \code{mclapply} is not available\footnote{except as a stub
+ which simply calls \code{lapply}.} on Windows and has further
+arguments discussed on its help page. They differ slightly in
+philosophy: \code{mclapply} sets up a pool of \code{mc.cores} workers
+just for this computation, whereas \code{parLapply} uses a less
+ephemeral pool specified by the object \code{cl} created by a call to
+\code{makeCluster} (which \emph{inter alia} specifies the size of the
+pool). So the workflow is
+\begin{verbatim}
+cl <- makeCluster(<size of pool>)
+# one or more parLapply calls
+stopCluster(cl)
+\end{verbatim}
+% we could arrange to stop a cluster when cl is gc-ed
+
+For matrices there are the rarely used \code{parApply} and
+\code{parCapply} functions, and the more commonly used
+\code{parRapply}, a parallel row \code{apply} for a matrix.
+
+\section{SNOW Clusters}
+
+The package contains a slightly revised copy of much of \CRANpkg{snow},
+and the functions it contains can also be used with clusters created
+by \CRANpkg{snow} (provided the package is on the search path).
+
+Two functions are provided to create SNOW clusters,
+\code{makePSOCKcluster} (a streamlined version of
+\code{snow::makeSOCKcluster}) and (except on Windows)
+\code{makeForkCluster}. They differ only in the way they spawn worker
+processes: \code{makePSOCKcluster} uses \code{Rscript} to launch
+further copies of \R{} (on the same host or optionally elsewhere)
+whereas \code{makeForkCluster} forks the workers on the current host
+(which thus inherit the environment of the current session).
+
+These functions would normally be called \emph{via} \code{makeCluster}.
+
+Both \code{stdout()} and \code{stderr()} of the workers are
+redirected, by default being discarded but they can be logged using
+the \code{outfile} option. Note that the previous sentence refers to
+the \emph{connections} of those names, not the C-level file handles.
+Thus properly written \R{} packages using \code{Rprintf} will have
+their output redirected, but not direct C-level output.
+
+A default cluster can be registered by a call to
+\code{setDefaultCluster()}: this is then used whenever one of the
+higher-level functions such as \code{parApply} is called without an
+explicit cluster. A little care is needed when repeatedly re-using a
+pool of workers, as their workspaces will accumulate objects from past
+usage, and packages may get added to the search path.
+
+If clusters are to be created on a host other than the current machine
+(\samp{localhost}), \code{makeCluster} may need to be be given more
+information in the shape of extra arguments.
+\begin{itemize}
+ \item If the worker machines are not set up in exactly the same way
+ as the master (for example if they are of a different
+ architecture), use \code{homogeneous = FALSE} and perhaps set
+ \code{rscript} to the full path to \command{Rscript} on the workers.
+ \item The worker machines need to know how to communicate with the
+ master: normally this can be done using the hostname found by
+ \code{Sys.info()}, but on private networks this need not be the
+ case and \code{master} may need to be supplied as a name or IP
+ address, e.g. \code{master = "192.168.1.111"}.
+ \item By default \command{ssh} is used to launch R on the workers.
+ If it is known by some other name, use e.g.{}
+ \code{rshcmd = "plink.exe"} for a Windows box using PUTTY.
+ SSH should be set
+ up to use silent authentication: setups which require a password
+ to be supplied may or may not work.
+ \item Socket communication is done over port 10187: site policies
+ might require some other port to be used, in which case set
+ argument \code{port} or environment variable \env{R\_PARALLEL\_PORT}.
+\end{itemize}
+
+\section{Forking}
+
+Except on Windows, the package contains a copy of \CRANpkg{multicore}:
+there a few names with the added prefix \code{mc}, e.g.{}
+\code{mccollect} and \code{mcparallel}. (Package \CRANpkg{multicore} used
+these names, but also the versions without the prefix which are too
+easily masked: e.g.{} package \CRANpkg{lattice} has a function
+\code{parallel}.)
+
+The low-level functions from \CRANpkg{multicore} are provided but not
+exported from the namespace.
+
+There are high-level functions \code{mclapply} and \code{pvec}: unlike
+the versions in \CRANpkg{multicore} these default to 2 cores, but this can
+be controlled by setting \code{options("mc.cores")}, and that takes
+its default from environment variable \code{MC\_CORES} when the
+package is loaded. (Setting this to \code{1} inhibits parallel
+operation: there are stub versions of these functions on Windows which
+force \code{mc.cores = 1}.)
+
+As from \R{} 2.15.0, \code{mcmapply} and \code{mcMap} provide
+analogues of \code{mapply} and \code{Map}.
+
+Note the earlier comments about using forking in a GUI environment.
+
+The parent and forked \R{} processes share the per-session temporary
+directory \code{tempdir()}, which can be a problem as a lot of code
+has assumed it is private to the \R{} process. Further, prior to \R{}
+2.14.1 it was possibly for \code{tempfile} in two processes to select
+the same filename in that temporary directory, and do it sufficiently
+simultaneously that neither saw it as being in use.
+
+The forked workers share file handles with the master: this means that
+any output from the worker should go to the same place as
+\file{stdout} and \file{stderr} of the master process. (This does not
+work reliably on all OSes: problems have also been noted when forking
+a session that is processing batch input from \file{stdin}.) Setting
+argument \code{mc.silent = TRUE} silences \file{stdout} for the child:
+\file{stderr} is not affected.
+
+Sharing file handles also impacts graphics devices as forked workers
+inherit all open graphics devices of the parent: they should not
+attempt to make use of them.
+
+
+\section{Random-number generation}
+
+Some care is needed with parallel computation using (pseudo-)random
+numbers: the processes/threads which run separate parts of the
+computation need to run independent (and preferably reproducible)
+random-number streams. One way to avoid any difficulties is (where
+possible) to do all the randomization in the master process: this is
+done where possible in package \CRANpkg{boot} (version 1.3-1 and later).
+
+When an \R{} process is started up it takes the random-number seed
+from the object \code{.Random.seed} in a saved workspace or constructs
+one from the clock time and process ID when random-number generation
+is first used (see the help on \code{RNG}). Thus worker processes
+might get the same seed because a workspace containing
+\code{.Random.seed} was restored or the random number generator has
+been used before forking: otherwise these get a non-reproducible seed
+(but with very high probability a different seed for each worker).
+
+The alternative is to set separate seeds for each worker process in
+some reproducible way from the seed in the master process. This is
+generally plenty safe enough, but there have been worries that the
+random-number streams in the workers might somehow get into step. One
+approach is to take the seeds a long way apart in the random-number
+stream: note that random numbers taken a long (fixed) distance apart
+in a single stream are not necessarily (and often are not) as
+independent as those taken a short distance apart. Yet another idea
+(as used by e.g.{} \pkg{JAGS}) is to use different random-number
+generators for each separate run/process.
+
+Package \pkg{parallel} contains an implementation of the ideas of
+\citet{lecuyer.2002}: this uses a single RNG and make \emph{streams}
+with seeds $2^{127}$ steps apart in the random number stream (which
+has period approximately $2^{191}$). This is based on the generator
+of \citet{lecuyer.1999}; the reason for choosing that
+generator\footnote{apart from the commonality of authors!} is that it
+has a fairly long period with a small seed (6 integers), and unlike
+\R{}'s default \code{"Mersenne-Twister"} RNG, it is simple to advance
+the seed by a fixed number of steps. The generator is the combination
+of two:
+\begin{eqnarray*}
+ x_n &=& 1403580 \times x_{n-2} - 810728 \times x_{n-3} \mod{(2^{32} - 209)}\\
+ y_n &=& 527612 \times y_{n-1} - 1370589 \times y_{n-3} \mod{(2^{32} - 22853)}\\
+ z_n &=& (x_n - y_n) \mod{4294967087}\\
+ u_n &=& z_n/4294967088\ \mbox{unless $z_n = 0$}
+\end{eqnarray*}
+The `seed' then consists of $(x_n, x_{n-1}, x_{n-2}, y_n, y_{n-1},
+y_{n-2})$, and the recursion for each of $x_n$ and $y_n$ can have
+pre-computed coefficients for $k$ steps ahead. For $k = 2^{127}$, the
+seed is advanced by $k$ steps by \R{} call
+\code{.Random.seed <- nextRNGStream(.Random.seed)}.
+
+% use \verb to get consistent quote mapping.
+The \citet{lecuyer.1999} generator is available in \R{} as from
+version 2.14.0 \emph{via} \verb|RNGkind("L'Ecuyer-CMRG")|. Thus using
+the ideas of \citet{lecuyer.2002} is as simple as
+\begin{verbatim}
+RNGkind("L'Ecuyer-CMRG")
+set.seed(<something>)
+## start M workers
+s <- .Random.seed
+for (i in 1:M) {
+ s <- nextRNGStream(s)
+ # send s to worker i as .Random.seed
+}
+\end{verbatim}
+and this is is implemented for SNOW clusters in function
+\code{clusterSetRNGStream}, and as part of \code{mcparallel} and
+\code{mclapply} (by default).
+
+Apart from \emph{streams} ($2^{127}$ steps apart), there is the concept of
+\emph{sub-streams} starting from seeds $2^{76}$ steps apart. Function
+\code{nextRNGSubStream} advances to the next substream.
+
+A direct \R{} interface to the (clunkier) original C implementation is
+available in CRAN package \CRANpkg{rlecuyer} \citep{rlecuyer}. That works
+with named streams, each of which have three 6-element seeds
+associated with them. This can easily be emulated in \R{} by storing
+\code{.Random.seed} at suitable times. There is another interface
+using S4 classes in package \CRANpkg{rstream} \citep{rstream}.
+
+\section{Load balancing}
+
+The introduction mentioned a different strategy which dynamically
+allocates tasks to workers: this is sometimes known as `load
+balancing' and is implemented in \code{mclapply(mc.preschedule =
+ FALSE)}, \code{clusterApplyLB} and wrappers such as
+\code{parLapplyLB} and \code{clusterMap(.scheduling = "dynamic")}.
+
+Load balancing is potentially advantageous when the tasks take quite
+dissimilar amounts of computation time, or where the nodes are of
+disparate capabilities. But some \emph{caveats} are in order:
+\begin{enumerate}[(a)]
+\item Random number streams are allocated to nodes, so if the tasks
+ involve random numbers they are likely to be non-repeatable (as the
+ allocation of tasks to nodes depends on the workloads of the nodes).
+ It would however take only slightly more work to allocate a stream to
+ each task.
+\item More care is needed is allocating the tasks. If 1000 tasks need
+ to be allocated to 10 nodes, the standard approach send chunks of
+ 100 tasks to each of the nodes. The load-balancing approach sends
+ tasks one at a time to a node, and the communication overhead may be
+ high. So it makes sense to have substantially more tasks than
+ nodes, but not by a factor of 100 (and maybe not by 10).
+\end{enumerate}
+
+\section{Portability considerations}
+
+People wanting to provide parallel facilities in their code need to
+decide how hard they want to try to be portable and efficient: no
+approach works optimally on all platforms.
+
+Using \code{mclapply} is usually the simplest approach, but will run
+serial versions of the code on Windows. This may suffice where
+parallel computation is only required for use on a single multi-core
+Unix-alike server---for \code{mclapply} can only run on a single
+shared-memory system. There is fallback to serial use when needed, by
+setting \code{mc.cores = 1}.
+
+Using \code{parLapply} will work everywhere that socket communication
+works, and can be used, for example, to harness all the CPU cores in a
+lab of machines that are not otherwise in use. But socket
+communication may be blocked even when using a single machine and is
+quite likely to be blocked between machines in a lab. There is not
+currently any fallback to serial use, nor could there easily be (as
+the workers start with a different \R{} environment from the one
+current on the master).
+
+An example of providing access to both approaches as well as serial
+code is package \CRANpkg{boot}, version \code{1.3-3} or later.
+
+\section{Extended examples}
+
+\SweaveOpts{eval=FALSE}
+<<hide=TRUE>>=
+library(parallel)
+@
+
+Probably the most common use of coarse-grained parallelization in
+statistics is to do multiple simulation runs, for example to do large
+numbers of bootstrap replicates or several runs of an MCMC simulation.
+We show an example of each.
+
+Note that some of the examples will only work serially on Windows and
+some actually are computer-intensive.
+
+\subsection{Bootstrapping}
+
+Package \CRANpkg{boot} \citep{boot} is support software for the monograph
+by \citet{Davison.Hinkley.97}. Bootstrapping is often used as an
+example of easy parallelization, and some methods of producing
+confidence intervals require many thousands of bootstrap samples.
+As from version \code{1.3-1} the package itself has parallel support
+within its main functions, but we illustrate how to use the original
+(serial) functions in parallel computations.
+
+We consider two examples using the \code{cd4} dataset from package
+\CRANpkg{boot} where the interest is in the correlation between before and
+after measurements. The first is a straight simulation, often called
+a \emph{parametric bootstrap}. The non-parallel form is
+<<>>=
+library(boot)
+cd4.rg <- function(data, mle) MASS::mvrnorm(nrow(data), mle$m, mle$v)
+cd4.mle <- list(m = colMeans(cd4), v = var(cd4))
+cd4.boot <- boot(cd4, corr, R = 999, sim = "parametric",
+ ran.gen = cd4.rg, mle = cd4.mle)
+boot.ci(cd4.boot, type = c("norm", "basic", "perc"),
+ conf = 0.9, h = atanh, hinv = tanh)
+@
+
+To do this with \code{mclapply} we need to break this into separate
+runs, and we will illustrate two runs of 500 simulations each:
+<<>>=
+cd4.rg <- function(data, mle) MASS::mvrnorm(nrow(data), mle$m, mle$v)
+cd4.mle <- list(m = colMeans(cd4), v = var(cd4))
+run1 <- function(...) boot(cd4, corr, R = 500, sim = "parametric",
+ ran.gen = cd4.rg, mle = cd4.mle)
+mc <- 2 # set as appropriate for your hardware
+## To make this reproducible:
+set.seed(123, "L'Ecuyer")
+cd4.boot <- do.call(c, mclapply(seq_len(mc), run1) )
+boot.ci(cd4.boot, type = c("norm", "basic", "perc"),
+ conf = 0.9, h = atanh, hinv = tanh)
+@
+There are many ways to program things like this: often the neatest is
+to encapsulate the computation in a function, so this is the parallel
+form of
+<<eval=FALSE>>=
+do.call(c, lapply(seq_len(mc), run1))
+@
+
+To run this with \code{parLapply} we could take a similar approach by
+<<>>=
+run1 <- function(...) {
+ library(boot)
+ cd4.rg <- function(data, mle) MASS::mvrnorm(nrow(data), mle$m, mle$v)
+ cd4.mle <- list(m = colMeans(cd4), v = var(cd4))
+ boot(cd4, corr, R = 500, sim = "parametric",
+ ran.gen = cd4.rg, mle = cd4.mle)
+}
+cl <- makeCluster(mc)
+## make this reproducible
+clusterSetRNGStream(cl, 123)
+library(boot) # needed for c() method on master
+cd4.boot <- do.call(c, parLapply(cl, seq_len(mc), run1) )
+boot.ci(cd4.boot, type = c("norm", "basic", "perc"),
+ conf = 0.9, h = atanh, hinv = tanh)
+stopCluster(cl)
+@
+Note that whereas with \code{mclapply} all the packages and objects
+we use are automatically available on the workers, this is not in
+general\footnote{it is with clusters set up with
+ \code{makeForkCluster}.} the case with the \code{parLapply}
+approach. There is often a delicate choice of where to do the
+computations: for example we could compute \code{cd4.mle} on the
+workers (as above) or on the master and send the value to the
+workers. We illustrate the latter by the following code
+<<>>=
+cl <- makeCluster(mc)
+cd4.rg <- function(data, mle) MASS::mvrnorm(nrow(data), mle$m, mle$v)
+cd4.mle <- list(m = colMeans(cd4), v = var(cd4))
+clusterExport(cl, c("cd4.rg", "cd4.mle"))
+junk <- clusterEvalQ(cl, library(boot)) # discard result
+clusterSetRNGStream(cl, 123)
+res <- clusterEvalQ(cl, boot(cd4, corr, R = 500,
+ sim = "parametric", ran.gen = cd4.rg, mle = cd4.mle))
+library(boot) # needed for c() method on master
+cd4.boot <- do.call(c, res)
+boot.ci(cd4.boot, type = c("norm", "basic", "perc"),
+ conf = 0.9, h = atanh, hinv = tanh)
+stopCluster(cl)
+@
+
+Running the double bootstrap on the same problem is far more
+computer-intensive. The standard version is
+<<fig=TRUE>>=
+R <- 999; M <- 999 ## we would like at least 999 each
+cd4.nest <- boot(cd4, nested.corr, R=R, stype="w", t0=corr(cd4), M=M)
+## nested.corr is a function in package boot
+op <- par(pty = "s", xaxs = "i", yaxs = "i")
+qqplot((1:R)/(R+1), cd4.nest$t[, 2], pch = ".", asp = 1,
+ xlab = "nominal", ylab = "estimated")
+abline(a = 0, b = 1, col = "grey")
+abline(h = 0.05, col = "grey")
+abline(h = 0.95, col = "grey")
+par(op)
+
+nominal <- (1:R)/(R+1)
+actual <- cd4.nest$t[, 2]
+100*nominal[c(sum(actual <= 0.05), sum(actual < 0.95))]
+@
+which took about 55 secs on one core of an 8-core Linux server.
+
+Using \code{mclapply} we could use
+<<eval=FALSE>>=
+mc <- 9
+R <- 999; M <- 999; RR <- floor(R/mc)
+run2 <- function(...)
+ cd4.nest <- boot(cd4, nested.corr, R=RR, stype="w", t0=corr(cd4), M=M)
+cd4.nest <- do.call(c, mclapply(seq_len(mc), run2, mc.cores = mc) )
+nominal <- (1:R)/(R+1)
+actual <- cd4.nest$t[, 2]
+100*nominal[c(sum(actual <= 0.05), sum(actual < 0.95))]
+@
+which ran in 11 secs (elapsed) using all of that server.
+
+\subsection{MCMC runs}
+
+\citet{Ripley.88} discusses the maximum-likelihood estimation of the
+Strauss process, which is done by solving a moment equation
+\[
+E_c T = t
+\]
+where $T$ is the number of $R$-close pairs and $t$ is the observed
+value, $30$ in the following example. A serial approach to the
+initial exploration might be
+<<>>=
+library(spatial)
+towns <- ppinit("towns.dat")
+tget <- function(x, r=3.5) sum(dist(cbind(x$x, x$y)) < r)
+t0 <- tget(towns)
+R <- 1000
+c <- seq(0, 1, 0.1)
+## res[1] = 0
+res <- c(0, sapply(c[-1], function(c)
+ mean(replicate(R, tget(Strauss(69, c=c, r=3.5))))))
+plot(c, res, type="l", ylab="E t")
+abline(h=t0, col="grey")
+@
+which takes about 20 seconds today, but many hours when first done
+in 1985. A parallel version might be
+<<>>=
+run3 <- function(c) {
+ library(spatial)
+ towns <- ppinit("towns.dat") # has side effects
+ mean(replicate(R, tget(Strauss(69, c=c, r=3.5))))
+}
+cl <- makeCluster(10, methods = FALSE)
+clusterExport(cl, c("R", "towns", "tget"))
+res <- c(0, parSapply(cl, c[-1], run3)) # 10 tasks
+stopCluster(cl)
+@
+which took about 4.5 secs, plus 2 secs to set up the cluster. Using a
+fork cluster (not on Windows) makes the startup much faster and setup easier:
+<<eval=FALSE>>=
+cl <- makeForkCluster(10) # fork after the variables have been set up
+run4 <- function(c) mean(replicate(R, tget(Strauss(69, c=c, r=3.5))))
+res <- c(0, parSapply(cl, c[-1], run4))
+stopCluster(cl)
+@
+As one might expect, the \code{mclapply} version is slightly simpler:
+<<eval=FALSE>>=
+run4 <- function(c) mean(replicate(R, tget(Strauss(69, c=c, r=3.5))))
+res <- c(0, unlist(mclapply(c[-1], run4, mc.cores = 10)))
+@
+If you do not have as many as 10 cores, you might want to consider
+load-balancing in a task like this as the time taken per simulation
+does vary with \code{c}. This can be done using
+\code{mclapply(mc.preschedule = FALSE)} or \code{parSapplyLB}. The
+disadvantage is that the results would not be reproducible (which does
+not matter here).
+
+\subsection{Package installation}
+
+With over 4000 \R{} packages available, it is often helpful to do a
+comprehensive install in parallel. We provide facilities to do so in
+\code{install.packages} \emph{via} a parallel \command{make}, but that
+approach may not be suitable.\footnote{A parallel \command{make} might
+ not be available, and we have seen a couple of instances of package
+ installation not working correctly when run from \command{make}.}
+Some of the tasks take many times longer than others, and we do not
+know in advance which these are.
+
+We illustrate an approach using package \pkg{parallel} which is used
+on part of the CRAN check farm. Suppose that there is a function
+\code{do\_one(pkg)} which installs a single package and then returns.
+Then the task is to run \code{do\_one} on as many of the \code{M}
+workers as possible whilst ensuring that all of the direct and
+indirect dependencies of \code{pkg} are installed before \code{pkg}
+itself. As the installation of a single package can block several
+others, we do need to allow the number of installs running
+simultaneously to vary: the following code achieves that, but needs to
+use low-level functions to do so.
+
+<<eval=FALSE>>=
+pkgs <- "<names of packages to be installed>"
+M <- 20 # number of parallel installs
+M <- min(M, length(pkgs))
+library(parallel)
+unlink("install_log")
+cl <- makeCluster(M, outfile = "install_log")
+clusterExport(cl, c("tars", "fakes", "gcc")) # variables needed by do_one
+
+## set up available via a call to available.packages() for
+## repositories containing all the packages involved and all their
+## dependencies.
+DL <- utils:::.make_dependency_list(pkgs, available, recursive = TRUE)
+DL <- lapply(DL, function(x) x[x %in% pkgs])
+lens <- sapply(DL, length)
+ready <- names(DL[lens == 0L])
+done <- character() # packages already installed
+n <- length(ready)
+submit <- function(node, pkg)
+ parallel:::sendCall(cl[[node]], do_one, list(pkg), tag = pkg)
+for (i in 1:min(n, M)) submit(i, ready[i])
+DL <- DL[!names(DL) %in% ready[1:min(n, M)]]
+av <- if(n < M) (n+1L):M else integer() # available workers
+while(length(done) < length(pkgs)) {
+ d <- parallel:::recvOneResult(cl)
+ av <- c(av, d$node)
+ done <- c(done, d$tag)
+ OK <- unlist(lapply(DL, function(x) all(x %in% done) ))
+ if (!any(OK)) next
+ p <- names(DL)[OK]
+ m <- min(length(p), length(av)) # >= 1
+ for (i in 1:m) submit(av[i], p[i])
+ av <- av[-(1:m)]
+ DL <- DL[!names(DL) %in% p[1:m]]
+}
+@
+
+\subsection{Passing \code{...}}
+
+The semantics of \code{...} do not fit well with parallel operation,
+since lazy evaluation may be delayed until the tasks have been sent to
+the workers. This is no problem in the forking approach, as the
+information needed for lazy evaluation will be present in the forked workers.
+
+For \pkg{snow}-like clusters the trick is to ensure that \code{...}
+has any promises forced whilst the information is still available.
+This is how \CRANpkg{boot} does it:
+<<eval=FALSE>>=
+ fn <- function(r) statistic(data, i[r, ], ...)
+ RR <- sum(R)
+ res <- if (ncpus > 1L && (have_mc || have_snow)) {
+ if (have_mc) {
+ parallel::mclapply(seq_len(RR), fn, mc.cores = ncpus)
+ } else if (have_snow) {
+ list(...) # evaluate any promises
+ if (is.null(cl)) {
+ cl <- parallel::makePSOCKcluster(rep("localhost", ncpus))
+ if(RNGkind()[1L] == "L'Ecuyer-CMRG")
+ parallel::clusterSetRNGStream(cl)
+ res <- parallel::parLapply(cl, seq_len(RR), fn)
+ parallel::stopCluster(cl)
+ res
+ } else parallel::parLapply(cl, seq_len(RR), fn)
+ }
+ } else lapply(seq_len(RR), fn)
+@
+Note that \code{...} is an argument to \code{boot}, and so after
+<<eval=FALSE>>=
+ list(...) # evaluate any promises
+@
+it refers to objects within the evaluation frame of \code{boot} and
+hence the environment of \code{fn} which will therefore be sent to the
+workers along with \code{fn}.
+
+\section{Differences from earlier versions}
+
+The support of parallel RNG differs from \CRANpkg{snow}: \CRANpkg{multicore}
+had no support.
+
+\subsection{Differences from multicore}
+
+\CRANpkg{multicore} had quite elaborate code to inhibit the Aqua event
+loop for \command{R.app} and the event loop for the \code{quartz}
+graphics device. This has been replaced by recording a flag in the
+\R{} executable for a child process.
+
+The version of \code{detectCores} here is biased towards the number of
+physical CPUs. This was occasioned by serious problems on Sparc Solaris
+where \CRANpkg{multicore} defaulted to a silly number of processes.
+
+Functions \code{fork} and \code{kill} have \code{mc} prefixes and are
+not exported. This avoids confusion with other packages (such as
+package \CRANpkg{fork}), and note that \code{mckill} is not as general as
+\code{tools::pskill}.
+
+Aliased functions \code{collect} and \code{parallel} are no longer provided.
+
+\subsection{Differences from snow}
+
+\CRANpkg{snow} set a timeout that exceeded the maximum value required by
+POSIX, and did not provide a means to set the timeout on the workers.
+This resulted in process interlocks on Solaris.
+
+\code{makeCluster} creates MPI or NWS clusters by calling \CRANpkg{snow}.
+
+\code{makePSOCKcluster} has been streamlined, as package \pkg{parallel} is in
+a known location on all systems, and \command{Rscript} is these days
+always available. Logging of workers is set up to append to the file,
+so multiple processes can be logged.
+
+\code{parSapply} has been brought into line with \code{sapply}.
+
+\code{clusterMap()} gains \code{SIMPLIFY} and \code{USE.NAMES}
+arguments to make it a parallel version of \code{mapply} and \code{Map}.
+
+The timing interface has not been copied.
+
+\bibliographystyle{jss}
+\bibliography{parallel}
+
+\end{document}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:
diff --git a/win32/deps/library/parallel/doc/parallel.pdf b/win32/deps/library/parallel/doc/parallel.pdf
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+parallel-package parallel-package
+clusterApply clusterApply
+clusterApplyLB clusterApply
+clusterCall clusterApply
+clusterEvalQ clusterApply
+clusterExport clusterApply
+clusterMap clusterApply
+clusterSetRNGStream RngStream
+clusterSplit clusterApply
+detectCores detectCores
+makeCluster makeCluster
+makeForkCluster makeCluster
+makePSOCKcluster makeCluster
+mc.reset.stream RngStream
+mclapply mcdummies
+mcMap mcdummies
+mcmapply mcdummies
+nextRNGStream RngStream
+nextRNGSubStream RngStream
+parallel parallel-package
+parApply clusterApply
+parCapply clusterApply
+parLapply clusterApply
+parLapplyLB clusterApply
+parRapply clusterApply
+parSapply clusterApply
+parSapplyLB clusterApply
+pvec mcdummies
+setDefaultCluster makeCluster
+splitIndices splitIndices
+stopCluster makeCluster
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+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Support for Parallel computation in R</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Support for Parallel computation in R
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘parallel’ version 2.15.2</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+<li><a href="../doc/index.html">Overview of user guides and package vignettes</a>; browse <a href="../doc">directory</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<table width="100%">
+<tr><td width="25%"><a href="parallel-package.html">parallel-package</a></td>
+<td>Support for Parallel Computation</td></tr>
+<tr><td width="25%"><a href="clusterApply.html">clusterApply</a></td>
+<td>Apply Operations using Clusters</td></tr>
+<tr><td width="25%"><a href="clusterApply.html">clusterApplyLB</a></td>
+<td>Apply Operations using Clusters</td></tr>
+<tr><td width="25%"><a href="clusterApply.html">clusterCall</a></td>
+<td>Apply Operations using Clusters</td></tr>
+<tr><td width="25%"><a href="clusterApply.html">clusterEvalQ</a></td>
+<td>Apply Operations using Clusters</td></tr>
+<tr><td width="25%"><a href="clusterApply.html">clusterExport</a></td>
+<td>Apply Operations using Clusters</td></tr>
+<tr><td width="25%"><a href="clusterApply.html">clusterMap</a></td>
+<td>Apply Operations using Clusters</td></tr>
+<tr><td width="25%"><a href="RngStream.html">clusterSetRNGStream</a></td>
+<td>Implementation of Pierre L'Ecuyer's RngStreams</td></tr>
+<tr><td width="25%"><a href="clusterApply.html">clusterSplit</a></td>
+<td>Apply Operations using Clusters</td></tr>
+<tr><td width="25%"><a href="detectCores.html">detectCores</a></td>
+<td>Detect the Number of CPU Cores</td></tr>
+<tr><td width="25%"><a href="makeCluster.html">makeCluster</a></td>
+<td>Create a Parallel Socket Cluster</td></tr>
+<tr><td width="25%"><a href="makeCluster.html">makeForkCluster</a></td>
+<td>Create a Parallel Socket Cluster</td></tr>
+<tr><td width="25%"><a href="makeCluster.html">makePSOCKcluster</a></td>
+<td>Create a Parallel Socket Cluster</td></tr>
+<tr><td width="25%"><a href="RngStream.html">mc.reset.stream</a></td>
+<td>Implementation of Pierre L'Ecuyer's RngStreams</td></tr>
+<tr><td width="25%"><a href="mcdummies.html">mclapply</a></td>
+<td>Serial versions of 'mclapply', 'mcmapply' and 'pvec'</td></tr>
+<tr><td width="25%"><a href="mcdummies.html">mcMap</a></td>
+<td>Serial versions of 'mclapply', 'mcmapply' and 'pvec'</td></tr>
+<tr><td width="25%"><a href="mcdummies.html">mcmapply</a></td>
+<td>Serial versions of 'mclapply', 'mcmapply' and 'pvec'</td></tr>
+<tr><td width="25%"><a href="RngStream.html">nextRNGStream</a></td>
+<td>Implementation of Pierre L'Ecuyer's RngStreams</td></tr>
+<tr><td width="25%"><a href="RngStream.html">nextRNGSubStream</a></td>
+<td>Implementation of Pierre L'Ecuyer's RngStreams</td></tr>
+<tr><td width="25%"><a href="parallel-package.html">parallel</a></td>
+<td>Support for Parallel Computation</td></tr>
+<tr><td width="25%"><a href="clusterApply.html">parApply</a></td>
+<td>Apply Operations using Clusters</td></tr>
+<tr><td width="25%"><a href="clusterApply.html">parCapply</a></td>
+<td>Apply Operations using Clusters</td></tr>
+<tr><td width="25%"><a href="clusterApply.html">parLapply</a></td>
+<td>Apply Operations using Clusters</td></tr>
+<tr><td width="25%"><a href="clusterApply.html">parLapplyLB</a></td>
+<td>Apply Operations using Clusters</td></tr>
+<tr><td width="25%"><a href="clusterApply.html">parRapply</a></td>
+<td>Apply Operations using Clusters</td></tr>
+<tr><td width="25%"><a href="clusterApply.html">parSapply</a></td>
+<td>Apply Operations using Clusters</td></tr>
+<tr><td width="25%"><a href="clusterApply.html">parSapplyLB</a></td>
+<td>Apply Operations using Clusters</td></tr>
+<tr><td width="25%"><a href="mcdummies.html">pvec</a></td>
+<td>Serial versions of 'mclapply', 'mcmapply' and 'pvec'</td></tr>
+<tr><td width="25%"><a href="makeCluster.html">setDefaultCluster</a></td>
+<td>Create a Parallel Socket Cluster</td></tr>
+<tr><td width="25%"><a href="splitIndices.html">splitIndices</a></td>
+<td>Divide Tasks for Distribution in a Cluster</td></tr>
+<tr><td width="25%"><a href="makeCluster.html">stopCluster</a></td>
+<td>Create a Parallel Socket Cluster</td></tr>
+</table>
+</body></html>
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+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
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diff --git a/win32/deps/library/parallel/po/zh_CN/LC_MESSAGES/R-parallel.mo b/win32/deps/library/parallel/po/zh_CN/LC_MESSAGES/R-parallel.mo
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diff --git a/win32/deps/library/parallel/po/zh_CN/LC_MESSAGES/parallel.mo b/win32/deps/library/parallel/po/zh_CN/LC_MESSAGES/parallel.mo
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diff --git a/win32/deps/library/parallel/tests/Master.R b/win32/deps/library/parallel/tests/Master.R
new file mode 100644
index 0000000..0c4f524
--- /dev/null
+++ b/win32/deps/library/parallel/tests/Master.R
@@ -0,0 +1,36 @@
+
+runone <- function(f)
+{
+ message(" Running ", sQuote(f))
+ infile <- paste(f, "RR", sep = ".")
+ outfile <- paste(f, "Rout", sep = ".")
+ cmd <- paste(shQuote(file.path(R.home("bin"), "R")),
+ "CMD BATCH --vanilla",
+ shQuote(infile), shQuote(outfile))
+ res <- system(cmd)
+ if (res) {
+ cat(readLines(outfile), sep="\n")
+ file.rename(outfile, paste(outfile, "fail", sep="."))
+ return(1L)
+ }
+ savefile <- paste(outfile, "save", sep = "." )
+ if (file.exists(savefile)) {
+ message(" Comparing ", sQuote(outfile), " to ",
+ sQuote(savefile), " ...", appendLF = FALSE)
+ res <- tools:::Rdiff(outfile, savefile, TRUE)
+ if (!res) message(" OK")
+ }
+ 0L
+}
+
+res <- 0L
+if(.Platform$OS.type == "unix") {
+ res <- res + runone("multicore1")
+ res <- res + runone("multicore2")
+ res <- res + runone("multicore3")
+}
+res <- res + runone("snow1")
+res <- res + runone("snow2")
+
+if(res) stop(gettextf("%d tests failed", res))
+
diff --git a/win32/deps/library/parallel/tests/multicore1.RR b/win32/deps/library/parallel/tests/multicore1.RR
new file mode 100644
index 0000000..9b614f0
--- /dev/null
+++ b/win32/deps/library/parallel/tests/multicore1.RR
@@ -0,0 +1,10 @@
+library(parallel)
+
+p <- parallel:::mcfork()
+if (inherits(p, "masterProcess")) {
+ cat("I'm a child! ", Sys.getpid(), "\n")
+ parallel:::mcexit(,"I was a child")
+}
+cat("I'm the master\n")
+unserialize(parallel:::readChildren(1.5))
+## don't do anything here as stdin is eaten.
diff --git a/win32/deps/library/parallel/tests/multicore2.RR b/win32/deps/library/parallel/tests/multicore2.RR
new file mode 100644
index 0000000..6a5c977
--- /dev/null
+++ b/win32/deps/library/parallel/tests/multicore2.RR
@@ -0,0 +1,14 @@
+library(parallel)
+
+library(boot)
+cd4.rg <- function(data, mle) MASS::mvrnorm(nrow(data), mle$m, mle$v)
+cd4.mle <- list(m = colMeans(cd4), v = var(cd4))
+mc <- getOption("mc.cores", 2)
+run1 <- function(...) boot(cd4, corr, R = 500, sim = "parametric",
+ ran.gen = cd4.rg, mle = cd4.mle)
+## To make this reproducible:
+set.seed(123, "L'Ecuyer"); mc.reset.stream()
+res <- mclapply(seq_len(mc), run1)
+cd4.boot <- do.call(c, res)
+boot.ci(cd4.boot, type = c("norm", "basic", "perc"),
+ conf = 0.9, h = atanh, hinv = tanh)
diff --git a/win32/deps/library/parallel/tests/multicore2.Rout.save b/win32/deps/library/parallel/tests/multicore2.Rout.save
new file mode 100644
index 0000000..83faebe
--- /dev/null
+++ b/win32/deps/library/parallel/tests/multicore2.Rout.save
@@ -0,0 +1,49 @@
+
+R Under development (unstable) (2011-08-04 r56618)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: i386-apple-darwin9.8.0/i386 (32-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+ Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(parallel)
+>
+> library(boot)
+> cd4.rg <- function(data, mle) MASS::mvrnorm(nrow(data), mle$m, mle$v)
+> cd4.mle <- list(m = colMeans(cd4), v = var(cd4))
+> mc <- getOption("mc.cores", 2)
+> run1 <- function(...) boot(cd4, corr, R = 500, sim = "parametric",
++ ran.gen = cd4.rg, mle = cd4.mle)
+> ## To make this reproducible:
+> set.seed(123, "L'Ecuyer"); mc.reset.stream()
+> res <- mclapply(seq_len(mc), run1)
+> cd4.boot <- do.call(c, res)
+> boot.ci(cd4.boot, type = c("norm", "basic", "perc"),
++ conf = 0.9, h = atanh, hinv = tanh)
+BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS
+Based on 1000 bootstrap replicates
+
+CALL :
+boot.ci(boot.out = cd4.boot, conf = 0.9, type = c("norm", "basic",
+ "perc"), h = atanh, hinv = tanh)
+
+Intervals :
+Level Normal Basic Percentile
+90% ( 0.4610, 0.8577 ) ( 0.4617, 0.8577 ) ( 0.4959, 0.8690 )
+Calculations on Transformed Scale; Intervals on Original Scale
+>
+> proc.time()
+ user system elapsed
+ 1.838 0.278 9.055
diff --git a/win32/deps/library/parallel/tests/multicore3.RR b/win32/deps/library/parallel/tests/multicore3.RR
new file mode 100644
index 0000000..b6faf1a
--- /dev/null
+++ b/win32/deps/library/parallel/tests/multicore3.RR
@@ -0,0 +1,7 @@
+library(parallel)
+
+simplify2array(mclapply(rep(4, 5), rnorm))
+# use the same random numbers for all values
+set.seed(1)
+simplify2array(mclapply(rep(4, 5), rnorm, mc.preschedule = FALSE,
+ mc.set.seed = FALSE))
diff --git a/win32/deps/library/parallel/tests/snow1.RR b/win32/deps/library/parallel/tests/snow1.RR
new file mode 100644
index 0000000..bd37abc
--- /dev/null
+++ b/win32/deps/library/parallel/tests/snow1.RR
@@ -0,0 +1,40 @@
+## not necessarily reproducible examples.
+
+library(parallel)
+
+
+cl <- makeCluster(getOption("cl.cores", 2))
+
+clusterApply(cl, 1:2, get("+"), 3)
+xx <- 1
+clusterExport(cl, "xx")
+clusterCall(cl, function(y) xx + y, 2)
+
+## Use clusterMap like an mapply example
+clusterMap(cl, function(x,y) seq_len(x) + y,
+ c(a = 1, b = 2, c = 3), c(A = 10, B = 0, C = -10))
+
+
+parSapply(cl, 1:20, get("+"), 3)
+
+## PR14898
+parSapply(cl, 1, identity)
+
+
+## A bootstrapping example, which can be done in many ways:
+clusterEvalQ(cl, {
+ ## set up each worker. Could also use clusterExport()
+ library(boot)
+ cd4.rg <- function(data, mle) MASS::mvrnorm(nrow(data), mle$m, mle$v)
+ cd4.mle <- list(m = colMeans(cd4), v = var(cd4))
+ NULL
+})
+res <- clusterEvalQ(cl, boot(cd4, corr, R = 100,
+ sim = "parametric", ran.gen = cd4.rg, mle = cd4.mle))
+library(boot)
+cd4.boot <- do.call(c, res)
+boot.ci(cd4.boot, type = c("norm", "basic", "perc"),
+ conf = 0.9, h = atanh, hinv = tanh)
+stopCluster(cl)
+
+
diff --git a/win32/deps/library/parallel/tests/snow2.RR b/win32/deps/library/parallel/tests/snow2.RR
new file mode 100644
index 0000000..f3d60a3
--- /dev/null
+++ b/win32/deps/library/parallel/tests/snow2.RR
@@ -0,0 +1,19 @@
+## reproducible examples.
+
+library(parallel)
+
+library(boot)
+run1 <- function(...) {
+ library(boot)
+ cd4.rg <- function(data, mle) MASS::mvrnorm(nrow(data), mle$m, mle$v)
+ cd4.mle <- list(m = colMeans(cd4), v = var(cd4))
+ boot(cd4, corr, R = 500, sim = "parametric",
+ ran.gen = cd4.rg, mle = cd4.mle)
+}
+cl <- makeCluster(mc <- 2)
+clusterSetRNGStream(cl, 123)
+cd4.boot <- do.call(c, parLapply(cl, seq_len(mc), run1))
+boot.ci(cd4.boot, type = c("norm", "basic", "perc"),
+ conf = 0.9, h = atanh, hinv = tanh)
+stopCluster(cl)
+
diff --git a/win32/deps/library/parallel/tests/snow2.Rout.save b/win32/deps/library/parallel/tests/snow2.Rout.save
new file mode 100644
index 0000000..3cf15bb
--- /dev/null
+++ b/win32/deps/library/parallel/tests/snow2.Rout.save
@@ -0,0 +1,54 @@
+
+R Under development (unstable) (2011-08-04 r56618)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: i386-apple-darwin9.8.0/i386 (32-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+ Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> ## reproducible examples.
+>
+> library(parallel)
+>
+> library(boot)
+> run1 <- function(...) {
++ library(boot)
++ cd4.rg <- function(data, mle) MASS::mvrnorm(nrow(data), mle$m, mle$v)
++ cd4.mle <- list(m = colMeans(cd4), v = var(cd4))
++ boot(cd4, corr, R = 500, sim = "parametric",
++ ran.gen = cd4.rg, mle = cd4.mle)
++ }
+> cl <- makeCluster(mc <- 2)
+> clusterSetRNGStream(cl, 123)
+> cd4.boot <- do.call(c, parLapply(cl, seq_len(mc), run1))
+> boot.ci(cd4.boot, type = c("norm", "basic", "perc"),
++ conf = 0.9, h = atanh, hinv = tanh)
+BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS
+Based on 1000 bootstrap replicates
+
+CALL :
+boot.ci(boot.out = cd4.boot, conf = 0.9, type = c("norm", "basic",
+ "perc"), h = atanh, hinv = tanh)
+
+Intervals :
+Level Normal Basic Percentile
+90% ( 0.4631, 0.8583 ) ( 0.4679, 0.8578 ) ( 0.4957, 0.8671 )
+Calculations on Transformed Scale; Intervals on Original Scale
+> stopCluster(cl)
+>
+>
+> proc.time()
+ user system elapsed
+ 1.092 0.164 4.819
diff --git a/win32/deps/library/rpart/DESCRIPTION b/win32/deps/library/rpart/DESCRIPTION
index 7e0d394..1347cf1 100644
--- a/win32/deps/library/rpart/DESCRIPTION
+++ b/win32/deps/library/rpart/DESCRIPTION
@@ -1,21 +1,26 @@
-Package: rpart
-Priority: recommended
-Version: 3.1-45
-Date: 2009-07-28
-DateNote: March 2002 version of rpart
-Author: Terry M Therneau and Beth Atkinson <atkinson mayo edu>. R port
- by Brian Ripley.
-Maintainer: Brian Ripley <ripley stats ox ac uk>
-Description: Recursive partitioning and regression trees
-Title: Recursive Partitioning
-Depends: R (>= 2.7.0), graphics, stats, grDevices
-Suggests: survival
-License: GPL-2 | file LICENCE
-LazyLoad: yes
-LazyData: yes
-URL:
- http://mayoresearch.mayo.edu/mayo/research/biostat/splusfunctions.cfm
-Packaged: 2009-07-28 12:36:05 UTC; ripley
-Repository: CRAN
-Date/Publication: 2009-08-05 11:22:00
-Built: R 2.9.2; i386-pc-mingw32; 2009-08-24 13:10:55 UTC; windows
+Package: rpart
+Priority: recommended
+Version: 3.1-55
+Date: 2012-10-07
+DateNote: March 2002 version of rpart
+Authors R: c(person("Terry", "Therneau", role = "aut", email =
+ "therneau mayo edu"), person("Beth", "Atkinson", role = "aut",
+ email = "atkinson mayo edu"), person("Brian", "Ripley", role =
+ c("aut", "trl", "cre"), email = "ripley stats ox ac uk",
+ comment = "author of R port"))
+Description: Recursive partitioning and regression trees
+Title: Recursive Partitioning
+Depends: R (>= 2.14.0), graphics, stats, grDevices
+Suggests: survival
+License: GPL-2 | GPL-3
+LazyData: yes
+Author: Terry Therneau [aut], Beth Atkinson [aut], Brian Ripley [aut,
+ trl, cre] (author of R port)
+Maintainer: Brian Ripley <ripley stats ox ac uk>
+Note: Maintainers are not available to give advice on using a package
+ they did not author.
+Packaged: 2012-10-12 06:33:35 UTC; ripley
+Repository: CRAN
+Date/Publication: 2012-10-07 09:32:08
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:15:07 UTC; windows
+Archs: i386, x64
diff --git a/win32/deps/library/rpart/Meta/Rd.rds b/win32/deps/library/rpart/Meta/Rd.rds
index b750851..478c900 100644
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index ae74c90..be68bb7 100644
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index 188382f..8ff041e 100644
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diff --git a/win32/deps/library/rpart/Meta/links.rds b/win32/deps/library/rpart/Meta/links.rds
new file mode 100644
index 0000000..56e9723
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diff --git a/win32/deps/library/rpart/Meta/nsInfo.rds b/win32/deps/library/rpart/Meta/nsInfo.rds
index cedaff5..554fdc4 100644
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diff --git a/win32/deps/library/rpart/Meta/package.rds b/win32/deps/library/rpart/Meta/package.rds
index dfa68b7..4994dc9 100644
Binary files a/win32/deps/library/rpart/Meta/package.rds and b/win32/deps/library/rpart/Meta/package.rds differ
diff --git a/win32/deps/library/rpart/R/rpart b/win32/deps/library/rpart/R/rpart
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/rpart/R/rpart
+++ b/win32/deps/library/rpart/R/rpart
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/rpart/R/rpart.rdb b/win32/deps/library/rpart/R/rpart.rdb
index 0c6a850..28b47ac 100644
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diff --git a/win32/deps/library/rpart/R/rpart.rdx b/win32/deps/library/rpart/R/rpart.rdx
index 7878a16..fae7a3a 100644
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diff --git a/win32/deps/library/rpart/data/Rdata.rdb b/win32/deps/library/rpart/data/Rdata.rdb
index 927541c..495c942 100644
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diff --git a/win32/deps/library/rpart/data/Rdata.rds b/win32/deps/library/rpart/data/Rdata.rds
index 035fba8..1ac116c 100644
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diff --git a/win32/deps/library/rpart/data/Rdata.rdx b/win32/deps/library/rpart/data/Rdata.rdx
index a1484e7..facb6ce 100644
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diff --git a/win32/deps/library/rpart/help/AnIndex b/win32/deps/library/rpart/help/AnIndex
index c8d9883..07f60c2 100644
--- a/win32/deps/library/rpart/help/AnIndex
+++ b/win32/deps/library/rpart/help/AnIndex
@@ -21,7 +21,6 @@ rpart rpart
rpart.control rpart.control
rpart.matrix rpart-internal
rpart.object rpart.object
-rpartcallback rpart
rpconvert rpconvert
rsq.rpart rsq.rpart
snip.rpart snip.rpart
diff --git a/win32/deps/library/rpart/help/aliases.rds b/win32/deps/library/rpart/help/aliases.rds
new file mode 100644
index 0000000..b527b56
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diff --git a/win32/deps/library/rpart/help/paths.rds b/win32/deps/library/rpart/help/paths.rds
new file mode 100644
index 0000000..ac2cfd7
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diff --git a/win32/deps/library/rpart/help/rpart.rdb b/win32/deps/library/rpart/help/rpart.rdb
new file mode 100644
index 0000000..870460a
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diff --git a/win32/deps/library/rpart/help/rpart.rdx b/win32/deps/library/rpart/help/rpart.rdx
new file mode 100644
index 0000000..598f7f3
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diff --git a/win32/deps/library/rpart/html/00Index.html b/win32/deps/library/rpart/html/00Index.html
new file mode 100644
index 0000000..72a23e6
--- /dev/null
+++ b/win32/deps/library/rpart/html/00Index.html
@@ -0,0 +1,79 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Recursive Partitioning</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Recursive Partitioning
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘rpart’ version 3.1-55</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<table width="100%">
+<tr><td width="25%"><a href="car.test.frame.html">car.test.frame</a></td>
+<td>Automobile Data from 'Consumer Reports' 1990</td></tr>
+<tr><td width="25%"><a href="cu.summary.html">cu.summary</a></td>
+<td>Automobile Data from 'Consumer Reports' 1990</td></tr>
+<tr><td width="25%"><a href="kyphosis.html">kyphosis</a></td>
+<td>Data on Children who have had Corrective Spinal Surgery</td></tr>
+<tr><td width="25%"><a href="labels.rpart.html">labels.rpart</a></td>
+<td>Create Split Labels For an Rpart Object</td></tr>
+<tr><td width="25%"><a href="meanvar.rpart.html">meanvar</a></td>
+<td>Mean-Variance Plot for an Rpart Object</td></tr>
+<tr><td width="25%"><a href="meanvar.rpart.html">meanvar.rpart</a></td>
+<td>Mean-Variance Plot for an Rpart Object</td></tr>
+<tr><td width="25%"><a href="na.rpart.html">na.rpart</a></td>
+<td>Handles Missing Values in an Rpart Object</td></tr>
+<tr><td width="25%"><a href="path.rpart.html">path.rpart</a></td>
+<td>Follow Paths to Selected Nodes of an Rpart Object</td></tr>
+<tr><td width="25%"><a href="plot.rpart.html">plot.rpart</a></td>
+<td>Plot an Rpart Object</td></tr>
+<tr><td width="25%"><a href="plotcp.html">plotcp</a></td>
+<td>Plot a Complexity Parameter Table for an Rpart Fit</td></tr>
+<tr><td width="25%"><a href="post.rpart.html">post</a></td>
+<td>PostScript Presentation Plot of an Rpart Object</td></tr>
+<tr><td width="25%"><a href="post.rpart.html">post.rpart</a></td>
+<td>PostScript Presentation Plot of an Rpart Object</td></tr>
+<tr><td width="25%"><a href="predict.rpart.html">predict.rpart</a></td>
+<td>Predictions from a Fitted Rpart Object</td></tr>
+<tr><td width="25%"><a href="print.rpart.html">print.rpart</a></td>
+<td>Print an Rpart Object</td></tr>
+<tr><td width="25%"><a href="printcp.html">printcp</a></td>
+<td>Displays CP table for Fitted Rpart Object</td></tr>
+<tr><td width="25%"><a href="prune.rpart.html">prune</a></td>
+<td>Cost-complexity Pruning of an Rpart Object</td></tr>
+<tr><td width="25%"><a href="prune.rpart.html">prune.rpart</a></td>
+<td>Cost-complexity Pruning of an Rpart Object</td></tr>
+<tr><td width="25%"><a href="residuals.rpart.html">residuals.rpart</a></td>
+<td>Residuals From a Fitted Rpart Object</td></tr>
+<tr><td width="25%"><a href="rpart.html">rpart</a></td>
+<td>Recursive Partitioning and Regression Trees</td></tr>
+<tr><td width="25%"><a href="rpart.control.html">rpart.control</a></td>
+<td>Control for Rpart Models</td></tr>
+<tr><td width="25%"><a href="rpart.object.html">rpart.object</a></td>
+<td>Recursive Partitioning and Regression Trees Object</td></tr>
+<tr><td width="25%"><a href="rpconvert.html">rpconvert</a></td>
+<td>Update an rpart object</td></tr>
+<tr><td width="25%"><a href="rsq.rpart.html">rsq.rpart</a></td>
+<td>Plots the Approximate R-Square for the Different Splits</td></tr>
+<tr><td width="25%"><a href="snip.rpart.html">snip.rpart</a></td>
+<td>Snip Subtrees of an Rpart Object</td></tr>
+<tr><td width="25%"><a href="solder.html">solder</a></td>
+<td>Soldering of Components on Printed-Circuit Boards</td></tr>
+<tr><td width="25%"><a href="summary.rpart.html">summary.rpart</a></td>
+<td>Summarize a Fitted Rpart Object</td></tr>
+<tr><td width="25%"><a href="text.rpart.html">text.rpart</a></td>
+<td>Place Text on a Dendrogram</td></tr>
+<tr><td width="25%"><a href="xpred.rpart.html">xpred.rpart</a></td>
+<td>Return Cross-Validated Predictions</td></tr>
+</table>
+</body></html>
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+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
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@@ -0,0 +1,971 @@
+
+R version 2.13.0 Under development (unstable) (2010-10-15 r53335)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: i386-apple-darwin9.8.0/i386 (32-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+ Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> pkgname <- "rpart"
+> source(file.path(R.home("share"), "R", "examples-header.R"))
+> options(warn = 1)
+> library('rpart')
+>
+> assign(".oldSearch", search(), pos = 'CheckExEnv')
+> cleanEx()
+> nameEx("car.test.frame")
+> ### * car.test.frame
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: car.test.frame
+> ### Title: Automobile Data from 'Consumer Reports' 1990
+> ### Aliases: car.test.frame
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> z.auto <- rpart(Mileage ~ Weight, car.test.frame)
+> summary(z.auto)
+Call:
+rpart(formula = Mileage ~ Weight, data = car.test.frame)
+ n= 60
+
+ CP nsplit rel error xerror xstd
+1 0.59534912 0 1.0000000 1.0319924 0.17931937
+2 0.13452819 1 0.4046509 0.4875114 0.07613003
+3 0.01282843 2 0.2701227 0.3802248 0.06685452
+4 0.01000000 3 0.2572943 0.3945980 0.06605572
+
+Node number 1: 60 observations, complexity param=0.5953491
+ mean=24.58333, MSE=22.57639
+ left son=2 (45 obs) right son=3 (15 obs)
+ Primary splits:
+ Weight < 2567.5 to the right, improve=0.5953491, (0 missing)
+
+Node number 2: 45 observations, complexity param=0.1345282
+ mean=22.46667, MSE=8.026667
+ left son=4 (22 obs) right son=5 (23 obs)
+ Primary splits:
+ Weight < 3087.5 to the right, improve=0.5045118, (0 missing)
+
+Node number 3: 15 observations
+ mean=30.93333, MSE=12.46222
+
+Node number 4: 22 observations
+ mean=20.40909, MSE=2.78719
+
+Node number 5: 23 observations, complexity param=0.01282843
+ mean=24.43478, MSE=5.115312
+ left son=10 (15 obs) right son=11 (8 obs)
+ Primary splits:
+ Weight < 2747.5 to the right, improve=0.1476996, (0 missing)
+
+Node number 10: 15 observations
+ mean=23.8, MSE=4.026667
+
+Node number 11: 8 observations
+ mean=25.625, MSE=4.984375
+
+>
+>
+>
+> cleanEx()
+> nameEx("cu.summary")
+> ### * cu.summary
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: cu.summary
+> ### Title: Automobile Data from 'Consumer Reports' 1990
+> ### Aliases: cu.summary
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> fit <- rpart(Price ~ Mileage + Type + Country, cu.summary)
+> plot(fit, compress=TRUE)
+> text(fit, use.n=TRUE)
+>
+>
+>
+> cleanEx()
+> nameEx("kyphosis")
+> ### * kyphosis
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: kyphosis
+> ### Title: Data on Children who have had Corrective Spinal Surgery
+> ### Aliases: kyphosis
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> fit <- rpart(Kyphosis ~ Age + Number + Start, data=kyphosis)
+> fit2 <- rpart(Kyphosis ~ Age + Number + Start, data=kyphosis,
++ parms=list(prior=c(.65,.35), split='information'))
+> fit3 <- rpart(Kyphosis ~ Age + Number + Start, data=kyphosis,
++ control=rpart.control(cp=.05))
+> par(mfrow=c(1,2))
+> plot(fit)
+> text(fit, use.n=TRUE)
+> plot(fit2)
+> text(fit2, use.n=TRUE)
+>
+>
+>
+> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
+> cleanEx()
+> nameEx("meanvar.rpart")
+> ### * meanvar.rpart
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: meanvar.rpart
+> ### Title: Mean-Variance Plot for an Rpart Object
+> ### Aliases: meanvar meanvar.rpart
+> ### Keywords: tree
+>
+> ### ** Examples
+>
+> z.auto <- rpart(Mileage ~ Weight, car.test.frame)
+> meanvar(z.auto, log='xy')
+>
+>
+>
+> cleanEx()
+> nameEx("path.rpart")
+> ### * path.rpart
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: path.rpart
+> ### Title: Follow Paths to Selected Nodes of an Rpart Object
+> ### Aliases: path.rpart
+> ### Keywords: tree
+>
+> ### ** Examples
+>
+> fit <- rpart(Kyphosis ~ Age + Number + Start, data=kyphosis)
+> summary(fit)
+Call:
+rpart(formula = Kyphosis ~ Age + Number + Start, data = kyphosis)
+ n= 81
+
+ CP nsplit rel error xerror xstd
+1 0.17647059 0 1.0000000 1.000000 0.2155872
+2 0.01960784 1 0.8235294 1.000000 0.2155872
+3 0.01000000 4 0.7647059 1.058824 0.2200975
+
+Node number 1: 81 observations, complexity param=0.1764706
+ predicted class=absent expected loss=0.2098765
+ class counts: 64 17
+ probabilities: 0.790 0.210
+ left son=2 (62 obs) right son=3 (19 obs)
+ Primary splits:
+ Start < 8.5 to the right, improve=6.762330, (0 missing)
+ Number < 5.5 to the left, improve=2.866795, (0 missing)
+ Age < 39.5 to the left, improve=2.250212, (0 missing)
+ Surrogate splits:
+ Number < 6.5 to the left, agree=0.802, adj=0.158, (0 split)
+
+Node number 2: 62 observations, complexity param=0.01960784
+ predicted class=absent expected loss=0.09677419
+ class counts: 56 6
+ probabilities: 0.903 0.097
+ left son=4 (29 obs) right son=5 (33 obs)
+ Primary splits:
+ Start < 14.5 to the right, improve=1.0205280, (0 missing)
+ Age < 55 to the left, improve=0.6848635, (0 missing)
+ Number < 4.5 to the left, improve=0.2975332, (0 missing)
+ Surrogate splits:
+ Number < 3.5 to the left, agree=0.645, adj=0.241, (0 split)
+ Age < 16 to the left, agree=0.597, adj=0.138, (0 split)
+
+Node number 3: 19 observations
+ predicted class=present expected loss=0.4210526
+ class counts: 8 11
+ probabilities: 0.421 0.579
+
+Node number 4: 29 observations
+ predicted class=absent expected loss=0
+ class counts: 29 0
+ probabilities: 1.000 0.000
+
+Node number 5: 33 observations, complexity param=0.01960784
+ predicted class=absent expected loss=0.1818182
+ class counts: 27 6
+ probabilities: 0.818 0.182
+ left son=10 (12 obs) right son=11 (21 obs)
+ Primary splits:
+ Age < 55 to the left, improve=1.2467530, (0 missing)
+ Start < 12.5 to the right, improve=0.2887701, (0 missing)
+ Number < 3.5 to the right, improve=0.1753247, (0 missing)
+ Surrogate splits:
+ Start < 9.5 to the left, agree=0.758, adj=0.333, (0 split)
+ Number < 5.5 to the right, agree=0.697, adj=0.167, (0 split)
+
+Node number 10: 12 observations
+ predicted class=absent expected loss=0
+ class counts: 12 0
+ probabilities: 1.000 0.000
+
+Node number 11: 21 observations, complexity param=0.01960784
+ predicted class=absent expected loss=0.2857143
+ class counts: 15 6
+ probabilities: 0.714 0.286
+ left son=22 (14 obs) right son=23 (7 obs)
+ Primary splits:
+ Age < 111 to the right, improve=1.71428600, (0 missing)
+ Start < 12.5 to the right, improve=0.79365080, (0 missing)
+ Number < 3.5 to the right, improve=0.07142857, (0 missing)
+
+Node number 22: 14 observations
+ predicted class=absent expected loss=0.1428571
+ class counts: 12 2
+ probabilities: 0.857 0.143
+
+Node number 23: 7 observations
+ predicted class=present expected loss=0.4285714
+ class counts: 3 4
+ probabilities: 0.429 0.571
+
+> path.rpart(fit, node=c(11, 22))
+
+ node number: 11
+ root
+ Start>=8.5
+ Start< 14.5
+ Age>=55
+
+ node number: 22
+ root
+ Start>=8.5
+ Start< 14.5
+ Age>=55
+ Age>=111
+>
+>
+>
+> cleanEx()
+> nameEx("plot.rpart")
+> ### * plot.rpart
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: plot.rpart
+> ### Title: Plot an Rpart Object
+> ### Aliases: plot.rpart
+> ### Keywords: tree
+>
+> ### ** Examples
+>
+> fit <- rpart(Price ~ Mileage + Type + Country, cu.summary)
+> plot(fit, compress=TRUE)
+> text(fit, use.n=TRUE)
+>
+>
+>
+> cleanEx()
+> nameEx("post.rpart")
+> ### * post.rpart
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: post.rpart
+> ### Title: PostScript Presentation Plot of an Rpart Object
+> ### Aliases: post.rpart post
+> ### Keywords: tree
+>
+> ### ** Examples
+>
+> z.auto <- rpart(Mileage ~ Weight, car.test.frame)
+> post(z.auto, file = "") # display tree on active device
+> # now construct postscript version on file "pretty.ps"
+> # with no title
+> post(z.auto, file = "pretty.ps", title = " ")
+> z.hp <- rpart(Mileage ~ Weight + HP, car.test.frame)
+> post(z.hp)
+>
+>
+>
+> cleanEx()
+> nameEx("predict.rpart")
+> ### * predict.rpart
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: predict.rpart
+> ### Title: Predictions from a Fitted Rpart Object
+> ### Aliases: predict.rpart
+> ### Keywords: tree
+>
+> ### ** Examples
+>
+> z.auto <- rpart(Mileage ~ Weight, car.test.frame)
+> predict(z.auto)
+ Eagle Summit 4 Ford Escort 4
+ 30.93333 30.93333
+ Ford Festiva 4 Honda Civic 4
+ 30.93333 30.93333
+ Mazda Protege 4 Mercury Tracer 4
+ 30.93333 30.93333
+ Nissan Sentra 4 Pontiac LeMans 4
+ 30.93333 30.93333
+ Subaru Loyale 4 Subaru Justy 3
+ 30.93333 30.93333
+ Toyota Corolla 4 Toyota Tercel 4
+ 30.93333 30.93333
+ Volkswagen Jetta 4 Chevrolet Camaro V8
+ 30.93333 20.40909
+ Dodge Daytona Ford Mustang V8
+ 23.80000 20.40909
+ Ford Probe Honda Civic CRX Si 4
+ 25.62500 30.93333
+ Honda Prelude Si 4WS 4 Nissan 240SX 4
+ 25.62500 23.80000
+ Plymouth Laser Subaru XT 4
+ 23.80000 30.93333
+ Audi 80 4 Buick Skylark 4
+ 25.62500 25.62500
+ Chevrolet Beretta 4 Chrysler Le Baron V6
+ 25.62500 23.80000
+ Ford Tempo 4 Honda Accord 4
+ 23.80000 23.80000
+ Mazda 626 4 Mitsubishi Galant 4
+ 23.80000 25.62500
+ Mitsubishi Sigma V6 Nissan Stanza 4
+ 20.40909 23.80000
+ Oldsmobile Calais 4 Peugeot 405 4
+ 25.62500 25.62500
+ Subaru Legacy 4 Toyota Camry 4
+ 23.80000 23.80000
+ Volvo 240 4 Acura Legend V6
+ 23.80000 20.40909
+ Buick Century 4 Chrysler Le Baron Coupe
+ 23.80000 23.80000
+ Chrysler New Yorker V6 Eagle Premier V6
+ 20.40909 20.40909
+ Ford Taurus V6 Ford Thunderbird V6
+ 20.40909 20.40909
+ Hyundai Sonata 4 Mazda 929 V6
+ 23.80000 20.40909
+ Nissan Maxima V6 Oldsmobile Cutlass Ciera 4
+ 20.40909 23.80000
+Oldsmobile Cutlass Supreme V6 Toyota Cressida 6
+ 20.40909 20.40909
+ Buick Le Sabre V6 Chevrolet Caprice V8
+ 20.40909 20.40909
+ Ford LTD Crown Victoria V8 Chevrolet Lumina APV V6
+ 20.40909 20.40909
+ Dodge Grand Caravan V6 Ford Aerostar V6
+ 20.40909 20.40909
+ Mazda MPV V6 Mitsubishi Wagon 4
+ 20.40909 20.40909
+ Nissan Axxess 4 Nissan Van 4
+ 20.40909 20.40909
+>
+> fit <- rpart(Kyphosis ~ Age + Number + Start, data=kyphosis)
+> predict(fit, type="prob") # class probabilities (default)
+ absent present
+1 0.4210526 0.5789474
+2 0.8571429 0.1428571
+3 0.4210526 0.5789474
+4 0.4210526 0.5789474
+5 1.0000000 0.0000000
+6 1.0000000 0.0000000
+7 1.0000000 0.0000000
+8 1.0000000 0.0000000
+9 1.0000000 0.0000000
+10 0.4285714 0.5714286
+11 0.4285714 0.5714286
+12 1.0000000 0.0000000
+13 0.4210526 0.5789474
+14 1.0000000 0.0000000
+15 1.0000000 0.0000000
+16 1.0000000 0.0000000
+17 1.0000000 0.0000000
+18 0.8571429 0.1428571
+19 1.0000000 0.0000000
+20 1.0000000 0.0000000
+21 1.0000000 0.0000000
+22 0.4210526 0.5789474
+23 0.4285714 0.5714286
+24 0.4210526 0.5789474
+25 0.4210526 0.5789474
+26 1.0000000 0.0000000
+27 0.4210526 0.5789474
+28 0.4285714 0.5714286
+29 1.0000000 0.0000000
+30 1.0000000 0.0000000
+31 1.0000000 0.0000000
+32 0.8571429 0.1428571
+33 0.8571429 0.1428571
+34 1.0000000 0.0000000
+35 0.8571429 0.1428571
+36 1.0000000 0.0000000
+37 1.0000000 0.0000000
+38 0.4210526 0.5789474
+39 1.0000000 0.0000000
+40 0.4285714 0.5714286
+41 0.4210526 0.5789474
+42 1.0000000 0.0000000
+43 0.4210526 0.5789474
+44 0.4210526 0.5789474
+45 1.0000000 0.0000000
+46 0.8571429 0.1428571
+47 1.0000000 0.0000000
+48 0.8571429 0.1428571
+49 0.4210526 0.5789474
+50 0.8571429 0.1428571
+51 0.4285714 0.5714286
+52 1.0000000 0.0000000
+53 0.4210526 0.5789474
+54 1.0000000 0.0000000
+55 1.0000000 0.0000000
+56 1.0000000 0.0000000
+57 1.0000000 0.0000000
+58 0.4210526 0.5789474
+59 1.0000000 0.0000000
+60 0.4285714 0.5714286
+61 0.4210526 0.5789474
+62 0.4210526 0.5789474
+63 0.4210526 0.5789474
+64 1.0000000 0.0000000
+65 1.0000000 0.0000000
+66 1.0000000 0.0000000
+67 1.0000000 0.0000000
+68 0.8571429 0.1428571
+69 1.0000000 0.0000000
+70 1.0000000 0.0000000
+71 0.8571429 0.1428571
+72 0.8571429 0.1428571
+73 1.0000000 0.0000000
+74 0.8571429 0.1428571
+75 1.0000000 0.0000000
+76 1.0000000 0.0000000
+77 0.8571429 0.1428571
+78 1.0000000 0.0000000
+79 0.8571429 0.1428571
+80 0.4210526 0.5789474
+81 1.0000000 0.0000000
+> predict(fit, type="vector") # level numbers
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
+ 2 1 2 2 1 1 1 1 1 2 2 1 2 1 1 1 1 1 1 1 1 2 2 2 2 1
+27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52
+ 2 2 1 1 1 1 1 1 1 1 1 2 1 2 2 1 2 2 1 1 1 1 2 1 2 1
+53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78
+ 2 1 1 1 1 2 1 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+79 80 81
+ 1 2 1
+> predict(fit, type="class") # factor
+ 1 2 3 4 5 6 7 8 9 10
+present absent present present absent absent absent absent absent present
+ 11 12 13 14 15 16 17 18 19 20
+present absent present absent absent absent absent absent absent absent
+ 21 22 23 24 25 26 27 28 29 30
+ absent present present present present absent present present absent absent
+ 31 32 33 34 35 36 37 38 39 40
+ absent absent absent absent absent absent absent present absent present
+ 41 42 43 44 45 46 47 48 49 50
+present absent present present absent absent absent absent present absent
+ 51 52 53 54 55 56 57 58 59 60
+present absent present absent absent absent absent present absent present
+ 61 62 63 64 65 66 67 68 69 70
+present present present absent absent absent absent absent absent absent
+ 71 72 73 74 75 76 77 78 79 80
+ absent absent absent absent absent absent absent absent absent present
+ 81
+ absent
+Levels: absent present
+> predict(fit, type="matrix") # level number, class frequencies, probabilities
+ [,1] [,2] [,3] [,4] [,5]
+1 2 8 11 0.4210526 0.5789474
+2 1 12 2 0.8571429 0.1428571
+3 2 8 11 0.4210526 0.5789474
+4 2 8 11 0.4210526 0.5789474
+5 1 29 0 1.0000000 0.0000000
+6 1 29 0 1.0000000 0.0000000
+7 1 29 0 1.0000000 0.0000000
+8 1 29 0 1.0000000 0.0000000
+9 1 29 0 1.0000000 0.0000000
+10 2 3 4 0.4285714 0.5714286
+11 2 3 4 0.4285714 0.5714286
+12 1 29 0 1.0000000 0.0000000
+13 2 8 11 0.4210526 0.5789474
+14 1 12 0 1.0000000 0.0000000
+15 1 29 0 1.0000000 0.0000000
+16 1 29 0 1.0000000 0.0000000
+17 1 29 0 1.0000000 0.0000000
+18 1 12 2 0.8571429 0.1428571
+19 1 29 0 1.0000000 0.0000000
+20 1 12 0 1.0000000 0.0000000
+21 1 29 0 1.0000000 0.0000000
+22 2 8 11 0.4210526 0.5789474
+23 2 3 4 0.4285714 0.5714286
+24 2 8 11 0.4210526 0.5789474
+25 2 8 11 0.4210526 0.5789474
+26 1 12 0 1.0000000 0.0000000
+27 2 8 11 0.4210526 0.5789474
+28 2 3 4 0.4285714 0.5714286
+29 1 29 0 1.0000000 0.0000000
+30 1 29 0 1.0000000 0.0000000
+31 1 29 0 1.0000000 0.0000000
+32 1 12 2 0.8571429 0.1428571
+33 1 12 2 0.8571429 0.1428571
+34 1 29 0 1.0000000 0.0000000
+35 1 12 2 0.8571429 0.1428571
+36 1 29 0 1.0000000 0.0000000
+37 1 12 0 1.0000000 0.0000000
+38 2 8 11 0.4210526 0.5789474
+39 1 12 0 1.0000000 0.0000000
+40 2 3 4 0.4285714 0.5714286
+41 2 8 11 0.4210526 0.5789474
+42 1 12 0 1.0000000 0.0000000
+43 2 8 11 0.4210526 0.5789474
+44 2 8 11 0.4210526 0.5789474
+45 1 29 0 1.0000000 0.0000000
+46 1 12 2 0.8571429 0.1428571
+47 1 29 0 1.0000000 0.0000000
+48 1 12 2 0.8571429 0.1428571
+49 2 8 11 0.4210526 0.5789474
+50 1 12 2 0.8571429 0.1428571
+51 2 3 4 0.4285714 0.5714286
+52 1 29 0 1.0000000 0.0000000
+53 2 8 11 0.4210526 0.5789474
+54 1 29 0 1.0000000 0.0000000
+55 1 29 0 1.0000000 0.0000000
+56 1 29 0 1.0000000 0.0000000
+57 1 12 0 1.0000000 0.0000000
+58 2 8 11 0.4210526 0.5789474
+59 1 12 0 1.0000000 0.0000000
+60 2 3 4 0.4285714 0.5714286
+61 2 8 11 0.4210526 0.5789474
+62 2 8 11 0.4210526 0.5789474
+63 2 8 11 0.4210526 0.5789474
+64 1 29 0 1.0000000 0.0000000
+65 1 29 0 1.0000000 0.0000000
+66 1 12 0 1.0000000 0.0000000
+67 1 29 0 1.0000000 0.0000000
+68 1 12 2 0.8571429 0.1428571
+69 1 12 0 1.0000000 0.0000000
+70 1 29 0 1.0000000 0.0000000
+71 1 12 2 0.8571429 0.1428571
+72 1 12 2 0.8571429 0.1428571
+73 1 29 0 1.0000000 0.0000000
+74 1 12 2 0.8571429 0.1428571
+75 1 29 0 1.0000000 0.0000000
+76 1 29 0 1.0000000 0.0000000
+77 1 12 2 0.8571429 0.1428571
+78 1 12 0 1.0000000 0.0000000
+79 1 12 2 0.8571429 0.1428571
+80 2 8 11 0.4210526 0.5789474
+81 1 12 0 1.0000000 0.0000000
+>
+> sub <- c(sample(1:50, 25), sample(51:100, 25), sample(101:150, 25))
+> fit <- rpart(Species ~ ., data=iris, subset=sub)
+> fit
+n= 75
+
+node), split, n, loss, yval, (yprob)
+ * denotes terminal node
+
+1) root 75 50 setosa (0.33333333 0.33333333 0.33333333)
+ 2) Petal.Length< 2.35 25 0 setosa (1.00000000 0.00000000 0.00000000) *
+ 3) Petal.Length>=2.35 50 25 versicolor (0.00000000 0.50000000 0.50000000)
+ 6) Petal.Width< 1.65 27 2 versicolor (0.00000000 0.92592593 0.07407407) *
+ 7) Petal.Width>=1.65 23 0 virginica (0.00000000 0.00000000 1.00000000) *
+> table(predict(fit, iris[-sub,], type="class"), iris[-sub, "Species"])
+
+ setosa versicolor virginica
+ setosa 25 0 0
+ versicolor 0 23 2
+ virginica 0 2 23
+>
+>
+>
+> cleanEx()
+> nameEx("print.rpart")
+> ### * print.rpart
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: print.rpart
+> ### Title: Print an Rpart Object
+> ### Aliases: print.rpart
+> ### Keywords: tree
+>
+> ### ** Examples
+>
+> z.auto <- rpart(Mileage ~ Weight, car.test.frame)
+> z.auto
+n= 60
+
+node), split, n, deviance, yval
+ * denotes terminal node
+
+ 1) root 60 1354.58300 24.58333
+ 2) Weight>=2567.5 45 361.20000 22.46667
+ 4) Weight>=3087.5 22 61.31818 20.40909 *
+ 5) Weight< 3087.5 23 117.65220 24.43478
+ 10) Weight>=2747.5 15 60.40000 23.80000 *
+ 11) Weight< 2747.5 8 39.87500 25.62500 *
+ 3) Weight< 2567.5 15 186.93330 30.93333 *
+> ## Not run:
+> ##D node), split, n, deviance, yval
+> ##D * denotes terminal node
+> ##D
+> ##D 1) root 60 1354.58300 24.58333
+> ##D 2) Weight>=2567.5 45 361.20000 22.46667
+> ##D 4) Weight>=3087.5 22 61.31818 20.40909 *
+> ##D 5) Weight<3087.5 23 117.65220 24.43478
+> ##D 10) Weight>=2747.5 15 60.40000 23.80000 *
+> ##D 11) Weight<2747.5 8 39.87500 25.62500 *
+> ##D 3) Weight<2567.5 15 186.93330 30.93333 *
+> ## End(Not run)
+>
+>
+> cleanEx()
+> nameEx("printcp")
+> ### * printcp
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: printcp
+> ### Title: Displays CP table for Fitted Rpart Object
+> ### Aliases: printcp
+> ### Keywords: tree
+>
+> ### ** Examples
+>
+> z.auto <- rpart(Mileage ~ Weight, car.test.frame)
+> printcp(z.auto)
+
+Regression tree:
+rpart(formula = Mileage ~ Weight, data = car.test.frame)
+
+Variables actually used in tree construction:
+[1] Weight
+
+Root node error: 1354.6/60 = 22.576
+
+n= 60
+
+ CP nsplit rel error xerror xstd
+1 0.595349 0 1.00000 1.03199 0.179319
+2 0.134528 1 0.40465 0.48751 0.076130
+3 0.012828 2 0.27012 0.38022 0.066855
+4 0.010000 3 0.25729 0.39460 0.066056
+> ## Not run:
+> ##D Regression tree:
+> ##D rpart(formula = Mileage ~ Weight, data = car.test.frame)
+> ##D
+> ##D Variables actually used in tree construction:
+> ##D [1] Weight
+> ##D
+> ##D Root node error: 1354.6/60 = 22.576
+> ##D
+> ##D CP nsplit rel error xerror xstd
+> ##D 1 0.595349 0 1.00000 1.03436 0.178526
+> ##D 2 0.134528 1 0.40465 0.60508 0.105217
+> ##D 3 0.012828 2 0.27012 0.45153 0.083330
+> ##D 4 0.010000 3 0.25729 0.44826 0.076998
+> ## End(Not run)
+>
+>
+> cleanEx()
+> nameEx("prune.rpart")
+> ### * prune.rpart
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: prune.rpart
+> ### Title: Cost-complexity Pruning of an Rpart Object
+> ### Aliases: prune.rpart prune
+> ### Keywords: tree
+>
+> ### ** Examples
+>
+> z.auto <- rpart(Mileage ~ Weight, car.test.frame)
+> zp <- prune(z.auto, cp=0.1)
+> plot(zp) #plot smaller rpart object
+>
+>
+>
+> cleanEx()
+> nameEx("residuals.rpart")
+> ### * residuals.rpart
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: residuals.rpart
+> ### Title: Residuals From a Fitted Rpart Object
+> ### Aliases: residuals.rpart
+> ### Keywords: tree
+>
+> ### ** Examples
+>
+> fit <- rpart(skips ~ Opening + Solder + Mask + PadType + Panel,
++ data=solder, method='anova')
+> summary(residuals(fit))
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+-13.8000 -1.0360 -0.6833 0.0000 0.9639 16.2000
+> plot(predict(fit),residuals(fit))
+>
+>
+>
+> cleanEx()
+> nameEx("rpart")
+> ### * rpart
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: rpart
+> ### Title: Recursive Partitioning and Regression Trees
+> ### Aliases: rpart
+> ### Keywords: tree
+>
+> ### ** Examples
+>
+> fit <- rpart(Kyphosis ~ Age + Number + Start, data=kyphosis)
+> fit2 <- rpart(Kyphosis ~ Age + Number + Start, data=kyphosis,
++ parms=list(prior=c(.65,.35), split='information'))
+> fit3 <- rpart(Kyphosis ~ Age + Number + Start, data=kyphosis,
++ control=rpart.control(cp=.05))
+> par(mfrow=c(1,2), xpd=NA) # otherwise on some devices the text is clipped
+> plot(fit)
+> text(fit, use.n=TRUE)
+> plot(fit2)
+> text(fit2, use.n=TRUE)
+>
+>
+>
+> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
+> cleanEx()
+> nameEx("rsq.rpart")
+> ### * rsq.rpart
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: rsq.rpart
+> ### Title: Plots the Approximate R-Square for the Different Splits
+> ### Aliases: rsq.rpart
+> ### Keywords: tree
+>
+> ### ** Examples
+>
+> z.auto <- rpart(Mileage ~ Weight, car.test.frame)
+> rsq.rpart(z.auto)
+
+Regression tree:
+rpart(formula = Mileage ~ Weight, data = car.test.frame)
+
+Variables actually used in tree construction:
+[1] Weight
+
+Root node error: 1354.6/60 = 22.576
+
+n= 60
+
+ CP nsplit rel error xerror xstd
+1 0.595349 0 1.00000 1.03199 0.179319
+2 0.134528 1 0.40465 0.48751 0.076130
+3 0.012828 2 0.27012 0.38022 0.066855
+4 0.010000 3 0.25729 0.39460 0.066056
+>
+>
+>
+> cleanEx()
+> nameEx("snip.rpart")
+> ### * snip.rpart
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: snip.rpart
+> ### Title: Snip Subtrees of an Rpart Object
+> ### Aliases: snip.rpart
+> ### Keywords: tree
+>
+> ### ** Examples
+>
+> ## dataset not in R
+> ## Not run:
+> ##D z.survey <- rpart(market.survey) #grow the rpart object
+> ##D plot(z.survey) #plot the tree
+> ##D z.survey2 <- snip.rpart(z.survey,toss=2) #trim subtree at node 2
+> ##D plot(z.survey2) #plot new tree
+> ##D
+> ##D # can also interactively select the node using the mouse in the
+> ##D # graphics window
+> ## End(Not run)
+>
+>
+> cleanEx()
+> nameEx("solder")
+> ### * solder
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: solder
+> ### Title: Soldering of Components on Printed-Circuit Boards
+> ### Aliases: solder
+> ### Keywords: datasets
+>
+> ### ** Examples
+>
+> fit <- rpart(skips ~ Opening + Solder + Mask + PadType + Panel,
++ data=solder, method='anova')
+> summary(residuals(fit))
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+-13.8000 -1.0360 -0.6833 0.0000 0.9639 16.2000
+> plot(predict(fit),residuals(fit))
+>
+>
+>
+> cleanEx()
+> nameEx("summary.rpart")
+> ### * summary.rpart
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: summary.rpart
+> ### Title: Summarize a Fitted Rpart Object
+> ### Aliases: summary.rpart
+> ### Keywords: tree
+>
+> ### ** Examples
+>
+> z.auto <- rpart(Mileage ~ Weight, car.test.frame)
+> summary(z.auto)
+Call:
+rpart(formula = Mileage ~ Weight, data = car.test.frame)
+ n= 60
+
+ CP nsplit rel error xerror xstd
+1 0.59534912 0 1.0000000 1.0319924 0.17931937
+2 0.13452819 1 0.4046509 0.4875114 0.07613003
+3 0.01282843 2 0.2701227 0.3802248 0.06685452
+4 0.01000000 3 0.2572943 0.3945980 0.06605572
+
+Node number 1: 60 observations, complexity param=0.5953491
+ mean=24.58333, MSE=22.57639
+ left son=2 (45 obs) right son=3 (15 obs)
+ Primary splits:
+ Weight < 2567.5 to the right, improve=0.5953491, (0 missing)
+
+Node number 2: 45 observations, complexity param=0.1345282
+ mean=22.46667, MSE=8.026667
+ left son=4 (22 obs) right son=5 (23 obs)
+ Primary splits:
+ Weight < 3087.5 to the right, improve=0.5045118, (0 missing)
+
+Node number 3: 15 observations
+ mean=30.93333, MSE=12.46222
+
+Node number 4: 22 observations
+ mean=20.40909, MSE=2.78719
+
+Node number 5: 23 observations, complexity param=0.01282843
+ mean=24.43478, MSE=5.115312
+ left son=10 (15 obs) right son=11 (8 obs)
+ Primary splits:
+ Weight < 2747.5 to the right, improve=0.1476996, (0 missing)
+
+Node number 10: 15 observations
+ mean=23.8, MSE=4.026667
+
+Node number 11: 8 observations
+ mean=25.625, MSE=4.984375
+
+>
+>
+>
+> cleanEx()
+> nameEx("text.rpart")
+> ### * text.rpart
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: text.rpart
+> ### Title: Place Text on a Dendrogram
+> ### Aliases: text.rpart
+> ### Keywords: tree
+>
+> ### ** Examples
+>
+> freen.tr <- rpart(y ~ ., freeny)
+> plot(freen.tr)
+> text(freen.tr, use.n=TRUE, all=TRUE)
+>
+>
+>
+> cleanEx()
+> nameEx("xpred.rpart")
+> ### * xpred.rpart
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: xpred.rpart
+> ### Title: Return Cross-Validated Predictions
+> ### Aliases: xpred.rpart
+> ### Keywords: tree
+>
+> ### ** Examples
+>
+> fit <- rpart(Mileage ~ Weight, car.test.frame)
+> xmat <- xpred.rpart(fit)
+> xerr <- (xmat - car.test.frame$Mileage)^2
+> apply(xerr, 2, sum) # cross-validated error estimate
+0.79767456 0.28300396 0.04154257 0.01132626
+ 1423.9568 740.4845 544.3925 536.6344
+>
+> # approx same result as rel. error from printcp(fit)
+> apply(xerr, 2, sum)/var(car.test.frame$Mileage)
+0.79767456 0.28300396 0.04154257 0.01132626
+ 62.02162 32.25242 23.71147 23.37355
+> printcp(fit)
+
+Regression tree:
+rpart(formula = Mileage ~ Weight, data = car.test.frame)
+
+Variables actually used in tree construction:
+[1] Weight
+
+Root node error: 1354.6/60 = 22.576
+
+n= 60
+
+ CP nsplit rel error xerror xstd
+1 0.595349 0 1.00000 1.03199 0.179319
+2 0.134528 1 0.40465 0.48751 0.076130
+3 0.012828 2 0.27012 0.38022 0.066855
+4 0.010000 3 0.25729 0.39460 0.066056
+>
+>
+>
+> ### * <FOOTER>
+> ###
+> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
+Time elapsed: 1.27 0.053 1.327 0 0
+> grDevices::dev.off()
+null device
+ 1
+> ###
+> ### Local variables: ***
+> ### mode: outline-minor ***
+> ### outline-regexp: "\\(> \\)?### [*]+" ***
+> ### End: ***
+> quit('no')
diff --git a/win32/deps/library/rpart/tests/backticks.R b/win32/deps/library/rpart/tests/backticks.R
new file mode 100644
index 0000000..b7e93e3
--- /dev/null
+++ b/win32/deps/library/rpart/tests/backticks.R
@@ -0,0 +1,7 @@
+## allow backticks in rpart.matrix: see
+## https://stat.ethz.ch/pipermail/r-help/2012-May/314081.html
+
+library(rpart)
+Iris <- iris
+names(Iris) <- sub(".", " ", names(iris), fixed=TRUE)
+rpart(Species ~ `Sepal Length`, data = Iris)
diff --git a/win32/deps/library/rpart/tests/data.stagec b/win32/deps/library/rpart/tests/data.stagec
new file mode 100644
index 0000000..1a06a9d
--- /dev/null
+++ b/win32/deps/library/rpart/tests/data.stagec
@@ -0,0 +1,146 @@
+ 6.130047 0 64 2 10.26 2 4 1
+ 9.374401 0 62 1 NA 3 8 3
+ 5.240246 1 59 2 9.99 3 7 1
+ 3.162217 1 62 2 3.57 2 4 1
+ 1.908282 1 64 2 22.56 4 8 2
+ 4.848733 0 69 1 6.14 3 7 1
+ 5.790554 0 75 2 13.69 2 NA 2
+ 7.304585 0 71 2 NA 3 7 3
+ 3.655030 1 73 2 11.77 3 6 1
+ 15.87132 0 64 2 27.27 3 7 2
+ 6.299794 0 65 2 19.34 3 7 2
+ 2.910335 1 58 2 14.82 4 8 2
+ 1.527720 1 70 2 10.22 3 8 1
+ 14.46132 0 67 2 15.66 2 6 2
+ 4.238193 1 66 2 17.79 3 7 2
+ 1.738535 1 74 2 11.11 3 8 1
+ 5.004791 0 70 2 11.44 2 5 1
+ 13.17727 0 57 2 14.78 2 4 2
+ 10.87200 0 63 2 54.93 3 8 2
+ 12.98015 0 65 2 24.58 3 7 2
+ 11.37303 0 62 2 27.79 2 5 2
+ 2.647501 1 72 2 14.86 3 6 2
+ 9.812457 0 64 1 10.51 2 5 1
+ 3.411362 1 67 NA 14.22 2 6 2
+ 7.638603 1 64 2 15.28 2 5 2
+ 4.799452 1 70 2 16.91 3 6 2
+ 3.674195 1 58 1 17.87 3 7 2
+ 13.89185 0 57 2 12.13 3 6 1
+ 4.881587 1 54 1 17.25 2 5 2
+ 15.92060 0 61 1 16.53 3 7 2
+ 2.850102 1 68 2 17.49 2 4 2
+ 9.273100 0 64 1 3.85 3 6 3
+ 6.510609 0 70 1 7.88 2 6 1
+ 1.686516 0 64 2 16.64 2 5 2
+ 6.932238 0 66 2 13.19 3 7 2
+ 5.492128 0 61 2 9.42 2 5 1
+ 5.719370 0 70 2 22.79 2 5 2
+ 4.076659 1 63 2 11.37 2 6 1
+ 0.3066393 1 59 2 3.77 3 6 3
+ 1.095140 1 66 1 13.76 3 6 2
+ 7.783710 0 53 2 14.52 2 5 2
+ 2.023271 1 62 2 7.55 3 7 1
+ 7.301847 0 69 2 8.46 2 5 1
+ 13.54688 0 63 2 7.66 3 7 1
+ 11.71800 0 61 2 8.40 2 5 1
+ 8.657084 0 70 1 4.43 1 3 1
+ 3.356605 0 61 2 10.37 3 7 1
+ 6.275154 0 62 2 10.82 2 6 1
+ 10.61738 0 55 2 7.81 2 5 1
+ 9.253935 0 61 2 11.23 2 5 1
+ 7.906913 0 63 2 13.99 3 6 2
+ 4.936345 0 67 2 6.41 2 5 1
+ 13.40725 0 59 2 16.05 2 5 2
+ 17.69199 0 58 2 22.97 3 6 2
+ 1.026694 1 61 1 2.40 4 10 1
+ 0.2546201 1 47 2 11.92 4 10 1
+ 13.07049 0 65 2 NA 3 6 2
+ 16.70088 0 56 2 5.29 1 3 1
+ 4.479124 0 63 2 5.75 2 5 1
+ 3.438740 1 69 1 7.64 3 8 3
+ 2.376454 1 50 1 16.81 3 7 2
+ 6.784394 0 70 2 29.56 2 5 2
+ 2.997946 1 55 1 13.35 3 6 3
+ 10.36276 0 55 2 8.10 2 5 1
+ 11.77002 0 62 1 12.62 2 5 1
+ 8.049281 1 66 2 14.14 2 5 2
+ 5.664613 0 71 1 10.16 2 6 1
+ 6.053388 0 63 2 17.21 2 5 2
+ 5.201916 0 54 2 11.35 2 6 1
+ 6.228610 0 65 2 11.35 2 5 1
+ 11.36481 0 59 2 7.61 2 5 1
+ 6.986995 1 61 2 20.82 3 6 2
+ 6.464065 0 65 1 12.93 3 7 1
+ 0.5366188 1 57 1 21.75 3 7 2
+ 6.067077 0 69 2 8.58 2 6 1
+ 5.111567 1 53 1 14.94 3 7 2
+ 3.660506 1 48 2 17.16 3 7 2
+ 12.16974 0 57 2 23.62 3 8 2
+ 7.707049 1 63 2 16.06 3 9 2
+ 7.028062 0 52 2 7.15 2 7 1
+ 7.230663 1 57 2 13.21 3 8 2
+ 4.350444 1 62 2 11.35 3 6 1
+ 6.694045 0 54 2 8.11 2 4 1
+ 6.765229 1 67 2 11.18 3 7 1
+ 5.185489 1 65 2 24.84 3 7 2
+ 8.662559 0 67 2 7.67 3 6 1
+ 10.79808 0 72 1 6.68 2 NA 1
+ 2.614647 1 66 2 15.23 3 8 2
+ 10.87474 0 72 2 6.80 2 5 1
+ 5.637234 1 60 2 14.58 3 7 2
+ 10.09993 0 70 2 13.17 2 6 2
+ 7.208761 0 63 1 9.76 2 5 1
+ 10.17659 0 64 1 7.61 2 NA 1
+ 7.718001 1 62 2 38.05 3 7 2
+ 2.696783 1 61 1 13.87 3 6 2
+ 1.949349 1 64 2 21.20 3 7 2
+ 3.630390 0 64 1 17.96 3 7 2
+ 8.229979 0 68 2 27.14 3 9 2
+ 9.174537 0 62 1 6.74 2 5 1
+ 6.121834 0 69 2 11.21 3 8 1
+ 8.698151 0 59 2 20.22 3 6 2
+ 7.411362 1 66 1 15.35 3 8 2
+ 1.645448 1 53 1 16.79 3 9 2
+ 8.353182 0 59 2 8.76 2 6 1
+ 4.717317 1 58 2 13.23 2 6 2
+ 5.746748 0 61 2 34.01 2 7 2
+ 3.156741 1 65 NA 14.68 3 8 2
+ 4.944558 0 67 1 17.95 3 8 2
+ 3.449692 1 57 1 23.34 3 8 2
+ 0.9883642 1 55 2 10.25 3 7 3
+ 5.445585 1 57 2 NA 3 8 3
+ 4.654346 0 57 1 15.10 3 7 2
+ 6.264202 0 68 1 26.55 2 6 2
+ 6.967830 0 67 2 7.78 2 6 1
+ 1.522245 1 60 1 NA 4 9 3
+ 7.055441 0 63 2 21.20 3 7 2
+ 6.045174 0 69 2 7.93 3 6 1
+ 3.843942 0 54 2 10.58 3 8 1
+ 6.516084 0 66 2 5.92 2 5 1
+ 3.112936 0 59 2 5.08 3 7 1
+ 6.795345 0 62 2 13.10 3 8 2
+ 6.669404 0 73 1 41.31 3 8 2
+ 5.749486 1 65 2 11.29 3 7 1
+ 1.516769 1 67 2 14.02 3 7 2
+ 5.169062 0 75 2 12.46 3 7 1
+ 1.253935 1 70 2 13.69 3 8 2
+ 6.160164 0 59 2 12.06 2 5 1
+ 6.480492 0 73 2 13.01 3 6 1
+ 1.163586 1 66 2 13.21 2 6 2
+ 5.697467 0 66 2 10.43 3 5 1
+ 3.397672 1 65 2 NA 3 7 3
+ 5.629021 0 66 1 13.33 2 5 2
+ 5.971252 0 66 2 37.49 3 7 2
+ 5.119781 0 59 2 11.69 3 7 1
+ 6.004106 0 52 2 9.90 2 4 1
+ 5.368925 0 68 2 13.01 2 5 1
+ 2.431211 0 63 2 4.81 3 8 1
+ 4.235455 0 67 2 14.71 2 5 2
+ 5.541409 0 59 1 9.01 2 5 1
+ 5.363449 0 57 1 10.90 3 6 1
+ 8.180698 0 62 2 10.72 3 7 1
+ 10.20123 0 63 2 5.14 2 5 1
+ 2.450376 1 73 2 46.92 4 9 2
+ 7.898699 0 68 2 NA 2 5 3
+ 5.634496 0 51 2 9.59 3 6 1
+ 2.058863 1 56 2 9.01 3 7 1
diff --git a/win32/deps/library/rpart/tests/rpartco.R b/win32/deps/library/rpart/tests/rpartco.R
new file mode 100644
index 0000000..1272cd2
--- /dev/null
+++ b/win32/deps/library/rpart/tests/rpartco.R
@@ -0,0 +1,6 @@
+## needs to be examimed for overlaps: formerly overlapped near Type=c
+pdf("rpartco-test.pdf")
+library(rpart)
+fit <- rpart(Price ~ Mileage + Type + Country, cu.summary)
+plot(fit, compress=TRUE, branch=0)
+text(fit, xpd = NA, cex = 0.7)
diff --git a/win32/deps/library/rpart/tests/surv_test.R b/win32/deps/library/rpart/tests/surv_test.R
new file mode 100644
index 0000000..837f957
--- /dev/null
+++ b/win32/deps/library/rpart/tests/surv_test.R
@@ -0,0 +1,9 @@
+## example from coxph: gave error in rpart 3.1-31
+## due to missing drop = FALSE
+test1 <- list(time= c(4, 3,1,1,2,2,3),
+ status=c(1,NA,1,0,1,1,0),
+ x= c(0, 2,1,1,1,0,0),
+ sex= c(0, 0,0,0,1,1,1))
+library(survival)
+library(rpart)
+rpart(Surv(time, status) ~ x + sex, test1)
diff --git a/win32/deps/library/rpart/tests/testall.R b/win32/deps/library/rpart/tests/testall.R
new file mode 100644
index 0000000..7433306
--- /dev/null
+++ b/win32/deps/library/rpart/tests/testall.R
@@ -0,0 +1,330 @@
+# Any necessary setup
+library(rpart)
+library(survival)
+options(na.action="na.omit")
+options(digits=4) # to match earlier output
+RNGversion("1.6.2")
+set.seed(1234)
+#
+# Read the data
+#
+# Time to progression in years
+# status 1=progressed, 0= censored
+# age
+# early endocrine therapy 1=no 2=yes
+# % of cells in g2 phase, from flow cytometry
+# tumor grade (Farrow) 1,2,3,4
+# Gleason score (competing grading system)
+# ploidy
+
+stagec <- read.table('data.stagec', col.names=c("pgtime", "pgstat", "age",
+ "eet", "g2", "grade", "gleason", "ploidy"))
+stagec$ploidy <- factor(stagec$ploidy, levels=1:3,
+ labels=c("diploid", "tetraploid", "aneuploid"))
+
+cox0 <- coxph(Surv(pgtime, pgstat) ~ 1, stagec)
+cox1 <- coxph(Surv(pgtime, pgstat) ~ age + eet + g2 + grade + ploidy, stagec)
+cox1
+
+fit1 <- rpart(Surv(pgtime, pgstat) ~ age + eet + g2+grade+gleason +ploidy,
+ stagec, control=rpart.control(usesurrogate=0, cp=0),
+ method='poisson')
+fit1
+summary(fit1)
+
+fit2 <- rpart(cox0$residual ~ age + eet + g2+grade+gleason +ploidy,
+ stagec)
+fit2
+summary(fit2)
+
+#
+# In 6/2001 rpart.exp changed to fix a bug. A side effect was reexamination
+# of one definition: the old version didn't count person-years after the
+# last death in computing the rescaling, the new one does. One could argue
+# about which is better. To match the old output, we modify the data.
+tdata <- stagec
+tdata$pgtime <- pmin(tdata$pgtime, max(tdata$pgtime[tdata$pgstat==1]))
+
+fit3 <- rpart(Surv(pgtime, pgstat) ~ age + eet + g2+grade+gleason +ploidy,
+ tdata, control=rpart.control(usesurrogate=1, cp=.001))
+
+summary(fit3)
+
+#
+# In order to compare the x-vals estimates of the mainline and S versions,
+# it is necessary that we use stratified xval sets (like the mainline
+# does).
+
+mystate <- data.frame(state.x77, region=factor(state.region))
+names(mystate) <- c("population","income" , "illiteracy","life" ,
+ "murder", "hs.grad", "frost", "area", "region")
+
+xvals <- 1:nrow(mystate)
+xvals[order(mystate$income)] <- rep(1:10, length=nrow(mystate))
+
+fit4 <- rpart(income ~ population + region + illiteracy +life + murder +
+ hs.grad + frost , mystate,
+ control=rpart.control(minsplit=10, xval=xvals))
+
+summary(fit4)
+
+
+#
+# Check out xpred.rpart
+#
+meany <- mean(mystate$income)
+xpr <- xpred.rpart(fit4, xval=xvals)
+xpr2 <- (xpr - mystate$income)^2
+risk0 <- mean((mystate$income - meany)^2)
+xpmean <- as.vector(apply(xpr2, 2, mean)) #kill the names
+all.equal(xpmean/risk0, as.vector(fit4$cptable[,'xerror']))
+
+xpstd <- as.vector(apply((sweep(xpr2, 2, xpmean))^2, 2, sum))
+xpstd <- sqrt(xpstd)/(50*risk0)
+all.equal(xpstd, as.vector(fit4$cptable[,'xstd']))
+
+#
+# recreate subset #3 of the xval
+#
+tfit4 <- rpart(income ~ population + region + illiteracy +life + murder +
+ hs.grad + frost , mystate, subset=(xvals!=3),
+ control=rpart.control(minsplit=10, xval=0))
+tpred <- predict(tfit4, mystate[xvals==3,])
+all.equal(tpred, xpr[xvals==3,ncol(xpr)])
+
+# How much does this differ from the "real" formula, more complex,
+# found on page 309 of Breiman et al. ?
+#xtemp <- (xpr2/outer(rep(1,50),xpmean)) - ((mystate$income - meany)^2)/risk0
+#real.se<- xpmean* sqrt(apply(xtemp^2,2,sum))/(risk0*50)
+
+fit5 <- rpart(factor(pgstat) ~ age + eet + g2+grade+gleason +ploidy,
+ stagec)
+
+fit5
+
+fit6 <- rpart(factor(pgstat) ~ age + eet + g2+grade+gleason +ploidy,
+ stagec, parm=list(prior=c(.5,.5)))
+summary(fit6)
+#
+# Fit a classification model to the car data.
+# Now, since Reliability is an ordered category, this model doesn't
+# make a lot of statistical sense, but it does test out some
+# areas of the code that nothing else does
+#
+
+carfit <- rpart(Reliability ~ Price + Country + Mileage + Type,
+ method='class', data=cu.summary)
+
+summary(carfit)
+#
+# Simplest weight test: treble the weights
+#
+# By using the unshrunken estimates the weights will nearly cancel
+# out: frame$wt, frame$dev, frame$yval2, and improvement will all
+# be threefold larger, other things will be the same.
+# The improvement is the splits matrix, column 3, rows with n>0. Other
+# rows are surrogate splits.
+
+tempc <- rpart.control(maxsurrogate=0, cp=0, xval=0)
+fit1 <- rpart(Surv(pgtime, pgstat) ~ age + eet + g2+grade+gleason +ploidy,
+ stagec, control=tempc,
+ method='poisson', parms=list(shrink=0))
+wts <- rep(3, nrow(stagec))
+fit1b <- rpart(Surv(pgtime, pgstat) ~ age + eet + g2+grade+gleason +ploidy,
+ stagec, control= tempc, parms=list(shrink=0),
+ method='poisson', weights=wts)
+fit1b$frame$wt <- fit1b$frame$wt/3
+fit1b$frame$dev <- fit1b$frame$dev/3
+fit1b$frame$yval2[,2] <- fit1b$frame$yval2[,2]/3
+fit1b$splits[,3] <- fit1b$splits[,3]/3
+all.equal(fit1[-3], fit1b[-3]) #all but the "call"
+
+#
+# Compare a pair of multiply weighted fits
+# In this one, the lengths of where and y won't match
+# I have to set minsplit to the smallest possible, because otherwise
+# the replicated data set will sometimes have enough "n" to split, but
+# the weighted one won't. Use of CP keeps the degenerate splits
+# (n=2, several covariates with exactly the same improvement) at bay.
+# For larger trees, the weighted split will sometimes have fewer
+# surrogates, because of the "at least two obs" rule.
+#
+set.seed(1234)
+wts <- sample(1:5, nrow(stagec), replace=TRUE)
+temp <- rep(1:nrow(stagec), wts) #row replicates
+xgrp <- rep(1:10, length=146)[order(runif(146))]
+xgrp2<- rep(xgrp, wts)
+# Direct: replicate rows in the data set, and use unweighted
+fit2 <- rpart(Surv(pgtime, pgstat) ~ age + eet + g2+grade+gleason +ploidy,
+ control=rpart.control(minsplit=2, xval=xgrp2, cp=.025),
+ data=stagec[temp,], method='poisson')
+# Weighted
+fit2b<- rpart(Surv(pgtime, pgstat) ~ age + eet + g2+grade+gleason +ploidy,
+ control=rpart.control(minsplit=2, xval=xgrp, cp=.025),
+ data=stagec, method='poisson', weight=wts)
+
+all.equal(fit2$frame[-2], fit2b$frame[-2]) # the "n" component won't match
+all.equal(fit2$cptable, fit2b$cptable)
+# next two depend on how ties are resolved, so platform-dependent
+# all.equal(fit2$splits[,-1],fit2b$splits[,-1]) #fails
+# all.equal(fit2$splits[-24,-1],fit2b$splits[-24,-1]) #ok
+all.equal(fit2$csplit, fit2b$csplit)
+# Line 24 is a surrogate split in a group whose 2 smallest ages are
+# 47 and 48. The weighted fit won't split there because it wants to
+# send at least 2 obs to the left; the replicate fit thinks that there
+# are several 47's.
+
+
+
+
+
+#
+# Test weights in a regression problem
+#
+
+xgrp <- rep(1:10,5)
+fit4 <- rpart(income ~ population + region + illiteracy +life + murder +
+ hs.grad + frost , mystate,
+ control=rpart.control(minsplit=10, xval=xgrp))
+wts <- rep(3, nrow(mystate))
+fit4b <- rpart(income ~ population + region + illiteracy +life + murder +
+ hs.grad + frost , mystate,
+ control=rpart.control(minsplit=10, xval=xgrp), weights=wts)
+fit4b$frame$wt <- fit4b$frame$wt/3
+fit4b$frame$dev <- fit4b$frame$dev/3
+fit4b$cptable[,5] <- fit4b$cptable[,5] * sqrt(3)
+temp <- c('frame', 'where', 'splits', 'csplit', 'cptable')
+all.equal(fit4[temp], fit4b[temp])
+
+
+# Next is a very simple case, but worth keeping
+dummy <- data.frame(y=1:10, x1=c(10:4, 1:3), x2=c(1,3,5,7,9,2,4,6,8,0))
+
+xx1 <- rpart(y ~ x1 + x2, dummy, minsplit=4, xval=0)
+xx2 <- rpart(y ~ x1 + x2, dummy, weights=rep(2,10), minsplit=4, xval=0)
+
+all.equal(xx1$frame$dev, c(82.5, 10, 2, .5, 10, .5, 2))
+all.equal(xx2$frame$dev, c(82.5, 10, 2, .5, 10, .5, 2)*2)
+summary(xx2)
+
+
+# Now for a set of non-equal weights
+# We need to set maxcompete=3 because there just happens to be, in one
+# of the lower nodes, an exact tie between variables "life" and "murder".
+# Round off error causes fit5 to choose one and fit5b the other.
+# Later -- cut it back to maxdepth=3 for the same reason (a tie).
+#
+nn <- nrow(mystate)
+wts <- sample(1:5, nn, replace=TRUE)
+temp <- rep(1:nn, wts) #row replicates
+xgrp <- rep(1:10, length=nn)[order(runif(nn))]
+xgrp2<- rep(xgrp, wts)
+tempc <- rpart.control(minsplit=2, xval=xgrp2, maxsurrogate=0,
+ maxcompete=3, maxdepth=3)
+# Direct: replicate rows in the data set, and use unweighted
+fit5 <- rpart(income ~ population + region + illiteracy +life + murder +
+ hs.grad + frost , data=mystate[temp,], control=tempc)
+# Weighted
+tempc <- rpart.control(minsplit=2, xval=xgrp, maxsurrogate=0,
+ maxcompete=3, maxdepth=3)
+fit5b <- rpart(income ~ population + region + illiteracy +life + murder +
+ hs.grad + frost , data=mystate, control=tempc,
+ weights=wts)
+all.equal(fit5$frame[-2], fit5b$frame[-2]) # the "n" component won't match
+all.equal(fit5$cptable, fit5b$cptable)
+all.equal(fit5$splits[,-1],fit5b$splits[,-1])
+all.equal(fit5$csplit, fit5b$csplit)
+#
+# The treble test for classification trees
+#
+#
+xgrp <- rep(1:10,length=nrow(cu.summary))
+carfit <- rpart(Country ~ Reliability + Price + Mileage + Type,
+ method='class', data=cu.summary,
+ control=rpart.control(xval=xgrp))
+
+carfit2 <- rpart(Country ~ Reliability + Price + Mileage + Type,
+ method='class', data=cu.summary,
+ weight=rep(3,nrow(cu.summary)),
+ control=rpart.control(xval=xgrp))
+
+all.equal(carfit$frame$wt, carfit2$frame$wt/3)
+all.equal(carfit$frame$dev, carfit2$frame$dev/3)
+all.equal(carfit$frame[,5:7], carfit2$frame[,5:7])
+all.equal(carfit$frame$yval2[,12:21], carfit2$frame$yval2[,12:21])
+all.equal(carfit[c('where', 'csplit')],
+ carfit2[c('where', 'csplit')])
+xx <- carfit2$splits
+xx[,'improve'] <- xx[,'improve'] / ifelse(xx[,5]> 0,1,3) # surrogate?
+all.equal(xx, carfit$splits)
+all.equal(as.vector(carfit$cptable),
+ as.vector(carfit2$cptable%*% diag(c(1,1,1,1,sqrt(3)))))
+
+summary(carfit2)
+
+#
+# Treble test for class trees with 2 outcomes
+#
+fit1 <- rpart(Kyphosis ~ Age + Number + Start, data=kyphosis,
+ control=rpart.control(maxsurrogate=0, cp=0, xval=0),
+ parms=list(prior=c(.7,.3),
+ loss=matrix(c(0,1,2,0),nrow=2,ncol=2)))
+wts <- rep(3, nrow(kyphosis))
+fit1b <- rpart(Kyphosis ~ Age + Number + Start, data=kyphosis,
+ control=rpart.control(maxsurrogate=0, cp=0, xval=0),
+ weights=wts,
+ parms=list(prior=c(.7,.3),
+ loss=matrix(c(0,1,2,0),nrow=2,ncol=2)))
+fit1b$frame$wt <- fit1b$frame$wt/3
+fit1b$frame$dev <- fit1b$frame$dev/3
+fit1b$frame$yval2[,2:3] <- fit1b$frame$yval2[,2:3]/3
+fit1b$splits[,3] <- fit1b$splits[,3]/3
+all.equal(fit1[-3], fit1b[-3]) #all but the "call"
+
+# Now for a set of non-equal weights
+nn <- nrow(kyphosis)
+wts <- sample(1:5, nn, replace=TRUE)
+temp <- rep(1:nn, wts) #row replicates
+xgrp <- rep(1:10, length=nn)[order(runif(nn))]
+xgrp2<- rep(xgrp, wts)
+tempc <- rpart.control(minsplit=2, xval=xgrp2, maxsurrogate=0)
+# Direct: replicate rows in the data set, and use unweighted
+fit2 <- rpart(Kyphosis ~ Age + Number + Start, data=kyphosis[temp,],
+ control=tempc,
+ parms=list(prior=c(.7,.3),
+ loss=matrix(c(0,1,2,0),nrow=2,ncol=2)))
+# Weighted
+tempc <- rpart.control(minsplit=2, xval=xgrp, maxsurrogate=0)
+fit2b <- rpart(Kyphosis ~ Age + Number + Start, data=kyphosis,
+ control=tempc, weights=wts,
+ parms=list(prior=c(.7,.3),
+ loss=matrix(c(0,1,2,0),nrow=2,ncol=2)))
+
+# all.equal(fit2$frame[-2], fit2b$frame[-2]) # the "n" component won't match
+all.equal(fit2$cptable, fit2b$cptable)
+# all.equal(fit2$splits[,-1],fit2b$splits[,-1]) #fails
+all.equal(fit2$csplit, fit2b$csplit)
+
+
+#
+# Check out using costs
+#
+fit1 <- rpart(Surv(time, status) ~ age + sex + ph.ecog + ph.karno + pat.karno
+ + meal.cal + wt.loss, data=lung,
+ maxdepth=1, maxcompete=6, xval=0)
+
+fit2 <- rpart(Surv(time, status) ~ age + sex + ph.ecog + ph.karno + pat.karno
+ + meal.cal + wt.loss, data=lung,
+ maxdepth=1, maxcompete=6, xval=0, cost=(1+ 1:7/10))
+
+temp1 <- fit1$splits[1:7,]
+temp2 <- fit2$splits[1:7,]
+temp3 <- c('age', 'sex', 'ph.ecog', 'ph.karno', 'pat.karno', 'meal.cal',
+ 'wt.loss')
+indx1 <- match(temp3, dimnames(temp1)[[1]])
+indx2 <- match(temp3, dimnames(temp2)[[1]])
+all.equal(temp1[indx1,1], temp2[indx2,1]) #same n's ?
+all.equal(temp1[indx1,3], temp2[indx2,3]*(1+ 1:7/10)) #scaled importance
+
+
+q()
diff --git a/win32/deps/library/rpart/tests/testall.Rout.save b/win32/deps/library/rpart/tests/testall.Rout.save
new file mode 100644
index 0000000..d431ad7
--- /dev/null
+++ b/win32/deps/library/rpart/tests/testall.Rout.save
@@ -0,0 +1,1506 @@
+
+R version 2.13.0 Under development (unstable) (2011-03-05 r54672)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> # Any necessary setup
+> library(rpart)
+> library(survival)
+Loading required package: splines
+> options(na.action="na.omit")
+> options(digits=4) # to match earlier output
+> RNGversion("1.6.2")
+Warning message:
+In RNGkind("Marsaglia-Multicarry", "Buggy Kinderman-Ramage") :
+ Buggy version of Kinderman-Ramage generator used
+> set.seed(1234)
+> #
+> # Read the data
+> #
+> # Time to progression in years
+> # status 1=progressed, 0= censored
+> # age
+> # early endocrine therapy 1=no 2=yes
+> # % of cells in g2 phase, from flow cytometry
+> # tumor grade (Farrow) 1,2,3,4
+> # Gleason score (competing grading system)
+> # ploidy
+>
+> stagec <- read.table('data.stagec', col.names=c("pgtime", "pgstat", "age",
++ "eet", "g2", "grade", "gleason", "ploidy"))
+> stagec$ploidy <- factor(stagec$ploidy, levels=1:3,
++ labels=c("diploid", "tetraploid", "aneuploid"))
+>
+> cox0 <- coxph(Surv(pgtime, pgstat) ~ 1, stagec)
+> cox1 <- coxph(Surv(pgtime, pgstat) ~ age + eet + g2 + grade + ploidy, stagec)
+> cox1
+Call:
+coxph(formula = Surv(pgtime, pgstat) ~ age + eet + g2 + grade +
+ ploidy, data = stagec)
+
+
+ coef exp(coef) se(coef) z p
+age -0.0173 0.983 0.0287 -0.604 5.5e-01
+eet 0.0704 1.073 0.3730 0.189 8.5e-01
+g2 -0.0527 0.949 0.0267 -1.973 4.9e-02
+grade 1.7289 5.634 0.3369 5.132 2.9e-07
+ploidytetraploid 1.0444 2.842 0.4225 2.472 1.3e-02
+ploidyaneuploid 1.1490 3.155 0.6611 1.738 8.2e-02
+
+Likelihood ratio test=48.6 on 6 df, p=8.92e-09 n= 137, number of events= 49
+ (9 observations deleted due to missingness)
+>
+> fit1 <- rpart(Surv(pgtime, pgstat) ~ age + eet + g2+grade+gleason +ploidy,
++ stagec, control=rpart.control(usesurrogate=0, cp=0),
++ method='poisson')
+> fit1
+n= 146
+
+node), split, n, deviance, yval
+ * denotes terminal node
+
+ 1) root 146 193.500 0.058500
+ 2) grade< 2.5 61 46.090 0.021290
+ 4) g2< 11.36 33 9.325 0.007180
+ 8) g2>=6.545 26 1.847 0.004466 *
+ 9) g2< 6.545 7 5.904 0.027880 *
+ 5) g2>=11.36 27 27.940 0.044910
+ 10) g2>=14.37 15 12.460 0.030970 *
+ 11) g2< 14.37 12 13.730 0.067920 *
+ 3) grade>=2.5 85 122.600 0.094370
+ 6) age>=56.5 75 104.300 0.082810
+ 12) g2>=22.77 12 14.840 0.039570 *
+ 13) g2< 22.77 57 75.780 0.100200
+ 26) gleason< 7.5 41 55.530 0.076840
+ 52) g2< 13.47 23 26.750 0.050850
+ 104) g2>=11.52 7 5.309 0.030860 *
+ 105) g2< 11.52 16 20.210 0.063860 *
+ 53) g2>=13.47 18 25.300 0.112100 *
+ 27) gleason>=7.5 16 15.170 0.163900 *
+ 7) age< 56.5 10 11.780 0.197100 *
+> summary(fit1)
+Call:
+rpart(formula = Surv(pgtime, pgstat) ~ age + eet + g2 + grade +
+ gleason + ploidy, data = stagec, method = "poisson", control = rpart.control(usesurrogate = 0,
+ cp = 0))
+ n= 146
+
+ CP nsplit rel error xerror xstd
+1 0.128138 0 1.0000 1.0187 0.06276
+2 0.052155 1 0.8719 0.9510 0.07306
+3 0.045615 3 0.7676 1.0155 0.08505
+4 0.026271 4 0.7219 1.0083 0.08603
+5 0.017966 5 0.6957 0.9905 0.09158
+6 0.009059 6 0.6777 1.0184 0.09407
+7 0.008132 7 0.6686 1.0107 0.09306
+8 0.006384 8 0.6605 1.0154 0.09288
+9 0.000000 9 0.6541 1.0033 0.09034
+
+Node number 1: 146 observations, complexity param=0.1281
+ events=54, estimated rate=0.0585 , mean deviance=1.325
+ left son=2 (61 obs) right son=3 (85 obs)
+ Primary splits:
+ grade < 2.5 to the left, improve=24.840, (0 missing)
+ gleason < 5.5 to the left, improve=21.620, (3 missing)
+ ploidy splits as LRR, improve=13.000, (0 missing)
+ g2 < 13.2 to the left, improve=11.440, (7 missing)
+ age < 53.5 to the right, improve= 2.482, (0 missing)
+ Surrogate splits:
+ gleason < 5.5 to the left, agree=0.863, adj=0.672, (0 split)
+ ploidy splits as LRR, agree=0.644, adj=0.148, (0 split)
+ g2 < 9.945 to the left, agree=0.630, adj=0.115, (0 split)
+ age < 66.5 to the right, agree=0.589, adj=0.016, (0 split)
+
+Node number 2: 61 observations, complexity param=0.04562
+ events=9, estimated rate=0.02129 , mean deviance=0.7556
+ left son=4 (33 obs) right son=5 (27 obs), 1 observation remains
+ Primary splits:
+ g2 < 11.36 to the left, improve=8.9660, (1 missing)
+ ploidy splits as LRL, improve=7.4650, (0 missing)
+ age < 68.5 to the right, improve=3.9540, (0 missing)
+ gleason < 5.5 to the left, improve=1.8060, (3 missing)
+ eet < 1.5 to the left, improve=0.5441, (1 missing)
+ Surrogate splits:
+ ploidy splits as LR-, agree=0.917, adj=0.815, (0 split)
+ age < 65.5 to the left, agree=0.617, adj=0.148, (0 split)
+
+Node number 3: 85 observations, complexity param=0.05215
+ events=45, estimated rate=0.09437 , mean deviance=1.442
+ left son=6 (75 obs) right son=7 (10 obs)
+ Primary splits:
+ age < 56.5 to the right, improve=7.3330, (0 missing)
+ g2 < 22.76 to the right, improve=6.8130, (6 missing)
+ gleason < 8.5 to the left, improve=4.8430, (0 missing)
+ ploidy splits as LLR, improve=1.7270, (0 missing)
+ eet < 1.5 to the right, improve=0.9572, (1 missing)
+
+Node number 4: 33 observations, complexity param=0.008132
+ events=1, estimated rate=0.00718 , mean deviance=0.2826
+ left son=8 (26 obs) right son=9 (7 obs)
+ Primary splits:
+ g2 < 6.545 to the right, improve=3.1310, (0 missing)
+ age < 62.5 to the right, improve=1.3530, (0 missing)
+ eet < 1.5 to the left, improve=0.6605, (0 missing)
+ gleason < 5.5 to the right, improve=0.4880, (2 missing)
+ Surrogate splits:
+ grade < 1.5 to the right, agree=0.848, adj=0.286, (0 split)
+
+Node number 5: 27 observations, complexity param=0.009059
+ events=8, estimated rate=0.04491 , mean deviance=1.035
+ left son=10 (15 obs) right son=11 (12 obs)
+ Primary splits:
+ g2 < 14.37 to the right, improve=1.818, (0 missing)
+ gleason < 5.5 to the left, improve=1.698, (1 missing)
+ age < 62.5 to the left, improve=1.137, (0 missing)
+ Surrogate splits:
+ ploidy splits as RL-, agree=0.741, adj=0.417, (0 split)
+ age < 65 to the left, agree=0.630, adj=0.167, (0 split)
+ gleason < 5.5 to the left, agree=0.630, adj=0.167, (0 split)
+
+Node number 6: 75 observations, complexity param=0.05215
+ events=37, estimated rate=0.08281 , mean deviance=1.391
+ left son=12 (12 obs) right son=13 (57 obs), 6 observations remain
+ Primary splits:
+ g2 < 22.76 to the right, improve=4.8340, (6 missing)
+ gleason < 7.5 to the left, improve=4.0830, (0 missing)
+ age < 69.5 to the left, improve=2.7450, (0 missing)
+ ploidy splits as LRR, improve=0.7867, (0 missing)
+ eet < 1.5 to the right, improve=0.1978, (1 missing)
+
+Node number 7: 10 observations
+ events=8, estimated rate=0.1971 , mean deviance=1.178
+
+Node number 8: 26 observations
+ events=0, estimated rate=0.004466 , mean deviance=0.07105
+
+Node number 9: 7 observations
+ events=1, estimated rate=0.02788 , mean deviance=0.8435
+
+Node number 10: 15 observations
+ events=3, estimated rate=0.03097 , mean deviance=0.8305
+
+Node number 11: 12 observations
+ events=5, estimated rate=0.06792 , mean deviance=1.144
+
+Node number 12: 12 observations
+ events=4, estimated rate=0.03957 , mean deviance=1.236
+
+Node number 13: 57 observations, complexity param=0.02627
+ events=30, estimated rate=0.1002 , mean deviance=1.33
+ left son=26 (41 obs) right son=27 (16 obs)
+ Primary splits:
+ gleason < 7.5 to the left, improve=5.37200, (0 missing)
+ g2 < 13.2 to the left, improve=4.45500, (0 missing)
+ ploidy splits as LRR, improve=3.48400, (0 missing)
+ age < 69.5 to the left, improve=3.14300, (0 missing)
+ eet < 1.5 to the left, improve=0.04885, (1 missing)
+ Surrogate splits:
+ grade < 3.5 to the left, agree=0.772, adj=0.187, (0 split)
+
+Node number 26: 41 observations, complexity param=0.01797
+ events=18, estimated rate=0.07684 , mean deviance=1.354
+ left son=52 (23 obs) right son=53 (18 obs)
+ Primary splits:
+ g2 < 13.48 to the left, improve=3.55300, (0 missing)
+ ploidy splits as LRR, improve=3.04200, (0 missing)
+ age < 65.5 to the left, improve=0.67910, (0 missing)
+ eet < 1.5 to the left, improve=0.09085, (0 missing)
+ gleason < 6.5 to the right, improve=0.01940, (0 missing)
+ Surrogate splits:
+ ploidy splits as LRL, agree=0.976, adj=0.944, (0 split)
+ eet < 1.5 to the right, agree=0.634, adj=0.167, (0 split)
+ age < 58.5 to the right, agree=0.585, adj=0.056, (0 split)
+
+Node number 27: 16 observations
+ events=12, estimated rate=0.1639 , mean deviance=0.9483
+
+Node number 52: 23 observations, complexity param=0.006384
+ events=7, estimated rate=0.05085 , mean deviance=1.163
+ left son=104 (7 obs) right son=105 (16 obs)
+ Primary splits:
+ g2 < 11.52 to the right, improve=1.40500, (0 missing)
+ age < 62.5 to the right, improve=1.24800, (0 missing)
+ gleason < 6.5 to the left, improve=0.01894, (0 missing)
+ Surrogate splits:
+ age < 71 to the right, agree=0.826, adj=0.429, (0 split)
+ ploidy splits as RLR, agree=0.739, adj=0.143, (0 split)
+
+Node number 53: 18 observations
+ events=11, estimated rate=0.1121 , mean deviance=1.405
+
+Node number 104: 7 observations
+ events=1, estimated rate=0.03086 , mean deviance=0.7585
+
+Node number 105: 16 observations
+ events=6, estimated rate=0.06386 , mean deviance=1.263
+
+>
+> fit2 <- rpart(cox0$residual ~ age + eet + g2+grade+gleason +ploidy,
++ stagec)
+> fit2
+n= 146
+
+node), split, n, deviance, yval
+ * denotes terminal node
+
+ 1) root 146 53.420 -4.563e-17
+ 2) grade< 2.5 61 11.330 -2.892e-01
+ 4) g2< 13.19 40 3.270 -4.119e-01 *
+ 5) g2>=13.19 21 6.314 -5.547e-02
+ 10) g2>=14.62 14 3.098 -1.913e-01 *
+ 11) g2< 14.62 7 2.440 2.163e-01 *
+ 3) grade>=2.5 85 33.320 2.075e-01
+ 6) age>=56.5 75 29.090 1.526e-01
+ 12) gleason< 7.5 50 18.400 5.706e-02
+ 24) g2< 13.47 25 7.725 -4.713e-02 *
+ 25) g2>=13.47 25 10.140 1.612e-01
+ 50) g2>=17.91 14 4.903 -6.099e-02 *
+ 51) g2< 17.91 11 3.662 4.441e-01 *
+ 13) gleason>=7.5 25 9.318 3.436e-01
+ 26) g2>=17 9 3.753 7.496e-02 *
+ 27) g2< 17 16 4.551 4.946e-01 *
+ 7) age< 56.5 10 2.304 6.199e-01 *
+> summary(fit2)
+Call:
+rpart(formula = cox0$residual ~ age + eet + g2 + grade + gleason +
+ ploidy, data = stagec)
+ n= 146
+
+ CP nsplit rel error xerror xstd
+1 0.16404 0 1.0000 1.0192 0.05787
+2 0.03608 1 0.8360 0.8708 0.06720
+3 0.03275 2 0.7999 1.0292 0.08526
+4 0.02561 3 0.7671 1.0005 0.08657
+5 0.01979 4 0.7415 1.0497 0.09136
+6 0.01899 6 0.7019 1.0494 0.09154
+7 0.01452 7 0.6830 1.0499 0.09209
+8 0.01000 8 0.6684 1.0801 0.09695
+
+Node number 1: 146 observations, complexity param=0.164
+ mean=-4.563e-17, MSE=0.3659
+ left son=2 (61 obs) right son=3 (85 obs)
+ Primary splits:
+ grade < 2.5 to the left, improve=0.16400, (0 missing)
+ gleason < 5.5 to the left, improve=0.13570, (3 missing)
+ ploidy splits as LRR, improve=0.09188, (0 missing)
+ g2 < 13.2 to the left, improve=0.08482, (7 missing)
+ age < 58.5 to the right, improve=0.01991, (0 missing)
+ Surrogate splits:
+ gleason < 5.5 to the left, agree=0.863, adj=0.672, (0 split)
+ ploidy splits as LRR, agree=0.644, adj=0.148, (0 split)
+ g2 < 9.945 to the left, agree=0.630, adj=0.115, (0 split)
+ age < 66.5 to the right, agree=0.589, adj=0.016, (0 split)
+
+Node number 2: 61 observations, complexity param=0.03275
+ mean=-0.2892, MSE=0.1858
+ left son=4 (40 obs) right son=5 (21 obs)
+ Primary splits:
+ g2 < 13.19 to the left, improve=0.14990, (1 missing)
+ ploidy splits as LRL, improve=0.13360, (0 missing)
+ gleason < 5.5 to the left, improve=0.03917, (3 missing)
+ age < 68.5 to the right, improve=0.03753, (0 missing)
+ eet < 1.5 to the left, improve=0.01233, (1 missing)
+ Surrogate splits:
+ ploidy splits as LR-, agree=0.983, adj=0.952, (0 split)
+
+Node number 3: 85 observations, complexity param=0.03608
+ mean=0.2075, MSE=0.392
+ left son=6 (75 obs) right son=7 (10 obs)
+ Primary splits:
+ age < 56.5 to the right, improve=0.05784, (0 missing)
+ g2 < 23.48 to the right, improve=0.05207, (6 missing)
+ gleason < 8.5 to the left, improve=0.04485, (0 missing)
+ ploidy splits as LRR, improve=0.02537, (0 missing)
+ eet < 1.5 to the right, improve=0.00724, (1 missing)
+
+Node number 4: 40 observations
+ mean=-0.4119, MSE=0.08176
+
+Node number 5: 21 observations, complexity param=0.01452
+ mean=-0.05547, MSE=0.3007
+ left son=10 (14 obs) right son=11 (7 obs)
+ Primary splits:
+ g2 < 14.62 to the right, improve=0.12280, (0 missing)
+ age < 63.5 to the left, improve=0.05198, (0 missing)
+
+Node number 6: 75 observations, complexity param=0.02561
+ mean=0.1526, MSE=0.3879
+ left son=12 (50 obs) right son=13 (25 obs)
+ Primary splits:
+ gleason < 7.5 to the left, improve=0.0470300, (0 missing)
+ g2 < 23.48 to the right, improve=0.0439100, (6 missing)
+ age < 69.5 to the left, improve=0.0255400, (0 missing)
+ ploidy splits as LRR, improve=0.0191000, (0 missing)
+ eet < 1.5 to the right, improve=0.0009644, (1 missing)
+ Surrogate splits:
+ grade < 3.5 to the left, agree=0.733, adj=0.2, (0 split)
+
+Node number 7: 10 observations
+ mean=0.6199, MSE=0.2304
+
+Node number 10: 14 observations
+ mean=-0.1913, MSE=0.2213
+
+Node number 11: 7 observations
+ mean=0.2163, MSE=0.3486
+
+Node number 12: 50 observations, complexity param=0.01979
+ mean=0.05706, MSE=0.3681
+ left son=24 (25 obs) right son=25 (25 obs)
+ Primary splits:
+ g2 < 13.48 to the left, improve=4.238e-02, (3 missing)
+ ploidy splits as LRR, improve=3.143e-02, (0 missing)
+ age < 62.5 to the right, improve=1.709e-02, (0 missing)
+ gleason < 6.5 to the left, improve=5.610e-04, (0 missing)
+ eet < 1.5 to the right, improve=6.361e-05, (0 missing)
+ Surrogate splits:
+ ploidy splits as LRL, agree=0.979, adj=0.957, (3 split)
+ age < 66.5 to the right, agree=0.596, adj=0.174, (0 split)
+ eet < 1.5 to the right, agree=0.553, adj=0.087, (0 split)
+ gleason < 6.5 to the left, agree=0.553, adj=0.087, (0 split)
+
+Node number 13: 25 observations, complexity param=0.01899
+ mean=0.3436, MSE=0.3727
+ left son=26 (9 obs) right son=27 (16 obs)
+ Primary splits:
+ g2 < 17 to the right, improve=1.562e-01, (3 missing)
+ age < 61.5 to the right, improve=5.841e-02, (0 missing)
+ ploidy splits as RLR, improve=1.562e-02, (0 missing)
+ eet < 1.5 to the right, improve=2.882e-05, (1 missing)
+ Surrogate splits:
+ age < 57.5 to the left, agree=0.682, adj=0.125, (3 split)
+
+Node number 24: 25 observations
+ mean=-0.04713, MSE=0.309
+
+Node number 25: 25 observations, complexity param=0.01979
+ mean=0.1612, MSE=0.4055
+ left son=50 (14 obs) right son=51 (11 obs)
+ Primary splits:
+ g2 < 17.92 to the right, improve=0.1271000, (1 missing)
+ eet < 1.5 to the right, improve=0.0309400, (0 missing)
+ age < 64.5 to the left, improve=0.0241800, (0 missing)
+ gleason < 6.5 to the right, improve=0.0003038, (0 missing)
+ Surrogate splits:
+ age < 65.5 to the left, agree=0.708, adj=0.364, (1 split)
+ eet < 1.5 to the right, agree=0.667, adj=0.273, (0 split)
+ gleason < 6.5 to the right, agree=0.625, adj=0.182, (0 split)
+
+Node number 26: 9 observations
+ mean=0.07496, MSE=0.417
+
+Node number 27: 16 observations
+ mean=0.4946, MSE=0.2844
+
+Node number 50: 14 observations
+ mean=-0.06099, MSE=0.3502
+
+Node number 51: 11 observations
+ mean=0.4441, MSE=0.3329
+
+>
+> #
+> # In 6/2001 rpart.exp changed to fix a bug. A side effect was reexamination
+> # of one definition: the old version didn't count person-years after the
+> # last death in computing the rescaling, the new one does. One could argue
+> # about which is better. To match the old output, we modify the data.
+> tdata <- stagec
+> tdata$pgtime <- pmin(tdata$pgtime, max(tdata$pgtime[tdata$pgstat==1]))
+>
+> fit3 <- rpart(Surv(pgtime, pgstat) ~ age + eet + g2+grade+gleason +ploidy,
++ tdata, control=rpart.control(usesurrogate=1, cp=.001))
+>
+> summary(fit3)
+Call:
+rpart(formula = Surv(pgtime, pgstat) ~ age + eet + g2 + grade +
+ gleason + ploidy, data = tdata, control = rpart.control(usesurrogate = 1,
+ cp = 0.001))
+ n= 146
+
+ CP nsplit rel error xerror xstd
+1 0.129126 0 1.0000 1.0078 0.07351
+2 0.041689 1 0.8709 0.9179 0.07705
+3 0.028803 2 0.8292 1.0148 0.09182
+4 0.017195 3 0.8004 1.0591 0.10192
+5 0.015181 4 0.7832 1.0864 0.10375
+6 0.013514 5 0.7680 1.0813 0.10384
+7 0.012706 6 0.7545 1.0803 0.10404
+8 0.009607 8 0.7291 1.0820 0.10423
+9 0.008959 9 0.7195 1.0904 0.10545
+10 0.001000 10 0.7105 1.0802 0.10404
+
+Node number 1: 146 observations, complexity param=0.1291
+ events=54, estimated rate=1 , mean deviance=1.338
+ left son=2 (61 obs) right son=3 (85 obs)
+ Primary splits:
+ grade < 2.5 to the left, improve=25.270, (0 missing)
+ gleason < 5.5 to the left, improve=21.630, (3 missing)
+ ploidy splits as LRR, improve=14.020, (0 missing)
+ g2 < 13.2 to the left, improve=12.580, (7 missing)
+ age < 58.5 to the right, improve= 2.796, (0 missing)
+ Surrogate splits:
+ gleason < 5.5 to the left, agree=0.863, adj=0.672, (0 split)
+ ploidy splits as LRR, agree=0.644, adj=0.148, (0 split)
+ g2 < 9.945 to the left, agree=0.630, adj=0.115, (0 split)
+ age < 66.5 to the right, agree=0.589, adj=0.016, (0 split)
+
+Node number 2: 61 observations, complexity param=0.04169
+ events=9, estimated rate=0.3617 , mean deviance=0.7373
+ left son=4 (33 obs) right son=5 (28 obs)
+ Primary splits:
+ g2 < 11.36 to the left, improve=9.0400, (1 missing)
+ ploidy splits as LRL, improve=7.6600, (0 missing)
+ age < 68.5 to the right, improve=4.1550, (0 missing)
+ gleason < 5.5 to the left, improve=1.6610, (3 missing)
+ eet < 1.5 to the left, improve=0.6096, (1 missing)
+ Surrogate splits:
+ ploidy splits as LR-, agree=0.917, adj=0.815, (0 split)
+ age < 65.5 to the left, agree=0.617, adj=0.148, (1 split)
+
+Node number 3: 85 observations, complexity param=0.0288
+ events=45, estimated rate=1.623 , mean deviance=1.472
+ left son=6 (75 obs) right son=7 (10 obs)
+ Primary splits:
+ age < 56.5 to the right, improve=6.3660, (0 missing)
+ g2 < 23.48 to the right, improve=4.6720, (6 missing)
+ gleason < 8.5 to the left, improve=4.2320, (0 missing)
+ ploidy splits as LRR, improve=1.5970, (0 missing)
+ eet < 1.5 to the right, improve=0.8234, (1 missing)
+
+Node number 4: 33 observations, complexity param=0.008959
+ events=1, estimated rate=0.122 , mean deviance=0.2767
+ left son=8 (26 obs) right son=9 (7 obs)
+ Primary splits:
+ g2 < 6.545 to the right, improve=3.2920, (0 missing)
+ age < 62.5 to the right, improve=1.4220, (0 missing)
+ eet < 1.5 to the left, improve=0.6913, (0 missing)
+ gleason < 5.5 to the right, improve=0.5440, (2 missing)
+ Surrogate splits:
+ grade < 1.5 to the right, agree=0.848, adj=0.286, (0 split)
+
+Node number 5: 28 observations, complexity param=0.01351
+ events=8, estimated rate=0.7341 , mean deviance=0.9894
+ left son=10 (19 obs) right son=11 (8 obs), 1 observation remains
+ Primary splits:
+ gleason < 5.5 to the left, improve=2.129, (1 missing)
+ age < 67.5 to the right, improve=1.667, (0 missing)
+ g2 < 14.37 to the right, improve=1.397, (1 missing)
+
+Node number 6: 75 observations, complexity param=0.0172
+ events=37, estimated rate=1.432 , mean deviance=1.386
+ left son=12 (50 obs) right son=13 (25 obs)
+ Primary splits:
+ gleason < 7.5 to the left, improve=3.4240, (0 missing)
+ g2 < 23.48 to the right, improve=3.3370, (6 missing)
+ age < 69.5 to the left, improve=2.2340, (0 missing)
+ ploidy splits as LRR, improve=1.1470, (0 missing)
+ eet < 1.5 to the right, improve=0.1427, (1 missing)
+ Surrogate splits:
+ grade < 3.5 to the left, agree=0.733, adj=0.2, (0 split)
+
+Node number 7: 10 observations
+ events=8, estimated rate=3.198 , mean deviance=1.552
+
+Node number 8: 26 observations
+ events=0, estimated rate=0.07451 , mean deviance=0.07119
+
+Node number 9: 7 observations
+ events=1, estimated rate=0.5041 , mean deviance=0.7898
+
+Node number 10: 19 observations
+ events=4, estimated rate=0.5521 , mean deviance=0.7319
+
+Node number 11: 8 observations
+ events=4, estimated rate=1.314 , mean deviance=1.395
+
+Node number 12: 50 observations, complexity param=0.01271
+ events=21, estimated rate=1.149 , mean deviance=1.33
+ left son=24 (25 obs) right son=25 (25 obs)
+ Primary splits:
+ g2 < 13.48 to the left, improve=1.94600, (3 missing)
+ ploidy splits as LRR, improve=1.49100, (0 missing)
+ age < 62.5 to the right, improve=0.80830, (0 missing)
+ gleason < 6.5 to the left, improve=0.02956, (0 missing)
+ eet < 1.5 to the right, improve=0.01135, (0 missing)
+ Surrogate splits:
+ ploidy splits as LRL, agree=0.979, adj=0.957, (3 split)
+ age < 66.5 to the right, agree=0.596, adj=0.174, (0 split)
+ eet < 1.5 to the right, agree=0.553, adj=0.087, (0 split)
+ gleason < 6.5 to the left, agree=0.553, adj=0.087, (0 split)
+
+Node number 13: 25 observations, complexity param=0.01518
+ events=16, estimated rate=2.028 , mean deviance=1.365
+ left son=26 (10 obs) right son=27 (15 obs)
+ Primary splits:
+ g2 < 15.29 to the right, improve=3.92900, (3 missing)
+ age < 68.5 to the left, improve=1.34300, (0 missing)
+ ploidy splits as RLR, improve=0.83660, (0 missing)
+ eet < 1.5 to the right, improve=0.00105, (1 missing)
+ Surrogate splits:
+ ploidy splits as RLR, agree=0.727, adj=0.4, (3 split)
+ gleason < 8.5 to the right, agree=0.636, adj=0.2, (0 split)
+ age < 57.5 to the left, agree=0.591, adj=0.1, (0 split)
+ eet < 1.5 to the left, agree=0.591, adj=0.1, (0 split)
+
+Node number 24: 25 observations, complexity param=0.009607
+ events=8, estimated rate=0.8817 , mean deviance=1.164
+ left son=48 (8 obs) right son=49 (17 obs)
+ Primary splits:
+ g2 < 11.52 to the right, improve=1.19200, (2 missing)
+ age < 65.5 to the right, improve=1.16600, (0 missing)
+ gleason < 6.5 to the left, improve=0.06199, (0 missing)
+ Surrogate splits:
+ age < 70 to the right, agree=0.826, adj=0.429, (2 split)
+ ploidy splits as RLR, agree=0.739, adj=0.143, (0 split)
+
+Node number 25: 25 observations, complexity param=0.01271
+ events=13, estimated rate=1.408 , mean deviance=1.442
+ left son=50 (14 obs) right son=51 (11 obs)
+ Primary splits:
+ g2 < 17.92 to the right, improve=3.122000, (1 missing)
+ eet < 1.5 to the right, improve=1.212000, (0 missing)
+ age < 64.5 to the left, improve=0.633000, (0 missing)
+ gleason < 6.5 to the right, improve=0.001267, (0 missing)
+ Surrogate splits:
+ age < 65.5 to the left, agree=0.708, adj=0.364, (1 split)
+ eet < 1.5 to the right, agree=0.667, adj=0.273, (0 split)
+ gleason < 6.5 to the right, agree=0.625, adj=0.182, (0 split)
+
+Node number 26: 10 observations
+ events=5, estimated rate=1.214 , mean deviance=1.181
+
+Node number 27: 15 observations
+ events=11, estimated rate=2.702 , mean deviance=1.291
+
+Node number 48: 8 observations
+ events=1, estimated rate=0.4749 , mean deviance=0.6646
+
+Node number 49: 17 observations
+ events=7, estimated rate=1.144 , mean deviance=1.289
+
+Node number 50: 14 observations
+ events=5, estimated rate=0.8795 , mean deviance=1.337
+
+Node number 51: 11 observations
+ events=8, estimated rate=2.183 , mean deviance=1.246
+
+>
+> #
+> # In order to compare the x-vals estimates of the mainline and S versions,
+> # it is necessary that we use stratified xval sets (like the mainline
+> # does).
+>
+> mystate <- data.frame(state.x77, region=factor(state.region))
+> names(mystate) <- c("population","income" , "illiteracy","life" ,
++ "murder", "hs.grad", "frost", "area", "region")
+>
+> xvals <- 1:nrow(mystate)
+> xvals[order(mystate$income)] <- rep(1:10, length=nrow(mystate))
+>
+> fit4 <- rpart(income ~ population + region + illiteracy +life + murder +
++ hs.grad + frost , mystate,
++ control=rpart.control(minsplit=10, xval=xvals))
+>
+> summary(fit4)
+Call:
+rpart(formula = income ~ population + region + illiteracy + life +
+ murder + hs.grad + frost, data = mystate, control = rpart.control(minsplit = 10,
+ xval = xvals))
+ n= 50
+
+ CP nsplit rel error xerror xstd
+1 0.42831 0 1.0000 1.0157 0.2265
+2 0.13514 1 0.5717 0.5948 0.1747
+3 0.06458 2 0.4365 0.7005 0.1802
+4 0.05485 3 0.3720 0.8606 0.2299
+5 0.05346 4 0.3171 0.8494 0.2297
+6 0.02479 5 0.2637 0.8289 0.2644
+7 0.01940 6 0.2389 0.8196 0.2641
+8 0.01394 7 0.2195 0.8196 0.2641
+9 0.01000 8 0.2055 0.8117 0.2640
+
+Node number 1: 50 observations, complexity param=0.4283
+ mean=4436, MSE=3.7e+05
+ left son=2 (10 obs) right son=3 (40 obs)
+ Primary splits:
+ hs.grad < 44.3 to the left, improve=0.4283, (0 missing)
+ illiteracy < 1.55 to the right, improve=0.3249, (0 missing)
+ region splits as RLRR, improve=0.2285, (0 missing)
+ murder < 11.55 to the right, improve=0.2012, (0 missing)
+ life < 68.9 to the left, improve=0.1672, (0 missing)
+ Surrogate splits:
+ illiteracy < 1.55 to the right, agree=0.90, adj=0.5, (0 split)
+ life < 69.26 to the left, agree=0.90, adj=0.5, (0 split)
+ region splits as RLRR, agree=0.88, adj=0.4, (0 split)
+ murder < 11.55 to the right, agree=0.88, adj=0.4, (0 split)
+ frost < 81 to the left, agree=0.82, adj=0.1, (0 split)
+
+Node number 2: 10 observations, complexity param=0.0194
+ mean=3640, MSE=6.688e+04
+ left son=4 (7 obs) right son=5 (3 obs)
+ Primary splits:
+ population < 3990 to the left, improve=0.53670, (0 missing)
+ frost < 55 to the left, improve=0.30250, (0 missing)
+ illiteracy < 2.2 to the right, improve=0.29240, (0 missing)
+ hs.grad < 40.8 to the right, improve=0.14540, (0 missing)
+ murder < 12.85 to the left, improve=0.08289, (0 missing)
+
+Node number 3: 40 observations, complexity param=0.1351
+ mean=4635, MSE=2.477e+05
+ left son=6 (34 obs) right son=7 (6 obs)
+ Primary splits:
+ life < 70.26 to the right, improve=0.25230, (0 missing)
+ murder < 10 to the left, improve=0.16790, (0 missing)
+ hs.grad < 60.95 to the left, improve=0.12350, (0 missing)
+ illiteracy < 0.75 to the left, improve=0.11520, (0 missing)
+ population < 659 to the right, improve=0.08106, (0 missing)
+ Surrogate splits:
+ population < 613.5 to the right, agree=0.875, adj=0.167, (0 split)
+ murder < 11.2 to the left, agree=0.875, adj=0.167, (0 split)
+ hs.grad < 64.55 to the left, agree=0.875, adj=0.167, (0 split)
+
+Node number 4: 7 observations
+ mean=3516, MSE=3.844e+04
+
+Node number 5: 3 observations
+ mean=3929, MSE=1.361e+04
+
+Node number 6: 34 observations, complexity param=0.06458
+ mean=4530, MSE=1.69e+05
+ left son=12 (12 obs) right son=13 (22 obs)
+ Primary splits:
+ population < 1374 to the left, improve=0.20790, (0 missing)
+ life < 70.41 to the left, improve=0.19010, (0 missing)
+ frost < 33.5 to the right, improve=0.10930, (0 missing)
+ illiteracy < 0.75 to the left, improve=0.08942, (0 missing)
+ hs.grad < 59.7 to the left, improve=0.06429, (0 missing)
+ Surrogate splits:
+ frost < 152 to the right, agree=0.794, adj=0.417, (0 split)
+ life < 70.41 to the left, agree=0.735, adj=0.250, (0 split)
+ murder < 2 to the left, agree=0.706, adj=0.167, (0 split)
+ region splits as RRRL, agree=0.676, adj=0.083, (0 split)
+ illiteracy < 1.85 to the right, agree=0.676, adj=0.083, (0 split)
+
+Node number 7: 6 observations
+ mean=5230, MSE=2.768e+05
+
+Node number 12: 12 observations, complexity param=0.05485
+ mean=4276, MSE=1.942e+05
+ left son=24 (3 obs) right son=25 (9 obs)
+ Primary splits:
+ population < 994.5 to the right, improve=0.4355, (0 missing)
+ life < 71.89 to the left, improve=0.2955, (0 missing)
+ frost < 172.5 to the left, improve=0.2333, (0 missing)
+ illiteracy < 0.75 to the left, improve=0.1965, (0 missing)
+ murder < 2.55 to the right, improve=0.1847, (0 missing)
+ Surrogate splits:
+ life < 70.47 to the left, agree=0.833, adj=0.333, (0 split)
+
+Node number 13: 22 observations, complexity param=0.05346
+ mean=4668, MSE=1.01e+05
+ left son=26 (4 obs) right son=27 (18 obs)
+ Primary splits:
+ hs.grad < 52.05 to the left, improve=0.44500, (0 missing)
+ region splits as RLLR, improve=0.35050, (0 missing)
+ life < 71.56 to the left, improve=0.12220, (0 missing)
+ murder < 5.65 to the right, improve=0.10520, (0 missing)
+ population < 2980 to the left, improve=0.06276, (0 missing)
+ Surrogate splits:
+ region splits as RLRR, agree=0.864, adj=0.25, (0 split)
+
+Node number 24: 3 observations
+ mean=3772, MSE=3.261e+04
+
+Node number 25: 9 observations
+ mean=4444, MSE=1.353e+05
+
+Node number 26: 4 observations
+ mean=4218, MSE=2.77e+04
+
+Node number 27: 18 observations, complexity param=0.02479
+ mean=4768, MSE=6.236e+04
+ left son=54 (8 obs) right son=55 (10 obs)
+ Primary splits:
+ region splits as RRLR, improve=0.4086, (0 missing)
+ illiteracy < 1 to the left, improve=0.3653, (0 missing)
+ murder < 3.05 to the left, improve=0.1805, (0 missing)
+ hs.grad < 52.75 to the right, improve=0.1507, (0 missing)
+ population < 2412 to the left, improve=0.1427, (0 missing)
+ Surrogate splits:
+ illiteracy < 1 to the left, agree=0.833, adj=0.625, (0 split)
+ frost < 108.5 to the right, agree=0.833, adj=0.625, (0 split)
+ life < 72.31 to the right, agree=0.778, adj=0.500, (0 split)
+ murder < 3.05 to the left, agree=0.778, adj=0.500, (0 split)
+ hs.grad < 59.95 to the left, agree=0.667, adj=0.250, (0 split)
+
+Node number 54: 8 observations
+ mean=4590, MSE=1.009e+04
+
+Node number 55: 10 observations, complexity param=0.01394
+ mean=4911, MSE=5.832e+04
+ left son=110 (7 obs) right son=111 (3 obs)
+ Primary splits:
+ frost < 109 to the left, improve=0.4423, (0 missing)
+ population < 2820 to the left, improve=0.3546, (0 missing)
+ hs.grad < 57.05 to the right, improve=0.3103, (0 missing)
+ region splits as RL-L, improve=0.2564, (0 missing)
+ illiteracy < 1.2 to the right, improve=0.1921, (0 missing)
+ Surrogate splits:
+ life < 71.94 to the left, agree=0.8, adj=0.333, (0 split)
+
+Node number 110: 7 observations
+ mean=4806, MSE=2.969e+04
+
+Node number 111: 3 observations
+ mean=5156, MSE=3.914e+04
+
+>
+>
+> #
+> # Check out xpred.rpart
+> #
+> meany <- mean(mystate$income)
+> xpr <- xpred.rpart(fit4, xval=xvals)
+> xpr2 <- (xpr - mystate$income)^2
+> risk0 <- mean((mystate$income - meany)^2)
+> xpmean <- as.vector(apply(xpr2, 2, mean)) #kill the names
+> all.equal(xpmean/risk0, as.vector(fit4$cptable[,'xerror']))
+[1] TRUE
+>
+> xpstd <- as.vector(apply((sweep(xpr2, 2, xpmean))^2, 2, sum))
+> xpstd <- sqrt(xpstd)/(50*risk0)
+> all.equal(xpstd, as.vector(fit4$cptable[,'xstd']))
+[1] TRUE
+>
+> #
+> # recreate subset #3 of the xval
+> #
+> tfit4 <- rpart(income ~ population + region + illiteracy +life + murder +
++ hs.grad + frost , mystate, subset=(xvals!=3),
++ control=rpart.control(minsplit=10, xval=0))
+> tpred <- predict(tfit4, mystate[xvals==3,])
+> all.equal(tpred, xpr[xvals==3,ncol(xpr)])
+[1] TRUE
+>
+> # How much does this differ from the "real" formula, more complex,
+> # found on page 309 of Breiman et al. ?
+> #xtemp <- (xpr2/outer(rep(1,50),xpmean)) - ((mystate$income - meany)^2)/risk0
+> #real.se<- xpmean* sqrt(apply(xtemp^2,2,sum))/(risk0*50)
+>
+> fit5 <- rpart(factor(pgstat) ~ age + eet + g2+grade+gleason +ploidy,
++ stagec)
+>
+> fit5
+n= 146
+
+node), split, n, loss, yval, (yprob)
+ * denotes terminal node
+
+ 1) root 146 54 0 (0.6301 0.3699)
+ 2) grade< 2.5 61 9 0 (0.8525 0.1475) *
+ 3) grade>=2.5 85 40 1 (0.4706 0.5294)
+ 6) g2< 13.2 40 17 0 (0.5750 0.4250)
+ 12) ploidy=diploid,tetraploid 31 11 0 (0.6452 0.3548)
+ 24) g2>=11.84 7 1 0 (0.8571 0.1429) *
+ 25) g2< 11.84 24 10 0 (0.5833 0.4167)
+ 50) g2< 11 17 5 0 (0.7059 0.2941) *
+ 51) g2>=11 7 2 1 (0.2857 0.7143) *
+ 13) ploidy=aneuploid 9 3 1 (0.3333 0.6667) *
+ 7) g2>=13.2 45 17 1 (0.3778 0.6222)
+ 14) g2>=17.91 22 8 0 (0.6364 0.3636)
+ 28) age>=62.5 15 4 0 (0.7333 0.2667) *
+ 29) age< 62.5 7 3 1 (0.4286 0.5714) *
+ 15) g2< 17.91 23 3 1 (0.1304 0.8696) *
+>
+> fit6 <- rpart(factor(pgstat) ~ age + eet + g2+grade+gleason +ploidy,
++ stagec, parm=list(prior=c(.5,.5)))
+> summary(fit6)
+Call:
+rpart(formula = factor(pgstat) ~ age + eet + g2 + grade + gleason +
+ ploidy, data = stagec, parms = list(prior = c(0.5, 0.5)))
+ n= 146
+
+ CP nsplit rel error xerror xstd
+1 0.39855 0 1.0000 1.1630 0.08486
+2 0.02335 1 0.6014 0.6341 0.07357
+3 0.02275 3 0.5548 0.7822 0.08197
+4 0.01892 5 0.5093 0.8007 0.08284
+5 0.01530 7 0.4714 0.8780 0.08508
+6 0.01000 9 0.4408 0.8422 0.08610
+
+Node number 1: 146 observations, complexity param=0.3986
+ predicted class=0 expected loss=0.5
+ class counts: 92 54
+ probabilities: 0.500 0.500
+ left son=2 (61 obs) right son=3 (85 obs)
+ Primary splits:
+ grade < 2.5 to the left, improve=12.490, (0 missing)
+ gleason < 5.5 to the left, improve=10.510, (3 missing)
+ ploidy splits as LRR, improve= 9.018, (0 missing)
+ g2 < 13.2 to the left, improve= 8.281, (7 missing)
+ age < 58.5 to the right, improve= 1.520, (0 missing)
+ Surrogate splits:
+ gleason < 5.5 to the left, agree=0.863, adj=0.672, (0 split)
+ ploidy splits as LRR, agree=0.644, adj=0.148, (0 split)
+ g2 < 9.945 to the left, agree=0.630, adj=0.115, (0 split)
+ age < 66.5 to the right, agree=0.589, adj=0.016, (0 split)
+
+Node number 2: 61 observations, complexity param=0.0153
+ predicted class=0 expected loss=0.1995
+ class counts: 52 9
+ probabilities: 0.772 0.228
+ left son=4 (33 obs) right son=5 (28 obs)
+ Primary splits:
+ g2 < 11.36 to the left, improve=3.5470, (1 missing)
+ ploidy splits as LRL, improve=3.2970, (0 missing)
+ age < 68.5 to the right, improve=1.2020, (0 missing)
+ gleason < 5.5 to the left, improve=0.6474, (3 missing)
+ eet < 1.5 to the left, improve=0.1910, (1 missing)
+ Surrogate splits:
+ ploidy splits as LR-, agree=0.917, adj=0.815, (0 split)
+ age < 65.5 to the left, agree=0.617, adj=0.148, (1 split)
+
+Node number 3: 85 observations, complexity param=0.02335
+ predicted class=1 expected loss=0.3734
+ class counts: 40 45
+ probabilities: 0.343 0.657
+ left son=6 (40 obs) right son=7 (45 obs)
+ Primary splits:
+ g2 < 13.2 to the left, improve=1.96800, (6 missing)
+ ploidy splits as LRR, improve=1.84100, (0 missing)
+ age < 56.5 to the right, improve=1.32300, (0 missing)
+ gleason < 8.5 to the left, improve=1.26900, (0 missing)
+ eet < 1.5 to the right, improve=0.09632, (1 missing)
+ Surrogate splits:
+ ploidy splits as LRL, agree=0.962, adj=0.914, (6 split)
+ age < 68.5 to the right, agree=0.608, adj=0.114, (0 split)
+ gleason < 6.5 to the left, agree=0.582, adj=0.057, (0 split)
+
+Node number 4: 33 observations
+ predicted class=0 expected loss=0.04097
+ class counts: 32 1
+ probabilities: 0.949 0.051
+
+Node number 5: 28 observations, complexity param=0.0153
+ predicted class=0 expected loss=0.3862
+ class counts: 20 8
+ probabilities: 0.595 0.405
+ left son=10 (20 obs) right son=11 (8 obs)
+ Primary splits:
+ gleason < 5.5 to the left, improve=1.1580, (1 missing)
+ age < 67.5 to the right, improve=1.1420, (0 missing)
+ g2 < 14.37 to the right, improve=0.8086, (1 missing)
+
+Node number 6: 40 observations, complexity param=0.02335
+ predicted class=1 expected loss=0.4563
+ class counts: 23 17
+ probabilities: 0.443 0.557
+ left son=12 (7 obs) right son=13 (33 obs)
+ Primary splits:
+ g2 < 11.84 to the right, improve=1.42400, (5 missing)
+ ploidy splits as LLR, improve=1.31000, (0 missing)
+ gleason < 7.5 to the left, improve=0.86340, (0 missing)
+ age < 61.5 to the right, improve=0.57940, (0 missing)
+ eet < 1.5 to the left, improve=0.05363, (0 missing)
+ Surrogate splits:
+ ploidy splits as RLR, agree=0.857, adj=0.286, (5 split)
+
+Node number 7: 45 observations, complexity param=0.02275
+ predicted class=1 expected loss=0.2998
+ class counts: 17 28
+ probabilities: 0.263 0.737
+ left son=14 (22 obs) right son=15 (23 obs)
+ Primary splits:
+ g2 < 17.91 to the right, improve=4.07900, (1 missing)
+ age < 62.5 to the right, improve=0.66100, (0 missing)
+ gleason < 7.5 to the left, improve=0.16170, (0 missing)
+ eet < 1.5 to the right, improve=0.09922, (1 missing)
+ Surrogate splits:
+ age < 61.5 to the right, agree=0.614, adj=0.190, (1 split)
+ eet < 1.5 to the right, agree=0.591, adj=0.143, (0 split)
+ grade < 3.5 to the right, agree=0.545, adj=0.048, (0 split)
+ gleason < 6.5 to the right, agree=0.545, adj=0.048, (0 split)
+
+Node number 10: 20 observations
+ predicted class=0 expected loss=0.2704
+ class counts: 16 4
+ probabilities: 0.701 0.299
+
+Node number 11: 8 observations
+ predicted class=1 expected loss=0.3967
+ class counts: 4 4
+ probabilities: 0.370 0.630
+
+Node number 12: 7 observations
+ predicted class=0 expected loss=0.1931
+ class counts: 6 1
+ probabilities: 0.779 0.221
+
+Node number 13: 33 observations, complexity param=0.01892
+ predicted class=1 expected loss=0.4088
+ class counts: 17 16
+ probabilities: 0.384 0.616
+ left son=26 (25 obs) right son=27 (8 obs)
+ Primary splits:
+ g2 < 11 to the left, improve=1.06300, (5 missing)
+ ploidy splits as L-R, improve=0.73950, (0 missing)
+ gleason < 6.5 to the left, improve=0.57220, (0 missing)
+ age < 62.5 to the right, improve=0.13320, (0 missing)
+ eet < 1.5 to the left, improve=0.05492, (0 missing)
+ Surrogate splits:
+ age < 70.5 to the left, agree=0.821, adj=0.286, (5 split)
+
+Node number 14: 22 observations, complexity param=0.02275
+ predicted class=0 expected loss=0.4916
+ class counts: 14 8
+ probabilities: 0.507 0.493
+ left son=28 (15 obs) right son=29 (7 obs)
+ Primary splits:
+ age < 62.5 to the right, improve=0.976400, (0 missing)
+ g2 < 23.48 to the right, improve=0.284300, (1 missing)
+ gleason < 7.5 to the left, improve=0.003765, (0 missing)
+ Surrogate splits:
+ gleason < 6.5 to the right, agree=0.773, adj=0.286, (0 split)
+
+Node number 15: 23 observations
+ predicted class=1 expected loss=0.1035
+ class counts: 3 20
+ probabilities: 0.081 0.919
+
+Node number 26: 25 observations, complexity param=0.01892
+ predicted class=1 expected loss=0.4443
+ class counts: 14 11
+ probabilities: 0.428 0.572
+ left son=52 (17 obs) right son=53 (8 obs)
+ Primary splits:
+ ploidy splits as L-R, improve=2.157000, (0 missing)
+ gleason < 6.5 to the left, improve=1.972000, (0 missing)
+ age < 61.5 to the right, improve=0.971800, (0 missing)
+ g2 < 7.65 to the right, improve=0.404500, (4 missing)
+ eet < 1.5 to the left, improve=0.002614, (0 missing)
+ Surrogate splits:
+ eet < 1.5 to the right, agree=0.72, adj=0.125, (0 split)
+ g2 < 4.33 to the right, agree=0.72, adj=0.125, (0 split)
+
+Node number 27: 8 observations
+ predicted class=1 expected loss=0.2976
+ class counts: 3 5
+ probabilities: 0.260 0.740
+
+Node number 28: 15 observations
+ predicted class=0 expected loss=0.3605
+ class counts: 11 4
+ probabilities: 0.617 0.383
+
+Node number 29: 7 observations
+ predicted class=1 expected loss=0.3401
+ class counts: 3 4
+ probabilities: 0.306 0.694
+
+Node number 52: 17 observations
+ predicted class=0 expected loss=0.3976
+ class counts: 12 5
+ probabilities: 0.585 0.415
+
+Node number 53: 8 observations
+ predicted class=1 expected loss=0.1984
+ class counts: 2 6
+ probabilities: 0.164 0.836
+
+> #
+> # Fit a classification model to the car data.
+> # Now, since Reliability is an ordered category, this model doesn't
+> # make a lot of statistical sense, but it does test out some
+> # areas of the code that nothing else does
+> #
+>
+> carfit <- rpart(Reliability ~ Price + Country + Mileage + Type,
++ method='class', data=cu.summary)
+>
+> summary(carfit)
+Call:
+rpart(formula = Reliability ~ Price + Country + Mileage + Type,
+ data = cu.summary, method = "class")
+ n=85 (32 observations deleted due to missingness)
+
+ CP nsplit rel error xerror xstd
+1 0.30508 0 1.0000 1.0000 0.07200
+2 0.08475 1 0.6949 0.6949 0.07808
+3 0.05085 2 0.6102 0.7119 0.07813
+4 0.03390 3 0.5593 0.7119 0.07813
+5 0.01000 4 0.5254 0.7119 0.07813
+
+Node number 1: 85 observations, complexity param=0.3051
+ predicted class=average expected loss=0.6941
+ class counts: 18 12 26 8 21
+ probabilities: 0.212 0.141 0.306 0.094 0.247
+ left son=2 (58 obs) right son=3 (27 obs)
+ Primary splits:
+ Country splits as ---LRRLLLL, improve=15.220, (0 missing)
+ Type splits as RLLRLL, improve= 4.288, (0 missing)
+ Price < 11970 to the right, improve= 3.200, (0 missing)
+ Mileage < 24.5 to the left, improve= 2.476, (36 missing)
+
+Node number 2: 58 observations, complexity param=0.08475
+ predicted class=average expected loss=0.6034
+ class counts: 18 12 23 5 0
+ probabilities: 0.310 0.207 0.397 0.086 0.000
+ left son=4 (9 obs) right son=5 (49 obs)
+ Primary splits:
+ Type splits as RRRRLR, improve=3.187, (0 missing)
+ Price < 11230 to the left, improve=2.564, (0 missing)
+ Mileage < 24.5 to the left, improve=1.802, (30 missing)
+ Country splits as ---L--RLRL, improve=1.329, (0 missing)
+
+Node number 3: 27 observations
+ predicted class=Much better expected loss=0.2222
+ class counts: 0 0 3 3 21
+ probabilities: 0.000 0.000 0.111 0.111 0.778
+
+Node number 4: 9 observations
+ predicted class=Much worse expected loss=0.2222
+ class counts: 7 0 2 0 0
+ probabilities: 0.778 0.000 0.222 0.000 0.000
+
+Node number 5: 49 observations, complexity param=0.05085
+ predicted class=average expected loss=0.5714
+ class counts: 11 12 21 5 0
+ probabilities: 0.224 0.245 0.429 0.102 0.000
+ left son=10 (27 obs) right son=11 (22 obs)
+ Primary splits:
+ Type splits as RLLR-L, improve=2.880, (0 missing)
+ Mileage < 24.5 to the left, improve=2.500, (25 missing)
+ Price < 11470 to the right, improve=2.424, (0 missing)
+ Country splits as ---R--LRLR, improve=1.027, (0 missing)
+ Surrogate splits:
+ Price < 11470 to the right, agree=0.898, adj=0.773, (0 split)
+ Country splits as ---R--RRRL, agree=0.755, adj=0.455, (0 split)
+
+Node number 10: 27 observations
+ predicted class=average expected loss=0.4074
+ class counts: 7 4 16 0 0
+ probabilities: 0.259 0.148 0.593 0.000 0.000
+
+Node number 11: 22 observations, complexity param=0.0339
+ predicted class=worse expected loss=0.6364
+ class counts: 4 8 5 5 0
+ probabilities: 0.182 0.364 0.227 0.227 0.000
+ left son=22 (14 obs) right son=23 (8 obs)
+ Primary splits:
+ Country splits as ---R--LRRL, improve=1.5190, (0 missing)
+ Price < 8646 to the left, improve=1.2720, (0 missing)
+ Type splits as L--R--, improve=0.1909, (0 missing)
+ Surrogate splits:
+ Price < 13970 to the left, agree=0.864, adj=0.625, (0 split)
+
+Node number 22: 14 observations
+ predicted class=worse expected loss=0.5714
+ class counts: 4 6 1 3 0
+ probabilities: 0.286 0.429 0.071 0.214 0.000
+
+Node number 23: 8 observations
+ predicted class=average expected loss=0.5
+ class counts: 0 2 4 2 0
+ probabilities: 0.000 0.250 0.500 0.250 0.000
+
+> #
+> # Simplest weight test: treble the weights
+> #
+> # By using the unshrunken estimates the weights will nearly cancel
+> # out: frame$wt, frame$dev, frame$yval2, and improvement will all
+> # be threefold larger, other things will be the same.
+> # The improvement is the splits matrix, column 3, rows with n>0. Other
+> # rows are surrogate splits.
+>
+> tempc <- rpart.control(maxsurrogate=0, cp=0, xval=0)
+> fit1 <- rpart(Surv(pgtime, pgstat) ~ age + eet + g2+grade+gleason +ploidy,
++ stagec, control=tempc,
++ method='poisson', parms=list(shrink=0))
+> wts <- rep(3, nrow(stagec))
+> fit1b <- rpart(Surv(pgtime, pgstat) ~ age + eet + g2+grade+gleason +ploidy,
++ stagec, control= tempc, parms=list(shrink=0),
++ method='poisson', weights=wts)
+> fit1b$frame$wt <- fit1b$frame$wt/3
+> fit1b$frame$dev <- fit1b$frame$dev/3
+> fit1b$frame$yval2[,2] <- fit1b$frame$yval2[,2]/3
+> fit1b$splits[,3] <- fit1b$splits[,3]/3
+> all.equal(fit1[-3], fit1b[-3]) #all but the "call"
+[1] TRUE
+>
+> #
+> # Compare a pair of multiply weighted fits
+> # In this one, the lengths of where and y won't match
+> # I have to set minsplit to the smallest possible, because otherwise
+> # the replicated data set will sometimes have enough "n" to split, but
+> # the weighted one won't. Use of CP keeps the degenerate splits
+> # (n=2, several covariates with exactly the same improvement) at bay.
+> # For larger trees, the weighted split will sometimes have fewer
+> # surrogates, because of the "at least two obs" rule.
+> #
+> set.seed(1234)
+> wts <- sample(1:5, nrow(stagec), replace=TRUE)
+> temp <- rep(1:nrow(stagec), wts) #row replicates
+> xgrp <- rep(1:10, length=146)[order(runif(146))]
+> xgrp2<- rep(xgrp, wts)
+> # Direct: replicate rows in the data set, and use unweighted
+> fit2 <- rpart(Surv(pgtime, pgstat) ~ age + eet + g2+grade+gleason +ploidy,
++ control=rpart.control(minsplit=2, xval=xgrp2, cp=.025),
++ data=stagec[temp,], method='poisson')
+> # Weighted
+> fit2b<- rpart(Surv(pgtime, pgstat) ~ age + eet + g2+grade+gleason +ploidy,
++ control=rpart.control(minsplit=2, xval=xgrp, cp=.025),
++ data=stagec, method='poisson', weight=wts)
+>
+> all.equal(fit2$frame[-2], fit2b$frame[-2]) # the "n" component won't match
+[1] "Component 7: Mean relative difference: 0.5"
+> all.equal(fit2$cptable, fit2b$cptable)
+[1] TRUE
+> # next two depend on how ties are resolved, so platform-dependent
+> # all.equal(fit2$splits[,-1],fit2b$splits[,-1]) #fails
+> # all.equal(fit2$splits[-24,-1],fit2b$splits[-24,-1]) #ok
+> all.equal(fit2$csplit, fit2b$csplit)
+[1] TRUE
+> # Line 24 is a surrogate split in a group whose 2 smallest ages are
+> # 47 and 48. The weighted fit won't split there because it wants to
+> # send at least 2 obs to the left; the replicate fit thinks that there
+> # are several 47's.
+>
+>
+>
+>
+>
+> #
+> # Test weights in a regression problem
+> #
+>
+> xgrp <- rep(1:10,5)
+> fit4 <- rpart(income ~ population + region + illiteracy +life + murder +
++ hs.grad + frost , mystate,
++ control=rpart.control(minsplit=10, xval=xgrp))
+> wts <- rep(3, nrow(mystate))
+> fit4b <- rpart(income ~ population + region + illiteracy +life + murder +
++ hs.grad + frost , mystate,
++ control=rpart.control(minsplit=10, xval=xgrp), weights=wts)
+> fit4b$frame$wt <- fit4b$frame$wt/3
+> fit4b$frame$dev <- fit4b$frame$dev/3
+> fit4b$cptable[,5] <- fit4b$cptable[,5] * sqrt(3)
+> temp <- c('frame', 'where', 'splits', 'csplit', 'cptable')
+> all.equal(fit4[temp], fit4b[temp])
+[1] TRUE
+>
+>
+> # Next is a very simple case, but worth keeping
+> dummy <- data.frame(y=1:10, x1=c(10:4, 1:3), x2=c(1,3,5,7,9,2,4,6,8,0))
+>
+> xx1 <- rpart(y ~ x1 + x2, dummy, minsplit=4, xval=0)
+> xx2 <- rpart(y ~ x1 + x2, dummy, weights=rep(2,10), minsplit=4, xval=0)
+>
+> all.equal(xx1$frame$dev, c(82.5, 10, 2, .5, 10, .5, 2))
+[1] TRUE
+> all.equal(xx2$frame$dev, c(82.5, 10, 2, .5, 10, .5, 2)*2)
+[1] TRUE
+> summary(xx2)
+Call:
+rpart(formula = y ~ x1 + x2, data = dummy, weights = rep(2, 10),
+ minsplit = 4, xval = 0)
+ n= 10
+
+ CP nsplit rel error
+1 0.75758 0 1.00000
+2 0.09091 1 0.24242
+3 0.01000 3 0.06061
+
+Node number 1: 10 observations, complexity param=0.7576
+ mean=5.5, MSE=8.25
+ left son=2 (5 obs) right son=3 (5 obs)
+ Primary splits:
+ x1 < 5.5 to the right, improve=0.7576, (0 missing)
+ x2 < 0.5 to the right, improve=0.2727, (0 missing)
+ Surrogate splits:
+ x2 < 2.5 to the right, agree=0.6, adj=0.2, (0 split)
+
+Node number 2: 5 observations, complexity param=0.09091
+ mean=3, MSE=2
+ left son=4 (3 obs) right son=5 (2 obs)
+ Primary splits:
+ x1 < 7.5 to the right, improve=0.75, (0 missing)
+ x2 < 4 to the left, improve=0.75, (0 missing)
+ Surrogate splits:
+ x2 < 6 to the left, agree=1, adj=1, (0 split)
+
+Node number 3: 5 observations, complexity param=0.09091
+ mean=8, MSE=2
+ left son=6 (2 obs) right son=7 (3 obs)
+ Primary splits:
+ x1 < 3.5 to the right, improve=0.75, (0 missing)
+ x2 < 1 to the right, improve=0.50, (0 missing)
+ Surrogate splits:
+ x2 < 5 to the left, agree=0.8, adj=0.5, (0 split)
+
+Node number 4: 3 observations
+ mean=2, MSE=0.6667
+
+Node number 5: 2 observations
+ mean=4.5, MSE=0.25
+
+Node number 6: 2 observations
+ mean=6.5, MSE=0.25
+
+Node number 7: 3 observations
+ mean=9, MSE=0.6667
+
+>
+>
+> # Now for a set of non-equal weights
+> # We need to set maxcompete=3 because there just happens to be, in one
+> # of the lower nodes, an exact tie between variables "life" and "murder".
+> # Round off error causes fit5 to choose one and fit5b the other.
+> # Later -- cut it back to maxdepth=3 for the same reason (a tie).
+> #
+> nn <- nrow(mystate)
+> wts <- sample(1:5, nn, replace=TRUE)
+> temp <- rep(1:nn, wts) #row replicates
+> xgrp <- rep(1:10, length=nn)[order(runif(nn))]
+> xgrp2<- rep(xgrp, wts)
+> tempc <- rpart.control(minsplit=2, xval=xgrp2, maxsurrogate=0,
++ maxcompete=3, maxdepth=3)
+> # Direct: replicate rows in the data set, and use unweighted
+> fit5 <- rpart(income ~ population + region + illiteracy +life + murder +
++ hs.grad + frost , data=mystate[temp,], control=tempc)
+> # Weighted
+> tempc <- rpart.control(minsplit=2, xval=xgrp, maxsurrogate=0,
++ maxcompete=3, maxdepth=3)
+> fit5b <- rpart(income ~ population + region + illiteracy +life + murder +
++ hs.grad + frost , data=mystate, control=tempc,
++ weights=wts)
+> all.equal(fit5$frame[-2], fit5b$frame[-2]) # the "n" component won't match
+[1] TRUE
+> all.equal(fit5$cptable, fit5b$cptable)
+[1] TRUE
+> all.equal(fit5$splits[,-1],fit5b$splits[,-1])
+[1] TRUE
+> all.equal(fit5$csplit, fit5b$csplit)
+[1] TRUE
+> #
+> # The treble test for classification trees
+> #
+> #
+> xgrp <- rep(1:10,length=nrow(cu.summary))
+> carfit <- rpart(Country ~ Reliability + Price + Mileage + Type,
++ method='class', data=cu.summary,
++ control=rpart.control(xval=xgrp))
+>
+> carfit2 <- rpart(Country ~ Reliability + Price + Mileage + Type,
++ method='class', data=cu.summary,
++ weight=rep(3,nrow(cu.summary)),
++ control=rpart.control(xval=xgrp))
+>
+> all.equal(carfit$frame$wt, carfit2$frame$wt/3)
+[1] TRUE
+> all.equal(carfit$frame$dev, carfit2$frame$dev/3)
+[1] TRUE
+> all.equal(carfit$frame[,5:7], carfit2$frame[,5:7])
+[1] TRUE
+> all.equal(carfit$frame$yval2[,12:21], carfit2$frame$yval2[,12:21])
+[1] TRUE
+> all.equal(carfit[c('where', 'csplit')],
++ carfit2[c('where', 'csplit')])
+[1] TRUE
+> xx <- carfit2$splits
+> xx[,'improve'] <- xx[,'improve'] / ifelse(xx[,5]> 0,1,3) # surrogate?
+> all.equal(xx, carfit$splits)
+[1] TRUE
+> all.equal(as.vector(carfit$cptable),
++ as.vector(carfit2$cptable%*% diag(c(1,1,1,1,sqrt(3)))))
+[1] TRUE
+>
+> summary(carfit2)
+Call:
+rpart(formula = Country ~ Reliability + Price + Mileage + Type,
+ data = cu.summary, weights = rep(3, nrow(cu.summary)), method = "class",
+ control = rpart.control(xval = xgrp))
+ n= 117
+
+ CP nsplit rel error xerror xstd
+1 0.23529 0 1.0000 1.0000 0.04531
+2 0.02941 1 0.7647 0.8088 0.04584
+3 0.02206 3 0.7059 0.9118 0.04584
+4 0.01000 5 0.6618 0.9559 0.04563
+
+Node number 1: 117 observations, complexity param=0.2353
+ predicted class=USA expected loss=0.5812
+ class counts: 3 3 6 33 93 27 15 9 15 147
+ probabilities: 0.009 0.009 0.017 0.094 0.265 0.077 0.043 0.026 0.043 0.419
+ left son=2 (33 obs) right son=3 (84 obs)
+ Primary splits:
+ Reliability splits as RRRLL, improve=44.780, (32 missing)
+ Type splits as LRRLRR, improve=11.250, (0 missing)
+ Price < 6923 to the left, improve=10.450, (0 missing)
+ Mileage < 22.5 to the right, improve= 6.084, (57 missing)
+ Surrogate splits:
+ Type splits as RRRLRR, agree=0.706, adj=0.138, (32 split)
+ Price < 6665 to the left, agree=0.682, adj=0.069, (0 split)
+
+Node number 2: 33 observations, complexity param=0.02206
+ predicted class=Japan expected loss=0.4545
+ class counts: 3 0 0 3 54 27 3 3 0 6
+ probabilities: 0.030 0.000 0.000 0.030 0.545 0.273 0.030 0.030 0.000 0.061
+ left son=4 (9 obs) right son=5 (24 obs)
+ Primary splits:
+ Price < 13200 to the right, improve=7.621, (0 missing)
+ Type splits as R-LRLL, improve=5.621, (0 missing)
+ Reliability splits as RRRRL, improve=5.406, (4 missing)
+ Mileage < 23.5 to the left, improve=3.916, (9 missing)
+ Surrogate splits:
+ Type splits as R-LRLL, agree=0.879, adj=0.556, (0 split)
+
+Node number 3: 84 observations, complexity param=0.02941
+ predicted class=USA expected loss=0.4405
+ class counts: 0 3 6 30 39 0 12 6 15 141
+ probabilities: 0.000 0.012 0.024 0.119 0.155 0.000 0.048 0.024 0.060 0.560
+ left son=6 (30 obs) right son=7 (54 obs)
+ Primary splits:
+ Price < 16670 to the right, improve=10.400, (0 missing)
+ Type splits as RRRLRR, improve= 6.026, (0 missing)
+ Mileage < 22.5 to the right, improve= 3.133, (48 missing)
+ Reliability splits as RLLLL, improve= 2.195, (28 missing)
+ Surrogate splits:
+ Type splits as RLLRRR, agree=0.714, adj=0.2, (0 split)
+
+Node number 4: 9 observations
+ predicted class=Japan expected loss=0.1111
+ class counts: 0 0 0 3 24 0 0 0 0 0
+ probabilities: 0.000 0.000 0.000 0.111 0.889 0.000 0.000 0.000 0.000 0.000
+
+Node number 5: 24 observations, complexity param=0.02206
+ predicted class=Japan expected loss=0.5833
+ class counts: 3 0 0 0 30 27 3 3 0 6
+ probabilities: 0.042 0.000 0.000 0.000 0.417 0.375 0.042 0.042 0.000 0.083
+ left son=10 (7 obs) right son=11 (17 obs)
+ Primary splits:
+ Price < 7038 to the left, improve=4.836, (0 missing)
+ Type splits as R--LR-, improve=1.967, (0 missing)
+ Mileage < 30.5 to the right, improve=1.717, (6 missing)
+
+Node number 6: 30 observations, complexity param=0.02941
+ predicted class=USA expected loss=0.6333
+ class counts: 0 3 3 24 12 0 0 0 15 33
+ probabilities: 0.000 0.033 0.033 0.267 0.133 0.000 0.000 0.000 0.167 0.367
+ left son=12 (10 obs) right son=13 (20 obs)
+ Primary splits:
+ Type splits as LRR-L-, improve=6.6000, (0 missing)
+ Price < 30510 to the right, improve=5.3740, (0 missing)
+ Reliability splits as RRLLL, improve=0.3333, (12 missing)
+ Surrogate splits:
+ Price < 19420 to the left, agree=0.767, adj=0.3, (0 split)
+
+Node number 7: 54 observations
+ predicted class=USA expected loss=0.3333
+ class counts: 0 0 3 6 27 0 12 6 0 108
+ probabilities: 0.000 0.000 0.019 0.037 0.167 0.000 0.074 0.037 0.000 0.667
+
+Node number 10: 7 observations
+ predicted class=Japan expected loss=0.2857
+ class counts: 0 0 0 0 15 3 3 0 0 0
+ probabilities: 0.000 0.000 0.000 0.000 0.714 0.143 0.143 0.000 0.000 0.000
+
+Node number 11: 17 observations
+ predicted class=Japan/USA expected loss=0.5294
+ class counts: 3 0 0 0 15 24 0 3 0 6
+ probabilities: 0.059 0.000 0.000 0.000 0.294 0.471 0.000 0.059 0.000 0.118
+
+Node number 12: 10 observations
+ predicted class=Germany expected loss=0.5
+ class counts: 0 0 0 15 3 0 0 0 9 3
+ probabilities: 0.000 0.000 0.000 0.500 0.100 0.000 0.000 0.000 0.300 0.100
+
+Node number 13: 20 observations
+ predicted class=USA expected loss=0.5
+ class counts: 0 3 3 9 9 0 0 0 6 30
+ probabilities: 0.000 0.050 0.050 0.150 0.150 0.000 0.000 0.000 0.100 0.500
+
+>
+> #
+> # Treble test for class trees with 2 outcomes
+> #
+> fit1 <- rpart(Kyphosis ~ Age + Number + Start, data=kyphosis,
++ control=rpart.control(maxsurrogate=0, cp=0, xval=0),
++ parms=list(prior=c(.7,.3),
++ loss=matrix(c(0,1,2,0),nrow=2,ncol=2)))
+> wts <- rep(3, nrow(kyphosis))
+> fit1b <- rpart(Kyphosis ~ Age + Number + Start, data=kyphosis,
++ control=rpart.control(maxsurrogate=0, cp=0, xval=0),
++ weights=wts,
++ parms=list(prior=c(.7,.3),
++ loss=matrix(c(0,1,2,0),nrow=2,ncol=2)))
+> fit1b$frame$wt <- fit1b$frame$wt/3
+> fit1b$frame$dev <- fit1b$frame$dev/3
+> fit1b$frame$yval2[,2:3] <- fit1b$frame$yval2[,2:3]/3
+> fit1b$splits[,3] <- fit1b$splits[,3]/3
+> all.equal(fit1[-3], fit1b[-3]) #all but the "call"
+[1] TRUE
+>
+> # Now for a set of non-equal weights
+> nn <- nrow(kyphosis)
+> wts <- sample(1:5, nn, replace=TRUE)
+> temp <- rep(1:nn, wts) #row replicates
+> xgrp <- rep(1:10, length=nn)[order(runif(nn))]
+> xgrp2<- rep(xgrp, wts)
+> tempc <- rpart.control(minsplit=2, xval=xgrp2, maxsurrogate=0)
+> # Direct: replicate rows in the data set, and use unweighted
+> fit2 <- rpart(Kyphosis ~ Age + Number + Start, data=kyphosis[temp,],
++ control=tempc,
++ parms=list(prior=c(.7,.3),
++ loss=matrix(c(0,1,2,0),nrow=2,ncol=2)))
+> # Weighted
+> tempc <- rpart.control(minsplit=2, xval=xgrp, maxsurrogate=0)
+> fit2b <- rpart(Kyphosis ~ Age + Number + Start, data=kyphosis,
++ control=tempc, weights=wts,
++ parms=list(prior=c(.7,.3),
++ loss=matrix(c(0,1,2,0),nrow=2,ncol=2)))
+>
+> # all.equal(fit2$frame[-2], fit2b$frame[-2]) # the "n" component won't match
+> all.equal(fit2$cptable, fit2b$cptable)
+[1] TRUE
+> # all.equal(fit2$splits[,-1],fit2b$splits[,-1]) #fails
+> all.equal(fit2$csplit, fit2b$csplit)
+[1] TRUE
+>
+>
+> #
+> # Check out using costs
+> #
+> fit1 <- rpart(Surv(time, status) ~ age + sex + ph.ecog + ph.karno + pat.karno
++ + meal.cal + wt.loss, data=lung,
++ maxdepth=1, maxcompete=6, xval=0)
+>
+> fit2 <- rpart(Surv(time, status) ~ age + sex + ph.ecog + ph.karno + pat.karno
++ + meal.cal + wt.loss, data=lung,
++ maxdepth=1, maxcompete=6, xval=0, cost=(1+ 1:7/10))
+>
+> temp1 <- fit1$splits[1:7,]
+> temp2 <- fit2$splits[1:7,]
+> temp3 <- c('age', 'sex', 'ph.ecog', 'ph.karno', 'pat.karno', 'meal.cal',
++ 'wt.loss')
+> indx1 <- match(temp3, dimnames(temp1)[[1]])
+> indx2 <- match(temp3, dimnames(temp2)[[1]])
+> all.equal(temp1[indx1,1], temp2[indx2,1]) #same n's ?
+[1] TRUE
+> all.equal(temp1[indx1,3], temp2[indx2,3]*(1+ 1:7/10)) #scaled importance
+[1] TRUE
+>
+>
+> q()
diff --git a/win32/deps/library/rpart/tests/usersplits.R b/win32/deps/library/rpart/tests/usersplits.R
new file mode 100644
index 0000000..b93928b
--- /dev/null
+++ b/win32/deps/library/rpart/tests/usersplits.R
@@ -0,0 +1,167 @@
+# Any necessary setup
+library(rpart)
+options(na.action="na.omit")
+options(digits=4) # to match earlier output
+set.seed(1234)
+
+mystate <- data.frame(state.x77, region=factor(state.region))
+names(mystate) <- c("population","income" , "illiteracy","life" ,
+ "murder", "hs.grad", "frost", "area", "region")
+#
+# Test out the "user mode" functions, with an anova variant
+#
+
+# The 'evaluation' function. Called once per node.
+# Produce a label (1 or more elements long) for labeling each node,
+# and a deviance. The latter is
+# - of length 1
+# - equal to 0 if the node is "pure" in some sense (unsplittable)
+# - does not need to be a deviance: any measure that gets larger
+# as the node is less acceptable is fine.
+# - the measure underlies cost-complexity pruning, however
+temp1 <- function(y, wt, parms) {
+ wmean <- sum(y*wt)/sum(wt)
+ rss <- sum(wt*(y-wmean)^2)
+ list(label= wmean, deviance=rss)
+ }
+
+# The split function, where most of the work occurs.
+# Called once per split variable per node.
+# If continuous=T
+# The actual x variable is ordered
+# y is supplied in the sort order of x, with no missings,
+# return two vectors of length (n-1):
+# goodness = goodness of the split, larger numbers are better.
+# 0 = couldn't find any worthwhile split
+# the ith value of goodness evaluates splitting obs 1:i vs (i+1):n
+# direction= -1 = send "y< cutpoint" to the left side of the tree
+# 1 = send "y< cutpoint" to the right
+# this is not a big deal, but making larger "mean y's" move towards
+# the right of the tree, as we do here, seems to make it easier to
+# read
+# If continuos=F, x is a set of integers defining the groups for an
+# unordered predictor. In this case:
+# direction = a vector of length m= "# groups". It asserts that the
+# best split can be found by lining the groups up in this order
+# and going from left to right, so that only m-1 splits need to
+# be evaluated rather than 2^(m-1)
+# goodness = m-1 values, as before.
+#
+# The reason for returning a vector of goodness is that the C routine
+# enforces the "minbucket" constraint. It selects the best return value
+# that is not too close to an edge.
+temp2 <- function(y, wt, x, parms, continuous) {
+ # Center y
+ n <- length(y)
+ y <- y- sum(y*wt)/sum(wt)
+
+ if (continuous) {
+ # continuous x variable
+ temp <- cumsum(y*wt)[-n]
+
+ left.wt <- cumsum(wt)[-n]
+ right.wt <- sum(wt) - left.wt
+ lmean <- temp/left.wt
+ rmean <- -temp/right.wt
+ goodness <- (left.wt*lmean^2 + right.wt*rmean^2)/sum(wt*y^2)
+ list(goodness= goodness, direction=sign(lmean))
+ }
+ else {
+ # Categorical X variable
+ ux <- sort(unique(x))
+ wtsum <- tapply(wt, x, sum)
+ ysum <- tapply(y*wt, x, sum)
+ means <- ysum/wtsum
+
+ # For anova splits, we can order the categories by their means
+ # then use the same code as for a non-categorical
+ ord <- order(means)
+ n <- length(ord)
+ temp <- cumsum(ysum[ord])[-n]
+ left.wt <- cumsum(wtsum[ord])[-n]
+ right.wt <- sum(wt) - left.wt
+ lmean <- temp/left.wt
+ rmean <- -temp/right.wt
+ list(goodness= (left.wt*lmean^2 + right.wt*rmean^2)/sum(wt*y^2),
+ direction = ux[ord])
+ }
+ }
+
+# The init function:
+# fix up y to deal with offsets
+# return a dummy parms list
+# numresp is the number of values produced by the eval routine's "label"
+# numy is the number of columns for y
+# summary is a function used to print one line in summary.rpart
+# In general, this function would also check for bad data, see rpart.poisson
+# for instace.
+temp3 <- function(y, offset, parms, wt) {
+ if (!is.null(offset)) y <- y-offset
+ list(y=y, parms=0, numresp=1, numy=1,
+ summary= function(yval, dev, wt, ylevel, digits ) {
+ paste(" mean=", format(signif(yval, digits)),
+ ", MSE=" , format(signif(dev/wt, digits)),
+ sep='')
+ })
+ }
+
+
+alist <- list(eval=temp1, split=temp2, init=temp3)
+
+fit0 <- rpart(income ~population +illiteracy + murder + hs.grad,
+ mystate, control=rpart.control(minsplit=10, xval=0),
+ method=alist)
+
+
+fit1 <- rpart(income ~population +illiteracy + murder + hs.grad + region,
+ mystate, control=rpart.control(minsplit=10, xval=0),
+ method=alist)
+
+fit2 <- rpart(income ~population +illiteracy + murder + hs.grad + region,
+ mystate, control=rpart.control(minsplit=10, xval=0),
+ method='anova')
+
+# Other than their call statement, and a longer "functions" component in
+# fit1, fit1 and fit2 should be identical.
+all.equal(fit1$frame, fit2$frame)
+all.equal(fit1$splits, fit2$splits)
+all.equal(fit1$csplit, fit2$csplit)
+all.equal(fit1$where, fit2$where)
+all.equal(fit1$cptable, fit2$cptable)
+
+# Now try xpred on it
+xvtemp <- rep(1:5, length=50)
+xp1 <- xpred.rpart(fit1, xval=xvtemp)
+xp2 <- xpred.rpart(fit2, xval=xvtemp)
+aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+aeq(xp1, xp2)
+
+fit3 <- rpart(income ~population +illiteracy + murder + hs.grad + region,
+ mystate, control=rpart.control(minsplit=10, xval=xvtemp),
+ method='anova')
+zz <- apply((mystate$income - xp1)^2,2, sum)
+aeq(zz/fit1$frame$dev[1], fit3$cptable[,4]) #reproduce xerror
+
+zz2 <- sweep((mystate$income-xp1)^2,2, zz/nrow(xp1))
+zz2 <- sqrt(apply(zz2^2, 2, sum))/ fit1$frame$dev[1]
+aeq(zz2, fit3$cptable[,5]) #reproduce se(xerror)
+
+#
+# Now try timing it on a multiplied data set (100 copies of mystate)
+#
+temp <- rbind(mystate, mystate, mystate, mystate)
+temp <- rbind(temp, temp, temp, temp, temp)
+temp <- rbind(temp, temp, temp, temp, temp)
+t1 <- system.time(rpart(income ~population +illiteracy + murder +
+ hs.grad + region +
+ life + area, temp, control=rpart.control(minsplit=10, xval=0),
+ method=alist))
+t2 <- system.time(rpart(income ~population +illiteracy + murder +
+ hs.grad + region +
+ life + area, temp, control=rpart.control(minsplit=10, xval=0),
+ method='anova'))
+cat("Timing ratio = ", round(t1[3]/t2[3], 1), "\n")
+
+rm(temp)
+
+q()
diff --git a/win32/deps/library/rpart/tests/usersplits.Rout.save b/win32/deps/library/rpart/tests/usersplits.Rout.save
new file mode 100644
index 0000000..fbe665a
--- /dev/null
+++ b/win32/deps/library/rpart/tests/usersplits.Rout.save
@@ -0,0 +1,193 @@
+
+R : Copyright 2006, The R Foundation for Statistical Computing
+Version 2.3.0 beta (2006-04-12 r37734)
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> # Any necessary setup
+> library(rpart)
+> options(na.action="na.omit")
+> options(digits=4) # to match earlier output
+> set.seed(1234)
+>
+> mystate <- data.frame(state.x77, region=factor(state.region))
+> names(mystate) <- c("population","income" , "illiteracy","life" ,
++ "murder", "hs.grad", "frost", "area", "region")
+> #
+> # Test out the "user mode" functions, with an anova variant
+> #
+>
+> # The 'evaluation' function. Called once per node.
+> # Produce a label (1 or more elements long) for labeling each node,
+> # and a deviance. The latter is
+> # - of length 1
+> # - equal to 0 if the node is "pure" in some sense (unsplittable)
+> # - does not need to be a deviance: any measure that gets larger
+> # as the node is less acceptable is fine.
+> # - the measure underlies cost-complexity pruning, however
+> temp1 <- function(y, wt, parms) {
++ wmean <- sum(y*wt)/sum(wt)
++ rss <- sum(wt*(y-wmean)^2)
++ list(label= wmean, deviance=rss)
++ }
+>
+> # The split function, where most of the work occurs.
+> # Called once per split variable per node.
+> # If continuous=T
+> # The actual x variable is ordered
+> # y is supplied in the sort order of x, with no missings,
+> # return two vectors of length (n-1):
+> # goodness = goodness of the split, larger numbers are better.
+> # 0 = couldn't find any worthwhile split
+> # the ith value of goodness evaluates splitting obs 1:i vs (i+1):n
+> # direction= -1 = send "y< cutpoint" to the left side of the tree
+> # 1 = send "y< cutpoint" to the right
+> # this is not a big deal, but making larger "mean y's" move towards
+> # the right of the tree, as we do here, seems to make it easier to
+> # read
+> # If continuos=F, x is a set of integers defining the groups for an
+> # unordered predictor. In this case:
+> # direction = a vector of length m= "# groups". It asserts that the
+> # best split can be found by lining the groups up in this order
+> # and going from left to right, so that only m-1 splits need to
+> # be evaluated rather than 2^(m-1)
+> # goodness = m-1 values, as before.
+> #
+> # The reason for returning a vector of goodness is that the C routine
+> # enforces the "minbucket" constraint. It selects the best return value
+> # that is not too close to an edge.
+> temp2 <- function(y, wt, x, parms, continuous) {
++ # Center y
++ n <- length(y)
++ y <- y- sum(y*wt)/sum(wt)
++
++ if (continuous) {
++ # continuous x variable
++ temp <- cumsum(y*wt)[-n]
++
++ left.wt <- cumsum(wt)[-n]
++ right.wt <- sum(wt) - left.wt
++ lmean <- temp/left.wt
++ rmean <- -temp/right.wt
++ goodness <- (left.wt*lmean^2 + right.wt*rmean^2)/sum(wt*y^2)
++ list(goodness= goodness, direction=sign(lmean))
++ }
++ else {
++ # Categorical X variable
++ ux <- sort(unique(x))
++ wtsum <- tapply(wt, x, sum)
++ ysum <- tapply(y*wt, x, sum)
++ means <- ysum/wtsum
++
++ # For anova splits, we can order the categories by their means
++ # then use the same code as for a non-categorical
++ ord <- order(means)
++ n <- length(ord)
++ temp <- cumsum(ysum[ord])[-n]
++ left.wt <- cumsum(wtsum[ord])[-n]
++ right.wt <- sum(wt) - left.wt
++ lmean <- temp/left.wt
++ rmean <- -temp/right.wt
++ list(goodness= (left.wt*lmean^2 + right.wt*rmean^2)/sum(wt*y^2),
++ direction = ux[ord])
++ }
++ }
+>
+> # The init function:
+> # fix up y to deal with offsets
+> # return a dummy parms list
+> # numresp is the number of values produced by the eval routine's "label"
+> # numy is the number of columns for y
+> # summary is a function used to print one line in summary.rpart
+> # In general, this function would also check for bad data, see rpart.poisson
+> # for instace.
+> temp3 <- function(y, offset, parms, wt) {
++ if (!is.null(offset)) y <- y-offset
++ list(y=y, parms=0, numresp=1, numy=1,
++ summary= function(yval, dev, wt, ylevel, digits ) {
++ paste(" mean=", format(signif(yval, digits)),
++ ", MSE=" , format(signif(dev/wt, digits)),
++ sep='')
++ })
++ }
+>
+>
+> alist <- list(eval=temp1, split=temp2, init=temp3)
+>
+> fit0 <- rpart(income ~population +illiteracy + murder + hs.grad,
++ mystate, control=rpart.control(minsplit=10, xval=0),
++ method=alist)
+>
+>
+> fit1 <- rpart(income ~population +illiteracy + murder + hs.grad + region,
++ mystate, control=rpart.control(minsplit=10, xval=0),
++ method=alist)
+>
+> fit2 <- rpart(income ~population +illiteracy + murder + hs.grad + region,
++ mystate, control=rpart.control(minsplit=10, xval=0),
++ method='anova')
+>
+> # Other than their call statement, and a longer "functions" component in
+> # fit1, fit1 and fit2 should be identical.
+> all.equal(fit1$frame, fit2$frame)
+[1] TRUE
+> all.equal(fit1$splits, fit2$splits)
+[1] TRUE
+> all.equal(fit1$csplit, fit2$csplit)
+[1] TRUE
+> all.equal(fit1$where, fit2$where)
+[1] TRUE
+> all.equal(fit1$cptable, fit2$cptable)
+[1] TRUE
+>
+> # Now try xpred on it
+> xvtemp <- rep(1:5, length=50)
+> xp1 <- xpred.rpart(fit1, xval=xvtemp)
+> xp2 <- xpred.rpart(fit2, xval=xvtemp)
+> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+> aeq(xp1, xp2)
+[1] TRUE
+>
+> fit3 <- rpart(income ~population +illiteracy + murder + hs.grad + region,
++ mystate, control=rpart.control(minsplit=10, xval=xvtemp),
++ method='anova')
+> zz <- apply((mystate$income - xp1)^2,2, sum)
+> aeq(zz/fit1$frame$dev[1], fit3$cptable[,4]) #reproduce xerror
+[1] TRUE
+>
+> zz2 <- sweep((mystate$income-xp1)^2,2, zz/nrow(xp1))
+> zz2 <- sqrt(apply(zz2^2, 2, sum))/ fit1$frame$dev[1]
+> aeq(zz2, fit3$cptable[,5]) #reproduce se(xerror)
+[1] TRUE
+>
+> #
+> # Now try timing it on a multiplied data set (100 copies of mystate)
+> #
+> temp <- rbind(mystate, mystate, mystate, mystate)
+> temp <- rbind(temp, temp, temp, temp, temp)
+> temp <- rbind(temp, temp, temp, temp, temp)
+> t1 <- system.time(rpart(income ~population +illiteracy + murder +
++ hs.grad + region +
++ life + area, temp, control=rpart.control(minsplit=10, xval=0),
++ method=alist))
+> t2 <- system.time(rpart(income ~population +illiteracy + murder +
++ hs.grad + region +
++ life + area, temp, control=rpart.control(minsplit=10, xval=0),
++ method='anova'))
+> cat("Timing ratio = ", round(t1[3]/t2[3], 1), "\n")
+Timing ratio = 5.9
+>
+> rm(temp)
+>
+> q()
diff --git a/win32/deps/library/spam/0NEWS b/win32/deps/library/spam/0NEWS
new file mode 100644
index 0000000..e8df599
--- /dev/null
+++ b/win32/deps/library/spam/0NEWS
@@ -0,0 +1,404 @@
+ Dear Emacs, please make this -*-Text-*- mode!
+
+
+ **************************************************
+ * *
+ * SPAM VERSION 0.21 *
+ * *
+ **************************************************
+
+ o New functions bandwidth, permutation, mle[.nomean][.spam],
+ neg2loglikelihood[.spam].
+
+ o Renamed adiag.spam to bdiag.spam.
+
+ o Cleaned up argument naming with the rmvnorm.*
+ suite.
+
+ o Varios Fortran code, R code and help file
+ improvements.
+
+
+ **************************************************
+ * *
+ * SPAM VERSION 0.20 *
+ * *
+ **************************************************
+
+ CHANGES IN R VERSION 0.20-3
+
+ o Resolved dependency issues.
+
+ CHANGES IN R VERSION 0.20-1,2
+
+ o Minor changes to pass the CRAN test.
+
+
+ CHANGES IN R VERSION 0.20-0
+
+ o New demos, test functions, datasets.
+
+ o Method t for spam.chol.NgPeyton.
+
+ o Method Math2 now with signature digits="ANY".
+
+ o Update in rmvnorm.canonical, can take a Cholesky structure
+ as argument.
+
+ o New functionality for a sparse times a full matrix
+ multiplication.
+
+ o Minor ajustment in memory allocation of chol.
+
+
+ **************************************************
+ * *
+ * SPAM VERSION 0.15 *
+ * *
+ **************************************************
+
+ CHANGES IN R VERSION 0.15-6
+
+ o Minor change in Fortran routines to accomodate some Intel
+ compilers (pointed out by Tim Hoar).
+
+
+ CHANGES IN R VERSION 0.15-5
+
+ o New function adiag.spam, creation of block diagonal sparse
+ matrices. No method though.
+
+ o New functions rmvnorm.spam, rmvnorm.canonical and
+ rmvnorm.prec to draw multivariate normals.
+
+ o New function apply.spam, similar functionality as apply.
+
+ o drop is implemented now when subsetting a sparse matrix
+ with a binary matrix.
+
+ o Major overhaul to nearest.dist: zeros are not included.
+ Old parameters are kept for backwards compatibility.
+
+ o Orders/complexities of major algorithms are now described
+ in the help 'complexity'.
+
+ o Using packageStartupMessage in .onAttach.
+
+ o Code clean up and help improvements. Changes reflecting the
+ change to UZH.
+
+ o Bugfix in assinging via a nx2 matrix.
+
+
+
+ CHANGES IN R VERSION 0.15-4
+
+ o Changes in help files. Minor code improvements.
+
+ o New function powerboost.
+
+ o Changes to if(getRversion() >= "x.y"), required for R 2.10.
+
+
+
+ CHANGES IN R VERSION 0.15-3
+
+ o Several bug fixes in the demos due to the changes in
+ the previous versions.
+
+ o Several minior changes in the help files to compile with
+ the new help parser and to correct for typos.
+
+ o Added the demos into the tests directory. Additionally,
+ tests contains now the proper Rout.saves files.
+
+ o In test files, library( spam, warn.conflict=FALSE)
+ is used to avoid masking messages in R-2.8.0.
+ Timing output in test files is suppressed.
+
+ o Added trivial headers to most files.
+
+
+ o Bug fix in spam.list(), negative values were not correctly
+ handled.
+
+ o Bug fix in subsetting (occured when subsetting very
+ sparse matrices, memory allocation problem).
+
+
+ CHANGES IN R VERSION 0.15-2
+
+ o Method all.equal for matrix-spam signature.
+
+ o Bug fix in Fortran function of nearest.dist. Numerical
+ instabilities could return NaN on diagonal. Additionally,
+ overhaul of tests/dist.R.
+
+ o Several minor improvements in the help files as well
+ as in function nearest.dist and tests/*.R.
+
+
+ CHANGES IN R VERSION 0.15-1
+
+ o Improvements in the nearest.dist function. The diagonals
+ are now handled consistenly.
+
+ o Symmetry check criterion for Cholesky decomposition has been
+ relaxed from (2+eps)*eps to 100*eps for an easier handling when
+ working with great circle distance induced covariance matrices.
+ Same cutoff is used with eigen. Instead of using norm,
+ we use essentially an isSymmetric.spam test.
+
+ o Methods isSymmetric and all.equal for spam.
+
+ o Methods image and display for spam.chol.NgPeyton.
+
+ o Method as.spam for distance class implemented.
+
+ o Complete rewrite of spam.list. Method as.spam for lists
+ are implemented as well.
+
+ o Method spam for spam objects (possibility to rearrange the
+ dimension) has been eliminated. The approach was based on
+ creating the full matrix and assigning it back to a spam
+ object.
+
+ o Binary subsetting and subassigning is implemented.
+
+ o Bug fix: the Cholesky Fortran routine checks if diagonal
+ elements are available (and positive).
+
+ o Bug fix: in dim<-.spam
+
+ o Minor improvements in the help files as well as the following
+ R functions: norm, .spam.matmul.
+
+
+ CHANGES IN R VERSION 0.15-0
+
+ o The devel versions of 14-x have been sitting around for
+ a while and I was inconsistent with the devel/gold numbering.
+ To avoid any confusion, I have decided to go to the next
+ minor version. An additional reason supporting this is
+ that the version number identification has changed over
+ the 0.14-devel.
+
+
+ **************************************************
+ * *
+ * SPAM VERSION 0.14 *
+ * *
+ **************************************************
+
+ CHANGES IN R VERSION 0.14-x
+
+ o A few rudimentary functions to change between the compressed
+ sparse row formats of the packages SparseM and Matrix.
+ Just the functions, no S3/S4 constructs available.
+
+ o Functionality to read matrices stored in the Harwell-Boeing
+ or MatrixMarket formats.Read MatrixMarket.
+
+ o Rewritten cbind.spam and rbind.spam. Both can take now
+ numeric and spam objects. cbind.spam calls now Fortran
+ code and is now very fast. Rewrite of their help.
+
+ o Implemented spam.list to go from a index based list to a
+ spam matrix. The function triplets does the inverse.
+
+ o forwardsolve and backsolve methods for spam objects.
+
+ o Implemented the function 'dim<-' for spam objects.
+
+ o Method diag and as.matrix for spam.chol.NgPeyton.
+
+ o eps is now tested for being at least double precision.
+
+ o as.spam.xxx and spam.yyy functions have been streamlined.
+
+ o Initializing an empty spam matrix causes a warning but still
+ coerces to a zero matrix, see new("spam",entries=rep(1,0))
+
+ o Eliminated bug in subsetting (occuring when subsetting
+ for an empty matrix). Clean out subsetting and assigning.
+
+ o Include a inst subdirectory containing this file, which
+ is renamed to NEWS. Once we have reached a stable version
+ I will maintain a proper CHANGELOG file in the root
+ directory.
+
+ o Proper method handling for kronecker and bug fixes in
+ kronecker.spam.
+
+ o Saved the datasets UScounties.storder/ndorder as spam
+ objects as assumed by demo article-jss.
+
+ o Implemented many 'identical' structures and homogenized zero
+ matrix handling, throughout the R code. int0, ..., int2 are
+ internally defined integers.
+
+ o Similar changes as for 13-3. Additionally, considerable
+ improvements in help, file structure, tests, timing, etc.
+
+
+ CHANGES IN R VERSION 0.14-0
+
+ Major revision. Slight loss of backwards compatibility.
+
+ o New demo article-jss.
+
+ o New variable spam.version, similar to the R version
+ variable.
+
+ o Change and adding of a few option names, for example
+ cholsymmetrycheck, cholpivotcheck, cholupdatesingular,
+ dopivoting, safemode, ...
+ See help files for details.
+
+ o Complete rewrite of chol. The argument ordering is
+ now called pivot, more consistent with the generic
+ function. Two different orderings are implemented.
+ Uses the new option cholsymmetrycheck.
+
+ o Similar changes as in chol in determinant.spam.
+
+ o New function update.spam.chol.NgPeyton.
+
+ o Invisible/minor changes in method c for spam, in solve.spam,
+ determinant.chol.NgPeyton
+
+ o The class spam.chol.NgPeyton is defined differently.
+ Accordingly, print and summary methods are updated.
+ Notably, fill-in ratios are given with summary.
+ Summary also hands back the length of the vectors holding the
+ factor and the column indices.
+
+ o New methods for spam.chol.NgPeyton, namely, dim, length, c,
+ dim<-, and length<-. The latter two giving simply errors.
+
+ o Along the redefinition of the class spam.chol.NgPeyton,
+ forwardsolve.spam and backsolve.spam are updated.
+ Use now the option dopivoting.
+
+ o kronecker.r is implemented.
+
+ o nearest.dist, a function to calculate close distances
+ within one or two sets of locations is implemented.
+ Roughly speaking, it is the union of dist in base and
+ rdist/rdist.earth in fields. (comes with options
+ nearestdistincreasefactor and nearestdistnnz).
+
+ o print and show now emphasize that the non-zero elements
+ are row-wise printed.
+
+ o UScounties is a dataset containing the adjacency matrix
+ of the first and second order neighbors of the counties
+ of the lower 48 US states.
+
+ o Some changes in help files, especially in the *-class
+ files.
+
+ o Eliminated warnings issued when compiling.
+
+ o Minor R and Fortran code cleaning.
+
+ o Along the new features, update of CHANGELOG, todo,
+ NAMESPACE files, etc.
+
+
+ **************************************************
+ * *
+ * SPAM VERSION SERIES 0.13 *
+ * *
+ **************************************************
+
+ CHANGES IN R VERSION 0.13-3
+
+ o Minor changes in R and Fortran code to eliminate warnings.
+
+ o In diag()'s argument list, drop the explicit default (' = n').
+ As is now in R-2.7.
+
+
+ CHANGES IN R VERSION 0.13-2
+
+ o New spam.options and getOption functions. .Spam
+ as a variable is not visible anymore.
+
+ o Retrieving information from the DESCRIPTION file directly
+ (thanks to Roger Bivand).
+
+
+ CHANGES IN R VERSION 0.13-1
+
+ o Minor Fortran Changes for g77 compatibility. Thanks to
+ Roger Bivand.
+
+ o Updated DESCRIPTION file.
+
+
+ CHANGES IN R VERSION 0.13
+
+ o Updated NAMESPACE (for versions > 2.5).
+
+ o Some changes in help files.
+
+ o Cleaned Fortran source files (eliminated unused
+ subroutines and used the posted complier output to
+ straighten details).
+
+ o Implemented more efficient transpose Fortran code.
+ This also eliminates a bug when transposing a 1 row
+ matrix.
+
+ o Eliminated bug when assigning with a 1 row matix.
+
+ o Eliminated bug (Fortran code) that could potentially
+ occur when assigning.
+
+ o Eliminated bug when plotting a 1 row matix.
+
+ o Minor R code cleaning.
+
+
+
+ **************************************************
+ * *
+ * SPAM VERSION 0.12 *
+ * *
+ **************************************************
+
+
+ o Updated NAMESPACE and DESCRIPTION file.
+
+ o print and summary pass back NULL instead of the
+ object.
+
+ o Changed to prod(x dimension) instead of nrow*ncol to
+ overcome integer overflow for very large matrices.
+
+ o Introduced a prototype in the definition of spam
+ and spam.chol.*.
+
+ o .Spam$safemode also determines if a spam object is
+ tested for validity, as well as for NAOK.
+
+ o In many functions sparse matrix construction is
+ done manually using slots (and check=FALSE, if
+ approprate).
+
+ o Increased the value of symmetry criteria to
+ (2+eps)*eps, as each element can be off by eps,
+ subtraction leads to a 2*eps offset and yet we are
+ symmetric.
+
+ o Major restructuration of chol/det with elimination
+ of auxiliarychol.
+
+ o Methods chol/backsolve/forwarsolve now call the *.spam
+ functions.
+
+ o Many internal changes to favour speed and efficiency.
+
+ o Bug fix in .spam.elemul. occuring when the result is the
+ zero matrix.
diff --git a/win32/deps/library/spam/CITATION b/win32/deps/library/spam/CITATION
new file mode 100644
index 0000000..ee1caab
--- /dev/null
+++ b/win32/deps/library/spam/CITATION
@@ -0,0 +1,19 @@
+citHeader("To cite spam in publications use:")
+
+citEntry(entry = "Article",
+ title = "{spam}: A Sparse Matrix {R} Package with Emphasis on MCMC Methods for Gaussian Markov Random Fields",
+ author = personList(as.person("Reinhard Furrer"),
+ as.person("Stephan R. Sain")),
+ journal = "Journal of Statistical Software",
+ year = "2010",
+ volume = "36",
+ number = "10",
+ pages = "1--25",
+ url = "http://www.jstatsoft.org/v36/i10/";,
+
+ textVersion =
+ paste("Reinhard Furrer, Stephan R. Sain (2010).",
+ "spam: A Sparse Matrix R Package with Emphasis on MCMC Methods for Gaussian Markov Random Fields.",
+ "Journal of Statistical Software, 36(10), 1-25.",
+ "URL http://www.jstatsoft.org/v36/i10/.";)
+)
diff --git a/win32/deps/library/spam/DESCRIPTION b/win32/deps/library/spam/DESCRIPTION
index a91bffd..8662c00 100644
--- a/win32/deps/library/spam/DESCRIPTION
+++ b/win32/deps/library/spam/DESCRIPTION
@@ -1,11 +1,11 @@
Package: spam
-Version: 0.20-3
-Date: 2010-01-13
+Version: 0.29-2
+Date: 2012-08-17
Author: Reinhard Furrer
Maintainer: Reinhard Furrer <reinhard furrer math uzh ch>
-Depends: R (>= 2.4), methods
+Depends: R (>= 2.11), methods
Suggests: fields, SparseM (>= 0.72), Matrix
-Description: Set of function for sparse matrix algebra. Differences
+Description: Set of function for sparse matrix algebra. Differences
with SparseM/Matrix are: (1) we only support (essentially) one
sparse matrix format, (2) based on transparent and simple
structure(s), (3) tailored for MCMC calculations within GMRF.
@@ -15,7 +15,8 @@ LazyData: Yes
License: GPL | file LICENSE
Title: SPArse Matrix
URL: http://www.math.uzh.ch/furrer/software/spam/
-Packaged: 2010-01-13 08:59:46 UTC; furrer
+Packaged: 2012-08-17 09:43:09 UTC; furrer
Repository: CRAN
-Date/Publication: 2010-01-13 11:29:37
-Built: R 2.9.2; i386-pc-mingw32; 2010-01-13 23:20:15 UTC; windows
+Date/Publication: 2012-08-17 11:09:49
+Built: R 2.15.2; x86_64-w64-mingw32; 2013-01-24 20:10:10 UTC; windows
+Archs: i386, x64
diff --git a/win32/deps/library/spam/INDEX b/win32/deps/library/spam/INDEX
index 08f8fa6..b8b6f92 100644
--- a/win32/deps/library/spam/INDEX
+++ b/win32/deps/library/spam/INDEX
@@ -7,36 +7,47 @@ UScounties Adjacency structure of the counties in the
contiguous United States
USprecip Monthly total precipitation (mm) for April 1948
in the contiguous United States
-adiag Binds Arrays Corner-to-Corner
all.equal.spam Test if Two 'spam' Objects are (Nearly) Equal
apply.spam Apply Functions Over Sparse Matrix Margins
+bandwidth Bandwidth of a Sparse Matrix
+bdiag Binds Arrays Corner-to-Corner
cbind Combine spam Matrices by Rows or Columns
-chol Cholesky Factorization for Sparse Matrices
+chol.spam Cholesky Factorization for Sparse Matrices
+circulant.spam Create Circulant Matrices
+cleanup Cleaning up sparse matrices
complexity Complexity for Sparse Matrices
det Calculate the determinant of a positive
definite Sparse Matrix
diag Sparse Matrix diagonals
-dim Dimensions of an Object
-display Graphially represent the nonzero entries
+dim<-.spam Dimensions of an Object
+display Graphially Represent the Nonzero Entries
dist.spam Distance Matrix Computation
foreign Transformation to other sparse formats
+head Return the First or Last Part of an Object
image Display a spam Object as Color Image
-import Read external matrix formats
+import Read External Matrix Formats
isSymmetric.spam Test if a spam matrix is Symmetric
-kronecker Kronecker products on sparse matrices
+kronecker.default Kronecker Products on Sparse Matrices
lower.tri Lower and Upper Triangular Part of a Sparse
Matrix
+make.prec Create Precision Matrices
map.landkreis Administrative districts of Germany
+mle Maximum likelihood estimates
ordering Extract the permutation
overview SPArse Matrix Package
+permutation Permute a matrix
powerboost Specific options Setting
+precmat IGMRF Precision Matrices
print Printing and summarizing sparse matrices
+rmvnorm.const Draw Constrainted Multivariate Normals
rmvnorm.spam Draw Multivariate Normals
+rowSums Form Row and Column Sums and Means
solve.spam Linear Equation Solving for Sparse Matrices
spam Sparse Matrix Class
spam-class Class "spam"
spam.chol.NgPeyton-class
Class "spam.chol.NgPeyton"
spam.options Options Settings
+toeplitz.spam Create Toeplitz Matrices
triplet Transform a spam format to triplets
version Spam Version Information
diff --git a/win32/deps/library/spam/MD5 b/win32/deps/library/spam/MD5
index 775dab7..b7e5d8d 100644
--- a/win32/deps/library/spam/MD5
+++ b/win32/deps/library/spam/MD5
@@ -1,73 +1,38 @@
-34428e5eaa439730735765db41b992b2 *CONTENTS
-5209247a5d8de7348c03af4d1197adf7 *DESCRIPTION
-872d3232bc4d1db97925711e6f003193 *INDEX
+512c41e65e4afe45afa7c4e54e753367 *0NEWS
+9c84294096a034b8f22f473187ddac2f *CITATION
+41a5ba2ed83f451f9920d0dd92f74b2f *DESCRIPTION
+2084ca5f776d6eca0ad57615945081e1 *INDEX
0981f20e64159b699b6f28b281905af8 *LICENSE
-bca7a7f8ad7cb26046dacf724d634924 *Meta/Rd.rds
-eb2fffcb02f4037905102cd94b6ddbe6 *Meta/data.rds
-aa39421fc88157931d6edf8c0a367d2d *Meta/demo.rds
-0bfb5ed52a59f044da2b5e44e698682f *Meta/hsearch.rds
-006a515221222e55802bd05216da2e0c *Meta/nsInfo.rds
-ede8c4b701670708aac25cd462284b8e *Meta/package.rds
-8a3a918c3f87c6fd0462740ea8bb75a7 *NAMESPACE
-44e9b2590cf3cfebff10b48983e38bea *NEWS
-f0fb9cd6da53d50c649011e2ebf026f8 *R-ex/Rex.zip
-f07d3015c4220dea7a7be8c741d2985b *R/spam
-2491e69d6ed62db5ef43b65c44243456 *R/spam.rdb
-a2634206939d6e4ce5012ef2484ef320 *R/spam.rdx
-5f5f16f169fefbc07314dc65f3ea8173 *chtml/spam.chm
-891fdd32b6dd71bad10e0525b4115ab7 *data/Rdata.rdb
-e153bcb3093f1798f3cf189ad119e342 *data/Rdata.rds
-97aea3c2e798277c027ef9a4d0cb9d1e *data/Rdata.rdx
-ffea98cc8460a7f5ddc8e1982d49bfc2 *demo/article-jss-example1.R
-f795e4ef203a65cf250ad265bb988de3 *demo/article-jss-example2.R
-0eb0fcac280445f3f04c171b7c1dcb27 *demo/article-jss.R
-40706f0ded4620ca1a6b4b94da5cbf9a *demo/cholesky.R
-40a4eb44f77cba5e3dbf124889ace30a *demo/spam.R
-b51b8cb0828ccbb44d02295d86ea5e5f *demo/timing.R
+387866d91d7781f6ad70223669546f6b *Meta/Rd.rds
+58642038b590127658741287d9355036 *Meta/data.rds
+0e8866ccba73133e1e26a1238396c8e7 *Meta/demo.rds
+137c7012e06f927695e6b0b76b4e7e6d *Meta/hsearch.rds
+1e66059a08c1e374e8821c6ec869c078 *Meta/links.rds
+ca70a647fb512b5bd02e2e95ae422df2 *Meta/nsInfo.rds
+40c1db4929c5fe68508ed2628099a4b7 *Meta/package.rds
+58bcfc6df6d218dbd4c3ba5374c27035 *NAMESPACE
+2f682d3d6b5a9b9272e71b07bd6629e0 *NEWS
+240d28d145138a75831809e31a480bad *R/spam
+81d5c33557eec8cf8e02240526ced627 *R/spam.rdb
+ce313b1645bf74a6034eecb7b698b023 *R/spam.rdx
+f857b5e1180aa6b49b8233d6f91f81cd *data/Rdata.rdb
+fe588ab1d708b2a19e7031a2646091f5 *data/Rdata.rds
+e62faf8e28b13ee71fb406eb014e4ef9 *data/Rdata.rdx
+777e3e94868c1414ec1f9c6b415d163d *demo/article-jss-example1.R
+eb97d62402d6fa6c299b869ba981d054 *demo/article-jss-example2.R
+0a46cd71466eba8d7cf994bcf77cf251 *demo/article-jss.R
+d5cb30f164ce3f8372b0b8980448557a *demo/cholesky.R
+f5088e9a56468a6b8b552ae3f742d8ff *demo/spam.R
+55eca567613e7c1b4943293f9da038a1 *demo/timing.R
0f7ff8c0275da9085576b25fa7437bfd *demodata/germany.adjacency
-21d9d7d211df35de5af4f8d3420118b3 *help/AnIndex
-3a4382461fdaa3b884e3d4eb4d0bbf17 *help/Rhelp.zip
-3a210c5dc1d93c65c3c9d5d808e2c198 *html/00Index.html
-8a35bd978b148b44fc000a3afc627589 *html/Oral.html
-ee2a2a891732aedff9336205c365787b *html/SPAM.html
-4990ac6f296952321dde7bf85d8f5000 *html/UScounties.html
-3ed477cf4e713fdfc43ad1bc95557722 *html/USprecip.html
-3450f7177b0d05b991fac487bcaaab28 *html/adiag.html
-25aa3d2f253c700ea0b1c88c6fc9ba27 *html/allequal.html
-7802c738f54e41d1eb6e2e734b5dd41e *html/apply.html
-b73ce3fbc1a8323f9784c5599437608a *html/chol.html
-51c3d9a1180eda1e54309602a72fc4ed *html/complexity.html
-710cbf0c000f7c64ab4e378c2e245d70 *html/det.html
-8469cf502192b6ba57aa972a69499ae9 *html/diag.html
-1b1cc4c9290b45b09baf1b0ef8390818 *html/dim.html
-4f4040d6d558a6a3151323fb41e55492 *html/display.html
-1023069f63ba970668090e695ea83f54 *html/foreign.html
-bef3a6ab57af15a1ad3b4793c7b3aee9 *html/germany.html
-8d1e60e93125c65de5c2bd39bc7e0227 *html/history.spam.html
-064531e56d00c71df86d42698d626793 *html/image.html
-84e34d2d6b506bd7e0ab9e8ae71fc9a1 *html/import.html
-acffb1e84646b2185f9df07b88f8dcc1 *html/isSymmetric.html
-dafdbc9d8cbbb88cc7348162dfe15669 *html/kronecker.html
-b6df7e5bb3d78184594938be8f1362a0 *html/lu.tri.html
-56a16d1a088639463b5276d84ab0263a *html/math.html
-1999db6432e3209487b9162eed13de1e *html/math2.html
-3a0c64e33d199b26367b1f4b907837d8 *html/nearestdist.html
-b219b3f13c3a5cd42d51379fde8c3777 *html/operations.html
-684cb2cecae13e64d5f4629ba2c81cee *html/options.html
-4a956144759106a55a4fed9e7b369a78 *html/ordering.html
-c8a26d06c91e1fe5125f06e01356d1f6 *html/powerboost.html
-efa91170f281cceec7c16bba7e741e5a *html/print.html
-4881d105ad9e0bf857066ba0f9dc3233 *html/rmvnorm.html
-c79f85960c58521d7c5bce7a267c4f16 *html/solve.html
-25f1de1b30dca3addc17e8b2fe10ae96 *html/spam-class.html
-90335d887daaf17fe6d959f560f92603 *html/spam.chol.NgPeyton-class.html
-d34ac3f608162bd07a23376dfdbc066c *html/spam.creation.html
-aaed0b0772002e2708b335576e0f9261 *html/spam.internal.html
-822272db7609d62e3479a4eafc9bba79 *html/summary.html
-4977665e3a620ecc3134437b1f55a1e3 *html/todo.html
-b5b6e25c2517a91607df2076573b24cd *html/triplet.html
-340a96a47820a1035e9cae0fa0a7d930 *html/version.html
-ad86492eb3083834007d139986a14ac5 *html/xybind.html
-07b7863f82ac5f17b4fc1a0721d8d35a *latex/Rhelp.zip
-277eda7fdae4f35008da1b1ed942adf0 *libs/spam.dll
-65e4f3d90172f90f69f07e2c80b1219e *man/spam.Rd.gz
+3abc1e86dc25fcdf208f17c76c9402b4 *help/AnIndex
+6e537666a594338de7c85802c58029b7 *help/aliases.rds
+c6b4893cffe3687cbf0f98791b173a1d *help/paths.rds
+614ff2d6616641d60bfb19a8b2286146 *help/spam.rdb
+e2abbeaf68381b16f62f66a805f34b38 *help/spam.rdx
+2e69154ec550efaf8c2b636d59a6cb48 *html/00Index.html
+444535b9cb76ddff1bab1e1865a3fb14 *html/R.css
+34dae2ee20d29ef912e837397ebb18cc *libs/i386/spam.dll
+d82c5767bafb90e7d498e35feaf7165f *libs/i386/symbols.rds
+39ab9f0812451064655c423b9a3ea580 *libs/x64/spam.dll
+5ae67cee102212cb8ced98d514a4ff1e *libs/x64/symbols.rds
diff --git a/win32/deps/library/spam/Meta/Rd.rds b/win32/deps/library/spam/Meta/Rd.rds
index 13020b6..12d08a5 100644
Binary files a/win32/deps/library/spam/Meta/Rd.rds and b/win32/deps/library/spam/Meta/Rd.rds differ
diff --git a/win32/deps/library/spam/Meta/data.rds b/win32/deps/library/spam/Meta/data.rds
index 72a65b6..1cb5040 100644
Binary files a/win32/deps/library/spam/Meta/data.rds and b/win32/deps/library/spam/Meta/data.rds differ
diff --git a/win32/deps/library/spam/Meta/demo.rds b/win32/deps/library/spam/Meta/demo.rds
index 86639c2..6b7affa 100644
Binary files a/win32/deps/library/spam/Meta/demo.rds and b/win32/deps/library/spam/Meta/demo.rds differ
diff --git a/win32/deps/library/spam/Meta/hsearch.rds b/win32/deps/library/spam/Meta/hsearch.rds
index 2f81d8d..ca1a5ec 100644
Binary files a/win32/deps/library/spam/Meta/hsearch.rds and b/win32/deps/library/spam/Meta/hsearch.rds differ
diff --git a/win32/deps/library/spam/Meta/links.rds b/win32/deps/library/spam/Meta/links.rds
new file mode 100644
index 0000000..899ddac
Binary files /dev/null and b/win32/deps/library/spam/Meta/links.rds differ
diff --git a/win32/deps/library/spam/Meta/nsInfo.rds b/win32/deps/library/spam/Meta/nsInfo.rds
index 42ccd0e..c3c7ea7 100644
Binary files a/win32/deps/library/spam/Meta/nsInfo.rds and b/win32/deps/library/spam/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/spam/Meta/package.rds b/win32/deps/library/spam/Meta/package.rds
index 03b9731..0891f2d 100644
Binary files a/win32/deps/library/spam/Meta/package.rds and b/win32/deps/library/spam/Meta/package.rds differ
diff --git a/win32/deps/library/spam/NAMESPACE b/win32/deps/library/spam/NAMESPACE
index 0dcf2cf..eeaa9f5 100644
--- a/win32/deps/library/spam/NAMESPACE
+++ b/win32/deps/library/spam/NAMESPACE
@@ -3,38 +3,12 @@ useDynLib(spam)
importFrom("graphics",image)
importFrom("graphics",plot)
-
# Next two paragraphs are from Matrix....
# Currently, group generics need to be explicitly imported (Bug?):
importFrom("methods", #Arith,Compare,
Math, Math2, Summary#, Complex
)
-if(paste(R.version$major, R.version$minor, sep=".") < "2.6")
-{
-## workaround S4-Group(generic|method) quirk: R/AllGeneric.R
-## needs setGeneric(*, group=) and this for all non-Primitives :
-export(
- ## "Math"
- "log",
- "gamma",
- "lgamma",
-
- ## "Math2"
- "round",
- "signif",
-
- ## "Summary"
- "max",
- "min",
- "range",
- "prod",
- "sum",
- "any",
- "all"
-)
-}
-
# Generic functions
export("dcheck",
"icheck",
@@ -79,6 +53,13 @@ export("dcheck",
"kronecker.default",
"kronecker.spam",
+
+ "diff.spam",
+
+ "circulant.spam",
+ "toeplitz.spam",
+
+ "make.prec",
"determinant.spam",
"determinant.spam.chol.NgPeyton",
@@ -104,12 +85,45 @@ export("dcheck",
"rmvnorm.spam",
"rmvnorm.canonical",
"rmvnorm.prec",
+ "rmvnorm.const",
+ "rmvnorm.canonical.const",
+ "rmvnorm.prec.const",
+
+ "precmat.RW1",
+ "precmat.RW2",
+ "precmat.season",
+ "precmat.IGMRFreglat",
+ "precmat.IGMRFirreglat",
+
+ "rowSums.spam",
+ "colSums.spam",
+ "rowMeans.spam",
+ "colMeans.spam",
+
+ "head.spam",
+ "tail.spam",
+
+ "chol2inv.spam",
+
+ "mle.spam",
+ "mle.nomean.spam",
+ "neg2loglikelihood.spam",
+ "mle",
+ "mle.nomean",
+ "neg2loglikelihood",
+
+ "bdiag.spam",
- "adiag.spam",
+ "bandwidth",
# ".spam.matmul.mat",
# ".spam.matmul",
+# "solve.spam.mat",
+# "solve.spam.dummy",
+ "subset.spam",
+ "subset.rows.spam",
+
"triplet",
"as.spam.matrix.csr",
"as.matrix.csr.spam",
@@ -121,8 +135,15 @@ export("dcheck",
"read.MM",
"read.HB",
+ "powerboost",
+
+ "permutation.spam",
+
"map.landkreis",
- "adjacency.landkreis"
+ "adjacency.landkreis",
+
+ "cleanup",
+ "backsolve"
)
@@ -166,14 +187,24 @@ exportMethods(
"lower.tri",
"norm",
+ "rowSums",
+ "rowMeans",
+ "colSums",
+ "colMeans",
+ "head",
+ "tail",
+
"chol",
"ordering",
"forwardsolve",
"backsolve",
"solve",
+ "chol2inv",
"kronecker",
+
+ "permutation",
"[",
"[<-",
diff --git a/win32/deps/library/spam/NEWS b/win32/deps/library/spam/NEWS
index 6e62011..a1c9f19 100644
--- a/win32/deps/library/spam/NEWS
+++ b/win32/deps/library/spam/NEWS
@@ -1,385 +1,232 @@
- Dear Emacs, please make this -*-Text-*- mode!
+ CHANGES IN VERSION 0.29-0, 0.29-1, 0.29-2
- **************************************************
- * *
- * SPAM VERSION 0.20 *
- * *
- **************************************************
+SIGNIFICANT USER-VISIBLE CHANGES
- CHANGES IN R VERSION 0.20-3
-
- o Resolved dependency issues.
-
- CHANGES IN R VERSION 0.20-1,2
-
- o Minor changes to pass the CRAN test.
-
-
- CHANGES IN R VERSION 0.20-0
-
- o New demos, test functions, datasets.
-
- o Method t for spam.chol.NgPeyton.
-
- o Method Math2 now with signature digits="ANY".
-
- o Update in rmvnorm.canonical, can take a Cholesky structure
- as argument.
-
- o New functionality for a sparse times a full matrix
- multiplication.
-
- o Minor ajustment in memory allocation of chol.
-
-
- **************************************************
- * *
- * SPAM VERSION 0.15 *
- * *
- **************************************************
-
- CHANGES IN R VERSION 0.15-6
-
- o Minor change in Fortran routines to accomodate some Intel
- compilers (pointed out by Tim Hoar).
+ o There is a generic conflict with 'backsolve' between spam
+ and other packages (e.g., bdsmatrix). To avoid the issue,
+ we use the standard generic implemented in 'methods' which
+ requires an additional argument for version 0.29-0 (see
+ also PR#14883).
+ However to maintain backwards compatibility with packages
+ that depend on spam, this was reverted in 0.29-1.
+ Currently, this conflict is not properly solved. I propose
+ to load 'spam' first then the other packages, followed by
+ manually calling:
- CHANGES IN R VERSION 0.15-5
+ setMethod("backsolve","spam.chol.NgPeyton",backsolve.spam)
+ setMethod("backsolve","spam",backsolve.spam)
- o New function adiag.spam, creation of block diagonal sparse
- matrices. No method though.
+ Stay tuned...
- o New functions rmvnorm.spam, rmvnorm.canonical and
- rmvnorm.prec to draw multivariate normals.
+ o Calls like:
+
+ mat <- diag.spam(4)
+ diag( mat[-1,]) <- 3
+ diag.spam( mat[,-1]) <-2
- o New function apply.spam, similar functionality as apply.
+ now work. They are, however, somewhat inefficient.
+ 'toeplitz.spam' is to be prefered. Pointed out by
+ Florian Gerber.
- o drop is implemented now when subsetting a sparse matrix
- with a binary matrix.
+ o The Gibbs sampler in the demo article-jss-example2 contains
+ several bugs, pointed out by Steve Geinitz and Andrea Riebler.
+ I'll post an updated sampler in a future release.
- o Major overhaul to nearest.dist: zeros are not included.
- Old parameters are kept for backwards compatibility.
- o Orders/complexities of major algorithms are now described
- in the help 'complexity'.
+NEW FEATURES
- o Using packageStartupMessage in .onAttach.
+ o New functions 'rmvnorm.const', 'rmvnorm.prec.const' and
+ 'rmvnorm.canonical.const' to draw constrained multivariate
+ normal variates.
- o Code clean up and help improvements. Changes reflecting the
- change to UZH.
+ o New functions 'precmat' (wrapper to), 'precmat.RW1', 'precmat.RW2',
+ 'precmat.season', 'precmat.IGMRFreglat' and 'precmat.IGMRFirreglat'
+ to create precision matrices for IGMRF.
- o Bugfix in assinging via a nx2 matrix.
-
+ o New methods 'rowSums', 'colSums' and 'rowMeans', 'colMeans' for
+ 'spam' objects.
-
- CHANGES IN R VERSION 0.15-4
+ o New methods 'head' and 'tail' for 'spam' and 'spam.chol.NgPeyton'
+ objects.
- o Changes in help files. Minor code improvements.
-
- o New function powerboost.
-
- o Changes to if(getRversion() >= "x.y"), required for R 2.10.
+ o New method 'chol2inv' for 'spam' object.
-
+ o New option 'inefficiencywarning': handling of warnings issued
+ in case of an inefficient calculation.
- CHANGES IN R VERSION 0.15-3
+ o New option 'structurebased': should operations be performed on
+ the nonzero entries or on including the zeros. Classical example:
+ what should the cosine of a sparse matrix look like?
+ In the near future, all operations from Math and Ops will include
+ this option. Some loss of backwards compatibility might be
+ lost in the future.
- o Several bug fixes in the demos due to the changes in
- the previous versions.
- o Several minior changes in the help files to compile with
- the new help parser and to correct for typos.
+INTERNAL CHANGES
- o Added the demos into the tests directory. Additionally,
- tests contains now the proper Rout.saves files.
+ o New much faster approach to extract rows. For not too sparse
+ large matrices improvements over two orders of magnitudes are
+ achieved.
- o In test files, library( spam, warn.conflict=FALSE)
- is used to avoid masking messages in R-2.8.0.
- Timing output in test files is suppressed.
-
- o Added trivial headers to most files.
+ o Elininated '.Internal()' calls that induce a 'Note' on CRAN
+ checks. This also implied a minor rewrite of 'image.spam'.
+ o Minor code improvements.
- o Bug fix in spam.list(), negative values were not correctly
- handled.
+ o Eliminated non-API calls (29.1).
- o Bug fix in subsetting (occured when subsetting very
- sparse matrices, memory allocation problem).
+ o Rewritten .C("bincode",...) call as suggested by Brian Ripley
+ (29.2).
+
+BUG FIXES
- CHANGES IN R VERSION 0.15-2
+ o Bug fix that occures when multiplying elementwise matrices
+ that have non-intersecting structures (pointed out by
+ Corentin Barbu).
- o Method all.equal for matrix-spam signature.
+ o Bug fix in triangular backsolves involving 'spam' objects
+ and rhs matrices.
- o Bug fix in Fortran function of nearest.dist. Numerical
- instabilities could return NaN on diagonal. Additionally,
- overhaul of tests/dist.R.
+ o Bug fix in triangular backsolve causing errors on some
+ architectures.
- o Several minor improvements in the help files as well
- as in function nearest.dist and tests/*.R.
- CHANGES IN R VERSION 0.15-1
- o Improvements in the nearest.dist function. The diagonals
- are now handled consistenly.
+ CHANGES IN VERSION 0.28
- o Symmetry check criterion for Cholesky decomposition has been
- relaxed from (2+eps)*eps to 100*eps for an easier handling when
- working with great circle distance induced covariance matrices.
- Same cutoff is used with eigen. Instead of using norm,
- we use essentially an isSymmetric.spam test.
+NEW FEATURES
- o Methods isSymmetric and all.equal for spam.
-
- o Methods image and display for spam.chol.NgPeyton.
+ o New function 'cleanup' (suggested by Simon Barthelme).
- o Method as.spam for distance class implemented.
+ o Extending help files.
- o Complete rewrite of spam.list. Method as.spam for lists
- are implemented as well.
+ o Improved functionality of 'isSymmetric'.
- o Method spam for spam objects (possibility to rearrange the
- dimension) has been eliminated. The approach was based on
- creating the full matrix and assigning it back to a spam
- object.
-
- o Binary subsetting and subassigning is implemented.
- o Bug fix: the Cholesky Fortran routine checks if diagonal
- elements are available (and positive).
+INTERNAL CHANGES
- o Bug fix: in dim<-.spam
+ o Proper storage of data files.
- o Minor improvements in the help files as well as the following
- R functions: norm, .spam.matmul.
+ o Cleaning up argument names within spam functions.
+ o Cleaning up old Fortran code, i.e., eliminating
+ unnecessary subroutines and write calls.
- CHANGES IN R VERSION 0.15-0
- o The devel versions of 14-x have been sitting around for
- a while and I was inconsistent with the devel/gold numbering.
- To avoid any confusion, I have decided to go to the next
- minor version. An additional reason supporting this is
- that the version number identification has changed over
- the 0.14-devel.
+BUG FIXES
+ o Bug fix that may occure when extracting zero elements
+ (pointed out by Corentin Barbu).
- **************************************************
- * *
- * SPAM VERSION 0.14 *
- * *
- **************************************************
- CHANGES IN R VERSION 0.14-x
- o A few rudimentary functions to change between the compressed
- sparse row formats of the packages SparseM and Matrix.
- Just the functions, no S3/S4 constructs available.
- o Functionality to read matrices stored in the Harwell-Boeing
- or MatrixMarket formats.Read MatrixMarket.
+ CHANGES IN VERSION 0.27
- o Rewritten cbind.spam and rbind.spam. Both can take now
- numeric and spam objects. cbind.spam calls now Fortran
- code and is now very fast. Rewrite of their help.
+NEW FEATURES
- o Implemented spam.list to go from a index based list to a
- spam matrix. The function triplets does the inverse.
-
- o forwardsolve and backsolve methods for spam objects.
+ o Requires now R2.10 and higher.
- o Implemented the function 'dim<-' for spam objects.
+ o Functions to create Toeplitz and circulant matrices.
- o Method diag and as.matrix for spam.chol.NgPeyton.
+ o Function to create precision matrices for gridded GMRF.
- o eps is now tested for being at least double precision.
-
- o as.spam.xxx and spam.yyy functions have been streamlined.
-
- o Initializing an empty spam matrix causes a warning but still
- coerces to a zero matrix, see new("spam",entries=rep(1,0))
+ o Improvements in the mle.* functions.
- o Eliminated bug in subsetting (occuring when subsetting
- for an empty matrix). Clean out subsetting and assigning.
+ o Method diff for sparse matrices (suggested by Paul Eilers).
- o Include a inst subdirectory containing this file, which
- is renamed to NEWS. Once we have reached a stable version
- I will maintain a proper CHANGELOG file in the root
- directory.
+ o Improvement of help pages.
- o Proper method handling for kronecker and bug fixes in
- kronecker.spam.
-
- o Saved the datasets UScounties.storder/ndorder as spam
- objects as assumed by demo article-jss.
+ o Eliminated some help aliases to base functions
+ (for which no 'usage' is given).
- o Implemented many 'identical' structures and homogenized zero
- matrix handling, throughout the R code. int0, ..., int2 are
- internally defined integers.
- o Similar changes as for 13-3. Additionally, considerable
- improvements in help, file structure, tests, timing, etc.
+INTERNAL CHANGES
+ o Change to iL coding.
- CHANGES IN R VERSION 0.14-0
+ o Start to using 'identical'.
- Major revision. Slight loss of backwards compatibility.
+ o Code cleaning due to requirement of R2.10 and higher.
- o New demo article-jss.
- o New variable spam.version, similar to the R version
- variable.
-
- o Change and adding of a few option names, for example
- cholsymmetrycheck, cholpivotcheck, cholupdatesingular,
- dopivoting, safemode, ...
- See help files for details.
+BUG FIXES
- o Complete rewrite of chol. The argument ordering is
- now called pivot, more consistent with the generic
- function. Two different orderings are implemented.
- Uses the new option cholsymmetrycheck.
+ o Bug fix in as.spam.list (thanks to Paul Eilers).
- o Similar changes as in chol in determinant.spam.
+ o Bug fix in demo(spam) (thanks to Thomas Gsponer).
- o New function update.spam.chol.NgPeyton.
-
- o Invisible/minor changes in method c for spam, in solve.spam,
- determinant.chol.NgPeyton
-
- o The class spam.chol.NgPeyton is defined differently.
- Accordingly, print and summary methods are updated.
- Notably, fill-in ratios are given with summary.
- Summary also hands back the length of the vectors holding the
- factor and the column indices.
-
- o New methods for spam.chol.NgPeyton, namely, dim, length, c,
- dim<-, and length<-. The latter two giving simply errors.
- o Along the redefinition of the class spam.chol.NgPeyton,
- forwardsolve.spam and backsolve.spam are updated.
- Use now the option dopivoting.
- o kronecker.r is implemented.
- o nearest.dist, a function to calculate close distances
- within one or two sets of locations is implemented.
- Roughly speaking, it is the union of dist in base and
- rdist/rdist.earth in fields. (comes with options
- nearestdistincreasefactor and nearestdistnnz).
- o print and show now emphasize that the non-zero elements
- are row-wise printed.
+ CHANGES IN VERSION 0.24, 0.25 and 0.26
- o UScounties is a dataset containing the adjacency matrix
- of the first and second order neighbors of the counties
- of the lower 48 US states.
-
- o Some changes in help files, especially in the *-class
- files.
-
- o Eliminated warnings issued when compiling.
+ o Devel versions, not released.
- o Minor R and Fortran code cleaning.
- o Along the new features, update of CHANGELOG, todo,
- NAMESPACE files, etc.
- **************************************************
- * *
- * SPAM VERSION SERIES 0.13 *
- * *
- **************************************************
- CHANGES IN R VERSION 0.13-3
+ CHANGES IN VERSION 0.23
- o Minor changes in R and Fortran code to eliminate warnings.
+NEW FEATURES
- o In diag()'s argument list, drop the explicit default (' = n').
- As is now in R-2.7.
+ o Further improved versions of demos.
+ o Some improvements to meet Rd standards.
+ Adjustments for future R versions.
- CHANGES IN R VERSION 0.13-2
- o New spam.options and getOption functions. .Spam
- as a variable is not visible anymore.
- o Retrieving information from the DESCRIPTION file directly
- (thanks to Roger Bivand).
- CHANGES IN R VERSION 0.13-1
+ CHANGES IN VERSION 0.22
- o Minor Fortran Changes for g77 compatibility. Thanks to
- Roger Bivand.
+NEW FEATURES
- o Updated DESCRIPTION file.
+ o Improved versions of demos. Synchronized with the JSS article.
-
- CHANGES IN R VERSION 0.13
+ o Additional changes and improvements in the help files (thanks
+ to Steve Geinitz).
- o Updated NAMESPACE (for versions > 2.5).
- o Some changes in help files.
- o Cleaned Fortran source files (eliminated unused
- subroutines and used the posted complier output to
- straighten details).
- o Implemented more efficient transpose Fortran code.
- This also eliminates a bug when transposing a 1 row
- matrix.
- o Eliminated bug when assigning with a 1 row matix.
- o Eliminated bug (Fortran code) that could potentially
- occur when assigning.
- o Eliminated bug when plotting a 1 row matix.
-
- o Minor R code cleaning.
+ CHANGES IN VERSION 0.21
+
+NEW FEATURES
- **************************************************
- * *
- * SPAM VERSION 0.12 *
- * *
- **************************************************
+ o New NEWS file, to work better with news() command.
+ The previous is available under ONEWS.
- o Updated NAMESPACE and DESCRIPTION file.
+ o New functions bandwidth, permutation, mle[.nomean][.spam],
+ neg2loglikelihood[.spam].
+
- o print and summary pass back NULL instead of the
- object.
+ o Renamed adiag.spam to bdiag.spam.
- o Changed to prod(x dimension) instead of nrow*ncol to
- overcome integer overflow for very large matrices.
- o Introduced a prototype in the definition of spam
- and spam.chol.*.
+ o Cleaned up argument naming with the rmvnorm.*
+ suite.
- o .Spam$safemode also determines if a spam object is
- tested for validity, as well as for NAOK.
- o In many functions sparse matrix construction is
- done manually using slots (and check=FALSE, if
- approprate).
+INTERNAL CHANGES
- o Increased the value of symmetry criteria to
- (2+eps)*eps, as each element can be off by eps,
- subtraction leads to a 2*eps offset and yet we are
- symmetric.
+ o Various Fortran code, R code and help file
+ improvements.
- o Major restructuration of chol/det with elimination
- of auxiliarychol.
- o Methods chol/backsolve/forwarsolve now call the *.spam
- functions.
+BUG FIXES
- o Many internal changes to favour speed and efficiency.
+ o Minor change in one of the demos (solves a 64bit issue).
- o Bug fix in .spam.elemul. occuring when the result is the
- zero matrix.
diff --git a/win32/deps/library/spam/R/spam b/win32/deps/library/spam/R/spam
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/spam/R/spam
+++ b/win32/deps/library/spam/R/spam
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/spam/R/spam.rdb b/win32/deps/library/spam/R/spam.rdb
index 0a9fdf2..0ae3d0a 100644
Binary files a/win32/deps/library/spam/R/spam.rdb and b/win32/deps/library/spam/R/spam.rdb differ
diff --git a/win32/deps/library/spam/R/spam.rdx b/win32/deps/library/spam/R/spam.rdx
index 5589873..ef3854d 100644
Binary files a/win32/deps/library/spam/R/spam.rdx and b/win32/deps/library/spam/R/spam.rdx differ
diff --git a/win32/deps/library/spam/data/Rdata.rdb b/win32/deps/library/spam/data/Rdata.rdb
index a9f2263..163ae99 100644
Binary files a/win32/deps/library/spam/data/Rdata.rdb and b/win32/deps/library/spam/data/Rdata.rdb differ
diff --git a/win32/deps/library/spam/data/Rdata.rds b/win32/deps/library/spam/data/Rdata.rds
index 6ba072a..ddd52e9 100644
Binary files a/win32/deps/library/spam/data/Rdata.rds and b/win32/deps/library/spam/data/Rdata.rds differ
diff --git a/win32/deps/library/spam/data/Rdata.rdx b/win32/deps/library/spam/data/Rdata.rdx
index fa46268..efc475b 100644
Binary files a/win32/deps/library/spam/data/Rdata.rdx and b/win32/deps/library/spam/data/Rdata.rdx differ
diff --git a/win32/deps/library/spam/demo/article-jss-example1.R b/win32/deps/library/spam/demo/article-jss-example1.R
index 473156a..a4be16c 100644
--- a/win32/deps/library/spam/demo/article-jss-example1.R
+++ b/win32/deps/library/spam/demo/article-jss-example1.R
@@ -1,4 +1,4 @@
-# This is file ../spam0.20-3/demo/article-jss-example1.R
+# This is file ../spam0.29-2/demo/article-jss-example1.R
# This file is part of the spam package,
# http://www.math.uzh.ch/furrer/software/spam/
# written and maintained by Reinhard Furrer.
@@ -6,9 +6,22 @@
-library(spam)
+# This demo contains the R code of the example in Section 5.1 of the
+# JSS article:
+# "spam: A Sparse Matrix R Package with Emphasis on
+# MCMC Methods for Gaussian Markov Random Fields"
+#
+# Compared to the R code given in the article, here we give:
+# - improved formatting
+# - more comments
+# - the R code to construct the figures
-data(UKDriverDeaths)
+
+
+# SETUP:
+library("spam")
+
+data("UKDriverDeaths")
y <- sqrt(c(UKDriverDeaths)) # square root counts
@@ -17,7 +30,7 @@ m <- 12 # We want to predict for one season.
nm <- n+m # Total length of s and t
-priorshape <- c(4,1,1) # alpha's, as in Rue & Held (2005)
+priorshape <- c(4, 1, 1) # alpha's, as in Rue & Held (2005)
priorinvscale <- c(4, 0.1, 0.0005) # beta's
# Construct the individual block precisions
@@ -25,19 +38,19 @@ priorinvscale <- c(4, 0.1, 0.0005) # beta's
# Qsy, Qty are trivial:
Qsy <- diag.spam(n)
-dim(Qsy) <- c(n+m,n)
+dim(Qsy) <- c(n+m, n)
Qty <- Qsy
-Qst <- spam(0,nm,nm)
-Qst[cbind(1:n,1:n)] <- rep(1,n)
+Qst <- spam(0, nm, nm)
+Qst[cbind(1:n, 1:n)] <- rep(1, n)
# The form of Qss is given by (Rue and Held equation 3.59).
# Qss can be constructed with a loop:
-Qss <- spam(0,nm,nm)
+Qss <- spam(0, nm, nm)
for (i in 0:(nm-m)) {
- Qss[i+1:m,i+1:m] <- Qss[i+1:m,i+1:m]+1
+ Qss[i+1:m,i+1:m] <- Qss[i+1:m, i+1:m]+1
}
# Note that for the final version we need:
@@ -65,12 +78,16 @@ Qst_yk <- rbind(cbind(k[2]*Qss + k[1]*diag.spam(nm), k[1]*Qst),
struct <- chol(Qst_yk)
+
+# Figure 6:
+display(Qst_yk)
+display(struct)
+
# Note that we do not provide the exactly the same ordering
# algorithms. Hence, the following is sightly different than
# Figure RH4.2.
-cholQst_yk <- chol(Qst_yk,pivot='RCM')
+cholQst_yk <- chol(Qst_yk,pivot="RCM")
P <- ordering(cholQst_yk)
-display(Qst_yk)
display(Qst_yk[P,P])
@@ -79,9 +96,10 @@ display(Qst_yk[P,P])
# k=( kappa_y, kappa_s, kappa_t)'
# Gibbs sampler
-ngibbs <- 100 # In the original version is 500!
+ngibbs <- 500 # Is very fast!
burnin <- 10 # > 0
totalg <- ngibbs+burnin
+set.seed(14)
# Initialize parameters:
spost <- tpost <- array(0, c(totalg, nm))
@@ -94,7 +112,7 @@ tpost[1,] <- 40
# calculation of a few variables:
postshape <- priorshape + c( n/2, (n+1)/2, (n+m-2)/2)
-
+# GIBBS' ITERATIONS:
timing <- system.time({
for (ig in 2:totalg) {
@@ -124,7 +142,7 @@ for (ig in 2:totalg) {
kpost[ig,] <- rgamma(3, postshape, postinvscale)
- if( (ig%%10)==0) cat('.')
+ if( (ig%%10)==0) cat(".")
}
@@ -132,7 +150,7 @@ for (ig in 2:totalg) {
# POSTPROCESSING:
-cat('\nTotal time:',timing[1],'per iteration:',timing[1]/totalg,'\n')
+cat("\nTotal time:",timing[1],"per iteration:",timing[1]/totalg,"\n")
# Eliminate burn-in:
@@ -140,11 +158,15 @@ kpost <- kpost[-c(1:burnin),]
spost <- spost[-c(1:burnin),]
tpost <- tpost[-c(1:burnin),]
+print(summary(kpost))
+
postquant <- apply(spost+tpost, 2, quantile,c(.025,.975))
postmean <- apply(spost+tpost, 2, mean)
postmedi <- apply(spost+tpost, 2, median)
+######################################################################
+# Figure 7:
par(mfcol=c(1,1),mai=c(.6,.8,.01,.01))
plot( y^2, ylim=c(800,2900),xlim=c(0,nm),ylab="Counts")
@@ -154,7 +176,7 @@ matlines( t(postquant)^2, col=4,lty=1)
legend("topright",legend=c("Posterior median", "Quantiles of posterior sample",
"Quantiles of predictive distribution"),
- bty='n',col=c(2,4,3),lty=1)
+ bty="n",col=c(2,4,3),lty=1)
@@ -165,13 +187,13 @@ dim(ypred) <- c(ngibbs,nm)
postpredquant <- apply(ypred, 2, quantile,c(.025,.975))
matlines( t(postpredquant)^2, col=3,lty=1)
points(y^2)
-dev.off()
+
kpostmedian <- apply(kpost,2,median)
par(mfcol=c(1,3),mai=c(.65,.65,.01,.01),cex=.85,mgp=c(2.6,1,0))
-matplot( log( kpost), lty=1, type='l',xlab='Index')
+matplot( log( kpost), lty=1, type="l",xlab="Index")
abline(h=log(kpostmedian),col=3)
acf( kpost[,3],ylab=expression(kappa[t]))
plot(kpost[,2:3],ylab=expression(kappa[t]),xlab=expression(kappa[s]),cex=.8)
@@ -182,20 +204,11 @@ allkappas <- rbind(apply(kpost,2,mean),
apply(kpost,2,median),
apply(1/kpost,2,mean),
apply(1/kpost,2,median))
-colnames(allkappas) <- c('kappa_y', 'kappa_s', 'kappa_t')
-rownames(allkappas) <- c('Prec (mean)', 'Prec (median)',
- 'Var (mean)', 'Var (median) ')
+colnames(allkappas) <- c("kappa_y", "kappa_s", "kappa_t")
+rownames(allkappas) <- c("Prec (mean)", "Prec (median)",
+ "Var (mean)", "Var (median) ")
print(allkappas,4)
-png("example1_m1.png",width=300,height=300)
-par(mai=c(.5,.5,.05,.05))
-display(Qst_yk)
-dev.off()
-
-png("example1_m2.png",width=300,height=300)
-par(mai=c(.5,.5,.05,.05))
-display(struct)
-summary(kpost)
diff --git a/win32/deps/library/spam/demo/article-jss-example2.R b/win32/deps/library/spam/demo/article-jss-example2.R
index 84c0d0d..d3f710e 100644
--- a/win32/deps/library/spam/demo/article-jss-example2.R
+++ b/win32/deps/library/spam/demo/article-jss-example2.R
@@ -1,12 +1,26 @@
-# This is file ../spam0.20-3/demo/article-jss-example2.R
+# This is file ../spam0.29-2/demo/article-jss-example2.R
# This file is part of the spam package,
# http://www.math.uzh.ch/furrer/software/spam/
# written and maintained by Reinhard Furrer.
+# This demo contains the R code of the example in Section 5.2 of the
+# JSS article:
+# "spam: A Sparse Matrix R Package with Emphasis on
+# MCMC Methods for Gaussian Markov Random Fields"
+
+
+# Compared to the R code in the article, here we give:
+# - improved formatting
+# - more comments, e.g. how to run the code using regular matrices
+# - the code to construct the figures
+
+cat("\nThis demo contains the R code of the second example\nin the JSS article. As pointed out by Steve Geinitz\nand Andrea Riebler, the Gibbs sampler is not correct\nand contains several bugs. \n\nI'll post an updated sampler in a future release.\n\n")
+
+
# INITALIZE AND FUNCTIONS:
-require( fields, warn.conflict=FALSE)
+require("fields", warn.conflict=FALSE)
# READ DATA:
@@ -71,8 +85,8 @@ postshape <- ahyper + c(n-1,n)/2
accept <- numeric(totalg)
-struct <- chol(Q1 + Q2,
- memory=list(nnzcolindices=6467))
+struct <- chol(Q1 + Q2 + diag.spam(2*n),
+ memory=list(nnzcolindices=5500))
# struct <- NULL # If no update steps are wanted
@@ -99,8 +113,7 @@ for (ig in 2:totalg) {
b,
# Precision matrix
Q,
- Rstruct=struct,
- memory=list(nnzcolindices=6467))
+ Rstruct=struct)
ustar <- xstar[1:n]
@@ -135,7 +148,7 @@ for (ig in 2:totalg) {
kpost[ig,] <- kpost[ig-1,]
}
- if( (ig%%10)==0) cat('.')
+ if( (ig%%10)==0) cat(".")
}
@@ -144,10 +157,10 @@ for (ig in 2:totalg) {
# POSTPROCESSING:
-cat('\nTotal time:',timing[1],'per iteration:',timing[1]/totalg)
+cat("\nTotal time:",timing[1],"per iteration:",timing[1]/totalg)
accept <- accept[-c(1:burnin)]
-cat('\nAcceptance rate:',mean(accept),'\n')
+cat("\nAcceptance rate:",mean(accept),"\n")
kpost <- kpost[-c(1:burnin),]
upost <- upost[-c(1:burnin),]
@@ -171,30 +184,32 @@ vpostmedian <- apply(vpost,2,median)
######################################################################
-# Figures
+# Figure 8:
+
par(mfcol=c(1,3),mai=rep(0,4))
map.landkreis(log(Y))
map.landkreis(Y/E,zlim=c(.1,2.4))
map.landkreis(exp(upostmedian),zlim=c(.1,2.4))
+# Figure 9:
par(mfcol=c(2,4),mai=c(.5,.5,.05,.1),mgp=c(2.3,.8,0))
-hist(kpost[,1],main='',xlab=expression(kappa[u]),prob=T)
+hist(kpost[,1],main="",xlab=expression(kappa[u]),prob=TRUE)
lines(density(kpost[,1]),col=2)
tmp <- seq(0,to=max(kpost[,1]),l=500)
lines(tmp,dgamma(tmp,ahyper[1],bhyper[1]),col=4)
abline(v=kpostmedian[1],col=3)
-hist(kpost[,2],main='',xlab=expression(kappa[y]),prob=T)
+hist(kpost[,2],main="",xlab=expression(kappa[y]),prob=TRUE)
lines(density(kpost[,2]),col=2)
tmp <- seq(0,to=max(kpost[,2]),l=500)
lines(tmp,dgamma(tmp,ahyper[2],bhyper[2]),col=4)
abline(v=kpostmedian[2],col=3)
# Trace plots:
-plot(kpost[,1],ylab=expression(kappa[u]),type='l')
+plot(kpost[,1],ylab=expression(kappa[u]),type="l")
abline(h=kpostmedian[1],col=3)
-plot(kpost[,2],ylab=expression(kappa[y]),type='l')
+plot(kpost[,2],ylab=expression(kappa[y]),type="l")
abline(h=kpostmedian[2],col=3)
# ACF:
@@ -208,9 +223,9 @@ plot(kpost[,1],kpost[,2],xlab=expression(kappa[u]),ylab=expression(kappa[y]))
abline(v=kpostmedian[1],h=kpostmedian[2],col=3)
-plot(accept+rnorm(ngibbs,sd=.05),pch='.',ylim=c(-1,2),yaxt='n',ylab='')
-text(ngibbs/2,1/2,paste('Acceptance rate:',round(mean(accept),3)))
-axis(2,at=c(0,1),label=c('Reject','Accept'))
+plot(accept+rnorm(ngibbs,sd=.05),pch=".",ylim=c(-1,2),yaxt="n",ylab="")
+text(ngibbs/2,1/2,paste("Acceptance rate:",round(mean(accept),3)))
+axis(2,at=c(0,1),label=c("Reject","Accept"))
detach(Oral)
######################################################################
diff --git a/win32/deps/library/spam/demo/article-jss.R b/win32/deps/library/spam/demo/article-jss.R
index 1eb542a..a4cbbaf 100644
--- a/win32/deps/library/spam/demo/article-jss.R
+++ b/win32/deps/library/spam/demo/article-jss.R
@@ -1,4 +1,4 @@
-# This is file ../spam0.20-3/demo/article-jss.R
+# This is file ../spam0.29-2/demo/article-jss.R
# This file is part of the spam package,
# http://www.math.uzh.ch/furrer/software/spam/
# written and maintained by Reinhard Furrer.
@@ -12,22 +12,21 @@
# This demo contains the R code to construct the figures and the table of the
-# article:
+# JSS article:
# "spam: A Sparse Matrix R Package with Emphasis on
# MCMC Methods for Gaussian Markov Random Fields"
-# submitted to JSS.
# The code presented here differs in the following points form the actually used
# one:
# - Very large grid sizes or very high order neighbor structures are not included
# here;
-# - Instead of (100+1) factorizations only (10+1) are performed here;
-# - The ratios in Fig 3 and 4 are not included here.
+# - Instead of (100+1) factorizations only (50+1) are performed here;
# - No figure fine-tuning is done here.
# - We had a few additional gc(), just to be sure.
+######################################################################
# Figure 1:
i <- c( 2,4,4,5,5)
j <- c( 1,1,2,1,3)
@@ -58,6 +57,7 @@ display( as.spam(R))
abline( h=-U supernodes+ 5,col=3,lty=2)
+######################################################################
# Figure 2:
theta1 <- .1
theta2 <- .01
@@ -81,19 +81,23 @@ display( as.spam(U))
text(400,-2200,"no permutation\nz=689615\nw=96463\ns=711",adj=0)
-# general parameters for the following
-N <- 25 # would be 100 in the article
+
+
+######################################################################
+# Figure 3:
+
+# general parameters for the following figures
+N <- 50 # would be 100 in the article
stsel <- 1 # user.self
rPsx <- 1 # for function "system.time"
rPsy <- 3 # memory usage
rPint <- .0001 # small interval
-# Figure 3:
-theta1 <- .1
+theta1 <- .1
theta2 <- .05
-xseq <- ceiling(4 + exp(seq(0,to=5,by=1))/2) # would be seq(0.5,to=6,by=.5) in the article
+xseq <- ceiling(4 + exp(seq(0.5,to=5.5,by=.5))/2) # would be seq(0,to=6,by=.5) in the article
xseql <- length(xseq)
table <- array(NA,c(xseql,4))
@@ -126,18 +130,30 @@ for (ix in 1:xseql) {
table <- pmax(table, 0.0001)
par(mfcol=c(1,2))
-plot(xseq, table[,1], type='l', log='xy', ylim=range(table[,c(1,3)]),
+plot(xseq, table[,1], type="l", log="xy", ylim=range(table[,c(1,3)]),
xlab="L (log scale)", ylab="seconds (log scale)")
lines(xseq, table[,3], lty=2)
+lines(xseq,table[,1]/table[,3],col=4,lty=3)
-plot(xseq, table[,2], type='l', log='xy', ylim=range(table[,c(2,4)]+0.01),
+plot(xseq, table[,2], type="l", log="xy", ylim=range(table[,c(2,4)]+0.01),
xlab="L (log scale)", ylab="Mbytes (log scale)")
lines(xseq, table[,4], lty=2)
+lines(xseq,table[,2]/table[,4],col=4,lty=3)
+
+
+######################################################################
# Figure 4:
-x <- 30 # was 50 in article
+# general parameters for the following figures
+N <- 50 # would be 100 in the article
+stsel <- 1 # user.self
+rPsx <- 1 # for function "system.time"
+rPsy <- 3 # memory usage
+rPint <- .0001 # small interval
+
+x <- 50 # was 50 in article
maxnn <- 6 # was 6 in article
egdx <- expand.grid( 1:(maxnn+1), 1:(maxnn+1))
@@ -173,20 +189,45 @@ for (id in 1:dvall) {
}
-# Since we have a small N, elements in table might be zero.
+# If we have a small N, elements in table might be zero.
table <- pmax(table, 0.0001)
par(mfcol=c(1,2))
-plot( dval, table[,1], type='l', log='xy',ylim=range(table[,c(1,3)]),
+plot( dval, table[,1], type="l", log="xy",ylim=range(table[,c(1,3)]),
xlab="distance (log scale)", ylab="seconds (log scale)")
lines( dval, table[,3],lty=2)
+lines( dval, table[,1]/table[,3],col=4,lty=3)
-plot( dval, table[,2], type='l', log='xy',ylim=range(table[,c(2,4)]),
+plot( dval, table[,2], type="l", log="xy",ylim=range(table[,c(2,4)]),
xlab="distance (log scale)", ylab="Mbytes (log scale)")
lines( dval, table[,4],lty=2)
+lines( dval, table[,2]/table[,4],col=4,lty=3)
+
+
+######################################################################
+# Figure 5
+In <- diag.spam(nrow(UScounties.storder))
+struct <- chol(In + .2 * UScounties.storder + .1 * UScounties.ndorder)
+
+len.1 <- 90 # in the article, is set to 180
+len.2 <- 50 # in the article, is set to 100
+theta.1 <- seq(-.225, to=.515, len=len.1)
+theta.2 <- seq(-.09, to=.235, len=len.2)
+
+grid <- array(NA, c(len.1, len.2))
+spam.options("cholupdatesingular"="null")
+
+for (i in 1:len.1)
+ for(j in 1:len.2)
+ grid[i,j] <- !is.null(update(struct, In + theta.1[i]*UScounties.storder
+ + theta.2[j]* UScounties.ndorder))
+image(theta.1, theta.2, grid, xlab=expression(theta[1]), ylab=expression(theta[2]),
+ xlim=c(-.3,.6),ylim=c(-.1,.25),col=c(0,"gray"))
+abline(v=0,h=0, lty=2)
+######################################################################
# Table 1:
table <- array(NA,c(9,4))
diff --git a/win32/deps/library/spam/demo/cholesky.R b/win32/deps/library/spam/demo/cholesky.R
index 070a487..26cfb3e 100644
--- a/win32/deps/library/spam/demo/cholesky.R
+++ b/win32/deps/library/spam/demo/cholesky.R
@@ -1,4 +1,4 @@
-# This is file ../spam0.20-3/demo/cholesky.R
+# This is file ../spam0.29-2/demo/cholesky.R
# This file is part of the spam package,
# http://www.math.uzh.ch/furrer/software/spam/
# written and maintained by Reinhard Furrer.
diff --git a/win32/deps/library/spam/demo/spam.R b/win32/deps/library/spam/demo/spam.R
index dbbbd95..f2d01f7 100644
--- a/win32/deps/library/spam/demo/spam.R
+++ b/win32/deps/library/spam/demo/spam.R
@@ -1,4 +1,4 @@
-# This is file ../spam0.20-3/demo/spam.R
+# This is file ../spam0.29-2/demo/spam.R
# This file is part of the spam package,
# http://www.math.uzh.ch/furrer/software/spam/
# written and maintained by Reinhard Furrer.
@@ -67,8 +67,7 @@ par(ask=interactive() &&
display(smat, main="'scatterplot'-type display, very efficient")
-
-.Spam$imagesize <- prod(smat dimension)+1
+spam.options("imagesize"=prod(smat dimension)+1)
display(smat, main="'image'-type display, may be slow and heavy")
par(opar)
diff --git a/win32/deps/library/spam/demo/timing.R b/win32/deps/library/spam/demo/timing.R
index 7b22ed5..a90bb54 100644
--- a/win32/deps/library/spam/demo/timing.R
+++ b/win32/deps/library/spam/demo/timing.R
@@ -1,4 +1,4 @@
-# This is file ../spam0.20-3/demo/timing.R
+# This is file ../spam0.29-2/demo/timing.R
# This file is part of the spam package,
# http://www.math.uzh.ch/furrer/software/spam/
# written and maintained by Reinhard Furrer.
diff --git a/win32/deps/library/spam/help/AnIndex b/win32/deps/library/spam/help/AnIndex
index 5c60544..e396669 100644
--- a/win32/deps/library/spam/help/AnIndex
+++ b/win32/deps/library/spam/help/AnIndex
@@ -50,8 +50,6 @@
abs math
acos math
acosh math
-adiag adiag
-adiag.spam adiag
adjacency.landkreis germany
all summary
all.equal,matrix,spam-method allequal
@@ -74,7 +72,7 @@ as.spam,list-method spam.creation
as.spam,matrix-method spam.creation
as.spam,numeric-method spam.creation
as.spam,spam-method spam.creation
-as.spam,spam.chol.NgPeyton-method spam.creation
+as.spam,spam.chol.NgPeyton-method spam.chol.NgPeyton-class
as.spam.chol.NgPeyton spam.creation
as.spam.dgCMatrix foreign
as.spam.dgRMatrix foreign
@@ -95,19 +93,33 @@ backsolve,matrix-method solve
backsolve,spam-method solve
backsolve,spam.chol.NgPeyton-method spam.chol.NgPeyton-class
backsolve-methods solve
-backsolve.default solve
backsolve.spam solve
+bandwidth bandwidth
+bdiag bdiag
+bdiag.spam bdiag
c,spam-method spam-class
c,spam.chol.NgPeyton-method spam.chol.NgPeyton-class
cbind xybind
cbind,spam-method xybind
cbind.spam xybind
ceiling math
-chol chol
chol,ANY-method chol
chol,matrix-method chol
chol,spam-method chol
+chol,spam.chol.NgPeyton-method spam.chol.NgPeyton-class
chol.spam chol
+chol2inv solve
+chol2inv,spam-method solve
+chol2inv,spam.chol.NgPeyton-method solve
+chol2inv.spam solve
+circulant.spam circulant
+cleanup cleanup
+colMeans rowcolstats
+colMeans,spam-method rowcolstats
+colMeans.spam rowcolstats
+colSums rowcolstats
+colSums,spam-method rowcolstats
+colSums.spam rowcolstats
Compare,numeric,spam-method spam-class
Compare,spam,numeric-method spam-class
complexities complexity
@@ -122,8 +134,9 @@ det,spam.chol.NgPeyton-method det
det.spam det
determinant det
determinant,spam-method det
-determinant,spam.chol.NgPeyton-method det
+determinant,spam.chol.NgPeyton-method spam.chol.NgPeyton-class
determinant.spam det
+determinant.spam.chol det
determinant.spam.chol.NgPeyton det
diag diag
diag,ANY-method diag
@@ -137,7 +150,7 @@ diag<- diag
diag<-,ANY-method diag
diag<-,spam-method diag
diag<-.spam diag
-dim dim
+diff.spam methods
dim,ANY-method operations
dim,spam-method operations
dim,spam.chol.NgPeyton-method spam.chol.NgPeyton-class
@@ -146,7 +159,7 @@ dim<-,spam.chol.NgPeyton-method spam.chol.NgPeyton-class
dim<-.spam dim
display display
display,spam-method display
-display,spam.chol.NgPeyton-method display
+display,spam.chol.NgPeyton-method spam.chol.NgPeyton-class
display.spam display
dist.spam nearestdist
distance nearestdist
@@ -159,24 +172,26 @@ forwardsolve,matrix-method solve
forwardsolve,spam-method solve
forwardsolve,spam.chol.NgPeyton-method spam.chol.NgPeyton-class
forwardsolve-methods solve
-forwardsolve.default solve
forwardsolve.spam solve
gamma math
germany Oral
germany.graph germany
+head headtail
+head,spam-method headtail
+head,spam.chol.NgPeyton-method headtail
+head.spam headtail
history history.spam
history.spam history.spam
icheck spam.internal
image image
image,spam-method image
-image,spam.chol.NgPeyton-method image
+image,spam.chol.NgPeyton-method spam.chol.NgPeyton-class
image.spam image
import import
initialize,spam-method spam.creation
is.spam spam.creation
isSymmetric,spam-method isSymmetric
isSymmetric.spam isSymmetric
-kronecker kronecker
kronecker,ANY,spam-method spam-class
kronecker,spam,ANY-method spam-class
kronecker,spam,spam-method spam-class
@@ -192,6 +207,7 @@ log10 math
lower.tri lu.tri
lower.tri,spam-method spam-class
lower.tri.spam lu.tri
+make.prec makeprec
map.landkreis germany
Math math
Math,spam-method math
@@ -200,10 +216,20 @@ Math2,spam,numeric-method math2
Math2,spam-method math2
max summary
min summary
+mle mle
+mle.nomean mle
+mle.nomean.spam mle
+mle.spam mle
ncol,spam-method operations
nearest.dist nearestdist
+neg2loglikelihood mle
+neg2loglikelihood.spam mle
norm operations
norm,ANY-method operations
+norm,matrix,character-method operations
+norm,matrix,missing-method operations
+norm,numeric,character-method operations
+norm,numeric,missing-method operations
norm,spam,character-method operations
norm,spam,missing-method operations
norm.spam operations
@@ -213,17 +239,30 @@ Oral Oral
ordering ordering
ordering,matrix-method ordering
ordering,spam-method ordering
-ordering,spam.chol.NgPeyton-method ordering
+ordering,spam.chol.NgPeyton-method spam.chol.NgPeyton-class
ordering-methods ordering
+ordering.spam.chol ordering
+ordering.spam.chol.NgPeyton ordering
overview SPAM
+permutation permutation
+permutation,matrix-method permutation
+permutation,spam-method permutation
+permutation.spam permutation
plot,spam,missing-method spam-class
plot,spam,spam-method spam-class
plot.spam operations
powerboost powerboost
+precmat precmat
+precmat.IGMRFirreglat precmat
+precmat.IGMRFreglat precmat
+precmat.RW1 precmat
+precmat.RW2 precmat
+precmat.season precmat
print print
print,spam-method print
-print,spam.chol.NgPeyton-method print
+print,spam.chol.NgPeyton-method spam.chol.NgPeyton-class
print.spam print
+print.spam.chol print
print.spam.chol.NgPeyton print
prod summary
range summary
@@ -233,14 +272,22 @@ rbind.spam xybind
read.HB import
read.MM import
rmvnorm.canonical rmvnorm
+rmvnorm.canonical.const rmvnorm.const
+rmvnorm.const rmvnorm.const
rmvnorm.prec rmvnorm
+rmvnorm.prec.const rmvnorm.const
rmvnorm.spam rmvnorm
round math2
+rowMeans rowcolstats
+rowMeans,spam-method rowcolstats
+rowMeans.spam rowcolstats
+rowSums rowcolstats
+rowSums,spam-method rowcolstats
+rowSums.spam rowcolstats
show,spam-method spam-class
show,spam.chol.NgPeyton-method spam.chol.NgPeyton-class
signif math2
sin math
-solve solve
solve,ANY-method solve
solve,spam-method solve
solve.spam solve
@@ -262,23 +309,29 @@ spam.options options
spam.Version version
spam.version version
sqrt math
+subset.rows.spam operations
subset.spam operations
sum summary
Summary summary
summary print
Summary,spam-method summary
summary,spam-method print
-summary,spam.chol.NgPeyton-method print
+summary,spam.chol.NgPeyton-method spam.chol.NgPeyton-class
Summary.spam summary
summary.spam print
+summary.spam.chol print
summary.spam.chol.NgPeyton print
-t,ANY-method operations
-t,spam-method operations
+t,spam-method spam-class
t,spam.chol.NgPeyton-method spam.chol.NgPeyton-class
t.spam operations
+tail headtail
+tail,spam-method headtail
+tail,spam.chol.NgPeyton-method headtail
+tail.spam headtail
tan math
todo todo
todo.spam todo
+toeplitz.spam toeplitz
triplet triplet
trunc math
update chol
@@ -293,31 +346,43 @@ UScounties.storder UScounties
USprecip USprecip
validspamobject spam.creation
version version
-[,spam,ANY,ANY-method operations
-[,spam,ANY-method spam-class
-[,spam,matrix,matrix-method spam-class
-[,spam,matrix,missing-method spam-class
-[,spam,missing,missing-method spam-class
-[,spam,missing,vector-method spam-class
-[,spam,spam,missing-method spam-class
-[,spam,vector,missing-method spam-class
-[,spam,vector,vector-method spam-class
+[,spam,ANY,ANY,ANY-method spam-class
+[,spam,matrix,matrix,ANY-method spam-class
+[,spam,matrix,missing,logical-method spam-class
+[,spam,matrix,missing,missing-method spam-class
+[,spam,missing,missing,ANY-method spam-class
+[,spam,missing,vector,ANY-method spam-class
+[,spam,spam,missing,ANY-method spam-class
+[,spam,vector,missing,logical-method spam-class
+[,spam,vector,missing,missing-method spam-class
+[,spam,vector,vector,ANY-method spam-class
[.spam operations
+[<-,spam,ANY,ANY,ANY-method spam-class
[<-,spam,ANY,ANY-method operations
[<-,spam,ANY-method spam-class
+[<-,spam,matrix,matrix,ANY-method spam-class
[<-,spam,matrix,matrix,numeric-method spam-class
[<-,spam,matrix,matrix-method operations
+[<-,spam,matrix,missing,ANY-method spam-class
[<-,spam,matrix,missing,numeric-method spam-class
[<-,spam,matrix,missing-method operations
+[<-,spam,missing,missing,ANY-method spam-class
[<-,spam,missing,missing,numeric-method spam-class
[<-,spam,missing,missing-method operations
+[<-,spam,missing,vector,ANY-method spam-class
[<-,spam,missing,vector,numeric-method spam-class
+[<-,spam,missing,vector,spam-method spam-class
[<-,spam,missing,vector-method operations
+[<-,spam,spam,missing,ANY-method spam-class
[<-,spam,spam,missing,numeric-method spam-class
[<-,spam,spam,missing-method operations
+[<-,spam,vector,missing,ANY-method spam-class
[<-,spam,vector,missing,numeric-method spam-class
+[<-,spam,vector,missing,spam-method spam-class
[<-,spam,vector,missing-method operations
+[<-,spam,vector,vector,ANY-method spam-class
[<-,spam,vector,vector,numeric-method spam-class
+[<-,spam,vector,vector,spam-method spam-class
[<-,spam,vector,vector-method operations
[<-.spam operations
^,spam-method operations
diff --git a/win32/deps/library/spam/help/aliases.rds b/win32/deps/library/spam/help/aliases.rds
new file mode 100644
index 0000000..02a8b34
Binary files /dev/null and b/win32/deps/library/spam/help/aliases.rds differ
diff --git a/win32/deps/library/spam/help/paths.rds b/win32/deps/library/spam/help/paths.rds
new file mode 100644
index 0000000..8e84b02
Binary files /dev/null and b/win32/deps/library/spam/help/paths.rds differ
diff --git a/win32/deps/library/spam/help/spam.rdb b/win32/deps/library/spam/help/spam.rdb
new file mode 100644
index 0000000..2ce70f5
Binary files /dev/null and b/win32/deps/library/spam/help/spam.rdb differ
diff --git a/win32/deps/library/spam/help/spam.rdx b/win32/deps/library/spam/help/spam.rdx
new file mode 100644
index 0000000..b995fd8
Binary files /dev/null and b/win32/deps/library/spam/help/spam.rdx differ
diff --git a/win32/deps/library/spam/html/00Index.html b/win32/deps/library/spam/html/00Index.html
index 6fc22f7..2e97600 100644
--- a/win32/deps/library/spam/html/00Index.html
+++ b/win32/deps/library/spam/html/00Index.html
@@ -1,25 +1,26 @@
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html><head><title>R: SPArse Matrix</title>
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><link rel="stylesheet" type="text/css" href="../../R.css">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
</head><body>
-<h1>SPArse Matrix <img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]"></h1>
-
+<h1> SPArse Matrix
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
<hr>
-
<div align="center">
-<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg"
-alt="[Package List]" width="30" height="30" border="0"></a>
-<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg"
-alt="[Top]" width="30" height="30" border="0"></a>
-</div>
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘spam’ version 0.29-2</h2>
-<h2>Documentation for package ‘spam’ version 0.20-3</h2>
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+<li><a href="../demo">Code demos</a>. Use <a href="../../utils/help/demo">demo()</a> to run them.</li>
+<li><a href="../NEWS">Package NEWS</a>.</li>
+</ul>
<h2>Help Pages</h2>
<p align="center">
-<a href="#"></a>
<a href="#A">A</a>
<a href="#B">B</a>
<a href="#C">C</a>
@@ -27,6 +28,7 @@ alt="[Top]" width="30" height="30" border="0"></a>
<a href="#E">E</a>
<a href="#F">F</a>
<a href="#G">G</a>
+<a href="#H">H</a>
<a href="#I">I</a>
<a href="#K">K</a>
<a href="#L">L</a>
@@ -43,109 +45,6 @@ alt="[Top]" width="30" height="30" border="0"></a>
</p>
-<h2><a name="">-- --</a></h2>
-
-<table width="100%">
-<tr><td width="25%"><a href="operations.html">!=,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%%,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%*%,ANY,ANY-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%*%,matrix,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%*%,numeric,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%*%,spam,matrix-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%*%,spam,numeric-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%*%,spam,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%*%-methods</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%/%,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%d*%</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%d*%,matrix,ANY-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%d*%,matrix,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%d*%,numeric,matrix-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%d*%,numeric,numeric-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%d*%,numeric,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%d*%,spam,ANY-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%d*%,spam,numeric-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%d*%,spam,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%d+%</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%d+%,matrix,ANY-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%d+%,matrix,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%d+%,numeric,matrix-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%d+%,numeric,numeric-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%d+%,numeric,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%d+%,spam,ANY-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%d+%,spam,numeric-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%d+%,spam,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">&,ANY,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">&,spam,ANY-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">&,spam,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">*,ANY,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">*,spam,ANY-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">*,spam,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">+,ANY,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">+,spam,ANY-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">+,spam,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">-,ANY,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">-,spam,ANY-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">-,spam,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="options.html">.Spam</a></td>
-<td>Options Settings</td></tr>
-<tr><td width="25%"><a href="operations.html">/,ANY,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">/,spam,ANY-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">/,spam,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html"><,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html"><=,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">==,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">>,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">>=,spam-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-</table>
-
<h2><a name="A">-- A --</a></h2>
<table width="100%">
@@ -155,17 +54,11 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Mathematical functions</td></tr>
<tr><td width="25%"><a href="math.html">acosh</a></td>
<td>Mathematical functions</td></tr>
-<tr><td width="25%"><a href="adiag.html">adiag</a></td>
-<td>Binds Arrays Corner-to-Corner</td></tr>
-<tr><td width="25%"><a href="adiag.html">adiag.spam</a></td>
-<td>Binds Arrays Corner-to-Corner</td></tr>
<tr><td width="25%"><a href="germany.html">adjacency.landkreis</a></td>
<td>Administrative districts of Germany</td></tr>
<tr><td width="25%"><a href="summary.html">all</a></td>
<td>Rounding of Numbers</td></tr>
-<tr><td width="25%"><a href="allequal.html">all.equal,matrix,spam-method</a></td>
-<td>Test if Two 'spam' Objects are (Nearly) Equal</td></tr>
-<tr><td width="25%"><a href="allequal.html">all.equal,spam,spam-method</a></td>
+<tr><td width="25%"><a href="allequal.html">all.equal-method</a></td>
<td>Test if Two 'spam' Objects are (Nearly) Equal</td></tr>
<tr><td width="25%"><a href="allequal.html">all.equal.spam</a></td>
<td>Test if Two 'spam' Objects are (Nearly) Equal</td></tr>
@@ -173,19 +66,15 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Rounding of Numbers</td></tr>
<tr><td width="25%"><a href="apply.html">apply.spam</a></td>
<td>Apply Functions Over Sparse Matrix Margins</td></tr>
-<tr><td width="25%"><a href="spam-class.html">Arith,numeric,spam-method</a></td>
-<td>Class "spam"</td></tr>
-<tr><td width="25%"><a href="spam-class.html">Arith,spam,missing-method</a></td>
-<td>Class "spam"</td></tr>
-<tr><td width="25%"><a href="spam-class.html">Arith,spam,numeric-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">Arith-method</a></td>
<td>Class "spam"</td></tr>
<tr><td width="25%"><a href="foreign.html">as.dgCMatrix.spam</a></td>
<td>Transformation to other sparse formats</td></tr>
<tr><td width="25%"><a href="foreign.html">as.dgRMatrix.spam</a></td>
<td>Transformation to other sparse formats</td></tr>
-<tr><td width="25%"><a href="spam-class.html">as.matrix,spam-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">as.matrix-method</a></td>
<td>Class "spam"</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">as.matrix,spam.chol.NgPeyton-method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">as.matrix-method</a></td>
<td>Class "spam.chol.NgPeyton"</td></tr>
<tr><td width="25%"><a href="foreign.html">as.matrix.csr.spam</a></td>
<td>Transformation to other sparse formats</td></tr>
@@ -193,17 +82,9 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Class "spam"</td></tr>
<tr><td width="25%"><a href="spam.creation.html">as.spam</a></td>
<td>Sparse Matrix Class</td></tr>
-<tr><td width="25%"><a href="spam.creation.html">as.spam,dist-method</a></td>
-<td>Sparse Matrix Class</td></tr>
-<tr><td width="25%"><a href="spam.creation.html">as.spam,list-method</a></td>
-<td>Sparse Matrix Class</td></tr>
-<tr><td width="25%"><a href="spam.creation.html">as.spam,matrix-method</a></td>
-<td>Sparse Matrix Class</td></tr>
-<tr><td width="25%"><a href="spam.creation.html">as.spam,numeric-method</a></td>
-<td>Sparse Matrix Class</td></tr>
-<tr><td width="25%"><a href="spam.creation.html">as.spam,spam-method</a></td>
-<td>Sparse Matrix Class</td></tr>
-<tr><td width="25%"><a href="spam.creation.html">as.spam,spam.chol.NgPeyton-method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">as.spam-method</a></td>
+<td>Class "spam.chol.NgPeyton"</td></tr>
+<tr><td width="25%"><a href="spam.creation.html">as.spam-method</a></td>
<td>Sparse Matrix Class</td></tr>
<tr><td width="25%"><a href="spam.creation.html">as.spam.chol.NgPeyton</a></td>
<td>Sparse Matrix Class</td></tr>
@@ -240,50 +121,66 @@ alt="[Top]" width="30" height="30" border="0"></a>
<table width="100%">
<tr><td width="25%"><a href="solve.html">backsolve</a></td>
<td>Linear Equation Solving for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="solve.html">backsolve,ANY-method</a></td>
-<td>Linear Equation Solving for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="solve.html">backsolve,matrix-method</a></td>
+<tr><td width="25%"><a href="solve.html">backsolve-method</a></td>
<td>Linear Equation Solving for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="solve.html">backsolve,spam-method</a></td>
-<td>Linear Equation Solving for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">backsolve,spam.chol.NgPeyton-method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">backsolve-method</a></td>
<td>Class "spam.chol.NgPeyton"</td></tr>
<tr><td width="25%"><a href="solve.html">backsolve-methods</a></td>
<td>Linear Equation Solving for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="solve.html">backsolve.default</a></td>
-<td>Linear Equation Solving for Sparse Matrices</td></tr>
<tr><td width="25%"><a href="solve.html">backsolve.spam</a></td>
<td>Linear Equation Solving for Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="bandwidth.html">bandwidth</a></td>
+<td>Bandwidth of a Sparse Matrix</td></tr>
+<tr><td width="25%"><a href="bdiag.html">bdiag</a></td>
+<td>Binds Arrays Corner-to-Corner</td></tr>
+<tr><td width="25%"><a href="bdiag.html">bdiag.spam</a></td>
+<td>Binds Arrays Corner-to-Corner</td></tr>
</table>
<h2><a name="C">-- C --</a></h2>
<table width="100%">
-<tr><td width="25%"><a href="spam-class.html">c,spam-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">c-method</a></td>
<td>Class "spam"</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">c,spam.chol.NgPeyton-method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">c-method</a></td>
<td>Class "spam.chol.NgPeyton"</td></tr>
<tr><td width="25%"><a href="xybind.html">cbind</a></td>
<td>Combine spam Matrices by Rows or Columns</td></tr>
-<tr><td width="25%"><a href="xybind.html">cbind,spam-method</a></td>
+<tr><td width="25%"><a href="xybind.html">cbind-method</a></td>
<td>Combine spam Matrices by Rows or Columns</td></tr>
<tr><td width="25%"><a href="xybind.html">cbind.spam</a></td>
<td>Combine spam Matrices by Rows or Columns</td></tr>
<tr><td width="25%"><a href="math.html">ceiling</a></td>
<td>Mathematical functions</td></tr>
-<tr><td width="25%"><a href="chol.html">chol</a></td>
-<td>Cholesky Factorization for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="chol.html">chol,ANY-method</a></td>
-<td>Cholesky Factorization for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="chol.html">chol,matrix-method</a></td>
-<td>Cholesky Factorization for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="chol.html">chol,spam-method</a></td>
+<tr><td width="25%"><a href="chol.html">chol-method</a></td>
<td>Cholesky Factorization for Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">chol-method</a></td>
+<td>Class "spam.chol.NgPeyton"</td></tr>
<tr><td width="25%"><a href="chol.html">chol.spam</a></td>
<td>Cholesky Factorization for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="spam-class.html">Compare,numeric,spam-method</a></td>
-<td>Class "spam"</td></tr>
-<tr><td width="25%"><a href="spam-class.html">Compare,spam,numeric-method</a></td>
+<tr><td width="25%"><a href="solve.html">chol2inv</a></td>
+<td>Linear Equation Solving for Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="solve.html">chol2inv-method</a></td>
+<td>Linear Equation Solving for Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="solve.html">chol2inv.spam</a></td>
+<td>Linear Equation Solving for Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="circulant.html">circulant.spam</a></td>
+<td>Create Circulant Matrices</td></tr>
+<tr><td width="25%"><a href="cleanup.html">cleanup</a></td>
+<td>Cleaning up sparse matrices</td></tr>
+<tr><td width="25%"><a href="rowcolstats.html">colMeans</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="rowcolstats.html">colMeans-method</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="rowcolstats.html">colMeans.spam</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="rowcolstats.html">colSums</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="rowcolstats.html">colSums-method</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="rowcolstats.html">colSums.spam</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="spam-class.html">Compare-method</a></td>
<td>Class "spam"</td></tr>
<tr><td width="25%"><a href="complexity.html">complexities</a></td>
<td>Complexity for Sparse Matrices</td></tr>
@@ -302,31 +199,29 @@ alt="[Top]" width="30" height="30" border="0"></a>
<table width="100%">
<tr><td width="25%"><a href="det.html">det</a></td>
<td>Calculate the determinant of a positive definite Sparse Matrix</td></tr>
-<tr><td width="25%"><a href="det.html">det,spam-method</a></td>
-<td>Calculate the determinant of a positive definite Sparse Matrix</td></tr>
-<tr><td width="25%"><a href="det.html">det,spam.chol.NgPeyton-method</a></td>
+<tr><td width="25%"><a href="det.html">det-method</a></td>
<td>Calculate the determinant of a positive definite Sparse Matrix</td></tr>
<tr><td width="25%"><a href="det.html">det.spam</a></td>
<td>Calculate the determinant of a positive definite Sparse Matrix</td></tr>
<tr><td width="25%"><a href="det.html">determinant</a></td>
<td>Calculate the determinant of a positive definite Sparse Matrix</td></tr>
-<tr><td width="25%"><a href="det.html">determinant,spam-method</a></td>
-<td>Calculate the determinant of a positive definite Sparse Matrix</td></tr>
-<tr><td width="25%"><a href="det.html">determinant,spam.chol.NgPeyton-method</a></td>
+<tr><td width="25%"><a href="det.html">determinant-method</a></td>
<td>Calculate the determinant of a positive definite Sparse Matrix</td></tr>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">determinant-method</a></td>
+<td>Class "spam.chol.NgPeyton"</td></tr>
<tr><td width="25%"><a href="det.html">determinant.spam</a></td>
<td>Calculate the determinant of a positive definite Sparse Matrix</td></tr>
+<tr><td width="25%"><a href="det.html">determinant.spam.chol</a></td>
+<td>Calculate the determinant of a positive definite Sparse Matrix</td></tr>
<tr><td width="25%"><a href="det.html">determinant.spam.chol.NgPeyton</a></td>
<td>Calculate the determinant of a positive definite Sparse Matrix</td></tr>
<tr><td width="25%"><a href="diag.html">diag</a></td>
<td>Sparse Matrix diagonals</td></tr>
-<tr><td width="25%"><a href="diag.html">diag,ANY-method</a></td>
-<td>Sparse Matrix diagonals</td></tr>
-<tr><td width="25%"><a href="diag.html">diag,spam-method</a></td>
+<tr><td width="25%"><a href="diag.html">diag-method</a></td>
<td>Sparse Matrix diagonals</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">diag,spam.chol.NgPeyton-method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">diag-method</a></td>
<td>Class "spam.chol.NgPeyton"</td></tr>
-<tr><td width="25%"><a href="diag.html">diag.assign,spam-method</a></td>
+<tr><td width="25%"><a href="diag.html">diag.assign-method</a></td>
<td>Sparse Matrix diagonals</td></tr>
<tr><td width="25%"><a href="diag.html">diag.of.spam</a></td>
<td>Sparse Matrix diagonals</td></tr>
@@ -336,34 +231,28 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Sparse Matrix diagonals</td></tr>
<tr><td width="25%"><a href="diag.html">diag<-</a></td>
<td>Sparse Matrix diagonals</td></tr>
-<tr><td width="25%"><a href="diag.html">diag<-,ANY-method</a></td>
-<td>Sparse Matrix diagonals</td></tr>
-<tr><td width="25%"><a href="diag.html">diag<-,spam-method</a></td>
+<tr><td width="25%"><a href="diag.html">diag<--method</a></td>
<td>Sparse Matrix diagonals</td></tr>
<tr><td width="25%"><a href="diag.html">diag<-.spam</a></td>
<td>Sparse Matrix diagonals</td></tr>
-<tr><td width="25%"><a href="dim.html">dim</a></td>
-<td>Dimensions of an Object</td></tr>
-<tr><td width="25%"><a href="operations.html">dim,ANY-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">dim,spam-method</a></td>
+<tr><td width="25%"><a href="operations.html">dim-method</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">dim,spam.chol.NgPeyton-method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">dim-method</a></td>
<td>Class "spam.chol.NgPeyton"</td></tr>
-<tr><td width="25%"><a href="dim.html">dim<-,spam-method</a></td>
+<tr><td width="25%"><a href="dim.html">dim<--method</a></td>
<td>Dimensions of an Object</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">dim<-,spam.chol.NgPeyton-method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">dim<--method</a></td>
<td>Class "spam.chol.NgPeyton"</td></tr>
<tr><td width="25%"><a href="dim.html">dim<-.spam</a></td>
<td>Dimensions of an Object</td></tr>
<tr><td width="25%"><a href="display.html">display</a></td>
-<td>Graphially represent the nonzero entries</td></tr>
-<tr><td width="25%"><a href="display.html">display,spam-method</a></td>
-<td>Graphially represent the nonzero entries</td></tr>
-<tr><td width="25%"><a href="display.html">display,spam.chol.NgPeyton-method</a></td>
-<td>Graphially represent the nonzero entries</td></tr>
+<td>Graphially Represent the Nonzero Entries</td></tr>
+<tr><td width="25%"><a href="display.html">display-method</a></td>
+<td>Graphially Represent the Nonzero Entries</td></tr>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">display-method</a></td>
+<td>Class "spam.chol.NgPeyton"</td></tr>
<tr><td width="25%"><a href="display.html">display.spam</a></td>
-<td>Graphially represent the nonzero entries</td></tr>
+<td>Graphially Represent the Nonzero Entries</td></tr>
<tr><td width="25%"><a href="nearestdist.html">dist.spam</a></td>
<td>Distance Matrix Computation</td></tr>
<tr><td width="25%"><a href="nearestdist.html">distance</a></td>
@@ -386,18 +275,12 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Transformation to other sparse formats</td></tr>
<tr><td width="25%"><a href="solve.html">forwardsolve</a></td>
<td>Linear Equation Solving for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="solve.html">forwardsolve,ANY-method</a></td>
-<td>Linear Equation Solving for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="solve.html">forwardsolve,matrix-method</a></td>
-<td>Linear Equation Solving for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="solve.html">forwardsolve,spam-method</a></td>
+<tr><td width="25%"><a href="solve.html">forwardsolve-method</a></td>
<td>Linear Equation Solving for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">forwardsolve,spam.chol.NgPeyton-method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">forwardsolve-method</a></td>
<td>Class "spam.chol.NgPeyton"</td></tr>
<tr><td width="25%"><a href="solve.html">forwardsolve-methods</a></td>
<td>Linear Equation Solving for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="solve.html">forwardsolve.default</a></td>
-<td>Linear Equation Solving for Sparse Matrices</td></tr>
<tr><td width="25%"><a href="solve.html">forwardsolve.spam</a></td>
<td>Linear Equation Solving for Sparse Matrices</td></tr>
</table>
@@ -413,24 +296,35 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Administrative districts of Germany</td></tr>
</table>
+<h2><a name="H">-- H --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="headtail.html">head</a></td>
+<td>Return the First or Last Part of an Object</td></tr>
+<tr><td width="25%"><a href="headtail.html">head-method</a></td>
+<td>Return the First or Last Part of an Object</td></tr>
+<tr><td width="25%"><a href="headtail.html">head.spam</a></td>
+<td>Return the First or Last Part of an Object</td></tr>
+</table>
+
<h2><a name="I">-- I --</a></h2>
<table width="100%">
<tr><td width="25%"><a href="image.html">image</a></td>
<td>Display a spam Object as Color Image</td></tr>
-<tr><td width="25%"><a href="image.html">image,spam-method</a></td>
-<td>Display a spam Object as Color Image</td></tr>
-<tr><td width="25%"><a href="image.html">image,spam.chol.NgPeyton-method</a></td>
+<tr><td width="25%"><a href="image.html">image-method</a></td>
<td>Display a spam Object as Color Image</td></tr>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">image-method</a></td>
+<td>Class "spam.chol.NgPeyton"</td></tr>
<tr><td width="25%"><a href="image.html">image.spam</a></td>
<td>Display a spam Object as Color Image</td></tr>
<tr><td width="25%"><a href="import.html">import</a></td>
-<td>Read external matrix formats</td></tr>
-<tr><td width="25%"><a href="spam.creation.html">initialize,spam-method</a></td>
+<td>Read External Matrix Formats</td></tr>
+<tr><td width="25%"><a href="spam.creation.html">initialize-method</a></td>
<td>Sparse Matrix Class</td></tr>
<tr><td width="25%"><a href="spam.creation.html">is.spam</a></td>
<td>Sparse Matrix Class</td></tr>
-<tr><td width="25%"><a href="isSymmetric.html">isSymmetric,spam-method</a></td>
+<tr><td width="25%"><a href="isSymmetric.html">isSymmetric-method</a></td>
<td>Test if a spam matrix is Symmetric</td></tr>
<tr><td width="25%"><a href="isSymmetric.html">isSymmetric.spam</a></td>
<td>Test if a spam matrix is Symmetric</td></tr>
@@ -439,30 +333,24 @@ alt="[Top]" width="30" height="30" border="0"></a>
<h2><a name="K">-- K --</a></h2>
<table width="100%">
-<tr><td width="25%"><a href="kronecker.html">kronecker</a></td>
-<td>Kronecker products on sparse matrices</td></tr>
-<tr><td width="25%"><a href="spam-class.html">kronecker,ANY,spam-method</a></td>
-<td>Class "spam"</td></tr>
-<tr><td width="25%"><a href="spam-class.html">kronecker,spam,ANY-method</a></td>
-<td>Class "spam"</td></tr>
-<tr><td width="25%"><a href="spam-class.html">kronecker,spam,spam-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">kronecker-method</a></td>
<td>Class "spam"</td></tr>
<tr><td width="25%"><a href="kronecker.html">kronecker.default</a></td>
-<td>Kronecker products on sparse matrices</td></tr>
+<td>Kronecker Products on Sparse Matrices</td></tr>
<tr><td width="25%"><a href="kronecker.html">kronecker.spam</a></td>
-<td>Kronecker products on sparse matrices</td></tr>
+<td>Kronecker Products on Sparse Matrices</td></tr>
</table>
<h2><a name="L">-- L --</a></h2>
<table width="100%">
-<tr><td width="25%"><a href="spam-class.html">length,spam-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">length-method</a></td>
<td>Class "spam"</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">length,spam.chol.NgPeyton-method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">length-method</a></td>
<td>Class "spam.chol.NgPeyton"</td></tr>
-<tr><td width="25%"><a href="spam-class.html">length<-,spam-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">length<--method</a></td>
<td>Class "spam"</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">length<-,spam.chol.NgPeyton-method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">length<--method</a></td>
<td>Class "spam.chol.NgPeyton"</td></tr>
<tr><td width="25%"><a href="math.html">lgamma</a></td>
<td>Mathematical functions</td></tr>
@@ -472,7 +360,7 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Mathematical functions</td></tr>
<tr><td width="25%"><a href="lu.tri.html">lower.tri</a></td>
<td>Lower and Upper Triangular Part of a Sparse Matrix</td></tr>
-<tr><td width="25%"><a href="spam-class.html">lower.tri,spam-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">lower.tri-method</a></td>
<td>Class "spam"</td></tr>
<tr><td width="25%"><a href="lu.tri.html">lower.tri.spam</a></td>
<td>Lower and Upper Triangular Part of a Sparse Matrix</td></tr>
@@ -481,42 +369,50 @@ alt="[Top]" width="30" height="30" border="0"></a>
<h2><a name="M">-- M --</a></h2>
<table width="100%">
+<tr><td width="25%"><a href="makeprec.html">make.prec</a></td>
+<td>Create Precision Matrices</td></tr>
<tr><td width="25%"><a href="germany.html">map.landkreis</a></td>
<td>Administrative districts of Germany</td></tr>
<tr><td width="25%"><a href="math.html">Math</a></td>
<td>Mathematical functions</td></tr>
-<tr><td width="25%"><a href="math.html">Math,spam-method</a></td>
+<tr><td width="25%"><a href="math.html">Math-method</a></td>
<td>Mathematical functions</td></tr>
<tr><td width="25%"><a href="math2.html">Math2</a></td>
<td>Rounding of Numbers</td></tr>
-<tr><td width="25%"><a href="math2.html">Math2,spam,numeric-method</a></td>
-<td>Rounding of Numbers</td></tr>
-<tr><td width="25%"><a href="math2.html">Math2,spam-method</a></td>
+<tr><td width="25%"><a href="math2.html">Math2-method</a></td>
<td>Rounding of Numbers</td></tr>
<tr><td width="25%"><a href="summary.html">max</a></td>
<td>Rounding of Numbers</td></tr>
<tr><td width="25%"><a href="summary.html">min</a></td>
<td>Rounding of Numbers</td></tr>
+<tr><td width="25%"><a href="mle.html">mle</a></td>
+<td>Maximum likelihood estimates</td></tr>
+<tr><td width="25%"><a href="mle.html">mle.nomean</a></td>
+<td>Maximum likelihood estimates</td></tr>
+<tr><td width="25%"><a href="mle.html">mle.nomean.spam</a></td>
+<td>Maximum likelihood estimates</td></tr>
+<tr><td width="25%"><a href="mle.html">mle.spam</a></td>
+<td>Maximum likelihood estimates</td></tr>
</table>
<h2><a name="N">-- N --</a></h2>
<table width="100%">
-<tr><td width="25%"><a href="operations.html">ncol,spam-method</a></td>
+<tr><td width="25%"><a href="operations.html">ncol-method</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
<tr><td width="25%"><a href="nearestdist.html">nearest.dist</a></td>
<td>Distance Matrix Computation</td></tr>
+<tr><td width="25%"><a href="mle.html">neg2loglikelihood</a></td>
+<td>Maximum likelihood estimates</td></tr>
+<tr><td width="25%"><a href="mle.html">neg2loglikelihood.spam</a></td>
+<td>Maximum likelihood estimates</td></tr>
<tr><td width="25%"><a href="operations.html">norm</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">norm,ANY-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">norm,spam,character-method</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">norm,spam,missing-method</a></td>
+<tr><td width="25%"><a href="operations.html">norm-method</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
<tr><td width="25%"><a href="operations.html">norm.spam</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">nrow,spam-method</a></td>
+<tr><td width="25%"><a href="operations.html">nrow-method</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
</table>
@@ -529,13 +425,15 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Oral Cavity Cancer</td></tr>
<tr><td width="25%"><a href="ordering.html">ordering</a></td>
<td>Extract the permutation</td></tr>
-<tr><td width="25%"><a href="ordering.html">ordering,matrix-method</a></td>
+<tr><td width="25%"><a href="ordering.html">ordering-method</a></td>
<td>Extract the permutation</td></tr>
-<tr><td width="25%"><a href="ordering.html">ordering,spam-method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">ordering-method</a></td>
+<td>Class "spam.chol.NgPeyton"</td></tr>
+<tr><td width="25%"><a href="ordering.html">ordering-methods</a></td>
<td>Extract the permutation</td></tr>
-<tr><td width="25%"><a href="ordering.html">ordering,spam.chol.NgPeyton-method</a></td>
+<tr><td width="25%"><a href="ordering.html">ordering.spam.chol</a></td>
<td>Extract the permutation</td></tr>
-<tr><td width="25%"><a href="ordering.html">ordering-methods</a></td>
+<tr><td width="25%"><a href="ordering.html">ordering.spam.chol.NgPeyton</a></td>
<td>Extract the permutation</td></tr>
<tr><td width="25%"><a href="SPAM.html">overview</a></td>
<td>SPArse Matrix Package</td></tr>
@@ -544,22 +442,40 @@ alt="[Top]" width="30" height="30" border="0"></a>
<h2><a name="P">-- P --</a></h2>
<table width="100%">
-<tr><td width="25%"><a href="spam-class.html">plot,spam,missing-method</a></td>
-<td>Class "spam"</td></tr>
-<tr><td width="25%"><a href="spam-class.html">plot,spam,spam-method</a></td>
+<tr><td width="25%"><a href="permutation.html">permutation</a></td>
+<td>Permute a matrix</td></tr>
+<tr><td width="25%"><a href="permutation.html">permutation-method</a></td>
+<td>Permute a matrix</td></tr>
+<tr><td width="25%"><a href="permutation.html">permutation.spam</a></td>
+<td>Permute a matrix</td></tr>
+<tr><td width="25%"><a href="spam-class.html">plot-method</a></td>
<td>Class "spam"</td></tr>
<tr><td width="25%"><a href="operations.html">plot.spam</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
<tr><td width="25%"><a href="powerboost.html">powerboost</a></td>
<td>Specific options Setting</td></tr>
+<tr><td width="25%"><a href="precmat.html">precmat</a></td>
+<td>IGMRF Precision Matrices</td></tr>
+<tr><td width="25%"><a href="precmat.html">precmat.IGMRFirreglat</a></td>
+<td>IGMRF Precision Matrices</td></tr>
+<tr><td width="25%"><a href="precmat.html">precmat.IGMRFreglat</a></td>
+<td>IGMRF Precision Matrices</td></tr>
+<tr><td width="25%"><a href="precmat.html">precmat.RW1</a></td>
+<td>IGMRF Precision Matrices</td></tr>
+<tr><td width="25%"><a href="precmat.html">precmat.RW2</a></td>
+<td>IGMRF Precision Matrices</td></tr>
+<tr><td width="25%"><a href="precmat.html">precmat.season</a></td>
+<td>IGMRF Precision Matrices</td></tr>
<tr><td width="25%"><a href="print.html">print</a></td>
<td>Printing and summarizing sparse matrices</td></tr>
-<tr><td width="25%"><a href="print.html">print,spam-method</a></td>
-<td>Printing and summarizing sparse matrices</td></tr>
-<tr><td width="25%"><a href="print.html">print,spam.chol.NgPeyton-method</a></td>
+<tr><td width="25%"><a href="print.html">print-method</a></td>
<td>Printing and summarizing sparse matrices</td></tr>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">print-method</a></td>
+<td>Class "spam.chol.NgPeyton"</td></tr>
<tr><td width="25%"><a href="print.html">print.spam</a></td>
<td>Printing and summarizing sparse matrices</td></tr>
+<tr><td width="25%"><a href="print.html">print.spam.chol</a></td>
+<td>Printing and summarizing sparse matrices</td></tr>
<tr><td width="25%"><a href="print.html">print.spam.chol.NgPeyton</a></td>
<td>Printing and summarizing sparse matrices</td></tr>
<tr><td width="25%"><a href="summary.html">prod</a></td>
@@ -573,40 +489,54 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Rounding of Numbers</td></tr>
<tr><td width="25%"><a href="xybind.html">rbind</a></td>
<td>Combine spam Matrices by Rows or Columns</td></tr>
-<tr><td width="25%"><a href="xybind.html">rbind,spam-method</a></td>
+<tr><td width="25%"><a href="xybind.html">rbind-method</a></td>
<td>Combine spam Matrices by Rows or Columns</td></tr>
<tr><td width="25%"><a href="xybind.html">rbind.spam</a></td>
<td>Combine spam Matrices by Rows or Columns</td></tr>
<tr><td width="25%"><a href="import.html">read.HB</a></td>
-<td>Read external matrix formats</td></tr>
+<td>Read External Matrix Formats</td></tr>
<tr><td width="25%"><a href="import.html">read.MM</a></td>
-<td>Read external matrix formats</td></tr>
+<td>Read External Matrix Formats</td></tr>
<tr><td width="25%"><a href="rmvnorm.html">rmvnorm.canonical</a></td>
<td>Draw Multivariate Normals</td></tr>
+<tr><td width="25%"><a href="rmvnorm.const.html">rmvnorm.canonical.const</a></td>
+<td>Draw Constrainted Multivariate Normals</td></tr>
+<tr><td width="25%"><a href="rmvnorm.const.html">rmvnorm.const</a></td>
+<td>Draw Constrainted Multivariate Normals</td></tr>
<tr><td width="25%"><a href="rmvnorm.html">rmvnorm.prec</a></td>
<td>Draw Multivariate Normals</td></tr>
+<tr><td width="25%"><a href="rmvnorm.const.html">rmvnorm.prec.const</a></td>
+<td>Draw Constrainted Multivariate Normals</td></tr>
<tr><td width="25%"><a href="rmvnorm.html">rmvnorm.spam</a></td>
<td>Draw Multivariate Normals</td></tr>
<tr><td width="25%"><a href="math2.html">round</a></td>
<td>Rounding of Numbers</td></tr>
+<tr><td width="25%"><a href="rowcolstats.html">rowMeans</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="rowcolstats.html">rowMeans-method</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="rowcolstats.html">rowMeans.spam</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="rowcolstats.html">rowSums</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="rowcolstats.html">rowSums-method</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
+<tr><td width="25%"><a href="rowcolstats.html">rowSums.spam</a></td>
+<td>Form Row and Column Sums and Means</td></tr>
</table>
<h2><a name="S">-- S --</a></h2>
<table width="100%">
-<tr><td width="25%"><a href="spam-class.html">show,spam-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">show-method</a></td>
<td>Class "spam"</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">show,spam.chol.NgPeyton-method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">show-method</a></td>
<td>Class "spam.chol.NgPeyton"</td></tr>
<tr><td width="25%"><a href="math2.html">signif</a></td>
<td>Rounding of Numbers</td></tr>
<tr><td width="25%"><a href="math.html">sin</a></td>
<td>Mathematical functions</td></tr>
-<tr><td width="25%"><a href="solve.html">solve</a></td>
-<td>Linear Equation Solving for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="solve.html">solve,ANY-method</a></td>
-<td>Linear Equation Solving for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="solve.html">solve,spam-method</a></td>
+<tr><td width="25%"><a href="solve.html">solve-method</a></td>
<td>Linear Equation Solving for Sparse Matrices</td></tr>
<tr><td width="25%"><a href="solve.html">solve.spam</a></td>
<td>Linear Equation Solving for Sparse Matrices</td></tr>
@@ -616,12 +546,10 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>SPArse Matrix Package</td></tr>
<tr><td width="25%"><a href="spam.creation.html">spam</a></td>
<td>Sparse Matrix Class</td></tr>
-<tr><td width="25%"><a href="spam.creation.html">spam,list-method</a></td>
-<td>Sparse Matrix Class</td></tr>
-<tr><td width="25%"><a href="spam.creation.html">spam,numeric-method</a></td>
-<td>Sparse Matrix Class</td></tr>
<tr><td width="25%"><a href="spam-class.html">spam-class</a></td>
<td>Class "spam"</td></tr>
+<tr><td width="25%"><a href="spam.creation.html">spam-method</a></td>
+<td>Sparse Matrix Class</td></tr>
<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">spam.chol.NgPeyton-class</a></td>
<td>Class "spam.chol.NgPeyton"</td></tr>
<tr><td width="25%"><a href="spam-class.html">spam.class</a></td>
@@ -644,6 +572,8 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Spam Version Information</td></tr>
<tr><td width="25%"><a href="math.html">sqrt</a></td>
<td>Mathematical functions</td></tr>
+<tr><td width="25%"><a href="operations.html">subset.rows.spam</a></td>
+<td>Basic Linear Algebra for Sparse Matrices</td></tr>
<tr><td width="25%"><a href="operations.html">subset.spam</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
<tr><td width="25%"><a href="summary.html">sum</a></td>
@@ -652,16 +582,18 @@ alt="[Top]" width="30" height="30" border="0"></a>
<td>Rounding of Numbers</td></tr>
<tr><td width="25%"><a href="print.html">summary</a></td>
<td>Printing and summarizing sparse matrices</td></tr>
-<tr><td width="25%"><a href="summary.html">Summary,spam-method</a></td>
+<tr><td width="25%"><a href="summary.html">Summary-method</a></td>
<td>Rounding of Numbers</td></tr>
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<td>Printing and summarizing sparse matrices</td></tr>
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@@ -669,16 +601,22 @@ alt="[Top]" width="30" height="30" border="0"></a>
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<td>Class "spam.chol.NgPeyton"</td></tr>
<tr><td width="25%"><a href="operations.html">t.spam</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="headtail.html">tail</a></td>
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<tr><td width="25%"><a href="math.html">tan</a></td>
<td>Mathematical functions</td></tr>
+<tr><td width="25%"><a href="toeplitz.html">toeplitz.spam</a></td>
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<tr><td width="25%"><a href="triplet.html">triplet</a></td>
<td>Transform a spam format to triplets</td></tr>
<tr><td width="25%"><a href="math.html">trunc</a></td>
@@ -690,13 +628,13 @@ alt="[Top]" width="30" height="30" border="0"></a>
<table width="100%">
<tr><td width="25%"><a href="chol.html">update</a></td>
<td>Cholesky Factorization for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="chol.html">update,spam.chol.NgPeyton-method</a></td>
+<tr><td width="25%"><a href="chol.html">update-method</a></td>
<td>Cholesky Factorization for Sparse Matrices</td></tr>
<tr><td width="25%"><a href="chol.html">update.spam.chol.NgPeyton</a></td>
<td>Cholesky Factorization for Sparse Matrices</td></tr>
<tr><td width="25%"><a href="lu.tri.html">upper.tri</a></td>
<td>Lower and Upper Triangular Part of a Sparse Matrix</td></tr>
-<tr><td width="25%"><a href="spam-class.html">upper.tri,spam-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">upper.tri-method</a></td>
<td>Class "spam"</td></tr>
<tr><td width="25%"><a href="lu.tri.html">upper.tri.spam</a></td>
<td>Lower and Upper Triangular Part of a Sparse Matrix</td></tr>
@@ -722,67 +660,59 @@ alt="[Top]" width="30" height="30" border="0"></a>
<h2><a name="misc">-- misc --</a></h2>
<table width="100%">
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+<tr><td width="25%"><a href="operations.html">!=-method</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="spam-class.html">[,spam,ANY-method</a></td>
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<td>Basic Linear Algebra for Sparse Matrices</td></tr>
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+<tr><td width="25%"><a href="operations.html">%*%-method</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
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<td>Basic Linear Algebra for Sparse Matrices</td></tr>
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+<tr><td width="25%"><a href="operations.html">^-method</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">|,spam,spam-method</a></td>
+<tr><td width="25%"><a href="operations.html">|-method</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
</table>
</body></html>
diff --git a/win32/deps/library/spam/html/R.css b/win32/deps/library/spam/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/spam/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
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+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
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+ font-size: large }
+
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+ color: rgb(40%, 40%, 40%);
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+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/spam/libs/i386/spam.dll b/win32/deps/library/spam/libs/i386/spam.dll
new file mode 100644
index 0000000..1558919
Binary files /dev/null and b/win32/deps/library/spam/libs/i386/spam.dll differ
diff --git a/win32/deps/library/spam/libs/i386/symbols.rds b/win32/deps/library/spam/libs/i386/symbols.rds
new file mode 100644
index 0000000..b56dd66
Binary files /dev/null and b/win32/deps/library/spam/libs/i386/symbols.rds differ
diff --git a/win32/deps/library/spam/libs/x64/spam.dll b/win32/deps/library/spam/libs/x64/spam.dll
new file mode 100644
index 0000000..d9f8ff8
Binary files /dev/null and b/win32/deps/library/spam/libs/x64/spam.dll differ
diff --git a/win32/deps/library/spam/libs/x64/symbols.rds b/win32/deps/library/spam/libs/x64/symbols.rds
new file mode 100644
index 0000000..73383e9
Binary files /dev/null and b/win32/deps/library/spam/libs/x64/symbols.rds differ
diff --git a/win32/deps/library/spatial/CITATION b/win32/deps/library/spatial/CITATION
index f6a6566..95a548e 100644
--- a/win32/deps/library/spatial/CITATION
+++ b/win32/deps/library/spatial/CITATION
@@ -1,4 +1,4 @@
-citHeader("To cite the VR bundle (MASS, class, nnet, spatial) in publications use:")
+citHeader("To cite the spatial package in publications use:")
citEntry(entry="Book",
title = "Modern Applied Statistics with S",
diff --git a/win32/deps/library/spatial/DESCRIPTION b/win32/deps/library/spatial/DESCRIPTION
index 87178b7..f666df9 100644
--- a/win32/deps/library/spatial/DESCRIPTION
+++ b/win32/deps/library/spatial/DESCRIPTION
@@ -1,23 +1,20 @@
-Bundle: VR
-Contains: MASS class nnet spatial
-Priority: recommended
-Version: 7.2-48
-Date: 2009-07-29
-Depends: R (>= 2.5.0), grDevices, graphics, stats, utils
-Suggests: lattice, nlme, survival
-Author: S original by Venables & Ripley. R port by Brian Ripley
- <ripley stats ox ac uk>, following earlier work by Kurt Hornik
- and Albrecht Gebhardt.
-Maintainer: Brian Ripley <ripley stats ox ac uk>
-BundleDescription: Functions and datasets to support Venables and
- Ripley, 'Modern Applied Statistics with S' (4th edition).
-License: GPL-2 | GPL-3
-URL: http://www.stats.ox.ac.uk/pub/MASS4/
-Packaged: 2009-07-31 13:56:57 UTC; ripley
-Repository: CRAN
-Date/Publication: 2009-08-05 11:20:53
-Package: spatial
-Description: Functions for kriging and point pattern analysis.
-Title: Functions for Kriging and Point Pattern Analysis
-LazyLoad: yes
-Built: R 2.9.2; i386-pc-mingw32; 2009-08-24 13:01:18 UTC; windows
+Package: spatial
+Priority: recommended
+Version: 7.3-5
+Date: 2012-10-08
+Depends: R (>= 2.5.0), graphics, stats, utils
+Suggests: MASS
+Authors R: c(person("Brian", "Ripley", role = c("aut", "cre", "cph"),
+ email = "ripley stats ox ac uk"), person("Roger", "Bivand",
+ role = "ctb"))
+Author: Brian Ripley <ripley stats ox ac uk>
+Maintainer: Brian Ripley <ripley stats ox ac uk>
+Description: Functions for kriging and point pattern analysis.
+Title: Functions for Kriging and Point Pattern Analysis
+LazyLoad: yes
+ByteCompile: yes
+License: GPL-2 | GPL-3
+URL: http://www.stats.ox.ac.uk/pub/MASS4/
+Packaged: 2012-10-14 08:12:31 UTC; ripley
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:15:22 UTC; windows
+Archs: i386, x64
diff --git a/win32/deps/library/spatial/LICENCE b/win32/deps/library/spatial/LICENCE
index e694c08..58b4304 100644
--- a/win32/deps/library/spatial/LICENCE
+++ b/win32/deps/library/spatial/LICENCE
@@ -15,16 +15,10 @@ possible individual files also carry brief copyright notices.
Copyrights
==========
-File MASS/R/profiles.R copyright (C) 1996 D. M. Bates and W. N. Venables.
- port to R by B. D. Ripley copyright (C) 1998
- corrections copyright (C) 2000,3,6 B. D. Ripley
-
-Our understanding is that the dataset files MASS/data/*.rda are not copyright.
-
Files spatial/data/*.dat were generated or digitized by B. D. Ripley: no
copyright is asserted.
-All other files are copyright (C) 1994-2007 W. N. Venables and
+All other files are copyright (C) 1994-2009 W. N. Venables and
B. D. Ripley. Those parts which were distributed with the first
edition are also copyright (C) 1994 Springer-Verlag New York Inc, with
all rights assigned to W. N. Venables and B. D. Ripley.
diff --git a/win32/deps/library/spatial/Meta/Rd.rds b/win32/deps/library/spatial/Meta/Rd.rds
index a485d91..fcefe55 100644
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diff --git a/win32/deps/library/spatial/Meta/hsearch.rds b/win32/deps/library/spatial/Meta/hsearch.rds
index 4aa579d..20d7513 100644
Binary files a/win32/deps/library/spatial/Meta/hsearch.rds and b/win32/deps/library/spatial/Meta/hsearch.rds differ
diff --git a/win32/deps/library/spatial/Meta/links.rds b/win32/deps/library/spatial/Meta/links.rds
new file mode 100644
index 0000000..d49d17e
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diff --git a/win32/deps/library/spatial/Meta/nsInfo.rds b/win32/deps/library/spatial/Meta/nsInfo.rds
index c19ae85..b75d566 100644
Binary files a/win32/deps/library/spatial/Meta/nsInfo.rds and b/win32/deps/library/spatial/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/spatial/Meta/package.rds b/win32/deps/library/spatial/Meta/package.rds
index fbf7bbf..72feeb3 100644
Binary files a/win32/deps/library/spatial/Meta/package.rds and b/win32/deps/library/spatial/Meta/package.rds differ
diff --git a/win32/deps/library/spatial/R/spatial b/win32/deps/library/spatial/R/spatial
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/spatial/R/spatial
+++ b/win32/deps/library/spatial/R/spatial
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/spatial/R/spatial.rdb b/win32/deps/library/spatial/R/spatial.rdb
index f74e5e5..d18da3d 100644
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diff --git a/win32/deps/library/spatial/R/spatial.rdx b/win32/deps/library/spatial/R/spatial.rdx
index cfcfc2c..7de8661 100644
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diff --git a/win32/deps/library/spatial/help/aliases.rds b/win32/deps/library/spatial/help/aliases.rds
new file mode 100644
index 0000000..db457e8
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diff --git a/win32/deps/library/spatial/help/paths.rds b/win32/deps/library/spatial/help/paths.rds
new file mode 100644
index 0000000..fc7e9e6
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new file mode 100644
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diff --git a/win32/deps/library/spatial/help/spatial.rdx b/win32/deps/library/spatial/help/spatial.rdx
new file mode 100644
index 0000000..0e7f77f
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diff --git a/win32/deps/library/spatial/html/00Index.html b/win32/deps/library/spatial/html/00Index.html
new file mode 100644
index 0000000..6a90cec
--- /dev/null
+++ b/win32/deps/library/spatial/html/00Index.html
@@ -0,0 +1,74 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Functions for Kriging and Point Pattern Analysis</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Functions for Kriging and Point Pattern Analysis
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘spatial’ version 7.3-5</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+<li><a href="../NEWS">Package NEWS</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<table width="100%">
+<tr><td width="25%"><a href="anova.trls.html">anova.trls</a></td>
+<td>Anova tables for fitted trend surface objects</td></tr>
+<tr><td width="25%"><a href="anova.trls.html">anovalist.trls</a></td>
+<td>Anova tables for fitted trend surface objects</td></tr>
+<tr><td width="25%"><a href="correlogram.html">correlogram</a></td>
+<td>Compute Spatial Correlograms</td></tr>
+<tr><td width="25%"><a href="expcov.html">expcov</a></td>
+<td>Spatial Covariance Functions</td></tr>
+<tr><td width="25%"><a href="expcov.html">gaucov</a></td>
+<td>Spatial Covariance Functions</td></tr>
+<tr><td width="25%"><a href="Kaver.html">Kaver</a></td>
+<td>Average K-functions from Simulations</td></tr>
+<tr><td width="25%"><a href="Kenvl.html">Kenvl</a></td>
+<td>Compute Envelope and Average of Simulations of K-fns</td></tr>
+<tr><td width="25%"><a href="Kfn.html">Kfn</a></td>
+<td>Compute K-fn of a Point Pattern</td></tr>
+<tr><td width="25%"><a href="trls.influence.html">plot.trls</a></td>
+<td>Regression diagnostics for trend surfaces</td></tr>
+<tr><td width="25%"><a href="ppgetregion.html">ppgetregion</a></td>
+<td>Get Domain for Spatial Point Pattern Analyses</td></tr>
+<tr><td width="25%"><a href="ppinit.html">ppinit</a></td>
+<td>Read a Point Process Object from a File</td></tr>
+<tr><td width="25%"><a href="pplik.html">pplik</a></td>
+<td>Pseudo-likelihood Estimation of a Strauss Spatial Point Process</td></tr>
+<tr><td width="25%"><a href="ppregion.html">ppregion</a></td>
+<td>Set Domain for Spatial Point Pattern Analyses</td></tr>
+<tr><td width="25%"><a href="predict.trls.html">predict.trls</a></td>
+<td>Predict method for trend surface fits</td></tr>
+<tr><td width="25%"><a href="prmat.html">prmat</a></td>
+<td>Evaluate Kriging Surface over a Grid</td></tr>
+<tr><td width="25%"><a href="Psim.html">Psim</a></td>
+<td>Simulate Binomial Spatial Point Process</td></tr>
+<tr><td width="25%"><a href="semat.html">semat</a></td>
+<td>Evaluate Kriging Standard Error of Prediction over a Grid</td></tr>
+<tr><td width="25%"><a href="expcov.html">sphercov</a></td>
+<td>Spatial Covariance Functions</td></tr>
+<tr><td width="25%"><a href="SSI.html">SSI</a></td>
+<td>Simulates Sequential Spatial Inhibition Point Process</td></tr>
+<tr><td width="25%"><a href="Strauss.html">Strauss</a></td>
+<td>Simulates Strauss Spatial Point Process</td></tr>
+<tr><td width="25%"><a href="surf.gls.html">surf.gls</a></td>
+<td>Fits a Trend Surface by Generalized Least-squares</td></tr>
+<tr><td width="25%"><a href="surf.ls.html">surf.ls</a></td>
+<td>Fits a Trend Surface by Least-squares</td></tr>
+<tr><td width="25%"><a href="trls.influence.html">trls.influence</a></td>
+<td>Regression diagnostics for trend surfaces</td></tr>
+<tr><td width="25%"><a href="trmat.html">trmat</a></td>
+<td>Evaluate Trend Surface over a Grid</td></tr>
+<tr><td width="25%"><a href="variogram.html">variogram</a></td>
+<td>Compute Spatial Variogram</td></tr>
+</table>
+</body></html>
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+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
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+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
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+ color: rgb(40%, 40%, 40%);
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+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
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diff --git a/win32/deps/library/spatial/tests/Examples/spatial-Ex.Rout.save b/win32/deps/library/spatial/tests/Examples/spatial-Ex.Rout.save
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+
+R version 2.13.0 Under development (unstable) (2011-03-05 r54672)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+ Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> pkgname <- "spatial"
+> source(file.path(R.home("share"), "R", "examples-header.R"))
+> options(warn = 1)
+> library('spatial')
+>
+> assign(".oldSearch", search(), pos = 'CheckExEnv')
+> cleanEx()
+> nameEx("Kaver")
+> ### * Kaver
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: Kaver
+> ### Title: Average K-functions from Simulations
+> ### Aliases: Kaver
+> ### Keywords: spatial
+>
+> ### ** Examples
+>
+> towns <- ppinit("towns.dat")
+> par(pty="s")
+> plot(Kfn(towns, 40), type="b")
+> plot(Kfn(towns, 10), type="b", xlab="distance", ylab="L(t)")
+> for(i in 1:10) lines(Kfn(Psim(69), 10))
+> lims <- Kenvl(10,100,Psim(69))
+> lines(lims$x,lims$lower, lty=2, col="green")
+> lines(lims$x,lims$upper, lty=2, col="green")
+> lines(Kaver(10,25,Strauss(69,0.5,3.5)), col="red")
+>
+>
+>
+> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
+> cleanEx()
+> nameEx("Kenvl")
+> ### * Kenvl
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: Kenvl
+> ### Title: Compute Envelope and Average of Simulations of K-fns
+> ### Aliases: Kenvl
+> ### Keywords: spatial
+>
+> ### ** Examples
+>
+> towns <- ppinit("towns.dat")
+> par(pty="s")
+> plot(Kfn(towns, 40), type="b")
+> plot(Kfn(towns, 10), type="b", xlab="distance", ylab="L(t)")
+> for(i in 1:10) lines(Kfn(Psim(69), 10))
+> lims <- Kenvl(10,100,Psim(69))
+> lines(lims$x,lims$lower, lty=2, col="green")
+> lines(lims$x,lims$upper, lty=2, col="green")
+> lines(Kaver(10,25,Strauss(69,0.5,3.5)), col="red")
+>
+>
+>
+> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
+> cleanEx()
+> nameEx("Kfn")
+> ### * Kfn
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: Kfn
+> ### Title: Compute K-fn of a Point Pattern
+> ### Aliases: Kfn
+> ### Keywords: spatial
+>
+> ### ** Examples
+>
+> towns <- ppinit("towns.dat")
+> par(pty="s")
+> plot(Kfn(towns, 10), type="s", xlab="distance", ylab="L(t)")
+>
+>
+>
+> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
+> cleanEx()
+> nameEx("Psim")
+> ### * Psim
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: Psim
+> ### Title: Simulate Binomial Spatial Point Process
+> ### Aliases: Psim
+> ### Keywords: spatial
+>
+> ### ** Examples
+>
+> towns <- ppinit("towns.dat")
+> par(pty="s")
+> plot(Kfn(towns, 10), type="s", xlab="distance", ylab="L(t)")
+> for(i in 1:10) lines(Kfn(Psim(69), 10))
+>
+>
+>
+> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
+> cleanEx()
+> nameEx("SSI")
+> ### * SSI
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: SSI
+> ### Title: Simulates Sequential Spatial Inhibition Point Process
+> ### Aliases: SSI
+> ### Keywords: spatial
+>
+> ### ** Examples
+>
+> towns <- ppinit("towns.dat")
+> par(pty = "s")
+> plot(Kfn(towns, 10), type = "b", xlab = "distance", ylab = "L(t)")
+> lines(Kaver(10, 25, SSI(69, 1.2)))
+>
+>
+>
+> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
+> cleanEx()
+> nameEx("Strauss")
+> ### * Strauss
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: Strauss
+> ### Title: Simulates Strauss Spatial Point Process
+> ### Aliases: Strauss
+> ### Keywords: spatial
+>
+> ### ** Examples
+>
+> towns <- ppinit("towns.dat")
+> par(pty="s")
+> plot(Kfn(towns, 10), type="b", xlab="distance", ylab="L(t)")
+> lines(Kaver(10, 25, Strauss(69,0.5,3.5)))
+>
+>
+>
+> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
+> cleanEx()
+> nameEx("anova.trls")
+> ### * anova.trls
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: anova.trls
+> ### Title: Anova tables for fitted trend surface objects
+> ### Aliases: anova.trls anovalist.trls
+> ### Keywords: spatial
+>
+> ### ** Examples
+>
+> library(stats)
+> data(topo, package="MASS")
+> topo0 <- surf.ls(0, topo)
+> topo1 <- surf.ls(1, topo)
+> topo2 <- surf.ls(2, topo)
+> topo3 <- surf.ls(3, topo)
+> topo4 <- surf.ls(4, topo)
+> anova(topo0, topo1, topo2, topo3, topo4)
+Analysis of Variance Table
+
+Model 1: surf.ls(np = 0, x = topo)
+Model 2: surf.ls(np = 1, x = topo)
+Model 3: surf.ls(np = 2, x = topo)
+Model 4: surf.ls(np = 3, x = topo)
+Model 5: surf.ls(np = 4, x = topo)
+ Res.Df Res.Sum Sq Df Sum Sq F value Pr(>F)
+1 51 196030
+2 49 67186 2 128844 46.9843 4.040e-12
+3 46 39958 3 27228 10.4482 2.325e-05
+4 42 21577 4 18381 8.9447 2.558e-05
+5 37 14886 5 6691 3.3265 0.014
+> summary(topo4)
+Analysis of Variance Table
+ Model: surf.ls(np = 4, x = topo)
+ Sum Sq Df Mean Sq F value Pr(>F)
+Regression 181144.0 14 12938.8567 32.16092 2.2204e-16
+Deviation 14885.7 37 402.3162
+Total 196029.7 51
+Multiple R-Squared: 0.9241, Adjusted R-squared: 0.8953
+AIC: (df = 15) 324.1594
+Fitted:
+ Min 1Q Median 3Q Max
+ 702.1 785.0 836.3 880.5 939.1
+Residuals:
+ Min 1Q Median 3Q Max
+-34.077 -12.568 -2.085 14.056 50.161
+>
+>
+>
+> cleanEx()
+> nameEx("correlogram")
+> ### * correlogram
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: correlogram
+> ### Title: Compute Spatial Correlograms
+> ### Aliases: correlogram
+> ### Keywords: spatial
+>
+> ### ** Examples
+>
+> data(topo, package="MASS")
+> topo.kr <- surf.ls(2, topo)
+> correlogram(topo.kr, 25)
+> d <- seq(0, 7, 0.1)
+> lines(d, expcov(d, 0.7))
+>
+>
+>
+> cleanEx()
+> nameEx("expcov")
+> ### * expcov
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: expcov
+> ### Title: Spatial Covariance Functions
+> ### Aliases: expcov gaucov sphercov
+> ### Keywords: spatial
+>
+> ### ** Examples
+>
+> data(topo, package="MASS")
+> topo.kr <- surf.ls(2, topo)
+> correlogram(topo.kr, 25)
+> d <- seq(0, 7, 0.1)
+> lines(d, expcov(d, 0.7))
+>
+>
+>
+> cleanEx()
+> nameEx("ppinit")
+> ### * ppinit
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: ppinit
+> ### Title: Read a Point Process Object from a File
+> ### Aliases: ppinit
+> ### Keywords: spatial
+>
+> ### ** Examples
+>
+> towns <- ppinit("towns.dat")
+> par(pty="s")
+> plot(Kfn(towns, 10), type="b", xlab="distance", ylab="L(t)")
+>
+>
+>
+> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
+> cleanEx()
+> nameEx("pplik")
+> ### * pplik
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: pplik
+> ### Title: Pseudo-likelihood Estimation of a Strauss Spatial Point Process
+> ### Aliases: pplik
+> ### Keywords: spatial
+>
+> ### ** Examples
+>
+> pines <- ppinit("pines.dat")
+> pplik(pines, 0.7)
+[1] 0.1508756
+>
+>
+>
+> cleanEx()
+> nameEx("predict.trls")
+> ### * predict.trls
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: predict.trls
+> ### Title: Predict method for trend surface fits
+> ### Aliases: predict.trls
+> ### Keywords: spatial
+>
+> ### ** Examples
+>
+> data(topo, package="MASS")
+> topo2 <- surf.ls(2, topo)
+> topo4 <- surf.ls(4, topo)
+> x <- c(1.78, 2.21)
+> y <- c(6.15, 6.15)
+> z2 <- predict(topo2, x, y)
+> z4 <- predict(topo4, x, y)
+> cat("2nd order predictions:", z2, "\n4th order predictions:", z4, "\n")
+2nd order predictions: 756.0682 747.0624
+4th order predictions: 765.5547 742.3738
+>
+>
+>
+> cleanEx()
+> nameEx("prmat")
+> ### * prmat
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: prmat
+> ### Title: Evaluate Kriging Surface over a Grid
+> ### Aliases: prmat
+> ### Keywords: spatial
+>
+> ### ** Examples
+>
+> data(topo, package="MASS")
+> topo.kr <- surf.gls(2, expcov, topo, d=0.7)
+> prsurf <- prmat(topo.kr, 0, 6.5, 0, 6.5, 50)
+> contour(prsurf, levels=seq(700, 925, 25))
+>
+>
+>
+> cleanEx()
+> nameEx("semat")
+> ### * semat
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: semat
+> ### Title: Evaluate Kriging Standard Error of Prediction over a Grid
+> ### Aliases: semat
+> ### Keywords: spatial
+>
+> ### ** Examples
+>
+> data(topo, package="MASS")
+> topo.kr <- surf.gls(2, expcov, topo, d=0.7)
+> prsurf <- prmat(topo.kr, 0, 6.5, 0, 6.5, 50)
+> contour(prsurf, levels=seq(700, 925, 25))
+> sesurf <- semat(topo.kr, 0, 6.5, 0, 6.5, 30)
+> contour(sesurf, levels=c(22,25))
+>
+>
+>
+> cleanEx()
+> nameEx("surf.gls")
+> ### * surf.gls
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: surf.gls
+> ### Title: Fits a Trend Surface by Generalized Least-squares
+> ### Aliases: surf.gls
+> ### Keywords: spatial
+>
+> ### ** Examples
+>
+> library(MASS) # for eqscplot
+> data(topo, package="MASS")
+> topo.kr <- surf.gls(2, expcov, topo, d=0.7)
+> trsurf <- trmat(topo.kr, 0, 6.5, 0, 6.5, 50)
+> eqscplot(trsurf, type = "n")
+> contour(trsurf, add = TRUE)
+>
+> prsurf <- prmat(topo.kr, 0, 6.5, 0, 6.5, 50)
+> contour(prsurf, levels=seq(700, 925, 25))
+> sesurf <- semat(topo.kr, 0, 6.5, 0, 6.5, 30)
+> eqscplot(sesurf, type = "n")
+> contour(sesurf, levels = c(22, 25), add = TRUE)
+>
+>
+>
+> cleanEx()
+
+detaching âpackage:MASSâ
+
+> nameEx("surf.ls")
+> ### * surf.ls
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: surf.ls
+> ### Title: Fits a Trend Surface by Least-squares
+> ### Aliases: surf.ls
+> ### Keywords: spatial
+>
+> ### ** Examples
+>
+> library(MASS) # for eqscplot
+> data(topo, package="MASS")
+> topo.kr <- surf.ls(2, topo)
+> trsurf <- trmat(topo.kr, 0, 6.5, 0, 6.5, 50)
+> eqscplot(trsurf, type = "n")
+> contour(trsurf, add = TRUE)
+> points(topo)
+>
+> eqscplot(trsurf, type = "n")
+> contour(trsurf, add = TRUE)
+> plot(topo.kr, add = TRUE)
+> title(xlab= "Circle radius proportional to Cook's influence statistic")
+>
+>
+>
+> cleanEx()
+
+detaching âpackage:MASSâ
+
+> nameEx("trls.influence")
+> ### * trls.influence
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: trls.influence
+> ### Title: Regression diagnostics for trend surfaces
+> ### Aliases: trls.influence plot.trls
+> ### Keywords: spatial
+>
+> ### ** Examples
+>
+> library(MASS) # for eqscplot
+> data(topo, package = "MASS")
+> topo2 <- surf.ls(2, topo)
+> infl.topo2 <- trls.influence(topo2)
+> (cand <- as.data.frame(infl.topo2)[abs(infl.topo2$stresid) > 1.5, ])
+ r hii stresid Di
+1 61.21889 0.35476783 2.585852 0.61275133
+4 -45.58507 0.13493260 -1.662930 0.07188916
+12 44.71663 0.21022336 1.707234 0.12930392
+31 52.05575 0.07154233 1.833006 0.04314966
+37 54.75944 0.06974770 1.926349 0.04637112
+48 97.75499 0.08574061 3.468809 0.18807312
+50 -63.25149 0.27530059 -2.520972 0.40237779
+> cand.xy <- topo[as.integer(rownames(cand)), c("x", "y")]
+> trsurf <- trmat(topo2, 0, 6.5, 0, 6.5, 50)
+> eqscplot(trsurf, type = "n")
+> contour(trsurf, add = TRUE, col = "grey")
+> plot(topo2, add = TRUE, div = 3)
+> points(cand.xy, pch = 16, col = "orange")
+> text(cand.xy, labels = rownames(cand.xy), pos = 4, offset = 0.5)
+>
+>
+>
+> cleanEx()
+
+detaching âpackage:MASSâ
+
+> nameEx("trmat")
+> ### * trmat
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: trmat
+> ### Title: Evaluate Trend Surface over a Grid
+> ### Aliases: trmat
+> ### Keywords: spatial
+>
+> ### ** Examples
+>
+> data(topo, package="MASS")
+> topo.kr <- surf.ls(2, topo)
+> trsurf <- trmat(topo.kr, 0, 6.5, 0, 6.5, 50)
+>
+>
+>
+> cleanEx()
+> nameEx("variogram")
+> ### * variogram
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: variogram
+> ### Title: Compute Spatial Variogram
+> ### Aliases: variogram
+> ### Keywords: spatial
+>
+> ### ** Examples
+>
+> data(topo, package="MASS")
+> topo.kr <- surf.ls(2, topo)
+> variogram(topo.kr, 25)
+>
+>
+>
+> ### * <FOOTER>
+> ###
+> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
+Time elapsed: 0.784 0.106 1.435 0 0
+> grDevices::dev.off()
+null device
+ 1
+> ###
+> ### Local variables: ***
+> ### mode: outline-minor ***
+> ### outline-regexp: "\\(> \\)?### [*]+" ***
+> ### End: ***
+> quit('no')
diff --git a/win32/deps/library/splines/DESCRIPTION b/win32/deps/library/splines/DESCRIPTION
index b03a72c..54009c9 100644
--- a/win32/deps/library/splines/DESCRIPTION
+++ b/win32/deps/library/splines/DESCRIPTION
@@ -1,11 +1,11 @@
Package: splines
-Version: 2.9.2
+Version: 2.15.2
Priority: base
Imports: graphics, stats
Title: Regression Spline Functions and Classes
-Author: Douglas M. Bates <bates stat wisc edu> and William N. Venables
- <Bill Venables csiro au>
+Author: Douglas M. Bates <bates stat wisc edu> and
+ William N. Venables <Bill Venables csiro au>
Maintainer: R Core Team <R-core r-project org>
Description: Regression spline functions and classes
-License: Part of R 2.9.2
-Built: R 2.9.2; i386-pc-mingw32; 2009-08-24 12:46:05 UTC; windows
+License: Part of R 2.15.2
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:07:55 UTC; windows
diff --git a/win32/deps/library/splines/INDEX b/win32/deps/library/splines/INDEX
index 5b9675f..ea12d63 100644
--- a/win32/deps/library/splines/INDEX
+++ b/win32/deps/library/splines/INDEX
@@ -12,4 +12,4 @@ splineDesign Design Matrix for B-splines
splineKnots Knot Vector from a Spline
splineOrder Determine the Order of a Spline
splines-package Regression Spline Functions and Classes
-xyVector Construct an xyVector Object
+xyVector Construct an 'xyVector' Object
diff --git a/win32/deps/library/splines/Meta/Rd.rds b/win32/deps/library/splines/Meta/Rd.rds
index 19b688d..f0ab2fa 100644
Binary files a/win32/deps/library/splines/Meta/Rd.rds and b/win32/deps/library/splines/Meta/Rd.rds differ
diff --git a/win32/deps/library/splines/Meta/hsearch.rds b/win32/deps/library/splines/Meta/hsearch.rds
index 7286b49..ff05ab5 100644
Binary files a/win32/deps/library/splines/Meta/hsearch.rds and b/win32/deps/library/splines/Meta/hsearch.rds differ
diff --git a/win32/deps/library/splines/Meta/links.rds b/win32/deps/library/splines/Meta/links.rds
new file mode 100644
index 0000000..bd91165
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diff --git a/win32/deps/library/splines/Meta/nsInfo.rds b/win32/deps/library/splines/Meta/nsInfo.rds
index f2db186..cb23c63 100644
Binary files a/win32/deps/library/splines/Meta/nsInfo.rds and b/win32/deps/library/splines/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/splines/Meta/package.rds b/win32/deps/library/splines/Meta/package.rds
index 3a03e08..d09d9c0 100644
Binary files a/win32/deps/library/splines/Meta/package.rds and b/win32/deps/library/splines/Meta/package.rds differ
diff --git a/win32/deps/library/splines/NAMESPACE b/win32/deps/library/splines/NAMESPACE
index 8cf91db..61ec3f1 100644
--- a/win32/deps/library/splines/NAMESPACE
+++ b/win32/deps/library/splines/NAMESPACE
@@ -1,3 +1,5 @@
+useDynLib(splines, .registration = TRUE, .fixes = "C_")
+
export(as.polySpline, asVector, backSpline, bs, interpSpline, ns,
periodicSpline, polySpline, spline.des, splineDesign,
splineKnots, splineOrder, xyVector)
diff --git a/win32/deps/library/splines/R/splines b/win32/deps/library/splines/R/splines
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/splines/R/splines
+++ b/win32/deps/library/splines/R/splines
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/splines/R/splines.rdb b/win32/deps/library/splines/R/splines.rdb
index e8908b1..6c6779f 100644
Binary files a/win32/deps/library/splines/R/splines.rdb and b/win32/deps/library/splines/R/splines.rdb differ
diff --git a/win32/deps/library/splines/R/splines.rdx b/win32/deps/library/splines/R/splines.rdx
index 145f4d7..5048981 100644
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diff --git a/win32/deps/library/splines/help/aliases.rds b/win32/deps/library/splines/help/aliases.rds
new file mode 100644
index 0000000..f9185d8
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diff --git a/win32/deps/library/splines/help/paths.rds b/win32/deps/library/splines/help/paths.rds
new file mode 100644
index 0000000..be52d00
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diff --git a/win32/deps/library/splines/help/splines.rdb b/win32/deps/library/splines/help/splines.rdb
new file mode 100644
index 0000000..e1be526
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diff --git a/win32/deps/library/splines/help/splines.rdx b/win32/deps/library/splines/help/splines.rdx
new file mode 100644
index 0000000..9cd364a
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diff --git a/win32/deps/library/splines/html/00Index.html b/win32/deps/library/splines/html/00Index.html
new file mode 100644
index 0000000..43185c1
--- /dev/null
+++ b/win32/deps/library/splines/html/00Index.html
@@ -0,0 +1,67 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Regression Spline Functions and Classes</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Regression Spline Functions and Classes
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘splines’ version 2.15.2</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<table width="100%">
+<tr><td width="25%"><a href="splines-package.html">splines-package</a></td>
+<td>Regression Spline Functions and Classes</td></tr>
+<tr><td width="25%"><a href="polySpline.html">as.polySpline</a></td>
+<td>Piecewise Polynomial Spline Representation</td></tr>
+<tr><td width="25%"><a href="asVector.html">asVector</a></td>
+<td>Coerce an Object to a Vector</td></tr>
+<tr><td width="25%"><a href="backSpline.html">backSpline</a></td>
+<td>Monotone Inverse Spline</td></tr>
+<tr><td width="25%"><a href="bs.html">bs</a></td>
+<td>B-Spline Basis for Polynomial Splines</td></tr>
+<tr><td width="25%"><a href="interpSpline.html">interpSpline</a></td>
+<td>Create an Interpolation Spline</td></tr>
+<tr><td width="25%"><a href="ns.html">ns</a></td>
+<td>Generate a Basis Matrix for Natural Cubic Splines</td></tr>
+<tr><td width="25%"><a href="periodicSpline.html">periodicSpline</a></td>
+<td>Create a Periodic Interpolation Spline</td></tr>
+<tr><td width="25%"><a href="polySpline.html">polySpline</a></td>
+<td>Piecewise Polynomial Spline Representation</td></tr>
+<tr><td width="25%"><a href="predict.bs.html">predict.bs</a></td>
+<td>Evaluate a Spline Basis</td></tr>
+<tr><td width="25%"><a href="predict.bSpline.html">predict.bSpline</a></td>
+<td>Evaluate a Spline at New Values of x</td></tr>
+<tr><td width="25%"><a href="predict.bSpline.html">predict.nbSpline</a></td>
+<td>Evaluate a Spline at New Values of x</td></tr>
+<tr><td width="25%"><a href="predict.bSpline.html">predict.npolySpline</a></td>
+<td>Evaluate a Spline at New Values of x</td></tr>
+<tr><td width="25%"><a href="predict.bs.html">predict.ns</a></td>
+<td>Evaluate a Spline Basis</td></tr>
+<tr><td width="25%"><a href="predict.bSpline.html">predict.pbSpline</a></td>
+<td>Evaluate a Spline at New Values of x</td></tr>
+<tr><td width="25%"><a href="predict.bSpline.html">predict.ppolySpline</a></td>
+<td>Evaluate a Spline at New Values of x</td></tr>
+<tr><td width="25%"><a href="splineDesign.html">spline.des</a></td>
+<td>Design Matrix for B-splines</td></tr>
+<tr><td width="25%"><a href="splineDesign.html">splineDesign</a></td>
+<td>Design Matrix for B-splines</td></tr>
+<tr><td width="25%"><a href="splineKnots.html">splineKnots</a></td>
+<td>Knot Vector from a Spline</td></tr>
+<tr><td width="25%"><a href="splineOrder.html">splineOrder</a></td>
+<td>Determine the Order of a Spline</td></tr>
+<tr><td width="25%"><a href="splines-package.html">splines</a></td>
+<td>Regression Spline Functions and Classes</td></tr>
+<tr><td width="25%"><a href="xyVector.html">xyVector</a></td>
+<td>Construct an 'xyVector' Object</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/splines/html/R.css b/win32/deps/library/splines/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/splines/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/splines/libs/i386/splines.dll b/win32/deps/library/splines/libs/i386/splines.dll
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index 0000000..da3a406
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diff --git a/win32/deps/library/splines/po/zh_CN/LC_MESSAGES/R-splines.mo b/win32/deps/library/splines/po/zh_CN/LC_MESSAGES/R-splines.mo
new file mode 100644
index 0000000..ecb82a3
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diff --git a/win32/deps/library/splines/po/zh_CN/LC_MESSAGES/splines.mo b/win32/deps/library/splines/po/zh_CN/LC_MESSAGES/splines.mo
new file mode 100644
index 0000000..6fd2f19
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diff --git a/win32/deps/library/stats/COPYRIGHTS.modreg b/win32/deps/library/stats/COPYRIGHTS.modreg
index 4f0e734..be2b1ec 100644
--- a/win32/deps/library/stats/COPYRIGHTS.modreg
+++ b/win32/deps/library/stats/COPYRIGHTS.modreg
@@ -39,5 +39,5 @@ src/loessf.f
The files are unchanged apart from the insertion of that statement.
-All other files are copyright the R Core Development Team and/or B. D. Ripley.
+All other files are copyright the R Core Team and/or B. D. Ripley.
diff --git a/win32/deps/library/stats/DESCRIPTION b/win32/deps/library/stats/DESCRIPTION
index b46cd69..8941be4 100644
--- a/win32/deps/library/stats/DESCRIPTION
+++ b/win32/deps/library/stats/DESCRIPTION
@@ -1,9 +1,9 @@
Package: stats
-Version: 2.9.2
+Version: 2.15.2
Priority: base
Title: The R Stats Package
-Author: R Development Core Team and contributors worldwide
+Author: R Core Team and contributors worldwide
Maintainer: R Core Team <R-core r-project org>
Description: R statistical functions
-License: Part of R 2.9.2
-Built: R 2.9.2; i386-pc-mingw32; 2009-08-24 12:44:09 UTC; windows
+License: Part of R 2.15.2
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:06:07 UTC; windows
diff --git a/win32/deps/library/stats/INDEX b/win32/deps/library/stats/INDEX
index 7c3c2f8..61dc293 100644
--- a/win32/deps/library/stats/INDEX
+++ b/win32/deps/library/stats/INDEX
@@ -9,6 +9,7 @@ Box.test Box-Pierce and Ljung-Box Tests
C Sets Contrasts for a Factor
Cauchy The Cauchy Distribution
Chisquare The (non-central) Chi-Squared Distribution
+Distributions Distributions in the stats package
Exponential The Exponential Distribution
FDist The F Distribution
GammaDist The Gamma Distribution
@@ -30,16 +31,18 @@ PP.test Phillips-Perron Test for Unit Roots
Poisson The Poisson Distribution
SSD SSD Matrix and Estimated Variance Matrix in
Multivariate Models
-SSasymp Asymptotic Regression Model
-SSasympOff Asymptotic Regression Model with an Offset
-SSasympOrig Asymptotic Regression Model through the Origin
-SSbiexp Biexponential model
-SSfol First-order Compartment Model
-SSfpl Four-parameter Logistic Model
-SSgompertz Gompertz Growth Model
-SSlogis Logistic Model
-SSmicmen Michaelis-Menten Model
-SSweibull Weibull growth curve model
+SSasymp Self-Starting Nls Asymptotic Regression Model
+SSasympOff Self-Starting Nls Asymptotic Regression Model
+ with an Offset
+SSasympOrig Self-Starting Nls Asymptotic Regression Model
+ through the Origin
+SSbiexp Self-Starting Nls Biexponential model
+SSfol Self-Starting Nls First-order Compartment Model
+SSfpl Self-Starting Nls Four-Parameter Logistic Model
+SSgompertz Self-Starting Nls Gompertz Growth Model
+SSlogis Self-Starting Nls Logistic Model
+SSmicmen Self-Starting Nls Michaelis-Menten Model
+SSweibull Self-Starting Nls Weibull Growth Curve Model
SignRank Distribution of the Wilcoxon Signed Rank
Statistic
StructTS Fit Structural Time Series
@@ -70,7 +73,7 @@ ar Fit Autoregressive Models to Time Series
ar.ols Fit Autoregressive Models to Time Series by OLS
arima ARIMA Modelling of Time Series
arima.sim Simulate from an ARIMA Model
-arima0 ARIMA Modelling of Time Series -- Preliminary
+arima0 ARIMA Modelling of Time Series - Preliminary
Version
as.hclust Convert Objects to Class hclust
asOneSidedFormula Convert to One-Sided Formula
@@ -85,15 +88,14 @@ bw.nrd0 Bandwidth Selectors for Kernel Density
cancor Canonical Correlations
case.names Case and Variable Names of Fitted Models
chisq.test Pearson's Chi-squared Test for Count Data
-clearNames Remove the Names from an Object
cmdscale Classical (Metric) Multidimensional Scaling
coef Extract Model Coefficients
complete.cases Find Complete Cases
confint Confidence Intervals for Model Parameters
-constrOptim Linearly constrained optimisation
-contr.helmert Contrast Matrices
+constrOptim Linearly Constrained Optimization
+contr.helmert (Possibly Sparse) Contrast Matrices
contrasts Get and Set Contrast Matrices
-convolve Fast Convolution
+convolve Convolution of Sequences via FFT
cophenetic Cophenetic Distances for a Hierarchical
Clustering
cor Correlation, Variance and Covariance (Matrices)
@@ -101,7 +103,7 @@ cor.test Test for Association/Correlation Between Paired
Samples
cov.wt Weighted Covariance Matrices
cpgram Plot Cumulative Periodogram
-cutree Cut a tree into groups of data
+cutree Cut a Tree into Groups of Data
decompose Classical Seasonal Decomposition by Moving
Averages
delete.response Modify Terms Objects
@@ -150,7 +152,7 @@ identify.hclust Identify Clusters in a Dendrogram
influence.measures Regression Deletion Diagnostics
integrate Integration of One-Dimensional Functions
interaction.plot Two-way Interaction Plot
-is.empty.model Check if a Model is Empty
+is.empty.model Test if a Model's Formula is Empty
isoreg Isotonic / Monotone Regression
kernapply Apply Smoothing Kernel
kernel Smoothing Kernel Objects
@@ -186,7 +188,8 @@ mcnemar.test McNemar's Chi-squared Test for Count Data
median Median Value
medpolish Median Polish of a Matrix
model.extract Extract Components from a Model Frame
-model.frame Extracting the "Environment" of a Model Formula
+model.frame Extracting the Model Frame from a Formula or
+ Fit
model.matrix Construct Design Matrices
model.tables Compute Tables of Results from an Aov Model Fit
monthplot Plot a Seasonal or other Subseries from a Time
@@ -202,7 +205,8 @@ nlm Non-Linear Minimization
nlminb Optimization using PORT routines
nls Nonlinear Least Squares
nls.control Control the Iterations in nls
-numericDeriv Evaluate derivatives numerically
+nobs Extract the Number of Observations from a Fit.
+numericDeriv Evaluate Derivatives Numerically
offset Include an Offset in a Model Formula
oneway.test Test for Equal Means in a One-Way Layout
optim General-purpose Optimization
@@ -213,7 +217,7 @@ p.adjust Adjust P-values for Multiple Comparisons
pairwise.prop.test Pairwise comparisons for proportions
pairwise.t.test Pairwise t tests
pairwise.table Tabulate p values for pairwise comparisons
-pairwise.wilcox.test Pairwise Wilcoxon rank sum tests
+pairwise.wilcox.test Pairwise Wilcoxon Rank Sum Tests
plot.HoltWinters Plot function for HoltWinters objects
plot.acf Plot Autocovariance and Autocorrelation
Functions
@@ -230,10 +234,10 @@ plot.ts Plotting Time-Series Objects
poisson.test Exact Poisson tests
poly Compute Orthogonal Polynomials
power Create a Power Link Object
-power.anova.test Power calculations for balanced one-way
- analysis of variance tests
-power.prop.test Power calculations two sample test for
- proportions
+power.anova.test Power Calculations for Balanced One-Way
+ Analysis of Variance Tests
+power.prop.test Power Calculations for Two-Sample Test for
+ Proportions
power.t.test Power calculations for one and two sample t
tests
ppoints Ordinates for Probability Plotting
@@ -241,14 +245,14 @@ ppr Projection Pursuit Regression
prcomp Principal Components Analysis
predict Model Predictions
predict.Arima Forecast from ARIMA fits
-predict.HoltWinters prediction function for fitted Holt-Winters
- models
+predict.HoltWinters Prediction Function for Fitted Holt-Winters
+ Models
predict.glm Predict Method for GLM Fits
predict.lm Predict method for Linear Model Fits
predict.loess Predict Loess Curve or Surface
predict.nls Predicting from Nonlinear Least Squares Fits
predict.smooth.spline Predict from Smoothing Spline Fit
-preplot Pre-computations for a Plotting Objeect
+preplot Pre-computations for a Plotting Object
princomp Principal Components Analysis
print.power.htest Print method for power calculation object
print.ts Printing Time-Series Objects
@@ -263,16 +267,16 @@ qqnorm Quantile-Quantile Plots
quade.test Quade Test
quantile Sample Quantiles
r2dtable Random 2-way Tables with Given Marginals
+rWishart Random Wishart Distributed Matrices
read.ftable Manipulate Flat Contingency Tables
rect.hclust Draw Rectangles Around Hierarchical Clusters
relevel Reorder Levels of Factor
+reorder.default Reorder Levels of a Factor
reorder.dendrogram Reorder a Dendrogram
-reorder.factor Reorder Levels of a Factor
replications Number of Replications of Terms
reshape Reshape Grouped Data
residuals Extract Model Residuals
-runmed Running Medians -- Robust Scatter Plot
- Smoothing
+runmed Running Medians - Robust Scatter Plot Smoothing
scatter.smooth Scatter Plot with Smooth Curve Fitted by Loess
screeplot Screeplots
sd Standard Deviation
@@ -284,7 +288,7 @@ simulate Simulate Responses
smooth Tukey's (Running Median) Smoothing
smooth.spline Fit a Smoothing Spline
smoothEnds End Points Smoothing (for Running Medians)
-sortedXyData Create a sortedXyData object
+sortedXyData Create a 'sortedXyData' Object
spec.ar Estimate Spectral Density of a Time Series from
AR Fit
spec.pgram Estimate Spectral Density of a Time Series by a
@@ -294,7 +298,7 @@ spectrum Spectral Density Estimation
splinefun Interpolating Splines
start Encode the Terminal Times of Time Series
stat.anova GLM Anova Statistics
-stats-deprecated Deprecated Functions in Stats package
+stats-deprecated Deprecated Functions in Package 'stats'
stats-package The R Stats Package
step Choose a model by AIC in a Stepwise Algorithm
stepfun Step Function Class
@@ -310,7 +314,7 @@ summary.princomp Summary method for Principal Components
supsmu Friedman's SuperSmoother
symnum Symbolic Number Coding
t.test Student's t-Test
-termplot Plot regression terms
+termplot Plot Regression Terms
terms Model Terms
terms.formula Construct a terms Object from a Formula
terms.object Description of Terms Objects
@@ -331,6 +335,7 @@ vcov Calculate Variance-Covariance Matrix for a
Fitted Model Object
weighted.mean Weighted Arithmetic Mean
weighted.residuals Compute Weighted Residuals
+weights Extract Model Weights
wilcox.test Wilcoxon Rank Sum and Signed Rank Tests
window Time Windows
xtabs Cross Tabulation
diff --git a/win32/deps/library/stats/Meta/Rd.rds b/win32/deps/library/stats/Meta/Rd.rds
index c46a14d..345fee8 100644
Binary files a/win32/deps/library/stats/Meta/Rd.rds and b/win32/deps/library/stats/Meta/Rd.rds differ
diff --git a/win32/deps/library/stats/Meta/demo.rds b/win32/deps/library/stats/Meta/demo.rds
index 6bdb416..8bb2fdf 100644
Binary files a/win32/deps/library/stats/Meta/demo.rds and b/win32/deps/library/stats/Meta/demo.rds differ
diff --git a/win32/deps/library/stats/Meta/hsearch.rds b/win32/deps/library/stats/Meta/hsearch.rds
index 5783d9d..9787d03 100644
Binary files a/win32/deps/library/stats/Meta/hsearch.rds and b/win32/deps/library/stats/Meta/hsearch.rds differ
diff --git a/win32/deps/library/stats/Meta/links.rds b/win32/deps/library/stats/Meta/links.rds
new file mode 100644
index 0000000..583c84d
Binary files /dev/null and b/win32/deps/library/stats/Meta/links.rds differ
diff --git a/win32/deps/library/stats/Meta/nsInfo.rds b/win32/deps/library/stats/Meta/nsInfo.rds
index a90bb71..1a34273 100644
Binary files a/win32/deps/library/stats/Meta/nsInfo.rds and b/win32/deps/library/stats/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/stats/Meta/package.rds b/win32/deps/library/stats/Meta/package.rds
index b63204d..473cb61 100644
Binary files a/win32/deps/library/stats/Meta/package.rds and b/win32/deps/library/stats/Meta/package.rds differ
diff --git a/win32/deps/library/stats/NAMESPACE b/win32/deps/library/stats/NAMESPACE
index 9b3c2b7..249c699 100644
--- a/win32/deps/library/stats/NAMESPACE
+++ b/win32/deps/library/stats/NAMESPACE
@@ -1,5 +1,11 @@
-# Refer to all C/Fortran routines by their name prefixed by R_
-useDynLib(stats, .registration = TRUE, .fixes = "R_")
+# Refer to all C/Fortran routines by their name prefixed by C_
+useDynLib(stats, .registration = TRUE, .fixes = "C_")
+
+import(graphics)
+importFrom(grDevices, dev.interactive, palette, extendrange, xy.coords)
+
+importFrom(utils, str)
+
# exportPattern("^[^\\.]")
export(.checkMFClasses, .getXlevels, .MFclass)
@@ -7,10 +13,10 @@ export(.checkMFClasses, .getXlevels, .MFclass)
export(add.scope, add1, addmargins, aggregate, aggregate.data.frame,
aggregate.default, aggregate.ts, AIC, alias, anova, anova.glm,
anova.glmlist, anova.lm, anova.lmlist, anova.mlm, aov, approx,
- approxfun, as.formula, as.ts, ave, binomial, bw.bcv, bw.nrd,
- bw.nrd0, bw.SJ, bw.ucv, C, case.names, coef, coefficients,
- complete.cases, confint, confint.default, constrOptim,
- contr.SAS, contr.helmert, contr.poly, contr.sum,
+ approxfun, as.formula, as.ts, ave, BIC, binomial, bw.bcv,
+ bw.nrd, bw.nrd0, bw.SJ, bw.ucv, C, case.names, coef,
+ coefficients, complete.cases, confint, confint.default,
+ constrOptim, contr.SAS, contr.helmert, contr.poly, contr.sum,
contr.treatment, contrasts, "contrasts<-", convolve,
cooks.distance, cor, cov, cov.wt, cov2cor, covratio, cycle, D,
dbeta, dbinom, dcauchy, dchisq, delete.response, deltat,
@@ -22,7 +28,7 @@ export(add.scope, add1, addmargins, aggregate, aggregate.data.frame,
dunif, dweibull, dwilcox, eff.aovlist, effects, estVar, end,
expand.model.frame, extractAIC, factor.scope, family, fft,
fitted, fitted.values, fivenum, formula, frequency, ftable,
- Gamma, gaussian, get_all_vars, glm, glm.control, glm.fit,
+ Gamma, gaussian, get_all_vars, getCall, glm, glm.control, glm.fit,
hasTsp, hat, hatvalues, hatvalues.lm, influence,
influence.measures, integrate, interaction.plot,
inverse.gaussian, IQR, is.empty.model, is.mts, is.ts, lines.ts,
@@ -34,31 +40,31 @@ export(add.scope, add1, addmargins, aggregate, aggregate.data.frame,
model.matrix.default, model.matrix.lm, model.offset,
model.response, model.tables, model.weights, mvfft, na.action,
na.exclude, na.fail, na.omit, na.pass, napredict, naprint,
- naresid, nextn, nlm, nlminb, offset, optim, optimise, optimize,
- p.adjust, p.adjust.methods, pbeta, pbinom, pcauchy, pchisq,
- pexp, pf, pgamma, pgeom, phyper, plnorm, plogis, plot.density,
- plot.lm, plot.mlm, plot.ts, plot.TukeyHSD, pnbinom, pnorm,
- poisson, poly, polym, power, ppoints, ppois, predict,
- predict.glm, predict.lm, predict.mlm, predict.poly, preplot,
- printCoefmat, print.anova, print.density, print.family,
- print.formula, print.ftable, print.glm, print.infl,
- print.integrate, print.lm, print.logLik, print.terms, print.ts,
- profile, proj, psignrank, pt, ptukey, punif, pweibull, pwilcox,
- qbeta, qbinom, qcauchy, qchisq, qexp, qf, qgamma, qgeom,
- qhyper, qlnorm, qlogis, qnbinom, qnorm, qpois, qqline, qqnorm,
- qqnorm.default, qqplot, qsignrank, qt, qtukey, quantile,
- quantile.default, quasi, quasibinomial, quasipoisson, qunif,
- qweibull, qwilcox, r2dtable, rbeta, rbinom, rcauchy, rchisq,
- read.ftable, reformulate, relevel, replications, reshape,
- resid, residuals, residuals.default, residuals.glm,
- residuals.lm, rexp, rf, rgamma, rgeom, rhyper, rlnorm, rlogis,
- rmultinom, rnbinom, rnorm, rpois, rsignrank, rstandard,
- rstandard.glm, rstandard.lm, rstudent, rstudent.glm,
- rstudent.lm, rt, runif, rweibull, rwilcox, sd, se.contrast,
- simulate, spline, splinefun, splinefunH, SSD, start, stat.anova, step,
- summary.aov, summary.aovlist, summary.glm, summary.infl,
- summary.lm, summary.manova, summary.mlm, symnum, termplot,
- terms, terms.aovlist, terms.default, terms.formula,
+ naresid, nextn, nlm, nlminb, nobs, offset, optim, optimHess, optimise,
+ optimize, p.adjust, p.adjust.methods, pbeta, pbinom, pcauchy,
+ pchisq, pexp, pf, pgamma, pgeom, phyper, plnorm, plogis,
+ plot.density, plot.lm, plot.mlm, plot.ts, plot.TukeyHSD,
+ pnbinom, pnorm, poisson, poly, polym, power, ppoints, ppois,
+ predict, predict.glm, predict.lm, predict.mlm, predict.poly,
+ preplot, printCoefmat, print.anova, print.density,
+ print.family, print.formula, print.ftable, print.glm,
+ print.infl, print.integrate, print.lm, print.logLik,
+ print.terms, print.ts, profile, proj, psignrank, pt, ptukey,
+ punif, pweibull, pwilcox, qbeta, qbinom, qcauchy, qchisq, qexp,
+ qf, qgamma, qgeom, qhyper, qlnorm, qlogis, qnbinom, qnorm,
+ qpois, qqline, qqnorm, qqnorm.default, qqplot, qsignrank, qt,
+ qtukey, quantile, quantile.default, quasi, quasibinomial,
+ quasipoisson, qunif, qweibull, qwilcox, r2dtable, rbeta,
+ rbinom, rcauchy, rchisq, read.ftable, reformulate, relevel,
+ replications, reshape, resid, residuals, residuals.default,
+ residuals.glm, residuals.lm, rexp, rf, rgamma, rgeom, rhyper,
+ rlnorm, rlogis, rmultinom, rnbinom, rnorm, rpois, rsignrank,
+ rstandard, rstandard.glm, rstandard.lm, rstudent, rstudent.glm,
+ rstudent.lm, rt, runif, rweibull, rwilcox, rWishart, sd, se.contrast,
+ simulate, spline, splinefun, splinefunH, SSD, start,
+ stat.anova, step, summary.aov, summary.aovlist, summary.glm,
+ summary.infl, summary.lm, summary.manova, summary.mlm, symnum,
+ termplot, terms, terms.aovlist, terms.default, terms.formula,
terms.terms, time, ts, tsp, "tsp<-", TukeyHSD, TukeyHSD.aov,
uniroot, update, update.default, update.formula, var,
variable.names, vcov, weighted.mean, weighted.residuals,
@@ -75,12 +81,6 @@ export(mauchley.test)
export(reshapeWide, reshapeLong, print.coefmat, anovalist.lm, lm.fit.null,
lm.wfit.null, glm.fit.null)
-import(graphics)
-## 'graphics' imports 'grDevices' completely; hence this is currently a noop:
-importFrom(grDevices, dev.interactive, palette, extendrange, xy.coords)
-
-importFrom(utils, str)
-
## register all the methods for generics elsewhere in case namespace is
## loaded but not currently attached.
S3method("[", acf)
@@ -92,14 +92,18 @@ S3method(add1, default)
S3method(add1, glm)
S3method(add1, lm)
S3method(add1, mlm)
+S3method("aggregate", "formula")
S3method(AIC, default)
S3method(AIC, logLik)
S3method(alias, formula)
S3method(alias, lm)
+S3method(as.data.frame, aovproj)
S3method(as.data.frame, ftable)
S3method(as.data.frame, logLik)
S3method(as.table, ftable)
S3method(as.ts, default)
+S3method(BIC, default)
+S3method(BIC, logLik)
S3method(case.names, default)
S3method(case.names, lm)
S3method(cbind, ts)
@@ -142,6 +146,7 @@ S3method(extractAIC, survreg)
S3method(family, glm)
S3method(family, lm)
S3method(fitted, default)
+S3method(fitted, kmeans)
S3method(format, ftable)
S3method(formula, character)
S3method(formula, data.frame)
@@ -153,6 +158,7 @@ S3method(formula, terms)
S3method(frequency, default)
S3method(ftable, default)
S3method(ftable, formula)
+S3method(getCall, default)
S3method(influence, glm)
S3method(influence, lm)
S3method(labels, dist)
@@ -160,6 +166,7 @@ S3method(labels, lm)
S3method(labels, terms)
S3method(logLik, glm)
S3method(logLik, lm)
+S3method(logLik, logLik)
S3method(makepredictcall, default)
S3method(makepredictcall, poly)
S3method(mauchly.test, SSD)
@@ -182,6 +189,11 @@ S3method(naprint, exclude)
S3method(naprint, omit)
S3method(naresid, default)
S3method(naresid, exclude)
+S3method(nobs, default)
+S3method(nobs, glm)
+S3method(nobs, lm)
+S3method(nobs, logLik)
+S3method(nobs, nls)
S3method(Ops, ts)
S3method(plot, density)
S3method(plot, lm)
@@ -226,12 +238,14 @@ S3method(proj, aov)
S3method(proj, aovlist)
S3method(proj, default)
S3method(proj, lm)
+S3method(qr, lm)
S3method(quantile, default)
+S3method(quantile, ecdf)
+S3method(quantile, POSIXt)
S3method(relevel, default)
S3method(relevel, factor)
S3method(relevel, ordered)
-S3method(reorder, factor)
-S3method(reorder, character)
+S3method(reorder, default)
S3method(se.contrast, aov)
S3method(se.contrast, aovlist)
S3method(simulate, lm)
@@ -256,6 +270,8 @@ S3method(variable.names, lm)
S3method(vcov, glm)
#S3method(vcov, gls)
S3method(vcov, lm)
+S3method(vcov, summary.lm)
+S3method(vcov, summary.glm)
S3method(vcov, mlm)
#S3method(vcov, lme)
S3method(weights, default)
@@ -359,6 +375,7 @@ export(as.dendrogram, dendrapply, heatmap, is.leaf,
S3method("[[", dendrogram)
S3method(as.dendrogram, hclust)
+S3method(as.hclust, dendrogram)
S3method(as.hclust, default)
S3method(as.hclust, twins)
S3method(as.matrix, dist)
@@ -369,6 +386,7 @@ S3method(cut, dendrogram)
S3method(format, dist)
S3method(identify, hclust)
S3method(labels, dendrogram)
+S3method(merge, dendrogram)
S3method(plot, dendrogram)
S3method(plot, hclust)
S3method(plot, prcomp)
@@ -527,3 +545,8 @@ S3method(summary, stepfun)
S3method(as.dist, default)
S3method(cophenetic, default)
S3method(cophenetic, dendrogram)
+S3method(weighted.mean, Date)
+S3method(weighted.mean, default)
+S3method(weighted.mean, difftime)
+S3method(weighted.mean, POSIXct)
+S3method(weighted.mean, POSIXlt)
diff --git a/win32/deps/library/stats/R/stats b/win32/deps/library/stats/R/stats
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/stats/R/stats
+++ b/win32/deps/library/stats/R/stats
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/stats/R/stats.rdb b/win32/deps/library/stats/R/stats.rdb
index c1b26f8..43850f1 100644
Binary files a/win32/deps/library/stats/R/stats.rdb and b/win32/deps/library/stats/R/stats.rdb differ
diff --git a/win32/deps/library/stats/R/stats.rdx b/win32/deps/library/stats/R/stats.rdx
index 773ccf5..02f5a1c 100644
Binary files a/win32/deps/library/stats/R/stats.rdx and b/win32/deps/library/stats/R/stats.rdx differ
diff --git a/win32/deps/library/stats/demo/glm.vr.R b/win32/deps/library/stats/demo/glm.vr.R
index e0024de..37393ac 100644
--- a/win32/deps/library/stats/demo/glm.vr.R
+++ b/win32/deps/library/stats/demo/glm.vr.R
@@ -1,3 +1,5 @@
+# Copyright (C) 1997-2009 The R Core Team
+
#### -*- R -*-
require(stats)
Fr <- c(68,42,42,30, 37,52,24,43,
diff --git a/win32/deps/library/stats/demo/lm.glm.R b/win32/deps/library/stats/demo/lm.glm.R
index 36b5c73..d291e53 100644
--- a/win32/deps/library/stats/demo/lm.glm.R
+++ b/win32/deps/library/stats/demo/lm.glm.R
@@ -2,6 +2,9 @@
### By Annette Dobson
###
### == with some additions ==
+
+# Copyright (C) 1997-2008 The R Core Team
+
require(stats); require(graphics)
## Plant Weight Data (Page 9)
@@ -9,8 +12,8 @@ ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
group <- gl(2,10, labels=c("Ctl","Trt"))
weight <- c(ctl,trt)
-anova(lm(weight~group))
-summary(lm(weight~group-1))
+anova (lm(weight~group))
+summary(lm(weight~group -1))
## Birth Weight Data (Page 14)
@@ -20,11 +23,13 @@ birthw <- c(2968, 2795, 3163, 2925, 2625, 2847, 3292, 3473, 2628, 3176,
3421, 2975, 3317, 2729, 2935, 2754, 3210, 2817, 3126, 2539,
2412, 2991, 2875, 3231)
sex <- gl(2,12, labels=c("M","F"))
-plot(age, birthw, col=as.numeric(sex), main="Dobson's Birth Weight Data")
-lines(lowess(age[sex=='F'], birthw[sex=='F']), col=1)
-lines(lowess(age[sex=='M'], birthw[sex=='M']), col=2)
+plot(age, birthw, col=as.numeric(sex), pch=3*as.numeric(sex),
+ main="Dobson's Birth Weight Data")
+lines(lowess(age[sex=='M'], birthw[sex=='M']), col=1)
+lines(lowess(age[sex=='F'], birthw[sex=='F']), col=2)
+legend("topleft", levels(sex), col=1:2, pch=3*(1:2), lty=1, bty="n")
-summary(l1 <- lm(birthw ~ sex + age), correlation=TRUE)
+summary(l1 <- lm(birthw ~ sex + age), correlation=TRUE)
summary(l0 <- lm(birthw ~ sex + age -1), correlation=TRUE)
anova(l1,l0)
summary(li <- lm(birthw ~ sex + sex:age -1), correlation=TRUE)
@@ -41,19 +46,19 @@ anova(z0,zz)
## Poisson Regression Data (Page 42)
x <- c(-1,-1,0,0,0,0,1,1,1)
y <- c(2,3,6,7,8,9,10,12,15)
-summary(glm(y~x,family=poisson(link="identity")))
+summary(glm(y~x, family=poisson(link="identity")))
## Calorie Data (Page 45)
calorie <- data.frame(
- carb = c(33,40,37,27,30,43,34,48,30,38,
- 50,51,30,36,41,42,46,24,35,37),
- age = c(33,47,49,35,46,52,62,23,32,42,
- 31,61,63,40,50,64,56,61,48,28),
- wgt = c(100, 92,135,144,140,101, 95,101, 98,105,
- 108, 85,130,127,109,107,117,100,118,102),
- prot = c(14,15,18,12,15,15,14,17,15,14,
- 17,19,19,20,15,16,18,13,18,14))
+ carb = c(33,40,37,27,30,43,34,48,30,38,
+ 50,51,30,36,41,42,46,24,35,37),
+ age = c(33,47,49,35,46,52,62,23,32,42,
+ 31,61,63,40,50,64,56,61,48,28),
+ wgt = c(100, 92,135,144,140,101, 95,101, 98,105,
+ 108, 85,130,127,109,107,117,100,118,102),
+ prot = c(14,15,18,12,15,15,14,17,15,14,
+ 17,19,19,20,15,16,18,13,18,14))
summary(lmcal <- lm(carb~age+wgt+prot, data= calorie))
diff --git a/win32/deps/library/stats/demo/nlm.R b/win32/deps/library/stats/demo/nlm.R
index 42d9b8b..8b63e3b 100644
--- a/win32/deps/library/stats/demo/nlm.R
+++ b/win32/deps/library/stats/demo/nlm.R
@@ -1,3 +1,5 @@
+# Copyright (C) 1997-2009 The R Core Team
+
### Helical Valley Function
### Page 362 Dennis + Schnabel
@@ -15,8 +17,8 @@ f <- function(x) {
}
## explore surface {at x3 = 0}
-x <- seq(-1, 2, length=50)
-y <- seq(-1, 1, length=50)
+x <- seq(-1, 2, length.out=50)
+y <- seq(-1, 1, length.out=50)
z <- apply(as.matrix(expand.grid(x, y)), 1, function(x) f(c(x, 0)))
contour(x, y, matrix(log10(z), 50, 50))
str(nlm.f <- nlm(f, c(-1,0,0), hessian = TRUE))
@@ -36,8 +38,8 @@ fx <- function(x)
x1 <- x[,1]; x2 <- x[,2]
100*(x2 - x1*x1)^2 + (1-x1)^2
}
-x <- seq(-2, 2, length=100)
-y <- seq(-0.5, 1.5, length=100)
+x <- seq(-2, 2, length.out=100)
+y <- seq(-0.5, 1.5, length.out=100)
z <- fx(expand.grid(x, y))
op <- par(mfrow = c(2,1), mar = 0.1 + c(3,3,0,0))
contour(x, y, matrix(log10(z), length(x)))
@@ -47,7 +49,7 @@ points(rbind(nlm.f2$estim[1:2]), col = "red", pch = 20)
## Zoom in :
rect(0.9, 0.9, 1.1, 1.1, border = "orange", lwd = 2)
-x <- y <- seq(0.9, 1.1, length=100)
+x <- y <- seq(0.9, 1.1, length.out=100)
z <- fx(expand.grid(x, y))
contour(x, y, matrix(log10(z), length(x)))
mtext("zoomed in");box(col = "orange")
diff --git a/win32/deps/library/stats/demo/smooth.R b/win32/deps/library/stats/demo/smooth.R
index 187368a..563974f 100644
--- a/win32/deps/library/stats/demo/smooth.R
+++ b/win32/deps/library/stats/demo/smooth.R
@@ -1,4 +1,5 @@
### This used to be in example(smooth) before we had package-specific demos
+# Copyright (C) 1997-2009 The R Core Team
require(stats); require(graphics); require(datasets)
op <- par(mfrow = c(1,1))
diff --git a/win32/deps/library/stats/help/AnIndex b/win32/deps/library/stats/help/AnIndex
index ff3c0c6..86bef5a 100644
--- a/win32/deps/library/stats/help/AnIndex
+++ b/win32/deps/library/stats/help/AnIndex
@@ -13,6 +13,7 @@ addmargins addmargins
aggregate aggregate
aggregate.data.frame aggregate
aggregate.default aggregate
+aggregate.formula aggregate
aggregate.ts aggregate
AIC AIC
alias alias
@@ -55,6 +56,7 @@ as.dist.default dist
as.formula formula
as.hclust as.hclust
as.hclust.default as.hclust
+as.hclust.dendrogram dendrogram
as.hclust.twins as.hclust
as.matrix.dist dist
as.stepfun stepfun
@@ -67,6 +69,7 @@ bartlett.test bartlett.test
bartlett.test.default bartlett.test
bartlett.test.formula bartlett.test
Beta Beta
+BIC AIC
binom.test binom.test
Binomial Binomial
binomial family
@@ -89,7 +92,7 @@ cbind.ts ts
ccf acf
chisq.test chisq.test
Chisquare Chisquare
-clearNames clearNames
+clearNames stats-defunct
cmdscale cmdscale
coef coef
coefficients coef
@@ -159,6 +162,9 @@ diffinv diffinv
diffinv.default diffinv
diffinv.ts diffinv
dist dist
+distribution Distributions
+Distributions Distributions
+distributions Distributions
dlnorm Lognormal
dlogis Logistic
dmultinom Multinom
@@ -203,6 +209,7 @@ filter filter
fisher.test fisher.test
fitted fitted.values
fitted.default fitted.values
+fitted.kmeans kmeans
fitted.values fitted.values
fivenum fivenum
fligner.test fligner.test
@@ -228,6 +235,8 @@ Gamma family
GammaDist GammaDist
gaussian family
Geometric Geometric
+getCall update
+getCall.default update
getInitial getInitial
getInitial.default getInitial
getInitial.formula getInitial
@@ -325,6 +334,7 @@ mcnemar.test mcnemar.test
median median
median.default median
medpolish medpolish
+merge.dendrogram dendrogram
model.extract model.extract
model.frame model.frame
model.frame.aovlist model.frame
@@ -388,12 +398,15 @@ NLSstLfAsymptote NLSstLfAsymptote
NLSstLfAsymptote.sortedXyData NLSstLfAsymptote
NLSstRtAsymptote NLSstRtAsymptote
NLSstRtAsymptote.sortedXyData NLSstRtAsymptote
+nobs nobs
+nobs.default nobs
Normal Normal
numericDeriv numericDeriv
offset offset
oneway.test oneway.test
Ops.ts ts
optim optim
+optimHess optim
optimise optimize
optimize optimize
order.dendrogram order.dendrogram
@@ -566,6 +579,7 @@ quade.test.default quade.test
quade.test.formula quade.test
quantile quantile
quantile.default quantile
+quantile.ecdf ecdf
quasi family
quasibinomial family
quasipoisson family
@@ -585,9 +599,8 @@ relevel.default relevel
relevel.factor relevel
relevel.ordered relevel
reorder reorder.factor
-reorder.character reorder.factor
+reorder.default reorder.factor
reorder.dendrogram reorder.dendrogram
-reorder.factor reorder.factor
replications replications
reshape reshape
reshapeLong stats-defunct
@@ -624,6 +637,7 @@ runif Uniform
runmed runmed
rweibull Weibull
rwilcox Wilcoxon
+rWishart rWishart
SafePrediction makepredictcall
scatter.smooth scatter.smooth
screeplot screeplot
@@ -735,11 +749,14 @@ vcov.glm vcov
vcov.gls vcov
vcov.lm vcov
vcov.lme vcov
+vcov.summary.glm vcov
+vcov.summary.lm vcov
Weibull Weibull
weighted.mean weighted.mean
+weighted.mean.default weighted.mean
weighted.residuals weighted.residuals
-weights lm.summaries
-weights.default lm.summaries
+weights weights
+weights.default weights
weights.glm glm
wilcox.test wilcox.test
wilcox.test.default wilcox.test
diff --git a/win32/deps/library/stats/help/aliases.rds b/win32/deps/library/stats/help/aliases.rds
new file mode 100644
index 0000000..0325d05
Binary files /dev/null and b/win32/deps/library/stats/help/aliases.rds differ
diff --git a/win32/deps/library/stats/help/paths.rds b/win32/deps/library/stats/help/paths.rds
new file mode 100644
index 0000000..e2f2ddc
Binary files /dev/null and b/win32/deps/library/stats/help/paths.rds differ
diff --git a/win32/deps/library/stats/help/stats.rdb b/win32/deps/library/stats/help/stats.rdb
new file mode 100644
index 0000000..a60a2d8
Binary files /dev/null and b/win32/deps/library/stats/help/stats.rdb differ
diff --git a/win32/deps/library/stats/help/stats.rdx b/win32/deps/library/stats/help/stats.rdx
new file mode 100644
index 0000000..60f3d89
Binary files /dev/null and b/win32/deps/library/stats/help/stats.rdx differ
diff --git a/win32/deps/library/stats/html/00Index.html b/win32/deps/library/stats/html/00Index.html
new file mode 100644
index 0000000..b649900
--- /dev/null
+++ b/win32/deps/library/stats/html/00Index.html
@@ -0,0 +1,1348 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: The R Stats Package</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> The R Stats Package
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘stats’ version 2.15.2</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+<li><a href="../demo">Code demos</a>. Use <a href="../../utils/help/demo">demo()</a> to run them.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<p align="center">
+<a href="# "> </a>
+<a href="#A">A</a>
+<a href="#B">B</a>
+<a href="#C">C</a>
+<a href="#D">D</a>
+<a href="#E">E</a>
+<a href="#F">F</a>
+<a href="#G">G</a>
+<a href="#H">H</a>
+<a href="#I">I</a>
+<a href="#K">K</a>
+<a href="#L">L</a>
+<a href="#M">M</a>
+<a href="#N">N</a>
+<a href="#O">O</a>
+<a href="#P">P</a>
+<a href="#Q">Q</a>
+<a href="#R">R</a>
+<a href="#S">S</a>
+<a href="#T">T</a>
+<a href="#U">U</a>
+<a href="#V">V</a>
+<a href="#W">W</a>
+<a href="#X">X</a>
+<a href="#misc">misc</a>
+</p>
+
+<table width="100%">
+<tr><td width="25%"><a href="stats-package.html">stats-package</a></td>
+<td>The R Stats Package</td></tr>
+</table>
+
+<h2><a name="A">-- A --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="acf.html">acf</a></td>
+<td>Auto- and Cross- Covariance and -Correlation Function Estimation</td></tr>
+<tr><td width="25%"><a href="acf2AR.html">acf2AR</a></td>
+<td>Compute an AR Process Exactly Fitting an ACF</td></tr>
+<tr><td width="25%"><a href="factor.scope.html">add.scope</a></td>
+<td>Compute Allowed Changes in Adding to or Dropping from a Formula</td></tr>
+<tr><td width="25%"><a href="add1.html">add1</a></td>
+<td>Add or Drop All Possible Single Terms to a Model</td></tr>
+<tr><td width="25%"><a href="addmargins.html">addmargins</a></td>
+<td>Puts Arbitrary Margins on Multidimensional Tables or Arrays</td></tr>
+<tr><td width="25%"><a href="aggregate.html">aggregate</a></td>
+<td>Compute Summary Statistics of Data Subsets</td></tr>
+<tr><td width="25%"><a href="AIC.html">AIC</a></td>
+<td>Akaike's An Information Criterion</td></tr>
+<tr><td width="25%"><a href="alias.html">alias</a></td>
+<td>Find Aliases (Dependencies) in a Model</td></tr>
+<tr><td width="25%"><a href="anova.html">anova</a></td>
+<td>Anova Tables</td></tr>
+<tr><td width="25%"><a href="anova.glm.html">anova.glm</a></td>
+<td>Analysis of Deviance for Generalized Linear Model Fits</td></tr>
+<tr><td width="25%"><a href="anova.lm.html">anova.lm</a></td>
+<td>ANOVA for Linear Model Fits</td></tr>
+<tr><td width="25%"><a href="anova.mlm.html">anova.mlm</a></td>
+<td>Comparisons between Multivariate Linear Models</td></tr>
+<tr><td width="25%"><a href="ansari.test.html">ansari.test</a></td>
+<td>Ansari-Bradley Test</td></tr>
+<tr><td width="25%"><a href="aov.html">aov</a></td>
+<td>Fit an Analysis of Variance Model</td></tr>
+<tr><td width="25%"><a href="approxfun.html">approx</a></td>
+<td>Interpolation Functions</td></tr>
+<tr><td width="25%"><a href="approxfun.html">approxfun</a></td>
+<td>Interpolation Functions</td></tr>
+<tr><td width="25%"><a href="ar.html">ar</a></td>
+<td>Fit Autoregressive Models to Time Series</td></tr>
+<tr><td width="25%"><a href="ar.html">ar.burg</a></td>
+<td>Fit Autoregressive Models to Time Series</td></tr>
+<tr><td width="25%"><a href="ar.html">ar.burg.default</a></td>
+<td>Fit Autoregressive Models to Time Series</td></tr>
+<tr><td width="25%"><a href="ar.html">ar.mle</a></td>
+<td>Fit Autoregressive Models to Time Series</td></tr>
+<tr><td width="25%"><a href="ar.ols.html">ar.ols</a></td>
+<td>Fit Autoregressive Models to Time Series by OLS</td></tr>
+<tr><td width="25%"><a href="ar.html">ar.yw</a></td>
+<td>Fit Autoregressive Models to Time Series</td></tr>
+<tr><td width="25%"><a href="ar.html">ar.yw.default</a></td>
+<td>Fit Autoregressive Models to Time Series</td></tr>
+<tr><td width="25%"><a href="arima.html">arima</a></td>
+<td>ARIMA Modelling of Time Series</td></tr>
+<tr><td width="25%"><a href="arima.sim.html">arima.sim</a></td>
+<td>Simulate from an ARIMA Model</td></tr>
+<tr><td width="25%"><a href="arima0.html">arima0</a></td>
+<td>ARIMA Modelling of Time Series - Preliminary Version</td></tr>
+<tr><td width="25%"><a href="ARMAacf.html">ARMAacf</a></td>
+<td>Compute Theoretical ACF for an ARMA Process</td></tr>
+<tr><td width="25%"><a href="ARMAtoMA.html">ARMAtoMA</a></td>
+<td>Convert ARMA Process to Infinite MA Process</td></tr>
+<tr><td width="25%"><a href="dendrogram.html">as.dendrogram</a></td>
+<td>General Tree Structures</td></tr>
+<tr><td width="25%"><a href="dist.html">as.dist</a></td>
+<td>Distance Matrix Computation</td></tr>
+<tr><td width="25%"><a href="formula.html">as.formula</a></td>
+<td>Model Formulae</td></tr>
+<tr><td width="25%"><a href="as.hclust.html">as.hclust</a></td>
+<td>Convert Objects to Class hclust</td></tr>
+<tr><td width="25%"><a href="dendrogram.html">as.hclust.dendrogram</a></td>
+<td>General Tree Structures</td></tr>
+<tr><td width="25%"><a href="dist.html">as.matrix.dist</a></td>
+<td>Distance Matrix Computation</td></tr>
+<tr><td width="25%"><a href="stepfun.html">as.stepfun</a></td>
+<td>Step Function Class</td></tr>
+<tr><td width="25%"><a href="ts.html">as.ts</a></td>
+<td>Time-Series Objects</td></tr>
+<tr><td width="25%"><a href="asOneSidedFormula.html">asOneSidedFormula</a></td>
+<td>Convert to One-Sided Formula</td></tr>
+<tr><td width="25%"><a href="ave.html">ave</a></td>
+<td>Group Averages Over Level Combinations of Factors</td></tr>
+</table>
+
+<h2><a name="B">-- B --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="kernel.html">bandwidth.kernel</a></td>
+<td>Smoothing Kernel Objects</td></tr>
+<tr><td width="25%"><a href="bartlett.test.html">bartlett.test</a></td>
+<td>Bartlett Test of Homogeneity of Variances</td></tr>
+<tr><td width="25%"><a href="Beta.html">Beta</a></td>
+<td>The Beta Distribution</td></tr>
+<tr><td width="25%"><a href="AIC.html">BIC</a></td>
+<td>Akaike's An Information Criterion</td></tr>
+<tr><td width="25%"><a href="binom.test.html">binom.test</a></td>
+<td>Exact Binomial Test</td></tr>
+<tr><td width="25%"><a href="Binomial.html">Binomial</a></td>
+<td>The Binomial Distribution</td></tr>
+<tr><td width="25%"><a href="family.html">binomial</a></td>
+<td>Family Objects for Models</td></tr>
+<tr><td width="25%"><a href="biplot.html">biplot</a></td>
+<td>Biplot of Multivariate Data</td></tr>
+<tr><td width="25%"><a href="biplot.princomp.html">biplot.princomp</a></td>
+<td>Biplot for Principal Components</td></tr>
+<tr><td width="25%"><a href="box.test.html">Box.test</a></td>
+<td>Box-Pierce and Ljung-Box Tests</td></tr>
+<tr><td width="25%"><a href="bandwidth.html">bw.bcv</a></td>
+<td>Bandwidth Selectors for Kernel Density Estimation</td></tr>
+<tr><td width="25%"><a href="bandwidth.html">bw.nrd</a></td>
+<td>Bandwidth Selectors for Kernel Density Estimation</td></tr>
+<tr><td width="25%"><a href="bandwidth.html">bw.nrd0</a></td>
+<td>Bandwidth Selectors for Kernel Density Estimation</td></tr>
+<tr><td width="25%"><a href="bandwidth.html">bw.SJ</a></td>
+<td>Bandwidth Selectors for Kernel Density Estimation</td></tr>
+<tr><td width="25%"><a href="bandwidth.html">bw.ucv</a></td>
+<td>Bandwidth Selectors for Kernel Density Estimation</td></tr>
+</table>
+
+<h2><a name="C">-- C --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="zC.html">C</a></td>
+<td>Sets Contrasts for a Factor</td></tr>
+<tr><td width="25%"><a href="cancor.html">cancor</a></td>
+<td>Canonical Correlations</td></tr>
+<tr><td width="25%"><a href="case.names.html">case.names</a></td>
+<td>Case and Variable Names of Fitted Models</td></tr>
+<tr><td width="25%"><a href="case.names.html">case.names.lm</a></td>
+<td>Case and Variable Names of Fitted Models</td></tr>
+<tr><td width="25%"><a href="Cauchy.html">Cauchy</a></td>
+<td>The Cauchy Distribution</td></tr>
+<tr><td width="25%"><a href="ts.html">cbind.ts</a></td>
+<td>Time-Series Objects</td></tr>
+<tr><td width="25%"><a href="acf.html">ccf</a></td>
+<td>Auto- and Cross- Covariance and -Correlation Function Estimation</td></tr>
+<tr><td width="25%"><a href="chisq.test.html">chisq.test</a></td>
+<td>Pearson's Chi-squared Test for Count Data</td></tr>
+<tr><td width="25%"><a href="Chisquare.html">Chisquare</a></td>
+<td>The (non-central) Chi-Squared Distribution</td></tr>
+<tr><td width="25%"><a href="cmdscale.html">cmdscale</a></td>
+<td>Classical (Metric) Multidimensional Scaling</td></tr>
+<tr><td width="25%"><a href="coef.html">coef</a></td>
+<td>Extract Model Coefficients</td></tr>
+<tr><td width="25%"><a href="coef.html">coefficients</a></td>
+<td>Extract Model Coefficients</td></tr>
+<tr><td width="25%"><a href="complete.cases.html">complete.cases</a></td>
+<td>Find Complete Cases</td></tr>
+<tr><td width="25%"><a href="confint.html">confint</a></td>
+<td>Confidence Intervals for Model Parameters</td></tr>
+<tr><td width="25%"><a href="constrOptim.html">constrOptim</a></td>
+<td>Linearly Constrained Optimization</td></tr>
+<tr><td width="25%"><a href="contrast.html">contr.helmert</a></td>
+<td>(Possibly Sparse) Contrast Matrices</td></tr>
+<tr><td width="25%"><a href="contrast.html">contr.poly</a></td>
+<td>(Possibly Sparse) Contrast Matrices</td></tr>
+<tr><td width="25%"><a href="contrast.html">contr.SAS</a></td>
+<td>(Possibly Sparse) Contrast Matrices</td></tr>
+<tr><td width="25%"><a href="contrast.html">contr.sum</a></td>
+<td>(Possibly Sparse) Contrast Matrices</td></tr>
+<tr><td width="25%"><a href="contrast.html">contr.treatment</a></td>
+<td>(Possibly Sparse) Contrast Matrices</td></tr>
+<tr><td width="25%"><a href="contrasts.html">contrasts</a></td>
+<td>Get and Set Contrast Matrices</td></tr>
+<tr><td width="25%"><a href="convolve.html">convolve</a></td>
+<td>Convolution of Sequences via FFT</td></tr>
+<tr><td width="25%"><a href="influence.measures.html">cooks.distance</a></td>
+<td>Regression Deletion Diagnostics</td></tr>
+<tr><td width="25%"><a href="influence.measures.html">cooks.distance.lm</a></td>
+<td>Regression Deletion Diagnostics</td></tr>
+<tr><td width="25%"><a href="cophenetic.html">cophenetic</a></td>
+<td>Cophenetic Distances for a Hierarchical Clustering</td></tr>
+<tr><td width="25%"><a href="cor.html">cor</a></td>
+<td>Correlation, Variance and Covariance (Matrices)</td></tr>
+<tr><td width="25%"><a href="cor.test.html">cor.test</a></td>
+<td>Test for Association/Correlation Between Paired Samples</td></tr>
+<tr><td width="25%"><a href="cor.html">cov</a></td>
+<td>Correlation, Variance and Covariance (Matrices)</td></tr>
+<tr><td width="25%"><a href="cov.wt.html">cov.wt</a></td>
+<td>Weighted Covariance Matrices</td></tr>
+<tr><td width="25%"><a href="cor.html">cov2cor</a></td>
+<td>Correlation, Variance and Covariance (Matrices)</td></tr>
+<tr><td width="25%"><a href="influence.measures.html">covratio</a></td>
+<td>Regression Deletion Diagnostics</td></tr>
+<tr><td width="25%"><a href="cpgram.html">cpgram</a></td>
+<td>Plot Cumulative Periodogram</td></tr>
+<tr><td width="25%"><a href="dendrogram.html">cut.dendrogram</a></td>
+<td>General Tree Structures</td></tr>
+<tr><td width="25%"><a href="cutree.html">cutree</a></td>
+<td>Cut a Tree into Groups of Data</td></tr>
+<tr><td width="25%"><a href="time.html">cycle</a></td>
+<td>Sampling Times of Time Series</td></tr>
+</table>
+
+<h2><a name="D">-- D --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="deriv.html">D</a></td>
+<td>Symbolic and Algorithmic Derivatives of Simple Expressions</td></tr>
+<tr><td width="25%"><a href="Beta.html">dbeta</a></td>
+<td>The Beta Distribution</td></tr>
+<tr><td width="25%"><a href="Binomial.html">dbinom</a></td>
+<td>The Binomial Distribution</td></tr>
+<tr><td width="25%"><a href="Cauchy.html">dcauchy</a></td>
+<td>The Cauchy Distribution</td></tr>
+<tr><td width="25%"><a href="Chisquare.html">dchisq</a></td>
+<td>The (non-central) Chi-Squared Distribution</td></tr>
+<tr><td width="25%"><a href="decompose.html">decompose</a></td>
+<td>Classical Seasonal Decomposition by Moving Averages</td></tr>
+<tr><td width="25%"><a href="delete.response.html">delete.response</a></td>
+<td>Modify Terms Objects</td></tr>
+<tr><td width="25%"><a href="time.html">deltat</a></td>
+<td>Sampling Times of Time Series</td></tr>
+<tr><td width="25%"><a href="dendrapply.html">dendrapply</a></td>
+<td>Apply a Function to All Nodes of a Dendrogram</td></tr>
+<tr><td width="25%"><a href="dendrogram.html">dendrogram</a></td>
+<td>General Tree Structures</td></tr>
+<tr><td width="25%"><a href="density.html">density</a></td>
+<td>Kernel Density Estimation</td></tr>
+<tr><td width="25%"><a href="deriv.html">deriv</a></td>
+<td>Symbolic and Algorithmic Derivatives of Simple Expressions</td></tr>
+<tr><td width="25%"><a href="deriv.html">deriv3</a></td>
+<td>Symbolic and Algorithmic Derivatives of Simple Expressions</td></tr>
+<tr><td width="25%"><a href="deviance.html">deviance</a></td>
+<td>Model Deviance</td></tr>
+<tr><td width="25%"><a href="Exponential.html">dexp</a></td>
+<td>The Exponential Distribution</td></tr>
+<tr><td width="25%"><a href="Fdist.html">df</a></td>
+<td>The F Distribution</td></tr>
+<tr><td width="25%"><a href="kernel.html">df.kernel</a></td>
+<td>Smoothing Kernel Objects</td></tr>
+<tr><td width="25%"><a href="df.residual.html">df.residual</a></td>
+<td>Residual Degrees-of-Freedom</td></tr>
+<tr><td width="25%"><a href="influence.measures.html">dfbeta</a></td>
+<td>Regression Deletion Diagnostics</td></tr>
+<tr><td width="25%"><a href="influence.measures.html">dfbetas</a></td>
+<td>Regression Deletion Diagnostics</td></tr>
+<tr><td width="25%"><a href="influence.measures.html">dffits</a></td>
+<td>Regression Deletion Diagnostics</td></tr>
+<tr><td width="25%"><a href="GammaDist.html">dgamma</a></td>
+<td>The Gamma Distribution</td></tr>
+<tr><td width="25%"><a href="Geometric.html">dgeom</a></td>
+<td>The Geometric Distribution</td></tr>
+<tr><td width="25%"><a href="Hypergeometric.html">dhyper</a></td>
+<td>The Hypergeometric Distribution</td></tr>
+<tr><td width="25%"><a href="ts-methods.html">diff.ts</a></td>
+<td>Methods for Time Series Objects</td></tr>
+<tr><td width="25%"><a href="diffinv.html">diffinv</a></td>
+<td>Discrete Integration: Inverse of Differencing</td></tr>
+<tr><td width="25%"><a href="dist.html">dist</a></td>
+<td>Distance Matrix Computation</td></tr>
+<tr><td width="25%"><a href="Distributions.html">distribution</a></td>
+<td>Distributions in the stats package</td></tr>
+<tr><td width="25%"><a href="Distributions.html">Distributions</a></td>
+<td>Distributions in the stats package</td></tr>
+<tr><td width="25%"><a href="Distributions.html">distributions</a></td>
+<td>Distributions in the stats package</td></tr>
+<tr><td width="25%"><a href="Lognormal.html">dlnorm</a></td>
+<td>The Log Normal Distribution</td></tr>
+<tr><td width="25%"><a href="Logistic.html">dlogis</a></td>
+<td>The Logistic Distribution</td></tr>
+<tr><td width="25%"><a href="Multinom.html">dmultinom</a></td>
+<td>The Multinomial Distribution</td></tr>
+<tr><td width="25%"><a href="NegBinomial.html">dnbinom</a></td>
+<td>The Negative Binomial Distribution</td></tr>
+<tr><td width="25%"><a href="Normal.html">dnorm</a></td>
+<td>The Normal Distribution</td></tr>
+<tr><td width="25%"><a href="Poisson.html">dpois</a></td>
+<td>The Poisson Distribution</td></tr>
+<tr><td width="25%"><a href="factor.scope.html">drop.scope</a></td>
+<td>Compute Allowed Changes in Adding to or Dropping from a Formula</td></tr>
+<tr><td width="25%"><a href="delete.response.html">drop.terms</a></td>
+<td>Modify Terms Objects</td></tr>
+<tr><td width="25%"><a href="add1.html">drop1</a></td>
+<td>Add or Drop All Possible Single Terms to a Model</td></tr>
+<tr><td width="25%"><a href="SignRank.html">dsignrank</a></td>
+<td>Distribution of the Wilcoxon Signed Rank Statistic</td></tr>
+<tr><td width="25%"><a href="TDist.html">dt</a></td>
+<td>The Student t Distribution</td></tr>
+<tr><td width="25%"><a href="dummy.coef.html">dummy.coef</a></td>
+<td>Extract Coefficients in Original Coding</td></tr>
+<tr><td width="25%"><a href="dummy.coef.html">dummy.coef.lm</a></td>
+<td>Extract Coefficients in Original Coding</td></tr>
+<tr><td width="25%"><a href="Uniform.html">dunif</a></td>
+<td>The Uniform Distribution</td></tr>
+<tr><td width="25%"><a href="Weibull.html">dweibull</a></td>
+<td>The Weibull Distribution</td></tr>
+<tr><td width="25%"><a href="Wilcoxon.html">dwilcox</a></td>
+<td>Distribution of the Wilcoxon Rank Sum Statistic</td></tr>
+</table>
+
+<h2><a name="E">-- E --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="ecdf.html">ecdf</a></td>
+<td>Empirical Cumulative Distribution Function</td></tr>
+<tr><td width="25%"><a href="eff.aovlist.html">eff.aovlist</a></td>
+<td>Compute Efficiencies of Multistratum Analysis of Variance</td></tr>
+<tr><td width="25%"><a href="effects.html">effects</a></td>
+<td>Effects from Fitted Model</td></tr>
+<tr><td width="25%"><a href="embed.html">embed</a></td>
+<td>Embedding a Time Series</td></tr>
+<tr><td width="25%"><a href="start.html">end</a></td>
+<td>Encode the Terminal Times of Time Series</td></tr>
+<tr><td width="25%"><a href="aov.html">Error</a></td>
+<td>Fit an Analysis of Variance Model</td></tr>
+<tr><td width="25%"><a href="SSD.html">estVar</a></td>
+<td>SSD Matrix and Estimated Variance Matrix in Multivariate Models</td></tr>
+<tr><td width="25%"><a href="expand.model.frame.html">expand.model.frame</a></td>
+<td>Add new variables to a model frame</td></tr>
+<tr><td width="25%"><a href="Exponential.html">Exponential</a></td>
+<td>The Exponential Distribution</td></tr>
+<tr><td width="25%"><a href="extractAIC.html">extractAIC</a></td>
+<td>Extract AIC from a Fitted Model</td></tr>
+</table>
+
+<h2><a name="F">-- F --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="factanal.html">factanal</a></td>
+<td>Factor Analysis</td></tr>
+<tr><td width="25%"><a href="factor.scope.html">factor.scope</a></td>
+<td>Compute Allowed Changes in Adding to or Dropping from a Formula</td></tr>
+<tr><td width="25%"><a href="family.html">family</a></td>
+<td>Family Objects for Models</td></tr>
+<tr><td width="25%"><a href="glm.summaries.html">family.glm</a></td>
+<td>Accessing Generalized Linear Model Fits</td></tr>
+<tr><td width="25%"><a href="lm.summaries.html">family.lm</a></td>
+<td>Accessing Linear Model Fits</td></tr>
+<tr><td width="25%"><a href="Fdist.html">FDist</a></td>
+<td>The F Distribution</td></tr>
+<tr><td width="25%"><a href="fft.html">fft</a></td>
+<td>Fast Discrete Fourier Transform</td></tr>
+<tr><td width="25%"><a href="filter.html">filter</a></td>
+<td>Linear Filtering on a Time Series</td></tr>
+<tr><td width="25%"><a href="fisher.test.html">fisher.test</a></td>
+<td>Fisher's Exact Test for Count Data</td></tr>
+<tr><td width="25%"><a href="kmeans.html">fitted.kmeans</a></td>
+<td>K-Means Clustering</td></tr>
+<tr><td width="25%"><a href="fitted.values.html">fitted.values</a></td>
+<td>Extract Model Fitted Values</td></tr>
+<tr><td width="25%"><a href="fivenum.html">fivenum</a></td>
+<td>Tukey Five-Number Summaries</td></tr>
+<tr><td width="25%"><a href="fligner.test.html">fligner.test</a></td>
+<td>Fligner-Killeen Test of Homogeneity of Variances</td></tr>
+<tr><td width="25%"><a href="dist.html">format.dist</a></td>
+<td>Distance Matrix Computation</td></tr>
+<tr><td width="25%"><a href="read.ftable.html">format.ftable</a></td>
+<td>Manipulate Flat Contingency Tables</td></tr>
+<tr><td width="25%"><a href="formula.html">formula</a></td>
+<td>Model Formulae</td></tr>
+<tr><td width="25%"><a href="lm.summaries.html">formula.lm</a></td>
+<td>Accessing Linear Model Fits</td></tr>
+<tr><td width="25%"><a href="formula.nls.html">formula.nls</a></td>
+<td>Extract Model Formula from nls Object</td></tr>
+<tr><td width="25%"><a href="time.html">frequency</a></td>
+<td>Sampling Times of Time Series</td></tr>
+<tr><td width="25%"><a href="friedman.test.html">friedman.test</a></td>
+<td>Friedman Rank Sum Test</td></tr>
+<tr><td width="25%"><a href="ftable.html">ftable</a></td>
+<td>Flat Contingency Tables</td></tr>
+<tr><td width="25%"><a href="ftable.formula.html">ftable.formula</a></td>
+<td>Formula Notation for Flat Contingency Tables</td></tr>
+</table>
+
+<h2><a name="G">-- G --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="family.html">Gamma</a></td>
+<td>Family Objects for Models</td></tr>
+<tr><td width="25%"><a href="GammaDist.html">GammaDist</a></td>
+<td>The Gamma Distribution</td></tr>
+<tr><td width="25%"><a href="family.html">gaussian</a></td>
+<td>Family Objects for Models</td></tr>
+<tr><td width="25%"><a href="Geometric.html">Geometric</a></td>
+<td>The Geometric Distribution</td></tr>
+<tr><td width="25%"><a href="update.html">getCall</a></td>
+<td>Update and Re-fit a Model Call</td></tr>
+<tr><td width="25%"><a href="getInitial.html">getInitial</a></td>
+<td>Get Initial Parameter Estimates</td></tr>
+<tr><td width="25%"><a href="model.frame.html">get_all_vars</a></td>
+<td>Extracting the Model Frame from a Formula or Fit</td></tr>
+<tr><td width="25%"><a href="glm.html">glm</a></td>
+<td>Fitting Generalized Linear Models</td></tr>
+<tr><td width="25%"><a href="glm.control.html">glm.control</a></td>
+<td>Auxiliary for Controlling GLM Fitting</td></tr>
+</table>
+
+<h2><a name="H">-- H --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="tsp.html">hasTsp</a></td>
+<td>Tsp Attribute of Time-Series-like Objects</td></tr>
+<tr><td width="25%"><a href="influence.measures.html">hat</a></td>
+<td>Regression Deletion Diagnostics</td></tr>
+<tr><td width="25%"><a href="influence.measures.html">hatvalues</a></td>
+<td>Regression Deletion Diagnostics</td></tr>
+<tr><td width="25%"><a href="hclust.html">hclust</a></td>
+<td>Hierarchical Clustering</td></tr>
+<tr><td width="25%"><a href="heatmap.html">heatmap</a></td>
+<td>Draw a Heat Map</td></tr>
+<tr><td width="25%"><a href="HoltWinters.html">HoltWinters</a></td>
+<td>Holt-Winters Filtering</td></tr>
+<tr><td width="25%"><a href="Hypergeometric.html">Hypergeometric</a></td>
+<td>The Hypergeometric Distribution</td></tr>
+</table>
+
+<h2><a name="I">-- I --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="identify.hclust.html">identify.hclust</a></td>
+<td>Identify Clusters in a Dendrogram</td></tr>
+<tr><td width="25%"><a href="lm.influence.html">influence</a></td>
+<td>Regression Diagnostics</td></tr>
+<tr><td width="25%"><a href="influence.measures.html">influence.measures</a></td>
+<td>Regression Deletion Diagnostics</td></tr>
+<tr><td width="25%"><a href="integrate.html">integrate</a></td>
+<td>Integration of One-Dimensional Functions</td></tr>
+<tr><td width="25%"><a href="interaction.plot.html">interaction.plot</a></td>
+<td>Two-way Interaction Plot</td></tr>
+<tr><td width="25%"><a href="family.html">inverse.gaussian</a></td>
+<td>Family Objects for Models</td></tr>
+<tr><td width="25%"><a href="IQR.html">IQR</a></td>
+<td>The Interquartile Range</td></tr>
+<tr><td width="25%"><a href="is.empty.html">is.empty.model</a></td>
+<td>Test if a Model's Formula is Empty</td></tr>
+<tr><td width="25%"><a href="dendrogram.html">is.leaf</a></td>
+<td>General Tree Structures</td></tr>
+<tr><td width="25%"><a href="ts.html">is.mts</a></td>
+<td>Time-Series Objects</td></tr>
+<tr><td width="25%"><a href="stepfun.html">is.stepfun</a></td>
+<td>Step Function Class</td></tr>
+<tr><td width="25%"><a href="ts.html">is.ts</a></td>
+<td>Time-Series Objects</td></tr>
+<tr><td width="25%"><a href="kernel.html">is.tskernel</a></td>
+<td>Smoothing Kernel Objects</td></tr>
+<tr><td width="25%"><a href="isoreg.html">isoreg</a></td>
+<td>Isotonic / Monotone Regression</td></tr>
+</table>
+
+<h2><a name="K">-- K --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="KalmanLike.html">KalmanForecast</a></td>
+<td>Kalman Filtering</td></tr>
+<tr><td width="25%"><a href="KalmanLike.html">KalmanLike</a></td>
+<td>Kalman Filtering</td></tr>
+<tr><td width="25%"><a href="KalmanLike.html">KalmanRun</a></td>
+<td>Kalman Filtering</td></tr>
+<tr><td width="25%"><a href="KalmanLike.html">KalmanSmooth</a></td>
+<td>Kalman Filtering</td></tr>
+<tr><td width="25%"><a href="kernapply.html">kernapply</a></td>
+<td>Apply Smoothing Kernel</td></tr>
+<tr><td width="25%"><a href="kernel.html">kernel</a></td>
+<td>Smoothing Kernel Objects</td></tr>
+<tr><td width="25%"><a href="kmeans.html">kmeans</a></td>
+<td>K-Means Clustering</td></tr>
+<tr><td width="25%"><a href="stepfun.html">knots</a></td>
+<td>Step Function Class</td></tr>
+<tr><td width="25%"><a href="kruskal.test.html">kruskal.test</a></td>
+<td>Kruskal-Wallis Rank Sum Test</td></tr>
+<tr><td width="25%"><a href="ks.test.html">ks.test</a></td>
+<td>Kolmogorov-Smirnov Tests</td></tr>
+<tr><td width="25%"><a href="ksmooth.html">ksmooth</a></td>
+<td>Kernel Regression Smoother</td></tr>
+</table>
+
+<h2><a name="L">-- L --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="order.dendrogram.html">labels.dendrogram</a></td>
+<td>Ordering or Labels of the Leaves in a Dendrogram</td></tr>
+<tr><td width="25%"><a href="dist.html">labels.dist</a></td>
+<td>Distance Matrix Computation</td></tr>
+<tr><td width="25%"><a href="lm.summaries.html">labels.lm</a></td>
+<td>Accessing Linear Model Fits</td></tr>
+<tr><td width="25%"><a href="terms.html">labels.terms</a></td>
+<td>Model Terms</td></tr>
+<tr><td width="25%"><a href="lag.html">lag</a></td>
+<td>Lag a Time Series</td></tr>
+<tr><td width="25%"><a href="lag.plot.html">lag.plot</a></td>
+<td>Time Series Lag Plots</td></tr>
+<tr><td width="25%"><a href="line.html">line</a></td>
+<td>Robust Line Fitting</td></tr>
+<tr><td width="25%"><a href="plot.isoreg.html">lines.isoreg</a></td>
+<td>Plot Method for isoreg Objects</td></tr>
+<tr><td width="25%"><a href="plot.stepfun.html">lines.stepfun</a></td>
+<td>Plot Step Functions</td></tr>
+<tr><td width="25%"><a href="plot.ts.html">lines.ts</a></td>
+<td>Plotting Time-Series Objects</td></tr>
+<tr><td width="25%"><a href="lm.html">lm</a></td>
+<td>Fitting Linear Models</td></tr>
+<tr><td width="25%"><a href="lmfit.html">lm.fit</a></td>
+<td>Fitter Functions for Linear Models</td></tr>
+<tr><td width="25%"><a href="lm.influence.html">lm.influence</a></td>
+<td>Regression Diagnostics</td></tr>
+<tr><td width="25%"><a href="lmfit.html">lm.wfit</a></td>
+<td>Fitter Functions for Linear Models</td></tr>
+<tr><td width="25%"><a href="loadings.html">loadings</a></td>
+<td>Print Loadings in Factor Analysis</td></tr>
+<tr><td width="25%"><a href="loess.html">loess</a></td>
+<td>Local Polynomial Regression Fitting</td></tr>
+<tr><td width="25%"><a href="loess.control.html">loess.control</a></td>
+<td>Set Parameters for Loess</td></tr>
+<tr><td width="25%"><a href="scatter.smooth.html">loess.smooth</a></td>
+<td>Scatter Plot with Smooth Curve Fitted by Loess</td></tr>
+<tr><td width="25%"><a href="Logistic.html">Logistic</a></td>
+<td>The Logistic Distribution</td></tr>
+<tr><td width="25%"><a href="logLik.html">logLik</a></td>
+<td>Extract Log-Likelihood</td></tr>
+<tr><td width="25%"><a href="logLik.html">logLik.lm</a></td>
+<td>Extract Log-Likelihood</td></tr>
+<tr><td width="25%"><a href="loglin.html">loglin</a></td>
+<td>Fitting Log-Linear Models</td></tr>
+<tr><td width="25%"><a href="Lognormal.html">Lognormal</a></td>
+<td>The Log Normal Distribution</td></tr>
+<tr><td width="25%"><a href="lowess.html">lowess</a></td>
+<td>Scatter Plot Smoothing</td></tr>
+<tr><td width="25%"><a href="ls.diag.html">ls.diag</a></td>
+<td>Compute Diagnostics for 'lsfit' Regression Results</td></tr>
+<tr><td width="25%"><a href="ls.print.html">ls.print</a></td>
+<td>Print 'lsfit' Regression Results</td></tr>
+<tr><td width="25%"><a href="lsfit.html">lsfit</a></td>
+<td>Find the Least Squares Fit</td></tr>
+</table>
+
+<h2><a name="M">-- M --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="mad.html">mad</a></td>
+<td>Median Absolute Deviation</td></tr>
+<tr><td width="25%"><a href="mahalanobis.html">mahalanobis</a></td>
+<td>Mahalanobis Distance</td></tr>
+<tr><td width="25%"><a href="make.link.html">make.link</a></td>
+<td>Create a Link for GLM Families</td></tr>
+<tr><td width="25%"><a href="KalmanLike.html">makeARIMA</a></td>
+<td>Kalman Filtering</td></tr>
+<tr><td width="25%"><a href="makepredictcall.html">makepredictcall</a></td>
+<td>Utility Function for Safe Prediction</td></tr>
+<tr><td width="25%"><a href="poly.html">makepredictcall.poly</a></td>
+<td>Compute Orthogonal Polynomials</td></tr>
+<tr><td width="25%"><a href="manova.html">manova</a></td>
+<td>Multivariate Analysis of Variance</td></tr>
+<tr><td width="25%"><a href="mantelhaen.test.html">mantelhaen.test</a></td>
+<td>Cochran-Mantel-Haenszel Chi-Squared Test for Count Data</td></tr>
+<tr><td width="25%"><a href="mauchly.test.html">mauchly.test</a></td>
+<td>Mauchly's Test of Sphericity</td></tr>
+<tr><td width="25%"><a href="mcnemar.test.html">mcnemar.test</a></td>
+<td>McNemar's Chi-squared Test for Count Data</td></tr>
+<tr><td width="25%"><a href="median.html">median</a></td>
+<td>Median Value</td></tr>
+<tr><td width="25%"><a href="medpolish.html">medpolish</a></td>
+<td>Median Polish of a Matrix</td></tr>
+<tr><td width="25%"><a href="dendrogram.html">merge.dendrogram</a></td>
+<td>General Tree Structures</td></tr>
+<tr><td width="25%"><a href="model.extract.html">model.extract</a></td>
+<td>Extract Components from a Model Frame</td></tr>
+<tr><td width="25%"><a href="model.frame.html">model.frame</a></td>
+<td>Extracting the Model Frame from a Formula or Fit</td></tr>
+<tr><td width="25%"><a href="model.matrix.html">model.matrix</a></td>
+<td>Construct Design Matrices</td></tr>
+<tr><td width="25%"><a href="model.extract.html">model.offset</a></td>
+<td>Extract Components from a Model Frame</td></tr>
+<tr><td width="25%"><a href="model.extract.html">model.response</a></td>
+<td>Extract Components from a Model Frame</td></tr>
+<tr><td width="25%"><a href="model.tables.html">model.tables</a></td>
+<td>Compute Tables of Results from an Aov Model Fit</td></tr>
+<tr><td width="25%"><a href="model.extract.html">model.weights</a></td>
+<td>Extract Components from a Model Frame</td></tr>
+<tr><td width="25%"><a href="monthplot.html">monthplot</a></td>
+<td>Plot a Seasonal or other Subseries from a Time Series</td></tr>
+<tr><td width="25%"><a href="mood.test.html">mood.test</a></td>
+<td>Mood Two-Sample Test of Scale</td></tr>
+<tr><td width="25%"><a href="Multinom.html">Multinomial</a></td>
+<td>The Multinomial Distribution</td></tr>
+<tr><td width="25%"><a href="fft.html">mvfft</a></td>
+<td>Fast Discrete Fourier Transform</td></tr>
+</table>
+
+<h2><a name="N">-- N --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="na.action.html">na.action</a></td>
+<td>NA Action</td></tr>
+<tr><td width="25%"><a href="na.contiguous.html">na.contiguous</a></td>
+<td>Find Longest Contiguous Stretch of non-NAs</td></tr>
+<tr><td width="25%"><a href="na.fail.html">na.exclude</a></td>
+<td>Handle Missing Values in Objects</td></tr>
+<tr><td width="25%"><a href="na.fail.html">na.fail</a></td>
+<td>Handle Missing Values in Objects</td></tr>
+<tr><td width="25%"><a href="na.fail.html">na.omit</a></td>
+<td>Handle Missing Values in Objects</td></tr>
+<tr><td width="25%"><a href="ts-methods.html">na.omit.ts</a></td>
+<td>Methods for Time Series Objects</td></tr>
+<tr><td width="25%"><a href="na.fail.html">na.pass</a></td>
+<td>Handle Missing Values in Objects</td></tr>
+<tr><td width="25%"><a href="nafns.html">napredict</a></td>
+<td>Adjust for Missing Values</td></tr>
+<tr><td width="25%"><a href="naprint.html">naprint</a></td>
+<td>Adjust for Missing Values</td></tr>
+<tr><td width="25%"><a href="nafns.html">naresid</a></td>
+<td>Adjust for Missing Values</td></tr>
+<tr><td width="25%"><a href="NegBinomial.html">NegBinomial</a></td>
+<td>The Negative Binomial Distribution</td></tr>
+<tr><td width="25%"><a href="nextn.html">nextn</a></td>
+<td>Highly Composite Numbers</td></tr>
+<tr><td width="25%"><a href="nlm.html">nlm</a></td>
+<td>Non-Linear Minimization</td></tr>
+<tr><td width="25%"><a href="nlminb.html">nlminb</a></td>
+<td>Optimization using PORT routines</td></tr>
+<tr><td width="25%"><a href="nls.html">nls</a></td>
+<td>Nonlinear Least Squares</td></tr>
+<tr><td width="25%"><a href="nls.control.html">nls.control</a></td>
+<td>Control the Iterations in nls</td></tr>
+<tr><td width="25%"><a href="NLSstAsymptotic.html">NLSstAsymptotic</a></td>
+<td>Fit the Asymptotic Regression Model</td></tr>
+<tr><td width="25%"><a href="NLSstClosestX.html">NLSstClosestX</a></td>
+<td>Inverse Interpolation</td></tr>
+<tr><td width="25%"><a href="NLSstLfAsymptote.html">NLSstLfAsymptote</a></td>
+<td>Horizontal Asymptote on the Left Side</td></tr>
+<tr><td width="25%"><a href="NLSstRtAsymptote.html">NLSstRtAsymptote</a></td>
+<td>Horizontal Asymptote on the Right Side</td></tr>
+<tr><td width="25%"><a href="nobs.html">nobs</a></td>
+<td>Extract the Number of Observations from a Fit.</td></tr>
+<tr><td width="25%"><a href="Normal.html">Normal</a></td>
+<td>The Normal Distribution</td></tr>
+<tr><td width="25%"><a href="numericDeriv.html">numericDeriv</a></td>
+<td>Evaluate Derivatives Numerically</td></tr>
+</table>
+
+<h2><a name="O">-- O --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="offset.html">offset</a></td>
+<td>Include an Offset in a Model Formula</td></tr>
+<tr><td width="25%"><a href="oneway.test.html">oneway.test</a></td>
+<td>Test for Equal Means in a One-Way Layout</td></tr>
+<tr><td width="25%"><a href="ts.html">Ops.ts</a></td>
+<td>Time-Series Objects</td></tr>
+<tr><td width="25%"><a href="optim.html">optim</a></td>
+<td>General-purpose Optimization</td></tr>
+<tr><td width="25%"><a href="optim.html">optimHess</a></td>
+<td>General-purpose Optimization</td></tr>
+<tr><td width="25%"><a href="optimize.html">optimise</a></td>
+<td>One Dimensional Optimization</td></tr>
+<tr><td width="25%"><a href="optimize.html">optimize</a></td>
+<td>One Dimensional Optimization</td></tr>
+<tr><td width="25%"><a href="order.dendrogram.html">order.dendrogram</a></td>
+<td>Ordering or Labels of the Leaves in a Dendrogram</td></tr>
+</table>
+
+<h2><a name="P">-- P --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="p.adjust.html">p.adjust</a></td>
+<td>Adjust P-values for Multiple Comparisons</td></tr>
+<tr><td width="25%"><a href="p.adjust.html">p.adjust.methods</a></td>
+<td>Adjust P-values for Multiple Comparisons</td></tr>
+<tr><td width="25%"><a href="acf.html">pacf</a></td>
+<td>Auto- and Cross- Covariance and -Correlation Function Estimation</td></tr>
+<tr><td width="25%"><a href="pairwise.prop.test.html">pairwise.prop.test</a></td>
+<td>Pairwise comparisons for proportions</td></tr>
+<tr><td width="25%"><a href="pairwise.t.test.html">pairwise.t.test</a></td>
+<td>Pairwise t tests</td></tr>
+<tr><td width="25%"><a href="pairwise.table.html">pairwise.table</a></td>
+<td>Tabulate p values for pairwise comparisons</td></tr>
+<tr><td width="25%"><a href="pairwise.wilcox.test.html">pairwise.wilcox.test</a></td>
+<td>Pairwise Wilcoxon Rank Sum Tests</td></tr>
+<tr><td width="25%"><a href="Beta.html">pbeta</a></td>
+<td>The Beta Distribution</td></tr>
+<tr><td width="25%"><a href="Binomial.html">pbinom</a></td>
+<td>The Binomial Distribution</td></tr>
+<tr><td width="25%"><a href="birthday.html">pbirthday</a></td>
+<td>Probability of coincidences</td></tr>
+<tr><td width="25%"><a href="Cauchy.html">pcauchy</a></td>
+<td>The Cauchy Distribution</td></tr>
+<tr><td width="25%"><a href="Chisquare.html">pchisq</a></td>
+<td>The (non-central) Chi-Squared Distribution</td></tr>
+<tr><td width="25%"><a href="Exponential.html">pexp</a></td>
+<td>The Exponential Distribution</td></tr>
+<tr><td width="25%"><a href="Fdist.html">pf</a></td>
+<td>The F Distribution</td></tr>
+<tr><td width="25%"><a href="GammaDist.html">pgamma</a></td>
+<td>The Gamma Distribution</td></tr>
+<tr><td width="25%"><a href="Geometric.html">pgeom</a></td>
+<td>The Geometric Distribution</td></tr>
+<tr><td width="25%"><a href="Hypergeometric.html">phyper</a></td>
+<td>The Hypergeometric Distribution</td></tr>
+<tr><td width="25%"><a href="hclust.html">plclust</a></td>
+<td>Hierarchical Clustering</td></tr>
+<tr><td width="25%"><a href="Lognormal.html">plnorm</a></td>
+<td>The Log Normal Distribution</td></tr>
+<tr><td width="25%"><a href="Logistic.html">plogis</a></td>
+<td>The Logistic Distribution</td></tr>
+<tr><td width="25%"><a href="plot.acf.html">plot.acf</a></td>
+<td>Plot Autocovariance and Autocorrelation Functions</td></tr>
+<tr><td width="25%"><a href="decompose.html">plot.decomposed.ts</a></td>
+<td>Classical Seasonal Decomposition by Moving Averages</td></tr>
+<tr><td width="25%"><a href="dendrogram.html">plot.dendrogram</a></td>
+<td>General Tree Structures</td></tr>
+<tr><td width="25%"><a href="plot.density.html">plot.density</a></td>
+<td>Plot Method for Kernel Density Estimation</td></tr>
+<tr><td width="25%"><a href="ecdf.html">plot.ecdf</a></td>
+<td>Empirical Cumulative Distribution Function</td></tr>
+<tr><td width="25%"><a href="hclust.html">plot.hclust</a></td>
+<td>Hierarchical Clustering</td></tr>
+<tr><td width="25%"><a href="plot.HoltWinters.html">plot.HoltWinters</a></td>
+<td>Plot function for HoltWinters objects</td></tr>
+<tr><td width="25%"><a href="plot.isoreg.html">plot.isoreg</a></td>
+<td>Plot Method for isoreg Objects</td></tr>
+<tr><td width="25%"><a href="plot.lm.html">plot.lm</a></td>
+<td>Plot Diagnostics for an lm Object</td></tr>
+<tr><td width="25%"><a href="plot.ppr.html">plot.ppr</a></td>
+<td>Plot Ridge Functions for Projection Pursuit Regression Fit</td></tr>
+<tr><td width="25%"><a href="prcomp.html">plot.prcomp</a></td>
+<td>Principal Components Analysis</td></tr>
+<tr><td width="25%"><a href="princomp.html">plot.princomp</a></td>
+<td>Principal Components Analysis</td></tr>
+<tr><td width="25%"><a href="plot.profile.nls.html">plot.profile.nls</a></td>
+<td>Plot a profile.nls Object</td></tr>
+<tr><td width="25%"><a href="plot.spec.html">plot.spec</a></td>
+<td>Plotting Spectral Densities</td></tr>
+<tr><td width="25%"><a href="plot.spec.html">plot.spec.coherency</a></td>
+<td>Plotting Spectral Densities</td></tr>
+<tr><td width="25%"><a href="plot.stepfun.html">plot.stepfun</a></td>
+<td>Plot Step Functions</td></tr>
+<tr><td width="25%"><a href="stlmethods.html">plot.stl</a></td>
+<td>Methods for STL Objects</td></tr>
+<tr><td width="25%"><a href="plot.ts.html">plot.ts</a></td>
+<td>Plotting Time-Series Objects</td></tr>
+<tr><td width="25%"><a href="kernel.html">plot.tskernel</a></td>
+<td>Smoothing Kernel Objects</td></tr>
+<tr><td width="25%"><a href="TukeyHSD.html">plot.TukeyHSD</a></td>
+<td>Compute Tukey Honest Significant Differences</td></tr>
+<tr><td width="25%"><a href="NegBinomial.html">pnbinom</a></td>
+<td>The Negative Binomial Distribution</td></tr>
+<tr><td width="25%"><a href="Normal.html">pnorm</a></td>
+<td>The Normal Distribution</td></tr>
+<tr><td width="25%"><a href="Poisson.html">Poisson</a></td>
+<td>The Poisson Distribution</td></tr>
+<tr><td width="25%"><a href="family.html">poisson</a></td>
+<td>Family Objects for Models</td></tr>
+<tr><td width="25%"><a href="poisson.test.html">poisson.test</a></td>
+<td>Exact Poisson tests</td></tr>
+<tr><td width="25%"><a href="poly.html">poly</a></td>
+<td>Compute Orthogonal Polynomials</td></tr>
+<tr><td width="25%"><a href="poly.html">polym</a></td>
+<td>Compute Orthogonal Polynomials</td></tr>
+<tr><td width="25%"><a href="power.html">power</a></td>
+<td>Create a Power Link Object</td></tr>
+<tr><td width="25%"><a href="power.anova.test.html">power.anova.test</a></td>
+<td>Power Calculations for Balanced One-Way Analysis of Variance Tests</td></tr>
+<tr><td width="25%"><a href="power.prop.test.html">power.prop.test</a></td>
+<td>Power Calculations for Two-Sample Test for Proportions</td></tr>
+<tr><td width="25%"><a href="power.t.test.html">power.t.test</a></td>
+<td>Power calculations for one and two sample t tests</td></tr>
+<tr><td width="25%"><a href="pp.test.html">PP.test</a></td>
+<td>Phillips-Perron Test for Unit Roots</td></tr>
+<tr><td width="25%"><a href="ppoints.html">ppoints</a></td>
+<td>Ordinates for Probability Plotting</td></tr>
+<tr><td width="25%"><a href="Poisson.html">ppois</a></td>
+<td>The Poisson Distribution</td></tr>
+<tr><td width="25%"><a href="ppr.html">ppr</a></td>
+<td>Projection Pursuit Regression</td></tr>
+<tr><td width="25%"><a href="prcomp.html">prcomp</a></td>
+<td>Principal Components Analysis</td></tr>
+<tr><td width="25%"><a href="predict.html">predict</a></td>
+<td>Model Predictions</td></tr>
+<tr><td width="25%"><a href="ar.html">predict.ar</a></td>
+<td>Fit Autoregressive Models to Time Series</td></tr>
+<tr><td width="25%"><a href="predict.arima.html">predict.Arima</a></td>
+<td>Forecast from ARIMA fits</td></tr>
+<tr><td width="25%"><a href="arima0.html">predict.arima0</a></td>
+<td>ARIMA Modelling of Time Series - Preliminary Version</td></tr>
+<tr><td width="25%"><a href="predict.glm.html">predict.glm</a></td>
+<td>Predict Method for GLM Fits</td></tr>
+<tr><td width="25%"><a href="predict.HoltWinters.html">predict.HoltWinters</a></td>
+<td>Prediction Function for Fitted Holt-Winters Models</td></tr>
+<tr><td width="25%"><a href="predict.lm.html">predict.lm</a></td>
+<td>Predict method for Linear Model Fits</td></tr>
+<tr><td width="25%"><a href="predict.loess.html">predict.loess</a></td>
+<td>Predict Loess Curve or Surface</td></tr>
+<tr><td width="25%"><a href="predict.nls.html">predict.nls</a></td>
+<td>Predicting from Nonlinear Least Squares Fits</td></tr>
+<tr><td width="25%"><a href="poly.html">predict.poly</a></td>
+<td>Compute Orthogonal Polynomials</td></tr>
+<tr><td width="25%"><a href="prcomp.html">predict.prcomp</a></td>
+<td>Principal Components Analysis</td></tr>
+<tr><td width="25%"><a href="princomp.html">predict.princomp</a></td>
+<td>Principal Components Analysis</td></tr>
+<tr><td width="25%"><a href="predict.smooth.spline.html">predict.smooth.spline</a></td>
+<td>Predict from Smoothing Spline Fit</td></tr>
+<tr><td width="25%"><a href="StructTS.html">predict.StructTS</a></td>
+<td>Fit Structural Time Series</td></tr>
+<tr><td width="25%"><a href="preplot.html">preplot</a></td>
+<td>Pre-computations for a Plotting Object</td></tr>
+<tr><td width="25%"><a href="princomp.html">princomp</a></td>
+<td>Principal Components Analysis</td></tr>
+<tr><td width="25%"><a href="anova.html">print.anova</a></td>
+<td>Anova Tables</td></tr>
+<tr><td width="25%"><a href="aov.html">print.aov</a></td>
+<td>Fit an Analysis of Variance Model</td></tr>
+<tr><td width="25%"><a href="ar.html">print.ar</a></td>
+<td>Fit Autoregressive Models to Time Series</td></tr>
+<tr><td width="25%"><a href="arima0.html">print.arima0</a></td>
+<td>ARIMA Modelling of Time Series - Preliminary Version</td></tr>
+<tr><td width="25%"><a href="dendrogram.html">print.dendrogram</a></td>
+<td>General Tree Structures</td></tr>
+<tr><td width="25%"><a href="density.html">print.density</a></td>
+<td>Kernel Density Estimation</td></tr>
+<tr><td width="25%"><a href="dist.html">print.dist</a></td>
+<td>Distance Matrix Computation</td></tr>
+<tr><td width="25%"><a href="ecdf.html">print.ecdf</a></td>
+<td>Empirical Cumulative Distribution Function</td></tr>
+<tr><td width="25%"><a href="family.html">print.family</a></td>
+<td>Family Objects for Models</td></tr>
+<tr><td width="25%"><a href="formula.html">print.formula</a></td>
+<td>Model Formulae</td></tr>
+<tr><td width="25%"><a href="ftable.html">print.ftable</a></td>
+<td>Flat Contingency Tables</td></tr>
+<tr><td width="25%"><a href="glm.html">print.glm</a></td>
+<td>Fitting Generalized Linear Models</td></tr>
+<tr><td width="25%"><a href="hclust.html">print.hclust</a></td>
+<td>Hierarchical Clustering</td></tr>
+<tr><td width="25%"><a href="HoltWinters.html">print.HoltWinters</a></td>
+<td>Holt-Winters Filtering</td></tr>
+<tr><td width="25%"><a href="influence.measures.html">print.infl</a></td>
+<td>Regression Deletion Diagnostics</td></tr>
+<tr><td width="25%"><a href="integrate.html">print.integrate</a></td>
+<td>Integration of One-Dimensional Functions</td></tr>
+<tr><td width="25%"><a href="kmeans.html">print.kmeans</a></td>
+<td>K-Means Clustering</td></tr>
+<tr><td width="25%"><a href="lm.html">print.lm</a></td>
+<td>Fitting Linear Models</td></tr>
+<tr><td width="25%"><a href="loadings.html">print.loadings</a></td>
+<td>Print Loadings in Factor Analysis</td></tr>
+<tr><td width="25%"><a href="logLik.html">print.logLik</a></td>
+<td>Extract Log-Likelihood</td></tr>
+<tr><td width="25%"><a href="print.power.htest.html">print.power.htest</a></td>
+<td>Print method for power calculation object</td></tr>
+<tr><td width="25%"><a href="prcomp.html">print.prcomp</a></td>
+<td>Principal Components Analysis</td></tr>
+<tr><td width="25%"><a href="princomp.html">print.princomp</a></td>
+<td>Principal Components Analysis</td></tr>
+<tr><td width="25%"><a href="stepfun.html">print.stepfun</a></td>
+<td>Step Function Class</td></tr>
+<tr><td width="25%"><a href="StructTS.html">print.StructTS</a></td>
+<td>Fit Structural Time Series</td></tr>
+<tr><td width="25%"><a href="summary.aov.html">print.summary.aov</a></td>
+<td>Summarize an Analysis of Variance Model</td></tr>
+<tr><td width="25%"><a href="summary.glm.html">print.summary.glm</a></td>
+<td>Summarizing Generalized Linear Model Fits</td></tr>
+<tr><td width="25%"><a href="summary.lm.html">print.summary.lm</a></td>
+<td>Summarizing Linear Model Fits</td></tr>
+<tr><td width="25%"><a href="summary.manova.html">print.summary.manova</a></td>
+<td>Summary Method for Multivariate Analysis of Variance</td></tr>
+<tr><td width="25%"><a href="summary.nls.html">print.summary.nls</a></td>
+<td>Summarizing Non-Linear Least-Squares Model Fits</td></tr>
+<tr><td width="25%"><a href="prcomp.html">print.summary.prcomp</a></td>
+<td>Principal Components Analysis</td></tr>
+<tr><td width="25%"><a href="summary.princomp.html">print.summary.princomp</a></td>
+<td>Summary method for Principal Components Analysis</td></tr>
+<tr><td width="25%"><a href="terms.html">print.terms</a></td>
+<td>Model Terms</td></tr>
+<tr><td width="25%"><a href="print.ts.html">print.ts</a></td>
+<td>Printing Time-Series Objects</td></tr>
+<tr><td width="25%"><a href="TukeyHSD.html">print.TukeyHSD</a></td>
+<td>Compute Tukey Honest Significant Differences</td></tr>
+<tr><td width="25%"><a href="xtabs.html">print.xtabs</a></td>
+<td>Cross Tabulation</td></tr>
+<tr><td width="25%"><a href="printCoefmat.html">printCoefmat</a></td>
+<td>Print Coefficient Matrices</td></tr>
+<tr><td width="25%"><a href="profile.html">profile</a></td>
+<td>Generic Function for Profiling Models</td></tr>
+<tr><td width="25%"><a href="profile.nls.html">profile.nls</a></td>
+<td>Method for Profiling nls Objects</td></tr>
+<tr><td width="25%"><a href="proj.html">proj</a></td>
+<td>Projections of Models</td></tr>
+<tr><td width="25%"><a href="varimax.html">promax</a></td>
+<td>Rotation Methods for Factor Analysis</td></tr>
+<tr><td width="25%"><a href="prop.test.html">prop.test</a></td>
+<td>Test of Equal or Given Proportions</td></tr>
+<tr><td width="25%"><a href="prop.trend.test.html">prop.trend.test</a></td>
+<td>Test for trend in proportions</td></tr>
+<tr><td width="25%"><a href="SignRank.html">psignrank</a></td>
+<td>Distribution of the Wilcoxon Signed Rank Statistic</td></tr>
+<tr><td width="25%"><a href="TDist.html">pt</a></td>
+<td>The Student t Distribution</td></tr>
+<tr><td width="25%"><a href="Tukey.html">ptukey</a></td>
+<td>The Studentized Range Distribution</td></tr>
+<tr><td width="25%"><a href="Uniform.html">punif</a></td>
+<td>The Uniform Distribution</td></tr>
+<tr><td width="25%"><a href="Weibull.html">pweibull</a></td>
+<td>The Weibull Distribution</td></tr>
+<tr><td width="25%"><a href="Wilcoxon.html">pwilcox</a></td>
+<td>Distribution of the Wilcoxon Rank Sum Statistic</td></tr>
+</table>
+
+<h2><a name="Q">-- Q --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Beta.html">qbeta</a></td>
+<td>The Beta Distribution</td></tr>
+<tr><td width="25%"><a href="Binomial.html">qbinom</a></td>
+<td>The Binomial Distribution</td></tr>
+<tr><td width="25%"><a href="birthday.html">qbirthday</a></td>
+<td>Probability of coincidences</td></tr>
+<tr><td width="25%"><a href="Cauchy.html">qcauchy</a></td>
+<td>The Cauchy Distribution</td></tr>
+<tr><td width="25%"><a href="Chisquare.html">qchisq</a></td>
+<td>The (non-central) Chi-Squared Distribution</td></tr>
+<tr><td width="25%"><a href="Exponential.html">qexp</a></td>
+<td>The Exponential Distribution</td></tr>
+<tr><td width="25%"><a href="Fdist.html">qf</a></td>
+<td>The F Distribution</td></tr>
+<tr><td width="25%"><a href="GammaDist.html">qgamma</a></td>
+<td>The Gamma Distribution</td></tr>
+<tr><td width="25%"><a href="Geometric.html">qgeom</a></td>
+<td>The Geometric Distribution</td></tr>
+<tr><td width="25%"><a href="Hypergeometric.html">qhyper</a></td>
+<td>The Hypergeometric Distribution</td></tr>
+<tr><td width="25%"><a href="Lognormal.html">qlnorm</a></td>
+<td>The Log Normal Distribution</td></tr>
+<tr><td width="25%"><a href="Logistic.html">qlogis</a></td>
+<td>The Logistic Distribution</td></tr>
+<tr><td width="25%"><a href="NegBinomial.html">qnbinom</a></td>
+<td>The Negative Binomial Distribution</td></tr>
+<tr><td width="25%"><a href="Normal.html">qnorm</a></td>
+<td>The Normal Distribution</td></tr>
+<tr><td width="25%"><a href="Poisson.html">qpois</a></td>
+<td>The Poisson Distribution</td></tr>
+<tr><td width="25%"><a href="qqnorm.html">qqline</a></td>
+<td>Quantile-Quantile Plots</td></tr>
+<tr><td width="25%"><a href="qqnorm.html">qqnorm</a></td>
+<td>Quantile-Quantile Plots</td></tr>
+<tr><td width="25%"><a href="qqnorm.html">qqplot</a></td>
+<td>Quantile-Quantile Plots</td></tr>
+<tr><td width="25%"><a href="SignRank.html">qsignrank</a></td>
+<td>Distribution of the Wilcoxon Signed Rank Statistic</td></tr>
+<tr><td width="25%"><a href="TDist.html">qt</a></td>
+<td>The Student t Distribution</td></tr>
+<tr><td width="25%"><a href="Tukey.html">qtukey</a></td>
+<td>The Studentized Range Distribution</td></tr>
+<tr><td width="25%"><a href="quade.test.html">quade.test</a></td>
+<td>Quade Test</td></tr>
+<tr><td width="25%"><a href="quantile.html">quantile</a></td>
+<td>Sample Quantiles</td></tr>
+<tr><td width="25%"><a href="ecdf.html">quantile.ecdf</a></td>
+<td>Empirical Cumulative Distribution Function</td></tr>
+<tr><td width="25%"><a href="family.html">quasi</a></td>
+<td>Family Objects for Models</td></tr>
+<tr><td width="25%"><a href="family.html">quasibinomial</a></td>
+<td>Family Objects for Models</td></tr>
+<tr><td width="25%"><a href="family.html">quasipoisson</a></td>
+<td>Family Objects for Models</td></tr>
+<tr><td width="25%"><a href="Uniform.html">qunif</a></td>
+<td>The Uniform Distribution</td></tr>
+<tr><td width="25%"><a href="Weibull.html">qweibull</a></td>
+<td>The Weibull Distribution</td></tr>
+<tr><td width="25%"><a href="Wilcoxon.html">qwilcox</a></td>
+<td>Distribution of the Wilcoxon Rank Sum Statistic</td></tr>
+</table>
+
+<h2><a name="R">-- R --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="r2dtable.html">r2dtable</a></td>
+<td>Random 2-way Tables with Given Marginals</td></tr>
+<tr><td width="25%"><a href="Beta.html">rbeta</a></td>
+<td>The Beta Distribution</td></tr>
+<tr><td width="25%"><a href="Binomial.html">rbinom</a></td>
+<td>The Binomial Distribution</td></tr>
+<tr><td width="25%"><a href="Cauchy.html">rcauchy</a></td>
+<td>The Cauchy Distribution</td></tr>
+<tr><td width="25%"><a href="Chisquare.html">rchisq</a></td>
+<td>The (non-central) Chi-Squared Distribution</td></tr>
+<tr><td width="25%"><a href="read.ftable.html">read.ftable</a></td>
+<td>Manipulate Flat Contingency Tables</td></tr>
+<tr><td width="25%"><a href="rect.hclust.html">rect.hclust</a></td>
+<td>Draw Rectangles Around Hierarchical Clusters</td></tr>
+<tr><td width="25%"><a href="delete.response.html">reformulate</a></td>
+<td>Modify Terms Objects</td></tr>
+<tr><td width="25%"><a href="relevel.html">relevel</a></td>
+<td>Reorder Levels of Factor</td></tr>
+<tr><td width="25%"><a href="reorder.factor.html">reorder</a></td>
+<td>Reorder Levels of a Factor</td></tr>
+<tr><td width="25%"><a href="reorder.dendrogram.html">reorder.dendrogram</a></td>
+<td>Reorder a Dendrogram</td></tr>
+<tr><td width="25%"><a href="replications.html">replications</a></td>
+<td>Number of Replications of Terms</td></tr>
+<tr><td width="25%"><a href="reshape.html">reshape</a></td>
+<td>Reshape Grouped Data</td></tr>
+<tr><td width="25%"><a href="residuals.html">resid</a></td>
+<td>Extract Model Residuals</td></tr>
+<tr><td width="25%"><a href="residuals.html">residuals</a></td>
+<td>Extract Model Residuals</td></tr>
+<tr><td width="25%"><a href="residuals.html">residuals.default</a></td>
+<td>Extract Model Residuals</td></tr>
+<tr><td width="25%"><a href="glm.summaries.html">residuals.glm</a></td>
+<td>Accessing Generalized Linear Model Fits</td></tr>
+<tr><td width="25%"><a href="HoltWinters.html">residuals.HoltWinters</a></td>
+<td>Holt-Winters Filtering</td></tr>
+<tr><td width="25%"><a href="lm.summaries.html">residuals.lm</a></td>
+<td>Accessing Linear Model Fits</td></tr>
+<tr><td width="25%"><a href="line.html">residuals.tukeyline</a></td>
+<td>Robust Line Fitting</td></tr>
+<tr><td width="25%"><a href="dendrogram.html">rev.dendrogram</a></td>
+<td>General Tree Structures</td></tr>
+<tr><td width="25%"><a href="Exponential.html">rexp</a></td>
+<td>The Exponential Distribution</td></tr>
+<tr><td width="25%"><a href="Fdist.html">rf</a></td>
+<td>The F Distribution</td></tr>
+<tr><td width="25%"><a href="GammaDist.html">rgamma</a></td>
+<td>The Gamma Distribution</td></tr>
+<tr><td width="25%"><a href="Geometric.html">rgeom</a></td>
+<td>The Geometric Distribution</td></tr>
+<tr><td width="25%"><a href="Hypergeometric.html">rhyper</a></td>
+<td>The Hypergeometric Distribution</td></tr>
+<tr><td width="25%"><a href="Lognormal.html">rlnorm</a></td>
+<td>The Log Normal Distribution</td></tr>
+<tr><td width="25%"><a href="Logistic.html">rlogis</a></td>
+<td>The Logistic Distribution</td></tr>
+<tr><td width="25%"><a href="Multinom.html">rmultinom</a></td>
+<td>The Multinomial Distribution</td></tr>
+<tr><td width="25%"><a href="NegBinomial.html">rnbinom</a></td>
+<td>The Negative Binomial Distribution</td></tr>
+<tr><td width="25%"><a href="Normal.html">rnorm</a></td>
+<td>The Normal Distribution</td></tr>
+<tr><td width="25%"><a href="Poisson.html">rpois</a></td>
+<td>The Poisson Distribution</td></tr>
+<tr><td width="25%"><a href="SignRank.html">rsignrank</a></td>
+<td>Distribution of the Wilcoxon Signed Rank Statistic</td></tr>
+<tr><td width="25%"><a href="influence.measures.html">rstandard</a></td>
+<td>Regression Deletion Diagnostics</td></tr>
+<tr><td width="25%"><a href="influence.measures.html">rstudent</a></td>
+<td>Regression Deletion Diagnostics</td></tr>
+<tr><td width="25%"><a href="TDist.html">rt</a></td>
+<td>The Student t Distribution</td></tr>
+<tr><td width="25%"><a href="Uniform.html">runif</a></td>
+<td>The Uniform Distribution</td></tr>
+<tr><td width="25%"><a href="runmed.html">runmed</a></td>
+<td>Running Medians - Robust Scatter Plot Smoothing</td></tr>
+<tr><td width="25%"><a href="Weibull.html">rweibull</a></td>
+<td>The Weibull Distribution</td></tr>
+<tr><td width="25%"><a href="Wilcoxon.html">rwilcox</a></td>
+<td>Distribution of the Wilcoxon Rank Sum Statistic</td></tr>
+<tr><td width="25%"><a href="rWishart.html">rWishart</a></td>
+<td>Random Wishart Distributed Matrices</td></tr>
+</table>
+
+<h2><a name="S">-- S --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="makepredictcall.html">SafePrediction</a></td>
+<td>Utility Function for Safe Prediction</td></tr>
+<tr><td width="25%"><a href="scatter.smooth.html">scatter.smooth</a></td>
+<td>Scatter Plot with Smooth Curve Fitted by Loess</td></tr>
+<tr><td width="25%"><a href="screeplot.html">screeplot</a></td>
+<td>Screeplots</td></tr>
+<tr><td width="25%"><a href="sd.html">sd</a></td>
+<td>Standard Deviation</td></tr>
+<tr><td width="25%"><a href="se.contrast.html">se.contrast</a></td>
+<td>Standard Errors for Contrasts in Model Terms</td></tr>
+<tr><td width="25%"><a href="se.contrast.html">se.contrast.aov</a></td>
+<td>Standard Errors for Contrasts in Model Terms</td></tr>
+<tr><td width="25%"><a href="selfStart.html">selfStart</a></td>
+<td>Construct Self-starting Nonlinear Models</td></tr>
+<tr><td width="25%"><a href="setNames.html">setNames</a></td>
+<td>Set the Names in an Object</td></tr>
+<tr><td width="25%"><a href="shapiro.test.html">shapiro.test</a></td>
+<td>Shapiro-Wilk Normality Test</td></tr>
+<tr><td width="25%"><a href="SignRank.html">SignRank</a></td>
+<td>Distribution of the Wilcoxon Signed Rank Statistic</td></tr>
+<tr><td width="25%"><a href="simulate.html">simulate</a></td>
+<td>Simulate Responses</td></tr>
+<tr><td width="25%"><a href="smooth.html">smooth</a></td>
+<td>Tukey's (Running Median) Smoothing</td></tr>
+<tr><td width="25%"><a href="smooth.spline.html">smooth.spline</a></td>
+<td>Fit a Smoothing Spline</td></tr>
+<tr><td width="25%"><a href="smoothEnds.html">smoothEnds</a></td>
+<td>End Points Smoothing (for Running Medians)</td></tr>
+<tr><td width="25%"><a href="sortedXyData.html">sortedXyData</a></td>
+<td>Create a 'sortedXyData' Object</td></tr>
+<tr><td width="25%"><a href="spectrum.html">spec</a></td>
+<td>Spectral Density Estimation</td></tr>
+<tr><td width="25%"><a href="spec.ar.html">spec.ar</a></td>
+<td>Estimate Spectral Density of a Time Series from AR Fit</td></tr>
+<tr><td width="25%"><a href="spec.pgram.html">spec.pgram</a></td>
+<td>Estimate Spectral Density of a Time Series by a Smoothed Periodogram</td></tr>
+<tr><td width="25%"><a href="spec.taper.html">spec.taper</a></td>
+<td>Taper a Time Series by a Cosine Bell</td></tr>
+<tr><td width="25%"><a href="spectrum.html">spectrum</a></td>
+<td>Spectral Density Estimation</td></tr>
+<tr><td width="25%"><a href="splinefun.html">spline</a></td>
+<td>Interpolating Splines</td></tr>
+<tr><td width="25%"><a href="splinefun.html">splinefun</a></td>
+<td>Interpolating Splines</td></tr>
+<tr><td width="25%"><a href="splinefun.html">splinefunH</a></td>
+<td>Interpolating Splines</td></tr>
+<tr><td width="25%"><a href="SSasymp.html">SSasymp</a></td>
+<td>Self-Starting Nls Asymptotic Regression Model</td></tr>
+<tr><td width="25%"><a href="SSasympOff.html">SSasympOff</a></td>
+<td>Self-Starting Nls Asymptotic Regression Model with an Offset</td></tr>
+<tr><td width="25%"><a href="SSasympOrig.html">SSasympOrig</a></td>
+<td>Self-Starting Nls Asymptotic Regression Model through the Origin</td></tr>
+<tr><td width="25%"><a href="SSbiexp.html">SSbiexp</a></td>
+<td>Self-Starting Nls Biexponential model</td></tr>
+<tr><td width="25%"><a href="SSD.html">SSD</a></td>
+<td>SSD Matrix and Estimated Variance Matrix in Multivariate Models</td></tr>
+<tr><td width="25%"><a href="SSfol.html">SSfol</a></td>
+<td>Self-Starting Nls First-order Compartment Model</td></tr>
+<tr><td width="25%"><a href="SSfpl.html">SSfpl</a></td>
+<td>Self-Starting Nls Four-Parameter Logistic Model</td></tr>
+<tr><td width="25%"><a href="SSgompertz.html">SSgompertz</a></td>
+<td>Self-Starting Nls Gompertz Growth Model</td></tr>
+<tr><td width="25%"><a href="SSlogis.html">SSlogis</a></td>
+<td>Self-Starting Nls Logistic Model</td></tr>
+<tr><td width="25%"><a href="SSmicmen.html">SSmicmen</a></td>
+<td>Self-Starting Nls Michaelis-Menten Model</td></tr>
+<tr><td width="25%"><a href="SSweibull.html">SSweibull</a></td>
+<td>Self-Starting Nls Weibull Growth Curve Model</td></tr>
+<tr><td width="25%"><a href="start.html">start</a></td>
+<td>Encode the Terminal Times of Time Series</td></tr>
+<tr><td width="25%"><a href="stat.anova.html">stat.anova</a></td>
+<td>GLM Anova Statistics</td></tr>
+<tr><td width="25%"><a href="stats-package.html">stats</a></td>
+<td>The R Stats Package</td></tr>
+<tr><td width="25%"><a href="stats-deprecated.html">stats-deprecated</a></td>
+<td>Deprecated Functions in Package 'stats'</td></tr>
+<tr><td width="25%"><a href="step.html">step</a></td>
+<td>Choose a model by AIC in a Stepwise Algorithm</td></tr>
+<tr><td width="25%"><a href="stepfun.html">stepfun</a></td>
+<td>Step Function Class</td></tr>
+<tr><td width="25%"><a href="stl.html">stl</a></td>
+<td>Seasonal Decomposition of Time Series by Loess</td></tr>
+<tr><td width="25%"><a href="dendrogram.html">str.dendrogram</a></td>
+<td>General Tree Structures</td></tr>
+<tr><td width="25%"><a href="logLik.html">str.logLik</a></td>
+<td>Extract Log-Likelihood</td></tr>
+<tr><td width="25%"><a href="StructTS.html">StructTS</a></td>
+<td>Fit Structural Time Series</td></tr>
+<tr><td width="25%"><a href="summary.aov.html">summary.aov</a></td>
+<td>Summarize an Analysis of Variance Model</td></tr>
+<tr><td width="25%"><a href="ecdf.html">summary.ecdf</a></td>
+<td>Empirical Cumulative Distribution Function</td></tr>
+<tr><td width="25%"><a href="summary.glm.html">summary.glm</a></td>
+<td>Summarizing Generalized Linear Model Fits</td></tr>
+<tr><td width="25%"><a href="influence.measures.html">summary.infl</a></td>
+<td>Regression Deletion Diagnostics</td></tr>
+<tr><td width="25%"><a href="summary.lm.html">summary.lm</a></td>
+<td>Summarizing Linear Model Fits</td></tr>
+<tr><td width="25%"><a href="summary.manova.html">summary.manova</a></td>
+<td>Summary Method for Multivariate Analysis of Variance</td></tr>
+<tr><td width="25%"><a href="summary.nls.html">summary.nls</a></td>
+<td>Summarizing Non-Linear Least-Squares Model Fits</td></tr>
+<tr><td width="25%"><a href="prcomp.html">summary.prcomp</a></td>
+<td>Principal Components Analysis</td></tr>
+<tr><td width="25%"><a href="summary.princomp.html">summary.princomp</a></td>
+<td>Summary method for Principal Components Analysis</td></tr>
+<tr><td width="25%"><a href="stepfun.html">summary.stepfun</a></td>
+<td>Step Function Class</td></tr>
+<tr><td width="25%"><a href="supsmu.html">supsmu</a></td>
+<td>Friedman's SuperSmoother</td></tr>
+<tr><td width="25%"><a href="symnum.html">symnum</a></td>
+<td>Symbolic Number Coding</td></tr>
+</table>
+
+<h2><a name="T">-- T --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="t.test.html">t.test</a></td>
+<td>Student's t-Test</td></tr>
+<tr><td width="25%"><a href="ts.html">t.ts</a></td>
+<td>Time-Series Objects</td></tr>
+<tr><td width="25%"><a href="TDist.html">TDist</a></td>
+<td>The Student t Distribution</td></tr>
+<tr><td width="25%"><a href="termplot.html">termplot</a></td>
+<td>Plot Regression Terms</td></tr>
+<tr><td width="25%"><a href="terms.html">terms</a></td>
+<td>Model Terms</td></tr>
+<tr><td width="25%"><a href="terms.formula.html">terms.formula</a></td>
+<td>Construct a terms Object from a Formula</td></tr>
+<tr><td width="25%"><a href="terms.object.html">terms.object</a></td>
+<td>Description of Terms Objects</td></tr>
+<tr><td width="25%"><a href="time.html">time</a></td>
+<td>Sampling Times of Time Series</td></tr>
+<tr><td width="25%"><a href="time.html">time.default</a></td>
+<td>Sampling Times of Time Series</td></tr>
+<tr><td width="25%"><a href="toeplitz.html">toeplitz</a></td>
+<td>Form Symmetric Toeplitz Matrix</td></tr>
+<tr><td width="25%"><a href="ts.html">ts</a></td>
+<td>Time-Series Objects</td></tr>
+<tr><td width="25%"><a href="ts.union.html">ts.intersect</a></td>
+<td>Bind Two or More Time Series</td></tr>
+<tr><td width="25%"><a href="ts.plot.html">ts.plot</a></td>
+<td>Plot Multiple Time Series</td></tr>
+<tr><td width="25%"><a href="ts.union.html">ts.union</a></td>
+<td>Bind Two or More Time Series</td></tr>
+<tr><td width="25%"><a href="tsdiag.html">tsdiag</a></td>
+<td>Diagnostic Plots for Time-Series Fits</td></tr>
+<tr><td width="25%"><a href="tsp.html">tsp</a></td>
+<td>Tsp Attribute of Time-Series-like Objects</td></tr>
+<tr><td width="25%"><a href="tsSmooth.html">tsSmooth</a></td>
+<td>Use Fixed-Interval Smoothing on Time Series</td></tr>
+<tr><td width="25%"><a href="Tukey.html">Tukey</a></td>
+<td>The Studentized Range Distribution</td></tr>
+<tr><td width="25%"><a href="TukeyHSD.html">TukeyHSD</a></td>
+<td>Compute Tukey Honest Significant Differences</td></tr>
+</table>
+
+<h2><a name="U">-- U --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Uniform.html">Uniform</a></td>
+<td>The Uniform Distribution</td></tr>
+<tr><td width="25%"><a href="uniroot.html">uniroot</a></td>
+<td>One Dimensional Root (Zero) Finding</td></tr>
+<tr><td width="25%"><a href="update.html">update</a></td>
+<td>Update and Re-fit a Model Call</td></tr>
+<tr><td width="25%"><a href="update.formula.html">update.formula</a></td>
+<td>Model Updating</td></tr>
+</table>
+
+<h2><a name="V">-- V --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="cor.html">var</a></td>
+<td>Correlation, Variance and Covariance (Matrices)</td></tr>
+<tr><td width="25%"><a href="var.test.html">var.test</a></td>
+<td>F Test to Compare Two Variances</td></tr>
+<tr><td width="25%"><a href="case.names.html">variable.names</a></td>
+<td>Case and Variable Names of Fitted Models</td></tr>
+<tr><td width="25%"><a href="case.names.html">variable.names.lm</a></td>
+<td>Case and Variable Names of Fitted Models</td></tr>
+<tr><td width="25%"><a href="varimax.html">varimax</a></td>
+<td>Rotation Methods for Factor Analysis</td></tr>
+<tr><td width="25%"><a href="vcov.html">vcov</a></td>
+<td>Calculate Variance-Covariance Matrix for a Fitted Model Object</td></tr>
+<tr><td width="25%"><a href="vcov.html">vcov.lme</a></td>
+<td>Calculate Variance-Covariance Matrix for a Fitted Model Object</td></tr>
+<tr><td width="25%"><a href="vcov.html">vcov.summary.lm</a></td>
+<td>Calculate Variance-Covariance Matrix for a Fitted Model Object</td></tr>
+</table>
+
+<h2><a name="W">-- W --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Weibull.html">Weibull</a></td>
+<td>The Weibull Distribution</td></tr>
+<tr><td width="25%"><a href="weighted.mean.html">weighted.mean</a></td>
+<td>Weighted Arithmetic Mean</td></tr>
+<tr><td width="25%"><a href="weighted.mean.html">weighted.mean.default</a></td>
+<td>Weighted Arithmetic Mean</td></tr>
+<tr><td width="25%"><a href="weighted.residuals.html">weighted.residuals</a></td>
+<td>Compute Weighted Residuals</td></tr>
+<tr><td width="25%"><a href="weights.html">weights</a></td>
+<td>Extract Model Weights</td></tr>
+<tr><td width="25%"><a href="glm.html">weights.glm</a></td>
+<td>Fitting Generalized Linear Models</td></tr>
+<tr><td width="25%"><a href="wilcox.test.html">wilcox.test</a></td>
+<td>Wilcoxon Rank Sum and Signed Rank Tests</td></tr>
+<tr><td width="25%"><a href="Wilcoxon.html">Wilcoxon</a></td>
+<td>Distribution of the Wilcoxon Rank Sum Statistic</td></tr>
+<tr><td width="25%"><a href="window.html">window</a></td>
+<td>Time Windows</td></tr>
+<tr><td width="25%"><a href="read.ftable.html">write.ftable</a></td>
+<td>Manipulate Flat Contingency Tables</td></tr>
+</table>
+
+<h2><a name="X">-- X --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="xtabs.html">xtabs</a></td>
+<td>Cross Tabulation</td></tr>
+</table>
+
+<h2><a name="misc">-- misc --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="checkMFClasses.html">.checkMFClasses</a></td>
+<td>Functions to Check the Type of Variables passed to Model Frames</td></tr>
+<tr><td width="25%"><a href="checkMFClasses.html">.getXlevels</a></td>
+<td>Functions to Check the Type of Variables passed to Model Frames</td></tr>
+<tr><td width="25%"><a href="checkMFClasses.html">.MFclass</a></td>
+<td>Functions to Check the Type of Variables passed to Model Frames</td></tr>
+<tr><td width="25%"><a href="acf.html">[.acf</a></td>
+<td>Auto- and Cross- Covariance and -Correlation Function Estimation</td></tr>
+<tr><td width="25%"><a href="formula.html">[.formula</a></td>
+<td>Model Formulae</td></tr>
+<tr><td width="25%"><a href="delete.response.html">[.terms</a></td>
+<td>Modify Terms Objects</td></tr>
+<tr><td width="25%"><a href="ts.html">[.ts</a></td>
+<td>Time-Series Objects</td></tr>
+<tr><td width="25%"><a href="dendrogram.html">[[.dendrogram</a></td>
+<td>General Tree Structures</td></tr>
+</table>
+</body></html>
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new file mode 100644
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+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
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diff --git a/win32/deps/library/stats/tests/NLSstClosest.R b/win32/deps/library/stats/tests/NLSstClosest.R
new file mode 100644
index 0000000..8ebb201
--- /dev/null
+++ b/win32/deps/library/stats/tests/NLSstClosest.R
@@ -0,0 +1,12 @@
+## PR#14384
+
+sXY <- structure(list(x = c(0, 24, 27, 48, 51, 72, 75, 96, 99),
+ y = c(4.98227, 6.38021, 6.90309, 7.77815, 7.64345, 7.23045, 7.27875, 7.11394, 6.95424)),
+ .Names = c("x", "y"), row.names = c(NA, 9L),
+ class = c("sortedXyData", "data.frame"))
+a <- NLSstLfAsymptote(sXY)
+d <- NLSstRtAsymptote(sXY)
+z <- NLSstClosestX(sXY, (a+d)/2)
+stopifnot(!is.na(z))
+## early versions gave NaN
+
diff --git a/win32/deps/library/stats/tests/cmdscale.R b/win32/deps/library/stats/tests/cmdscale.R
new file mode 100644
index 0000000..aff5060
--- /dev/null
+++ b/win32/deps/library/stats/tests/cmdscale.R
@@ -0,0 +1,10 @@
+## regression tests on cmdscale from R 2.13.0
+
+cmdsE <- cmdscale(eurodist, k = 20, eig = TRUE, x.ret = TRUE)
+utils::str(cmdsE)
+cmdsE2 <- cmdscale(eurodist, k = 20, add = TRUE, eig = TRUE, x.ret = TRUE)
+utils::str(cmdsE2)
+stopifnot(identical(rownames(cmdsE2$points), attr(eurodist, "Labels")))
+
+## the exact answers diff by platform, since eigenvalue calculations are
+## involved
diff --git a/win32/deps/library/stats/tests/drop1-polr.R b/win32/deps/library/stats/tests/drop1-polr.R
new file mode 100644
index 0000000..962cc86
--- /dev/null
+++ b/win32/deps/library/stats/tests/drop1-polr.R
@@ -0,0 +1,32 @@
+### Test calling drop1.default() "deep down" -- via
+### correct formula environment
+
+library(stats)
+stopifnot(require(MASS))
+
+regr <- function(formula, data, ...)
+{
+ lform <- formula(formula)
+ d1 <- data
+ i.polr(lform, d1, ...)
+}
+
+i.polr <- function(form, data, ...)
+{
+ lfo <- form
+ d2 <- data
+ environment(lfo) <- environment()
+ lreg <- polr(lfo, data=d2, ...)
+ do.drop(lreg, lreg1$coef, ltesttype="Chisq")
+}
+
+do.drop <- function(lreg, lcoeftab, ltesttype)
+{
+ drop1(lreg, test=ltesttype, scope=terms(lreg), trace=FALSE)
+}
+
+m <- polr(Sat ~ Infl + Type + Cont, data = housing)
+rr <- regr(formula(m), data = housing)
+dr1 <- drop1(m)
+stopifnot(is.data.frame(rr),
+ all.equal(rr[-(3:4)], dr1, check.attributes=FALSE))
diff --git a/win32/deps/library/stats/tests/ig_glm.R b/win32/deps/library/stats/tests/ig_glm.R
new file mode 100644
index 0000000..db040a6
--- /dev/null
+++ b/win32/deps/library/stats/tests/ig_glm.R
@@ -0,0 +1,61 @@
+## some tests of inverse-gaussian GLMs based on a file suppled by
+## David Firth, Feb 2009.
+
+options(digits=5)
+
+## Data from Whitmore, G A (1986), Inverse Gaussian Ratio Estimation.
+## Applied Statistics 35(1), 8-15.
+##
+## A "real, but disguised" set of data (Whitmore, 1986, p8).
+##
+## For each of 20 products, x is projected sales and y is actual sales.
+
+x <- c(5959, 3534, 2641, 1965, 1738, 1182, 667, 613, 610, 549,
+ 527, 353, 331, 290, 253, 193, 156, 133, 122, 114)
+y <- c(5673, 3659, 2565, 2182, 1839, 1236, 918, 902, 756, 500,
+ 487, 463, 225, 257, 311, 212, 166, 123, 198, 99)
+
+## Whitmore's model (2.4) is
+
+fit <- glm(y ~ x - 1, weights = x^2,
+ family = inverse.gaussian(link = "identity"),
+ epsilon = 1e-12)
+fit
+coef(summary(fit))
+## Alternatively, use the explicit formula that's available for the MLE
+## in this example. It's just a ratio estimate:
+(beta.exact <- sum(y)/sum(x))
+stopifnot(all.equal(beta.exact, as.vector(coef(fit))))
+## and for a confidence interval via confint
+(ci <- confint(fit, 1, level = 0.95))
+## and via asymptotic normality
+sterr <- coef(summary(fit))[, "Std. Error"]
+coef(fit) + (1.96 * sterr * c(-1, 1))
+
+## David suggested the use of an inverse link
+
+fit2 <- glm(y ~ I(1/x) - 1, weights = x^2,
+ family = inverse.gaussian(link = "inverse"),
+ epsilon = 1e-12)
+coef(summary(fit2))
+## which gives the same CIs both ways
+ci1 <- rev(1/(confint(fit2, 1, level = 0.95)))
+sterr <- (summary(fit2)$coefficients)[, "Std. Error"]
+ci2 <- 1/(coef(fit2) - (1.96 * sterr * c(-1, 1)))
+stopifnot(all.equal(as.vector(ci), as.vector(ci1), 1e-5),
+ all.equal(as.vector(ci), ci2, 1e-3))
+
+## because the log likelihood for 1/beta is exactly quadratic.
+
+## The approximate intervals above differ slightly from the exact
+## confidence interval given in Whitmore (1986) -- as is to be
+## expected (they are based on asymptotic approximations, not the
+## exact pivot).
+
+
+## Now simulate from this model
+if(require("SuppDists")) {
+ print( ys <- simulate(fit, nsim = 3, seed = 1) )
+ for(i in seq_len(3))
+ print(coef(summary(update(fit, ys[, i] ~ .))))
+}
diff --git a/win32/deps/library/stats/tests/ks-test.R b/win32/deps/library/stats/tests/ks-test.R
new file mode 100644
index 0000000..dc380ec
--- /dev/null
+++ b/win32/deps/library/stats/tests/ks-test.R
@@ -0,0 +1,22 @@
+## some examples of the KS test
+
+## unrealistic one of PR#14561
+ds1 <- c(1.7,2,3,3,4,4,5,5,6,6)
+ks.test(ds1, "pnorm", mean = 3.3, sd = 1.55216)
+# how on earth can sigma = 1.55216 be known?
+
+# R >= 2.14.0 allows the equally invalid
+ks.test(ds1, "pnorm", mean = 3.3, sd = 1.55216, exact = TRUE)
+
+## Try out the effects of rounding
+set.seed(123)
+ds2 <- rnorm(1000)
+ks.test(ds2, "pnorm") # exact = FALSE is default for n = 1000
+ks.test(ds2, "pnorm", exact = TRUE)
+## next two are still close
+ks.test(round(ds2, 2), "pnorm")
+ks.test(round(ds2, 2), "pnorm", exact = TRUE)
+# now D has doubled, but p-values remain similar (if very different from ds2)
+ks.test(round(ds2, 1), "pnorm")
+ks.test(round(ds2, 1), "pnorm", exact = TRUE)
+
diff --git a/win32/deps/library/stats/tests/ks-test.Rout.save b/win32/deps/library/stats/tests/ks-test.Rout.save
new file mode 100644
index 0000000..991451a
--- /dev/null
+++ b/win32/deps/library/stats/tests/ks-test.Rout.save
@@ -0,0 +1,115 @@
+
+R Under development (unstable) (2011-08-04 r56621)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> ## some examples of the KS test
+>
+> ## unrealistic one of PR#14561
+> ds1 <- c(1.7,2,3,3,4,4,5,5,6,6)
+> ks.test(ds1, "pnorm", mean = 3.3, sd = 1.55216)
+
+ One-sample Kolmogorov-Smirnov test
+
+data: ds1
+D = 0.274, p-value = 0.4407
+alternative hypothesis: two-sided
+
+Warning message:
+In ks.test(ds1, "pnorm", mean = 3.3, sd = 1.55216) :
+ ties should not be present for the Kolmogorov-Smirnov test
+> # how on earth can sigma = 1.55216 be known?
+>
+> # R >= 2.14.0 allows the equally invalid
+> ks.test(ds1, "pnorm", mean = 3.3, sd = 1.55216, exact = TRUE)
+
+ One-sample Kolmogorov-Smirnov test
+
+data: ds1
+D = 0.274, p-value = 0.3715
+alternative hypothesis: two-sided
+
+Warning message:
+In ks.test(ds1, "pnorm", mean = 3.3, sd = 1.55216, exact = TRUE) :
+ ties should not be present for the Kolmogorov-Smirnov test
+>
+> ## Try out the effects of rounding
+> set.seed(123)
+> ds2 <- rnorm(1000)
+> ks.test(ds2, "pnorm") # exact = FALSE is default for n = 1000
+
+ One-sample Kolmogorov-Smirnov test
+
+data: ds2
+D = 0.0194, p-value = 0.8452
+alternative hypothesis: two-sided
+
+> ks.test(ds2, "pnorm", exact = TRUE)
+
+ One-sample Kolmogorov-Smirnov test
+
+data: ds2
+D = 0.0194, p-value = 0.8379
+alternative hypothesis: two-sided
+
+> ## next two are still close
+> ks.test(round(ds2, 2), "pnorm")
+
+ One-sample Kolmogorov-Smirnov test
+
+data: round(ds2, 2)
+D = 0.0192, p-value = 0.856
+alternative hypothesis: two-sided
+
+Warning message:
+In ks.test(round(ds2, 2), "pnorm") :
+ ties should not be present for the Kolmogorov-Smirnov test
+> ks.test(round(ds2, 2), "pnorm", exact = TRUE)
+
+ One-sample Kolmogorov-Smirnov test
+
+data: round(ds2, 2)
+D = 0.0192, p-value = 0.8489
+alternative hypothesis: two-sided
+
+Warning message:
+In ks.test(round(ds2, 2), "pnorm", exact = TRUE) :
+ ties should not be present for the Kolmogorov-Smirnov test
+> # now D has doubled, but p-values remain similar (if very different from ds2)
+> ks.test(round(ds2, 1), "pnorm")
+
+ One-sample Kolmogorov-Smirnov test
+
+data: round(ds2, 1)
+D = 0.0367, p-value = 0.1344
+alternative hypothesis: two-sided
+
+Warning message:
+In ks.test(round(ds2, 1), "pnorm") :
+ ties should not be present for the Kolmogorov-Smirnov test
+> ks.test(round(ds2, 1), "pnorm", exact = TRUE)
+
+ One-sample Kolmogorov-Smirnov test
+
+data: round(ds2, 1)
+D = 0.0367, p-value = 0.1311
+alternative hypothesis: two-sided
+
+Warning message:
+In ks.test(round(ds2, 1), "pnorm", exact = TRUE) :
+ ties should not be present for the Kolmogorov-Smirnov test
+>
+>
diff --git a/win32/deps/library/stats/tests/nafns.R b/win32/deps/library/stats/tests/nafns.R
new file mode 100644
index 0000000..a531306
--- /dev/null
+++ b/win32/deps/library/stats/tests/nafns.R
@@ -0,0 +1,135 @@
+# File src/library/stats/tests/nafns.R
+# Part of the R package, http://www.R-project.org
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# A copy of the GNU General Public License is available at
+# http://www.r-project.org/Licenses/
+
+## Tests of functions handling NAs in fits
+## These functions were introduced in 1.3.0.
+## They are used by lm and glm in base R, and by
+## packages MASS, rpart and survival.
+
+## Comparison strictness is set at 256eps, increased from 100eps for v.2.1.0
+## May look lenient, but notice that the Ozone levels that are being modeled
+## can be more than 100.
+
+dim(airquality)
+nd <- airquality[c(6,25:27), ]
+
+sm <- function(x) cat("length", length(x), "with", sum(is.na(x)), "NAs\n")
+
+# default is to omit some rows
+fit <- lm(Ozone ~ ., data=airquality, na.action=na.omit)
+summary(fit)
+sm(fitted(fit))
+sm(resid(fit))
+sm(predict(fit))
+(pp <- predict(fit, nd))
+
+fit2 <- lm(Ozone ~ ., data=airquality, na.action=na.exclude)
+summary(fit2) # same as before
+sm(fitted(fit2))
+sm(resid(fit2))
+sm(predict(fit2))
+(pp2 <- predict(fit2, nd))
+
+## same as before: napredict is only applied to predictions on the
+## original data, following Therneau's original code (and S-PLUS).
+## However, as from R 1.8.0 there is a separate na.action arg to predict.lm()
+stopifnot(all.equal(pp, pp2))
+
+## should fail
+try(fit3 <- lm(Ozone ~ ., data=airquality, na.action=na.fail))
+
+## more precise tests.
+f1 <- fitted(fit)
+f2 <- fitted(fit2)
+common <- match(names(f1), names(f2))
+stopifnot(max(abs(f1 - f2[common])) <= 256*.Machine$double.eps)
+stopifnot(all(is.na(f2[-common])))
+
+r1 <- resid(fit)
+r2 <- resid(fit2)
+common <- match(names(r1), names(r2))
+stopifnot(max(abs(r1 - r2[common])) <= 256*.Machine$double.eps)
+stopifnot(all(is.na(r2[-common])))
+
+p1 <- predict(fit)
+p2 <- predict(fit2)
+common <- match(names(p1), names(p2))
+stopifnot(max(abs(p1 - p2[common])) <= 256*.Machine$double.eps)
+stopifnot(all(is.na(p2[-common])))
+
+
+### now try out glm
+gfit <- glm(Ozone ~ ., data=airquality, na.action=na.omit)
+summary(gfit)
+sm(fitted(gfit))
+sm(resid(gfit))
+sm(predict(gfit))
+predict(gfit, nd)
+(pp <- predict(gfit, nd))
+
+gfit2 <- glm(Ozone ~ ., data=airquality, na.action=na.exclude)
+summary(gfit2) # same as before
+sm(fitted(gfit2))
+sm(resid(gfit2))
+sm(predict(gfit2))
+(pp2 <- predict(gfit2, nd))
+stopifnot(all.equal(pp, pp2))
+
+## more precise tests.
+f1 <- fitted(gfit)
+f2 <- fitted(gfit2)
+common <- match(names(f1), names(f2))
+stopifnot(max(abs(f1 - f2[common])) <= 256*.Machine$double.eps)
+stopifnot(all(is.na(f2[-common])))
+
+r1 <- resid(gfit)
+r2 <- resid(gfit2)
+common <- match(names(r1), names(r2))
+stopifnot(max(abs(r1 - r2[common])) <= 256*.Machine$double.eps)
+stopifnot(all(is.na(r2[-common])))
+
+p1 <- predict(gfit)
+p2 <- predict(gfit2)
+common <- match(names(p1), names(p2))
+stopifnot(max(abs(p1 - p2[common])) <= 256*.Machine$double.eps)
+stopifnot(all(is.na(p2[-common])))
+
+## tests of diagnostic measures.
+x <- 1:10
+y <- c(rnorm(9),NA)
+fit <- lm(y ~ x, na.action=na.exclude)
+fit2 <- lm(y ~ x, subset=-10)
+
+lm.influence(fit2); lm.influence(fit)
+
+rstandard(fit2); rstandard(fit)
+rstudent(fit2); rstudent(fit)
+
+dffits(fit2); dffits(fit)
+
+dfbetas(fit2); dfbetas(fit)
+
+covratio(fit2); covratio(fit)
+
+cooks.distance(fit2); cooks.distance(fit)
+
+(inf <- influence.measures(fit))
+(inf2 <- influence.measures(fit2))
+
+summary(inf)
+summary(inf2)
+
+plot(fit)
diff --git a/win32/deps/library/stats/tests/nls.R b/win32/deps/library/stats/tests/nls.R
new file mode 100644
index 0000000..870edaf
--- /dev/null
+++ b/win32/deps/library/stats/tests/nls.R
@@ -0,0 +1,263 @@
+# File src/library/stats/tests/nls.R
+# Part of the R package, http://www.R-project.org
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# A copy of the GNU General Public License is available at
+# http://www.r-project.org/Licenses/
+
+## tests of nls, especially of weighted fits
+
+.proctime00 <- proc.time()
+library(stats)
+options(digits=5) # to avoid trivial printed differences
+options(show.signif.stars=FALSE) # avoid fancy quotes in o/p
+options(show.nls.convergence=FALSE) # avoid non-diffable output
+pdf("nls-test.pdf")
+
+## selfStart.default() w/ no parameters:
+logist <- deriv( ~Asym/(1+exp(-(x-xmid)/scal)), c("Asym", "xmid", "scal"),
+ function(x, Asym, xmid, scal){} )
+logistInit <- function(mCall, LHS, data) {
+ xy <- sortedXyData(mCall[["x"]], LHS, data)
+ if(nrow(xy) < 3) stop("Too few distinct input values to fit a logistic")
+ Asym <- max(abs(xy[,"y"]))
+ if (Asym != max(xy[,"y"])) Asym <- -Asym # negative asymptote
+ xmid <- NLSstClosestX(xy, 0.5 * Asym)
+ scal <- NLSstClosestX(xy, 0.75 * Asym) - xmid
+ value <- c(Asym, xmid, scal)
+ names(value) <- mCall[c("Asym", "xmid", "scal")]
+ value
+}
+logist <- selfStart(logist, initial = logistInit) ##-> Error in R 1.5.0
+str(logist)
+
+## lower and upper in algorithm="port"
+set.seed(123)
+x <- runif(200)
+a <- b <- 1; c <- -0.1
+y <- a+b*x+c*x^2+rnorm(200, sd=0.05)
+plot(x,y)
+curve(a+b*x+c*x^2, add = TRUE)
+nls(y ~ a+b*x+c*I(x^2), start = c(a=1, b=1, c=0.1), algorithm = "port")
+(fm <- nls(y ~ a+b*x+c*I(x^2), start = c(a=1, b=1, c=0.1),
+ algorithm = "port", lower = c(0, 0, 0)))
+confint(fm)
+
+
+## weighted nls fit: unsupported < 2.3.0
+set.seed(123)
+y <- x <- 1:10
+yeps <- y + rnorm(length(y), sd = 0.01)
+wts <- rep(c(1, 2), length = 10); wts[5] <- 0
+fit0 <- lm(yeps ~ x, weights = wts)
+summary(fit0, cor = TRUE)
+cf0 <- coef(summary(fit0))[, 1:2]
+fit <- nls(yeps ~ a + b*x, start = list(a = 0.12345, b = 0.54321),
+ weights = wts, trace = TRUE)
+summary(fit, cor = TRUE)
+stopifnot(all.equal(residuals(fit), residuals(fit0), 1e5,
+ check.attributes = FALSE))
+stopifnot(df.residual(fit) == df.residual(fit0))
+cf1 <- coef(summary(fit))[, 1:2]
+fit2 <- nls(yeps ~ a + b*x, start = list(a = 0.12345, b = 0.54321),
+ weights = wts, trace = TRUE, algorithm = "port")
+summary(fit2, cor = TRUE)
+cf2 <- coef(summary(fit2))[, 1:2]
+rownames(cf0) <- c("a", "b")
+# expect relative errors ca 2e-08
+stopifnot(all.equal(cf1, cf0, 1e-6), all.equal(cf1, cf0, 1e-6))
+stopifnot(all.equal(residuals(fit2), residuals(fit0), 1e5,
+ check.attributes = FALSE))
+
+
+DNase1 <- subset(DNase, Run == 1)
+DNase1$wts <- rep(8:1, each = 2)
+fm1 <- nls(density ~ SSlogis(log(conc), Asym, xmid, scal),
+ data = DNase1, weights = wts)
+summary(fm1)
+
+## directly
+fm2 <- nls(density ~ Asym/(1 + exp((xmid - log(conc))/scal)),
+ data = DNase1, weights = wts,
+ start = list(Asym = 3, xmid = 0, scal = 1))
+summary(fm2)
+stopifnot(all.equal(coef(summary(fm2)), coef(summary(fm1)), tol = 1e-6))
+stopifnot(all.equal(residuals(fm2), residuals(fm1), tol = 1e-5))
+stopifnot(all.equal(fitted(fm2), fitted(fm1), tol = 1e-6))
+fm2a <- nls(density ~ Asym/(1 + exp((xmid - log(conc)))),
+ data = DNase1, weights = wts,
+ start = list(Asym = 3, xmid = 0))
+anova(fm2a, fm2)
+
+## and without using weights
+fm3 <- nls(~ sqrt(wts) * (density - Asym/(1 + exp((xmid - log(conc))/scal))),
+ data = DNase1, start = list(Asym = 3, xmid = 0, scal = 1))
+summary(fm3)
+stopifnot(all.equal(coef(summary(fm3)), coef(summary(fm1)), tol = 1e-6))
+ft <- with(DNase1, density - fitted(fm3)/sqrt(wts))
+stopifnot(all.equal(ft, fitted(fm1), tol = 1e-6))
+# sign of residuals is reversed
+r <- with(DNase1, -residuals(fm3)/sqrt(wts))
+all.equal(r, residuals(fm1), tol = 1e05)
+fm3a <- nls(~ sqrt(wts) * (density - Asym/(1 + exp((xmid - log(conc))))),
+ data = DNase1, start = list(Asym = 3, xmid = 0))
+anova(fm3a, fm3)
+
+## using conditional linearity
+fm4 <- nls(density ~ 1/(1 + exp((xmid - log(conc))/scal)),
+ data = DNase1, weights = wts,
+ start = list(xmid = 0, scal = 1), algorithm = "plinear")
+summary(fm4)
+cf <- coef(summary(fm4))[c(3,1,2), ]
+rownames(cf)[2] <- "Asym"
+stopifnot(all.equal(cf, coef(summary(fm1)), tol = 1e-6,
+ check.attributes = FALSE))
+stopifnot(all.equal(residuals(fm4), residuals(fm1), tol = 1e-5))
+stopifnot(all.equal(fitted(fm4), fitted(fm1), tol = 1e-6))
+fm4a <- nls(density ~ 1/(1 + exp((xmid - log(conc)))),
+ data = DNase1, weights = wts,
+ start = list(xmid = 0), algorithm = "plinear")
+anova(fm4a, fm4)
+
+## using 'port'
+fm5 <- nls(density ~ Asym/(1 + exp((xmid - log(conc))/scal)),
+ data = DNase1, weights = wts,
+ start = list(Asym = 3, xmid = 0, scal = 1),
+ algorithm = "port")
+summary(fm5)
+stopifnot(all.equal(coef(summary(fm5)), coef(summary(fm1)), tol = 1e-6))
+stopifnot(all.equal(residuals(fm5), residuals(fm1), tol = 1e-5))
+stopifnot(all.equal(fitted(fm5), fitted(fm1), tol = 1e-6))
+
+## check profiling
+pfm1 <- profile(fm1)
+pfm3 <- profile(fm3)
+for(m in names(pfm1)) stopifnot(all.equal(pfm1[[m]], pfm3[[m]], tol=1e-5))
+pfm5 <- profile(fm5)
+for(m in names(pfm1))
+ stopifnot(all.equal(pfm1[[m]], pfm5[[m]], tol=1e-5))
+(c1 <- confint(fm1))
+(c4 <- confint(fm4, 1:2))
+stopifnot(all.equal(c1[2:3, ], c4, tol = 1e-3))
+
+## some low-dimensional examples
+npts <- 1000
+set.seed(1001)
+x <- runif(npts)
+b <- 0.7
+y <- x^b+rnorm(npts, sd=0.05)
+a <- 0.5
+y2 <- a*x^b+rnorm(npts, sd=0.05)
+c <- 1.0
+y3 <- a*(x+c)^b+rnorm(npts, sd=0.05)
+d <- 0.5
+y4 <- a*(x^d+c)^b+rnorm(npts, sd=0.05)
+m1 <- c(y ~ x^b, y2 ~ a*x^b, y3 ~ a*(x+exp(logc))^b)
+s1 <- list(c(b=1), c(a=1,b=1), c(a=1,b=1,logc=0))
+for(p in 1:3) {
+ fm <- nls(m1[[p]], start = s1[[p]])
+ print(fm)
+ print(confint(fm))
+ fm <- nls(m1[[p]], start = s1[[p]], algorithm="port")
+ print(fm)
+ print(confint(fm))
+}
+
+fm <- nls(y2~x^b, start=c(b=1), algorithm="plinear")
+confint(profile(fm))
+fm <- nls(y3 ~ (x+exp(logc))^b, start=c(b=1, logc=0), algorithm="plinear")
+confint(profile(fm))
+
+
+## more profiling with bounds
+op <- options(digits=3)
+npts <- 10
+set.seed(1001)
+a <- 2
+b <- 0.5
+x <- runif(npts)
+y <- a*x/(1+a*b*x) + rnorm(npts, sd=0.2)
+gfun <- function(a,b,x) {
+ if(a < 0 || b < 0) stop("bounds violated")
+ a*x/(1+a*b*x)
+}
+m1 <- nls(y ~ gfun(a,b,x), algorithm = "port",
+ lower = c(0,0), start = c(a=1, b=1))
+(pr1 <- profile(m1))
+confint(pr1)
+
+gfun <- function(a,b,x) {
+ if(a < 0 || b < 0 || a > 1.5 || b > 1) stop("bounds violated")
+ a*x/(1+a*b*x)
+}
+m2 <- nls(y ~ gfun(a,b,x), algorithm = "port",
+ lower = c(0, 0), upper=c(1.5, 1), start = c(a=1, b=1))
+profile(m2)
+confint(m2)
+options(op)
+
+## scoping problems
+test <- function()
+{
+ x <- seq(0,5,len=20)
+ n <- 1
+ y <- 2*x^2 + n + rnorm(x)
+ xy <- data.frame(x=x,y=y)
+ myf <- function(x,a,b,c) a*x^b+c
+ nls(y ~ myf(x,a,b,n), data=xy, start=c(a=1,b=1), trace=TRUE)
+}
+test()
+## failed to find n in 2.2.x
+## found wrong n in 2.3.x
+## finally worked in 2.4.0
+
+
+## list 'start'
+getExpmat <- function(theta, t)
+{
+ conc <- matrix(nrow = length(t), ncol = length(theta))
+ for(i in 1:length(theta)) conc[, i] <- exp(-theta[i] * t)
+ conc
+}
+
+expsum <- as.vector(getExpmat(c(.05,.005), 1:100) %*% c(1,1))
+expsumNoisy <- expsum + max(expsum) *.001 * rnorm(100)
+expsum.df <-data.frame(expsumNoisy)
+
+## estimate decay rates, amplitudes with default Gauss-Newton
+summary (nls(expsumNoisy ~ getExpmat(k, 1:100) %*% sp, expsum.df,
+ start = list(k = c(.6,.02), sp = c(1,2))))
+
+## didn't work with port in 2.4.1
+summary (nls(expsumNoisy ~ getExpmat(k, 1:100) %*% sp, expsum.df,
+ start = list(k = c(.6,.02), sp = c(1,2)),
+ algorithm = "port"))
+
+
+## PR13540
+
+x <- runif(200)
+b0 <- c(rep(0,100),runif(100))
+b1 <- 1
+fac <- as.factor(rep(c(0,1), each = 100))
+y <- b0 + b1*x + rnorm(200, sd=0.05)
+# next failed in 2.8.1
+fit <- nls(y~b0[fac] + b1*x, start = list(b0=c(1,1), b1=1),
+ algorithm ="port", upper = c(100, 100, 100))
+# next did not "fail" in proposed fix:
+fit <- nls(y~b0[fac] + b1*x, start = list(b0=c(1,1), b1=101),
+ algorithm ="port", upper = c(100, 100, 100),
+ control = list(warnOnly=TRUE))# warning ..
+with(fit$convInfo, ## start par. violates constraints
+ stopifnot(isConv == FALSE, stopCode == 300))
+
+cat('Time elapsed: ', proc.time() - .proctime00,'\n')
diff --git a/win32/deps/library/stats/tests/nls.Rout.save b/win32/deps/library/stats/tests/nls.Rout.save
new file mode 100644
index 0000000..6937a94
--- /dev/null
+++ b/win32/deps/library/stats/tests/nls.Rout.save
@@ -0,0 +1,662 @@
+
+R version 2.15.0 Patched (2012-04-11 r58983) -- "Easter Beagle"
+Copyright (C) 2012 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> # File src/library/stats/tests/nls.R
+> # Part of the R package, http://www.R-project.org
+> #
+> # This program is free software; you can redistribute it and/or modify
+> # it under the terms of the GNU General Public License as published by
+> # the Free Software Foundation; either version 2 of the License, or
+> # (at your option) any later version.
+> #
+> # This program is distributed in the hope that it will be useful,
+> # but WITHOUT ANY WARRANTY; without even the implied warranty of
+> # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+> # GNU General Public License for more details.
+> #
+> # A copy of the GNU General Public License is available at
+> # http://www.r-project.org/Licenses/
+>
+> ## tests of nls, especially of weighted fits
+>
+> .proctime00 <- proc.time()
+> library(stats)
+> options(digits=5) # to avoid trivial printed differences
+> options(show.signif.stars=FALSE) # avoid fancy quotes in o/p
+> options(show.nls.convergence=FALSE) # avoid non-diffable output
+> pdf("nls-test.pdf")
+>
+> ## selfStart.default() w/ no parameters:
+> logist <- deriv( ~Asym/(1+exp(-(x-xmid)/scal)), c("Asym", "xmid", "scal"),
++ function(x, Asym, xmid, scal){} )
+> logistInit <- function(mCall, LHS, data) {
++ xy <- sortedXyData(mCall[["x"]], LHS, data)
++ if(nrow(xy) < 3) stop("Too few distinct input values to fit a logistic")
++ Asym <- max(abs(xy[,"y"]))
++ if (Asym != max(xy[,"y"])) Asym <- -Asym # negative asymptote
++ xmid <- NLSstClosestX(xy, 0.5 * Asym)
++ scal <- NLSstClosestX(xy, 0.75 * Asym) - xmid
++ value <- c(Asym, xmid, scal)
++ names(value) <- mCall[c("Asym", "xmid", "scal")]
++ value
++ }
+> logist <- selfStart(logist, initial = logistInit) ##-> Error in R 1.5.0
+> str(logist)
+function (x, Asym, xmid, scal)
+ - attr(*, "initial")=function (mCall, LHS, data)
+ - attr(*, "class")= chr "selfStart"
+>
+> ## lower and upper in algorithm="port"
+> set.seed(123)
+> x <- runif(200)
+> a <- b <- 1; c <- -0.1
+> y <- a+b*x+c*x^2+rnorm(200, sd=0.05)
+> plot(x,y)
+> curve(a+b*x+c*x^2, add = TRUE)
+> nls(y ~ a+b*x+c*I(x^2), start = c(a=1, b=1, c=0.1), algorithm = "port")
+Nonlinear regression model
+ model: y ~ a + b * x + c * I(x^2)
+ data: parent.frame()
+ a b c
+ 1.0058 0.9824 -0.0897
+ residual sum-of-squares: 0.46
+
+Algorithm "port", convergence message: relative convergence (4)
+> (fm <- nls(y ~ a+b*x+c*I(x^2), start = c(a=1, b=1, c=0.1),
++ algorithm = "port", lower = c(0, 0, 0)))
+Nonlinear regression model
+ model: y ~ a + b * x + c * I(x^2)
+ data: parent.frame()
+ a b c
+1.02 0.89 0.00
+ residual sum-of-squares: 0.468
+
+Algorithm "port", convergence message: both X-convergence and relative convergence (5)
+> confint(fm)
+Waiting for profiling to be done...
+ 2.5% 97.5%
+a 1.00875 1.037847
+b 0.84138 0.914645
+c NA 0.042807
+>
+>
+> ## weighted nls fit: unsupported < 2.3.0
+> set.seed(123)
+> y <- x <- 1:10
+> yeps <- y + rnorm(length(y), sd = 0.01)
+> wts <- rep(c(1, 2), length = 10); wts[5] <- 0
+> fit0 <- lm(yeps ~ x, weights = wts)
+> summary(fit0, cor = TRUE)
+
+Call:
+lm(formula = yeps ~ x, weights = wts)
+
+Weighted Residuals:
+ Min 1Q Median 3Q Max
+-0.01562 -0.00723 -0.00158 0.00403 0.02413
+
+Coefficients:
+ Estimate Std. Error t value Pr(>|t|)
+(Intercept) 0.00517 0.00764 0.68 0.52
+x 0.99915 0.00119 841.38 <2e-16
+
+Residual standard error: 0.0132 on 7 degrees of freedom
+Multiple R-squared: 1, Adjusted R-squared: 1
+F-statistic: 7.08e+05 on 1 and 7 DF, p-value: <2e-16
+
+Correlation of Coefficients:
+ (Intercept)
+x -0.89
+
+> cf0 <- coef(summary(fit0))[, 1:2]
+> fit <- nls(yeps ~ a + b*x, start = list(a = 0.12345, b = 0.54321),
++ weights = wts, trace = TRUE)
+112.14 : 0.12345 0.54321
+0.0012128 : 0.0051705 0.9991529
+> summary(fit, cor = TRUE)
+
+Formula: yeps ~ a + b * x
+
+Parameters:
+ Estimate Std. Error t value Pr(>|t|)
+a 0.00517 0.00764 0.68 0.52
+b 0.99915 0.00119 841.37 <2e-16
+
+Residual standard error: 0.0132 on 7 degrees of freedom
+
+Correlation of Parameter Estimates:
+ a
+b -0.89
+
+> stopifnot(all.equal(residuals(fit), residuals(fit0), 1e5,
++ check.attributes = FALSE))
+> stopifnot(df.residual(fit) == df.residual(fit0))
+> cf1 <- coef(summary(fit))[, 1:2]
+> fit2 <- nls(yeps ~ a + b*x, start = list(a = 0.12345, b = 0.54321),
++ weights = wts, trace = TRUE, algorithm = "port")
+ 0: 56.070572: 0.123450 0.543210
+ 1: 6.3964587: 1.34546 0.700840
+ 2: 0.00060639084: 0.00517053 0.999153
+ 3: 0.00060639084: 0.00517051 0.999153
+> summary(fit2, cor = TRUE)
+
+Formula: yeps ~ a + b * x
+
+Parameters:
+ Estimate Std. Error t value Pr(>|t|)
+a 0.00517 0.00764 0.68 0.52
+b 0.99915 0.00119 841.38 <2e-16
+
+Residual standard error: 0.0132 on 7 degrees of freedom
+
+Correlation of Parameter Estimates:
+ a
+b -0.89
+
+Algorithm "port", convergence message: both X-convergence and relative convergence (5)
+
+> cf2 <- coef(summary(fit2))[, 1:2]
+> rownames(cf0) <- c("a", "b")
+> # expect relative errors ca 2e-08
+> stopifnot(all.equal(cf1, cf0, 1e-6), all.equal(cf1, cf0, 1e-6))
+> stopifnot(all.equal(residuals(fit2), residuals(fit0), 1e5,
++ check.attributes = FALSE))
+>
+>
+> DNase1 <- subset(DNase, Run == 1)
+> DNase1$wts <- rep(8:1, each = 2)
+> fm1 <- nls(density ~ SSlogis(log(conc), Asym, xmid, scal),
++ data = DNase1, weights = wts)
+> summary(fm1)
+
+Formula: density ~ SSlogis(log(conc), Asym, xmid, scal)
+
+Parameters:
+ Estimate Std. Error t value Pr(>|t|)
+Asym 2.3350 0.0966 24.2 3.5e-12
+xmid 1.4731 0.0947 15.6 8.8e-10
+scal 1.0385 0.0304 34.1 4.2e-14
+
+Residual standard error: 0.0355 on 13 degrees of freedom
+
+>
+> ## directly
+> fm2 <- nls(density ~ Asym/(1 + exp((xmid - log(conc))/scal)),
++ data = DNase1, weights = wts,
++ start = list(Asym = 3, xmid = 0, scal = 1))
+> summary(fm2)
+
+Formula: density ~ Asym/(1 + exp((xmid - log(conc))/scal))
+
+Parameters:
+ Estimate Std. Error t value Pr(>|t|)
+Asym 2.3350 0.0966 24.2 3.5e-12
+xmid 1.4731 0.0947 15.6 8.8e-10
+scal 1.0385 0.0304 34.1 4.2e-14
+
+Residual standard error: 0.0355 on 13 degrees of freedom
+
+> stopifnot(all.equal(coef(summary(fm2)), coef(summary(fm1)), tol = 1e-6))
+> stopifnot(all.equal(residuals(fm2), residuals(fm1), tol = 1e-5))
+> stopifnot(all.equal(fitted(fm2), fitted(fm1), tol = 1e-6))
+> fm2a <- nls(density ~ Asym/(1 + exp((xmid - log(conc)))),
++ data = DNase1, weights = wts,
++ start = list(Asym = 3, xmid = 0))
+> anova(fm2a, fm2)
+Analysis of Variance Table
+
+Model 1: density ~ Asym/(1 + exp((xmid - log(conc))))
+Model 2: density ~ Asym/(1 + exp((xmid - log(conc))/scal))
+ Res.Df Res.Sum Sq Df Sum Sq F value Pr(>F)
+1 14 0.0186
+2 13 0.0164 1 0.00212 1.68 0.22
+>
+> ## and without using weights
+> fm3 <- nls(~ sqrt(wts) * (density - Asym/(1 + exp((xmid - log(conc))/scal))),
++ data = DNase1, start = list(Asym = 3, xmid = 0, scal = 1))
+> summary(fm3)
+
+Formula: 0 ~ sqrt(wts) * (density - Asym/(1 + exp((xmid - log(conc))/scal)))
+
+Parameters:
+ Estimate Std. Error t value Pr(>|t|)
+Asym 2.3350 0.0966 24.2 3.5e-12
+xmid 1.4731 0.0947 15.6 8.8e-10
+scal 1.0385 0.0304 34.1 4.2e-14
+
+Residual standard error: 0.0355 on 13 degrees of freedom
+
+> stopifnot(all.equal(coef(summary(fm3)), coef(summary(fm1)), tol = 1e-6))
+> ft <- with(DNase1, density - fitted(fm3)/sqrt(wts))
+> stopifnot(all.equal(ft, fitted(fm1), tol = 1e-6))
+> # sign of residuals is reversed
+> r <- with(DNase1, -residuals(fm3)/sqrt(wts))
+> all.equal(r, residuals(fm1), tol = 1e05)
+[1] TRUE
+> fm3a <- nls(~ sqrt(wts) * (density - Asym/(1 + exp((xmid - log(conc))))),
++ data = DNase1, start = list(Asym = 3, xmid = 0))
+> anova(fm3a, fm3)
+Analysis of Variance Table
+
+Model 1: 0 ~ sqrt(wts) * (density - Asym/(1 + exp((xmid - log(conc)))))
+Model 2: 0 ~ sqrt(wts) * (density - Asym/(1 + exp((xmid - log(conc))/scal)))
+ Res.Df Res.Sum Sq Df Sum Sq F value Pr(>F)
+1 14 0.0186
+2 13 0.0164 1 0.00212 1.68 0.22
+>
+> ## using conditional linearity
+> fm4 <- nls(density ~ 1/(1 + exp((xmid - log(conc))/scal)),
++ data = DNase1, weights = wts,
++ start = list(xmid = 0, scal = 1), algorithm = "plinear")
+> summary(fm4)
+
+Formula: density ~ 1/(1 + exp((xmid - log(conc))/scal))
+
+Parameters:
+ Estimate Std. Error t value Pr(>|t|)
+xmid 1.4731 0.0947 15.6 8.8e-10
+scal 1.0385 0.0304 34.1 4.2e-14
+.lin 2.3350 0.0966 24.2 3.5e-12
+
+Residual standard error: 0.0355 on 13 degrees of freedom
+
+> cf <- coef(summary(fm4))[c(3,1,2), ]
+> rownames(cf)[2] <- "Asym"
+> stopifnot(all.equal(cf, coef(summary(fm1)), tol = 1e-6,
++ check.attributes = FALSE))
+> stopifnot(all.equal(residuals(fm4), residuals(fm1), tol = 1e-5))
+> stopifnot(all.equal(fitted(fm4), fitted(fm1), tol = 1e-6))
+> fm4a <- nls(density ~ 1/(1 + exp((xmid - log(conc)))),
++ data = DNase1, weights = wts,
++ start = list(xmid = 0), algorithm = "plinear")
+> anova(fm4a, fm4)
+Analysis of Variance Table
+
+Model 1: density ~ 1/(1 + exp((xmid - log(conc))))
+Model 2: density ~ 1/(1 + exp((xmid - log(conc))/scal))
+ Res.Df Res.Sum Sq Df Sum Sq F value Pr(>F)
+1 14 0.0186
+2 13 0.0164 1 0.00212 1.68 0.22
+>
+> ## using 'port'
+> fm5 <- nls(density ~ Asym/(1 + exp((xmid - log(conc))/scal)),
++ data = DNase1, weights = wts,
++ start = list(Asym = 3, xmid = 0, scal = 1),
++ algorithm = "port")
+> summary(fm5)
+
+Formula: density ~ Asym/(1 + exp((xmid - log(conc))/scal))
+
+Parameters:
+ Estimate Std. Error t value Pr(>|t|)
+Asym 2.3350 0.0966 24.2 3.5e-12
+xmid 1.4731 0.0947 15.6 8.8e-10
+scal 1.0385 0.0304 34.1 4.2e-14
+
+Residual standard error: 0.0355 on 13 degrees of freedom
+
+Algorithm "port", convergence message: relative convergence (4)
+
+> stopifnot(all.equal(coef(summary(fm5)), coef(summary(fm1)), tol = 1e-6))
+> stopifnot(all.equal(residuals(fm5), residuals(fm1), tol = 1e-5))
+> stopifnot(all.equal(fitted(fm5), fitted(fm1), tol = 1e-6))
+>
+> ## check profiling
+> pfm1 <- profile(fm1)
+> pfm3 <- profile(fm3)
+> for(m in names(pfm1)) stopifnot(all.equal(pfm1[[m]], pfm3[[m]], tol=1e-5))
+> pfm5 <- profile(fm5)
+> for(m in names(pfm1))
++ stopifnot(all.equal(pfm1[[m]], pfm5[[m]], tol=1e-5))
+> (c1 <- confint(fm1))
+Waiting for profiling to be done...
+ 2.5% 97.5%
+Asym 2.14936 2.5724
+xmid 1.28535 1.6966
+scal 0.97526 1.1068
+> (c4 <- confint(fm4, 1:2))
+Waiting for profiling to be done...
+ 2.5% 97.5%
+xmid 1.2866 1.6949
+scal 0.9757 1.1063
+> stopifnot(all.equal(c1[2:3, ], c4, tol = 1e-3))
+>
+> ## some low-dimensional examples
+> npts <- 1000
+> set.seed(1001)
+> x <- runif(npts)
+> b <- 0.7
+> y <- x^b+rnorm(npts, sd=0.05)
+> a <- 0.5
+> y2 <- a*x^b+rnorm(npts, sd=0.05)
+> c <- 1.0
+> y3 <- a*(x+c)^b+rnorm(npts, sd=0.05)
+> d <- 0.5
+> y4 <- a*(x^d+c)^b+rnorm(npts, sd=0.05)
+> m1 <- c(y ~ x^b, y2 ~ a*x^b, y3 ~ a*(x+exp(logc))^b)
+> s1 <- list(c(b=1), c(a=1,b=1), c(a=1,b=1,logc=0))
+> for(p in 1:3) {
++ fm <- nls(m1[[p]], start = s1[[p]])
++ print(fm)
++ print(confint(fm))
++ fm <- nls(m1[[p]], start = s1[[p]], algorithm="port")
++ print(fm)
++ print(confint(fm))
++ }
+Nonlinear regression model
+ model: y ~ x^b
+ data: parent.frame()
+ b
+0.695
+ residual sum-of-squares: 2.39
+Waiting for profiling to be done...
+ 2.5% 97.5%
+0.68704 0.70281
+Nonlinear regression model
+ model: y ~ x^b
+ data: parent.frame()
+ b
+0.695
+ residual sum-of-squares: 2.39
+
+Algorithm "port", convergence message: relative convergence (4)
+Waiting for profiling to be done...
+ 2.5% 97.5%
+0.68704 0.70281
+Nonlinear regression model
+ model: y2 ~ a * x^b
+ data: parent.frame()
+ a b
+0.502 0.724
+ residual sum-of-squares: 2.51
+Waiting for profiling to be done...
+ 2.5% 97.5%
+a 0.49494 0.50893
+b 0.70019 0.74767
+Nonlinear regression model
+ model: y2 ~ a * x^b
+ data: parent.frame()
+ a b
+0.502 0.724
+ residual sum-of-squares: 2.51
+
+Algorithm "port", convergence message: relative convergence (4)
+Waiting for profiling to be done...
+ 2.5% 97.5%
+a 0.49494 0.50893
+b 0.70019 0.74767
+Nonlinear regression model
+ model: y3 ~ a * (x + exp(logc))^b
+ data: parent.frame()
+ a b logc
+ 0.558 0.603 -0.176
+ residual sum-of-squares: 2.44
+Waiting for profiling to be done...
+ 2.5% 97.5%
+a 0.35006 0.66057
+b 0.45107 0.91473
+logc -0.64627 0.40946
+Nonlinear regression model
+ model: y3 ~ a * (x + exp(logc))^b
+ data: parent.frame()
+ a b logc
+ 0.558 0.603 -0.176
+ residual sum-of-squares: 2.44
+
+Algorithm "port", convergence message: relative convergence (4)
+Waiting for profiling to be done...
+ 2.5% 97.5%
+a 0.35006 0.66057
+b 0.45107 0.91473
+logc -0.64627 0.40946
+>
+> fm <- nls(y2~x^b, start=c(b=1), algorithm="plinear")
+> confint(profile(fm))
+ 2.5% 97.5%
+0.70019 0.74767
+> fm <- nls(y3 ~ (x+exp(logc))^b, start=c(b=1, logc=0), algorithm="plinear")
+> confint(profile(fm))
+ 2.5% 97.5%
+b 0.45105 0.91471
+logc -0.64625 0.40933
+>
+>
+> ## more profiling with bounds
+> op <- options(digits=3)
+> npts <- 10
+> set.seed(1001)
+> a <- 2
+> b <- 0.5
+> x <- runif(npts)
+> y <- a*x/(1+a*b*x) + rnorm(npts, sd=0.2)
+> gfun <- function(a,b,x) {
++ if(a < 0 || b < 0) stop("bounds violated")
++ a*x/(1+a*b*x)
++ }
+> m1 <- nls(y ~ gfun(a,b,x), algorithm = "port",
++ lower = c(0,0), start = c(a=1, b=1))
+> (pr1 <- profile(m1))
+$a
+ tau par.vals.a par.vals.b
+1 -3.869 0.706 0.000
+2 -3.114 0.802 0.000
+3 -0.863 1.124 0.000
+4 0.000 1.538 0.263
+5 0.590 1.952 0.446
+6 1.070 2.423 0.592
+7 1.534 3.082 0.737
+8 1.969 4.034 0.878
+9 2.376 5.502 1.014
+10 2.751 7.929 1.144
+11 3.090 12.263 1.264
+12 3.375 20.845 1.373
+
+$b
+ tau par.vals.a par.vals.b
+1 -0.673 1.2087 0.0272
+2 0.000 1.5381 0.2633
+3 0.707 2.0026 0.4994
+4 1.365 2.6295 0.7236
+5 1.994 3.5762 0.9522
+6 2.611 5.1820 1.1962
+7 3.225 8.2162 1.4614
+8 3.820 17.3946 1.7512
+
+attr(,"original.fit")
+Nonlinear regression model
+ model: y ~ gfun(a, b, x)
+ data: parent.frame()
+ a b
+1.538 0.263
+ residual sum-of-squares: 0.389
+
+Algorithm "port", convergence message: relative convergence (4)
+attr(,"summary")
+
+Formula: y ~ gfun(a, b, x)
+
+Parameters:
+ Estimate Std. Error t value Pr(>|t|)
+a 1.538 0.617 2.49 0.037
+b 0.263 0.352 0.75 0.476
+
+Residual standard error: 0.221 on 8 degrees of freedom
+
+Algorithm "port", convergence message: relative convergence (4)
+
+attr(,"class")
+[1] "profile.nls" "profile"
+> confint(pr1)
+ 2.5% 97.5%
+a 0.96 5.20
+b NA 1.07
+>
+> gfun <- function(a,b,x) {
++ if(a < 0 || b < 0 || a > 1.5 || b > 1) stop("bounds violated")
++ a*x/(1+a*b*x)
++ }
+> m2 <- nls(y ~ gfun(a,b,x), algorithm = "port",
++ lower = c(0, 0), upper=c(1.5, 1), start = c(a=1, b=1))
+> profile(m2)
+$a
+ tau par.vals.a par.vals.b
+1 -3.681 0.729 0.000
+2 -2.945 0.823 0.000
+3 -0.977 1.099 0.000
+4 0.000 1.500 0.243
+
+$b
+ tau par.vals.a par.vals.b
+1 -0.733 1.18200 0.00395
+2 0.000 1.50000 0.24263
+3 1.645 1.50000 0.48132
+4 2.154 1.50000 0.57869
+5 2.727 1.50000 0.70706
+6 3.288 1.50000 0.85748
+
+attr(,"original.fit")
+Nonlinear regression model
+ model: y ~ gfun(a, b, x)
+ data: parent.frame()
+ a b
+1.500 0.243
+ residual sum-of-squares: 0.39
+
+Algorithm "port", convergence message: relative convergence (4)
+attr(,"summary")
+
+Formula: y ~ gfun(a, b, x)
+
+Parameters:
+ Estimate Std. Error t value Pr(>|t|)
+a 1.500 0.598 2.51 0.036
+b 0.243 0.356 0.68 0.514
+
+Residual standard error: 0.221 on 8 degrees of freedom
+
+Algorithm "port", convergence message: relative convergence (4)
+
+attr(,"class")
+[1] "profile.nls" "profile"
+> confint(m2)
+Waiting for profiling to be done...
+ 2.5% 97.5%
+a 0.907 NA
+b NA 0.611
+> options(op)
+>
+> ## scoping problems
+> test <- function()
++ {
++ x <- seq(0,5,len=20)
++ n <- 1
++ y <- 2*x^2 + n + rnorm(x)
++ xy <- data.frame(x=x,y=y)
++ myf <- function(x,a,b,c) a*x^b+c
++ nls(y ~ myf(x,a,b,n), data=xy, start=c(a=1,b=1), trace=TRUE)
++ }
+> test()
+8291.9 : 1 1
+726.02 : 0.80544 2.42971
+552.85 : 1.290 2.129
+70.431 : 1.9565 1.9670
+26.555 : 1.9788 2.0064
+26.503 : 1.9798 2.0046
+26.503 : 1.9799 2.0046
+Nonlinear regression model
+ model: y ~ myf(x, a, b, n)
+ data: xy
+ a b
+1.98 2.00
+ residual sum-of-squares: 26.5
+> ## failed to find n in 2.2.x
+> ## found wrong n in 2.3.x
+> ## finally worked in 2.4.0
+>
+>
+> ## list 'start'
+> getExpmat <- function(theta, t)
++ {
++ conc <- matrix(nrow = length(t), ncol = length(theta))
++ for(i in 1:length(theta)) conc[, i] <- exp(-theta[i] * t)
++ conc
++ }
+>
+> expsum <- as.vector(getExpmat(c(.05,.005), 1:100) %*% c(1,1))
+> expsumNoisy <- expsum + max(expsum) *.001 * rnorm(100)
+> expsum.df <-data.frame(expsumNoisy)
+>
+> ## estimate decay rates, amplitudes with default Gauss-Newton
+> summary (nls(expsumNoisy ~ getExpmat(k, 1:100) %*% sp, expsum.df,
++ start = list(k = c(.6,.02), sp = c(1,2))))
+
+Formula: expsumNoisy ~ getExpmat(k, 1:100) %*% sp
+
+Parameters:
+ Estimate Std. Error t value Pr(>|t|)
+k1 5.00e-02 3.07e-04 162.5 <2e-16
+k2 4.99e-03 5.38e-05 92.8 <2e-16
+sp1 1.00e+00 4.47e-03 224.0 <2e-16
+sp2 9.99e-01 5.00e-03 199.8 <2e-16
+
+Residual standard error: 0.00205 on 96 degrees of freedom
+
+>
+> ## didn't work with port in 2.4.1
+> summary (nls(expsumNoisy ~ getExpmat(k, 1:100) %*% sp, expsum.df,
++ start = list(k = c(.6,.02), sp = c(1,2)),
++ algorithm = "port"))
+
+Formula: expsumNoisy ~ getExpmat(k, 1:100) %*% sp
+
+Parameters:
+ Estimate Std. Error t value Pr(>|t|)
+k1 5.00e-02 3.07e-04 162.5 <2e-16
+k2 4.99e-03 5.38e-05 92.8 <2e-16
+sp1 1.00e+00 4.47e-03 224.0 <2e-16
+sp2 9.99e-01 5.00e-03 199.8 <2e-16
+
+Residual standard error: 0.00205 on 96 degrees of freedom
+
+Algorithm "port", convergence message: both X-convergence and relative convergence (5)
+
+>
+>
+> ## PR13540
+>
+> x <- runif(200)
+> b0 <- c(rep(0,100),runif(100))
+> b1 <- 1
+> fac <- as.factor(rep(c(0,1), each = 100))
+> y <- b0 + b1*x + rnorm(200, sd=0.05)
+> # next failed in 2.8.1
+> fit <- nls(y~b0[fac] + b1*x, start = list(b0=c(1,1), b1=1),
++ algorithm ="port", upper = c(100, 100, 100))
+> # next did not "fail" in proposed fix:
+> fit <- nls(y~b0[fac] + b1*x, start = list(b0=c(1,1), b1=101),
++ algorithm ="port", upper = c(100, 100, 100),
++ control = list(warnOnly=TRUE))# warning ..
+Warning message:
+In nls(y ~ b0[fac] + b1 * x, start = list(b0 = c(1, 1), b1 = 101), :
+ Convergence failure: initial par violates constraints
+> with(fit$convInfo, ## start par. violates constraints
++ stopifnot(isConv == FALSE, stopCode == 300))
+>
+> cat('Time elapsed: ', proc.time() - .proctime00,'\n')
+Time elapsed: 2.168 0.023 2.201 0 0
+>
diff --git a/win32/deps/library/stats/tests/offsets.R b/win32/deps/library/stats/tests/offsets.R
new file mode 100644
index 0000000..eea721a
--- /dev/null
+++ b/win32/deps/library/stats/tests/offsets.R
@@ -0,0 +1,27 @@
+## tests of offsets, and prediction from them.
+
+data(anorexia, package = "MASS")
+
+## via formula
+fit1 <- lm(Postwt ~ Prewt + Treat + offset(Prewt), data = anorexia)
+summary(fit1)
+pred <- fitted(fit1)
+stopifnot(all.equal(predict(fit1, anorexia), pred))
+
+## via argument
+fit2 <- lm(Postwt ~ Prewt + Treat, data = anorexia, offset=Prewt)
+summary(fit2)
+stopifnot(all.equal(predict(fit2, anorexia), pred))
+
+## now spili into two parts
+anorexia$o1 <- 0.9*anorexia$Prewt
+anorexia$o2 <- 0.1*anorexia$Prewt
+fit3 <- lm(Postwt ~ Prewt + Treat + offset(o1) + offset(o2), data = anorexia)
+summary(fit3)
+stopifnot(all.equal(predict(fit3, anorexia), pred))
+
+fit4 <- lm(Postwt ~ Prewt + Treat + offset(o1), data = anorexia, offset = o2)
+summary(fit4)
+stopifnot(all.equal(predict(fit4, anorexia), pred))
+
+## using more than one offset failed in R 2.8.1
diff --git a/win32/deps/library/stats/tests/ppr.R b/win32/deps/library/stats/tests/ppr.R
new file mode 100644
index 0000000..f582956
--- /dev/null
+++ b/win32/deps/library/stats/tests/ppr.R
@@ -0,0 +1,6 @@
+## example from PR#13571: should fail, not crash.
+
+require("stats")
+bad <- as.matrix(read.csv("ppr_test.csv"))
+try(ppr(bad[,-3], bad[, 3], nterms=1))
+
diff --git a/win32/deps/library/stats/tests/ppr_test.csv b/win32/deps/library/stats/tests/ppr_test.csv
new file mode 100644
index 0000000..3efcefd
--- /dev/null
+++ b/win32/deps/library/stats/tests/ppr_test.csv
@@ -0,0 +1,443 @@
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+"384",-0.0288709420636975,1,-0.157806820134940
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+"387",-0.0175975974392743,2,-0.251533189535103
+"388",-0.0172844489774848,2,0.758893789787943
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+"390",-0.0166581520539057,1,-0.362704477405226
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+"404",-0.0238605666750649,2,0.199286515264368
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+"406",-0.10089508827529,1,0.114498290097875
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+"427",0.0688313780146366,1,-0.386184997207579
+"428",-0.062690975936967,1,-0.503984283937765
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+"435",0.0108989125835731,2,-0.556213330349359
+"436",0.0046359433477825,2,-0.47603482348101
+"437",-0.0470335528474903,2,-0.290496276509039
+"438",-0.00256647127337676,1,-0.174951863141946
+"439",0.0791652772536912,1,-0.0941605505892384
+"440",-0.0138398158977999,1,0.0900586677437571
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+"442",0.0278089295202079,2,-0.215872199044323
diff --git a/win32/deps/library/stats/tests/simulate.R b/win32/deps/library/stats/tests/simulate.R
new file mode 100644
index 0000000..7b6d4c2
--- /dev/null
+++ b/win32/deps/library/stats/tests/simulate.R
@@ -0,0 +1,78 @@
+## tests of the simulate.lm method, added Feb 2009
+
+options(digits = 5)
+
+# recommended packages should be present
+if(!require("MASS")) q()
+
+## cases should be named
+fit1 <- lm(time ~ dist, data = hills)
+set.seed(1)
+simulate(fit1, nsim = 3)
+
+## and weights should be takedn into account
+fit2 <- lm(time ~ -1 + dist + climb, hills[-18, ], weight = 1/dist^2)
+coef(summary(fit2))
+set.seed(1)
+( ys <- simulate(fit2, nsim = 3) )
+for(i in seq_len(3))
+ print(coef(summary(update(fit2, ys[, i] ~ .))))
+
+## Poisson fit
+fit3 <- glm(Postwt ~ Prewt + Treat + offset(Prewt),
+ family = gaussian, data = anorexia)
+coef(summary(fit3))
+set.seed(1)
+simulate(fit3, nsim = 8)
+
+## two-column binomial fit
+ldose <- rep(0:5, 2)
+numdead <- c(1, 4, 9, 13, 18, 20, 0, 2, 6, 10, 12, 16)
+sex <- factor(rep(c("M", "F"), c(6, 6)))
+SF <- cbind(numdead, numalive = 20 - numdead)
+fit4 <- glm(SF ~ sex + ldose - 1, family = binomial)
+coef(summary(fit4))
+set.seed(1)
+( ys <- simulate(fit4, nsim = 3) )
+for(i in seq_len(3))
+ print(coef(summary(update(fit4, ys[, i] ~ .))))
+
+## same via proportions
+fit5 <- glm(numdead/20 ~ sex + ldose - 1, family = binomial,
+ weights = rep(20, 12))
+set.seed(1)
+( ys <- simulate(fit5, nsim = 3) )
+for(i in seq_len(3))
+ print(coef(summary(update(fit5, ys[, i] ~ .))))
+
+
+## factor binomial fit
+bwt <- with(birthwt, {
+ race <- factor(race, labels = c("white", "black", "other"))
+ table(ptl)
+ ptd <- factor(ptl > 0)
+ table(ftv)
+ ftv <- factor(ftv)
+ levels(ftv)[-(1:2)] <- "2+"
+ data.frame(low = factor(low), age, lwt, race,
+ smoke = (smoke > 0), ptd, ht = (ht > 0), ui = (ui > 0), ftv)
+})
+fit6 <- glm(low ~ ., family = binomial, data = bwt)
+coef(summary(fit6))
+set.seed(1)
+ys <- simulate(fit6, nsim = 3)
+ys[1:10, ]
+for(i in seq_len(3))
+ print(coef(summary(update(fit6, ys[, i] ~ .))))
+
+
+## gamma fit, from example(glm)
+clotting <- data.frame(u = c(5,10,15,20,30,40,60,80,100),
+ lot1 = c(118,58,42,35,27,25,21,19,18))
+fit7 <- glm(lot1 ~ log(u), data=clotting, family=Gamma)
+coef(summary(fit7))
+set.seed(1)
+( ys <- simulate(fit7, nsim = 3) )
+for(i in seq_len(3))
+ print(coef(summary(update(fit7, ys[, i] ~ .))))
+
diff --git a/win32/deps/library/stats/tests/simulate.Rout.save b/win32/deps/library/stats/tests/simulate.Rout.save
new file mode 100644
index 0000000..c5d8880
--- /dev/null
+++ b/win32/deps/library/stats/tests/simulate.Rout.save
@@ -0,0 +1,407 @@
+
+R version 2.13.0 Under development (unstable) (2011-03-04 r54667)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> ## tests of the simulate.lm method, added Feb 2009
+>
+> options(digits = 5)
+>
+> # recommended packages should be present
+> if(!require("MASS")) q()
+Loading required package: MASS
+>
+> ## cases should be named
+> fit1 <- lm(time ~ dist, data = hills)
+> set.seed(1)
+> simulate(fit1, nsim = 3)
+ sim_1 sim_2 sim_3
+Greenmantle 3.4841 7.7039 25.4746
+Carnethy 48.8068 37.2737 30.9745
+Craig Dunain 28.4665 43.9584 57.3295
+Ben Rha 89.4727 79.5895 38.9971
+Ben Lomond 68.3785 77.0326 36.7858
+Goatfell 45.4299 58.5197 67.6189
+Bens of Jura 138.1736 123.3906 119.6004
+Cairnpapple 59.8758 59.0504 45.1641
+Scolty 48.3017 47.9202 38.2951
+Traprain 39.0478 31.3974 33.3777
+Lairig Ghru 258.5807 214.2935 217.0639
+Dollar 44.5912 44.0871 34.1140
+Lomonds 61.9013 89.6352 97.8082
+Cairn Table 0.9461 42.9001 14.7382
+Eildon Two 55.0951 50.2295 44.4990
+Cairngorm 77.5672 86.4083 85.1081
+Seven Hills 111.4626 99.5722 133.0006
+Knock Hill 38.9856 26.9579 14.0804
+Black Hill 49.0344 10.1091 40.0303
+Creag Beag 52.8285 69.5738 46.3069
+Kildcon Hill 38.4895 59.6709 9.3243
+Meall Ant-Suidhe 39.9240 16.9877 48.4197
+Half Ben Nevis 46.6300 24.3056 68.2987
+Cow Hill -27.8787 23.1894 25.7935
+N Berwick Law 32.5197 17.4555 51.8170
+Creag Dubh 27.3610 76.4071 39.6261
+Burnswark 42.0330 44.3590 19.6667
+Largo Law 7.4616 50.5758 25.3716
+Criffel 39.7654 49.8660 24.8692
+Acmony 45.1519 21.9790 27.3645
+Ben Nevis 105.5773 82.2313 66.0840
+Knockfarrel 43.0908 9.1228 45.9825
+Two Breweries 152.8438 174.3537 126.9294
+Cockleroi 31.5726 35.7046 35.7999
+Moffat Chase 134.2882 205.1244 148.7057
+>
+> ## and weights should be takedn into account
+> fit2 <- lm(time ~ -1 + dist + climb, hills[-18, ], weight = 1/dist^2)
+> coef(summary(fit2))
+ Estimate Std. Error t value Pr(>|t|)
+dist 4.8999847 0.4737032 10.3440 9.8468e-12
+climb 0.0084718 0.0016869 5.0221 1.8636e-05
+> set.seed(1)
+> ( ys <- simulate(fit2, nsim = 3) )
+ sim_1 sim_2 sim_3
+Greenmantle 15.754 13.355 18.247
+Carnethy 51.988 47.396 67.247
+Craig Dunain 30.614 34.000 40.672
+Ben Rha 58.825 42.959 36.719
+Ben Lomond 68.579 76.460 71.455
+Goatfell 55.088 71.287 53.926
+Bens of Jura 151.910 138.573 116.292
+Cairnpapple 41.841 34.234 38.413
+Scolty 34.958 35.733 28.443
+Traprain 32.564 39.177 34.915
+Lairig Ghru 209.113 130.333 157.652
+Dollar 43.936 36.921 37.675
+Lomonds 57.642 69.616 58.280
+Cairn Table 16.646 39.532 32.599
+Eildon Two 41.230 34.111 41.536
+Cairngorm 73.841 85.681 54.935
+Seven Hills 86.948 94.364 97.870
+Black Hill 35.952 27.000 32.437
+Creag Beag 37.808 34.432 39.509
+Kildcon Hill 19.520 12.910 16.075
+Meall Ant-Suidhe 33.970 36.271 31.514
+Half Ben Nevis 54.038 63.231 50.087
+Cow Hill 17.615 16.486 16.037
+N Berwick Law 12.152 15.778 24.416
+Creag Dubh 39.714 39.457 42.478
+Burnswark 35.747 35.141 41.549
+Largo Law 31.552 47.902 42.693
+Criffel 34.452 46.350 51.317
+Acmony 25.679 33.145 20.575
+Ben Nevis 91.620 86.634 78.946
+Knockfarrel 44.906 28.781 25.088
+Two Breweries 129.888 136.598 121.358
+Cockleroi 31.482 18.866 25.682
+Moffat Chase 138.983 177.836 141.436
+> for(i in seq_len(3))
++ print(coef(summary(update(fit2, ys[, i] ~ .))))
+ Estimate Std. Error t value Pr(>|t|)
+dist 4.8759333 0.4295826 11.3504 9.3646e-13
+climb 0.0091824 0.0015298 6.0023 1.0781e-06
+ Estimate Std. Error t value Pr(>|t|)
+dist 4.6969341 0.4406227 10.66 4.6417e-12
+climb 0.0099795 0.0015691 6.36 3.8442e-07
+ Estimate Std. Error t value Pr(>|t|)
+dist 4.8215499 0.420077 11.4778 7.0162e-13
+climb 0.0090388 0.001496 6.0422 9.6065e-07
+>
+> ## Poisson fit
+> fit3 <- glm(Postwt ~ Prewt + Treat + offset(Prewt),
++ family = gaussian, data = anorexia)
+> coef(summary(fit3))
+ Estimate Std. Error t value Pr(>|t|)
+(Intercept) 49.77111 13.39096 3.7168 0.00041011
+Prewt -0.56554 0.16118 -3.5087 0.00080343
+TreatCont -4.09707 1.89349 -2.1638 0.03399931
+TreatFT 4.56306 2.13334 2.1389 0.03603508
+> set.seed(1)
+> simulate(fit3, nsim = 8)
+ sim_1 sim_2 sim_3 sim_4 sim_5 sim_6 sim_7 sim_8
+1 76.364 84.997 72.948 78.581 83.762 62.645 70.046 87.655
+2 85.796 77.997 79.276 75.769 91.529 93.684 84.340 95.638
+3 79.726 76.809 100.122 90.039 82.835 81.123 89.696 75.979
+4 88.956 79.858 77.946 77.512 80.451 74.824 76.441 76.082
+5 81.905 76.512 70.629 67.511 81.309 78.424 85.830 87.696
+6 78.312 84.045 72.589 84.052 74.084 88.309 83.858 76.262
+7 87.004 84.121 86.744 79.204 96.013 88.336 79.083 65.958
+8 83.454 74.188 78.173 75.923 79.240 82.265 82.812 71.771
+9 84.710 76.723 78.472 72.621 86.034 76.696 77.664 73.942
+10 77.605 78.792 73.251 92.318 86.401 70.223 92.105 80.067
+11 89.938 87.609 69.008 77.078 79.035 76.676 79.261 76.571
+12 86.931 73.579 76.708 73.007 82.077 86.150 90.162 85.826
+13 76.661 85.140 87.974 82.372 87.232 75.252 82.427 78.048
+14 64.151 81.929 75.270 81.442 72.297 79.125 58.615 82.216
+15 84.154 83.722 66.643 69.424 90.060 68.155 66.771 73.749
+16 78.944 77.135 92.302 59.098 76.581 79.200 76.298 87.563
+17 82.577 85.272 85.657 78.221 94.233 83.589 84.343 77.545
+18 89.624 84.902 81.372 87.019 93.590 82.020 66.690 85.066
+19 87.943 78.426 89.599 81.795 82.791 81.068 88.923 76.038
+20 84.445 88.729 86.486 79.615 84.259 92.607 76.083 81.752
+21 89.233 90.918 78.499 86.734 75.671 88.142 77.567 82.487
+22 87.800 87.229 97.737 74.063 84.597 90.098 71.487 70.588
+23 80.777 91.330 78.478 87.911 87.540 73.815 70.112 79.251
+24 65.463 83.242 69.404 79.307 80.036 80.492 79.738 87.581
+25 81.411 68.177 76.078 82.021 73.917 85.144 80.640 81.841
+26 83.949 80.341 85.789 91.557 79.765 83.947 69.702 85.341
+27 83.658 76.200 100.851 86.305 84.495 69.886 77.737 76.425
+28 76.394 83.353 87.395 80.525 94.118 89.063 90.396 94.816
+29 81.843 80.851 88.369 93.295 81.802 71.887 82.018 85.732
+30 88.574 85.951 85.119 71.700 84.813 79.997 100.768 82.505
+31 93.966 78.128 82.154 80.683 75.454 93.724 93.178 95.943
+32 87.591 89.411 88.065 86.524 91.757 92.604 92.463 82.937
+33 93.707 86.434 96.498 89.842 100.128 98.619 91.036 93.118
+34 82.545 95.253 97.402 90.041 93.367 85.060 84.870 91.865
+35 75.353 89.964 92.132 85.913 90.648 84.194 80.037 89.165
+36 81.849 91.097 93.174 87.587 71.698 78.295 89.128 82.603
+37 83.949 89.381 78.108 86.214 90.064 97.816 97.030 83.781
+38 88.111 100.264 95.391 86.797 91.708 88.839 96.085 91.003
+39 92.769 80.657 86.627 89.946 82.627 80.103 79.418 88.676
+40 88.333 79.786 72.769 91.006 84.197 89.045 71.711 83.137
+41 79.035 90.178 83.819 63.414 74.154 87.681 79.418 89.384
+42 82.934 80.161 83.594 88.698 89.442 97.930 87.778 84.242
+43 90.825 84.515 96.182 88.577 83.679 81.754 95.389 81.075
+44 89.716 83.090 80.486 82.864 74.882 83.104 76.630 89.581
+45 83.067 85.640 84.871 94.510 85.309 84.969 90.416 72.509
+46 81.416 84.405 79.890 83.637 95.874 83.731 87.982 89.088
+47 89.853 90.757 86.073 85.324 84.976 84.750 95.640 90.776
+48 88.370 81.770 85.813 88.991 88.121 80.944 82.813 81.438
+49 83.831 81.084 79.509 96.615 91.220 94.676 82.122 76.819
+50 94.065 97.289 93.711 89.801 87.947 83.049 79.914 85.160
+51 88.740 84.464 77.532 83.016 83.503 83.253 82.351 96.777
+52 80.127 83.145 77.085 76.100 80.701 88.951 81.871 79.209
+53 88.863 85.784 96.540 84.173 91.644 94.332 102.886 70.212
+54 76.995 89.849 77.787 78.317 77.455 79.488 101.948 90.544
+55 97.743 87.230 90.618 85.936 89.461 84.197 86.580 84.245
+56 104.562 90.479 88.083 93.494 88.722 94.396 83.459 87.177
+57 87.962 85.768 93.382 84.580 74.720 97.627 76.757 82.044
+58 84.412 89.435 103.483 110.184 81.867 89.945 95.289 91.540
+59 94.153 90.597 101.249 91.266 96.569 80.198 82.567 95.071
+60 91.060 87.893 89.693 99.889 90.667 103.929 107.945 87.902
+61 105.676 92.626 72.970 72.943 94.523 98.931 82.737 84.683
+62 87.470 77.149 105.173 92.915 100.915 82.787 88.520 95.397
+63 100.074 97.400 99.915 86.075 105.545 94.806 121.849 93.533
+64 86.419 75.502 90.001 92.642 90.950 73.946 78.485 85.108
+65 84.122 87.208 89.215 92.087 91.960 93.284 91.455 84.941
+66 91.104 86.100 93.346 86.942 88.441 101.037 82.062 96.070
+67 77.408 85.453 88.856 99.244 101.014 78.578 92.429 83.066
+68 98.275 87.651 90.984 83.155 92.209 82.608 81.955 93.975
+69 91.681 77.253 87.819 86.560 82.422 86.137 91.151 96.234
+70 108.553 101.603 83.831 86.407 92.306 88.639 91.321 90.129
+71 95.016 80.079 98.591 87.035 78.307 77.509 83.441 97.618
+72 87.308 89.028 102.868 98.858 90.900 95.758 92.341 99.148
+>
+> ## two-column binomial fit
+> ldose <- rep(0:5, 2)
+> numdead <- c(1, 4, 9, 13, 18, 20, 0, 2, 6, 10, 12, 16)
+> sex <- factor(rep(c("M", "F"), c(6, 6)))
+> SF <- cbind(numdead, numalive = 20 - numdead)
+> fit4 <- glm(SF ~ sex + ldose - 1, family = binomial)
+> coef(summary(fit4))
+ Estimate Std. Error z value Pr(>|z|)
+sexF -3.4732 0.46852 -7.4130 1.2344e-13
+sexM -2.3724 0.38551 -6.1539 7.5579e-10
+ldose 1.0642 0.13108 8.1190 4.7015e-16
+> set.seed(1)
+> ( ys <- simulate(fit4, nsim = 3) )
+ sim_1.numdead sim_1.numalive sim_2.numdead sim_2.numalive sim_3.numdead
+1 1 19 2 18 1
+2 4 16 4 16 4
+3 9 11 10 10 4
+4 11 9 14 6 15
+5 19 1 17 3 16
+6 18 2 16 4 20
+7 2 18 0 20 0
+8 2 18 3 17 2
+9 5 15 7 13 4
+10 5 15 7 13 7
+11 15 5 13 7 12
+12 19 1 19 1 17
+ sim_3.numalive
+1 19
+2 16
+3 16
+4 5
+5 4
+6 0
+7 20
+8 18
+9 16
+10 13
+11 8
+12 3
+> for(i in seq_len(3))
++ print(coef(summary(update(fit4, ys[, i] ~ .))))
+ Estimate Std. Error z value Pr(>|z|)
+sexF -3.3079 0.45218 -7.3154 2.5656e-13
+sexM -2.5067 0.39240 -6.3880 1.6812e-10
+ldose 1.0482 0.12869 8.1454 3.7800e-16
+ Estimate Std. Error z value Pr(>|z|)
+sexF -2.84478 0.40661 -6.9963 2.6289e-12
+sexM -2.11845 0.35818 -5.9145 3.3286e-09
+ldose 0.90935 0.11578 7.8541 4.0273e-15
+ Estimate Std. Error z value Pr(>|z|)
+sexF -3.9838 0.52156 -7.6384 2.1996e-14
+sexM -2.8717 0.43047 -6.6712 2.5376e-11
+ldose 1.1487 0.14102 8.1459 3.7655e-16
+>
+> ## same via proportions
+> fit5 <- glm(numdead/20 ~ sex + ldose - 1, family = binomial,
++ weights = rep(20, 12))
+> set.seed(1)
+> ( ys <- simulate(fit5, nsim = 3) )
+ sim_1 sim_2 sim_3
+1 0.05 0.10 0.05
+2 0.20 0.20 0.20
+3 0.45 0.50 0.20
+4 0.55 0.70 0.75
+5 0.95 0.85 0.80
+6 0.90 0.80 1.00
+7 0.10 0.00 0.00
+8 0.10 0.15 0.10
+9 0.25 0.35 0.20
+10 0.25 0.35 0.35
+11 0.75 0.65 0.60
+12 0.95 0.95 0.85
+> for(i in seq_len(3))
++ print(coef(summary(update(fit5, ys[, i] ~ .))))
+ Estimate Std. Error z value Pr(>|z|)
+sexF -3.3079 0.45218 -7.3154 2.5656e-13
+sexM -2.5067 0.39240 -6.3880 1.6812e-10
+ldose 1.0482 0.12869 8.1454 3.7800e-16
+ Estimate Std. Error z value Pr(>|z|)
+sexF -2.84478 0.40661 -6.9963 2.6289e-12
+sexM -2.11845 0.35818 -5.9145 3.3286e-09
+ldose 0.90935 0.11578 7.8541 4.0273e-15
+ Estimate Std. Error z value Pr(>|z|)
+sexF -3.9838 0.52156 -7.6384 2.1996e-14
+sexM -2.8717 0.43047 -6.6712 2.5376e-11
+ldose 1.1487 0.14102 8.1459 3.7655e-16
+>
+>
+> ## factor binomial fit
+> bwt <- with(birthwt, {
++ race <- factor(race, labels = c("white", "black", "other"))
++ table(ptl)
++ ptd <- factor(ptl > 0)
++ table(ftv)
++ ftv <- factor(ftv)
++ levels(ftv)[-(1:2)] <- "2+"
++ data.frame(low = factor(low), age, lwt, race,
++ smoke = (smoke > 0), ptd, ht = (ht > 0), ui = (ui > 0), ftv)
++ })
+> fit6 <- glm(low ~ ., family = binomial, data = bwt)
+> coef(summary(fit6))
+ Estimate Std. Error z value Pr(>|z|)
+(Intercept) 0.823019 1.2447143 0.66121 0.5084769
+age -0.037234 0.0387024 -0.96207 0.3360159
+lwt -0.015653 0.0070804 -2.21075 0.0270532
+raceblack 1.192413 0.5359646 2.22480 0.0260948
+raceother 0.740685 0.4617443 1.60410 0.1086916
+smokeTRUE 0.755528 0.4250166 1.77764 0.0754623
+ptdTRUE 1.343763 0.4806207 2.79589 0.0051757
+htTRUE 1.913166 0.7207369 2.65446 0.0079436
+uiTRUE 0.680195 0.4643403 1.46486 0.1429580
+ftv1 -0.436380 0.4793936 -0.91027 0.3626779
+ftv2+ 0.179009 0.4563778 0.39224 0.6948827
+> set.seed(1)
+> ys <- simulate(fit6, nsim = 3)
+> ys[1:10, ]
+ sim_1 sim_2 sim_3
+1 0 0 0
+2 0 0 0
+3 0 0 0
+4 1 0 1
+5 0 1 1
+6 1 0 1
+7 1 0 0
+8 0 0 0
+9 0 0 0
+10 0 0 1
+> for(i in seq_len(3))
++ print(coef(summary(update(fit6, ys[, i] ~ .))))
+ Estimate Std. Error z value Pr(>|z|)
+(Intercept) -0.284354 1.2297301 -0.23123 0.817134
+age -0.011485 0.0389166 -0.29513 0.767897
+lwt -0.012314 0.0069041 -1.78353 0.074500
+raceblack 0.844051 0.5514350 1.53064 0.125857
+raceother 0.565993 0.4665978 1.21302 0.225122
+smokeTRUE 1.024337 0.4253416 2.40827 0.016028
+ptdTRUE 1.578045 0.4887012 3.22906 0.001242
+htTRUE 1.171556 0.7060321 1.65935 0.097045
+uiTRUE 0.384214 0.4835840 0.79451 0.426897
+ftv1 -0.790699 0.5271049 -1.50008 0.133594
+ftv2+ 0.522245 0.4498448 1.16094 0.245665
+ Estimate Std. Error z value Pr(>|z|)
+(Intercept) 0.916922 1.433819 0.63950 5.2250e-01
+age 0.034662 0.041752 0.83019 4.0643e-01
+lwt -0.036299 0.009577 -3.79021 1.5052e-04
+raceblack 2.588992 0.631372 4.10058 4.1211e-05
+raceother 1.073046 0.522576 2.05338 4.0036e-02
+smokeTRUE 0.710930 0.478870 1.48460 1.3765e-01
+ptdTRUE 0.679588 0.503299 1.35027 1.7693e-01
+htTRUE 1.988224 0.801811 2.47967 1.3151e-02
+uiTRUE 1.080176 0.489033 2.20880 2.7189e-02
+ftv1 -0.418153 0.549009 -0.76165 4.4627e-01
+ftv2+ 0.657962 0.500605 1.31433 1.8873e-01
+ Estimate Std. Error z value Pr(>|z|)
+(Intercept) 1.4927579 1.2779154 1.168119 0.24275859
+age -0.0986485 0.0415094 -2.376532 0.01747625
+lwt -0.0088426 0.0070635 -1.251885 0.21061194
+raceblack 0.2106382 0.5622160 0.374657 0.70791549
+raceother 0.8608985 0.4814556 1.788116 0.07375727
+smokeTRUE 0.7884781 0.4449757 1.771958 0.07640158
+ptdTRUE 1.9686209 0.5435116 3.622040 0.00029229
+htTRUE 1.7835637 0.7279712 2.450047 0.01428375
+uiTRUE 1.4816743 0.5139743 2.882779 0.00394184
+ftv1 -0.7388479 0.5090637 -1.451386 0.14667244
+ftv2+ -0.0097438 0.4670024 -0.020865 0.98335371
+>
+>
+> ## gamma fit, from example(glm)
+> clotting <- data.frame(u = c(5,10,15,20,30,40,60,80,100),
++ lot1 = c(118,58,42,35,27,25,21,19,18))
+> fit7 <- glm(lot1 ~ log(u), data=clotting, family=Gamma)
+> coef(summary(fit7))
+ Estimate Std. Error t value Pr(>|t|)
+(Intercept) -0.016554 0.00092755 -17.847 4.2791e-07
+log(u) 0.015343 0.00041496 36.975 2.7512e-09
+> set.seed(1)
+> ( ys <- simulate(fit7, nsim = 3) )
+ sim_1 sim_2 sim_3
+1 119.451 118.552 123.140
+2 56.310 51.798 48.747
+3 42.193 39.456 40.843
+4 34.581 33.905 35.580
+5 26.208 26.971 27.210
+6 25.476 25.840 24.437
+7 22.287 22.151 21.375
+8 20.206 20.503 19.626
+9 18.224 19.094 17.952
+> for(i in seq_len(3))
++ print(coef(summary(update(fit7, ys[, i] ~ .))))
+ Estimate Std. Error t value Pr(>|t|)
+(Intercept) -0.016008 0.00077887 -20.553 1.6197e-07
+log(u) 0.015044 0.00034611 43.465 8.9084e-10
+ Estimate Std. Error t value Pr(>|t|)
+(Intercept) -0.015483 0.00050102 -30.903 9.5910e-09
+log(u) 0.014935 0.00021999 67.889 3.9547e-11
+ Estimate Std. Error t value Pr(>|t|)
+(Intercept) -0.016850 0.00075120 -22.431 8.8554e-08
+log(u) 0.015569 0.00033659 46.256 5.7704e-10
+>
+>
diff --git a/win32/deps/library/stats/tests/smooth.spline.R b/win32/deps/library/stats/tests/smooth.spline.R
new file mode 100644
index 0000000..b7f47e0
--- /dev/null
+++ b/win32/deps/library/stats/tests/smooth.spline.R
@@ -0,0 +1,15 @@
+## moved from ?smooth.spline, quite system-specific.
+y18 <- c(1:3,5,4,7:3,2*(2:5),rep(10,4))
+xx <- seq(1,length(y18), len=201)
+s2. <- smooth.spline(y18, cv = TRUE,
+ control = list(trace=TRUE, tol=1e-6,low= -3,maxit=20))
+s2. ## i386-Linux: Df ~= (even! > ) 18 : interpolating -- much smaller PRESS
+## {others, e.g., may end quite differently!}
+plot(y18)
+lines(predict(s2., xx), col = 4)
+mtext(deparse(s2.$call,200), side= 1, line= -1, cex= 0.8, col= 4)
+
+(sdf8 <- smooth.spline(y18, df = 8, control=list(trace=TRUE)))
+sdf8$df - 8
+
+try(smooth.spline(y18, spar = 50)) #>> error : spar 'way too large'
diff --git a/win32/deps/library/stats/tests/ts-tests.R b/win32/deps/library/stats/tests/ts-tests.R
new file mode 100644
index 0000000..1589982
--- /dev/null
+++ b/win32/deps/library/stats/tests/ts-tests.R
@@ -0,0 +1,143 @@
+# File src/library/stats/tests/ts-tests.R
+# Part of the R package, http://www.R-project.org
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# A copy of the GNU General Public License is available at
+# http://www.r-project.org/Licenses/
+
+## tests of time-series functionality
+
+.proctime00 <- proc.time()
+library(stats)
+
+postscript("ts-test.ps")
+
+### ar
+ar(lh)
+ar(lh, method = "burg")
+ar(lh, method = "ols")
+ar(lh, FALSE, 4) # fit ar(4)
+ar.ols(lh)
+ar.ols(lh, FALSE, 4) # fit ar(4) by OLS
+
+ar(LakeHuron)
+ar(LakeHuron, method = "burg")
+ar(LakeHuron, method = "ols")
+ar(LakeHuron, method = "mle")
+
+ar(sunspot.year, method = "yw")
+ar(sunspot.year, method = "burg")
+ar(sunspot.year, method = "ols")
+ar(sunspot.year, method = "mle")
+
+
+### tests using presidents, contains missing values
+acf(presidents, na.action = na.pass)
+pacf(presidents, na.action = na.pass)
+## graphs in example(acf) suggest order 1 or 3
+(fit1 <- arima(presidents, c(1, 0, 0)))
+tsdiag(fit1)
+(fit3 <- arima(presidents, c(3, 0, 0))) # smaller AIC
+tsdiag(fit3)
+
+
+### tests of arima:
+arima(USAccDeaths, order = c(0,1,1), seasonal = list(order=c(0,1,1)))
+arima(USAccDeaths, order = c(0,1,1), seasonal = list(order=c(0,1,1)),
+ method = "CSS") # drops first 13 observations.
+
+## test fitting with NAs
+tmp <- LakeHuron
+trend <- time(LakeHuron) - 1920
+tmp[c(17, 45, 96)] <- NA
+arima(tmp, order=c(2,0,0), xreg=trend)
+arima(tmp, order=c(1,1,1), xreg=trend)
+trend[c(20, 67)] <- NA
+arima(tmp, order=c(2,0,0), xreg=trend)
+
+## tests of prediction
+predict(arima(lh, order=c(1,0,1)), n.ahead=5)
+predict(arima(lh, order=c(1,1,0)), n.ahead=5)
+predict(arima(lh, order=c(0,2,1)), n.ahead=5)
+
+## test of init
+arima(lh, order = c(1,0,1), init = c(0.5, 0.5, NA))
+arima(lh, order = c(1,0,1), init = c(0.5, 2, NA))
+try(arima(lh, order = c(1,0,1), init = c(2, NA, NA)))
+
+## test of fixed
+arima(lh, order = c(1,0,1), fixed = c(0.5, NA, NA), trans = FALSE)
+trend <- time(LakeHuron) - 1920
+arima(LakeHuron, order=c(2,0,0), xreg=trend)
+arima(x = LakeHuron, order = c(2, 0, 0), xreg = trend,
+ fixed = c(NA, NA, 580, -0.02))
+arima(x = LakeHuron, order = c(2, 0, 0), xreg = trend,
+ fixed = c(NA, NA, 580, 0))
+
+
+### model selection from WWWusage
+aics <- matrix(, 6, 6, dimnames=list(p=0:5, q=0:5))
+for(q in 1:5) aics[1, 1+q] <- arima(WWWusage, c(0,1,q),
+ optim.control = list(maxit = 500))$aic
+for(p in 1:5)
+ for(q in 0:5) aics[1+p, 1+q] <- arima(WWWusage, c(p,1,q),
+ optim.control = list(maxit = 500))$aic
+round(aics - min(aics, na.rm=TRUE), 2)
+
+
+
+### nottem
+nott <- window(nottem, end=c(1936,12))
+fit <- arima(nott,order=c(1,0,0), list(order=c(2,1,0), period=12))
+nott.fore <- predict(fit, n.ahead=36)
+ts.plot(nott, nott.fore$pred, nott.fore$pred+2*nott.fore$se,
+ nott.fore$pred-2*nott.fore$se, gpars=list(col=c(1,1,4,4)))
+
+
+### StructTS
+(fit <- StructTS(log10(UKgas), type = "BSM"))
+(fit <- StructTS(log10(UKgas), type = "BSM", fixed=c(0, NA, NA, NA)))
+(fit <- StructTS(log10(UKgas), type = "BSM", fixed=c(NA, 0, NA, NA)))
+(fit <- StructTS(log10(UKgas), type = "BSM", fixed=c(NA, NA, NA, 0)))
+
+### from AirPassengers
+## The classic `airline model', by full ML
+(fit <- arima(log10(AirPassengers), c(0, 1, 1),
+ seasonal = list(order=c(0, 1 ,1), period=12)))
+update(fit, method = "CSS")
+update(fit, x=window(log10(AirPassengers), start = 1954))
+pred <- predict(fit, n.ahead = 24)
+tl <- pred$pred - 1.96 * pred$se
+tu <- pred$pred + 1.96 * pred$se
+ts.plot(AirPassengers, 10^tl, 10^tu, log = "y", lty = c(1,2,2))
+
+## full ML fit is the same if the series is reversed, CSS fit is not
+ap0 <- rev(log10(AirPassengers))
+attributes(ap0) <- attributes(AirPassengers)
+arima(ap0, c(0, 1, 1), seasonal = list(order=c(0, 1 ,1), period=12))
+arima(ap0, c(0, 1, 1), seasonal = list(order=c(0, 1 ,1), period=12),
+ method = "CSS")
+
+## Structural Time Series
+ap <- log10(AirPassengers) - 2
+(fit <- StructTS(ap, type= "BSM"))
+par(mfrow=c(1,2))
+plot(cbind(ap, fitted(fit)), plot.type = "single")
+plot(cbind(ap, tsSmooth(fit)), plot.type = "single")
+
+## PR14925
+a <- ts(matrix(1:36, 12), start = 2000, freq = 12)
+b <- ts(matrix(1:48, 16), start = c(1999,9), freq = 12)
+window(a, start = c(2000,6)) <- window(b, start = c(2000,6), end = c(2000,12))
+## failed in R < 2.15.1
+
+cat('Time elapsed: ', proc.time() - .proctime00,'\n')
diff --git a/win32/deps/library/stats4/DESCRIPTION b/win32/deps/library/stats4/DESCRIPTION
index 34d0a00..48c8c17 100644
--- a/win32/deps/library/stats4/DESCRIPTION
+++ b/win32/deps/library/stats4/DESCRIPTION
@@ -1,11 +1,10 @@
Package: stats4
Title: Statistical Functions using S4 Classes
-Version: 2.9.2
+Version: 2.15.2
Priority: base
-Author: R Development Core Team and contributors worldwide
+Author: R Core Team and contributors worldwide
Description: Statistical Functions using S4 classes
Maintainer: R Core Team <R-core r-project org>
Depends: methods, graphics, stats
-LazyLoad: yes
-License: Part of R 2.9.2
-Built: R 2.9.2; ; 2009-08-24 12:46:12 UTC; windows
+License: Part of R 2.15.2
+Built: R 2.15.2; ; 2012-10-27 03:07:58 UTC; windows
diff --git a/win32/deps/library/stats4/INDEX b/win32/deps/library/stats4/INDEX
index 86357be..871a1f9 100644
--- a/win32/deps/library/stats4/INDEX
+++ b/win32/deps/library/stats4/INDEX
@@ -1,23 +1,22 @@
-AIC-methods Methods for Function 'AIC' in Package 'stats4'
-BIC Bayesian Information Criterion
coef-methods Methods for Function 'coef' in Package 'stats4'
confint-methods Methods for Function 'confint' in Package
'stats4'
logLik-methods Methods for Function 'logLik' in Package
'stats4'
mle Maximum Likelihood Estimation
-mle-class Class "mle" for Results of Maximum Likelihood
+mle-class Class '"mle"' for Results of Maximum Likelihood
Estimation
plot-methods Methods for Function 'plot' in Package 'stats4'
-profile-methods Methods for Function profile in Package
+profile-methods Methods for Function 'profile' in Package
'stats4'
-profile.mle-class Class "profile.mle"; Profiling information for
- "mle" object
-show-methods Methods for Function show in Package 'stats4'
+profile.mle-class Class '"profile.mle"'; Profiling information
+ for '"mle"' object
+show-methods Methods for Function 'show' in Package 'stats4'
stats4-package Statistical Functions using S4 Classes
-summary-methods Methods for Function summary in Package
+summary-methods Methods for Function 'summary' in Package
'stats4'
-summary.mle-class Class "summary.mle", summary of "mle" objects
+summary.mle-class Class '"summary.mle"', Summary of '"mle"'
+ Objects
update-methods Methods for Function 'update' in Package
'stats4'
vcov-methods Methods for Function 'vcov' in Package 'stats4'
diff --git a/win32/deps/library/stats4/Meta/Rd.rds b/win32/deps/library/stats4/Meta/Rd.rds
index 42b4d1d..b766621 100644
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diff --git a/win32/deps/library/stats4/Meta/hsearch.rds b/win32/deps/library/stats4/Meta/hsearch.rds
index 17f8c46..68e4b81 100644
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diff --git a/win32/deps/library/stats4/Meta/links.rds b/win32/deps/library/stats4/Meta/links.rds
new file mode 100644
index 0000000..282664e
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diff --git a/win32/deps/library/stats4/Meta/nsInfo.rds b/win32/deps/library/stats4/Meta/nsInfo.rds
index 91e3ddb..53402a8 100644
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diff --git a/win32/deps/library/stats4/Meta/package.rds b/win32/deps/library/stats4/Meta/package.rds
index 72cf813..90138d7 100644
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diff --git a/win32/deps/library/stats4/NAMESPACE b/win32/deps/library/stats4/NAMESPACE
index df0d269..8170874 100644
--- a/win32/deps/library/stats4/NAMESPACE
+++ b/win32/deps/library/stats4/NAMESPACE
@@ -1,13 +1,13 @@
export(mle) # exporting methods implicitly exports the generics
-importFrom(graphics, plot)
-## need AIC to make an implicit generic from
-importFrom(stats, AIC, coef, confint, logLik, optim, profile,
- qchisq, update, vcov)
+importFrom("graphics", plot)
+importFrom("methods", show)
+importFrom("stats", optim, qchisq)
+## For these, we define methods or (AIC, BIC, nobs) an implicit generic:
+importFrom("stats", AIC, BIC, coef, confint, logLik, nobs, profile, update, vcov)
## S4
exportClasses(mle, profile.mle, summary.mle)
-## All methods, for own or "foreign" generics:
-exportMethods(BIC, coef, confint, logLik, plot, profile,
- summary, show, update, vcov)
-## implicit generic does not have any methods here (but in flexmix)
-export(AIC)
+## All methods for imported generics:
+exportMethods(coef, confint, logLik, nobs, plot, profile, summary, show, update, vcov)
+## implicit generics do not have any methods here
+export(AIC, BIC)
diff --git a/win32/deps/library/stats4/R/stats4 b/win32/deps/library/stats4/R/stats4
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/stats4/R/stats4
+++ b/win32/deps/library/stats4/R/stats4
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/stats4/R/stats4.rdb b/win32/deps/library/stats4/R/stats4.rdb
index f1c0ecf..60f3f67 100644
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diff --git a/win32/deps/library/stats4/R/stats4.rdx b/win32/deps/library/stats4/R/stats4.rdx
index fc93321..6157e1e 100644
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diff --git a/win32/deps/library/stats4/help/AnIndex b/win32/deps/library/stats4/help/AnIndex
index 676c074..e525ea2 100644
--- a/win32/deps/library/stats4/help/AnIndex
+++ b/win32/deps/library/stats4/help/AnIndex
@@ -1,9 +1,4 @@
stats4-package stats4-package
-AIC,ANY-method AIC-methods
-AIC-methods AIC-methods
-BIC BIC
-BIC,ANY-method BIC
-BIC,logLik-method BIC
coef,ANY-method coef-methods
coef,mle-method coef-methods
coef,summary.mle-method coef-methods
@@ -17,6 +12,7 @@ logLik,mle-method logLik-methods
logLik-methods logLik-methods
mle mle
mle-class mle-class
+nobs,mle-method mle-class
plot,ANY,ANY-method plot-methods
plot,profile.mle,missing-method plot-methods
plot-methods plot-methods
diff --git a/win32/deps/library/stats4/help/aliases.rds b/win32/deps/library/stats4/help/aliases.rds
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index 0000000..c485c43
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index 0000000..444d550
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diff --git a/win32/deps/library/stats4/html/00Index.html b/win32/deps/library/stats4/html/00Index.html
new file mode 100644
index 0000000..16e9324
--- /dev/null
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+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Statistical Functions using S4 Classes</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Statistical Functions using S4 Classes
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘stats4’ version 2.15.2</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<table width="100%">
+<tr><td width="25%"><a href="stats4-package.html">stats4-package</a></td>
+<td>Statistical Functions using S4 Classes</td></tr>
+<tr><td width="25%"><a href="coef-methods.html">coef-method</a></td>
+<td>Methods for Function 'coef' in Package 'stats4'</td></tr>
+<tr><td width="25%"><a href="coef-methods.html">coef-methods</a></td>
+<td>Methods for Function 'coef' in Package 'stats4'</td></tr>
+<tr><td width="25%"><a href="confint-methods.html">confint-method</a></td>
+<td>Methods for Function 'confint' in Package 'stats4'</td></tr>
+<tr><td width="25%"><a href="confint-methods.html">confint-methods</a></td>
+<td>Methods for Function 'confint' in Package 'stats4'</td></tr>
+<tr><td width="25%"><a href="logLik-methods.html">logLik-method</a></td>
+<td>Methods for Function 'logLik' in Package 'stats4'</td></tr>
+<tr><td width="25%"><a href="logLik-methods.html">logLik-methods</a></td>
+<td>Methods for Function 'logLik' in Package 'stats4'</td></tr>
+<tr><td width="25%"><a href="mle.html">mle</a></td>
+<td>Maximum Likelihood Estimation</td></tr>
+<tr><td width="25%"><a href="mle-class.html">mle-class</a></td>
+<td>Class '"mle"' for Results of Maximum Likelihood Estimation</td></tr>
+<tr><td width="25%"><a href="mle-class.html">nobs-method</a></td>
+<td>Class '"mle"' for Results of Maximum Likelihood Estimation</td></tr>
+<tr><td width="25%"><a href="plot-methods.html">plot-method</a></td>
+<td>Methods for Function 'plot' in Package 'stats4'</td></tr>
+<tr><td width="25%"><a href="plot-methods.html">plot-methods</a></td>
+<td>Methods for Function 'plot' in Package 'stats4'</td></tr>
+<tr><td width="25%"><a href="profile-methods.html">profile-method</a></td>
+<td>Methods for Function 'profile' in Package 'stats4'</td></tr>
+<tr><td width="25%"><a href="profile-methods.html">profile-methods</a></td>
+<td>Methods for Function 'profile' in Package 'stats4'</td></tr>
+<tr><td width="25%"><a href="profile.mle-class.html">profile.mle-class</a></td>
+<td>Class '"profile.mle"'; Profiling information for '"mle"' object</td></tr>
+<tr><td width="25%"><a href="show-methods.html">show-method</a></td>
+<td>Methods for Function 'show' in Package 'stats4'</td></tr>
+<tr><td width="25%"><a href="show-methods.html">show-methods</a></td>
+<td>Methods for Function 'show' in Package 'stats4'</td></tr>
+<tr><td width="25%"><a href="stats4-package.html">stats4</a></td>
+<td>Statistical Functions using S4 Classes</td></tr>
+<tr><td width="25%"><a href="summary-methods.html">summary-method</a></td>
+<td>Methods for Function 'summary' in Package 'stats4'</td></tr>
+<tr><td width="25%"><a href="summary-methods.html">summary-methods</a></td>
+<td>Methods for Function 'summary' in Package 'stats4'</td></tr>
+<tr><td width="25%"><a href="summary.mle-class.html">summary.mle-class</a></td>
+<td>Class '"summary.mle"', Summary of '"mle"' Objects</td></tr>
+<tr><td width="25%"><a href="update-methods.html">update-method</a></td>
+<td>Methods for Function 'update' in Package 'stats4'</td></tr>
+<tr><td width="25%"><a href="update-methods.html">update-methods</a></td>
+<td>Methods for Function 'update' in Package 'stats4'</td></tr>
+<tr><td width="25%"><a href="vcov-methods.html">vcov-method</a></td>
+<td>Methods for Function 'vcov' in Package 'stats4'</td></tr>
+<tr><td width="25%"><a href="vcov-methods.html">vcov-methods</a></td>
+<td>Methods for Function 'vcov' in Package 'stats4'</td></tr>
+</table>
+</body></html>
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+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
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+
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+ color: rgb(40%, 40%, 40%);
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+ font-size: large }
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+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
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diff --git a/win32/deps/library/stats4/tests/confint.R b/win32/deps/library/stats4/tests/confint.R
new file mode 100644
index 0000000..105640f
--- /dev/null
+++ b/win32/deps/library/stats4/tests/confint.R
@@ -0,0 +1,23 @@
+## PR#14646
+
+library(stats4)
+minusLogL1 <- function(mu, logsigma2)
+ N*log(2*pi*exp(logsigma2))/2 + N*(var(x)+(mean(x)-mu)^2)/(2*exp(logsigma2))
+
+minusLogL2 <- function(mu) {
+ logsigma2 <- 0;
+ N*log(2*pi*exp(logsigma2))/2 + N*(var(x)+(mean(x)-mu)^2)/(2*exp(logsigma2))
+}
+
+N <- 100
+set.seed(123)
+x <- rnorm(N, 0, 1)
+
+fit <- mle(minusLogL1, start = list(mu=0, logsigma2=0))
+confint(fit)
+
+fit2 <- mle(minusLogL1, start = list(mu=0), fixed = list(logsigma2=0))
+confint(fit2) # failed
+
+fit3 <- mle(minusLogL2, start = list(mu=0))
+confint(fit3) # same
diff --git a/win32/deps/library/survival/CITATION b/win32/deps/library/survival/CITATION
new file mode 100644
index 0000000..366c43f
--- /dev/null
+++ b/win32/deps/library/survival/CITATION
@@ -0,0 +1,15 @@
+citHeader("To cite package 'survival' in publications use:")
+
+# Grab the version and date from the DESCRIPTION file
+if(!exists("meta") || is.null(meta)) meta <- packageDescription("survival")
+year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", meta$Date)
+vers <- paste("R package version", meta$Version)
+
+citEntry(entry="Manual",
+ title = "A Package for Survival Analysis in S",
+ author= personList(as.person("Terry Therneau")),
+ year =year,
+ note =vers,
+ textVersion= paste("Terry Therneau (", year,
+ "). A Package for Survival Analysis in S. ",
+ vers, ".", sep=""))
diff --git a/win32/deps/library/survival/DESCRIPTION b/win32/deps/library/survival/DESCRIPTION
index 09fa300..f46c1a9 100644
--- a/win32/deps/library/survival/DESCRIPTION
+++ b/win32/deps/library/survival/DESCRIPTION
@@ -1,20 +1,19 @@
-Title: Survival analysis, including penalised likelihood.
-Maintainer: Thomas Lumley <tlumley u washington edu>
-Priority: recommended
-Package: survival
-Version: 2.35-4
-Date: 2009-04-01
-Depends: stats, utils, graphics, splines, R (>= 2.0.0)
-LazyData: Yes
-LazyLoad: Yes
-Author: Terry Therneau, original R port by Thomas Lumley
-Description: survival analysis: descriptive statistics, two-sample
- tests, parametric accelerated failure models, Cox model.
- Delayed entry (truncation) allowed for all models; interval
- censoring for parametric models. Case-cohort designs.
-License: GPL-2
-URL: http://r-forge.r-project.org
-Packaged: Wed Apr 1 13:56:03 2009; tlumley
-Repository: CRAN
-Date/Publication: 2009-04-01 17:02:08
-Built: R 2.9.2; i386-pc-mingw32; 2009-08-24 13:11:31 UTC; windows
+Title: Survival analysis, including penalised likelihood.
+Maintainer: Terry Therneau <therneau terry mayo edu>
+Priority: recommended
+Package: survival
+Version: 2.36-14
+Date: 2012-02-03
+Depends: stats, utils, graphics, splines, R (>= 2.13.0)
+LazyData: Yes
+LazyLoad: Yes
+Author: Terry Therneau, original Splus->R port by Thomas Lumley
+Description: survival analysis: descriptive statistics, two-sample
+ tests, parametric accelerated failure models, Cox model. Delayed entry
+ (truncation) allowed for all models; interval censoring for parametric
+ models. Case-cohort designs.
+License: GPL (>=2)
+URL: http://r-forge.r-project.org
+Packaged: 2012-04-25 17:11:24 UTC; therneau
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:14:03 UTC; windows
+Archs: i386, x64
diff --git a/win32/deps/library/survival/INDEX b/win32/deps/library/survival/INDEX
index 93eff05..aebf0a0 100644
--- a/win32/deps/library/survival/INDEX
+++ b/win32/deps/library/survival/INDEX
@@ -1,33 +1,88 @@
-Surv Package a survival variable
-clogit Conditional logistic regression
-cluster Identify clusters.
-cox.zph Test the proportional hazards assumption of a Cox regression.
-coxph Proportional Hazards Regression
-coxph.detail Details of a cox model fit
-coxph.object Proportional Hazards Regression Object
-coxph.rvar Robust variance for a Cox model
-frailty Frailty models by penalised likelihood
-is.ratetable Verify that an object is of class ratetable.
-lines.survfit Add lines to a survival plot
-plot.cox.zph Graphical test of proportional hazards (requires splines)
-plot.survfit Plot method for survfit.
-print.survfit Short summary of a survival curve
-pspline Penalised (smoothing) splines
-pyears Person Years
-residuals.coxph Calculate residuals for a coxph fit.
-residuals.survreg Compute Residuals for survreg Objects
-ridge ridge regression
-strata Identify strata variables.
-summary.survfit Print a Survival Curve
-survdiff Test Survival Curve Differences
-survexp Compute Expected Survival
-survexp.fit Compute expected survival
-survexp.usr Mortality tables for US and some states (requires date)
-survfit Compute a survival Curve for Censored Data
-survfit.object Survival Curve Object
-survobrien O'Brien's test for association of a variable with survival
-survreg Regression for a parametric survival model
-survreg.object Parametric Survival Model Object
-survSplit Split data for creating time-dependent covariates.
-anova.survreg ANOVA tables for survreg objects
-untangle.specials Help process the 'specials' argument of the terms function.
+Surv Create a Survival Object
+aareg Aalen's additive regression model for censored
+ data
+aml Acute Myelogenous Leukemia survival data
+anova.coxph Analysis of Deviance for a Cox model.
+attrassign Create new-style "assign" attribute
+basehaz Compute the baseline survival curve for a Cox
+ model
+bladder Bladder Cancer Recurrences
+cch Fits proportional hazards regression model to
+ case-cohort data
+cgd Chronic Granulotomous Disease data
+clogit Conditional logistic regression
+cluster Identify clusters.
+colon Chemotherapy for Stage B/C colon cancer
+cox.zph Test the Proportional Hazards Assumption of a
+ Cox Regression
+coxph Fit Proportional Hazards Regression Model
+coxph.control Ancillary arguments for controling coxph fits
+coxph.detail Details of a Cox Model Fit
+coxph.object Proportional Hazards Regression Object
+dsurvreg Distributions available in survreg.
+frailty Random effects terms
+heart Stanford Heart Transplant data
+is.ratetable Verify that an object is of class ratetable.
+kidney Kidney catheter data
+lines.survfit Add Lines or Points to a Survival Plot
+logan Data from the 1972-78 GSS data used by Logan
+lung NCCTG Lung Cancer Data
+mgus Monoclonal gammapothy data
+model.frame.coxph Model.frame method for coxph objects
+model.matrix.coxph Model.matrix method for coxph models
+nwtco Data from the National Wilm's Tumor Study
+ovarian Ovarian Cancer Survival Data
+pbc Mayo Clinic Primary Biliary Cirrhosis Data
+pbcseq Mayo Clinic Primary Biliary Cirrhosis,
+ sequential data
+plot.aareg Plot an aareg object.
+plot.cox.zph Graphical Test of Proportional Hazards
+plot.survfit Plot Method for 'survfit'
+predict.coxph Predictions for a Cox model
+predict.survreg Predicted Values for a 'survreg' Object
+print.aareg Print an aareg object
+print.summary.coxph Print method for summary.coxph objects
+print.summary.survexp Print Survexp Summary
+print.summary.survfit Print Survfit Summary
+print.survfit Print a Short Summary of a Survival Curve
+pspline Smoothing splines using a pspline basis
+pyears Person Years
+quantile.survfit Quantiles from a survfit object
+ratetable Ratetable reference in formula
+ratetableDate Convert date objects to ratetable form
+rats Rat data from Gail et al.
+residuals.coxph Calculate Residuals for a 'coxph' Fit
+residuals.survreg Compute Residuals for 'survreg' Objects
+ridge Ridge regression
+stanford2 More Stanford Heart Transplant data
+strata Identify Stratification Variables
+summary.aareg Summarize an aareg fit
+summary.coxph Summary method for Cox models
+summary.survexp Summary function for a survexp object
+summary.survfit Summary of a Survival Curve
+survConcordance Compute a concordance measure.
+survSplit Split a survival data set at specified times
+survdiff Test Survival Curve Differences
+survexp Compute Expected Survival
+survexp.fit Compute Expected Survival
+survexp.us Census Data Sets for the Expected Survival and
+ Person Years Functions
+survfit Create survival curves
+survfit.coxph Compute a Survival Curve from a Cox model
+survfit.formula Compute a Survival Curve for Censored Data
+survfit.object Survival Curve Object
+survfitcoxph.fit A direct interface to the 'computational
+ engine' of survfit.coxph
+survobrien O'Brien's Test for Association of a Single
+ Variable with Survival
+survreg Regression for a Parametric Survival Model
+survreg.control Package options for survreg and coxph
+survreg.distributions Parametric Survival Distributions
+survreg.object Parametric Survival Model Object
+survregDtest Verify a survreg distribution
+tcut Factors for person-year calculations
+tobin Tobin's Tobit data
+tt Mark time tranform terms
+untangle.specials Help Process the 'specials' Argument of the
+ 'terms' Function.
+veteran Veterans' Administration Lung Cancer study
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diff --git a/win32/deps/library/survival/Meta/nsInfo.rds b/win32/deps/library/survival/Meta/nsInfo.rds
index e603578..5569735 100644
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diff --git a/win32/deps/library/survival/Meta/package.rds b/win32/deps/library/survival/Meta/package.rds
index 032f1fd..8367e7b 100644
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diff --git a/win32/deps/library/survival/Meta/vignette.rds b/win32/deps/library/survival/Meta/vignette.rds
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diff --git a/win32/deps/library/survival/NAMESPACE b/win32/deps/library/survival/NAMESPACE
index 4274399..6b9a9f3 100644
--- a/win32/deps/library/survival/NAMESPACE
+++ b/win32/deps/library/survival/NAMESPACE
@@ -11,11 +11,12 @@ export("Surv", "aareg", "attrassign",
"is.na.ratetable", "is.ratetable",
"labels.survreg", "match.ratetable",
"psurvreg", "qsurvreg", "dsurvreg",
- "pspline", "pyears", "ratetable",
+ "pspline", "pyears", "ratetable", "ratetableDate",
"ridge", "strata", "survConcordance",
"survSplit", "survdiff", "survexp", "survfit" ,
+ "survfitcoxph.fit",
"survobrien", "survreg", "survreg.control", "survreg.fit",
- "survreg.distributions", "survregDtest", "tcut",
+ "survreg.distributions", "survregDtest", "tcut", "tt",
"untangle.specials")
S3method(`[`, Surv)
S3method(`[`, cox.zph)
@@ -43,14 +44,16 @@ S3method(attrassign, lm)
S3method(extractAIC,coxph.penal)
S3method(lines, aareg)
S3method(lines, survfit)
+S3method(makepredictcall, pspline)
S3method(model.frame, coxph)
-S3method(model.frame, survreg)
+S3method(model.matrix, coxph)
S3method(plot, aareg)
S3method(plot, cox.zph)
S3method(plot, survfit)
S3method(points, survfit)
S3method(predict, coxph)
S3method(predict, coxph.penal)
+S3method(predict, pspline)
S3method(predict, survreg)
S3method(predict, survreg.penal)
S3method(print, Surv)
@@ -66,14 +69,17 @@ S3method(print, summary.cch)
S3method(print, summary.coxph)
S3method(print, summary.survfit)
S3method(print, summary.survreg)
+S3method(print, survConcordance)
S3method(print, survdiff)
S3method(print, survexp)
S3method(print, survfit)
S3method(print, survreg)
S3method(print, survreg.penal)
+S3method(quantile, survfit)
S3method(ratetableDate, POSIXt)
+S3method(ratetableDate, Date)
S3method(ratetableDate, date)
-S3method(ratetableDate, timeDate)
+S3method(ratetableDate, chron)
S3method(residuals, coxph)
S3method(residuals, coxph.null)
S3method(residuals, coxph.penal)
@@ -83,11 +89,11 @@ S3method(summary, aareg)
S3method(summary, coxph)
S3method(summary, coxph.penal)
S3method(summary, ratetable)
+S3method(summary, pyears)
S3method(summary, survfit)
S3method(summary, survreg)
S3method(summary,cch)
S3method(survfit, coxph)
-S3method(survfit, coxph.null)
S3method(survfit, formula)
S3method(vcov, cch)
S3method(vcov, coxph)
diff --git a/win32/deps/library/survival/NEWS.Rd b/win32/deps/library/survival/NEWS.Rd
new file mode 100644
index 0000000..dab613f
--- /dev/null
+++ b/win32/deps/library/survival/NEWS.Rd
@@ -0,0 +1,702 @@
+\name{NEWS}
+\title{NEWS file for the survival package}
+\section{Changes in version 2.36-14}{
+ \itemize{
+ \item A supposedly cosmetic change to coxph in the last release
+ caused formulas with a "." on the right hand side to fail. Fix this
+ and add a case with "." to the test suite.
+ }}
+
+\section{Changes in version 2.36-13}{
+ \itemize{
+ \item Add the anova.coxmelist function. This is in the survival
+ package rather than in coxme since "anova(fit1, fit2)" is valid when
+ fit1 is a coxph and fit2 a coxme object, a case which will cause this
+ function to be called by way of anova.coxph.
+
+ \item More work on "predvars" handling for the pspline function,
+ when used in predict calls. Add a new test of this to the suite,
+ and the makepredictcall method to the namespace.
+ Fixes a bug pointed out by C Crowson.
+
+ \item Deprecate the "robust" option of coxph. When there are
+ multiple observations per subject it is almost surely the wrong
+ thing to do, while adding a "cluster(id)" term does the correct
+ thing. When there is only one obs per subject both methods work
+ correctly.
+
+ \item Add documentation of the output structure to the aareg help
+ file.
+
+ \item Change ratetableDate so that it still allows use of chron
+ objects, but doesn't need the chron library. This eliminates a
+ warning messge from the package checks, but is also a reasonable
+ support strategy for a moribund package. (Some of the local users keep
+ datasets for a long long time.)
+
+ \item Fix a bug in summary.survfit for a multiple-strata survival
+ object. If one of the curves had no data after application of the
+ times argument, an output label was the wrong length.
+
+ \item Fix a bug pointed out by Charles Berry: predict for a Cox
+ model which has strata, and the strata is a factor with not all its
+ levels represented in the data. I had a mistake in the subscripting
+ logic: number of groups is not equal to max(as.integer(strata)).
+
+ \item Changes to avoid overflow in the exponent made in 2.36-6
+ caused failure for one special usage: in case-cohort designs a dummy
+ offset of -100 could be added to some observations. This was being
+ rounded away. The solution is to 1: have coxsafe not truncate small
+ exponents and 2: do not recenter user provided offset values.
+
+ \item Fix bug in survfit.coxph. Due to an indexing error I would
+ sometimes create a huge scratch vector midway through the
+ calculations (size = max value of "id"); the final result was always
+ correct however. Data set provided by Cindy Crowson which had a
+ user id in the billions.
+
+ \item Fix bug pointed out by Nicholas Horton: predictions of
+ type expected, with newdata, from a Cox model without a strata
+ statement would fail with "x not found". A misplaced parenthesis
+ from an earlier update caused it to not recreate the X matrix even
+ though it was needed later. Also add some further information to
+ the predict manual page to clarify an issue when there is a frailty term.
+ }}
+
+\section{Changes in version 2.36-12}{
+ \itemize{
+ \item Fix a bug in the new fast subsets code. The test suite had no
+ examples of strata + lots of tied times, so of course that's the
+ case where I had an indexing error. Add a test case using the
+ clogit function, which exercises this.
+
+ \item Further memory tuning for survexp.
+ }}
+
+ \section{Changes in version 2.36-11}{
+ \itemize{
+ \item Make survexp more efficient. The X matrix was being modified
+ in several places, leading to multiple copies of the data. When the
+ data set was large this would lead to a memory shortage.
+
+ \item Cause anova.coxph to call anova.coxme when a list of models
+ has both coxph and coxme objects.
+
+ \item Add the quantile.survfit function. This allows a user to
+ extract arbitrary quantiles from a fitted curve (and std err).
+
+ \item Fix an error in predict.coxph. When the model had a strata
+ and the newdata and reference="sample" arguments were used, it
+ would (incorrectly) ask for a strata variable in the new data set.
+
+ \item Incorporate the fast subsets algorithm of Gail et al, when
+ using coxph with the "exact" option. The speed increase is profound
+ though at the cost of some memory. Reflect this in the
+ documentation for the clogit routine.
+ Note that the fast computation is not yet implemented for
+ (start,stop) coxph models.
+
+ \item Change the C routine used by coxph.fit from .C to .Call
+ semantics to improve memory efficiency, in particular fewer copies
+ of the X matrix.
+
+ \item Add scaling to the above routine. This was prompted by a user
+ who had some variables with a 0-1 range and others that were
+ 0 - 10^7, resulting in 0 digits of accuracy in the variance matrix.
+ (Economics data).
+
+ \item Comment out some code sections that are specific to Splus.
+ This reduced the number of "function not found" warnings from R CMD check.
+}}
+
+\section{Changes in version 2.36-10}{
+ \itemize{
+ \item 30 Sept 2011: The na.action argument was being ignored in
+ predict.coxph; pointed out by Cindy Crowson.
+
+ \item The log-likelihood for survreg was incorrect when there are
+ case weights in the model. The error is a fixed constant for any
+ given data set, so had no impact on tests or inferences. The error
+ and correction were pointed out by Robert Kusher.
+
+ \item A variable name was incorrect in survpenal.fit. This was in a
+ program path that had never been traversed until Carina Salt used
+ survreg with a psline(..., method='aic') call, leading to a
+ "variable not found" message.
+
+ \item Punctuation error in psline made it impossible for a user to
+ specify the boundary.knots argument. Pointed out by Brandon
+ Stewart.
+
+ \item Add an "id" variable to the output of survobrien.
+
+ \item The survfitCI routine would fail for a curve with only one
+ jump point (a matrix collapsed into a vector).
+
+ \item Fix an error in survfit.coxph when the coxph model has both a
+ strata by covariate interaction and a cluster statement. The
+ cluster term was not dropped from the Terms object as it should have
+ been, led to a spurious "variable not found" error. Pointed out
+ by Eva Bouguen.
+
+ \item If a coxph model with penalized terms (frailty, pspline) also
+ had a redundant covariate, the linear predictor would be returned as
+ NA. Pointed out by Pavel Krivitsky.
+}}
+
+\section{Changes in version 2.36-9}{
+ \itemize{
+ \item Due to a mistake in my script that submits to CRAN, the fix in
+ 2.36-8 below was actually not propogated to the CRAN submission.
+
+ \item Fix an error in the Cauchy example found in the survreg.distributions
+ help page, pointed out by James Price.
+
+ \item Update the coxph.getdata routine to use the model.frame.coxph
+ and model.matrix.coxph methods.
+
+ \item Add the concordance statistic to the printout for penalized models.
+}}
+
+\section{Changes in version 2.36-8}{
+ \itemize{
+ \item Unitialized variable in calcuation of the variance of the
+ concordance. Found on platform cross-checking by Brian Ripley.
+ \item Changed testci to use a fixed file of results from cmprsk
+ rather than invoking that package on-the-fly. Suggested by the CRAN
+ maintainers.
+ }
+ }
+\section{Changes in version 2.36-7}{
+ \itemize{
+ \item Due to changes in R 2.13 default printout, the results of many of
+ the test programs change in trivial way (one more or fewer digits).
+ Update the necessary test/___.Rout.save files. Per the core team's
+ suggestion the dependency for the package is marked as >=2.13.
+ }}
+
+\section{Changes in version 2.36-6}{
+ \itemize{
+ \item An example from A Drummond caused iteration failure in
+ coxph: x=c(1,1,1,0,1, rep(0,35)), time=1:40, status=1. The first
+ iteration overshoots the solution and lands on an almost perfectly
+ linear part of the loglik surface, which made the second iteration
+ go to a huge number and exp() overflows. A sanity check routine
+ coxsafe is now invoked on all values of the linear predictor.
+
+ \item 1 April: Fix minor bug in survfit. For left censored data
+ where all the left censored are on the very left, it would give a
+ spurious warning message when trying to create a 0 row matrix that
+ it didn't need or use. Pointed out by Steve Su.
+
+ \item 31 March 2011: One of the plots in the r_sas test was wrong
+ (it's been a long time since I visually checked these). The error
+ was in predict.survreg; it had not taken into account a change in
+ R2.7.1: the intercept attribute is reset to 1 whenever one
+ subscripts a terms object, leading to incorrect results for a model
+ with "-1" in the formula and a strata(): the intercept returned
+ when removing the strata. I used this opportunity to move most of
+ the logic into model.frame.survreg and model.matrix.survreg
+ functions. Small change to the model.frame.coxph and
+ model.matrix.coxph functions due to a better understanding of
+ xlevels processing.
+
+ \item Round off error issue in survfit: it used both unique(time)
+ and table(time), and the resulting number of unique values is not
+ guarranteed to be the same for times that differ by a tiny amount.
+ Now times are coverted to a factor first. Peter Savicky from the R
+ core team provided a nice discussion of the issue and helped me
+ clarify how best to deal with it. The prior fix of first rounding
+ to 15 digits was good enough for almost every data set -- except the
+ one found by a local user just last week.
+
+ \item Round off error in print.survfit pointed out by Micheal Faye.
+ If a survival value was .5 in truth, but .5- eps due to round off
+ the printed median was wrong. But it was ok for .5+eps. Simple
+ if-then logic error.
+
+ \item Re-fix a bug in survfit. It uses both unique and table in
+ various places, which do not round the same; I had added a
+ pre-rounding step to the code. A data set from Fan Chun showed that
+ I didn't round quite enough. But the prior rounding did work for a
+ time of 2 vs (sqrt(2))^2: this bug is very hard to produce. I now
+ use as.numeric(as.character(factor(x))), which induces exactly the
+ same rounding as table, since it is the same compuation path.
+
+ \item Further changes to pspline. The new Boundary.knots argument
+ allows a user to set the boundary knots inside the range of data.
+ Code for extrapolation outside that range was needed,
+ essentially a copy of the code found in ns() for the same issue.
+ Also added a psplineinverse function, which may be useful with
+ certain tt() calls in coxph.
+
+ \item 10 Mar 2011: Add the capablilty for time-dependent
+ transformations to coxph, along with a small vignette describing use
+ of the feature. This code is still incompletely incorporated in
+ that the models work but other methods (residuals, predict, etc) are
+ not yet defined.
+
+ \item 8 Mar 2011: Expand the survConcordance function. The function
+ now correctly handles strata and time dependent covariates, and
+ computes a standard error for the estimate. All computation is based
+ on a balanced binary tree strucure, which leads to computation in
+ \eqn{O(n \log_2(n))}{O(n log(n))} time.
+ The \code{coxph} function now adds concordance to its output, and
+ \code{summary.coxph} displays the result.
+
+ \item 8 Mar 2011: Add the "reference" option to predict.coxph, a
+ feature and need pointed out by Stephen Bond.
+
+ \item 4 Mar 2011: Add a makepredictcall method for pspline(), which
+ in turn required addition of a Boundary.knots argument to the
+ function.
+
+ \item 25 Feb 2011: Bug in pyears pointed out by Norm Phillips. If a
+ subject started out with "off table" time, their age was not
+ incremented by that amount as they moved forward to the next "in
+ table" cell of the result. This could lead to using the wrong
+ expected rate from the rate table.
+ }
+}
+
+\section{Changes in version 2.36-5}{
+ \itemize{
+ \item 20 Feb 2011: Update survConcordance to correctly handle case
+ weights, time dependent covariates, and strata.
+
+ \item 18 Feb 2011: Bug in predict.coxph found by a user (1 day after
+ 36-4!). If the coxph call had a subset and predict used newdata,
+ the subset clause was "remembered" in the newdata construction,
+ which is not appropriate.
+}}
+
+\section{Changes in version 2.36-4}{
+\itemize{
+ \item 17 Feb 2011: Fix to predict.coxph. A small typo that only was
+ exercised if the coxph model had x=T. Discovered via induced error in
+ the rankhazard package. Added lines to the test suite to test for
+ this in the future.
+
+ \item Removed some files from test and src that are no longer needed.
+
+ \item Update the configure script per suggestion from Kurt H.
+ }}
+\section{Changes in version 2.36-3}{
+ \itemize{
+
+ \item 13 Feb 2011: Add the rmap argument to pyears, as was done for
+ survexp, and update the manual pages and examples. Fix one last bug
+ in predict.coxph (na.action use). Passes all the
+ tests for inclusion on the next R release.
+
+ \item 8 Feb 2011: Change the name of the new survfit.coxph.fit routine to
+ survfitcoxph.fit; R was mistaking it for a survfit method. Fix
+ errors in predict.coxph when there is a newdata argument, including
+ adding yet another test program.
+
+ \item 1 Feb 2011: Fix bugs in coxph and survreg pointed out by Heinz
+ Tuechler and dtdenes cogpsyphy hu, independently, that were the same
+ wrong line in both programs. With interactions, a non-penalized
+ term could be marked as penalized due to a mismatched vector length,
+ leading to a spurious error message later in the code.
+
+ \item 1 Feb 2011: Update survfit.coxph to handle the case of a strata by
+ covariate interaction. All prior releases of the code did this
+ wrong, but it is a very rare case (found by Frank Harrell). Added a
+ new test routine coxsurv4. Also found a bug in [.survfit; for a
+ curve with both strata and multiple columns, as produced by
+ survfit.coxph, it could drop the n.censored item when subscripting.
+ A minor issue was fixed in coxph: when iter=0 the output coefficient
+ vector should be equal to the input even when the variance is
+ singular.
+
+ \item 30 Jan 2011: Move the noweb files to a top level directory, out of
+ inst/. They don't need to be copied to binary installs.
+
+ \item 22 Jan 2011: Convert the Changelog files to the new inst/NEWS.Rd
+ format.
+
+ \item 1 Jan 202011: The match.ratetable would fail when passed a data
+ frame with a character variable. This was pointed out by Heinz
+ Tuechler, who also did most of the legwork to find it. It was
+ triggered by the first few lines of tests/jasa.R (expect <- ....)
+ when options(stringsAsFactors=FALSE) is set.
+ }
+}
+
+\section{Changes in version 2.36-2}{
+\itemize{
+ \item 20 Dec 2010: Add more test cases for survfit.coxph,
+ which led to significant updates in the code.
+
+ \item 18 Nov 2010: Add nevent to the coxph output and printout in
+ response to a long standing user request.
+
+ \item 14 Dec 2010: Add an as.matrix method for Surv objects.
+
+ \item 11 Nov 2010: The prior changes broke 5 packages: the dependencies form a bigger
+test suite than mine! 1. Survival curve for a coxph model with sparse
+frailty fit; fixed and added a new test case. 2. survexp could fail if
+called from within a function due to a scoping error. 3. "Tsiatis" was once
+a valid type (alias for 'aalen') for survfit.coxph; now removed from the
+documentation but the code needed to be backwards compatable. The other two
+conflicts were fixed in the packages that call survival. There are still
+issues with the rms package which I am working out with Frank H.
+ }
+}
+
+\section{Changes in version 2.36-1}{
+ \itemize{
+ \item{27 Oct 2010: Finish corrections and test to the new code. It now passes
+the checks. The predict.coxph routine now does strata and standard errors
+correctly, factors propogate through to predictions, and numerous small
+errors are addressed. Predicted survival curves for a Cox model has been
+rewritten in noweb and expanded. Change the version number to 2.36-1.}
+
+ \item{17 Oct 2010: Per a request from Frank Harrell (interaction with his library),
+survfit.coxph no longer reconstructs the model frame unless it really needs
+it: in some cases the 'x' and 'y' matrices may be sufficient, and may be
+saved in the result. Add an argument "mf" to model.matrix.coxph for more
+efficient interaction when a parent routine has already recovered the model
+frame.
+ In general, we are trying to make use of model.matrix.coxph in many of the
+routines, so that the logic contained there (remove cluster() calls, pull
+out strata, how to handle intercepts) need not be replicated in multiple
+places.}
+
+ \item{12 Oct 2010: Fix a bug in the modified lower limits for survfit (Dory & Korn).
+A logical vector was being inadvertently converted to numeric. Pointed out
+by Andy Mugglin. A new case was added to the test suite. }
+ }
+}
+
+\section{Changes in version 2.35}{
+ \itemize{
+ \item{15 July 2010: Add a coxph method for the logLik function. This is used by
+the AIC function and was requested by a user.}
+
+ \item{29 July 2010: Fix 2 bugs in pyears. The check for a US rate table was off
+(minor effect on calculations), and there was a call to julian which assumed
+that the origin argument could be a vector. }
+
+ \item{21 July 2010: Fix a problem pointed out by a user: calling survfit with almost
+tied times, e.g., c(2, sqrt(2)^2), could lead to an inconsistent result. Some
+parts of the code saw these as 2 unique values per the unique() function, some
+as a single value using the results of table(). We now pre-round the input
+times to one less decimal digit than the max from .Machine$double.digits.
+ Also added the noweb.R processing function from the coxme package, so that
+the noweb code can be extracted "on the fly" during installation using
+commands in the configure and cleanup scripts. }
+
+ \item{11 July 2010: A rewrite of the majority of the survfit.coxph code. The primary
+benefits are 1: finally tracked down and eliminated the bug for standard errors
+of case weights + Cox survival + Efron method; 2: the individual=TRUE and FALSE
+options now use the same underlying code for curves, before there were some
+options valid only for one or the other; 3: code was rewritten using noweb
+with a considerable increase in documentation; 4: during the verification
+process some errors were found in the test suite and corrected, e.g., a
+typo in my book led to failure of an all.equal test in book4.R. Similar
+to the rewrite for survfit several years ago, the new code has far less use
+of .C to help transparency.}
+
+ \item{21 May 2010: Fix bug in summary.survfit. For a survival curve from a Cox model
+with start,stop data, the 'times' argument would generate an error.}
+
+ \item{24 May 2010: Fix an annoyance in summary.survfit. When the survival data
+had an event or censor at time 0 and summary is called with a times argument,
+then my constructed call to approx() would have duplicate x values. The answer
+was always right, but approx has begun to print a bothersome warning message.
+A small change to the constructed argument vector avoids it.}
+
+ \item{7 April 2010: Minor bug pointed out by Fredrik Lundgren. In survfit if the
+method was KM (default) and error = Tsiatis an error message results. Simple
+fix: code went down the wrong branch.}
+
+ \item{24 Feb 2010: Serious bug pointed out by Kevin Buhr. In Surv(time1, time2,stat)
+if there were i) missing values in time1 and/or time2, ii) illegal value
+sets with time1 >=time2, and iii) all the instances of ii do not preceed all
+the instances of i, then the wrong observation (not the illegal) will be
+thrown out. Repaired, and a new test added.
+ Minor updates to 3 test files: survreg2, testci, ratetable.}
+
+ \item{8 Feb 2010: Bug pointed out by Heinz Tuechler -- if a subscript was dropped from
+a rate table the 'type' attribute got dropped, e.g. survexp.usr[,1,,].}
+
+ \item{26 Jan 2010: At the request of Alex Bokov, added the xmax, xscale, and fun
+arguments to points.survfit.}
+
+ \item{26 Jan 2010: Fix bug pointed out by Thomas Lumley -- with case weights <1 a Cox
+model with (start, stop) input would inappropriately decide it needed to do
+step halving to find a solution, eventually failing to converge. It was
+treating a loglik >0 as an indication of failure, but such values arise for
+small case weights. Let L(w) be the loglik for a data set where everyone is
+given a weight of w, then L(w)= wL(1) - d log(w) where d=number of deaths in
+the data. For small enough w positivity of L(w) is certain.}
+
+ \item{25 Jan 2010: Fix bug in summary.ratetable pointed out by Heinze Tuechler. Added
+a call to the function to the test suite as well.}
+
+ \item{15 Dec 2009: Two users pointed out a bug that crept into survreg() with a
+cluster statement, when a t(x)%*%x was replaced with crossprod. A trivial
+fix, but in response I added another test that more formally checks the
+dfbeta residuals and found a major oversight for the case of multiple
+strata. }
+
+ \item{14 Dec 2009: 1.Fix bug in frailty.xxx, if there is a missing value in the levels
+it gets counted by "length(unique(x))" (frailty is called before NA
+removal.) 2.SurvfitCI had an incorrect CI with case weights, and 3. in
+survreg a call to resid instead of residuals.survreg, before the class
+was attached.}
+
+ \item{11 Nov 2009: The 'type' argument does not make sense for plot.survfit. (If
+type='p', should one plot the tops of the step function, the bottoms, or
+both?). Make it explicitly disallowed in response to an R-help query,
+rather than the confusing error message that currently arose.}
+
+ \item{28 Oct 2009: The basehaz function would reorder the labels of the strata
+factor. Not a bug really, but a "why do this?" Unintended consequence of
+a character -> factor conversion.}
+
+ \item{1 Oct 2009: Fix a bug pointed out by Ben Domingue. There was one if-then-else
+path into step-halving in the frailty.controldf routine that would refer to
+a non-existent variable. A very rarely followed path, obviously, and with
+the obvious fix. The mathematics of the update was fine.}
+
+ \item{30 Sep 2009: For coxph and model.matrix.coxph, re-attach the
+attributues lost from the X matrix when the intercept is removed,
+i.e., X <- X[,1]. In particular, some downstream libraries depend on
+the assign attribute.
+ For predict.coxph remove an earlier edit so that a single variable model
++ type='terms' returns a matrix, not a vector. This is expected by the
+termplot() function. It led to a whole lot of changes in the test suite
+results, though, due to more "matrix" printouts.}
+
+ \item{4 Sep 2009: Added a model.matrix.coxph and model.frame.coxph methods. The
+model.matrix.default function ceased to work for coxph models sometime
+between R 2.9 and 2.9.2 (best guess). This wasn't picked up in the test
+suite but rather by failure of 3 packages that depend on survival. Also added
+a test. Update CRAN since this broke other's packages.}
+
+ \item{20 Aug 2009: One more fix to predict.coxph. It needed to use
+delete.response(Terms) rather than Terms, so as to not look for (unnecessarily)
+the response variable when the newdata argment is used. Pointed out by Michael
+Conklin.}
+
+ \item{17 Aug 2009: Small bug in survfit.coxph.null pointed out by Frank Harrell. The
+'n' component would be missing if the input data included strata, i.e., the
+initial model had used x=TRUE. He also pointed out the fix.}
+
+ \item{10 June 2009: Fix an error pointed out by Nick Reich, who was the first to use
+interval censored data + user defined distribution in survreg, jointly. There
+was no test case and creating one uncovered several errors (but only for this
+combination). All the error cases led to catastrophic failure, highlighting
+the extreme rarity of a user requesting this combination.}
+
+ \item{2 June 2009: Surv(time1, time2, status, type='interval') would fail for an NA
+status code. Pointed out by Achim Zeilus.}
+
+ \item{22 May 2009: Allow single subscripts to rate tables, e.g. survexp[1:10: .
+Returns a simple vector of values. The str() function does this to print out
+a short summary. Problem pointed out by Heinz Tuechler.}
+
+ \item{21 May 2009: Create a test case for factor variables/newdata/predict for coxph
+and survreg. This led to a set of minor fixes; the code is now in line with
+the R standard for model functions. One consequence is that model.frame.coxph
+and model.frame.survreg are no longer needed, so have been removed.}
+
+ \item{20 May 2009: The manual page for survfit was confusing, since it tries to
+document both the standard KM (formula method) and the coxph method. I've
+split them out so that now survfit documents only the basic method and points
+a user the appropriate specialized page.}
+
+ \item{1 May 2009: The anova.coxph function was incorrect for models with a strata
+term. Fixed this, and made chisquare tests the default.}
+
+ \item{22 April 2009: The coxph code had an override to iter and eps, making both of
+them more strict for a penalized model. However, the overall default values
+have changed over time, so that these lines actually decreased accuracy - the
+opposite of their intent. Removed the lines. Also removed the iter.miss and
+eps.miss components (on which this check depended) from coxph.control, which
+makes that function match its documentation.}
+
+ }
+}
+
+\section{Changes in version 2.34 and earlier}{
+\subsection{Merge of the TMT source code tree with the Lumley code tree}{
+ \itemize{
+
+ \item Issues/decisions in remerging the Mayo and R code:
+ For most of routines, it was easier to start with the Lumley code and add
+the Therneau fixes. This is because Tom had expanded a lot of partial
+matches, e.g., fit$coef in the TT code vs fit$coefficients. Routines with
+substantial changes were, of course, a special case.
+ The most common change is an is.R() construct to choose class vs oldClass.
+ \item xtras.R: Move anova.coxph and anova.coxphlist to their own
+ source files.
+ The remainder of the code is R only.
+
+ \item survsum: removed from package
+
+ \item survreg.old: has been removed from the package
+
+ \item survfit.s:
+ Depreciate the "formula with no ~1" option
+ Mayo code for [ allows for reordering curves
+ Separate out the R "basehaz" function as a separate source file
+
+ \item survfit.km.s: The major change of did not get copied into R, so lots of
+changes. R had "new.time" and Splus 'start.time' for the same argument. Allow
+them both as synonyms.
+ The output structure also changed: adapt the new one. This is mostly some
+name changes in the components, removing unneeded redundancies created by
+a different programmer.
+
+ \item survfit.coxph.s: TMT code finally fixed the "Can't (yet) to case weights"
+problem. There must have been 10 years been the intent and execution.
+
+ \item survexp.s: Add "bareterms" function from R, which replaces a prior use of
+ terms.inner (in Splus but not R).
+
+ \item survdiff.s: R code had the old (incorrect) expected <- sum(1-offset), since
+corrected to sum(-log(offset)) .
+
+ \item{summary.coxph.s: This was a mess, since Tom and I had independently made the
+ addition of a print.summary.coxph function. Below, TMT means that it was the
+ choice in the Splus code, TL means that it was the choice in R
+ 1. Put the coef=T argument in the print function, not summary (TMT)
+ 2. Change the output's name from coef to coefficients (suggestion of
+ Peter Dalgaard). Also change one column name to Pr(>|z|) for R.
+ 3. Remove last vestiges of a reference to the 'icc' component (TMT)
+ 4. Do not include score, rscore, naive.var in the result (TL)
+ 5. Do include loglik in the result (TMT)
+ 6. Compute the test statistics (loglik, Wald, etc) in the summary
+ function rather than in the print.summary function (TL)
+ 7. Remove the digits option from summary, it belongs in print.summary.
+ (neither)}
+
+ \item{strata.s: R code added a sep argument, this is ok
+ R changed the character string NA to as.character(NA). Not okay
+ 1. won't work with Splus,
+ 2. This is a label, designed for printing,
+ and so it should be a character string. }
+
+ \item{residuals.coxph.s: R had added type='partial'. (Which I'm not very partial to,
+ from their statistical properties. But they are legal, and I assume that
+ someone requested them).}
+
+ \item{print.survfit.s: Rewritten as a part of the general survival rewrite. Created
+the function 'survmean' which does most of the work, and is shared by print and
+summary, so that the values from 'print' are now available.
+ Fix the minmin function: min(NULL) gives NA in Splus, which is the right
+answer for a non-estimable median, but Inf in R. Explicitly deal with this
+case, and add a bunch of comments.
+ R had the print.rmean option, this has been expanded to a more general
+rmean option that allows setting the cutoff point.
+ R added a print.n option with 3 choices, my code includes all 3 in the
+output. }
+
+ \item{lines.survfit.s:
+ The S version has a new block of code for guessing "firstx" more
+intellegently when it is missing. (Or, one hopes is is more intellegent!)}
+
+ \item{coxph.control.s:
+ The R code had tighter tolerances (eps= 1e-9) than Splus (1e-4) and
+a higher iterationn count (20 vs 10).
+ Set eps to 1e-8 and iter to 15, mostly bending to the world. The tighter
+iteration is defensible, but I still maintain that a Cox model that takes >10
+iterations is not going to finish if you give it 100. The likelihood surface
+is almost perfectly quadratic near the minimum. (Not true for survreg by the
+way).}
+
+ \item{: In Surv, the Mayo code creates NA's out of invalid status values or
+start,stop pairs, rather than a stop and error message. This is to
+allow for example
+ coxph(Surv(time1,time2, status).... , subset=(goodlines))
+succeed, when "goodlines" is the subset with correct values.}
+}
+}
+
+\subsection{Older changes}{
+ \itemize{
+ \item{25SepO7: How embarrassing -- someone pointed out that I had Dave Harrington's
+name spelled wrong in the options to survfit.coxph!}
+
+ \item{9Jul07: In a model with offsets, survreg mistakenly omitted the offset
+from the returned linear.predictor component.}
+
+ \item{10May07: Change summary.coxph so that it returns an object of class
+summary.coxph, and add a print method for that object.}
+
+ \item{22Jun06: Update match.ratetable, so that more liberal matches are now
+allowed. For instance, 'F', 'f', 'female', 'fem', 'FEMA', etc are
+now all considered matches to the dimname "female" in survexp.us.}
+
+ \item{26Apr06: Fix bug in summary.survfit, pointed out by Bob Treder. With
+the times option, the value of n.risk would be wrong for "in between"
+times; e.g., the data had events and/or censoring at times 10,
+20,... and we asked for printout at time 15. It should give n.risk at time
+20, it was returning the value at time 10. Interestingly, the code had
+a very careful treatment of this case, along with an example in the
+comments, and the "the right answer is" part of the comment was wrong!
+So the code correctly computed an incorrect answer. Added another
+test case to the test suite, survtest2.}
+
+ \item{21Apr06: Fix problem in [.survfit, pointed out by Thomas Lumley. If
+fit <- survfit(Surv(time, status) ~ ph.ecog, lung), then fit[2:1] did
+not reorder the output correctly. I had never tested putting the
+subscripts in non-increasing order.}
+
+ \item{7Feb06: Fix a problem in the coxph iteration (coxfit2.c, coxfit5, agfit3,
+agfit5, agexact). It will likely never catch anyone again, even if I
+didn't fix it. In a particular data set, beta overshot and step halving
+was invoked. During step halving, a loglik happened to occur that was
+within eps of the prior step's loglik --- and the routine decided, erroneously,
+that it had converged! (A nice quadratic curve, a first guess b1 to the
+left of the desired max of the curve. The next guess b2 overshot and ends
+up with a lower loglik, on the right side of the max. Back up to the
+midpoint of b1 and b2, and this guess, still to the right of the max (still
+too large) has EXACTLY the same value of y as b1 did, but on the other side
+of the max from b1. "Last two guesses give the same answer, I'm done" said
+the routine).}
+
+ \item{27Sep05: Found and fixed a nasty bug in survfit. When method='fh2' and
+there were multiple groups I had a subscripting bug, leading to vectors
+that were supposed to be the same length, but weren't, passed into C.
+The resulting curves were obviously wrong -- survival precipitously drops
+to zero.}
+
+ \item{5May05: Add the drop=F arg to one subscripting selection in survfit.coxph.
+ temp <- (matrix(surv$y, ncol=3))[ntime,,drop=F]
+If you selected only 1 time point (1 row) in the final output, the code
+would fail. Pointed out by Cindy Crowson.}
+
+ \item{18Apr05: Bug in survfit.turnbull. The strata variable was not being
+filled in (number of points per curve). So if multiple curves were
+generated at once, i.e., with something on the right hand side of ~ in
+the formula, all the downstream print/plot functions would not work
+with the result.}
+
+ \item{8Feb05: Fix small typo in is.ratetable, introduced on 24Nov04: (Today
+was the first time I added to the standard library, and thus ended
+up using the non-verbose mode.)}
+
+ \item{8Feb05: Add the data.frame argument to pyears. This causes the output
+to contain a dataframe rather than a set of arrays. It is useful for
+further processing of the data using Poisson regression.}
+
+ \item{7Feb05: Modified print.ratetable to be more useful. It now tells
+about the ratetable, rather than printing all of its values.}
+
+ \item{8Dec04: Fix a small bug in survfit.turnbull. If there are people left
+censored before the first
+time point of any other kind (interval, exact, or right censored),
+the the plotted height of the curve from "rightmost left censoring time"
+to "leftmost event time", that is the flat tail on the left, was at
+the wrong height.
+ Added another test to testreg/reliability.s for this.}
+
+ \item{24Nov04: Change is.ratetable to give longer messages}
+}
+}
+}
diff --git a/win32/deps/library/survival/R/survival b/win32/deps/library/survival/R/survival
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/survival/R/survival
+++ b/win32/deps/library/survival/R/survival
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/survival/R/survival.rdb b/win32/deps/library/survival/R/survival.rdb
index b2cae16..9b73f54 100644
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diff --git a/win32/deps/library/survival/R/survival.rdx b/win32/deps/library/survival/R/survival.rdx
index d1ac08c..78ba92b 100644
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diff --git a/win32/deps/library/survival/data/Rdata.rdb b/win32/deps/library/survival/data/Rdata.rdb
index 56aa883..d365f62 100644
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diff --git a/win32/deps/library/survival/data/Rdata.rds b/win32/deps/library/survival/data/Rdata.rds
index 0c13cba..e8c9b02 100644
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diff --git a/win32/deps/library/survival/data/Rdata.rdx b/win32/deps/library/survival/data/Rdata.rdx
index ddbc442..76c18ea 100644
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diff --git a/win32/deps/library/survival/doc/index.html b/win32/deps/library/survival/doc/index.html
new file mode 100644
index 0000000..6923ac9
--- /dev/null
+++ b/win32/deps/library/survival/doc/index.html
@@ -0,0 +1,27 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Vignettes</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="/doc/html/R.css">
+</head><body>
+<h1> Vignettes
+<img class="toplogo" src="/doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="/doc/html/index.html"><img src="/doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div>
+<h2>Vignettes from package 'survival'</h2>
+<table width="100%">
+<col width="22%">
+<col width="2%">
+<col width="50%">
+<col width="8%">
+<col width="8%">
+<col width="8%">
+<tr><td align="right" valign="top"><a href="../../../library/survival/doc/timedep.pdf">survival::timedep</a></td>
+<td></td><td valign="top">Using Time Dependent Covariates</td>
+<td valign="top"><a href="../../../library/survival/doc/timedep.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/survival/doc/timedep.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/survival/doc/timedep.R">R code</a></td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/survival/doc/timedep.R b/win32/deps/library/survival/doc/timedep.R
new file mode 100644
index 0000000..1fe59de
--- /dev/null
+++ b/win32/deps/library/survival/doc/timedep.R
@@ -0,0 +1,121 @@
+### R code from vignette source 'timedep.Rnw'
+
+###################################################
+### code chunk number 1: preamble
+###################################################
+options(width=60, continue=" ")
+makefig <- function(file, top=1, right=1, left=4) {
+ pdf(file, width=9.5, height=7, pointsize=18)
+ par(mar=c(4, left, top, right) +.1)
+ }
+library(survival)
+
+
+###################################################
+### code chunk number 2: timedep.Rnw:75-77 (eval = FALSE)
+###################################################
+## fit <- coxph(Surv(time1, time2, status) ~ age + creatinine,
+## data=mydata)
+
+
+###################################################
+### code chunk number 3: timedep.Rnw:153-186
+###################################################
+cgdname <- c("id", "center", "random.dt", "trt", "sex", "age",
+ "height", "weight", "inheritance", "steroids",
+ "antibiotic", "inst", "futime", paste("e", 1:7, sep=''))
+cgd1 <- read.table('cgd.dat', header=F, fill=T, col.names=cgdname,
+ colClasses=c("integer", "integer", "character",
+ rep("integer", 3), rep("numeric",2),
+ rep("integer", 12)))
+
+cgd1$ninfect <- rowSums(!is.na(as.matrix(cgd1[,14:20])))
+cgd1$random.dt <- as.Date(cgd1$random.dt, format="%m%d%y")
+cgd1$sex <- factor(cgd1$sex, labels=c("M", "F"))
+cgd1$inst <- factor(cgd1$inst, labels=c("NIH", "US-Other",
+ "Amsterdam", "Europe-Other"))
+
+temp <- apply(as.matrix(cgd1[,13:20]), 1, function(x) {
+ z <- as.vector(x[!is.na(x)])
+ if (length(z)==1) cbind(0, z, 0)
+ else {
+ temp <- cbind(c(0, z[-1]),
+ c(z[-1], z[1]),
+ c(rep(1, length(z)-1), 0))
+ if (z[1]== z[length(z)]) temp[-nrow(temp),]
+ else temp
+ }})
+
+index <- rep(1:nrow(cgd1), unlist(lapply(temp, nrow)))
+cgd2 <- data.frame( cgd1[index, 1:12],
+ time1= unlist(lapply(temp, function(x) x[,1])),
+ time2= unlist(lapply(temp, function(x) x[,2])),
+ event= unlist(lapply(temp, function(x) x[,3])),
+ enum = unlist(lapply(temp, function(x) 1:nrow(x))))
+cfit <- coxph(Surv(time1, time2, event) ~ trt + sex + age +
+ inheritance + cluster(id), data=cgd2)
+
+
+###################################################
+### code chunk number 4: timedep.Rnw:260-268
+###################################################
+load('raheart.rda')
+age2 <- tcut(raheart$agechf*365.25, 0:110* 365.25, labels=0:109)
+rowid <- 1:nrow(raheart)
+pfit <- pyears(Surv(startday, stopday, hospevt) ~ age2 + rowid,
+ data=raheart, data.frame=TRUE, scale=1)
+print(pfit$offtable)
+pdata <- pfit$data
+print(pdata[1:6,])
+
+
+###################################################
+### code chunk number 5: timedep.Rnw:297-314
+###################################################
+index <- as.integer(pdata$rowid)
+lagtime <- c(0, pdata$pyears[-nrow(pdata)])
+lagtime[1+ which(diff(index)==0)] <- 0 #starts at 0 for each subject
+temp <- raheart$startday[index] + lagtime #start of each new interval
+data2 <- data.frame(raheart[index,],
+ time1= temp,
+ time2= temp + pdata$pyears,
+ event= pdata$event,
+ age2= 1+ as.numeric(pdata$age2) )
+
+afit1 <- coxph(Surv(startday, stopday, hospevt) ~ male + pspline(agechf),
+ data=raheart)
+afit2 <- coxph(Surv(time1, time2, event) ~ male + pspline(age2), data2)
+#termplot(afit1, terms=2, se=TRUE, xlab="Age at Diagnosis of CHF")
+#termplot(afit2, terms=2, se=TRUE, xlab="Current Age")
+
+table(with(raheart, tapply(hospevt, patid, sum)))
+
+
+###################################################
+### code chunk number 6: timedep.Rnw:330-334
+###################################################
+afit2b <- coxph(Surv(startday, stopday, hospevt) ~ male + tt(agechf),
+ data=raheart,
+ tt=function(x, t, ...) pspline(x + t/365.25))
+afit2b
+
+
+###################################################
+### code chunk number 7: timedep.Rnw:360-367
+###################################################
+function(x, t, riskset, weights){
+ obrien <- function(x) {
+ r <- rank(x)
+ (r-.5)/(.5+length(r)-r)
+ }
+ unlist(tapply(x, riskset, obrien))
+}
+
+
+###################################################
+### code chunk number 8: timedep.Rnw:377-379
+###################################################
+function(x, t, riskset, weights)
+ unlist(tapply(x, riskset, rank))
+
+
diff --git a/win32/deps/library/survival/doc/timedep.Rnw b/win32/deps/library/survival/doc/timedep.Rnw
new file mode 100644
index 0000000..10b60f3
--- /dev/null
+++ b/win32/deps/library/survival/doc/timedep.Rnw
@@ -0,0 +1,419 @@
+\documentclass{article}
+\usepackage{amsmath}
+\usepackage{Sweave}
+\addtolength{\textwidth}{1in}
+\addtolength{\oddsidemargin}{-.5in}
+\setlength{\evensidemargin}{\oddsidemargin}
+
+%\VignetteIndexEntry{Using Time Dependent Covariates}
+
+\title{Using Time Dependent Covariates and Time Dependent Coefficients
+ in the Cox Model}
+\author{Terry Therneau \and Cindy Crowson\\ Mayo Clinic}
+
+\begin{document}
+\maketitle
+
+\SweaveOpts{keep.source=TRUE}
+<<preamble, echo=F>>=
+options(width=60, continue=" ")
+makefig <- function(file, top=1, right=1, left=4) {
+ pdf(file, width=9.5, height=7, pointsize=18)
+ par(mar=c(4, left, top, right) +.1)
+ }
+library(survival)
+@
+
+\section{Introduction}
+One of the strengths of the Cox model is its ability to encompass covariates
+that change over time, due to the theoretical foundation in martigales.
+A \emph{martingale} (original definition) is a betting strategy in games of
+chance. One of the simplest and best known is doubling the bet each time
+you lose. For instance consider the following game of roulette:
+\begin{equation*}
+ \begin{tabular}{rcc|c}
+ Bet & Outcome & Win & Running total \\ \hline
+ R \$1 & Red & 2 & 1 \\ &&&\\
+ R \$1 & Black & 0 & 0 \\
+ R \$2 & Black & 0 & -2 \\
+ B \$4 & Red & 0 & -6 \\
+ R \$8 & Black & 0 & -14 \\
+ B \$16& Black & 32 & 2 \\ &&&\\
+ B \$1 & Red & 0 & 1 \\
+ B \$2 & Black & 4 & 3 \\&&&\\
+ \vdots & \vdots & \vdots &\vdots
+ \end{tabular}
+\end{equation*}
+At the end of each cycle of bets the player is another \$1 ahead.
+The problem is that a modest sequence of losses will exhaust their stake.
+
+The rule for time dependent covariates in a Cox model is simple
+and essentially the same as that for gambling: you cannot look into
+the future.
+A covariate may change in any way based on past data or outcomes, but it
+may not reach ``forward'' in time.
+One of the more well known examples of this error is analysis by response:
+at the end of a trial a survival curve is made comparing those who had an
+early response to treatment (shrinkage of tumor, lowering of cholesterol,
+or whatever), and it discovered that response predicts survival.
+The problem arises because subjects are classified as responders or
+non-responders from the beginning of the study, i.e., they are placed into
+group A or B before the response has occurred.
+As a consequence, any early deaths that occur before response can be
+assessed will be assigned to the non-responder group, even deaths that have
+nothing to do with the condition under study.
+
+There are many variations on the error: interpolation of the values of a
+laboratory test linearly between observation times, removing subjects who do
+not finish the treatment plan, imputing the date of an adverse event midway
+between observation times, etc.
+All of these are similar to running a red light in your car:
+disaster is not guarranteed --- but it is likely.
+
+The most common way to encode time-dependent covariates is to use the
+(start, stop] form of the model.
+<<echo=TRUE, eval=FALSE>>=
+fit <- coxph(Surv(time1, time2, status) ~ age + creatinine,
+ data=mydata)
+@
+In this data set a patient might have the following observations
+\begin{center}
+ \begin{tabular}{ccccccc}
+ subject & time1 & time2 & status & age & creatinine & \ldots \\ \hline
+ 1 & 0 & 15 & 0 & 25 & 1.3 \\
+ 1 & 15& 46 & 0 & 25 & 1.5 \\
+ 1 & 46& 73 & 0 & 25 & 1.4 \\
+ 1 & 73& 100& 1 & 25 & 1.6 \\
+\end{tabular}
+\end{center}
+In this case the variable \emph{age} = age at entry to the study stays the
+same from line to line, while the value of creatinine varies and is treated as
+1.3 over the interval $(0, 15]$, 1.5 over $(15, 46]$, etc. The intervals are
+open on the left and closed on the right, which means that the creatinine
+is taken to be 1.3 on day 15.
+The status variable describes whether or not each interval ended in an event.
+
+One commmon question with this data setup is whether we need to worry about
+correlated data, since a given subject has multiple observations.
+The answer is no, we do not. The reason is that this representation is
+simply a bookkeeping trick; the likelihood equations at any time point
+use only one copy of any subject, the program picks out the correct
+row of data at any given time.
+There are two exceptions to this rule, in which case the cluster variance
+is necessary:
+\begin{itemize}
+ \item When subjects have multiple events.
+ \item When a subject appears in overlapping intervals. This however is
+ almost always a data error, since it corresponds to two copies of the
+ subject being present at the same time, e.g., they could meet themselves
+ on the sidewalk.
+\end{itemize}
+
+
+\section{Examples}
+\subsection{Multiple events}
+Chronic granulomatous disease (CGD) is a heterogenous group of uncommon
+inherited disorders characterized by recurrent pyogenic infections that
+usually begin early in life and may lead to death in childhood. Interferon
+gamma is a principal macrophage-activating factor shown to partially correct
+the metabolic defect in phagocytes.
+It was hypothesized that treatment with interferon might reduce
+the frequency of serious
+infections in patients with CGD.
+In 1986, Genentech, Inc. conducted a
+randomized, double-blind, placebo-controlled trial in 128 CGD patients who
+received Genentech's humanized interferon gamma (rIFN-g) or placebo three %'
+times daily for a year. The primary endpoint of the study was the time to
+the first serious infection. However, data were collected on all serious
+infections until the end of followup,
+which occurred before day 400 for most
+patients. Thirty of the 65 patients in the placebo group and 14 of the 63
+patients in the rIFN-g group had at least one serious infection.
+The total number of infections was 56 and 20 in the placebo and treatment
+groups, respectively.
+ One patient was taken off on the day of his last infection; all others
+have some followup after their last episode.
+Below are the first 10 observations, but with the listing truncatated
+beyond the fourth infection. Subject 2 has 7 infections, no one in the
+study has more.
+\small\begin{verbatim}
+ 1 204 082888 1 2 12 147.0 62.0 2 2 2 2 414 219 373
+ 2 204 082888 0 1 15 159.0 47.5 2 2 1 2 439 8 26 152 241 249 322 350
+ 3 204 082988 1 1 19 171.0 72.7 1 2 1 2 382
+ 4 204 091388 1 1 12 142.0 34.0 1 2 1 2 388
+ 5 238 092888 0 1 17 162.5 52.7 1 2 1 1 383 246 253
+ 6 245 093088 1 2 44 153.3 45.0 2 2 2 2 364
+ 7 245 093088 0 1 22 175.0 59.7 1 2 1 2 364 292
+ 8 245 093088 1 1 7 111.0 17.4 1 2 1 2 363
+ 9 238 100488 0 1 27 176.0 82.8 2 2 1 1 349 294
+ 10 238 100488 1 1 5 113.0 19.5 1 2 1 1 371
+\end{verbatim}
+\normalsize
+
+<<>>=
+cgdname <- c("id", "center", "random.dt", "trt", "sex", "age",
+ "height", "weight", "inheritance", "steroids",
+ "antibiotic", "inst", "futime", paste("e", 1:7, sep=''))
+cgd1 <- read.table('cgd.dat', header=F, fill=T, col.names=cgdname,
+ colClasses=c("integer", "integer", "character",
+ rep("integer", 3), rep("numeric",2),
+ rep("integer", 12)))
+
+cgd1$ninfect <- rowSums(!is.na(as.matrix(cgd1[,14:20])))
+cgd1$random.dt <- as.Date(cgd1$random.dt, format="%m%d%y")
+cgd1$sex <- factor(cgd1$sex, labels=c("M", "F"))
+cgd1$inst <- factor(cgd1$inst, labels=c("NIH", "US-Other",
+ "Amsterdam", "Europe-Other"))
+
+temp <- apply(as.matrix(cgd1[,13:20]), 1, function(x) {
+ z <- as.vector(x[!is.na(x)])
+ if (length(z)==1) cbind(0, z, 0)
+ else {
+ temp <- cbind(c(0, z[-1]),
+ c(z[-1], z[1]),
+ c(rep(1, length(z)-1), 0))
+ if (z[1]== z[length(z)]) temp[-nrow(temp),]
+ else temp
+ }})
+
+index <- rep(1:nrow(cgd1), unlist(lapply(temp, nrow)))
+cgd2 <- data.frame( cgd1[index, 1:12],
+ time1= unlist(lapply(temp, function(x) x[,1])),
+ time2= unlist(lapply(temp, function(x) x[,2])),
+ event= unlist(lapply(temp, function(x) x[,3])),
+ enum = unlist(lapply(temp, function(x) 1:nrow(x))))
+cfit <- coxph(Surv(time1, time2, event) ~ trt + sex + age +
+ inheritance + cluster(id), data=cgd2)
+@
+
+The logic for creating the time variables is
+\begin{itemize}
+ \item If a subject has no events there is a single interval from 0 to
+ last follow-up, with a status of 0.
+ \item If there are events
+ \begin{itemize}
+ \item There is an interval for each event (0, event1], (event1, event2],
+ etc. each with status =1.
+ \item If the follow-up time exceeds the last event there will be a
+ final interval with status =0.
+ \end{itemize}
+\end{itemize}
+
+The result of the \texttt{apply} function above will be a list with one
+item per patient, each item being a 3 column matrix with time1,
+time2, and status.
+The as.vector command removes names, which can speed the operation.
+The resulting data frame \texttt{cgd2} is in the proper format for the
+analysis.
+
+
+\subsection{Changing lab tests}
+ To be filled in.
+
+\subsection{Predictable time-dependent covariates}
+Occasionaly one has a time-dependent covariate whose values in the future
+are predictable.
+The most obvious of these is patient age, occasionally this may also be
+true for the cumulative dose of a drug.
+If age is entered as a linear term in the model, then the effect of changing
+age can be ignored in a Cox model, due to the structure of the partial
+likelihood. Assume that subject $i$ has an event at time $t_i$, with other
+subject $j \in R_i$ at risk at that time, with $a$ denoting age.
+The partial likelihood term is
+\begin{equation*}
+ \frac{e^{\beta * a_i}}{\sum_{j \in R_i} e^{\beta* a_j}} =
+ \frac{e^{\beta * (a_i + t_i)}}{\sum_{j \in R_i} e^{\beta* (a_j + t_i)}}
+\end{equation*}
+We see that using time-dependent age (the right hand version) or age at
+baseline (left hand), the partial likelihood term is identical since
+$\exp(\beta t_i)$ cancels out of the fraction.
+Howevever, if the effect of age on risk is \emph{non-linear}, this
+cancellation does not occur.
+
+Since age changes continuously, we would in theory need a very large
+(start, stop] data set to completely capture the effect --- an interval
+per day to match the usual resolution for death times.
+In practice this level of resolution is not necessary; though we all
+grow older, risk does not increase so rapidly that we need to know
+out age to the day!
+For most medical applications year is sufficient, but this still leads
+to a large data set.
+One useful way to generate this data set is through use of the \texttt{pyears}
+function.
+The following example uses data on rehospitalization for cohort of
+rheumatoid arthritis
+patients who also have conjestive heart failure (CHF)\cite{Nicola05}.
+The variables are
+\begin{itemize}
+ \item patid: patient identifier
+ \item agechf: age at onset of CHF
+ \item yearchf calendar year of CHF, relative to the start of the study
+ \item startday, stopday: an interval of risk
+ \item hospevt: =1 if the interval ends with a hospitalization
+ \item prevhosp: number of prior hosptializations
+ \item duration: duration of RA prior to CHF
+ \item male sex: 1 for male, 0 for female
+\end{itemize}
+The age and duration variables have been rounded to .1 year to
+maintain patient privacy.
+
+<<>>=
+load('raheart.rda')
+age2 <- tcut(raheart$agechf*365.25, 0:110* 365.25, labels=0:109)
+rowid <- 1:nrow(raheart)
+pfit <- pyears(Surv(startday, stopday, hospevt) ~ age2 + rowid,
+ data=raheart, data.frame=TRUE, scale=1)
+print(pfit$offtable)
+pdata <- pfit$data
+print(pdata[1:6,])
+@
+The \texttt{tcut} function attaches a set of cutpoints to the starting age
+for each subject, it's primary job is to mark the variable as time-increasing%'
+for the \texttt{pyears} function.
+In the \texttt{pyears} call we set scale=1 to prevent the age intervals from
+being rescaled to years, this is not critical.
+Printing out the value of offtable is important, however. One of them
+most common mistakes in using \texttt{pyears} is mismatched scales, for
+instance if the age were in years and the follow-up time in days, and
+a common result of that error is to have follow-up time that fits into
+none of the categories.
+This will give a large amount of time that is outside the boundaries of the
+table.
+In the resulting data frame the first observation has 7 days of follow-up,
+exactly as in the starting data.
+The second observation has been broken into 4 rows, 109.6 days at age 92,
+then a year each at age 93 and 94, and a final 234.9 days at age 95
+ending with a hospitalization.
+(The odd fractions of a day like .575 are a consequence of rounding the
+age values to 1 digit.)
+
+Now we combine this with the original data set using the same indexing
+trick found in the first example.
+We also need a variable containing the end time for the prior row of
+each subject and zero for the first row of each subject, which is
+\texttt{lagtime} below.
+We then fit two models. The first looks at the effect of age at
+diagnosis of CHF, the second at the effect of current age.
+<<>>=
+index <- as.integer(pdata$rowid)
+lagtime <- c(0, pdata$pyears[-nrow(pdata)])
+lagtime[1+ which(diff(index)==0)] <- 0 #starts at 0 for each subject
+temp <- raheart$startday[index] + lagtime #start of each new interval
+data2 <- data.frame(raheart[index,],
+ time1= temp,
+ time2= temp + pdata$pyears,
+ event= pdata$event,
+ age2= 1+ as.numeric(pdata$age2) )
+
+afit1 <- coxph(Surv(startday, stopday, hospevt) ~ male + pspline(agechf),
+ data=raheart)
+afit2 <- coxph(Surv(time1, time2, event) ~ male + pspline(age2), data2)
+#termplot(afit1, terms=2, se=TRUE, xlab="Age at Diagnosis of CHF")
+#termplot(afit2, terms=2, se=TRUE, xlab="Current Age")
+
+table(with(raheart, tapply(hospevt, patid, sum)))
+@
+In this particular case the two fits are quite similar.
+In retrospect this perhaps should have been expected: the mean age
+for onset of CHF in this group is 75 years, which does leave a lot
+of time for aging.
+(This analysis is very preliminary, however. As shown by the last line
+above there are a few patients with a very large number of admissions,
+sometimes referred to as ``entering a revolving door'' near the end of
+their disease. These have an untoward influence on the fit.)
+
+
+\subsection{Predictable covariates, method 2}
+
+Another method to create a time-changing covariate is to use the
+\emph{time-transform} feature of coxph.
+<<>>=
+afit2b <- coxph(Surv(startday, stopday, hospevt) ~ male + tt(agechf),
+ data=raheart,
+ tt=function(x, t, ...) pspline(x + t/365.25))
+afit2b
+@
+
+If there are one or more terms on the right hand side of the equation
+marked with the tt() operator, the program will pre-compute the values
+of that variable for each unique event time and strata combination.
+A user-defined function is called with arguments of
+\begin{itemize}
+ \item the covariate: whatever is inside the tt() call
+ \item the event time
+ \item the event number: if there are multiple strata and the same event
+ time occurs in two of them, they are treated separately
+ \item the weight for the observation, if the call used weights
+\end{itemize}
+There is a single call to the function with a very large $x$ vector,
+it contains an element for each subject at risk at each event time.
+If there are multiple tt() terms in the formula, then the tt argument
+should be a list of functions with the requisite number of elements.
+
+There are other interesting uses for the time-transform capability.
+One example is O'Brien's logit-rank test procedure \cite{obrien78}.
+He proposed replacing the covariate at each event time with a logit
+transform of its ranks.
+This removes the influence of any outliers in the predictor $x$.
+For this case we ingore the event time argument and concentrate on the
+groupings.
+<<>>=
+function(x, t, riskset, weights){
+ obrien <- function(x) {
+ r <- rank(x)
+ (r-.5)/(.5+length(r)-r)
+ }
+ unlist(tapply(x, riskset, obrien))
+}
+@
+This relies on the fact that the input argments to tt() are ordered by the
+event number or riskset.
+This function is used as a default if no tt argument is present in the
+coxph call, but there are tt terms in the model formula.
+(Doing so allowed me to depreciate the survobrien function).
+
+Another interesting useage is to replace the data by simple ranks, not
+rescaled to 0--1.
+<<>>=
+function(x, t, riskset, weights)
+ unlist(tapply(x, riskset, rank))
+@
+The score statistic for this model is $(C-D)/2$, where $C$ and $D$ are the
+number of concordant and discordant pairs, see the
+survConcordance function.
+The score statistic from this fit is then a test for significance of the
+concordance statistics, and is in fact the basis for the standard error
+reported by survConcordance.
+The O'Brien test can be viewed as concordance statistic that gives equal %'
+weight to each event time, whereas the standard concordance weights each
+event proportionally to the size of the risk set.
+(The Cox score statistic depends on the mean $x$ at each event time;
+since ranks go from 1 to number at risk the mean also scales.)
+
+Although handy, the computational impact of the tt argument should be
+considered before using it.
+The Cox model requires computation of a weighted mean and variance of
+the covariates at each event time, a process that is inherently
+$O(ndp^2)$ where $n$ = the sample size, $d$ = the number of events and $p$=
+the number of covariates.
+Much of the algorithmic effort in coxph() is to use updating methods for
+the mean and variance matrices, reducing the compute time to $O((n+d) p^2)$.
+When a tt term appears updating is not possible; for even moderate size
+data sets the impact of $nd$ versus $n+d$ can be surprising.
+
+
+The time-transform is a new addition and still has some rough edges.
+At this moment the $x=T$ argment is needed to get proper residuals and
+predicted values, and termplot is unable to properly reconstruct the
+data to plot the spline fit.
+Please communicate any concerns or interesting examples to the author.
+
+\begin{thebibliography}{9}
+ \bibitem{Nicola05} Nicola PJ, Maradit-Kremers H, Roger VL, Jacobsen SJ,
+ Crowson CS, Ballman KV, Gabriel SE. ``The risk of Congestive Heart Failure
+ in Rheumatoid Arthritis: a Population-Based Study Over 46 Years.''
+ \emph{Arthritis Rheum} 52: 412--20, 2005.
+ \bibitem{obrien78} O'Brien, Peter, ``A non-parametric test for %'
+ association with censored data'', \emph{Biometrics} 34:243--250, 1978.
+\end{thebibliography}
+\end{document}
diff --git a/win32/deps/library/survival/doc/timedep.pdf b/win32/deps/library/survival/doc/timedep.pdf
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diff --git a/win32/deps/library/survival/help/AnIndex b/win32/deps/library/survival/help/AnIndex
index f7a12f1..5a09688 100644
--- a/win32/deps/library/survival/help/AnIndex
+++ b/win32/deps/library/survival/help/AnIndex
@@ -55,6 +55,7 @@ kidney kidney
labels.survreg survreg
leukemia aml
lines.survfit lines.survfit
+logan logan
lung lung
match.ratetable survival-internal
Math.ratetable is.ratetable
@@ -62,9 +63,9 @@ Math.Surv Surv
mgus mgus
mgus1 mgus
mgus2 mgus
-model.frame.coxph coxph
+model.frame.coxph model.frame.coxph
model.frame.survreg survreg
-model.newframe survival-internal
+model.matrix.coxph model.matrix.coxph
nwtco nwtco
Ops.ratetable is.ratetable
Ops.Surv Surv
@@ -86,6 +87,7 @@ print.coxph.null coxph
print.coxph.penal coxph
print.ratetable ratetable
print.summary.coxph print.summary.coxph
+print.summary.survexp print.summary.survexp
print.summary.survfit print.summary.survfit
print.summary.survreg survreg
print.Surv Surv
@@ -95,10 +97,13 @@ print.survfit print.survfit
print.survreg survreg.object
print.survreg.penal survreg
pspline pspline
+psplineinverse pspline
psurvreg dsurvreg
pyears pyears
qsurvreg dsurvreg
+quantile.survfit quantile.survfit
ratetable ratetable
+ratetableDate ratetableDate
rats rats
residuals.coxph residuals.coxph
residuals.coxph.null residuals.coxph
@@ -113,6 +118,7 @@ summary.coxph summary.coxph
summary.coxph.penal coxph
summary.ratetable ratetable
Summary.Surv Surv
+summary.survexp summary.survexp
summary.survfit summary.survfit
summary.survreg survreg.object
Surv Surv
@@ -132,8 +138,11 @@ survexp.usr survexp.us
survexp.wnc survexp.us
survfit survfit
survfit.coxph survfit.coxph
-survfit.formula survfit
+survfit.formula survfit.formula
survfit.object survfit.object
+survfitCI survival-internal
+survfitcoxph.fit survfitcoxph.fit
+survfitKM survival-internal
survival-internal survival-internal
survobrien survobrien
survpenal.fit survival-internal
@@ -147,6 +156,7 @@ survregDtest survregDtest
survSplit survSplit
tcut tcut
tobin tobin
+tt tt
untangle.specials untangle.specials
vcov.coxph coxph
vcov.survreg survreg
@@ -156,5 +166,5 @@ veteran veteran
[.ratetable ratetable
[.ratetable2 ratetable
[.Surv Surv
-[.survfit survfit
+[.survfit survfit.formula
[.tcut tcut
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+++ b/win32/deps/library/survival/html/00Index.html
@@ -0,0 +1,463 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Survival analysis, including penalised likelihood.</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Survival analysis, including penalised likelihood.
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘survival’ version 2.36-14</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+<li><a href="../doc/index.html">Overview of user guides and package vignettes</a>; browse <a href="../doc">directory</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<p align="center">
+<a href="#A">A</a>
+<a href="#B">B</a>
+<a href="#C">C</a>
+<a href="#D">D</a>
+<a href="#E">E</a>
+<a href="#F">F</a>
+<a href="#H">H</a>
+<a href="#I">I</a>
+<a href="#J">J</a>
+<a href="#K">K</a>
+<a href="#L">L</a>
+<a href="#M">M</a>
+<a href="#N">N</a>
+<a href="#O">O</a>
+<a href="#P">P</a>
+<a href="#Q">Q</a>
+<a href="#R">R</a>
+<a href="#S">S</a>
+<a href="#T">T</a>
+<a href="#U">U</a>
+<a href="#V">V</a>
+<a href="#misc">misc</a>
+</p>
+
+
+<h2><a name="A">-- A --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="aareg.html">aareg</a></td>
+<td>Aalen's additive regression model for censored data</td></tr>
+<tr><td width="25%"><a href="aml.html">aml</a></td>
+<td>Acute Myelogenous Leukemia survival data</td></tr>
+<tr><td width="25%"><a href="anova.coxph.html">anova.coxph</a></td>
+<td>Analysis of Deviance for a Cox model.</td></tr>
+<tr><td width="25%"><a href="anova.coxph.html">anova.coxphlist</a></td>
+<td>Analysis of Deviance for a Cox model.</td></tr>
+<tr><td width="25%"><a href="survreg.html">anova.survreg</a></td>
+<td>Regression for a Parametric Survival Model</td></tr>
+<tr><td width="25%"><a href="survreg.html">anova.survreglist</a></td>
+<td>Regression for a Parametric Survival Model</td></tr>
+<tr><td width="25%"><a href="Surv.html">as.character.Surv</a></td>
+<td>Create a Survival Object</td></tr>
+<tr><td width="25%"><a href="Surv.html">as.data.frame.Surv</a></td>
+<td>Create a Survival Object</td></tr>
+<tr><td width="25%"><a href="Surv.html">as.matrix.Surv</a></td>
+<td>Create a Survival Object</td></tr>
+<tr><td width="25%"><a href="attrassign.html">attrassign</a></td>
+<td>Create new-style "assign" attribute</td></tr>
+<tr><td width="25%"><a href="attrassign.html">attrassign.default</a></td>
+<td>Create new-style "assign" attribute</td></tr>
+<tr><td width="25%"><a href="attrassign.html">attrassign.lm</a></td>
+<td>Create new-style "assign" attribute</td></tr>
+</table>
+
+<h2><a name="B">-- B --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="basehaz.html">basehaz</a></td>
+<td>Compute the baseline survival curve for a Cox model</td></tr>
+<tr><td width="25%"><a href="bladder.html">bladder</a></td>
+<td>Bladder Cancer Recurrences</td></tr>
+<tr><td width="25%"><a href="bladder.html">bladder1</a></td>
+<td>Bladder Cancer Recurrences</td></tr>
+<tr><td width="25%"><a href="bladder.html">bladder2</a></td>
+<td>Bladder Cancer Recurrences</td></tr>
+</table>
+
+<h2><a name="C">-- C --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="lung.html">cancer</a></td>
+<td>NCCTG Lung Cancer Data</td></tr>
+<tr><td width="25%"><a href="cch.html">cch</a></td>
+<td>Fits proportional hazards regression model to case-cohort data</td></tr>
+<tr><td width="25%"><a href="cgd.html">cgd</a></td>
+<td>Chronic Granulotomous Disease data</td></tr>
+<tr><td width="25%"><a href="clogit.html">clogit</a></td>
+<td>Conditional logistic regression</td></tr>
+<tr><td width="25%"><a href="cluster.html">cluster</a></td>
+<td>Identify clusters.</td></tr>
+<tr><td width="25%"><a href="colon.html">colon</a></td>
+<td>Chemotherapy for Stage B/C colon cancer</td></tr>
+<tr><td width="25%"><a href="cox.zph.html">cox.zph</a></td>
+<td>Test the Proportional Hazards Assumption of a Cox Regression</td></tr>
+<tr><td width="25%"><a href="coxph.html">coxph</a></td>
+<td>Fit Proportional Hazards Regression Model</td></tr>
+<tr><td width="25%"><a href="coxph.control.html">coxph.control</a></td>
+<td>Ancillary arguments for controling coxph fits</td></tr>
+<tr><td width="25%"><a href="coxph.detail.html">coxph.detail</a></td>
+<td>Details of a Cox Model Fit</td></tr>
+<tr><td width="25%"><a href="coxph.html">coxph.getdata</a></td>
+<td>Fit Proportional Hazards Regression Model</td></tr>
+<tr><td width="25%"><a href="coxph.object.html">coxph.object</a></td>
+<td>Proportional Hazards Regression Object</td></tr>
+<tr><td width="25%"><a href="coxph.html">coxph.penalty</a></td>
+<td>Fit Proportional Hazards Regression Model</td></tr>
+</table>
+
+<h2><a name="D">-- D --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="dsurvreg.html">dsurvreg</a></td>
+<td>Distributions available in survreg.</td></tr>
+</table>
+
+<h2><a name="E">-- E --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="coxph.object.html">extractAIC.coxph.penal</a></td>
+<td>Proportional Hazards Regression Object</td></tr>
+</table>
+
+<h2><a name="F">-- F --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Surv.html">format.Surv</a></td>
+<td>Create a Survival Object</td></tr>
+<tr><td width="25%"><a href="frailty.html">frailty</a></td>
+<td>Random effects terms</td></tr>
+<tr><td width="25%"><a href="frailty.html">frailty.gamma</a></td>
+<td>Random effects terms</td></tr>
+<tr><td width="25%"><a href="frailty.html">frailty.gaussian</a></td>
+<td>Random effects terms</td></tr>
+<tr><td width="25%"><a href="frailty.html">frailty.t</a></td>
+<td>Random effects terms</td></tr>
+</table>
+
+<h2><a name="H">-- H --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="heart.html">heart</a></td>
+<td>Stanford Heart Transplant data</td></tr>
+</table>
+
+<h2><a name="I">-- I --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="ratetable.html">is.na.ratetable</a></td>
+<td>Ratetable reference in formula</td></tr>
+<tr><td width="25%"><a href="Surv.html">is.na.Surv</a></td>
+<td>Create a Survival Object</td></tr>
+<tr><td width="25%"><a href="is.ratetable.html">is.ratetable</a></td>
+<td>Verify that an object is of class ratetable.</td></tr>
+<tr><td width="25%"><a href="Surv.html">is.Surv</a></td>
+<td>Create a Survival Object</td></tr>
+</table>
+
+<h2><a name="J">-- J --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="heart.html">jasa</a></td>
+<td>Stanford Heart Transplant data</td></tr>
+<tr><td width="25%"><a href="heart.html">jasa1</a></td>
+<td>Stanford Heart Transplant data</td></tr>
+</table>
+
+<h2><a name="K">-- K --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="kidney.html">kidney</a></td>
+<td>Kidney catheter data</td></tr>
+</table>
+
+<h2><a name="L">-- L --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="survreg.html">labels.survreg</a></td>
+<td>Regression for a Parametric Survival Model</td></tr>
+<tr><td width="25%"><a href="aml.html">leukemia</a></td>
+<td>Acute Myelogenous Leukemia survival data</td></tr>
+<tr><td width="25%"><a href="lines.survfit.html">lines.survfit</a></td>
+<td>Add Lines or Points to a Survival Plot</td></tr>
+<tr><td width="25%"><a href="logan.html">logan</a></td>
+<td>Data from the 1972-78 GSS data used by Logan</td></tr>
+<tr><td width="25%"><a href="lung.html">lung</a></td>
+<td>NCCTG Lung Cancer Data</td></tr>
+</table>
+
+<h2><a name="M">-- M --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="is.ratetable.html">Math.ratetable</a></td>
+<td>Verify that an object is of class ratetable.</td></tr>
+<tr><td width="25%"><a href="Surv.html">Math.Surv</a></td>
+<td>Create a Survival Object</td></tr>
+<tr><td width="25%"><a href="mgus.html">mgus</a></td>
+<td>Monoclonal gammapothy data</td></tr>
+<tr><td width="25%"><a href="mgus.html">mgus1</a></td>
+<td>Monoclonal gammapothy data</td></tr>
+<tr><td width="25%"><a href="mgus.html">mgus2</a></td>
+<td>Monoclonal gammapothy data</td></tr>
+<tr><td width="25%"><a href="model.frame.coxph.html">model.frame.coxph</a></td>
+<td>Model.frame method for coxph objects</td></tr>
+<tr><td width="25%"><a href="survreg.html">model.frame.survreg</a></td>
+<td>Regression for a Parametric Survival Model</td></tr>
+<tr><td width="25%"><a href="model.matrix.coxph.html">model.matrix.coxph</a></td>
+<td>Model.matrix method for coxph models</td></tr>
+</table>
+
+<h2><a name="N">-- N --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="nwtco.html">nwtco</a></td>
+<td>Data from the National Wilm's Tumor Study</td></tr>
+</table>
+
+<h2><a name="O">-- O --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="is.ratetable.html">Ops.ratetable</a></td>
+<td>Verify that an object is of class ratetable.</td></tr>
+<tr><td width="25%"><a href="Surv.html">Ops.Surv</a></td>
+<td>Create a Survival Object</td></tr>
+<tr><td width="25%"><a href="ovarian.html">ovarian</a></td>
+<td>Ovarian Cancer Survival Data</td></tr>
+</table>
+
+<h2><a name="P">-- P --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="pbc.html">pbc</a></td>
+<td>Mayo Clinic Primary Biliary Cirrhosis Data</td></tr>
+<tr><td width="25%"><a href="pbcseq.html">pbcseq</a></td>
+<td>Mayo Clinic Primary Biliary Cirrhosis, sequential data</td></tr>
+<tr><td width="25%"><a href="plot.aareg.html">plot.aareg</a></td>
+<td>Plot an aareg object.</td></tr>
+<tr><td width="25%"><a href="plot.cox.zph.html">plot.cox.zph</a></td>
+<td>Graphical Test of Proportional Hazards</td></tr>
+<tr><td width="25%"><a href="plot.survfit.html">plot.survfit</a></td>
+<td>Plot Method for 'survfit'</td></tr>
+<tr><td width="25%"><a href="lines.survfit.html">points.survfit</a></td>
+<td>Add Lines or Points to a Survival Plot</td></tr>
+<tr><td width="25%"><a href="predict.coxph.html">predict.coxph</a></td>
+<td>Predictions for a Cox model</td></tr>
+<tr><td width="25%"><a href="predict.coxph.html">predict.coxph.penal</a></td>
+<td>Predictions for a Cox model</td></tr>
+<tr><td width="25%"><a href="predict.survreg.html">predict.survreg</a></td>
+<td>Predicted Values for a 'survreg' Object</td></tr>
+<tr><td width="25%"><a href="predict.survreg.html">predict.survreg.penal</a></td>
+<td>Predicted Values for a 'survreg' Object</td></tr>
+<tr><td width="25%"><a href="print.aareg.html">print.aareg</a></td>
+<td>Print an aareg object</td></tr>
+<tr><td width="25%"><a href="cox.zph.html">print.cox.zph</a></td>
+<td>Test the Proportional Hazards Assumption of a Cox Regression</td></tr>
+<tr><td width="25%"><a href="coxph.object.html">print.coxph</a></td>
+<td>Proportional Hazards Regression Object</td></tr>
+<tr><td width="25%"><a href="coxph.html">print.coxph.null</a></td>
+<td>Fit Proportional Hazards Regression Model</td></tr>
+<tr><td width="25%"><a href="coxph.html">print.coxph.penal</a></td>
+<td>Fit Proportional Hazards Regression Model</td></tr>
+<tr><td width="25%"><a href="ratetable.html">print.ratetable</a></td>
+<td>Ratetable reference in formula</td></tr>
+<tr><td width="25%"><a href="print.summary.coxph.html">print.summary.coxph</a></td>
+<td>Print method for summary.coxph objects</td></tr>
+<tr><td width="25%"><a href="print.summary.survexp.html">print.summary.survexp</a></td>
+<td>Print Survexp Summary</td></tr>
+<tr><td width="25%"><a href="print.summary.survfit.html">print.summary.survfit</a></td>
+<td>Print Survfit Summary</td></tr>
+<tr><td width="25%"><a href="survreg.html">print.summary.survreg</a></td>
+<td>Regression for a Parametric Survival Model</td></tr>
+<tr><td width="25%"><a href="Surv.html">print.Surv</a></td>
+<td>Create a Survival Object</td></tr>
+<tr><td width="25%"><a href="survdiff.html">print.survdiff</a></td>
+<td>Test Survival Curve Differences</td></tr>
+<tr><td width="25%"><a href="survexp.html">print.survexp</a></td>
+<td>Compute Expected Survival</td></tr>
+<tr><td width="25%"><a href="print.survfit.html">print.survfit</a></td>
+<td>Print a Short Summary of a Survival Curve</td></tr>
+<tr><td width="25%"><a href="survreg.object.html">print.survreg</a></td>
+<td>Parametric Survival Model Object</td></tr>
+<tr><td width="25%"><a href="survreg.html">print.survreg.penal</a></td>
+<td>Regression for a Parametric Survival Model</td></tr>
+<tr><td width="25%"><a href="pspline.html">pspline</a></td>
+<td>Smoothing splines using a pspline basis</td></tr>
+<tr><td width="25%"><a href="pspline.html">psplineinverse</a></td>
+<td>Smoothing splines using a pspline basis</td></tr>
+<tr><td width="25%"><a href="dsurvreg.html">psurvreg</a></td>
+<td>Distributions available in survreg.</td></tr>
+<tr><td width="25%"><a href="pyears.html">pyears</a></td>
+<td>Person Years</td></tr>
+</table>
+
+<h2><a name="Q">-- Q --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="dsurvreg.html">qsurvreg</a></td>
+<td>Distributions available in survreg.</td></tr>
+<tr><td width="25%"><a href="quantile.survfit.html">quantile.survfit</a></td>
+<td>Quantiles from a survfit object</td></tr>
+</table>
+
+<h2><a name="R">-- R --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="ratetable.html">ratetable</a></td>
+<td>Ratetable reference in formula</td></tr>
+<tr><td width="25%"><a href="ratetableDate.html">ratetableDate</a></td>
+<td>Convert date objects to ratetable form</td></tr>
+<tr><td width="25%"><a href="rats.html">rats</a></td>
+<td>Rat data from Gail et al.</td></tr>
+<tr><td width="25%"><a href="residuals.coxph.html">residuals.coxph</a></td>
+<td>Calculate Residuals for a 'coxph' Fit</td></tr>
+<tr><td width="25%"><a href="residuals.coxph.html">residuals.coxph.null</a></td>
+<td>Calculate Residuals for a 'coxph' Fit</td></tr>
+<tr><td width="25%"><a href="residuals.coxph.html">residuals.coxph.penal</a></td>
+<td>Calculate Residuals for a 'coxph' Fit</td></tr>
+<tr><td width="25%"><a href="residuals.survreg.html">residuals.survreg</a></td>
+<td>Compute Residuals for 'survreg' Objects</td></tr>
+<tr><td width="25%"><a href="residuals.survreg.html">residuals.survreg.penal</a></td>
+<td>Compute Residuals for 'survreg' Objects</td></tr>
+<tr><td width="25%"><a href="ridge.html">ridge</a></td>
+<td>Ridge regression</td></tr>
+</table>
+
+<h2><a name="S">-- S --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="stanford2.html">stanford2</a></td>
+<td>More Stanford Heart Transplant data</td></tr>
+<tr><td width="25%"><a href="strata.html">strata</a></td>
+<td>Identify Stratification Variables</td></tr>
+<tr><td width="25%"><a href="summary.aareg.html">summary.aareg</a></td>
+<td>Summarize an aareg fit</td></tr>
+<tr><td width="25%"><a href="summary.coxph.html">summary.coxph</a></td>
+<td>Summary method for Cox models</td></tr>
+<tr><td width="25%"><a href="coxph.html">summary.coxph.penal</a></td>
+<td>Fit Proportional Hazards Regression Model</td></tr>
+<tr><td width="25%"><a href="ratetable.html">summary.ratetable</a></td>
+<td>Ratetable reference in formula</td></tr>
+<tr><td width="25%"><a href="Surv.html">Summary.Surv</a></td>
+<td>Create a Survival Object</td></tr>
+<tr><td width="25%"><a href="summary.survexp.html">summary.survexp</a></td>
+<td>Summary function for a survexp object</td></tr>
+<tr><td width="25%"><a href="summary.survfit.html">summary.survfit</a></td>
+<td>Summary of a Survival Curve</td></tr>
+<tr><td width="25%"><a href="survreg.object.html">summary.survreg</a></td>
+<td>Parametric Survival Model Object</td></tr>
+<tr><td width="25%"><a href="Surv.html">Surv</a></td>
+<td>Create a Survival Object</td></tr>
+<tr><td width="25%"><a href="survConcordance.html">survConcordance</a></td>
+<td>Compute a concordance measure.</td></tr>
+<tr><td width="25%"><a href="survdiff.html">survdiff</a></td>
+<td>Test Survival Curve Differences</td></tr>
+<tr><td width="25%"><a href="survexp.html">survexp</a></td>
+<td>Compute Expected Survival</td></tr>
+<tr><td width="25%"><a href="survexp.us.html">survexp.az</a></td>
+<td>Census Data Sets for the Expected Survival and Person Years Functions</td></tr>
+<tr><td width="25%"><a href="survexp.us.html">survexp.azr</a></td>
+<td>Census Data Sets for the Expected Survival and Person Years Functions</td></tr>
+<tr><td width="25%"><a href="survexp.fit.html">survexp.fit</a></td>
+<td>Compute Expected Survival</td></tr>
+<tr><td width="25%"><a href="survexp.us.html">survexp.fl</a></td>
+<td>Census Data Sets for the Expected Survival and Person Years Functions</td></tr>
+<tr><td width="25%"><a href="survexp.us.html">survexp.flr</a></td>
+<td>Census Data Sets for the Expected Survival and Person Years Functions</td></tr>
+<tr><td width="25%"><a href="survexp.us.html">survexp.mn</a></td>
+<td>Census Data Sets for the Expected Survival and Person Years Functions</td></tr>
+<tr><td width="25%"><a href="survexp.us.html">survexp.mnwhite</a></td>
+<td>Census Data Sets for the Expected Survival and Person Years Functions</td></tr>
+<tr><td width="25%"><a href="survexp.us.html">survexp.us</a></td>
+<td>Census Data Sets for the Expected Survival and Person Years Functions</td></tr>
+<tr><td width="25%"><a href="survexp.us.html">survexp.usr</a></td>
+<td>Census Data Sets for the Expected Survival and Person Years Functions</td></tr>
+<tr><td width="25%"><a href="survexp.us.html">survexp.wnc</a></td>
+<td>Census Data Sets for the Expected Survival and Person Years Functions</td></tr>
+<tr><td width="25%"><a href="survfit.html">survfit</a></td>
+<td>Create survival curves</td></tr>
+<tr><td width="25%"><a href="survfit.coxph.html">survfit.coxph</a></td>
+<td>Compute a Survival Curve from a Cox model</td></tr>
+<tr><td width="25%"><a href="survfit.formula.html">survfit.formula</a></td>
+<td>Compute a Survival Curve for Censored Data</td></tr>
+<tr><td width="25%"><a href="survfit.object.html">survfit.object</a></td>
+<td>Survival Curve Object</td></tr>
+<tr><td width="25%"><a href="survfitcoxph.fit.html">survfitcoxph.fit</a></td>
+<td>A direct interface to the 'computational engine' of survfit.coxph</td></tr>
+<tr><td width="25%"><a href="survobrien.html">survobrien</a></td>
+<td>O'Brien's Test for Association of a Single Variable with Survival</td></tr>
+<tr><td width="25%"><a href="survreg.html">survReg</a></td>
+<td>Regression for a Parametric Survival Model</td></tr>
+<tr><td width="25%"><a href="survreg.html">survreg</a></td>
+<td>Regression for a Parametric Survival Model</td></tr>
+<tr><td width="25%"><a href="survreg.control.html">survreg.control</a></td>
+<td>Package options for survreg and coxph</td></tr>
+<tr><td width="25%"><a href="survreg.distributions.html">survreg.distributions</a></td>
+<td>Parametric Survival Distributions</td></tr>
+<tr><td width="25%"><a href="survreg.object.html">survreg.object</a></td>
+<td>Parametric Survival Model Object</td></tr>
+<tr><td width="25%"><a href="survregDtest.html">survregDtest</a></td>
+<td>Verify a survreg distribution</td></tr>
+<tr><td width="25%"><a href="survSplit.html">survSplit</a></td>
+<td>Split a survival data set at specified times</td></tr>
+</table>
+
+<h2><a name="T">-- T --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="tcut.html">tcut</a></td>
+<td>Factors for person-year calculations</td></tr>
+<tr><td width="25%"><a href="tobin.html">tobin</a></td>
+<td>Tobin's Tobit data</td></tr>
+<tr><td width="25%"><a href="tt.html">tt</a></td>
+<td>Mark time tranform terms</td></tr>
+</table>
+
+<h2><a name="U">-- U --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="untangle.specials.html">untangle.specials</a></td>
+<td>Help Process the 'specials' Argument of the 'terms' Function.</td></tr>
+</table>
+
+<h2><a name="V">-- V --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="coxph.html">vcov.coxph</a></td>
+<td>Fit Proportional Hazards Regression Model</td></tr>
+<tr><td width="25%"><a href="survreg.html">vcov.survreg</a></td>
+<td>Regression for a Parametric Survival Model</td></tr>
+<tr><td width="25%"><a href="veteran.html">veteran</a></td>
+<td>Veterans' Administration Lung Cancer study</td></tr>
+</table>
+
+<h2><a name="misc">-- misc --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="cox.zph.html">[.cox.zph</a></td>
+<td>Test the Proportional Hazards Assumption of a Cox Regression</td></tr>
+<tr><td width="25%"><a href="coxph.html">[.coxph.penalty</a></td>
+<td>Fit Proportional Hazards Regression Model</td></tr>
+<tr><td width="25%"><a href="ratetable.html">[.ratetable</a></td>
+<td>Ratetable reference in formula</td></tr>
+<tr><td width="25%"><a href="ratetable.html">[.ratetable2</a></td>
+<td>Ratetable reference in formula</td></tr>
+<tr><td width="25%"><a href="Surv.html">[.Surv</a></td>
+<td>Create a Survival Object</td></tr>
+<tr><td width="25%"><a href="survfit.formula.html">[.survfit</a></td>
+<td>Compute a Survival Curve for Censored Data</td></tr>
+<tr><td width="25%"><a href="tcut.html">[.tcut</a></td>
+<td>Factors for person-year calculations</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/survival/html/R.css b/win32/deps/library/survival/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/survival/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/survival/libs/i386/survival.dll b/win32/deps/library/survival/libs/i386/survival.dll
new file mode 100644
index 0000000..e06d51f
Binary files /dev/null and b/win32/deps/library/survival/libs/i386/survival.dll differ
diff --git a/win32/deps/library/survival/tests/aareg.R b/win32/deps/library/survival/tests/aareg.R
new file mode 100644
index 0000000..02a309e
--- /dev/null
+++ b/win32/deps/library/survival/tests/aareg.R
@@ -0,0 +1,210 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Test aareg, for some simple data where the answers can be computed
+# in closed form
+#
+aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+
+test1 <- data.frame(time= c(4, 3,1,1,2,2,3),
+ status=c(1,NA,1,0,1,1,0),
+ x= c(0, 2,1,1,1,0,0),
+ wt= c(1, 1:6))
+
+tfit <- aareg(Surv(time, status) ~ x, test1)
+aeq(tfit$times, c(1,2,2))
+aeq(tfit$nrisk, c(6,4,4))
+aeq(tfit$coefficient, matrix(c(0,0,1/3, 1/3, 1, -1/3), ncol=2))
+aeq(tfit$tweight, matrix(c(3,3,3, 3/2, 3/4, 3/4), ncol=2))
+aeq(tfit$test.statistic, c(1,1))
+aeq(tfit$test.var, c(1, -1/4, -1/4, 1/4 + 9/16 + 1/16))
+
+tfit <- aareg(Surv(time, status) ~ x, test1, test='nrisk')
+aeq(tfit$tweight, matrix(c(3,3,3, 3/2, 3/4, 3/4), ncol=2)) #should be as before
+aeq(tfit$test.statistic, c(4/3, 6/3+ 4 - 4/3))
+aeq(tfit$test.var, c(16/9, -16/9, -16/9, 36/9 + 16 + 16/9))
+
+# In the 1-variable case, this is the same as the default Aalen weight
+tfit <- aareg(Surv(time, status) ~ x, test1, test='variance')
+aeq(tfit$test.statistic, c(1,1))
+aeq(tfit$test.var, c(1, -1/4, -1/4, 1/4 + 9/16 + 1/16))
+
+#
+# Repeat the above, with case weights
+#
+tfit <- aareg(Surv(time, status) ~x, test1, weights=wt)
+aeq(tfit$times, c(1,2,2))
+aeq(tfit$nrisk, c(21,16,16))
+aeq(tfit$coefficient, matrix(c(0,0,5/12, 2/9, 1, -5/12), ncol=2))
+aeq(tfit$tweight, matrix(c(12,12,12, 36/7, 3,3), ncol=2))
+aeq(tfit$test.statistic, c(5, 72/63 + 3 - 15/12))
+aeq(tfit$test.var, c(25, -25/4, -25/4, (72/63)^2 + 9 + (5/4)^2))
+
+tfit <- aareg(Surv(time, status) ~x, test1, weights=wt, test='nrisk')
+aeq(tfit$test.statistic, c(20/3, 42/9 + 16 - 16*5/12))
+aeq(tfit$test.var, c(400/9, -400/9, -400/9,
+ (42/9)^2 + 16^2 + (16*5/12)^2))
+
+#
+# Make a test data set with no NAs, in sorted order, no ties,
+# 15 observations
+tdata <- lung[15:29, c('time', 'status', 'age', 'sex', 'ph.ecog')]
+tdata$status <- tdata$status -1
+tdata <- tdata[order(tdata$time, tdata$status),]
+row.names(tdata) <- 1:15
+tdata$status[8] <- 0 #for some variety
+
+afit <- aareg(Surv(time, status) ~ age + sex + ph.ecog, tdata, nmin=6)
+#
+# Now, do it "by hand"
+cfit <- coxph(Surv(time, status) ~ age + sex + ph.ecog, tdata, iter=0,
+ method='breslow')
+dt1 <- coxph.detail(cfit)
+sch1 <- resid(cfit, type='schoen')
+
+# First estimate of Aalen: from the Cox computations, first 9
+# The first and last cols of the ninth are somewhat unstable (approx =0)
+mine <- rbind(solve(dt1$imat[,,1], sch1[1,]),
+ solve(dt1$imat[,,2], sch1[2,]),
+ solve(dt1$imat[,,3], sch1[3,]),
+ solve(dt1$imat[,,4], sch1[4,]),
+ solve(dt1$imat[,,5], sch1[5,]),
+ solve(dt1$imat[,,6], sch1[6,]),
+ solve(dt1$imat[,,7], sch1[7,]),
+ solve(dt1$imat[,,8], sch1[8,]),
+ solve(dt1$imat[,,9], sch1[9,]))
+mine <- diag(1/dt1$nrisk[1:9]) %*% mine
+
+aeq(mine, afit$coef[1:9, -1])
+
+rm(tfit, afit, mine, dt1, cfit, sch1)
+
+#
+# Check out the dfbeta matrix from aareg
+# Note that it is kept internally in time order, not data set order
+# Those who want residuals should use the resid function!
+
+#
+# First, the simple test case where I know the anwers
+#
+afit <- aareg(Surv(time, status) ~ x, test1, dfbeta=T)
+temp <- c(rep(0,6), #intercepts at time 1
+ c(2,-1,-1,0,0,0)/9, #alpha at time 1
+ c(0,0,0,2, -1, -1)/9, #intercepts at time 2
+ c(0,0,0,-2,1,1)/9) #alpha at time 2
+aeq(afit$dfbeta, temp)
+
+#
+#Now a multivariate data set
+#
+afit <- aareg(Surv(time, status) ~ age + sex + ph.ecog, lung, dfbeta=T)
+
+ord <- order(lung$time, -lung$status)
+cfit <- coxph(Surv(time, status) ~ age + sex + ph.ecog, lung[ord,],
+ method='breslow', iter=0, x=T)
+cdt <- coxph.detail(cfit, riskmat=T)
+
+# an arbitrary list of times
+acoef <- rowsum(afit$coef, afit$times) #per death time coefs
+indx <- match(cdt$time, afit$times)
+for (i in c(2,5,27,54,101, 135)) {
+ lwho <- (cdt$riskmat[,i]==1)
+ lmx <- cfit$x[lwho,]
+ lmy <- 1*( cfit$y[lwho,2]==1 & cfit$y[lwho,1] == cdt$time[i])
+ fit <- lm(lmy~ lmx)
+ cat("i=", i, "coef=", aeq(fit$coef, acoef[i,]))
+
+ rr <- diag(resid(fit))
+ zz <- cbind(1,lmx)
+ zzinv <- solve(t(zz) %*% zz)
+ cat(" twt=", aeq(1/(diag(zzinv)), afit$tweight[indx[i],]))
+
+ df <- t(zzinv %*% t(zz) %*% rr)
+ cat(" dfbeta=", aeq(df, afit$dfbeta[lwho,,i]), "\n")
+ }
+
+rm(afit, cfit, cdt, lwho, lmx, lmy, fit, rr, zz, df)
+
+
+# Repeat it with case weights
+ww <- rep(1:5, length=nrow(lung))/ 3.0
+afit <- aareg(Surv(time, status) ~ age + sex + ph.ecog, lung, dfbeta=T,
+ weights=ww)
+cfit <- coxph(Surv(time, status) ~ age + sex + ph.ecog, lung[ord,],
+ method='breslow', iter=0, x=T, weight=ww[ord])
+cdt <- coxph.detail(cfit, riskmat=T)
+
+acoef <- rowsum(afit$coef, afit$times) #per death time coefs
+for (i in c(2,5,27,54,101, 135)) {
+ who <- (cdt$riskmat[,i]==1)
+ x <- cfit$x[who,]
+ y <- 1*( cfit$y[who,2]==1 & cfit$y[who,1] == cdt$time[i])
+ w <- cfit$weight[who]
+ fit <- lm(y~x, weights=w)
+ cat("i=", i, "coef=", aeq(fit$coef, acoef[i,]))
+
+ rr <- diag(resid(fit))
+ zz <- cbind(1,x)
+ zzinv <- solve(t(zz)%*% (w*zz))
+ cat(" twt=", aeq(1/(diag(zzinv)), afit$tweight[indx[i],]))
+
+ df <- t(zzinv %*% t(zz) %*% (w*rr))
+ cat(" dfbeta=", aeq(df, afit$dfbeta[who,,i]), "\n")
+ }
+
+rm(afit, cfit, cdt, who, x, y, fit, rr, zz, df)
+rm(ord, acoef)
+
+#
+# Check that the test statistic computed within aareg and
+# the one recomputed within summary.aareg are the same.
+# Of course, they could both be wrong, but at least they'll agree!
+# If the maxtime argument is used in summary, it recomputes the test,
+# even if we know that it wouldn't have had to.
+#
+# Because the 1-variable and >1 variable case have different code, test
+# them both.
+#
+afit <- aareg(Surv(time, status) ~ age, lung, dfbeta=T)
+asum <- summary(afit, maxtime=max(afit$times))
+aeq(afit$test.stat, asum$test.stat)
+aeq(afit$test.var, asum$test.var)
+aeq(afit$test.var2, asum$test.var2)
+
+print(afit)
+
+afit <- aareg(Surv(time, status) ~ age, lung, dfbeta=T, test='nrisk')
+asum <- summary(afit, maxtime=max(afit$times))
+aeq(afit$test.stat, asum$test.stat)
+aeq(afit$test.var, asum$test.var)
+aeq(afit$test.var2, asum$test.var2)
+
+summary(afit)
+
+#
+# Mulitvariate
+#
+afit <- aareg(Surv(time, status) ~ age + sex + ph.karno + pat.karno, lung,
+ dfbeta=T)
+asum <- summary(afit, maxtime=max(afit$times))
+aeq(afit$test.stat, asum$test.stat)
+aeq(afit$test.var, asum$test.var)
+aeq(afit$test.var2, asum$test.var2)
+
+print(afit)
+
+afit <- aareg(Surv(time, status) ~ age + sex + ph.karno + pat.karno, lung,
+ dfbeta=T, test='nrisk')
+asum <- summary(afit, maxtime=max(afit$times))
+aeq(afit$test.stat, asum$test.stat)
+aeq(afit$test.var, asum$test.var)
+aeq(afit$test.var2, asum$test.var2)
+
+summary(afit)
+
+# Weights play no role in the final computation of the test statistic, given
+# the coefficient matrix, nrisk, and dfbeta as inputs. (Weights do
+# change the inputs). So there is no need to reprise the above with
+# case weights.
diff --git a/win32/deps/library/survival/tests/aareg.Rout.save b/win32/deps/library/survival/tests/aareg.Rout.save
new file mode 100644
index 0000000..894a49e
--- /dev/null
+++ b/win32/deps/library/survival/tests/aareg.Rout.save
@@ -0,0 +1,381 @@
+
+R version 2.14.0 Under development (unstable) (2011-04-10 r55401)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Test aareg, for some simple data where the answers can be computed
+> # in closed form
+> #
+> aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+>
+> test1 <- data.frame(time= c(4, 3,1,1,2,2,3),
++ status=c(1,NA,1,0,1,1,0),
++ x= c(0, 2,1,1,1,0,0),
++ wt= c(1, 1:6))
+>
+> tfit <- aareg(Surv(time, status) ~ x, test1)
+> aeq(tfit$times, c(1,2,2))
+[1] TRUE
+> aeq(tfit$nrisk, c(6,4,4))
+[1] TRUE
+> aeq(tfit$coefficient, matrix(c(0,0,1/3, 1/3, 1, -1/3), ncol=2))
+[1] TRUE
+> aeq(tfit$tweight, matrix(c(3,3,3, 3/2, 3/4, 3/4), ncol=2))
+[1] TRUE
+> aeq(tfit$test.statistic, c(1,1))
+[1] TRUE
+> aeq(tfit$test.var, c(1, -1/4, -1/4, 1/4 + 9/16 + 1/16))
+[1] TRUE
+>
+> tfit <- aareg(Surv(time, status) ~ x, test1, test='nrisk')
+> aeq(tfit$tweight, matrix(c(3,3,3, 3/2, 3/4, 3/4), ncol=2)) #should be as before
+[1] TRUE
+> aeq(tfit$test.statistic, c(4/3, 6/3+ 4 - 4/3))
+[1] TRUE
+> aeq(tfit$test.var, c(16/9, -16/9, -16/9, 36/9 + 16 + 16/9))
+[1] TRUE
+>
+> # In the 1-variable case, this is the same as the default Aalen weight
+> tfit <- aareg(Surv(time, status) ~ x, test1, test='variance')
+> aeq(tfit$test.statistic, c(1,1))
+[1] TRUE
+> aeq(tfit$test.var, c(1, -1/4, -1/4, 1/4 + 9/16 + 1/16))
+[1] TRUE
+>
+> #
+> # Repeat the above, with case weights
+> #
+> tfit <- aareg(Surv(time, status) ~x, test1, weights=wt)
+> aeq(tfit$times, c(1,2,2))
+[1] TRUE
+> aeq(tfit$nrisk, c(21,16,16))
+[1] TRUE
+> aeq(tfit$coefficient, matrix(c(0,0,5/12, 2/9, 1, -5/12), ncol=2))
+[1] TRUE
+> aeq(tfit$tweight, matrix(c(12,12,12, 36/7, 3,3), ncol=2))
+[1] TRUE
+> aeq(tfit$test.statistic, c(5, 72/63 + 3 - 15/12))
+[1] TRUE
+> aeq(tfit$test.var, c(25, -25/4, -25/4, (72/63)^2 + 9 + (5/4)^2))
+[1] TRUE
+>
+> tfit <- aareg(Surv(time, status) ~x, test1, weights=wt, test='nrisk')
+> aeq(tfit$test.statistic, c(20/3, 42/9 + 16 - 16*5/12))
+[1] TRUE
+> aeq(tfit$test.var, c(400/9, -400/9, -400/9,
++ (42/9)^2 + 16^2 + (16*5/12)^2))
+[1] TRUE
+>
+> #
+> # Make a test data set with no NAs, in sorted order, no ties,
+> # 15 observations
+> tdata <- lung[15:29, c('time', 'status', 'age', 'sex', 'ph.ecog')]
+> tdata$status <- tdata$status -1
+> tdata <- tdata[order(tdata$time, tdata$status),]
+> row.names(tdata) <- 1:15
+> tdata$status[8] <- 0 #for some variety
+>
+> afit <- aareg(Surv(time, status) ~ age + sex + ph.ecog, tdata, nmin=6)
+> #
+> # Now, do it "by hand"
+> cfit <- coxph(Surv(time, status) ~ age + sex + ph.ecog, tdata, iter=0,
++ method='breslow')
+> dt1 <- coxph.detail(cfit)
+> sch1 <- resid(cfit, type='schoen')
+>
+> # First estimate of Aalen: from the Cox computations, first 9
+> # The first and last cols of the ninth are somewhat unstable (approx =0)
+> mine <- rbind(solve(dt1$imat[,,1], sch1[1,]),
++ solve(dt1$imat[,,2], sch1[2,]),
++ solve(dt1$imat[,,3], sch1[3,]),
++ solve(dt1$imat[,,4], sch1[4,]),
++ solve(dt1$imat[,,5], sch1[5,]),
++ solve(dt1$imat[,,6], sch1[6,]),
++ solve(dt1$imat[,,7], sch1[7,]),
++ solve(dt1$imat[,,8], sch1[8,]),
++ solve(dt1$imat[,,9], sch1[9,]))
+> mine <- diag(1/dt1$nrisk[1:9]) %*% mine
+>
+> aeq(mine, afit$coef[1:9, -1])
+[1] TRUE
+>
+> rm(tfit, afit, mine, dt1, cfit, sch1)
+>
+> #
+> # Check out the dfbeta matrix from aareg
+> # Note that it is kept internally in time order, not data set order
+> # Those who want residuals should use the resid function!
+>
+> #
+> # First, the simple test case where I know the anwers
+> #
+> afit <- aareg(Surv(time, status) ~ x, test1, dfbeta=T)
+> temp <- c(rep(0,6), #intercepts at time 1
++ c(2,-1,-1,0,0,0)/9, #alpha at time 1
++ c(0,0,0,2, -1, -1)/9, #intercepts at time 2
++ c(0,0,0,-2,1,1)/9) #alpha at time 2
+> aeq(afit$dfbeta, temp)
+[1] TRUE
+>
+> #
+> #Now a multivariate data set
+> #
+> afit <- aareg(Surv(time, status) ~ age + sex + ph.ecog, lung, dfbeta=T)
+>
+> ord <- order(lung$time, -lung$status)
+> cfit <- coxph(Surv(time, status) ~ age + sex + ph.ecog, lung[ord,],
++ method='breslow', iter=0, x=T)
+> cdt <- coxph.detail(cfit, riskmat=T)
+>
+> # an arbitrary list of times
+> acoef <- rowsum(afit$coef, afit$times) #per death time coefs
+> indx <- match(cdt$time, afit$times)
+> for (i in c(2,5,27,54,101, 135)) {
++ lwho <- (cdt$riskmat[,i]==1)
++ lmx <- cfit$x[lwho,]
++ lmy <- 1*( cfit$y[lwho,2]==1 & cfit$y[lwho,1] == cdt$time[i])
++ fit <- lm(lmy~ lmx)
++ cat("i=", i, "coef=", aeq(fit$coef, acoef[i,]))
++
++ rr <- diag(resid(fit))
++ zz <- cbind(1,lmx)
++ zzinv <- solve(t(zz) %*% zz)
++ cat(" twt=", aeq(1/(diag(zzinv)), afit$tweight[indx[i],]))
++
++ df <- t(zzinv %*% t(zz) %*% rr)
++ cat(" dfbeta=", aeq(df, afit$dfbeta[lwho,,i]), "\n")
++ }
+i= 2 coef= TRUE twt= TRUE dfbeta= TRUE
+i= 5 coef= TRUE twt= TRUE dfbeta= TRUE
+i= 27 coef= TRUE twt= TRUE dfbeta= TRUE
+i= 54 coef= TRUE twt= TRUE dfbeta= TRUE
+i= 101 coef= TRUE twt= TRUE dfbeta= TRUE
+i= 135 coef= TRUE twt= TRUE dfbeta= TRUE
+>
+> rm(afit, cfit, cdt, lwho, lmx, lmy, fit, rr, zz, df)
+>
+>
+> # Repeat it with case weights
+> ww <- rep(1:5, length=nrow(lung))/ 3.0
+> afit <- aareg(Surv(time, status) ~ age + sex + ph.ecog, lung, dfbeta=T,
++ weights=ww)
+> cfit <- coxph(Surv(time, status) ~ age + sex + ph.ecog, lung[ord,],
++ method='breslow', iter=0, x=T, weight=ww[ord])
+> cdt <- coxph.detail(cfit, riskmat=T)
+>
+> acoef <- rowsum(afit$coef, afit$times) #per death time coefs
+> for (i in c(2,5,27,54,101, 135)) {
++ who <- (cdt$riskmat[,i]==1)
++ x <- cfit$x[who,]
++ y <- 1*( cfit$y[who,2]==1 & cfit$y[who,1] == cdt$time[i])
++ w <- cfit$weight[who]
++ fit <- lm(y~x, weights=w)
++ cat("i=", i, "coef=", aeq(fit$coef, acoef[i,]))
++
++ rr <- diag(resid(fit))
++ zz <- cbind(1,x)
++ zzinv <- solve(t(zz)%*% (w*zz))
++ cat(" twt=", aeq(1/(diag(zzinv)), afit$tweight[indx[i],]))
++
++ df <- t(zzinv %*% t(zz) %*% (w*rr))
++ cat(" dfbeta=", aeq(df, afit$dfbeta[who,,i]), "\n")
++ }
+i= 2 coef= TRUE twt= TRUE dfbeta= TRUE
+i= 5 coef= TRUE twt= TRUE dfbeta= TRUE
+i= 27 coef= TRUE twt= TRUE dfbeta= TRUE
+i= 54 coef= TRUE twt= TRUE dfbeta= TRUE
+i= 101 coef= TRUE twt= TRUE dfbeta= TRUE
+i= 135 coef= TRUE twt= TRUE dfbeta= TRUE
+>
+> rm(afit, cfit, cdt, who, x, y, fit, rr, zz, df)
+> rm(ord, acoef)
+>
+> #
+> # Check that the test statistic computed within aareg and
+> # the one recomputed within summary.aareg are the same.
+> # Of course, they could both be wrong, but at least they'll agree!
+> # If the maxtime argument is used in summary, it recomputes the test,
+> # even if we know that it wouldn't have had to.
+> #
+> # Because the 1-variable and >1 variable case have different code, test
+> # them both.
+> #
+> afit <- aareg(Surv(time, status) ~ age, lung, dfbeta=T)
+> asum <- summary(afit, maxtime=max(afit$times))
+> aeq(afit$test.stat, asum$test.stat)
+[1] TRUE
+> aeq(afit$test.var, asum$test.var)
+[1] TRUE
+> aeq(afit$test.var2, asum$test.var2)
+[1] TRUE
+>
+> print(afit)
+Call:
+aareg(formula = Surv(time, status) ~ age, data = lung, dfbeta = T)
+
+ n= 228
+ 139 out of 139 unique event times used
+
+ slope coef se(coef) robust se z p
+Intercept -0.000872 -0.000905 4.26e-03 4.13e-03 -0.219 0.8270
+age 0.000110 0.000142 6.96e-05 6.75e-05 2.110 0.0351
+
+Chisq=4.44 on 1 df, p=0.035; test weights=aalen
+>
+> afit <- aareg(Surv(time, status) ~ age, lung, dfbeta=T, test='nrisk')
+> asum <- summary(afit, maxtime=max(afit$times))
+> aeq(afit$test.stat, asum$test.stat)
+[1] TRUE
+> aeq(afit$test.var, asum$test.var)
+[1] TRUE
+> aeq(afit$test.var2, asum$test.var2)
+[1] TRUE
+>
+> summary(afit)
+$table
+ slope coef se(coef) robust se z
+Intercept -0.0009538483 -0.11693804 0.534885651 0.533148054 -0.219335
+age 0.0001053024 0.01795521 0.008746523 0.008734005 2.055782
+ p
+Intercept 0.82638908
+age 0.03980352
+
+$test
+[1] "nrisk"
+
+$test.statistic
+Intercept age
+-19.29478 2.96261
+
+$test.var
+ [,1] [,2]
+[1,] 7789.1449 -126.055872
+[2,] -126.0559 2.082758
+
+$test.var2
+ [,1] [,2]
+[1,] 7738.6204 -125.5077
+[2,] -125.5077 2.0768
+
+$chisq
+ [,1]
+[1,] 4.22624
+
+$n
+[1] 228 139 139
+
+attr(,"class")
+[1] "summary.aareg"
+>
+> #
+> # Mulitvariate
+> #
+> afit <- aareg(Surv(time, status) ~ age + sex + ph.karno + pat.karno, lung,
++ dfbeta=T)
+> asum <- summary(afit, maxtime=max(afit$times))
+> aeq(afit$test.stat, asum$test.stat)
+[1] TRUE
+> aeq(afit$test.var, asum$test.var)
+[1] TRUE
+> aeq(afit$test.var2, asum$test.var2)
+[1] TRUE
+>
+> print(afit)
+Call:
+aareg(formula = Surv(time, status) ~ age + sex + ph.karno + pat.karno,
+ data = lung, dfbeta = T)
+
+ n=224 (4 observations deleted due to missingness)
+ 132 out of 136 unique event times used
+
+ slope coef se(coef) robust se z p
+Intercept 2.15e-02 0.025000 8.45e-03 7.72e-03 3.25 0.00117
+age 3.09e-05 0.000076 7.32e-05 6.49e-05 1.17 0.24100
+sex -2.96e-03 -0.004020 1.25e-03 1.23e-03 -3.27 0.00109
+ph.karno -6.77e-05 -0.000083 6.69e-05 8.30e-05 -1.00 0.31700
+pat.karno -1.01e-04 -0.000112 5.59e-05 5.70e-05 -1.96 0.05010
+
+Chisq=23.36 on 4 df, p=0.00011; test weights=aalen
+>
+> afit <- aareg(Surv(time, status) ~ age + sex + ph.karno + pat.karno, lung,
++ dfbeta=T, test='nrisk')
+> asum <- summary(afit, maxtime=max(afit$times))
+> aeq(afit$test.stat, asum$test.stat)
+[1] TRUE
+> aeq(afit$test.var, asum$test.var)
+[1] TRUE
+> aeq(afit$test.var2, asum$test.var2)
+[1] TRUE
+>
+> summary(afit)
+$table
+ slope coef se(coef) robust se z
+Intercept 2.119015e-02 3.05872822 1.044992929 0.955953617 3.199662
+age 3.181122e-05 0.01071085 0.009280348 0.008182931 1.308926
+sex -2.985556e-03 -0.49368373 0.153217001 0.151559500 -3.257359
+ph.karno -8.371983e-05 -0.01131957 0.007825769 0.009654398 -1.172478
+pat.karno -8.501076e-05 -0.01328844 0.007241150 0.007669582 -1.732617
+ p
+Intercept 0.00137589
+age 0.19055946
+sex 0.00112454
+ph.karno 0.24100515
+pat.karno 0.08316385
+
+$test
+[1] "nrisk"
+
+$test.statistic
+ Intercept age sex ph.karno pat.karno
+480.220330 1.681604 -77.508345 -1.777173 -2.086286
+
+$test.var
+ b0
+b0 26916.95995 -177.3767597 -791.4141458 -103.5540756 -69.1210402
+ -177.37676 2.1228915 0.1752574 0.4055099 0.1622945
+ -791.41415 0.1752574 578.6463538 -0.9726495 -0.6320578
+ -103.55408 0.4055099 -0.9726495 1.5095704 -0.5793466
+ -69.12104 0.1622945 -0.6320578 -0.5793466 1.2924520
+
+$test.var2
+ [,1] [,2] [,3] [,4] [,5]
+[1,] 22525.42254 -109.0376340 -1294.620657 -135.7477106 -24.1718358
+[2,] -109.03763 1.6505060 2.562655 0.1774270 -0.1206339
+[3,] -1294.62066 2.5626546 566.194480 7.4865489 -4.7691882
+[4,] -135.74771 0.1774270 7.486549 2.2974694 -0.9877341
+[5,] -24.17184 -0.1206339 -4.769188 -0.9877341 1.4499155
+
+$chisq
+ [,1]
+[1,] 22.3874
+
+$n
+[1] 224 132 136
+
+attr(,"class")
+[1] "summary.aareg"
+>
+> # Weights play no role in the final computation of the test statistic, given
+> # the coefficient matrix, nrisk, and dfbeta as inputs. (Weights do
+> # change the inputs). So there is no need to reprise the above with
+> # case weights.
+>
diff --git a/win32/deps/library/survival/tests/anova.R b/win32/deps/library/survival/tests/anova.R
new file mode 100644
index 0000000..18b9b32
--- /dev/null
+++ b/win32/deps/library/survival/tests/anova.R
@@ -0,0 +1,31 @@
+#
+# Test out anova, with strata terms
+#
+options(na.action=na.omit)
+library(survival)
+
+fit1 <- coxph(Surv(time, status) ~ ph.ecog + wt.loss + strata(sex) +
+ poly(age,3), lung)
+ztemp <- anova(fit1)
+
+tdata <- na.omit(lung[, c('time', 'status', 'ph.ecog', 'wt.loss', 'sex', 'age')])
+fit2 <- coxph(Surv(time, status)~ ph.ecog + wt.loss + poly(age,3) + strata(sex),
+ data=tdata)
+ztemp2 <- anova(fit2)
+all.equal(ztemp, ztemp2)
+
+
+fit2 <- coxph(Surv(time, status) ~ ph.ecog + wt.loss + strata(sex), tdata)
+fit3 <- coxph(Surv(time, status) ~ ph.ecog + strata(sex), tdata)
+
+all.equal(ztemp$loglik, c(fit1$loglik[1], fit3$loglik[2], fit2$loglik[2],
+ fit1$loglik[2]))
+all.equal(ztemp$Chisq[-1], 2* diff(ztemp$loglik))
+all.equal(ztemp$Df[-1], c(1,1,3))
+
+ztemp2 <- anova(fit3, fit2, fit1)
+all.equal(ztemp2$loglik, ztemp$loglik[-1])
+all.equal(ztemp2$Chisq[2:3], ztemp$Chisq[3:4])
+all.equal(ztemp2$P[2:3], ztemp$P[3:4])
+
+
diff --git a/win32/deps/library/survival/tests/anova.Rout.save b/win32/deps/library/survival/tests/anova.Rout.save
new file mode 100644
index 0000000..b39e4f4
--- /dev/null
+++ b/win32/deps/library/survival/tests/anova.Rout.save
@@ -0,0 +1,57 @@
+
+R version 2.9.0 (2009-04-17)
+Copyright (C) 2009 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> #
+> # Test out anova, with strata terms
+> #
+> options(na.action=na.omit)
+> library(survival)
+Loading required package: splines
+>
+> fit1 <- coxph(Surv(time, status) ~ ph.ecog + wt.loss + strata(sex) +
++ poly(age,3), lung)
+> ztemp <- anova(fit1)
+>
+> tdata <- na.omit(lung[, c('time', 'status', 'ph.ecog', 'wt.loss', 'sex', 'age')])
+> fit2 <- coxph(Surv(time, status)~ ph.ecog + wt.loss + poly(age,3) + strata(sex),
++ data=tdata)
+> ztemp2 <- anova(fit2)
+> all.equal(ztemp, ztemp2)
+[1] TRUE
+>
+>
+> fit2 <- coxph(Surv(time, status) ~ ph.ecog + wt.loss + strata(sex), tdata)
+> fit3 <- coxph(Surv(time, status) ~ ph.ecog + strata(sex), tdata)
+>
+> all.equal(ztemp$loglik, c(fit1$loglik[1], fit3$loglik[2], fit2$loglik[2],
++ fit1$loglik[2]))
+[1] TRUE
+> all.equal(ztemp$Chisq[-1], 2* diff(ztemp$loglik))
+[1] TRUE
+> all.equal(ztemp$Df[-1], c(1,1,3))
+[1] TRUE
+>
+> ztemp2 <- anova(fit3, fit2, fit1)
+> all.equal(ztemp2$loglik, ztemp$loglik[-1])
+[1] TRUE
+> all.equal(ztemp2$Chisq[2:3], ztemp$Chisq[3:4])
+[1] TRUE
+> all.equal(ztemp2$P[2:3], ztemp$P[3:4])
+[1] TRUE
+>
+>
+>
diff --git a/win32/deps/library/survival/tests/bladder.R b/win32/deps/library/survival/tests/bladder.R
new file mode 100644
index 0000000..4dabeaa
--- /dev/null
+++ b/win32/deps/library/survival/tests/bladder.R
@@ -0,0 +1,37 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Fit the models found in Wei et. al.
+#
+wfit <- coxph(Surv(stop, event) ~ (rx + size + number)* strata(enum) +
+ cluster(id), bladder, method='breslow')
+wfit
+
+# Check the rx coefs versus Wei, et al, JASA 1989
+rx <- c(1,4,5,6) # the treatment coefs above
+cmat <- diag(4); cmat[1,] <- 1; #contrast matrix
+wfit$coef[rx] %*% cmat # the coefs in their paper (table 5)
+t(cmat) %*% wfit$var[rx,rx] %*% cmat # var matrix (eqn 3.2)
+
+# Anderson-Gill fit
+fita <- coxph(Surv(start, stop, event) ~ rx + size + number + cluster(id),
+ bladder2, method='breslow')
+summary(fita)
+
+# Prentice fits. Their model 1 a and b are the same
+fit1p <- coxph(Surv(stop, event) ~ rx + size + number, bladder2,
+ subset=(enum==1), method='breslow')
+fit2pa <- coxph(Surv(stop, event) ~ rx + size + number, bladder2,
+ subset=(enum==2), method='breslow')
+fit2pb <- coxph(Surv(stop-start, event) ~ rx + size + number, bladder2,
+ subset=(enum==2), method='breslow')
+fit3pa <- coxph(Surv(stop, event) ~ rx + size + number, bladder2,
+ subset=(enum==3), method='breslow')
+ #and etc.
+fit1p
+fit2pa
+fit2pb
+fit3pa
+rm(rx, cmat, wfit, fita, fit1p, fit2pa, fit2pb, fit3pa)
diff --git a/win32/deps/library/survival/tests/bladder.Rout.save b/win32/deps/library/survival/tests/bladder.Rout.save
new file mode 100644
index 0000000..2038b8e
--- /dev/null
+++ b/win32/deps/library/survival/tests/bladder.Rout.save
@@ -0,0 +1,154 @@
+
+R version 2.14.0 Under development (unstable) (2011-04-10 r55401)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Fit the models found in Wei et. al.
+> #
+> wfit <- coxph(Surv(stop, event) ~ (rx + size + number)* strata(enum) +
++ cluster(id), bladder, method='breslow')
+> wfit
+Call:
+coxph(formula = Surv(stop, event) ~ (rx + size + number) * strata(enum) +
+ cluster(id), data = bladder, method = "breslow")
+
+
+ coef exp(coef) se(coef) robust se z p
+rx -0.5176 0.596 0.3158 0.3075 -1.683 0.0920
+size 0.0679 1.070 0.1012 0.0853 0.796 0.4300
+number 0.2360 1.266 0.0761 0.0721 3.274 0.0011
+rx:strata(enum)enum=2 -0.1018 0.903 0.5043 0.3265 -0.312 0.7600
+rx:strata(enum)enum=3 -0.1823 0.833 0.5579 0.3916 -0.465 0.6400
+rx:strata(enum)enum=4 -0.1332 0.875 0.6581 0.4968 -0.268 0.7900
+size:strata(enum)enum=2 -0.1440 0.866 0.1680 0.1119 -1.287 0.2000
+size:strata(enum)enum=3 -0.2792 0.756 0.2086 0.1511 -1.847 0.0650
+size:strata(enum)enum=4 -0.2711 0.763 0.2515 0.1856 -1.460 0.1400
+number:strata(enum)enum=2 -0.0984 0.906 0.1193 0.1144 -0.861 0.3900
+number:strata(enum)enum=3 -0.0662 0.936 0.1298 0.1167 -0.567 0.5700
+number:strata(enum)enum=4 0.0928 1.097 0.1466 0.1175 0.790 0.4300
+
+Likelihood ratio test=29.4 on 12 df, p=0.00344 n= 340, number of events= 112
+>
+> # Check the rx coefs versus Wei, et al, JASA 1989
+> rx <- c(1,4,5,6) # the treatment coefs above
+> cmat <- diag(4); cmat[1,] <- 1; #contrast matrix
+> wfit$coef[rx] %*% cmat # the coefs in their paper (table 5)
+ [,1] [,2] [,3] [,4]
+[1,] -0.5176209 -0.6194404 -0.6998771 -0.6507935
+> t(cmat) %*% wfit$var[rx,rx] %*% cmat # var matrix (eqn 3.2)
+ [,1] [,2] [,3] [,4]
+[1,] 0.09455501 0.06017669 0.05677331 0.0437777
+[2,] 0.06017669 0.13242834 0.13011557 0.1160420
+[3,] 0.05677331 0.13011557 0.17235879 0.1590865
+[4,] 0.04377770 0.11604200 0.15908650 0.2398112
+>
+> # Anderson-Gill fit
+> fita <- coxph(Surv(start, stop, event) ~ rx + size + number + cluster(id),
++ bladder2, method='breslow')
+> summary(fita)
+Call:
+coxph(formula = Surv(start, stop, event) ~ rx + size + number +
+ cluster(id), data = bladder2, method = "breslow")
+
+ n= 178, number of events= 112
+
+ coef exp(coef) se(coef) robust se z Pr(>|z|)
+rx -0.45979 0.63142 0.19996 0.25801 -1.782 0.07474 .
+size -0.04256 0.95833 0.06903 0.07555 -0.563 0.57317
+number 0.17164 1.18726 0.04733 0.06131 2.799 0.00512 **
+---
+Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
+
+ exp(coef) exp(-coef) lower .95 upper .95
+rx 0.6314 1.5837 0.3808 1.047
+size 0.9583 1.0435 0.8264 1.111
+number 1.1873 0.8423 1.0528 1.339
+
+Concordance= 0.634 (se = 0.03 )
+Rsquare= 0.09 (max possible= 0.994 )
+Likelihood ratio test= 16.77 on 3 df, p=0.000787
+Wald test = 11.76 on 3 df, p=0.008256
+Score (logrank) test = 18.57 on 3 df, p=0.0003355, Robust = 11.44 p=0.009588
+
+ (Note: the likelihood ratio and score tests assume independence of
+ observations within a cluster, the Wald and robust score tests do not).
+>
+> # Prentice fits. Their model 1 a and b are the same
+> fit1p <- coxph(Surv(stop, event) ~ rx + size + number, bladder2,
++ subset=(enum==1), method='breslow')
+> fit2pa <- coxph(Surv(stop, event) ~ rx + size + number, bladder2,
++ subset=(enum==2), method='breslow')
+> fit2pb <- coxph(Surv(stop-start, event) ~ rx + size + number, bladder2,
++ subset=(enum==2), method='breslow')
+> fit3pa <- coxph(Surv(stop, event) ~ rx + size + number, bladder2,
++ subset=(enum==3), method='breslow')
+> #and etc.
+> fit1p
+Call:
+coxph(formula = Surv(stop, event) ~ rx + size + number, data = bladder2,
+ subset = (enum == 1), method = "breslow")
+
+
+ coef exp(coef) se(coef) z p
+rx -0.5176 0.596 0.3158 -1.639 0.1000
+size 0.0679 1.070 0.1012 0.671 0.5000
+number 0.2360 1.266 0.0761 3.102 0.0019
+
+Likelihood ratio test=9.66 on 3 df, p=0.0216 n= 85, number of events= 47
+> fit2pa
+Call:
+coxph(formula = Surv(stop, event) ~ rx + size + number, data = bladder2,
+ subset = (enum == 2), method = "breslow")
+
+
+ coef exp(coef) se(coef) z p
+rx -0.42421 0.654 0.4022 -1.0547 0.29
+size -0.12503 0.882 0.1171 -1.0679 0.29
+number 0.00199 1.002 0.0938 0.0212 0.98
+
+Likelihood ratio test=2.02 on 3 df, p=0.569 n= 46, number of events= 29
+> fit2pb
+Call:
+coxph(formula = Surv(stop - start, event) ~ rx + size + number,
+ data = bladder2, subset = (enum == 2), method = "breslow")
+
+
+ coef exp(coef) se(coef) z p
+rx -0.25911 0.772 0.4051 -0.6396 0.52
+size -0.11636 0.890 0.1192 -0.9759 0.33
+number -0.00571 0.994 0.0967 -0.0591 0.95
+
+Likelihood ratio test=1.27 on 3 df, p=0.735 n= 46, number of events= 29
+> fit3pa
+Call:
+coxph(formula = Surv(stop, event) ~ rx + size + number, data = bladder2,
+ subset = (enum == 3), method = "breslow")
+
+
+ coef exp(coef) se(coef) z p
+rx -0.8985 0.407 0.554 -1.623 0.10
+size 0.0850 1.089 0.209 0.407 0.68
+number -0.0172 0.983 0.128 -0.134 0.89
+
+Likelihood ratio test=4.16 on 3 df, p=0.245 n= 27, number of events= 22
+> rm(rx, cmat, wfit, fita, fit1p, fit2pa, fit2pb, fit3pa)
+>
diff --git a/win32/deps/library/survival/tests/book1.R b/win32/deps/library/survival/tests/book1.R
new file mode 100644
index 0000000..b36aa83
--- /dev/null
+++ b/win32/deps/library/survival/tests/book1.R
@@ -0,0 +1,106 @@
+library(survival)
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+
+#
+# Tests from the appendix of Therneau and Grambsch
+# a. Data set 1 and Breslow estimate
+# The data below is not in time order, to also test sorting, and has 1 NA
+#
+test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
+ status=c(1,NA,1,0,1,1,0),
+ x= c(0, 2,1,1,1,0,0))
+
+# Breslow estimate
+byhand1 <- function(beta, newx=0) {
+ r <- exp(beta)
+ loglik <- 2*beta - (log(3*r+3) + 2*log(r+3))
+ u <- (6 + 3*r - r^2) / ((r+1)*(r+3))
+ imat <- r/(r+1)^2 + 6*r/(r+3)^2
+
+ x <- c(1,1,1,0,0,0)
+ status <- c(1,0,1,1,0,1)
+ xbar <- c(r/(r+1), r/(r+3), 0, 0) # at times 1, 6, 8 and 9
+ haz <- c(1/(3*r+3), 2/(r+3), 0, 1 )
+ ties <- c(1,1,2,2,3,4)
+ wt <- c(r,r,r,1,1,1)
+ mart <- c(1,0,1,1,0,1) - wt* (cumsum(haz))[ties] #martingale residual
+
+ a <- 3*(r+1)^2; b<- (r+3)^2
+ score <- c((2*r+3)/a, -r/a, -r/a + 3*(3-r)/b, r/a - r*(r+1)/b,
+ r/a + 2*r/b, r/a + 2*r/b)
+
+ # Schoenfeld residual
+ scho <- c(1/(r+1), 1- (r/(3+r)), 0-(r/(3+r)) , 0)
+
+ surv <- exp(-cumsum(haz)* exp(beta*newx))
+ varhaz.g <- cumsum(c(1/(3*r+3)^2, 2/(r+3)^2, 0, 1 ))
+
+ varhaz.d <- cumsum((newx-xbar) * haz)
+
+ varhaz <- (varhaz.g + varhaz.d^2/ imat) * exp(2*beta*newx)
+
+ names(xbar) <- names(haz) <- 1:4
+ names(surv) <- names(varhaz) <- 1:4
+ list(loglik=loglik, u=u, imat=imat, xbar=xbar, haz=haz,
+ mart=mart, score=score,
+ scho=scho, surv=surv, var=varhaz,
+ varhaz.g=varhaz.g, varhaz.d=varhaz.d)
+ }
+
+
+aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+
+fit0 <-coxph(Surv(time, status) ~x, test1, iter=0, method='breslow')
+truth0 <- byhand1(0,0)
+aeq(truth0$loglik, fit0$loglik[1])
+aeq(1/truth0$imat, fit0$var)
+aeq(truth0$mart, fit0$resid[c(2:6,1)])
+aeq(truth0$scho, resid(fit0, 'schoen'))
+aeq(truth0$score, resid(fit0, 'score')[c(3:7,1)])
+sfit <- survfit(fit0, list(x=0))
+aeq(sfit$std.err^2, c(7/180, 2/9, 2/9, 11/9))
+aeq(resid(fit0, 'score'), c(5/24, NA, 5/12, -1/12, 7/24, -1/24, 5/24))
+
+fit1 <- coxph(Surv(time, status) ~x, test1, iter=1, method='breslow')
+aeq(fit1$coef, 8/5)
+
+# This next gives an ignorable warning message
+fit2 <- coxph(Surv(time, status) ~x, test1, method='breslow', iter=2)
+aeq(round(fit2$coef, 6), 1.472724)
+
+fit <- coxph(Surv(time, status) ~x, test1, method='breslow', eps=1e-8)
+aeq(round(fit$coef,7), 1.4752849)
+truth <- byhand1(fit$coef, 0)
+aeq(truth$loglik, fit$loglik[2])
+aeq(1/truth$imat, fit$var)
+aeq(truth$mart, fit$resid[c(2:6,1)])
+aeq(truth$scho, resid(fit, 'schoen'))
+aeq(truth$score, resid(fit, 'score')[c(3:7,1)])
+
+sfit <- survfit(fit, list(x=0), censor=FALSE)
+aeq(sfit$std.err^2, truth$var[c(1,2,4)]) # sfit skips time 8 (no events there)
+aeq(-log(sfit$surv), (cumsum(truth$haz))[c(1,2,4)])
+sfit <- survfit(fit, list(x=0), censor=TRUE)
+aeq(sfit$std.err^2, truth$var)
+aeq(-log(sfit$surv), (cumsum(truth$haz)))
+
+
+#
+# Done with the formal test, now print out lots of bits
+#
+resid(fit)
+resid(fit, 'scor')
+resid(fit, 'scho')
+
+predict(fit, type='lp')
+predict(fit, type='risk')
+predict(fit, type='expected')
+predict(fit, type='terms')
+predict(fit, type='lp', se.fit=T)
+predict(fit, type='risk', se.fit=T)
+predict(fit, type='expected', se.fit=T)
+predict(fit, type='terms', se.fit=T)
+
+summary(survfit(fit))
+summary(survfit(fit, list(x=2)))
diff --git a/win32/deps/library/survival/tests/book1.Rout.save b/win32/deps/library/survival/tests/book1.Rout.save
new file mode 100644
index 0000000..b65ce26
--- /dev/null
+++ b/win32/deps/library/survival/tests/book1.Rout.save
@@ -0,0 +1,222 @@
+
+R version 2.11.1 (2010-05-31)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+>
+> #
+> # Tests from the appendix of Therneau and Grambsch
+> # a. Data set 1 and Breslow estimate
+> # The data below is not in time order, to also test sorting, and has 1 NA
+> #
+> test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
++ status=c(1,NA,1,0,1,1,0),
++ x= c(0, 2,1,1,1,0,0))
+>
+> # Breslow estimate
+> byhand1 <- function(beta, newx=0) {
++ r <- exp(beta)
++ loglik <- 2*beta - (log(3*r+3) + 2*log(r+3))
++ u <- (6 + 3*r - r^2) / ((r+1)*(r+3))
++ imat <- r/(r+1)^2 + 6*r/(r+3)^2
++
++ x <- c(1,1,1,0,0,0)
++ status <- c(1,0,1,1,0,1)
++ xbar <- c(r/(r+1), r/(r+3), 0, 0) # at times 1, 6, 8 and 9
++ haz <- c(1/(3*r+3), 2/(r+3), 0, 1 )
++ ties <- c(1,1,2,2,3,4)
++ wt <- c(r,r,r,1,1,1)
++ mart <- c(1,0,1,1,0,1) - wt* (cumsum(haz))[ties] #martingale residual
++
++ a <- 3*(r+1)^2; b<- (r+3)^2
++ score <- c((2*r+3)/a, -r/a, -r/a + 3*(3-r)/b, r/a - r*(r+1)/b,
++ r/a + 2*r/b, r/a + 2*r/b)
++
++ # Schoenfeld residual
++ scho <- c(1/(r+1), 1- (r/(3+r)), 0-(r/(3+r)) , 0)
++
++ surv <- exp(-cumsum(haz)* exp(beta*newx))
++ varhaz.g <- cumsum(c(1/(3*r+3)^2, 2/(r+3)^2, 0, 1 ))
++
++ varhaz.d <- cumsum((newx-xbar) * haz)
++
++ varhaz <- (varhaz.g + varhaz.d^2/ imat) * exp(2*beta*newx)
++
++ names(xbar) <- names(haz) <- 1:4
++ names(surv) <- names(varhaz) <- 1:4
++ list(loglik=loglik, u=u, imat=imat, xbar=xbar, haz=haz,
++ mart=mart, score=score,
++ scho=scho, surv=surv, var=varhaz,
++ varhaz.g=varhaz.g, varhaz.d=varhaz.d)
++ }
+>
+>
+> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+>
+> fit0 <-coxph(Surv(time, status) ~x, test1, iter=0, method='breslow')
+> truth0 <- byhand1(0,0)
+> aeq(truth0$loglik, fit0$loglik[1])
+[1] TRUE
+> aeq(1/truth0$imat, fit0$var)
+[1] TRUE
+> aeq(truth0$mart, fit0$resid[c(2:6,1)])
+[1] TRUE
+> aeq(truth0$scho, resid(fit0, 'schoen'))
+[1] TRUE
+> aeq(truth0$score, resid(fit0, 'score')[c(3:7,1)])
+[1] TRUE
+> sfit <- survfit(fit0, list(x=0))
+> aeq(sfit$std.err^2, c(7/180, 2/9, 2/9, 11/9))
+[1] TRUE
+> aeq(resid(fit0, 'score'), c(5/24, NA, 5/12, -1/12, 7/24, -1/24, 5/24))
+[1] TRUE
+>
+> fit1 <- coxph(Surv(time, status) ~x, test1, iter=1, method='breslow')
+> aeq(fit1$coef, 8/5)
+[1] TRUE
+>
+> # This next gives an ignorable warning message
+> fit2 <- coxph(Surv(time, status) ~x, test1, method='breslow', iter=2)
+Warning message:
+In fitter(X, Y, strats, offset, init, control, weights = weights, :
+ Ran out of iterations and did not converge
+> aeq(round(fit2$coef, 6), 1.472724)
+[1] TRUE
+>
+> fit <- coxph(Surv(time, status) ~x, test1, method='breslow', eps=1e-8)
+> aeq(round(fit$coef,7), 1.4752849)
+[1] TRUE
+> truth <- byhand1(fit$coef, 0)
+> aeq(truth$loglik, fit$loglik[2])
+[1] TRUE
+> aeq(1/truth$imat, fit$var)
+[1] TRUE
+> aeq(truth$mart, fit$resid[c(2:6,1)])
+[1] TRUE
+> aeq(truth$scho, resid(fit, 'schoen'))
+[1] TRUE
+> aeq(truth$score, resid(fit, 'score')[c(3:7,1)])
+[1] TRUE
+>
+> sfit <- survfit(fit, list(x=0), censor=FALSE)
+> aeq(sfit$std.err^2, truth$var[c(1,2,4)]) # sfit skips time 8 (no events there)
+[1] TRUE
+> aeq(-log(sfit$surv), (cumsum(truth$haz))[c(1,2,4)])
+[1] TRUE
+> sfit <- survfit(fit, list(x=0), censor=TRUE)
+> aeq(sfit$std.err^2, truth$var)
+[1] TRUE
+> aeq(-log(sfit$surv), (cumsum(truth$haz)))
+[1] TRUE
+>
+>
+> #
+> # Done with the formal test, now print out lots of bits
+> #
+> resid(fit)
+ 1 2 3 4 5 6 7
+-0.3333333 NA 0.7287136 -0.2712864 -0.4574271 0.6666667 -0.3333333
+> resid(fit, 'scor')
+ 1 2 3 4 5 6
+ 0.21138938 NA 0.13564322 -0.05049744 -0.12624360 -0.38168095
+ 7
+ 0.21138938
+> resid(fit, 'scho')
+ 1 6 6 9
+ 0.1861407 0.4069297 -0.5930703 0.0000000
+>
+> predict(fit, type='lp')
+[1] -0.7376425 NA 0.7376425 0.7376425 0.7376425 -0.7376425 -0.7376425
+> predict(fit, type='risk')
+[1] 0.4782401 NA 2.0910001 2.0910001 2.0910001 0.4782401 0.4782401
+> predict(fit, type='expected')
+ 1 2 3 4 5 6 7
+1.3333333 NA 0.2712864 0.2712864 1.4574271 0.3333333 0.3333333
+> predict(fit, type='terms')
+ x
+1 -0.7376425
+2 NA
+3 0.7376425
+4 0.7376425
+5 0.7376425
+6 -0.7376425
+7 -0.7376425
+> predict(fit, type='lp', se.fit=T)
+$fit
+ 1 2 3 4 5 6 7
+-0.7376425 NA 0.7376425 0.7376425 0.7376425 -0.7376425 -0.7376425
+
+$se.fit
+ 1 2 3 4 5 6 7
+0.6278672 NA 0.6278672 0.6278672 0.6278672 0.6278672 0.6278672
+
+> predict(fit, type='risk', se.fit=T)
+$fit
+ 1 2 3 4 5 6 7
+0.4782401 NA 2.0910001 2.0910001 2.0910001 0.4782401 0.4782401
+
+$se.fit
+ 1 2 3 4 5 6 7
+0.4342009 NA 0.9079142 0.9079142 0.9079142 0.4342009 0.4342009
+
+> predict(fit, type='expected', se.fit=T)
+$fit
+ 1 2 3 4 5 6 7
+1.3333333 NA 0.2712864 0.2712864 1.4574271 0.3333333 0.3333333
+
+$se.fit
+[1] 1.0540926 NA 0.2785989 0.2785989 1.1069433 0.3333333 0.3333333
+
+> predict(fit, type='terms', se.fit=T)
+$fit
+ x
+1 -0.7376425
+2 NA
+3 0.7376425
+4 0.7376425
+5 0.7376425
+6 -0.7376425
+7 -0.7376425
+
+$se.fit
+ x
+1 0.6278672
+2 NA
+3 0.6278672
+4 0.6278672
+5 0.6278672
+6 0.6278672
+7 0.6278672
+
+>
+> summary(survfit(fit))
+Call: survfit(formula = fit)
+
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 1 6 1 0.8783 0.122 0.66827 1
+ 6 4 2 0.4981 0.218 0.21125 1
+ 9 1 1 0.0615 0.150 0.00051 1
+> summary(survfit(fit, list(x=2)))
+Call: survfit(formula = fit, newdata = list(x = 2))
+
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 1 6 1 3.05e-01 6.50e-01 4.72e-03 1
+ 6 4 2 1.71e-03 1.98e-02 2.33e-13 1
+ 9 1 1 8.52e-12 5.29e-10 1.22e-64 1
+>
diff --git a/win32/deps/library/survival/tests/book2.R b/win32/deps/library/survival/tests/book2.R
new file mode 100644
index 0000000..9da9ca0
--- /dev/null
+++ b/win32/deps/library/survival/tests/book2.R
@@ -0,0 +1,105 @@
+library(survival)
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+
+#
+# Tests from the appendix of Therneau and Grambsch
+# b. Data set 1 and Efron estimate
+#
+test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
+ status=c(1,NA,1,0,1,1,0),
+ x= c(0, 2,1,1,1,0,0))
+
+byhand <- function(beta, newx=0) {
+ r <- exp(beta)
+ loglik <- 2*beta - (log(3*r +3) + log((r+5)/2) + log(r+3))
+ u <- (30 + 23*r - r^3)/ ((r+1)*(r+3)*(r+5))
+ tfun <- function(x) x - x^2
+ imat <- tfun(r/(r+1)) + tfun(r/(r+5)) + tfun(r/(r+3))
+
+ # The matrix of weights, one row per obs, one col per time
+ # Time of 1, 6, 6+0 (second death), and 9
+ wtmat <- matrix(c(1,1,1,1,1,1,
+ 0,0,1,1,1,1,
+ 0,0,.5, .5, 1,1,
+ 0,0,0,0,0,1), ncol=4)
+ wtmat <- diag(c(r,r,r,1,1,1)) %*% wtmat
+
+ x <- c(1,1,1,0,0,0)
+ status <- c(1,0,1,1,0,1)
+ xbar <- colSums(wtmat*x)/ colSums(wtmat)
+ haz <- 1/ colSums(wtmat) # one death at each of the times
+
+ hazmat <- wtmat %*% diag(haz) #each subject's hazard over time
+ mart <- status - rowSums(hazmat)
+
+ a <- r+1; b<- r+3; d<- r+5 # 'c' in the book, 'd' here
+ score <- c((2*r + 3)/ (3*a^2),
+ -r/ (3*a^2),
+ (675+ r*(1305 +r*(756 + r*(-4 +r*(-79 -13*r)))))/(3*(a*b*d)^2),
+ r*(1/(3*a^2) - a/(2*b^2) - b/(2*d^2)),
+ 2*r*(177 + r*(282 +r*(182 + r*(50 + 5*r)))) /(3*(a*b*d)^2),
+ 2*r*(177 + r*(282 +r*(182 + r*(50 + 5*r)))) /(3*(a*b*d)^2))
+
+ # Schoenfeld residual
+ d <- mean(xbar[2:3])
+ scho <- c(1/(r+1), 1- d, 0- d , 0)
+
+ surv <- exp(-cumsum(haz)* exp(beta*newx))[c(1,3,4)]
+ varhaz.g <- cumsum(haz^2) # since all numerators are 1
+
+ varhaz.d <- cumsum((newx-xbar) * haz)
+
+ varhaz <- (varhaz.g + varhaz.d^2/ imat) * exp(2*beta*newx)
+
+ list(loglik=loglik, u=u, imat=imat, xbar=xbar, haz=haz,
+ mart=mart, score=score, var.g=varhaz.g, var.d=varhaz.d,
+ scho=scho, surv=surv, var=varhaz[c(1,3,4)])
+ }
+
+
+aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+
+fit0 <-coxph(Surv(time, status) ~x, test1, iter=0)
+truth0 <- byhand(0,0)
+aeq(truth0$loglik, fit0$loglik[1])
+aeq(1/truth0$imat, fit0$var)
+aeq(truth0$mart, fit0$resid[c(2:6,1)])
+aeq(resid(fit0), c(-3/4, NA, 5/6, -1/6, 5/12, 5/12, -3/4))
+aeq(truth0$scho, resid(fit0, 'schoen'))
+aeq(truth0$score, resid(fit0, 'score')[c(3:7,1)])
+sfit <- survfit(fit0, list(x=0), censor=FALSE)
+aeq(sfit$std.err^2, truth0$var)
+aeq(sfit$surv, truth0$surv)
+
+fit <- coxph(Surv(time, status) ~x, test1, eps=1e-8)
+aeq(round(fit$coef,6), 1.676857)
+truth <- byhand(fit$coef, 0)
+aeq(truth$loglik, fit$loglik[2])
+aeq(1/truth$imat, fit$var)
+aeq(truth$mart, fit$resid[c(2:6,1)])
+aeq(truth$scho, resid(fit, 'schoen'))
+aeq(truth$score, resid(fit, 'score')[c(3:7,1)])
+
+sfit <- survfit(fit, list(x=0), censor=FALSE)
+aeq(sfit$surv, truth$surv)
+aeq(sfit$std.err^2, truth$var)
+
+#
+# Done with the formal test, now print out lots of bits
+#
+resid(fit)
+resid(fit, 'scor')
+resid(fit, 'scho')
+
+predict(fit, type='lp')
+predict(fit, type='risk')
+predict(fit, type='expected')
+predict(fit, type='terms')
+predict(fit, type='lp', se.fit=T)
+predict(fit, type='risk', se.fit=T)
+predict(fit, type='expected', se.fit=T)
+predict(fit, type='terms', se.fit=T)
+
+summary(survfit(fit))
+summary(survfit(fit, list(x=2)))
diff --git a/win32/deps/library/survival/tests/book2.Rout.save b/win32/deps/library/survival/tests/book2.Rout.save
new file mode 100644
index 0000000..b4461b5
--- /dev/null
+++ b/win32/deps/library/survival/tests/book2.Rout.save
@@ -0,0 +1,214 @@
+
+R version 2.14.0 Under development (unstable) (2011-04-10 r55401)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+>
+> #
+> # Tests from the appendix of Therneau and Grambsch
+> # b. Data set 1 and Efron estimate
+> #
+> test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
++ status=c(1,NA,1,0,1,1,0),
++ x= c(0, 2,1,1,1,0,0))
+>
+> byhand <- function(beta, newx=0) {
++ r <- exp(beta)
++ loglik <- 2*beta - (log(3*r +3) + log((r+5)/2) + log(r+3))
++ u <- (30 + 23*r - r^3)/ ((r+1)*(r+3)*(r+5))
++ tfun <- function(x) x - x^2
++ imat <- tfun(r/(r+1)) + tfun(r/(r+5)) + tfun(r/(r+3))
++
++ # The matrix of weights, one row per obs, one col per time
++ # Time of 1, 6, 6+0 (second death), and 9
++ wtmat <- matrix(c(1,1,1,1,1,1,
++ 0,0,1,1,1,1,
++ 0,0,.5, .5, 1,1,
++ 0,0,0,0,0,1), ncol=4)
++ wtmat <- diag(c(r,r,r,1,1,1)) %*% wtmat
++
++ x <- c(1,1,1,0,0,0)
++ status <- c(1,0,1,1,0,1)
++ xbar <- colSums(wtmat*x)/ colSums(wtmat)
++ haz <- 1/ colSums(wtmat) # one death at each of the times
++
++ hazmat <- wtmat %*% diag(haz) #each subject's hazard over time
++ mart <- status - rowSums(hazmat)
++
++ a <- r+1; b<- r+3; d<- r+5 # 'c' in the book, 'd' here
++ score <- c((2*r + 3)/ (3*a^2),
++ -r/ (3*a^2),
++ (675+ r*(1305 +r*(756 + r*(-4 +r*(-79 -13*r)))))/(3*(a*b*d)^2),
++ r*(1/(3*a^2) - a/(2*b^2) - b/(2*d^2)),
++ 2*r*(177 + r*(282 +r*(182 + r*(50 + 5*r)))) /(3*(a*b*d)^2),
++ 2*r*(177 + r*(282 +r*(182 + r*(50 + 5*r)))) /(3*(a*b*d)^2))
++
++ # Schoenfeld residual
++ d <- mean(xbar[2:3])
++ scho <- c(1/(r+1), 1- d, 0- d , 0)
++
++ surv <- exp(-cumsum(haz)* exp(beta*newx))[c(1,3,4)]
++ varhaz.g <- cumsum(haz^2) # since all numerators are 1
++
++ varhaz.d <- cumsum((newx-xbar) * haz)
++
++ varhaz <- (varhaz.g + varhaz.d^2/ imat) * exp(2*beta*newx)
++
++ list(loglik=loglik, u=u, imat=imat, xbar=xbar, haz=haz,
++ mart=mart, score=score, var.g=varhaz.g, var.d=varhaz.d,
++ scho=scho, surv=surv, var=varhaz[c(1,3,4)])
++ }
+>
+>
+> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+>
+> fit0 <-coxph(Surv(time, status) ~x, test1, iter=0)
+> truth0 <- byhand(0,0)
+> aeq(truth0$loglik, fit0$loglik[1])
+[1] TRUE
+> aeq(1/truth0$imat, fit0$var)
+[1] TRUE
+> aeq(truth0$mart, fit0$resid[c(2:6,1)])
+[1] TRUE
+> aeq(resid(fit0), c(-3/4, NA, 5/6, -1/6, 5/12, 5/12, -3/4))
+[1] TRUE
+> aeq(truth0$scho, resid(fit0, 'schoen'))
+[1] TRUE
+> aeq(truth0$score, resid(fit0, 'score')[c(3:7,1)])
+[1] TRUE
+> sfit <- survfit(fit0, list(x=0), censor=FALSE)
+> aeq(sfit$std.err^2, truth0$var)
+[1] TRUE
+> aeq(sfit$surv, truth0$surv)
+[1] TRUE
+>
+> fit <- coxph(Surv(time, status) ~x, test1, eps=1e-8)
+> aeq(round(fit$coef,6), 1.676857)
+[1] TRUE
+> truth <- byhand(fit$coef, 0)
+> aeq(truth$loglik, fit$loglik[2])
+[1] TRUE
+> aeq(1/truth$imat, fit$var)
+[1] TRUE
+> aeq(truth$mart, fit$resid[c(2:6,1)])
+[1] TRUE
+> aeq(truth$scho, resid(fit, 'schoen'))
+[1] TRUE
+> aeq(truth$score, resid(fit, 'score')[c(3:7,1)])
+[1] TRUE
+>
+> sfit <- survfit(fit, list(x=0), censor=FALSE)
+> aeq(sfit$surv, truth$surv)
+[1] TRUE
+> aeq(sfit$std.err^2, truth$var)
+[1] TRUE
+>
+> #
+> # Done with the formal test, now print out lots of bits
+> #
+> resid(fit)
+ 1 2 3 4 5 6 7
+-0.3655434 NA 0.7191707 -0.2808293 -0.4383414 0.7310869 -0.3655434
+> resid(fit, 'scor')
+ 1 2 3 4 5 6 7
+ 0.2208584 NA 0.1132780 -0.0442340 -0.1029199 -0.4078409 0.2208584
+> resid(fit, 'scho')
+ 1 6 6 9
+ 0.157512 0.421244 -0.578756 0.000000
+>
+> predict(fit, type='lp')
+[1] -0.8384287 NA 0.8384287 0.8384287 0.8384287 -0.8384287 -0.8384287
+> predict(fit, type='risk')
+[1] 0.4323894 NA 2.3127302 2.3127302 2.3127302 0.4323894 0.4323894
+> predict(fit, type='expected')
+ 1 2 3 4 5 6 7
+1.3655434 NA 0.2808293 0.2808293 1.4383414 0.2689131 0.3655434
+> predict(fit, type='terms')
+ x
+1 -0.8384287
+2 NA
+3 0.8384287
+4 0.8384287
+5 0.8384287
+6 -0.8384287
+7 -0.8384287
+> predict(fit, type='lp', se.fit=T)
+$fit
+ 1 2 3 4 5 6 7
+-0.8384287 NA 0.8384287 0.8384287 0.8384287 -0.8384287 -0.8384287
+
+$se.fit
+ 1 2 3 4 5 6 7
+0.6388078 NA 0.6388078 0.6388078 0.6388078 0.6388078 0.6388078
+
+> predict(fit, type='risk', se.fit=T)
+$fit
+ 1 2 3 4 5 6 7
+0.4323894 NA 2.3127302 2.3127302 2.3127302 0.4323894 0.4323894
+
+$se.fit
+ 1 2 3 4 5 6 7
+0.4200565 NA 0.9714774 0.9714774 0.9714774 0.4200565 0.4200565
+
+> predict(fit, type='expected', se.fit=T)
+$fit
+ 1 2 3 4 5 6 7
+1.3655434 NA 0.2808293 0.2808293 1.4383414 0.2689131 0.3655434
+
+$se.fit
+[1] 1.0649293 NA 0.2864593 0.2864593 1.5922983 0.3661617 0.3661617
+
+> predict(fit, type='terms', se.fit=T)
+$fit
+ x
+1 -0.8384287
+2 NA
+3 0.8384287
+4 0.8384287
+5 0.8384287
+6 -0.8384287
+7 -0.8384287
+
+$se.fit
+ x
+1 0.6388078
+2 NA
+3 0.6388078
+4 0.6388078
+5 0.6388078
+6 0.6388078
+7 0.6388078
+
+>
+> summary(survfit(fit))
+Call: survfit(formula = fit)
+
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 1 6 1 0.8857 0.117 0.683036 1
+ 6 4 2 0.4294 0.237 0.145743 1
+ 9 1 1 0.0425 0.116 0.000198 1
+> summary(survfit(fit, list(x=2)))
+Call: survfit(formula = fit, newdata = list(x = 2))
+
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 1 6 1 2.23e-01 5.97e-01 1.16e-03 1
+ 6 4 2 2.87e-05 5.69e-04 3.96e-22 1
+ 9 1 1 1.08e-17 1.04e-15 1.07e-99 1
+>
diff --git a/win32/deps/library/survival/tests/book3.R b/win32/deps/library/survival/tests/book3.R
new file mode 100644
index 0000000..25b1233
--- /dev/null
+++ b/win32/deps/library/survival/tests/book3.R
@@ -0,0 +1,109 @@
+library(survival)
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+
+#
+# Tests from the appendix of Therneau and Grambsch
+# c. Data set 2 and Breslow estimate
+#
+test2 <- data.frame(start=c(1, 2, 5, 2, 1, 7, 3, 4, 8, 8),
+ stop =c(2, 3, 6, 7, 8, 9, 9, 9,14,17),
+ event=c(1, 1, 1, 1, 1, 1, 1, 0, 0, 0),
+ x =c(1, 0, 0, 1, 0, 1, 1, 1, 0, 0) )
+
+byhand <- function(beta, newx=0) {
+ r <- exp(beta)
+ loglik <- 4*beta - log(r+1) - log(r+2) - 3*log(3*r+2) - 2*log(3*r+1)
+ u <- 1/(r+1) + 1/(3*r+1) + 4/(3*r+2) -
+ ( r/(r+2) +3*r/(3*r+2) + 3*r/(3*r+1))
+ imat <- r/(r+1)^2 + 2*r/(r+2)^2 + 6*r/(3*r+2)^2 +
+ 3*r/(3*r+1)^2 + 3*r/(3*r+1)^2 + 12*r/(3*r+2)^2
+
+ hazard <-c( 1/(r+1), 1/(r+2), 1/(3*r+2), 1/(3*r+1), 1/(3*r+1), 2/(3*r+2) )
+ xbar <- c(r/(r+1), r/(r+2), 3*r/(3*r+2), 3*r/(3*r+1), 3*r/(3*r+1),
+ 3*r/(3*r+2))
+
+ # The matrix of weights, one row per obs, one col per time
+ # deaths at 2,3,6,7,8,9
+ wtmat <- matrix(c(1,0,0,0,1,0,0,0,0,0,
+ 0,1,0,1,1,0,0,0,0,0,
+ 0,0,1,1,1,0,1,1,0,0,
+ 0,0,0,1,1,0,1,1,0,0,
+ 0,0,0,0,1,1,1,1,0,0,
+ 0,0,0,0,0,1,1,1,1,1), ncol=6)
+ wtmat <- diag(c(r,1,1,r,1,r,r,r,1,1)) %*% wtmat
+
+ x <- c(1,0,0,1,0,1,1,1,0,0)
+ status <- c(1,1,1,1,1,1,1,0,0,0)
+ xbar <- colSums(wtmat*x)/ colSums(wtmat)
+ n <- length(x)
+
+ # Table of sums for score and Schoenfeld resids
+ hazmat <- wtmat %*% diag(hazard) #each subject's hazard over time
+ dM <- -hazmat #Expected part
+ for (i in 1:6) dM[i,i] <- dM[i,i] +1 #observed
+ dM[7,6] <- dM[7,6] +1 # observed
+ mart <- rowSums(dM)
+
+ # Table of sums for score and Schoenfeld resids
+ # Looks like the last table of appendix E.2.1 of the book
+ resid <- dM * outer(x, xbar, '-')
+ score <- rowSums(resid)
+ scho <- colSums(resid)
+ # We need to split the two tied times up, to match coxph
+ scho <- c(scho[1:5], scho[6]/2, scho[6]/2)
+ var.g <- cumsum(hazard*hazard /c(1,1,1,1,1,2))
+ var.d <- cumsum( (xbar-newx)*hazard)
+
+ surv <- exp(-cumsum(hazard) * exp(beta*newx))
+ varhaz <- (var.g + var.d^2/imat)* exp(2*beta*newx)
+
+ list(loglik=loglik, u=u, imat=imat, xbar=xbar, haz=hazard,
+ mart=mart, score=score, rmat=resid,
+ scho=scho, surv=surv, var=varhaz)
+ }
+
+
+aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+
+fit0 <-coxph(Surv(start, stop, event) ~x, test2, iter=0, method='breslow')
+truth0 <- byhand(0,0)
+aeq(truth0$loglik, fit0$loglik[1])
+aeq(1/truth0$imat, fit0$var)
+aeq(truth0$mart, fit0$resid)
+aeq(truth0$scho, resid(fit0, 'schoen'))
+aeq(truth0$score, resid(fit0, 'score'))
+sfit <- survfit(fit0, list(x=0), censor=FALSE)
+aeq(sfit$std.err^2, truth0$var)
+aeq(sfit$surv, truth0$surv)
+
+fit <- coxph(Surv(start, stop, event) ~x, test2, eps=1e-8, method='breslow')
+truth <- byhand(fit$coef, 0)
+aeq(truth$loglik, fit$loglik[2])
+aeq(1/truth$imat, fit$var)
+aeq(truth$mart, fit$resid)
+aeq(truth$scho, resid(fit, 'schoen'))
+aeq(truth$score, resid(fit, 'score'))
+
+sfit <- survfit(fit, list(x=0), censor=FALSE)
+aeq(sfit$std.err^2, truth$var)
+aeq(-log(sfit$surv), (cumsum(truth$haz)))
+
+#
+# Done with the formal test, now print out lots of bits
+#
+resid(fit)
+resid(fit, 'scor')
+resid(fit, 'scho')
+
+predict(fit, type='lp')
+predict(fit, type='risk')
+predict(fit, type='expected')
+predict(fit, type='terms')
+predict(fit, type='lp', se.fit=T)
+predict(fit, type='risk', se.fit=T)
+predict(fit, type='expected', se.fit=T)
+predict(fit, type='terms', se.fit=T)
+
+summary(survfit(fit))
+summary(survfit(fit, list(x=2)))
diff --git a/win32/deps/library/survival/tests/book3.Rout.save b/win32/deps/library/survival/tests/book3.Rout.save
new file mode 100644
index 0000000..7514b92
--- /dev/null
+++ b/win32/deps/library/survival/tests/book3.Rout.save
@@ -0,0 +1,254 @@
+
+R version 2.14.0 Under development (unstable) (2011-04-10 r55401)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+>
+> #
+> # Tests from the appendix of Therneau and Grambsch
+> # c. Data set 2 and Breslow estimate
+> #
+> test2 <- data.frame(start=c(1, 2, 5, 2, 1, 7, 3, 4, 8, 8),
++ stop =c(2, 3, 6, 7, 8, 9, 9, 9,14,17),
++ event=c(1, 1, 1, 1, 1, 1, 1, 0, 0, 0),
++ x =c(1, 0, 0, 1, 0, 1, 1, 1, 0, 0) )
+>
+> byhand <- function(beta, newx=0) {
++ r <- exp(beta)
++ loglik <- 4*beta - log(r+1) - log(r+2) - 3*log(3*r+2) - 2*log(3*r+1)
++ u <- 1/(r+1) + 1/(3*r+1) + 4/(3*r+2) -
++ ( r/(r+2) +3*r/(3*r+2) + 3*r/(3*r+1))
++ imat <- r/(r+1)^2 + 2*r/(r+2)^2 + 6*r/(3*r+2)^2 +
++ 3*r/(3*r+1)^2 + 3*r/(3*r+1)^2 + 12*r/(3*r+2)^2
++
++ hazard <-c( 1/(r+1), 1/(r+2), 1/(3*r+2), 1/(3*r+1), 1/(3*r+1), 2/(3*r+2) )
++ xbar <- c(r/(r+1), r/(r+2), 3*r/(3*r+2), 3*r/(3*r+1), 3*r/(3*r+1),
++ 3*r/(3*r+2))
++
++ # The matrix of weights, one row per obs, one col per time
++ # deaths at 2,3,6,7,8,9
++ wtmat <- matrix(c(1,0,0,0,1,0,0,0,0,0,
++ 0,1,0,1,1,0,0,0,0,0,
++ 0,0,1,1,1,0,1,1,0,0,
++ 0,0,0,1,1,0,1,1,0,0,
++ 0,0,0,0,1,1,1,1,0,0,
++ 0,0,0,0,0,1,1,1,1,1), ncol=6)
++ wtmat <- diag(c(r,1,1,r,1,r,r,r,1,1)) %*% wtmat
++
++ x <- c(1,0,0,1,0,1,1,1,0,0)
++ status <- c(1,1,1,1,1,1,1,0,0,0)
++ xbar <- colSums(wtmat*x)/ colSums(wtmat)
++ n <- length(x)
++
++ # Table of sums for score and Schoenfeld resids
++ hazmat <- wtmat %*% diag(hazard) #each subject's hazard over time
++ dM <- -hazmat #Expected part
++ for (i in 1:6) dM[i,i] <- dM[i,i] +1 #observed
++ dM[7,6] <- dM[7,6] +1 # observed
++ mart <- rowSums(dM)
++
++ # Table of sums for score and Schoenfeld resids
++ # Looks like the last table of appendix E.2.1 of the book
++ resid <- dM * outer(x, xbar, '-')
++ score <- rowSums(resid)
++ scho <- colSums(resid)
++ # We need to split the two tied times up, to match coxph
++ scho <- c(scho[1:5], scho[6]/2, scho[6]/2)
++ var.g <- cumsum(hazard*hazard /c(1,1,1,1,1,2))
++ var.d <- cumsum( (xbar-newx)*hazard)
++
++ surv <- exp(-cumsum(hazard) * exp(beta*newx))
++ varhaz <- (var.g + var.d^2/imat)* exp(2*beta*newx)
++
++ list(loglik=loglik, u=u, imat=imat, xbar=xbar, haz=hazard,
++ mart=mart, score=score, rmat=resid,
++ scho=scho, surv=surv, var=varhaz)
++ }
+>
+>
+> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+>
+> fit0 <-coxph(Surv(start, stop, event) ~x, test2, iter=0, method='breslow')
+> truth0 <- byhand(0,0)
+> aeq(truth0$loglik, fit0$loglik[1])
+[1] TRUE
+> aeq(1/truth0$imat, fit0$var)
+[1] TRUE
+> aeq(truth0$mart, fit0$resid)
+[1] TRUE
+> aeq(truth0$scho, resid(fit0, 'schoen'))
+[1] TRUE
+> aeq(truth0$score, resid(fit0, 'score'))
+[1] TRUE
+> sfit <- survfit(fit0, list(x=0), censor=FALSE)
+> aeq(sfit$std.err^2, truth0$var)
+[1] TRUE
+> aeq(sfit$surv, truth0$surv)
+[1] TRUE
+>
+> fit <- coxph(Surv(start, stop, event) ~x, test2, eps=1e-8, method='breslow')
+> truth <- byhand(fit$coef, 0)
+> aeq(truth$loglik, fit$loglik[2])
+[1] TRUE
+> aeq(1/truth$imat, fit$var)
+[1] TRUE
+> aeq(truth$mart, fit$resid)
+[1] TRUE
+> aeq(truth$scho, resid(fit, 'schoen'))
+[1] TRUE
+> aeq(truth$score, resid(fit, 'score'))
+[1] TRUE
+>
+> sfit <- survfit(fit, list(x=0), censor=FALSE)
+> aeq(sfit$std.err^2, truth$var)
+[1] TRUE
+> aeq(-log(sfit$surv), (cumsum(truth$haz)))
+[1] TRUE
+>
+> #
+> # Done with the formal test, now print out lots of bits
+> #
+> resid(fit)
+ 1 2 3 4 5 6
+ 0.52111895 0.65741078 0.78977654 0.24738772 -0.60629349 0.36902492
+ 7 8 9 10
+-0.06876579 -1.06876579 -0.42044692 -0.42044692
+> resid(fit, 'scor')
+ 1 2 3 4 5 6
+ 0.27156496 -0.20696709 -0.45771743 -0.09586133 0.13608234 0.19288983
+ 7 8 9 10
+ 0.04655651 -0.37389040 0.24367131 0.24367131
+> resid(fit, 'scho')
+ 2 3 6 7 8 9 9
+ 0.5211189 -0.3148216 -0.5795531 0.2661809 -0.7338191 0.4204469 0.4204469
+>
+> predict(fit, type='lp')
+ [1] -0.04226304 0.04226304 0.04226304 -0.04226304 0.04226304 -0.04226304
+ [7] -0.04226304 -0.04226304 0.04226304 0.04226304
+> predict(fit, type='risk')
+ [1] 0.9586176 1.0431688 1.0431688 0.9586176 1.0431688 0.9586176 0.9586176
+ [8] 0.9586176 1.0431688 1.0431688
+> predict(fit, type='expected')
+ 1 2 3 4 5 6 7 8
+0.4788811 0.3425892 0.2102235 0.7526123 1.6062935 0.6309751 1.0687658 1.0687658
+ 9 10
+0.4204469 0.4204469
+> predict(fit, type='terms')
+ x
+1 -0.04226304
+2 0.04226304
+3 0.04226304
+4 -0.04226304
+5 0.04226304
+6 -0.04226304
+7 -0.04226304
+8 -0.04226304
+9 0.04226304
+10 0.04226304
+attr(,"constant")
+[1] -0.04226304
+> predict(fit, type='lp', se.fit=T)
+$fit
+ 1 2 3 4 5 6
+-0.04226304 0.04226304 0.04226304 -0.04226304 0.04226304 -0.04226304
+ 7 8 9 10
+-0.04226304 -0.04226304 0.04226304 0.04226304
+
+$se.fit
+ 1 2 3 4 5 6 7 8
+0.3969086 0.3969086 0.3969086 0.3969086 0.3969086 0.3969086 0.3969086 0.3969086
+ 9 10
+0.3969086 0.3969086
+
+> predict(fit, type='risk', se.fit=T)
+$fit
+ 1 2 3 4 5 6 7 8
+0.9586176 1.0431688 1.0431688 0.9586176 1.0431688 0.9586176 0.9586176 0.9586176
+ 9 10
+1.0431688 1.0431688
+
+$se.fit
+ 1 2 3 4 5 6 7 8
+0.3886094 0.4053852 0.4053852 0.3886094 0.4053852 0.3886094 0.3886094 0.3886094
+ 9 10
+0.4053852 0.4053852
+
+> predict(fit, type='expected', se.fit=T)
+$fit
+ 1 2 3 4 5 6 7 8
+0.4788811 0.3425892 0.2102235 0.7526123 1.6062935 0.6309751 1.0687658 1.0687658
+ 9 10
+0.4204469 0.4204469
+
+$se.fit
+ [1] 0.5182381 0.3982700 0.3292830 0.6266797 1.0255146 0.5852364 0.7341340
+ [8] 0.7341340 0.6268550 0.6268550
+
+> predict(fit, type='terms', se.fit=T)
+$fit
+ x
+1 -0.04226304
+2 0.04226304
+3 0.04226304
+4 -0.04226304
+5 0.04226304
+6 -0.04226304
+7 -0.04226304
+8 -0.04226304
+9 0.04226304
+10 0.04226304
+attr(,"constant")
+[1] -0.04226304
+
+$se.fit
+ x
+1 0.3969086
+2 0.3969086
+3 0.3969086
+4 0.3969086
+5 0.3969086
+6 0.3969086
+7 0.3969086
+8 0.3969086
+9 0.3969086
+10 0.3969086
+
+>
+> summary(survfit(fit))
+Call: survfit(formula = fit)
+
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 2 2 1 0.607 0.303 0.2279 1.000
+ 3 3 1 0.437 0.262 0.1347 1.000
+ 6 5 1 0.357 0.226 0.1034 1.000
+ 7 4 1 0.277 0.188 0.0729 1.000
+ 8 4 1 0.214 0.156 0.0514 0.894
+ 9 5 2 0.143 0.112 0.0308 0.667
+> summary(survfit(fit, list(x=2)))
+Call: survfit(formula = fit, newdata = list(x = 2))
+
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 2 2 1 0.644 0.444 0.16657 1
+ 3 3 1 0.482 0.511 0.06055 1
+ 6 5 1 0.404 0.504 0.03491 1
+ 7 4 1 0.322 0.475 0.01801 1
+ 8 4 1 0.258 0.437 0.00928 1
+ 9 5 2 0.181 0.377 0.00302 1
+>
diff --git a/win32/deps/library/survival/tests/book4.R b/win32/deps/library/survival/tests/book4.R
new file mode 100644
index 0000000..7491c4e
--- /dev/null
+++ b/win32/deps/library/survival/tests/book4.R
@@ -0,0 +1,101 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Tests from the appendix of Therneau and Grambsch
+# d. Data set 2 and Efron estimate
+#
+test2 <- data.frame(start=c(1, 2, 5, 2, 1, 7, 3, 4, 8, 8),
+ stop =c(2, 3, 6, 7, 8, 9, 9, 9,14,17),
+ event=c(1, 1, 1, 1, 1, 1, 1, 0, 0, 0),
+ x =c(1, 0, 0, 1, 0, 1, 1, 1, 0, 0) )
+
+byhand <- function(beta, newx=0) {
+ r <- exp(beta)
+ loglik <- 4*beta - (log(r+1) + log(r+2) + 2*log(3*r+2) + 2*log(3*r+1) +
+ log(2*r +2))
+ u <- 1/(r+1) + 1/(3*r+1) + 2*(1/(3*r+2) + 1/(2*r+2)) -
+ ( r/(r+2) +3*r/(3*r+2) + 3*r/(3*r+1))
+ imat <- r*(1/(r+1)^2 + 2/(r+2)^2 + 6/(3*r+2)^2 +
+ 6/(3*r+1)^2 + 6/(3*r+2)^2 + 4/(2*r +2)^2)
+
+ hazard <-c( 1/(r+1), 1/(r+2), 1/(3*r+2), 1/(3*r+1), 1/(3*r+1),
+ 1/(3*r+2), 1/(2*r +2) )
+
+
+ # The matrix of weights, one row per obs, one col per time
+ # deaths at 2,3,6,7,8,9
+ wtmat <- matrix(c(1,0,0,0,1, 0, 0,0,0,0,
+ 0,1,0,1,1, 0, 0,0,0,0,
+ 0,0,1,1,1, 0, 1,1,0,0,
+ 0,0,0,1,1, 0, 1,1,0,0,
+ 0,0,0,0,1, 1, 1,1,0,0,
+ 0,0,0,0,0, 1, 1,1,1,1,
+ 0,0,0,0,0,.5,.5,1,1,1), ncol=7)
+ wtmat <- diag(c(r,1,1,r,1,r,r,r,1,1)) %*% wtmat
+
+ x <- c(1,0,0,1,0,1,1,1,0,0)
+ status <- c(1,1,1,1,1,1,1,0,0,0)
+ xbar <- colSums(wtmat*x)/ colSums(wtmat)
+ n <- length(x)
+
+ # Table of sums for score and Schoenfeld resids
+ hazmat <- wtmat %*% diag(hazard) #each subject's hazard over time
+ dM <- -hazmat #Expected part
+ for (i in 1:5) dM[i,i] <- dM[i,i] +1 #observed
+ dM[6:7,6:7] <- dM[6:7,6:7] +.5 # observed
+ mart <- rowSums(dM)
+
+ # Table of sums for score and Schoenfeld resids
+ # Looks like the last table of appendix E.2.1 of the book
+ resid <- dM * outer(x, xbar, '-')
+ score <- rowSums(resid)
+ scho <- colSums(resid)
+
+ # We need to add the ties back up (they are symmetric)
+ scho[6:7] <- rep(mean(scho[6:7]), 2)
+
+ list(loglik=loglik, u=u, imat=imat, xbar=xbar, haz=hazard,
+ mart=mart, score=score, rmat=resid,
+ scho=scho)
+ }
+
+
+aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+
+fit0 <-coxph(Surv(start, stop, event) ~x, test2, iter=0)
+truth0 <- byhand(0,0)
+aeq(truth0$loglik, fit0$loglik[1])
+aeq(1/truth0$imat, fit0$var)
+aeq(truth0$mart, fit0$resid)
+aeq(truth0$scho, resid(fit0, 'schoen'))
+aeq(truth0$score, resid(fit0, 'score'))
+
+
+fit <- coxph(Surv(start, stop, event) ~x, test2, eps=1e-8)
+truth <- byhand(fit$coef, 0)
+aeq(truth$loglik, fit$loglik[2])
+aeq(1/truth$imat, fit$var)
+aeq(truth$mart, fit$resid)
+aeq(truth$scho, resid(fit, 'schoen'))
+aeq(truth$score, resid(fit, 'score'))
+
+#
+# Done with the formal test, now print out lots of bits
+#
+resid(fit)
+resid(fit, 'scor')
+resid(fit, 'scho')
+
+predict(fit, type='lp')
+predict(fit, type='risk')
+predict(fit, type='expected')
+predict(fit, type='terms')
+predict(fit, type='lp', se.fit=T)
+predict(fit, type='risk', se.fit=T)
+predict(fit, type='expected', se.fit=T)
+predict(fit, type='terms', se.fit=T)
+
+summary(survfit(fit))
+summary(survfit(fit, list(x=2)))
diff --git a/win32/deps/library/survival/tests/book4.Rout.save b/win32/deps/library/survival/tests/book4.Rout.save
new file mode 100644
index 0000000..a646e11
--- /dev/null
+++ b/win32/deps/library/survival/tests/book4.Rout.save
@@ -0,0 +1,242 @@
+
+R version 2.14.0 Under development (unstable) (2011-04-10 r55401)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Tests from the appendix of Therneau and Grambsch
+> # d. Data set 2 and Efron estimate
+> #
+> test2 <- data.frame(start=c(1, 2, 5, 2, 1, 7, 3, 4, 8, 8),
++ stop =c(2, 3, 6, 7, 8, 9, 9, 9,14,17),
++ event=c(1, 1, 1, 1, 1, 1, 1, 0, 0, 0),
++ x =c(1, 0, 0, 1, 0, 1, 1, 1, 0, 0) )
+>
+> byhand <- function(beta, newx=0) {
++ r <- exp(beta)
++ loglik <- 4*beta - (log(r+1) + log(r+2) + 2*log(3*r+2) + 2*log(3*r+1) +
++ log(2*r +2))
++ u <- 1/(r+1) + 1/(3*r+1) + 2*(1/(3*r+2) + 1/(2*r+2)) -
++ ( r/(r+2) +3*r/(3*r+2) + 3*r/(3*r+1))
++ imat <- r*(1/(r+1)^2 + 2/(r+2)^2 + 6/(3*r+2)^2 +
++ 6/(3*r+1)^2 + 6/(3*r+2)^2 + 4/(2*r +2)^2)
++
++ hazard <-c( 1/(r+1), 1/(r+2), 1/(3*r+2), 1/(3*r+1), 1/(3*r+1),
++ 1/(3*r+2), 1/(2*r +2) )
++
++
++ # The matrix of weights, one row per obs, one col per time
++ # deaths at 2,3,6,7,8,9
++ wtmat <- matrix(c(1,0,0,0,1, 0, 0,0,0,0,
++ 0,1,0,1,1, 0, 0,0,0,0,
++ 0,0,1,1,1, 0, 1,1,0,0,
++ 0,0,0,1,1, 0, 1,1,0,0,
++ 0,0,0,0,1, 1, 1,1,0,0,
++ 0,0,0,0,0, 1, 1,1,1,1,
++ 0,0,0,0,0,.5,.5,1,1,1), ncol=7)
++ wtmat <- diag(c(r,1,1,r,1,r,r,r,1,1)) %*% wtmat
++
++ x <- c(1,0,0,1,0,1,1,1,0,0)
++ status <- c(1,1,1,1,1,1,1,0,0,0)
++ xbar <- colSums(wtmat*x)/ colSums(wtmat)
++ n <- length(x)
++
++ # Table of sums for score and Schoenfeld resids
++ hazmat <- wtmat %*% diag(hazard) #each subject's hazard over time
++ dM <- -hazmat #Expected part
++ for (i in 1:5) dM[i,i] <- dM[i,i] +1 #observed
++ dM[6:7,6:7] <- dM[6:7,6:7] +.5 # observed
++ mart <- rowSums(dM)
++
++ # Table of sums for score and Schoenfeld resids
++ # Looks like the last table of appendix E.2.1 of the book
++ resid <- dM * outer(x, xbar, '-')
++ score <- rowSums(resid)
++ scho <- colSums(resid)
++
++ # We need to add the ties back up (they are symmetric)
++ scho[6:7] <- rep(mean(scho[6:7]), 2)
++
++ list(loglik=loglik, u=u, imat=imat, xbar=xbar, haz=hazard,
++ mart=mart, score=score, rmat=resid,
++ scho=scho)
++ }
+>
+>
+> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+>
+> fit0 <-coxph(Surv(start, stop, event) ~x, test2, iter=0)
+> truth0 <- byhand(0,0)
+> aeq(truth0$loglik, fit0$loglik[1])
+[1] TRUE
+> aeq(1/truth0$imat, fit0$var)
+[1] TRUE
+> aeq(truth0$mart, fit0$resid)
+[1] TRUE
+> aeq(truth0$scho, resid(fit0, 'schoen'))
+[1] TRUE
+> aeq(truth0$score, resid(fit0, 'score'))
+[1] TRUE
+>
+>
+> fit <- coxph(Surv(start, stop, event) ~x, test2, eps=1e-8)
+> truth <- byhand(fit$coef, 0)
+> aeq(truth$loglik, fit$loglik[2])
+[1] TRUE
+> aeq(1/truth$imat, fit$var)
+[1] TRUE
+> aeq(truth$mart, fit$resid)
+[1] TRUE
+> aeq(truth$scho, resid(fit, 'schoen'))
+[1] TRUE
+> aeq(truth$score, resid(fit, 'score'))
+[1] TRUE
+>
+> #
+> # Done with the formal test, now print out lots of bits
+> #
+> resid(fit)
+ 1 2 3 4 5 6
+ 0.50527611 0.66432995 0.79746211 0.22435805 -0.55144018 0.42933697
+ 7 8 9 10
+-0.01764508 -1.14132605 -0.45517594 -0.45517594
+> resid(fit, 'scor')
+ 1 2 3 4 5 6 7
+ 0.2553039 -0.2183386 -0.4744295 -0.1101520 0.1137126 0.2491954 0.1057078
+ 8 9 10
+-0.4119611 0.2454808 0.2454808
+> resid(fit, 'scho')
+ 2 3 6 7 8 9 9
+ 0.5052761 -0.3286599 -0.5949242 0.2539781 -0.7460219 0.4551759 0.4551759
+>
+> predict(fit, type='lp')
+ [1] -0.0105526 0.0105526 0.0105526 -0.0105526 0.0105526 -0.0105526
+ [7] -0.0105526 -0.0105526 0.0105526 0.0105526
+> predict(fit, type='risk')
+ [1] 0.9895029 1.0106085 1.0106085 0.9895029 1.0106085 0.9895029 0.9895029
+ [8] 0.9895029 1.0106085 1.0106085
+> predict(fit, type='expected')
+ 1 2 3 4 5 6 7 8
+0.4947239 0.3356701 0.2025379 0.7756420 1.5514402 0.5706630 1.0176451 1.1413261
+ 9 10
+0.4551759 0.4551759
+> predict(fit, type='terms')
+ x
+1 -0.0105526
+2 0.0105526
+3 0.0105526
+4 -0.0105526
+5 0.0105526
+6 -0.0105526
+7 -0.0105526
+8 -0.0105526
+9 0.0105526
+10 0.0105526
+attr(,"constant")
+[1] -0.0105526
+> predict(fit, type='lp', se.fit=T)
+$fit
+ 1 2 3 4 5 6 7
+-0.0105526 0.0105526 0.0105526 -0.0105526 0.0105526 -0.0105526 -0.0105526
+ 8 9 10
+-0.0105526 0.0105526 0.0105526
+
+$se.fit
+ 1 2 3 4 5 6 7 8
+0.3975884 0.3975884 0.3975884 0.3975884 0.3975884 0.3975884 0.3975884 0.3975884
+ 9 10
+0.3975884 0.3975884
+
+> predict(fit, type='risk', se.fit=T)
+$fit
+ 1 2 3 4 5 6 7 8
+0.9895029 1.0106085 1.0106085 0.9895029 1.0106085 0.9895029 0.9895029 0.9895029
+ 9 10
+1.0106085 1.0106085
+
+$se.fit
+ 1 2 3 4 5 6 7 8
+0.3954962 0.3996918 0.3996918 0.3954962 0.3996918 0.3954962 0.3954962 0.3954962
+ 9 10
+0.3996918 0.3996918
+
+> predict(fit, type='expected', se.fit=T)
+$fit
+ 1 2 3 4 5 6 7 8
+0.4947239 0.3356701 0.2025379 0.7756420 1.5514402 0.5706630 1.0176451 1.1413261
+ 9 10
+0.4551759 0.4551759
+
+$se.fit
+ [1] 0.5331623 0.3940109 0.3241963 0.6388491 1.0026838 0.6453101 0.7848594
+ [8] 0.7848594 0.6401915 0.6401915
+
+> predict(fit, type='terms', se.fit=T)
+$fit
+ x
+1 -0.0105526
+2 0.0105526
+3 0.0105526
+4 -0.0105526
+5 0.0105526
+6 -0.0105526
+7 -0.0105526
+8 -0.0105526
+9 0.0105526
+10 0.0105526
+attr(,"constant")
+[1] -0.0105526
+
+$se.fit
+ x
+1 0.3975884
+2 0.3975884
+3 0.3975884
+4 0.3975884
+5 0.3975884
+6 0.3975884
+7 0.3975884
+8 0.3975884
+9 0.3975884
+10 0.3975884
+
+>
+> summary(survfit(fit))
+Call: survfit(formula = fit)
+
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 2 2 1 0.607 0.303 0.2277 1.000
+ 3 3 1 0.435 0.262 0.1337 1.000
+ 6 5 1 0.356 0.226 0.1029 1.000
+ 7 4 1 0.277 0.189 0.0729 1.000
+ 8 4 1 0.215 0.157 0.0516 0.899
+ 9 5 2 0.137 0.109 0.0288 0.655
+> summary(survfit(fit, list(x=2)))
+Call: survfit(formula = fit, newdata = list(x = 2))
+
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 2 2 1 0.616 0.465 0.14013 1
+ 3 3 1 0.447 0.519 0.04568 1
+ 6 5 1 0.368 0.504 0.02512 1
+ 7 4 1 0.288 0.464 0.01232 1
+ 8 4 1 0.226 0.418 0.00603 1
+ 9 5 2 0.146 0.343 0.00147 1
+>
diff --git a/win32/deps/library/survival/tests/book5.R b/win32/deps/library/survival/tests/book5.R
new file mode 100644
index 0000000..4792624
--- /dev/null
+++ b/win32/deps/library/survival/tests/book5.R
@@ -0,0 +1,124 @@
+library(survival)
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+
+# Tests of the weighted Cox model
+# This is section 1.3 of my appendix -- no yet found in any of the
+# printings though, it awaits the next edition
+#
+# Similar data set to test1, but add weights,
+# a double-death/censor tied time
+# a censored last subject
+# The latter two are cases covered only feebly elsewhere.
+#
+# The data set testw2 has the same data, but done via replication
+#
+aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+
+testw1 <- data.frame(time= c(1,1,2,2,2,2,3,4,5),
+ status= c(1,0,1,1,1,0,0,1,0),
+ x= c(2,0,1,1,0,1,0,1,0),
+ wt = c(1,2,3,4,3,2,1,2,1))
+xx <- testw1$wt
+testw2 <- data.frame(time= rep(c(1,1,2,2,2,2,3,4,5), xx),
+ status= rep(c(1,0,1,1,1,0,0,1,0), xx),
+ x= rep(c(2,0,1,1,0,1,0,1,0), xx),
+ id= rep(1:9, xx))
+indx <- match(1:9, testw2$id)
+
+# Breslow estimate
+byhand <- function(beta, newx=0) {
+ r <- exp(beta)
+ loglik <- 11*beta - (log(r^2 + 11*r +7) + 10*log(11*r +5) +2*log(2*r+1))
+ hazard <- c(1/(r^2 + 11*r +7), 10/(11*r +5), 2/(2*r+1))
+ xbar <- c((2*r^2 + 11*r)*hazard[1], 11*r/(11*r +5), r*hazard[3])
+ imat <- (4*r^2 + 11*r)*hazard[1] - xbar[1]^2 +
+ 10*(xbar[2] - xbar[2]^2) + 2*(xbar[3] - xbar[3]^2)
+
+ temp <- cumsum(hazard)
+ risk <- c(r^2, 1,r,r,1,r,1,r,1)
+ expected <- risk* temp[c(1,1,2,2,2,2,2,3,3)]
+
+ # The matrix of weights, one row per obs, one col per death
+ # deaths at 1,2,2,2, and 4
+ riskmat <- matrix(c(1,1,1,1,1,1,1,1,1,
+ 0,0,1,1,1,1,1,1,1,
+ 0,0,1,1,1,1,1,1,1,
+ 0,0,1,1,1,1,1,1,1,
+ 0,0,0,0,0,0,0,1,1), ncol=5)
+ wtmat <- diag(c(r^2, 2, 3*r, 4*r, 3, 2*r, 1, 2*r, 1)) %*% riskmat
+
+ x <- c(2,0,1,1,0,1,0,1,0)
+ status <- c(1,0,1,1,1,0,0,1,0)
+ wt <- c(1,2,3,4,3,2,1,2,1)
+ # Table of sums for score and Schoenfeld resids
+ hazmat <- riskmat %*% diag(c(1,3,4,3,2)/colSums(wtmat))
+ dM <- -risk*hazmat #Expected part
+ dM[1,1] <- dM[1,1] +1 # deaths at time 1
+ for (i in 2:4) dM[i+1, i] <- dM[i+1,i] +1
+ dM[8,5] <- dM[8,5] +1
+ mart <- rowSums(dM)
+ resid <-dM * outer(x, xbar[c(1,2,2,2,3)] ,'-')
+
+ # Increments to the variance of the hazard
+ var.g <- cumsum(hazard^2/ c(1,10,2))
+ var.d <- cumsum((xbar-newx)*hazard)
+
+ list(loglik=loglik, imat=imat, hazard=hazard, xbar=xbar,
+ mart=c(1,0,1,1,1,0,0,1,0)-expected, expected=expected,
+ score=rowSums(resid), schoen=c(2,1,1,0,1) - xbar[c(1,2,2,2,3)],
+ varhaz=(var.g + var.d^2/imat)* exp(2*beta*newx))
+ }
+
+aeq(byhand(0)$expected, c(1/19, 1/19, rep(103/152, 5), rep(613/456,2))) #verify
+
+fit0 <- coxph(Surv(time, status) ~x, testw1, weights=wt,
+ method='breslow', iter=0)
+fit0b <- coxph(Surv(time, status) ~x, testw2, method='breslow', iter=0)
+fit <- coxph(Surv(time, status) ~x, testw1, weights=wt, method='breslow')
+fitb <- coxph(Surv(time, status) ~x, testw2, method='breslow')
+
+aeq(resid(fit0, type='mart'), (resid(fit0b, type='mart'))[indx])
+aeq(resid(fit0, type='scor'), (resid(fit0b, type='scor'))[indx])
+aeq(unique(resid(fit0, type='scho')), unique(resid(fit0b, type='scho')))
+
+truth0 <- byhand(0,pi)
+aeq(fit0$loglik[1], truth0$loglik)
+aeq(1/truth0$imat, fit0$var)
+aeq(truth0$mart, fit0$resid)
+aeq(truth0$scho, resid(fit0, 'schoen'))
+aeq(truth0$score, resid(fit0, 'score'))
+sfit <- survfit(fit0, list(x=pi), censor=FALSE)
+aeq(sfit$std.err^2, truth0$var)
+aeq(-log(sfit$surv), cumsum(truth0$haz))
+
+truth <- byhand(fit$coef, .3)
+aeq(truth$loglik, fit$loglik[2])
+aeq(1/truth$imat, fit$var)
+aeq(truth$mart, fit$resid)
+aeq(truth$scho, resid(fit, 'schoen'))
+aeq(truth$score, resid(fit, 'score'))
+
+sfit <- survfit(fit, list(x=.3), censor=FALSE)
+aeq(sfit$std.err^2, truth$var)
+aeq(-log(sfit$surv), (cumsum(truth$haz)* exp(fit$coef*.3)))
+
+
+fit0
+summary(fit)
+resid(fit0, type='score')
+resid(fit0, type='scho')
+
+resid(fit, type='score')
+resid(fit, type='scho')
+aeq(resid(fit, type='mart'), (resid(fitb, type='mart'))[indx])
+aeq(resid(fit, type='scor'), (resid(fitb, type='scor'))[indx])
+aeq(unique(resid(fit, type='scho')), unique(resid(fitb, type='scho')))
+rr1 <- resid(fit, type='mart')
+rr2 <- resid(fit, type='mart', weighted=T)
+aeq(rr2/rr1, testw1$wt)
+
+rr1 <- resid(fit, type='score')
+rr2 <- resid(fit, type='score', weighted=T)
+aeq(rr2/rr1, testw1$wt)
+
diff --git a/win32/deps/library/survival/tests/book5.Rout.save b/win32/deps/library/survival/tests/book5.Rout.save
new file mode 100644
index 0000000..0e17a35
--- /dev/null
+++ b/win32/deps/library/survival/tests/book5.Rout.save
@@ -0,0 +1,206 @@
+
+R version 2.12.2 (2011-02-25)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+>
+> # Tests of the weighted Cox model
+> # This is section 1.3 of my appendix -- no yet found in any of the
+> # printings though, it awaits the next edition
+> #
+> # Similar data set to test1, but add weights,
+> # a double-death/censor tied time
+> # a censored last subject
+> # The latter two are cases covered only feebly elsewhere.
+> #
+> # The data set testw2 has the same data, but done via replication
+> #
+> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+>
+> testw1 <- data.frame(time= c(1,1,2,2,2,2,3,4,5),
++ status= c(1,0,1,1,1,0,0,1,0),
++ x= c(2,0,1,1,0,1,0,1,0),
++ wt = c(1,2,3,4,3,2,1,2,1))
+> xx <- testw1$wt
+> testw2 <- data.frame(time= rep(c(1,1,2,2,2,2,3,4,5), xx),
++ status= rep(c(1,0,1,1,1,0,0,1,0), xx),
++ x= rep(c(2,0,1,1,0,1,0,1,0), xx),
++ id= rep(1:9, xx))
+> indx <- match(1:9, testw2$id)
+>
+> # Breslow estimate
+> byhand <- function(beta, newx=0) {
++ r <- exp(beta)
++ loglik <- 11*beta - (log(r^2 + 11*r +7) + 10*log(11*r +5) +2*log(2*r+1))
++ hazard <- c(1/(r^2 + 11*r +7), 10/(11*r +5), 2/(2*r+1))
++ xbar <- c((2*r^2 + 11*r)*hazard[1], 11*r/(11*r +5), r*hazard[3])
++ imat <- (4*r^2 + 11*r)*hazard[1] - xbar[1]^2 +
++ 10*(xbar[2] - xbar[2]^2) + 2*(xbar[3] - xbar[3]^2)
++
++ temp <- cumsum(hazard)
++ risk <- c(r^2, 1,r,r,1,r,1,r,1)
++ expected <- risk* temp[c(1,1,2,2,2,2,2,3,3)]
++
++ # The matrix of weights, one row per obs, one col per death
++ # deaths at 1,2,2,2, and 4
++ riskmat <- matrix(c(1,1,1,1,1,1,1,1,1,
++ 0,0,1,1,1,1,1,1,1,
++ 0,0,1,1,1,1,1,1,1,
++ 0,0,1,1,1,1,1,1,1,
++ 0,0,0,0,0,0,0,1,1), ncol=5)
++ wtmat <- diag(c(r^2, 2, 3*r, 4*r, 3, 2*r, 1, 2*r, 1)) %*% riskmat
++
++ x <- c(2,0,1,1,0,1,0,1,0)
++ status <- c(1,0,1,1,1,0,0,1,0)
++ wt <- c(1,2,3,4,3,2,1,2,1)
++ # Table of sums for score and Schoenfeld resids
++ hazmat <- riskmat %*% diag(c(1,3,4,3,2)/colSums(wtmat))
++ dM <- -risk*hazmat #Expected part
++ dM[1,1] <- dM[1,1] +1 # deaths at time 1
++ for (i in 2:4) dM[i+1, i] <- dM[i+1,i] +1
++ dM[8,5] <- dM[8,5] +1
++ mart <- rowSums(dM)
++ resid <-dM * outer(x, xbar[c(1,2,2,2,3)] ,'-')
++
++ # Increments to the variance of the hazard
++ var.g <- cumsum(hazard^2/ c(1,10,2))
++ var.d <- cumsum((xbar-newx)*hazard)
++
++ list(loglik=loglik, imat=imat, hazard=hazard, xbar=xbar,
++ mart=c(1,0,1,1,1,0,0,1,0)-expected, expected=expected,
++ score=rowSums(resid), schoen=c(2,1,1,0,1) - xbar[c(1,2,2,2,3)],
++ varhaz=(var.g + var.d^2/imat)* exp(2*beta*newx))
++ }
+>
+> aeq(byhand(0)$expected, c(1/19, 1/19, rep(103/152, 5), rep(613/456,2))) #verify
+[1] TRUE
+>
+> fit0 <- coxph(Surv(time, status) ~x, testw1, weights=wt,
++ method='breslow', iter=0)
+> fit0b <- coxph(Surv(time, status) ~x, testw2, method='breslow', iter=0)
+> fit <- coxph(Surv(time, status) ~x, testw1, weights=wt, method='breslow')
+> fitb <- coxph(Surv(time, status) ~x, testw2, method='breslow')
+>
+> aeq(resid(fit0, type='mart'), (resid(fit0b, type='mart'))[indx])
+[1] TRUE
+> aeq(resid(fit0, type='scor'), (resid(fit0b, type='scor'))[indx])
+[1] TRUE
+> aeq(unique(resid(fit0, type='scho')), unique(resid(fit0b, type='scho')))
+[1] TRUE
+>
+> truth0 <- byhand(0,pi)
+> aeq(fit0$loglik[1], truth0$loglik)
+[1] TRUE
+> aeq(1/truth0$imat, fit0$var)
+[1] TRUE
+> aeq(truth0$mart, fit0$resid)
+[1] TRUE
+> aeq(truth0$scho, resid(fit0, 'schoen'))
+[1] TRUE
+> aeq(truth0$score, resid(fit0, 'score'))
+[1] TRUE
+> sfit <- survfit(fit0, list(x=pi), censor=FALSE)
+> aeq(sfit$std.err^2, truth0$var)
+[1] TRUE
+> aeq(-log(sfit$surv), cumsum(truth0$haz))
+[1] TRUE
+>
+> truth <- byhand(fit$coef, .3)
+> aeq(truth$loglik, fit$loglik[2])
+[1] TRUE
+> aeq(1/truth$imat, fit$var)
+[1] TRUE
+> aeq(truth$mart, fit$resid)
+[1] TRUE
+> aeq(truth$scho, resid(fit, 'schoen'))
+[1] TRUE
+> aeq(truth$score, resid(fit, 'score'))
+[1] TRUE
+>
+> sfit <- survfit(fit, list(x=.3), censor=FALSE)
+> aeq(sfit$std.err^2, truth$var)
+[1] TRUE
+> aeq(-log(sfit$surv), (cumsum(truth$haz)* exp(fit$coef*.3)))
+[1] TRUE
+>
+>
+> fit0
+Call:
+coxph(formula = Surv(time, status) ~ x, data = testw1, weights = wt,
+ method = "breslow", iter = 0)
+
+
+ coef exp(coef) se(coef) z p
+x 0 1 0.586 0 1
+
+Likelihood ratio test=0 on 1 df, p=1 n= 9, number of events= 5
+> summary(fit)
+Call:
+coxph(formula = Surv(time, status) ~ x, data = testw1, weights = wt,
+ method = "breslow")
+
+ n= 9, number of events= 5
+
+ coef exp(coef) se(coef) z Pr(>|z|)
+x 0.8596 2.3621 0.7131 1.205 0.228
+
+ exp(coef) exp(-coef) lower .95 upper .95
+x 2.362 0.4233 0.5839 9.556
+
+Concordance= 0.638 (se = 0.159 )
+Rsquare= 0.171 (max possible= 0.999 )
+Likelihood ratio test= 1.69 on 1 df, p=0.1932
+Wald test = 1.45 on 1 df, p=0.2281
+Score (logrank) test = 1.52 on 1 df, p=0.217
+
+> resid(fit0, type='score')
+ 1 2 3 4 5 6
+ 1.24653740 0.03601108 0.10056700 0.10056700 -0.22180142 -0.21193300
+ 7 8 9
+ 0.46569858 -0.10082189 0.91014302
+> resid(fit0, type='scho')
+ 1 2 2 2 4
+ 1.3157895 0.3125000 0.3125000 -0.6875000 0.3333333
+>
+> resid(fit, type='score')
+ 1 2 3 4 5 6
+ 0.88681615 0.02497653 0.03608964 0.03608964 -0.54297652 -0.12528780
+ 7 8 9
+ 0.29564605 -0.09476911 0.58400064
+> resid(fit, type='scho')
+ 1 2 2 2 4
+ 1.0368337 0.1613774 0.1613774 -0.8386226 0.1746960
+> aeq(resid(fit, type='mart'), (resid(fitb, type='mart'))[indx])
+[1] TRUE
+> aeq(resid(fit, type='scor'), (resid(fitb, type='scor'))[indx])
+[1] TRUE
+> aeq(unique(resid(fit, type='scho')), unique(resid(fitb, type='scho')))
+[1] TRUE
+> rr1 <- resid(fit, type='mart')
+> rr2 <- resid(fit, type='mart', weighted=T)
+> aeq(rr2/rr1, testw1$wt)
+[1] TRUE
+>
+> rr1 <- resid(fit, type='score')
+> rr2 <- resid(fit, type='score', weighted=T)
+> aeq(rr2/rr1, testw1$wt)
+[1] TRUE
+>
+>
diff --git a/win32/deps/library/survival/tests/book6.R b/win32/deps/library/survival/tests/book6.R
new file mode 100644
index 0000000..8bcad17
--- /dev/null
+++ b/win32/deps/library/survival/tests/book6.R
@@ -0,0 +1,114 @@
+library(survival)
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+
+# Tests of the weighted Cox model
+# This is section 1.3 of my appendix -- no yet found in any of the
+# printings though, it awaits the next edition
+#
+# Efron approximation
+#
+aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+
+testw1 <- data.frame(time= c(1,1,2,2,2,2,3,4,5),
+ status= c(1,0,1,1,1,0,0,1,0),
+ x= c(2,0,1,1,0,1,0,1,0),
+ wt = c(1,2,3,4,3,2,1,2,1))
+xx <- testw1$wt
+
+# Efron estimate
+byhand <- function(beta, newx=0) {
+ r <- exp(beta)
+ a <- 7*r +3; b<- 4*r+2
+ loglik <- 11*beta - (log(r^2 + 11*r +7) + 10*log(11*r +5)/3 +
+ 10*log(a*2/3 +b)/3 + 10*log(a/3 +b)/3 +2*log(2*r+1))
+
+ hazard <- c(1/(r^2 + 11*r +7),
+ 10/(3*c(11*r +5, a*2/3 +b, a/3+b)), 2/(2*r+1))
+ temp <- c(hazard[1], hazard[1]+hazard[2] + hazard[3]*2/3 + hazard[4]/3,
+ cumsum(hazard)[4:5])
+ risk <- c(r^2, 1,r,r,1,r,1,r,1)
+ expected <- risk* temp[c(1,1,2,2,2,3,3,4,4)]
+
+ # The matrix of weights, one row per obs, one col per death
+ # deaths at 1,2,2,2, and 4
+ riskmat <- matrix(c(1,1,1,1,1,1,1,1,1,
+ 0,0,1,1,1,1,1,1,1,
+ 0,0,2/3,2/3,2/3,1,1,1,1,
+ 0,0,1/3,1/3,1/3,1,1,1,1,
+ 0,0,0,0,0,0,0,1,1), ncol=5)
+ wtmat <- diag(c(r^2, 2, 3*r, 4*r, 3, 2*r, 1, 2*r, 1)) %*% riskmat
+
+ x <- c(2,0,1,1,0,1,0,1,0)
+ xbar <- colSums(x*wtmat)/ colSums(wtmat)
+ imat <- (4*r^2 + 11*r)*hazard[1] - xbar[1]^2 +
+ 10* mean(xbar[2:4] - xbar[2:4]^2) + 2*(xbar[5] - xbar[5]^2)
+
+ status <- c(1,0,1,1,1,0,0,1,0)
+ wt <- c(1,2,3,4,3,2,1,2,1)
+ # Table of sums for score resids
+ hazmat <- riskmat %*% diag(c(1,10/3,10/3, 10/3,2)/colSums(wtmat))
+ dM <- -risk*hazmat #Expected part
+ dM[1,1] <- dM[1,1] +1 # deaths at time 1
+ for (i in 2:4) dM[3:5, i] <- dM[3:5,i] + 1/3
+ dM[8,5] <- dM[8,5] +1
+ mart <- rowSums(dM)
+ resid <-dM * outer(x, xbar ,'-')
+
+ # Increments to the variance of the hazard
+ var.g <- cumsum(hazard^2* c(1,3/10, 3/10, 3/10, 1/2))
+ var.d <- cumsum((xbar-newx)*hazard)
+
+ sxbar <- c(xbar[1], mean(xbar[2:4]), xbar[5]) #xbar for Schoen
+ list(loglik=loglik, imat=imat, hazard=hazard, xbar=xbar,
+ mart=status-expected, expected=expected,
+ score=rowSums(resid), schoen=c(2,1,1,0,1) - sxbar[c(1,2,2,2,3)],
+ varhaz=((var.g + var.d^2/imat)* exp(2*beta*newx))[c(1,4,5)])
+ }
+
+# Verify
+temp <- byhand(0,0)
+aeq(temp$xbar, c(13/19, 11/16, 26/38, 19/28, 2/3))
+aeq(temp$hazard, c(1/19, 5/24, 5/19, 5/14, 2/3))
+
+fit0 <- coxph(Surv(time, status) ~x, testw1, weights=wt, iter=0)
+fit <- coxph(Surv(time, status) ~x, testw1, weights=wt)
+
+truth0 <- byhand(0,pi)
+aeq(fit0$loglik[1], truth0$loglik)
+aeq(1/truth0$imat, fit0$var)
+aeq(truth0$mart, fit0$resid)
+aeq(truth0$scho, resid(fit0, 'schoen'))
+aeq(truth0$score, resid(fit0, 'score'))
+sfit <- survfit(fit0, list(x=pi), censor=FALSE)
+aeq(sfit$std.err^2, truth0$var)
+aeq(-log(sfit$surv), cumsum(truth0$hazard)[c(1,4,5)])
+
+truth <- byhand(fit$coef, .3)
+aeq(truth$loglik, fit$loglik[2])
+aeq(1/truth$imat, fit$var)
+aeq(truth$mart, fit$resid)
+aeq(truth$scho, resid(fit, 'schoen'))
+aeq(truth$score, resid(fit, 'score'))
+
+sfit <- survfit(fit, list(x=.3), censor=FALSE)
+aeq(sfit$std.err^2, truth$var)
+aeq(-log(sfit$surv), (cumsum(truth$hazard)* exp(fit$coef*.3))[c(1,4,5)])
+
+
+fit0
+summary(fit)
+resid(fit0, type='score')
+resid(fit0, type='scho')
+
+resid(fit, type='score')
+resid(fit, type='scho')
+
+rr1 <- resid(fit, type='mart')
+rr2 <- resid(fit, type='mart', weighted=T)
+aeq(rr2/rr1, testw1$wt)
+
+rr1 <- resid(fit, type='score')
+rr2 <- resid(fit, type='score', weighted=T)
+aeq(rr2/rr1, testw1$wt)
+
diff --git a/win32/deps/library/survival/tests/book6.Rout.save b/win32/deps/library/survival/tests/book6.Rout.save
new file mode 100644
index 0000000..66e543e
--- /dev/null
+++ b/win32/deps/library/survival/tests/book6.Rout.save
@@ -0,0 +1,190 @@
+
+R version 2.12.2 (2011-02-25)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+>
+> # Tests of the weighted Cox model
+> # This is section 1.3 of my appendix -- no yet found in any of the
+> # printings though, it awaits the next edition
+> #
+> # Efron approximation
+> #
+> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+>
+> testw1 <- data.frame(time= c(1,1,2,2,2,2,3,4,5),
++ status= c(1,0,1,1,1,0,0,1,0),
++ x= c(2,0,1,1,0,1,0,1,0),
++ wt = c(1,2,3,4,3,2,1,2,1))
+> xx <- testw1$wt
+>
+> # Efron estimate
+> byhand <- function(beta, newx=0) {
++ r <- exp(beta)
++ a <- 7*r +3; b<- 4*r+2
++ loglik <- 11*beta - (log(r^2 + 11*r +7) + 10*log(11*r +5)/3 +
++ 10*log(a*2/3 +b)/3 + 10*log(a/3 +b)/3 +2*log(2*r+1))
++
++ hazard <- c(1/(r^2 + 11*r +7),
++ 10/(3*c(11*r +5, a*2/3 +b, a/3+b)), 2/(2*r+1))
++ temp <- c(hazard[1], hazard[1]+hazard[2] + hazard[3]*2/3 + hazard[4]/3,
++ cumsum(hazard)[4:5])
++ risk <- c(r^2, 1,r,r,1,r,1,r,1)
++ expected <- risk* temp[c(1,1,2,2,2,3,3,4,4)]
++
++ # The matrix of weights, one row per obs, one col per death
++ # deaths at 1,2,2,2, and 4
++ riskmat <- matrix(c(1,1,1,1,1,1,1,1,1,
++ 0,0,1,1,1,1,1,1,1,
++ 0,0,2/3,2/3,2/3,1,1,1,1,
++ 0,0,1/3,1/3,1/3,1,1,1,1,
++ 0,0,0,0,0,0,0,1,1), ncol=5)
++ wtmat <- diag(c(r^2, 2, 3*r, 4*r, 3, 2*r, 1, 2*r, 1)) %*% riskmat
++
++ x <- c(2,0,1,1,0,1,0,1,0)
++ xbar <- colSums(x*wtmat)/ colSums(wtmat)
++ imat <- (4*r^2 + 11*r)*hazard[1] - xbar[1]^2 +
++ 10* mean(xbar[2:4] - xbar[2:4]^2) + 2*(xbar[5] - xbar[5]^2)
++
++ status <- c(1,0,1,1,1,0,0,1,0)
++ wt <- c(1,2,3,4,3,2,1,2,1)
++ # Table of sums for score resids
++ hazmat <- riskmat %*% diag(c(1,10/3,10/3, 10/3,2)/colSums(wtmat))
++ dM <- -risk*hazmat #Expected part
++ dM[1,1] <- dM[1,1] +1 # deaths at time 1
++ for (i in 2:4) dM[3:5, i] <- dM[3:5,i] + 1/3
++ dM[8,5] <- dM[8,5] +1
++ mart <- rowSums(dM)
++ resid <-dM * outer(x, xbar ,'-')
++
++ # Increments to the variance of the hazard
++ var.g <- cumsum(hazard^2* c(1,3/10, 3/10, 3/10, 1/2))
++ var.d <- cumsum((xbar-newx)*hazard)
++
++ sxbar <- c(xbar[1], mean(xbar[2:4]), xbar[5]) #xbar for Schoen
++ list(loglik=loglik, imat=imat, hazard=hazard, xbar=xbar,
++ mart=status-expected, expected=expected,
++ score=rowSums(resid), schoen=c(2,1,1,0,1) - sxbar[c(1,2,2,2,3)],
++ varhaz=((var.g + var.d^2/imat)* exp(2*beta*newx))[c(1,4,5)])
++ }
+>
+> # Verify
+> temp <- byhand(0,0)
+> aeq(temp$xbar, c(13/19, 11/16, 26/38, 19/28, 2/3))
+[1] TRUE
+> aeq(temp$hazard, c(1/19, 5/24, 5/19, 5/14, 2/3))
+[1] TRUE
+>
+> fit0 <- coxph(Surv(time, status) ~x, testw1, weights=wt, iter=0)
+> fit <- coxph(Surv(time, status) ~x, testw1, weights=wt)
+>
+> truth0 <- byhand(0,pi)
+> aeq(fit0$loglik[1], truth0$loglik)
+[1] TRUE
+> aeq(1/truth0$imat, fit0$var)
+[1] TRUE
+> aeq(truth0$mart, fit0$resid)
+[1] TRUE
+> aeq(truth0$scho, resid(fit0, 'schoen'))
+[1] TRUE
+> aeq(truth0$score, resid(fit0, 'score'))
+[1] TRUE
+> sfit <- survfit(fit0, list(x=pi), censor=FALSE)
+> aeq(sfit$std.err^2, truth0$var)
+[1] TRUE
+> aeq(-log(sfit$surv), cumsum(truth0$hazard)[c(1,4,5)])
+[1] TRUE
+>
+> truth <- byhand(fit$coef, .3)
+> aeq(truth$loglik, fit$loglik[2])
+[1] TRUE
+> aeq(1/truth$imat, fit$var)
+[1] TRUE
+> aeq(truth$mart, fit$resid)
+[1] TRUE
+> aeq(truth$scho, resid(fit, 'schoen'))
+[1] TRUE
+> aeq(truth$score, resid(fit, 'score'))
+[1] TRUE
+>
+> sfit <- survfit(fit, list(x=.3), censor=FALSE)
+> aeq(sfit$std.err^2, truth$var)
+[1] TRUE
+> aeq(-log(sfit$surv), (cumsum(truth$hazard)* exp(fit$coef*.3))[c(1,4,5)])
+[1] TRUE
+>
+>
+> fit0
+Call:
+coxph(formula = Surv(time, status) ~ x, data = testw1, weights = wt,
+ iter = 0)
+
+
+ coef exp(coef) se(coef) z p
+x 0 1 0.584 0 1
+
+Likelihood ratio test=0 on 1 df, p=1 n= 9, number of events= 5
+> summary(fit)
+Call:
+coxph(formula = Surv(time, status) ~ x, data = testw1, weights = wt)
+
+ n= 9, number of events= 5
+
+ coef exp(coef) se(coef) z Pr(>|z|)
+x 0.8726 2.3931 0.7126 1.225 0.221
+
+ exp(coef) exp(-coef) lower .95 upper .95
+x 2.393 0.4179 0.5921 9.672
+
+Concordance= 0.638 (se = 0.159 )
+Rsquare= 0.177 (max possible= 0.999 )
+Likelihood ratio test= 1.75 on 1 df, p=0.1858
+Wald test = 1.5 on 1 df, p=0.2207
+Score (logrank) test = 1.58 on 1 df, p=0.2094
+
+> resid(fit0, type='score')
+ 1 2 3 4 5 6
+ 1.24653740 0.03601108 0.14118105 0.14118105 -0.30336782 -0.27962308
+ 7 8 9
+ 0.60164259 -0.16851197 1.04608703
+> resid(fit0, type='scho')
+ 1 2 2 2 4
+ 1.3157895 0.3165727 0.3165727 -0.6834273 0.3333333
+>
+> resid(fit, type='score')
+ 1 2 3 4 5 6
+ 0.88116056 0.02477248 0.06057806 0.06057806 -0.59724033 -0.16737066
+ 7 8 9
+ 0.38040295 -0.13750290 0.66631324
+> resid(fit, type='scho')
+ 1 2 2 2 4
+ 1.0325955 0.1621759 0.1621759 -0.8378241 0.1728229
+>
+> rr1 <- resid(fit, type='mart')
+> rr2 <- resid(fit, type='mart', weighted=T)
+> aeq(rr2/rr1, testw1$wt)
+[1] TRUE
+>
+> rr1 <- resid(fit, type='score')
+> rr2 <- resid(fit, type='score', weighted=T)
+> aeq(rr2/rr1, testw1$wt)
+[1] TRUE
+>
+>
diff --git a/win32/deps/library/survival/tests/book7.R b/win32/deps/library/survival/tests/book7.R
new file mode 100644
index 0000000..8d0431b
--- /dev/null
+++ b/win32/deps/library/survival/tests/book7.R
@@ -0,0 +1,55 @@
+library(survival)
+options(na.action=na.exclude)
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+
+#
+# Tests from the appendix of Therneau and Grambsch
+# Data set 1 + exact method
+
+test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
+ status=c(1,NA,1,0,1,1,0),
+ x= c(0, 2,1,1,1,0,0))
+
+byhand7 <- function(beta) {
+ r <- exp(beta)
+ loglik <- 2*(beta - log(3*r + 3))
+ u <- 2/(r+1)
+ imat <- 2*r/(r+1)^2
+ haz <- c(1/(3*r+3), 2/(r+3), 0, 1 )
+
+ ties <- c(1,1,2,2,3,4)
+ wt <- c(r,r,r,1,1,1)
+ mart <- c(1,0,1,1,0,1) - wt* (cumsum(haz))[ties] #martingale residual
+
+ list(loglik=loglik, u=u, imat=imat, mart=mart)
+}
+aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+
+fit0 <-coxph(Surv(time, status) ~x, test1, iter=0, method='exact')
+truth0 <- byhand7(0)
+aeq(truth0$loglik, fit0$loglik[1])
+aeq(1/truth0$imat, fit0$var)
+aeq(truth0$mart, fit0$resid[c(2:6,1)])
+
+fit1 <- coxph(Surv(time, status) ~x, test1, iter=1, method='exact')
+aeq(fit1$coef, truth0$u*fit0$var)
+truth1 <- byhand7(fit1$coef)
+aeq(fit1$loglik[2], truth1$loglik)
+aeq(1/truth1$imat, fit1$var)
+aeq(truth1$mart, resid(fit1)[c(3:7,1)])
+
+fit2 <- coxph(Surv(time, status) ~x, test1, method='exact')
+aeq(resid(fit2)[-2], c(0, 2/3, -1/3, -4/3, 1, 0)) #values from the book
+
+
+#
+# Now a multivariate case: start/stop data uses a different C routine
+#
+zz <- rep(0, nrow(lung))
+fit1 <- coxph(Surv(time, status) ~ age + ph.ecog + sex, lung, method="exact")
+fit2 <- coxph(Surv(zz, time, status) ~ age + ph.ecog + sex, lung,
+ method="exact")
+aeq(fit1$loglik, fit2$loglik)
+aeq(fit1$var, fit2$var)
+aeq(fit1$score, fit2$score)
+aeq(fit1$resid, fit2$resid)
diff --git a/win32/deps/library/survival/tests/book7.Rout.save b/win32/deps/library/survival/tests/book7.Rout.save
new file mode 100644
index 0000000..2fcaf56
--- /dev/null
+++ b/win32/deps/library/survival/tests/book7.Rout.save
@@ -0,0 +1,90 @@
+
+R version 2.14.0 (2011-10-31)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: i686-pc-linux-gnu (32-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+> options(na.action=na.exclude)
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+>
+> #
+> # Tests from the appendix of Therneau and Grambsch
+> # Data set 1 + exact method
+>
+> test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
++ status=c(1,NA,1,0,1,1,0),
++ x= c(0, 2,1,1,1,0,0))
+>
+> byhand7 <- function(beta) {
++ r <- exp(beta)
++ loglik <- 2*(beta - log(3*r + 3))
++ u <- 2/(r+1)
++ imat <- 2*r/(r+1)^2
++ haz <- c(1/(3*r+3), 2/(r+3), 0, 1 )
++
++ ties <- c(1,1,2,2,3,4)
++ wt <- c(r,r,r,1,1,1)
++ mart <- c(1,0,1,1,0,1) - wt* (cumsum(haz))[ties] #martingale residual
++
++ list(loglik=loglik, u=u, imat=imat, mart=mart)
++ }
+> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+>
+> fit0 <-coxph(Surv(time, status) ~x, test1, iter=0, method='exact')
+> truth0 <- byhand7(0)
+> aeq(truth0$loglik, fit0$loglik[1])
+[1] TRUE
+> aeq(1/truth0$imat, fit0$var)
+[1] TRUE
+> aeq(truth0$mart, fit0$resid[c(2:6,1)])
+[1] TRUE
+>
+> fit1 <- coxph(Surv(time, status) ~x, test1, iter=1, method='exact')
+> aeq(fit1$coef, truth0$u*fit0$var)
+[1] TRUE
+> truth1 <- byhand7(fit1$coef)
+> aeq(fit1$loglik[2], truth1$loglik)
+[1] TRUE
+> aeq(1/truth1$imat, fit1$var)
+[1] TRUE
+> aeq(truth1$mart, resid(fit1)[c(3:7,1)])
+[1] TRUE
+>
+> fit2 <- coxph(Surv(time, status) ~x, test1, method='exact')
+Warning message:
+In fitter(X, Y, strats, offset, init, control, weights = weights, :
+ Loglik converged before variable 1 ; beta may be infinite.
+> aeq(resid(fit2)[-2], c(0, 2/3, -1/3, -4/3, 1, 0)) #values from the book
+[1] TRUE
+>
+>
+> #
+> # Now a multivariate case: start/stop data uses a different C routine
+> #
+> zz <- rep(0, nrow(lung))
+> fit1 <- coxph(Surv(time, status) ~ age + ph.ecog + sex, lung, method="exact")
+> fit2 <- coxph(Surv(zz, time, status) ~ age + ph.ecog + sex, lung,
++ method="exact")
+> aeq(fit1$loglik, fit2$loglik)
+[1] TRUE
+> aeq(fit1$var, fit2$var)
+[1] TRUE
+> aeq(fit1$score, fit2$score)
+[1] TRUE
+> aeq(fit1$resid, fit2$resid)
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/cancer.R b/win32/deps/library/survival/tests/cancer.R
new file mode 100644
index 0000000..3a4bcf9
--- /dev/null
+++ b/win32/deps/library/survival/tests/cancer.R
@@ -0,0 +1,34 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Test out all of the routines on a more complex data set
+#
+temp <- survfit(Surv(time, status) ~ ph.ecog, lung)
+summary(temp, times=c(30*1:11, 365*1:3))
+print(temp[2:3])
+
+temp <- survfit(Surv(time, status)~1, lung, type='fleming',
+ conf.int=.9, conf.type='log-log', error='tsiatis')
+summary(temp, times=30 *1:5)
+
+temp <- survdiff(Surv(time, status) ~ inst, lung, rho=.5)
+print(temp, digits=6)
+
+temp <- coxph(Surv(time, status) ~ ph.ecog + ph.karno + pat.karno + wt.loss
+ + sex + age + meal.cal + strata(inst), lung)
+summary(temp)
+cox.zph(temp)
+cox.zph(temp, transform='identity')
+
+coxph(Surv(rep(0,length(time)), time, status) ~ ph.ecog + ph.karno + pat.karno
+ + wt.loss + sex + age + meal.cal + strata(inst), lung)
+
+#
+# Tests of using "."
+#
+fit1 <- coxph(Surv(time, status) ~ . - meal.cal - wt.loss - inst, lung)
+fit2 <- update(fit1, .~. - ph.karno)
+fit3 <- coxph(Surv(time, status) ~ age + sex + ph.ecog + pat.karno, lung)
+all.equal(fit2, fit3)
diff --git a/win32/deps/library/survival/tests/cancer.Rout.save b/win32/deps/library/survival/tests/cancer.Rout.save
new file mode 100644
index 0000000..de03a3a
--- /dev/null
+++ b/win32/deps/library/survival/tests/cancer.Rout.save
@@ -0,0 +1,224 @@
+
+R version 2.15.0 (2012-03-30)
+Copyright (C) 2012 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Test out all of the routines on a more complex data set
+> #
+> temp <- survfit(Surv(time, status) ~ ph.ecog, lung)
+> summary(temp, times=c(30*1:11, 365*1:3))
+Call: survfit(formula = Surv(time, status) ~ ph.ecog, data = lung)
+
+1 observation deleted due to missingness
+ ph.ecog=0
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 30 60 3 0.952 0.0268 0.9012 1.000
+ 60 58 2 0.921 0.0341 0.8562 0.990
+ 90 56 2 0.889 0.0396 0.8146 0.970
+ 120 56 0 0.889 0.0396 0.8146 0.970
+ 150 55 1 0.873 0.0419 0.7946 0.959
+ 180 52 2 0.841 0.0461 0.7553 0.936
+ 210 48 2 0.808 0.0498 0.7164 0.912
+ 240 45 0 0.808 0.0498 0.7164 0.912
+ 270 38 2 0.770 0.0543 0.6709 0.884
+ 300 33 2 0.727 0.0591 0.6203 0.853
+ 330 29 2 0.681 0.0637 0.5670 0.818
+ 365 22 6 0.535 0.0728 0.4100 0.699
+ 730 5 11 0.193 0.0707 0.0943 0.396
+
+ ph.ecog=1
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 30 111 2 0.982 0.0124 0.9583 1.000
+ 60 110 3 0.956 0.0193 0.9186 0.994
+ 90 104 4 0.920 0.0255 0.8718 0.972
+ 120 99 5 0.876 0.0310 0.8174 0.939
+ 150 93 6 0.823 0.0359 0.7556 0.896
+ 180 82 8 0.751 0.0407 0.6756 0.836
+ 210 68 9 0.666 0.0450 0.5831 0.760
+ 240 57 6 0.604 0.0474 0.5176 0.704
+ 270 53 4 0.561 0.0487 0.4729 0.665
+ 300 46 3 0.527 0.0495 0.4384 0.633
+ 330 40 4 0.480 0.0504 0.3903 0.589
+ 365 34 4 0.431 0.0509 0.3417 0.543
+ 730 7 21 0.114 0.0388 0.0582 0.222
+
+ ph.ecog=2
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 30 46 5 0.9000 0.0424 0.82057 0.987
+ 60 43 2 0.8600 0.0491 0.76900 0.962
+ 90 40 3 0.8000 0.0566 0.69647 0.919
+ 120 34 4 0.7174 0.0641 0.60216 0.855
+ 150 31 3 0.6541 0.0680 0.53342 0.802
+ 180 26 6 0.5275 0.0719 0.40385 0.689
+ 210 21 4 0.4431 0.0717 0.32266 0.608
+ 240 17 3 0.3766 0.0705 0.26100 0.543
+ 270 17 0 0.3766 0.0705 0.26100 0.543
+ 300 13 3 0.3102 0.0677 0.20223 0.476
+ 330 11 2 0.2624 0.0651 0.16135 0.427
+ 365 9 2 0.2147 0.0614 0.12258 0.376
+ 730 1 6 0.0371 0.0345 0.00601 0.229
+
+ ph.ecog=3
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 30 1 0 1 0 1 1
+ 60 1 0 1 0 1 1
+ 90 1 0 1 0 1 1
+
+> print(temp[2:3])
+Call: survfit(formula = Surv(time, status) ~ ph.ecog, data = lung)
+
+ 1 observation deleted due to missingness
+ records n.max n.start events median 0.95LCL 0.95UCL
+ph.ecog=1 113 113 113 82 306 268 429
+ph.ecog=2 50 50 50 44 199 156 288
+>
+> temp <- survfit(Surv(time, status)~1, lung, type='fleming',
++ conf.int=.9, conf.type='log-log', error='tsiatis')
+> summary(temp, times=30 *1:5)
+Call: survfit(formula = Surv(time, status) ~ 1, data = lung, type = "fleming",
+ conf.int = 0.9, conf.type = "log-log", error = "tsiatis")
+
+ time n.risk n.event survival std.err lower 90% CI upper 90% CI
+ 30 219 10 0.956 0.0135 0.928 0.974
+ 60 213 7 0.926 0.0173 0.891 0.950
+ 90 201 10 0.882 0.0213 0.842 0.913
+ 120 189 10 0.838 0.0244 0.793 0.874
+ 150 179 10 0.794 0.0268 0.745 0.834
+>
+> temp <- survdiff(Surv(time, status) ~ inst, lung, rho=.5)
+> print(temp, digits=6)
+Call:
+survdiff(formula = Surv(time, status) ~ inst, data = lung, rho = 0.5)
+
+n=227, 1 observation deleted due to missingness.
+
+ N Observed Expected (O-E)^2/E (O-E)^2/V
+inst=1 36 21.190058 17.455181 0.799149708 1.171232977
+inst=2 5 3.173330 1.964395 0.744007932 0.860140808
+inst=3 19 10.663476 11.958755 0.140294489 0.200472362
+inst=4 4 2.245347 3.559344 0.485085848 0.677874608
+inst=5 9 5.010883 4.500982 0.057765161 0.077128402
+inst=6 14 8.862602 7.078516 0.449665221 0.582743947
+inst=7 8 4.445647 4.416133 0.000197254 0.000253632
+inst=10 4 2.901923 2.223283 0.207150016 0.249077097
+inst=11 18 7.807867 9.525163 0.309611863 0.422142221
+inst=12 23 14.009656 12.216768 0.263117640 0.365712493
+inst=13 20 9.140983 11.863298 0.624699853 0.874238212
+inst=15 6 3.170744 3.558447 0.042241456 0.057938955
+inst=16 16 8.870360 9.992612 0.126038005 0.175170113
+inst=21 13 9.263733 4.460746 5.171484268 6.149354145
+inst=22 17 8.278566 11.971473 1.139171459 1.645863937
+inst=26 6 1.627074 3.542694 1.035821659 1.286365543
+inst=32 7 1.792468 2.679904 0.293869782 0.343966668
+inst=33 2 0.929177 0.416202 0.632249272 0.676682390
+
+ Chisq= 15.1 on 17 degrees of freedom, p= 0.590384
+>
+> temp <- coxph(Surv(time, status) ~ ph.ecog + ph.karno + pat.karno + wt.loss
++ + sex + age + meal.cal + strata(inst), lung)
+> summary(temp)
+Call:
+coxph(formula = Surv(time, status) ~ ph.ecog + ph.karno + pat.karno +
+ wt.loss + sex + age + meal.cal + strata(inst), data = lung)
+
+ n= 167, number of events= 120
+ (61 observations deleted due to missingness)
+
+ coef exp(coef) se(coef) z Pr(>|z|)
+ph.ecog 0.7299987 2.0750779 0.2689397 2.714 0.00664 **
+ph.karno 0.0130512 1.0131368 0.0137362 0.950 0.34204
+pat.karno -0.0140955 0.9860034 0.0093680 -1.505 0.13242
+wt.loss -0.0148821 0.9852281 0.0084811 -1.755 0.07931 .
+sex -0.6612534 0.5162039 0.2339979 -2.826 0.00471 **
+age 0.0050920 1.0051050 0.0137288 0.371 0.71071
+meal.cal -0.0002398 0.9997602 0.0003019 -0.794 0.42701
+---
+Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
+
+ exp(coef) exp(-coef) lower .95 upper .95
+ph.ecog 2.0751 0.4819 1.2249 3.5153
+ph.karno 1.0131 0.9870 0.9862 1.0408
+pat.karno 0.9860 1.0142 0.9681 1.0043
+wt.loss 0.9852 1.0150 0.9690 1.0017
+sex 0.5162 1.9372 0.3263 0.8166
+age 1.0051 0.9949 0.9784 1.0325
+meal.cal 0.9998 1.0002 0.9992 1.0004
+
+Concordance= 0.696 (se = 0.115 )
+Rsquare= 0.167 (max possible= 0.912 )
+Likelihood ratio test= 30.6 on 7 df, p=7.377e-05
+Wald test = 28.15 on 7 df, p=0.0002066
+Score (logrank) test = 30.72 on 7 df, p=7e-05
+
+> cox.zph(temp)
+ rho chisq p
+ph.ecog 0.0276 0.1078 0.7427
+ph.karno 0.1331 2.0018 0.1571
+pat.karno 0.0250 0.0841 0.7718
+wt.loss -0.0386 0.2122 0.6451
+sex 0.0399 0.1800 0.6713
+age 0.0639 0.5600 0.4543
+meal.cal 0.1611 3.6945 0.0546
+GLOBAL NA 9.0115 0.2518
+> cox.zph(temp, transform='identity')
+ rho chisq p
+ph.ecog 0.0221 0.0688 0.793
+ph.karno 0.1217 1.6743 0.196
+pat.karno 0.0302 0.1227 0.726
+wt.loss -0.0516 0.3790 0.538
+sex 0.0449 0.2280 0.633
+age 0.0719 0.7085 0.400
+meal.cal 0.1808 4.6537 0.031
+GLOBAL NA 10.0537 0.186
+>
+> coxph(Surv(rep(0,length(time)), time, status) ~ ph.ecog + ph.karno + pat.karno
++ + wt.loss + sex + age + meal.cal + strata(inst), lung)
+Call:
+coxph(formula = Surv(rep(0, length(time)), time, status) ~ ph.ecog +
+ ph.karno + pat.karno + wt.loss + sex + age + meal.cal + strata(inst),
+ data = lung)
+
+
+ coef exp(coef) se(coef) z p
+ph.ecog 0.73000 2.075 0.268940 2.714 0.0066
+ph.karno 0.01305 1.013 0.013736 0.950 0.3400
+pat.karno -0.01410 0.986 0.009368 -1.505 0.1300
+wt.loss -0.01488 0.985 0.008481 -1.755 0.0790
+sex -0.66125 0.516 0.233998 -2.826 0.0047
+age 0.00509 1.005 0.013729 0.371 0.7100
+meal.cal -0.00024 1.000 0.000302 -0.794 0.4300
+
+Likelihood ratio test=30.6 on 7 df, p=7.38e-05 n= 167, number of events= 120
+ (61 observations deleted due to missingness)
+>
+> #
+> # Tests of using "."
+> #
+> fit1 <- coxph(Surv(time, status) ~ . - meal.cal - wt.loss - inst, lung)
+> fit2 <- update(fit1, .~. - ph.karno)
+> fit3 <- coxph(Surv(time, status) ~ age + sex + ph.ecog + pat.karno, lung)
+> all.equal(fit2, fit3)
+[1] TRUE
+>
+> proc.time()
+ user system elapsed
+ 0.412 0.076 0.526
diff --git a/win32/deps/library/survival/tests/clogit.R b/win32/deps/library/survival/tests/clogit.R
new file mode 100644
index 0000000..3a09b47
--- /dev/null
+++ b/win32/deps/library/survival/tests/clogit.R
@@ -0,0 +1,28 @@
+library(survival)
+#
+# Test of the clogit function, and indirectly of the exact option
+#
+# Data set logan has the occupation of fathers, we create a
+# multinomial response
+#
+nresp <- length(levels(logan$occupation))
+n <- nrow(logan)
+indx <- rep(1:n, nresp)
+logan2 <- data.frame(logan[indx,],
+ id = indx,
+ occ2 = factor(rep(levels(logan$occupation), each=n)))
+logan2$y <- (logan2$occupation == logan2$occ2)
+
+#We expect two NA coefficients, so ignore the warning
+fit1 <- clogit(y ~ occ2 + occ2:education + occ2:race + strata(id), logan2)
+
+#since there is only one death per group, all methods are equal
+dummy <- rep(1, nrow(logan2))
+fit2 <- coxph(Surv(dummy, y) ~ occ2 + occ2:education + occ2:race + strata(id),
+ logan2, method='breslow')
+
+all.equal(fit1$coef, fit2$coef)
+all.equal(fit1$loglik, fit2$loglik)
+all.equal(fit1$var, fit2$var)
+all.equal(fit1$resid, fit2$resid)
+
diff --git a/win32/deps/library/survival/tests/clogit.Rout.save b/win32/deps/library/survival/tests/clogit.Rout.save
new file mode 100644
index 0000000..e6a1f47
--- /dev/null
+++ b/win32/deps/library/survival/tests/clogit.Rout.save
@@ -0,0 +1,58 @@
+
+R version 2.14.0 (2011-10-31)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: i686-pc-linux-gnu (32-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+> #
+> # Test of the clogit function, and indirectly of the exact option
+> #
+> # Data set logan has the occupation of fathers, we create a
+> # multinomial response
+> #
+> nresp <- length(levels(logan$occupation))
+> n <- nrow(logan)
+> indx <- rep(1:n, nresp)
+> logan2 <- data.frame(logan[indx,],
++ id = indx,
++ occ2 = factor(rep(levels(logan$occupation), each=n)))
+> logan2$y <- (logan2$occupation == logan2$occ2)
+>
+> #We expect two NA coefficients, so ignore the warning
+> fit1 <- clogit(y ~ occ2 + occ2:education + occ2:race + strata(id), logan2)
+Warning message:
+In coxph(formula = Surv(rep(1, 4190L), y) ~ occ2 + occ2:education + :
+ X matrix deemed to be singular; variable 9 14
+>
+> #since there is only one death per group, all methods are equal
+> dummy <- rep(1, nrow(logan2))
+> fit2 <- coxph(Surv(dummy, y) ~ occ2 + occ2:education + occ2:race + strata(id),
++ logan2, method='breslow')
+Warning message:
+In coxph(Surv(dummy, y) ~ occ2 + occ2:education + occ2:race + strata(id), :
+ X matrix deemed to be singular; variable 9 14
+>
+> all.equal(fit1$coef, fit2$coef)
+[1] TRUE
+> all.equal(fit1$loglik, fit2$loglik)
+[1] TRUE
+> all.equal(fit1$var, fit2$var)
+[1] TRUE
+> all.equal(fit1$resid, fit2$resid)
+[1] TRUE
+>
+>
diff --git a/win32/deps/library/survival/tests/concordance.R b/win32/deps/library/survival/tests/concordance.R
new file mode 100644
index 0000000..a3a8c30
--- /dev/null
+++ b/win32/deps/library/survival/tests/concordance.R
@@ -0,0 +1,109 @@
+library(survival)
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+
+#
+# Simple tests of concordance. These numbers were derived in multiple
+# codes.
+#
+aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+
+grank <- function(x, time, grp, wt)
+ unlist(tapply(x, grp, rank))
+grank2 <- function(x, time, grp, wt) { #for case weights
+ if (length(wt)==0) wt <- rep(1, length(x))
+ z <- double(length(x))
+ for (i in unique(grp)) {
+ indx <- which(grp==i)
+ temp <- tapply(wt[indx], x[indx], sum)
+ temp <- temp/2 + c(0, cumsum(temp)[-length(temp)])
+ z[indx] <- temp[match(x[indx], names(temp))]
+ }
+ z
+}
+
+
+tdata <- aml[aml$x=='Maintained',]
+tdata$y <- c(1,6,2,7,3,7,3,8,4,4,5)
+tdata$wt <- c(1,2,3,2,1,2,3,4,3,2,1)
+fit <- survConcordance(Surv(time, status) ~y, tdata)
+aeq(fit$stats[1:4], c(14,24,2,0))
+cfit <- coxph(Surv(time, status) ~ tt(y), tdata, tt=grank, method='breslow',
+ iter=0, x=T)
+cdt <- coxph.detail(cfit)
+aeq(4*sum(cdt$imat),fit$stats[5]^2)
+aeq(2*sum(cdt$score), diff(fit$stats[2:1]))
+
+
+# Lots of ties
+tempx <- Surv(c(1,2,2,2,3,4,4,4,5,2), c(1,0,1,0,1,0,1,1,0,1))
+tempy <- c(5,5,4,4,3,3,7,6,5,4)
+fit2 <- survConcordance(tempx ~ tempy)
+aeq(fit2$stats[1:4], c(13,13,5,2))
+cfit2 <- coxph(tempx ~ tt(tempy), tt=grank, method='breslow', iter=0)
+aeq(4/cfit2$var, fit2$stats[5]^2)
+
+# Bigger data
+fit3 <- survConcordance(Surv(time, status) ~ age, lung)
+aeq(fit3$stats[1:4], c(10717, 8706, 591, 28))
+cfit3 <- coxph(Surv(time, status) ~ tt(age), lung,
+ iter=0, method='breslow', tt=grank, x=T)
+cdt <- coxph.detail(cfit3)
+aeq(4*sum(cdt$imat),fit3$stats[5]^2)
+aeq(2*sum(cdt$score), diff(fit3$stats[2:1]))
+
+
+# More ties
+fit4 <- survConcordance(Surv(time, status) ~ ph.ecog, lung)
+aeq(fit4$stats[1:4], c(8392, 4258, 7137, 28))
+cfit4 <- coxph(Surv(time, status) ~ tt(ph.ecog), lung,
+ iter=0, method='breslow', tt=grank)
+aeq(4/cfit4$var, fit4$stats[5]^2)
+
+# Case weights
+fit5 <- survConcordance(Surv(time, status) ~ y, tdata, weight=wt)
+fit6 <- survConcordance(Surv(time, status) ~y, tdata[rep(1:11,tdata$wt),])
+aeq(fit5$stats[1:4], c(70, 91, 7, 0)) # checked by hand
+aeq(fit5$stats[1:3], fit6$stats[1:3]) #spurious "tied on time" value, ignore
+aeq(fit5$std, fit6$std)
+cfit5 <- coxph(Surv(time, status) ~ tt(y), tdata, weight=wt,
+ iter=0, method='breslow', tt=grank2)
+cfit6 <- coxph(Surv(time, status) ~ tt(y), tdata[rep(1:11,tdata$wt),],
+ iter=0, method='breslow', tt=grank)
+aeq(4/cfit6$var, fit6$stats[5]^2)
+aeq(cfit5$var, cfit6$var)
+
+# Start, stop simplest cases
+fit7 <- survConcordance(Surv(rep(0,11), time, status) ~ y, tdata)
+aeq(fit7$stats, fit$stats)
+aeq(fit7$std.err, fit$std.err)
+fit7 <- survConcordance(Surv(rep(0,11), time, status) ~ y, tdata, weight=wt)
+aeq(fit5$stats, fit7$stats)
+
+# Multiple intervals for some, but same risk sets as tdata
+tdata2 <- data.frame(time1=c(0,3, 5, 6,7, 0, 4,17, 7, 0,16, 2, 0,
+ 0,9, 5),
+ time2=c(3,9, 13, 7,13, 18, 17,23, 28, 16,31, 34, 45,
+ 9,48, 60),
+ status=c(0,1, 1, 0,0, 1, 0,1, 0, 0,1, 1, 0, 0,1, 0),
+ y = c(1,1, 6, 2,2, 7, 3,3, 7, 3,3, 8, 4, 4,4, 5),
+ wt= c(1,1, 2, 3,3, 2, 1,1, 2, 3,3, 4, 3, 2,2, 1))
+fit8 <- survConcordance(Surv(time1, time2, status) ~y, tdata2, weight=wt)
+aeq(fit5$stats, fit8$stats)
+aeq(fit5$std.err, fit8$std.err)
+cfit8 <- coxph(Surv(time1, time2, status) ~ tt(y), tdata2, weight=wt,
+ iter=0, method='breslow', tt=grank2)
+aeq(4/cfit8$var, fit8$stats[5]^2)
+aeq(fit8$stats[5]/(2*sum(fit8$stats[1:3])), fit8$std.err)
+
+# Stratified
+tdata3 <- data.frame(time1=c(tdata2$time1, rep(0, nrow(lung))),
+ time2=c(tdata2$time2, lung$time),
+ status = c(tdata2$status, lung$status -1),
+ x = c(tdata2$y, lung$ph.ecog),
+ wt= c(tdata2$wt, rep(1, nrow(lung))),
+ grp=rep(1:2, c(nrow(tdata2), nrow(lung))))
+fit9 <- survConcordance(Surv(time1, time2, status) ~x + strata(grp),
+ data=tdata3, weight=wt)
+aeq(fit9$stats[1,], fit5$stats)
+aeq(fit9$stats[2,], fit4$stats)
diff --git a/win32/deps/library/survival/tests/concordance.Rout.save b/win32/deps/library/survival/tests/concordance.Rout.save
new file mode 100644
index 0000000..138ea39
--- /dev/null
+++ b/win32/deps/library/survival/tests/concordance.Rout.save
@@ -0,0 +1,153 @@
+
+R version 2.12.2 (2011-02-25)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+>
+> #
+> # Simple tests of concordance. These numbers were derived in multiple
+> # codes.
+> #
+> aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+>
+> grank <- function(x, time, grp, wt)
++ unlist(tapply(x, grp, rank))
+> grank2 <- function(x, time, grp, wt) { #for case weights
++ if (length(wt)==0) wt <- rep(1, length(x))
++ z <- double(length(x))
++ for (i in unique(grp)) {
++ indx <- which(grp==i)
++ temp <- tapply(wt[indx], x[indx], sum)
++ temp <- temp/2 + c(0, cumsum(temp)[-length(temp)])
++ z[indx] <- temp[match(x[indx], names(temp))]
++ }
++ z
++ }
+>
+>
+> tdata <- aml[aml$x=='Maintained',]
+> tdata$y <- c(1,6,2,7,3,7,3,8,4,4,5)
+> tdata$wt <- c(1,2,3,2,1,2,3,4,3,2,1)
+> fit <- survConcordance(Surv(time, status) ~y, tdata)
+> aeq(fit$stats[1:4], c(14,24,2,0))
+[1] TRUE
+> cfit <- coxph(Surv(time, status) ~ tt(y), tdata, tt=grank, method='breslow',
++ iter=0, x=T)
+> cdt <- coxph.detail(cfit)
+> aeq(4*sum(cdt$imat),fit$stats[5]^2)
+[1] TRUE
+> aeq(2*sum(cdt$score), diff(fit$stats[2:1]))
+[1] TRUE
+>
+>
+> # Lots of ties
+> tempx <- Surv(c(1,2,2,2,3,4,4,4,5,2), c(1,0,1,0,1,0,1,1,0,1))
+> tempy <- c(5,5,4,4,3,3,7,6,5,4)
+> fit2 <- survConcordance(tempx ~ tempy)
+> aeq(fit2$stats[1:4], c(13,13,5,2))
+[1] TRUE
+> cfit2 <- coxph(tempx ~ tt(tempy), tt=grank, method='breslow', iter=0)
+> aeq(4/cfit2$var, fit2$stats[5]^2)
+[1] TRUE
+>
+> # Bigger data
+> fit3 <- survConcordance(Surv(time, status) ~ age, lung)
+> aeq(fit3$stats[1:4], c(10717, 8706, 591, 28))
+[1] TRUE
+> cfit3 <- coxph(Surv(time, status) ~ tt(age), lung,
++ iter=0, method='breslow', tt=grank, x=T)
+> cdt <- coxph.detail(cfit3)
+> aeq(4*sum(cdt$imat),fit3$stats[5]^2)
+[1] TRUE
+> aeq(2*sum(cdt$score), diff(fit3$stats[2:1]))
+[1] TRUE
+>
+>
+> # More ties
+> fit4 <- survConcordance(Surv(time, status) ~ ph.ecog, lung)
+> aeq(fit4$stats[1:4], c(8392, 4258, 7137, 28))
+[1] TRUE
+> cfit4 <- coxph(Surv(time, status) ~ tt(ph.ecog), lung,
++ iter=0, method='breslow', tt=grank)
+> aeq(4/cfit4$var, fit4$stats[5]^2)
+[1] TRUE
+>
+> # Case weights
+> fit5 <- survConcordance(Surv(time, status) ~ y, tdata, weight=wt)
+> fit6 <- survConcordance(Surv(time, status) ~y, tdata[rep(1:11,tdata$wt),])
+> aeq(fit5$stats[1:4], c(70, 91, 7, 0)) # checked by hand
+[1] TRUE
+> aeq(fit5$stats[1:3], fit6$stats[1:3]) #spurious "tied on time" value, ignore
+[1] TRUE
+> aeq(fit5$std, fit6$std)
+[1] TRUE
+> cfit5 <- coxph(Surv(time, status) ~ tt(y), tdata, weight=wt,
++ iter=0, method='breslow', tt=grank2)
+> cfit6 <- coxph(Surv(time, status) ~ tt(y), tdata[rep(1:11,tdata$wt),],
++ iter=0, method='breslow', tt=grank)
+> aeq(4/cfit6$var, fit6$stats[5]^2)
+[1] TRUE
+> aeq(cfit5$var, cfit6$var)
+[1] TRUE
+>
+> # Start, stop simplest cases
+> fit7 <- survConcordance(Surv(rep(0,11), time, status) ~ y, tdata)
+> aeq(fit7$stats, fit$stats)
+[1] TRUE
+> aeq(fit7$std.err, fit$std.err)
+[1] TRUE
+> fit7 <- survConcordance(Surv(rep(0,11), time, status) ~ y, tdata, weight=wt)
+> aeq(fit5$stats, fit7$stats)
+[1] TRUE
+>
+> # Multiple intervals for some, but same risk sets as tdata
+> tdata2 <- data.frame(time1=c(0,3, 5, 6,7, 0, 4,17, 7, 0,16, 2, 0,
++ 0,9, 5),
++ time2=c(3,9, 13, 7,13, 18, 17,23, 28, 16,31, 34, 45,
++ 9,48, 60),
++ status=c(0,1, 1, 0,0, 1, 0,1, 0, 0,1, 1, 0, 0,1, 0),
++ y = c(1,1, 6, 2,2, 7, 3,3, 7, 3,3, 8, 4, 4,4, 5),
++ wt= c(1,1, 2, 3,3, 2, 1,1, 2, 3,3, 4, 3, 2,2, 1))
+> fit8 <- survConcordance(Surv(time1, time2, status) ~y, tdata2, weight=wt)
+> aeq(fit5$stats, fit8$stats)
+[1] TRUE
+> aeq(fit5$std.err, fit8$std.err)
+[1] TRUE
+> cfit8 <- coxph(Surv(time1, time2, status) ~ tt(y), tdata2, weight=wt,
++ iter=0, method='breslow', tt=grank2)
+> aeq(4/cfit8$var, fit8$stats[5]^2)
+[1] TRUE
+> aeq(fit8$stats[5]/(2*sum(fit8$stats[1:3])), fit8$std.err)
+[1] TRUE
+>
+> # Stratified
+> tdata3 <- data.frame(time1=c(tdata2$time1, rep(0, nrow(lung))),
++ time2=c(tdata2$time2, lung$time),
++ status = c(tdata2$status, lung$status -1),
++ x = c(tdata2$y, lung$ph.ecog),
++ wt= c(tdata2$wt, rep(1, nrow(lung))),
++ grp=rep(1:2, c(nrow(tdata2), nrow(lung))))
+> fit9 <- survConcordance(Surv(time1, time2, status) ~x + strata(grp),
++ data=tdata3, weight=wt)
+> aeq(fit9$stats[1,], fit5$stats)
+[1] TRUE
+> aeq(fit9$stats[2,], fit4$stats)
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/counting.R b/win32/deps/library/survival/tests/counting.R
new file mode 100644
index 0000000..ff25354
--- /dev/null
+++ b/win32/deps/library/survival/tests/counting.R
@@ -0,0 +1,47 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+# Create a "counting process" version of the simplest test data set
+#
+test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
+ status=c(1,NA,1,0,1,1,0),
+ x= c(0, 2,1,1,1,0,0))
+
+test1b<- list(start= c(0, 3, 0, 0, 5, 0, 6,14, 0, 0, 10,20,30, 0),
+ stop = c(3,10, 10, 5,20, 6,14,20, 30, 10,20,30,40, 10),
+ status=c(0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0),
+ x= c(1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, NA),
+ id = c(3, 3, 4, 5, 5, 6, 6, 6, 7, 1, 1, 1, 1, 2))
+
+aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+#
+# Check out the various residuals under an Efron approximation
+#
+fit0 <- coxph(Surv(time, status)~ x, test1, iter=0)
+fit <- coxph(Surv(time, status) ~x, test1)
+fit0b <- coxph(Surv(start, stop, status) ~ x, test1b, iter=0)
+fitb <- coxph(Surv(start, stop, status) ~x, test1b)
+fitc <- coxph(Surv(time, status) ~ offset(fit$coef*x), test1)
+fitd <- coxph(Surv(start, stop, status) ~ offset(fit$coef*x), test1b)
+
+aeq(fit0b$coef, fit0$coef)
+
+aeq(resid(fit0), resid(fit0b, collapse=test1b$id))
+aeq(resid(fit), resid(fitb, collapse=test1b$id))
+aeq(resid(fitc), resid(fitd, collapse=test1b$id))
+aeq(resid(fitc), resid(fit))
+
+aeq(resid(fit0, type='score'), resid(fit0b, type='score', collapse=test1b$id))
+aeq(resid(fit, type='score'), resid(fitb, type='score', collapse=test1b$id))
+
+aeq(resid(fit0, type='scho'), resid(fit0b, type='scho', collapse=test1b$id))
+aeq(resid(fit, type='scho'), resid(fitb, type='scho', collapse=test1b$id))
+
+# The two survivals will have different censoring times
+# nrisk, nevent, surv, and std should be the same
+temp1 <- survfit(fit, list(x=1), censor=FALSE)
+temp2 <- survfit(fitb, list(x=1), censor=FALSE)
+all.equal(unclass(temp1)[c(3,4,6,8)], unclass(temp2)[c(3,4,6,8)])
+
+
diff --git a/win32/deps/library/survival/tests/counting.Rout.save b/win32/deps/library/survival/tests/counting.Rout.save
new file mode 100644
index 0000000..c90bcad
--- /dev/null
+++ b/win32/deps/library/survival/tests/counting.Rout.save
@@ -0,0 +1,76 @@
+
+R version 2.10.0 (2009-10-26)
+Copyright (C) 2009 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> # Create a "counting process" version of the simplest test data set
+> #
+> test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
++ status=c(1,NA,1,0,1,1,0),
++ x= c(0, 2,1,1,1,0,0))
+>
+> test1b<- list(start= c(0, 3, 0, 0, 5, 0, 6,14, 0, 0, 10,20,30, 0),
++ stop = c(3,10, 10, 5,20, 6,14,20, 30, 10,20,30,40, 10),
++ status=c(0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0),
++ x= c(1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, NA),
++ id = c(3, 3, 4, 5, 5, 6, 6, 6, 7, 1, 1, 1, 1, 2))
+>
+> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+> #
+> # Check out the various residuals under an Efron approximation
+> #
+> fit0 <- coxph(Surv(time, status)~ x, test1, iter=0)
+> fit <- coxph(Surv(time, status) ~x, test1)
+> fit0b <- coxph(Surv(start, stop, status) ~ x, test1b, iter=0)
+> fitb <- coxph(Surv(start, stop, status) ~x, test1b)
+> fitc <- coxph(Surv(time, status) ~ offset(fit$coef*x), test1)
+> fitd <- coxph(Surv(start, stop, status) ~ offset(fit$coef*x), test1b)
+>
+> aeq(fit0b$coef, fit0$coef)
+[1] TRUE
+>
+> aeq(resid(fit0), resid(fit0b, collapse=test1b$id))
+[1] TRUE
+> aeq(resid(fit), resid(fitb, collapse=test1b$id))
+[1] TRUE
+> aeq(resid(fitc), resid(fitd, collapse=test1b$id))
+[1] TRUE
+> aeq(resid(fitc), resid(fit))
+[1] TRUE
+>
+> aeq(resid(fit0, type='score'), resid(fit0b, type='score', collapse=test1b$id))
+[1] TRUE
+> aeq(resid(fit, type='score'), resid(fitb, type='score', collapse=test1b$id))
+[1] TRUE
+>
+> aeq(resid(fit0, type='scho'), resid(fit0b, type='scho', collapse=test1b$id))
+[1] TRUE
+> aeq(resid(fit, type='scho'), resid(fitb, type='scho', collapse=test1b$id))
+[1] TRUE
+>
+> # The two survivals will have different censoring times
+> # nrisk, nevent, surv, and std should be the same
+> temp1 <- survfit(fit, list(x=1), censor=FALSE)
+> temp2 <- survfit(fitb, list(x=1), censor=FALSE)
+> all.equal(unclass(temp1)[c(3,4,6,8)], unclass(temp2)[c(3,4,6,8)])
+[1] TRUE
+>
+>
+>
diff --git a/win32/deps/library/survival/tests/coxsurv.R b/win32/deps/library/survival/tests/coxsurv.R
new file mode 100644
index 0000000..fabc295
--- /dev/null
+++ b/win32/deps/library/survival/tests/coxsurv.R
@@ -0,0 +1,80 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Test out subscripting in the case of a coxph survival curve
+#
+aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+
+fit <- coxph(Surv(time, status) ~ age + sex + meal.cal + strata(ph.ecog),
+ data=cancer)
+
+surv1 <- survfit(fit)
+temp <- surv1[2:3]
+
+which <- cumsum(surv1$strata)
+zed <- (which[1]+1):(which[3])
+aeq(surv1$surv[zed], temp$surv)
+aeq(surv1$time[zed], temp$time)
+
+# This call should not create a model frame in the code -- so same
+# answer but a different path through the underlying code
+fit <- coxph(Surv(time, status) ~ age + sex + meal.cal + strata(ph.ecog),
+ x=T, data=cancer)
+surv2 <- survfit(fit)
+all.equal(surv1, surv2)
+
+#
+# Now a result with a matrix of survival curves
+#
+dummy <- data.frame(age=c(30,40,60), sex=c(1,2,2), meal.cal=c(500, 1000, 1500))
+surv2 <- survfit(fit, newdata=dummy)
+
+zed <- 1:which[1]
+aeq(surv2$surv[zed,1], surv2[1,1]$surv)
+aeq(surv2$surv[zed,2], surv2[1,2]$surv)
+aeq(surv2$surv[zed,3], surv2[1,3]$surv)
+aeq(surv2$surv[zed, ], surv2[1,1:3]$surv)
+aeq(surv2$surv[zed], (surv2[1]$surv)[,1])
+aeq(surv2$surv[zed, ], surv2[1, ]$surv)
+
+fit <- coxph(Surv(time, status) ~ age + sex + meal.cal + strata(ph.ecog),
+ data=cancer)
+
+surv1 <- survfit(fit)
+temp <- surv1[2:3]
+
+which <- cumsum(surv1$strata)
+zed <- (which[1]+1):(which[3])
+aeq(surv1$surv[zed], temp$surv)
+aeq(surv1$time[zed], temp$time)
+
+# This call should not create a model frame in the code -- so same
+# answer but a different path through the underlying code
+fit <- coxph(Surv(time, status) ~ age + sex + meal.cal + strata(ph.ecog),
+ x=T, data=cancer)
+surv2 <- survfit(fit)
+all.equal(surv1, surv2)
+
+#
+# Now a result with a matrix of survival curves
+#
+dummy <- data.frame(age=c(30,40,60), sex=c(1,2,2), meal.cal=c(500, 1000, 1500))
+surv2 <- survfit(fit, newdata=dummy)
+
+zed <- 1:which[1]
+aeq(surv2$surv[zed,1], surv2[1,1]$surv)
+aeq(surv2$surv[zed,2], surv2[1,2]$surv)
+aeq(surv2$surv[zed,3], surv2[1,3]$surv)
+aeq(surv2$surv[zed, ], surv2[1,1:3]$surv)
+aeq(surv2$surv[zed], (surv2[1]$surv)[,1])
+aeq(surv2$surv[zed, ], surv2[1, ]$surv)
+
+# And the depreciated form - call with a named vector as 'newdata'
+# the resulting $call component won't match so delete it before comparing
+surv3 <- survfit(fit, c(age=40, sex=2, meal.cal=1000))
+all.equal(unclass(surv2[,2])[-length(surv3)], unclass(surv3)[-length(surv3)])
+
+rm(fit, surv1, temp, which, zed,dummy, surv2, surv3)
+
diff --git a/win32/deps/library/survival/tests/coxsurv.Rout.save b/win32/deps/library/survival/tests/coxsurv.Rout.save
new file mode 100644
index 0000000..ef2f7a1
--- /dev/null
+++ b/win32/deps/library/survival/tests/coxsurv.Rout.save
@@ -0,0 +1,119 @@
+
+R version 2.12.1 (2010-12-16)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: i686-pc-linux-gnu (32-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Test out subscripting in the case of a coxph survival curve
+> #
+> aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+>
+> fit <- coxph(Surv(time, status) ~ age + sex + meal.cal + strata(ph.ecog),
++ data=cancer)
+>
+> surv1 <- survfit(fit)
+> temp <- surv1[2:3]
+>
+> which <- cumsum(surv1$strata)
+> zed <- (which[1]+1):(which[3])
+> aeq(surv1$surv[zed], temp$surv)
+[1] TRUE
+> aeq(surv1$time[zed], temp$time)
+[1] TRUE
+>
+> # This call should not create a model frame in the code -- so same
+> # answer but a different path through the underlying code
+> fit <- coxph(Surv(time, status) ~ age + sex + meal.cal + strata(ph.ecog),
++ x=T, data=cancer)
+> surv2 <- survfit(fit)
+> all.equal(surv1, surv2)
+[1] TRUE
+>
+> #
+> # Now a result with a matrix of survival curves
+> #
+> dummy <- data.frame(age=c(30,40,60), sex=c(1,2,2), meal.cal=c(500, 1000, 1500))
+> surv2 <- survfit(fit, newdata=dummy)
+>
+> zed <- 1:which[1]
+> aeq(surv2$surv[zed,1], surv2[1,1]$surv)
+[1] TRUE
+> aeq(surv2$surv[zed,2], surv2[1,2]$surv)
+[1] TRUE
+> aeq(surv2$surv[zed,3], surv2[1,3]$surv)
+[1] TRUE
+> aeq(surv2$surv[zed, ], surv2[1,1:3]$surv)
+[1] TRUE
+> aeq(surv2$surv[zed], (surv2[1]$surv)[,1])
+[1] TRUE
+> aeq(surv2$surv[zed, ], surv2[1, ]$surv)
+[1] TRUE
+>
+> fit <- coxph(Surv(time, status) ~ age + sex + meal.cal + strata(ph.ecog),
++ data=cancer)
+>
+> surv1 <- survfit(fit)
+> temp <- surv1[2:3]
+>
+> which <- cumsum(surv1$strata)
+> zed <- (which[1]+1):(which[3])
+> aeq(surv1$surv[zed], temp$surv)
+[1] TRUE
+> aeq(surv1$time[zed], temp$time)
+[1] TRUE
+>
+> # This call should not create a model frame in the code -- so same
+> # answer but a different path through the underlying code
+> fit <- coxph(Surv(time, status) ~ age + sex + meal.cal + strata(ph.ecog),
++ x=T, data=cancer)
+> surv2 <- survfit(fit)
+> all.equal(surv1, surv2)
+[1] TRUE
+>
+> #
+> # Now a result with a matrix of survival curves
+> #
+> dummy <- data.frame(age=c(30,40,60), sex=c(1,2,2), meal.cal=c(500, 1000, 1500))
+> surv2 <- survfit(fit, newdata=dummy)
+>
+> zed <- 1:which[1]
+> aeq(surv2$surv[zed,1], surv2[1,1]$surv)
+[1] TRUE
+> aeq(surv2$surv[zed,2], surv2[1,2]$surv)
+[1] TRUE
+> aeq(surv2$surv[zed,3], surv2[1,3]$surv)
+[1] TRUE
+> aeq(surv2$surv[zed, ], surv2[1,1:3]$surv)
+[1] TRUE
+> aeq(surv2$surv[zed], (surv2[1]$surv)[,1])
+[1] TRUE
+> aeq(surv2$surv[zed, ], surv2[1, ]$surv)
+[1] TRUE
+>
+> # And the depreciated form - call with a named vector as 'newdata'
+> # the resulting $call component won't match so delete it before comparing
+> surv3 <- survfit(fit, c(age=40, sex=2, meal.cal=1000))
+> all.equal(unclass(surv2[,2])[-length(surv3)], unclass(surv3)[-length(surv3)])
+[1] TRUE
+>
+> rm(fit, surv1, temp, which, zed,dummy, surv2, surv3)
+>
+>
diff --git a/win32/deps/library/survival/tests/coxsurv2.R b/win32/deps/library/survival/tests/coxsurv2.R
new file mode 100644
index 0000000..21ff309
--- /dev/null
+++ b/win32/deps/library/survival/tests/coxsurv2.R
@@ -0,0 +1,58 @@
+library(survival)
+#
+# Check that the survival curves from a Cox model with beta=0
+# match ordinary survival
+#
+# Aalen
+surv1 <- survfit(Surv(time,status) ~ sex, data=lung, type='fleming',
+ error='tsiatis')
+fit1 <- coxph(Surv(time, status) ~ age + strata(sex), data=lung, iter=0,
+ method='breslow')
+fit1$var <- 0*fit1$var #sneaky, causes the extra term in the Cox variance
+ # calculation to be zero
+surv2 <- survfit(fit1, type='aalen', vartype='tsiatis')
+surv3 <- survfit(fit1)
+
+arglist <- c('n', 'time', 'n.risk','n.event', 'n.censor', 'surv', 'strata',
+ 'std.err', 'upper', 'lower')
+all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist])
+all.equal(unclass(surv1)[arglist], unclass(surv3)[arglist])
+
+
+# Efron method
+surv1 <- survfit(Surv(time,status) ~ sex, data=lung, type='fh2',
+ error='tsiatis')
+surv2 <- survfit(fit1, type='efron', vartype='efron')
+all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist])
+
+# Kaplan-Meier
+surv1 <- survfit(Surv(time,status) ~ sex, data=lung)
+surv2 <- survfit(fit1, type='kalb', vartype='green')
+all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist])
+
+
+# Now add some random weights
+rwt <- runif(nrow(lung), .5, 3)
+surv1 <- survfit(Surv(time,status) ~ sex, data=lung, type='fleming',
+ error='tsiatis', weight=rwt)
+fit1 <- coxph(Surv(time, status) ~ age + strata(sex), data=lung, iter=0,
+ method='breslow', weight=rwt)
+fit1$var <- 0*fit1$var #sneaky
+surv2 <- survfit(fit1, type='aalen', vartype='tsiatis')
+surv3 <- survfit(fit1)
+
+all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist])
+all.equal(unclass(surv1)[arglist], unclass(surv3)[arglist])
+
+
+# Efron method
+surv1 <- survfit(Surv(time,status) ~ sex, data=lung, type='fh2',
+ error='tsiatis', weight=rwt)
+surv2 <- survfit(fit1, type='efron', vartype='efron')
+all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist])
+
+# Kaplan-Meier
+surv1 <- survfit(Surv(time,status) ~ sex, data=lung, weight=rwt)
+surv2 <- survfit(fit1, type='kalb', vartype='green')
+all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist])
+
diff --git a/win32/deps/library/survival/tests/coxsurv2.Rout.save b/win32/deps/library/survival/tests/coxsurv2.Rout.save
new file mode 100644
index 0000000..226a5d7
--- /dev/null
+++ b/win32/deps/library/survival/tests/coxsurv2.Rout.save
@@ -0,0 +1,85 @@
+
+R version 2.11.1 (2010-05-31)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+> #
+> # Check that the survival curves from a Cox model with beta=0
+> # match ordinary survival
+> #
+> # Aalen
+> surv1 <- survfit(Surv(time,status) ~ sex, data=lung, type='fleming',
++ error='tsiatis')
+> fit1 <- coxph(Surv(time, status) ~ age + strata(sex), data=lung, iter=0,
++ method='breslow')
+> fit1$var <- 0*fit1$var #sneaky, causes the extra term in the Cox variance
+> # calculation to be zero
+> surv2 <- survfit(fit1, type='aalen', vartype='tsiatis')
+> surv3 <- survfit(fit1)
+>
+> arglist <- c('n', 'time', 'n.risk','n.event', 'n.censor', 'surv', 'strata',
++ 'std.err', 'upper', 'lower')
+> all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist])
+[1] TRUE
+> all.equal(unclass(surv1)[arglist], unclass(surv3)[arglist])
+[1] TRUE
+>
+>
+> # Efron method
+> surv1 <- survfit(Surv(time,status) ~ sex, data=lung, type='fh2',
++ error='tsiatis')
+> surv2 <- survfit(fit1, type='efron', vartype='efron')
+> all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist])
+[1] TRUE
+>
+> # Kaplan-Meier
+> surv1 <- survfit(Surv(time,status) ~ sex, data=lung)
+> surv2 <- survfit(fit1, type='kalb', vartype='green')
+> all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist])
+[1] TRUE
+>
+>
+> # Now add some random weights
+> rwt <- runif(nrow(lung), .5, 3)
+> surv1 <- survfit(Surv(time,status) ~ sex, data=lung, type='fleming',
++ error='tsiatis', weight=rwt)
+> fit1 <- coxph(Surv(time, status) ~ age + strata(sex), data=lung, iter=0,
++ method='breslow', weight=rwt)
+> fit1$var <- 0*fit1$var #sneaky
+> surv2 <- survfit(fit1, type='aalen', vartype='tsiatis')
+> surv3 <- survfit(fit1)
+>
+> all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist])
+[1] TRUE
+> all.equal(unclass(surv1)[arglist], unclass(surv3)[arglist])
+[1] TRUE
+>
+>
+> # Efron method
+> surv1 <- survfit(Surv(time,status) ~ sex, data=lung, type='fh2',
++ error='tsiatis', weight=rwt)
+> surv2 <- survfit(fit1, type='efron', vartype='efron')
+> all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist])
+[1] TRUE
+>
+> # Kaplan-Meier
+> surv1 <- survfit(Surv(time,status) ~ sex, data=lung, weight=rwt)
+> surv2 <- survfit(fit1, type='kalb', vartype='green')
+> all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist])
+[1] TRUE
+>
+>
diff --git a/win32/deps/library/survival/tests/coxsurv3.R b/win32/deps/library/survival/tests/coxsurv3.R
new file mode 100644
index 0000000..902130e
--- /dev/null
+++ b/win32/deps/library/survival/tests/coxsurv3.R
@@ -0,0 +1,98 @@
+library(survival)
+aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+# One more test on coxph survival curves, to test out the individual
+# option. First fit a model with a time dependent covariate
+#
+test2 <- data.frame(start=c(1, 2, 5, 2, 1, 7, 3, 4, 8, 8),
+ stop =c(2, 3, 6, 7, 8, 9, 9, 9,14,17),
+ event=c(1, 1, 1, 1, 1, 1, 1, 0, 0, 0),
+ x =c(1, 0, 0, 1, 0, 1, 1, 1, 0, 0) )
+
+# True hazard function, from the validation document
+lambda <- function(beta, x=0, method='efron') {
+ r <- exp(beta)
+ lambda <- c(1/(r+1), 1/(r+2), 1/(3*r +2), 1/(3*r+1),
+ 1/(3*r+1), 1/(3*r+2) + 1/(2*r +2))
+ if (method == 'breslow') lambda[9] <- 2/(3*r +2)
+ list(time=c(2,3,6,7,8,9), lambda=lambda)
+ }
+
+fit <- coxph(Surv(start, stop, event) ~x, test2)
+# A curve for someone who never changes
+surv1 <-survfit(fit, newdata=list(x=0), censor=FALSE)
+
+true <- lambda(fit$coef, 0)
+
+aeq(true$time, surv1$time)
+aeq(-log(surv1$surv), cumsum(true$lambda))
+
+# Reprise it with a time dependent subject who doesn't change
+data2 <- data.frame(start=c(0, 4, 9, 11), stop=c(4, 9, 11, 17),
+ event=c(0,0,0,0), x=c(0,0,0,0))
+surv2 <- survfit(fit, newdata=data2, individual=TRUE, censor=FALSE)
+aeq(surv2$surv, surv1$surv)
+
+
+#
+# Now a more complex data set with multiple strata
+#
+test3 <- data.frame(start=c(1, 2, 5, 2, 1, 7, 3, 4, 8, 8,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
+ stop =c(2, 3, 6, 7, 8, 9, 9, 9,14,17,
+ 1:11),
+ event=c(1, 1, 1, 1, 1, 1, 1, 0, 0, 0,
+ 0, 1, 1, 0, 0, 1, 1, 0, 1, 0,1),
+ x =c(1, 0, 0, 1, 0, 1, 1, 1, 0, 0,
+ 1, 2, 3, 2, 1, 1, 1, 0, 2, 1,0),
+ grp = c(rep('a', 10), rep('b', 11)))
+
+fit2 <- coxph(Surv(start, stop, event) ~ x + strata(grp), test3)
+
+# The above tests show the program works for a simple case, use it to
+# get a true baseline for strata 2
+fit2b <- coxph(Surv(start, stop, event) ~x, test3,
+ subset=(grp=='b'), init=fit2$coef, iter=0)
+temp <- survfit(fit2b, newdata=list(x=0), censor=F)
+true2 <- list(time=temp$time, lambda=diff(c(0, -log(temp$surv))))
+true1 <- lambda(fit2$coef, x=0)
+
+# Separate strata, one value
+surv3 <- survfit(fit2, list(x=0), censor=FALSE)
+aeq(true1$time, (surv3[1])$time)
+aeq(-log(surv3[1]$surv), cumsum(true1$lambda))
+
+data4 <- data.frame(start=c(0, 4, 9, 11), stop=c(4, 9, 11, 17),
+ event=c(0,0,0,0), x=c(0,0,0,0), grp=rep('a', 4))
+surv4a <- survfit(fit2, newdata=data4, individual=T, censor=FALSE)
+aeq(-log(surv4a$surv), cumsum(true1$lambda))
+
+data4$grp <- rep('b',4)
+surv4b <- survfit(fit2, newdata=data4, individual=T, censor=FALSE)
+aeq(-log(surv4b$surv), cumsum(true2$lambda))
+
+
+# Now for something more complex
+# Subject 1 skips day 4. Since there were no events that day the survival
+# will be the same, but the times will be different.
+# Subject 2 spends some time in strata 1, some in strata 2, with
+# moving covariates
+#
+data5 <- data.frame(start=c(0,5,9,11,
+ 0, 4, 3),
+ stop =c(4,9,11,17, 4,8,7),
+ event=rep(0,7),
+ x=c(1,1,1,1, 0,1,2),
+ grp=c('a', 'a', 'a', 'a', 'a', 'a', 'b'),
+ subject=c(1,1,1,1, 2,2,2))
+surv5 <- survfit(fit2, newdata=data5, censor=FALSE, id=subject)
+
+aeq(surv5[1]$time, c(2,3,5,6,7,8)) #surv1 has 2, 3, 6, 7, 8, 9
+aeq(surv5[1]$surv, surv3[1]$surv ^ exp(fit2$coef))
+
+tlam <- c(true1$lambda[1:2]* exp(fit2$coef * data5$x[5]),
+ true1$lambda[3:5]* exp(fit2$coef * data5$x[6]),
+ true2$lambda[3:4]* exp(fit2$coef * data5$x[7]))
+aeq(-log(surv5[2]$surv), cumsum(tlam))
+
+
+
diff --git a/win32/deps/library/survival/tests/coxsurv3.Rout.save b/win32/deps/library/survival/tests/coxsurv3.Rout.save
new file mode 100644
index 0000000..bc1b1cc
--- /dev/null
+++ b/win32/deps/library/survival/tests/coxsurv3.Rout.save
@@ -0,0 +1,127 @@
+
+R version 2.11.0 (2010-04-22)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+> # One more test on coxph survival curves, to test out the individual
+> # option. First fit a model with a time dependent covariate
+> #
+> test2 <- data.frame(start=c(1, 2, 5, 2, 1, 7, 3, 4, 8, 8),
++ stop =c(2, 3, 6, 7, 8, 9, 9, 9,14,17),
++ event=c(1, 1, 1, 1, 1, 1, 1, 0, 0, 0),
++ x =c(1, 0, 0, 1, 0, 1, 1, 1, 0, 0) )
+>
+> # True hazard function, from the validation document
+> lambda <- function(beta, x=0, method='efron') {
++ r <- exp(beta)
++ lambda <- c(1/(r+1), 1/(r+2), 1/(3*r +2), 1/(3*r+1),
++ 1/(3*r+1), 1/(3*r+2) + 1/(2*r +2))
++ if (method == 'breslow') lambda[9] <- 2/(3*r +2)
++ list(time=c(2,3,6,7,8,9), lambda=lambda)
++ }
+>
+> fit <- coxph(Surv(start, stop, event) ~x, test2)
+> # A curve for someone who never changes
+> surv1 <-survfit(fit, newdata=list(x=0), censor=FALSE)
+>
+> true <- lambda(fit$coef, 0)
+>
+> aeq(true$time, surv1$time)
+[1] TRUE
+> aeq(-log(surv1$surv), cumsum(true$lambda))
+[1] TRUE
+>
+> # Reprise it with a time dependent subject who doesn't change
+> data2 <- data.frame(start=c(0, 4, 9, 11), stop=c(4, 9, 11, 17),
++ event=c(0,0,0,0), x=c(0,0,0,0))
+> surv2 <- survfit(fit, newdata=data2, individual=TRUE, censor=FALSE)
+> aeq(surv2$surv, surv1$surv)
+[1] TRUE
+>
+>
+> #
+> # Now a more complex data set with multiple strata
+> #
+> test3 <- data.frame(start=c(1, 2, 5, 2, 1, 7, 3, 4, 8, 8,
++ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
++ stop =c(2, 3, 6, 7, 8, 9, 9, 9,14,17,
++ 1:11),
++ event=c(1, 1, 1, 1, 1, 1, 1, 0, 0, 0,
++ 0, 1, 1, 0, 0, 1, 1, 0, 1, 0,1),
++ x =c(1, 0, 0, 1, 0, 1, 1, 1, 0, 0,
++ 1, 2, 3, 2, 1, 1, 1, 0, 2, 1,0),
++ grp = c(rep('a', 10), rep('b', 11)))
+>
+> fit2 <- coxph(Surv(start, stop, event) ~ x + strata(grp), test3)
+>
+> # The above tests show the program works for a simple case, use it to
+> # get a true baseline for strata 2
+> fit2b <- coxph(Surv(start, stop, event) ~x, test3,
++ subset=(grp=='b'), init=fit2$coef, iter=0)
+> temp <- survfit(fit2b, newdata=list(x=0), censor=F)
+> true2 <- list(time=temp$time, lambda=diff(c(0, -log(temp$surv))))
+> true1 <- lambda(fit2$coef, x=0)
+>
+> # Separate strata, one value
+> surv3 <- survfit(fit2, list(x=0), censor=FALSE)
+> aeq(true1$time, (surv3[1])$time)
+[1] TRUE
+> aeq(-log(surv3[1]$surv), cumsum(true1$lambda))
+[1] TRUE
+>
+> data4 <- data.frame(start=c(0, 4, 9, 11), stop=c(4, 9, 11, 17),
++ event=c(0,0,0,0), x=c(0,0,0,0), grp=rep('a', 4))
+> surv4a <- survfit(fit2, newdata=data4, individual=T, censor=FALSE)
+> aeq(-log(surv4a$surv), cumsum(true1$lambda))
+[1] TRUE
+>
+> data4$grp <- rep('b',4)
+> surv4b <- survfit(fit2, newdata=data4, individual=T, censor=FALSE)
+> aeq(-log(surv4b$surv), cumsum(true2$lambda))
+[1] TRUE
+>
+>
+> # Now for something more complex
+> # Subject 1 skips day 4. Since there were no events that day the survival
+> # will be the same, but the times will be different.
+> # Subject 2 spends some time in strata 1, some in strata 2, with
+> # moving covariates
+> #
+> data5 <- data.frame(start=c(0,5,9,11,
++ 0, 4, 3),
++ stop =c(4,9,11,17, 4,8,7),
++ event=rep(0,7),
++ x=c(1,1,1,1, 0,1,2),
++ grp=c('a', 'a', 'a', 'a', 'a', 'a', 'b'),
++ subject=c(1,1,1,1, 2,2,2))
+> surv5 <- survfit(fit2, newdata=data5, censor=FALSE, id=subject)
+>
+> aeq(surv5[1]$time, c(2,3,5,6,7,8)) #surv1 has 2, 3, 6, 7, 8, 9
+[1] TRUE
+> aeq(surv5[1]$surv, surv3[1]$surv ^ exp(fit2$coef))
+[1] TRUE
+>
+> tlam <- c(true1$lambda[1:2]* exp(fit2$coef * data5$x[5]),
++ true1$lambda[3:5]* exp(fit2$coef * data5$x[6]),
++ true2$lambda[3:4]* exp(fit2$coef * data5$x[7]))
+> aeq(-log(surv5[2]$surv), cumsum(tlam))
+[1] TRUE
+>
+>
+>
+>
diff --git a/win32/deps/library/survival/tests/coxsurv4.R b/win32/deps/library/survival/tests/coxsurv4.R
new file mode 100644
index 0000000..d6f82bc
--- /dev/null
+++ b/win32/deps/library/survival/tests/coxsurv4.R
@@ -0,0 +1,49 @@
+library(survival)
+
+# Strata by covariate interactions, a case pointed out in early 2011
+# by Frank Harrell, which as it turns out had never been computed
+# correctly by any version of the package. This shows how often this
+# case arises in practice.
+#
+
+fit1 <- coxph(Surv(time, status) ~ wt.loss + age*strata(sex) + strata(ph.ecog),
+ data=lung)
+surv1 <- survfit(fit1, newdata=list(wt.loss=c(10,5), age=c(50,60)))
+
+fit2 <- coxph(Surv(time, status) ~ wt.loss + age + I(age*0), data=lung,
+ init=fit1$coef, iter=0, subset=(sex==1 & ph.ecog==0))
+fit2$var <- fit1$var
+
+surv2 <- survfit(fit2, newdata=list(wt.loss=c(10,5), age=c(50,60)))
+
+nocall <- length(surv2) # the calls won't be the same
+all.equal(unclass(surv1[1,])[-nocall], unclass(surv2)[-nocall])
+
+fit3 <- coxph(Surv(time, status) ~ wt.loss + age + I(age*0),
+ data=lung, init=fit1$coef, iter=0,
+ subset=(sex==1 & ph.ecog==1))
+fit3$var <- fit1$var
+surv3 <- survfit(fit3, newdata=list(wt.loss=c(10,5), age=c(50,60)))
+all.equal(surv1[2,]$surv, surv3$surv)
+all.equal(surv1[2,]$std, surv3$std)
+
+fit4 <- coxph(Surv(time, status) ~ wt.loss + age + I(age),
+ data=lung, init=fit1$coef, iter=0,
+ subset=(sex==2 & ph.ecog==1))
+fit4$var <- fit1$var
+surv4 <- survfit(fit4, newdata=list(wt.loss=c(10,5), age=c(50,60)))
+
+all.equal(surv1[6,]$surv, surv4$surv)
+all.equal(surv1[6,]$std.err, surv4$std.err)
+
+fit5 <- coxph(Surv(time, status) ~ wt.loss + age + I(age) + strata(ph.ecog),
+ data=lung, init=fit1$coef, iter=0,
+ subset=(sex==2))
+fit5$var <- fit1$var
+surv5 <- survfit(fit5, newdata=list(wt.loss=c(10,5), age=c(50,60)))
+temp1 <- surv1[5:7,]
+temp2 <- surv5[1:3,]
+all.equal(temp1$strata, temp2$strata, check.attributes=FALSE)
+nlist <- c('n', 'time', 'n.risk', 'n.event', 'n.censor', 'surv',
+ 'std.err')
+all.equal(unclass(temp1)[nlist], unclass(temp2)[nlist])
diff --git a/win32/deps/library/survival/tests/coxsurv4.Rout.save b/win32/deps/library/survival/tests/coxsurv4.Rout.save
new file mode 100644
index 0000000..19c9e66
--- /dev/null
+++ b/win32/deps/library/survival/tests/coxsurv4.Rout.save
@@ -0,0 +1,75 @@
+
+R version 2.11.0 (2010-04-22)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+>
+> # Strata by covariate interactions, a case pointed out in early 2011
+> # by Frank Harrell, which as it turns out had never been computed
+> # correctly by any version of the package. This shows how often this
+> # case arises in practice.
+> #
+>
+> fit1 <- coxph(Surv(time, status) ~ wt.loss + age*strata(sex) + strata(ph.ecog),
++ data=lung)
+> surv1 <- survfit(fit1, newdata=list(wt.loss=c(10,5), age=c(50,60)))
+>
+> fit2 <- coxph(Surv(time, status) ~ wt.loss + age + I(age*0), data=lung,
++ init=fit1$coef, iter=0, subset=(sex==1 & ph.ecog==0))
+> fit2$var <- fit1$var
+>
+> surv2 <- survfit(fit2, newdata=list(wt.loss=c(10,5), age=c(50,60)))
+>
+> nocall <- length(surv2) # the calls won't be the same
+> all.equal(unclass(surv1[1,])[-nocall], unclass(surv2)[-nocall])
+[1] TRUE
+>
+> fit3 <- coxph(Surv(time, status) ~ wt.loss + age + I(age*0),
++ data=lung, init=fit1$coef, iter=0,
++ subset=(sex==1 & ph.ecog==1))
+> fit3$var <- fit1$var
+> surv3 <- survfit(fit3, newdata=list(wt.loss=c(10,5), age=c(50,60)))
+> all.equal(surv1[2,]$surv, surv3$surv)
+[1] TRUE
+> all.equal(surv1[2,]$std, surv3$std)
+[1] TRUE
+>
+> fit4 <- coxph(Surv(time, status) ~ wt.loss + age + I(age),
++ data=lung, init=fit1$coef, iter=0,
++ subset=(sex==2 & ph.ecog==1))
+> fit4$var <- fit1$var
+> surv4 <- survfit(fit4, newdata=list(wt.loss=c(10,5), age=c(50,60)))
+>
+> all.equal(surv1[6,]$surv, surv4$surv)
+[1] TRUE
+> all.equal(surv1[6,]$std.err, surv4$std.err)
+[1] TRUE
+>
+> fit5 <- coxph(Surv(time, status) ~ wt.loss + age + I(age) + strata(ph.ecog),
++ data=lung, init=fit1$coef, iter=0,
++ subset=(sex==2))
+> fit5$var <- fit1$var
+> surv5 <- survfit(fit5, newdata=list(wt.loss=c(10,5), age=c(50,60)))
+> temp1 <- surv1[5:7,]
+> temp2 <- surv5[1:3,]
+> all.equal(temp1$strata, temp2$strata, check.attributes=FALSE)
+[1] TRUE
+> nlist <- c('n', 'time', 'n.risk', 'n.event', 'n.censor', 'surv',
++ 'std.err')
+> all.equal(unclass(temp1)[nlist], unclass(temp2)[nlist])
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/data.capacitor b/win32/deps/library/survival/tests/data.capacitor
new file mode 100644
index 0000000..0cbea67
--- /dev/null
+++ b/win32/deps/library/survival/tests/data.capacitor
@@ -0,0 +1,125 @@
+ 1 300.00 0 20
+ 2 300.00 0 20
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+ 26 277.33 1 26
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+ 29 12.95 1 26
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diff --git a/win32/deps/library/survival/tests/data.cracks b/win32/deps/library/survival/tests/data.cracks
new file mode 100644
index 0000000..48041a7
--- /dev/null
+++ b/win32/deps/library/survival/tests/data.cracks
@@ -0,0 +1,9 @@
+NA 6.12 5
+6.12 19.92 16
+19.92 29.64 12
+29.64 35.40 18
+35.40 39.72 18
+39.72 45.24 2
+45.24 52.32 6
+52.32 63.48 17
+63.48 NA 73
diff --git a/win32/deps/library/survival/tests/data.donnell b/win32/deps/library/survival/tests/data.donnell
new file mode 100644
index 0000000..5eaf8d1
--- /dev/null
+++ b/win32/deps/library/survival/tests/data.donnell
@@ -0,0 +1,210 @@
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diff --git a/win32/deps/library/survival/tests/data.fluid b/win32/deps/library/survival/tests/data.fluid
new file mode 100644
index 0000000..cd55d26
--- /dev/null
+++ b/win32/deps/library/survival/tests/data.fluid
@@ -0,0 +1,41 @@
+ 5.79 26kV
+1579.52 26kV
+2323.70 26kV
+ 7.74 30kV
+ 17.05 30kV
+ 20.46 30kV
+ 21.02 30kV
+ 22.66 30kV
+ 43.40 30kV
+ 47.30 30kV
+ 139.07 30kV
+ 144.12 30kV
+ 175.88 30kV
+ 194.90 30kV
+ 0.19 34kV
+ 0.78 34kV
+ 0.96 34kV
+ 1.31 34kV
+ 2.78 34kV
+ 3.16 34kV
+ 4.15 34kV
+ 4.67 34kV
+ 4.85 34kV
+ 6.50 34kV
+ 7.35 34kV
+ 8.01 34kV
+ 8.27 34kV
+ 12.06 34kV
+ 31.75 34kV
+ 32.52 34kV
+ 33.91 34kV
+ 36.71 34kV
+ 72.89 34kV
+ 0.09 38kV
+ 0.39 38kV
+ 0.47 38kV
+ 0.73 38kV
+ 0.74 38kV
+ 1.13 38kV
+ 1.40 38kV
+ 2.38 38kV
diff --git a/win32/deps/library/survival/tests/data.interval b/win32/deps/library/survival/tests/data.interval
new file mode 100644
index 0000000..309d59d
--- /dev/null
+++ b/win32/deps/library/survival/tests/data.interval
@@ -0,0 +1,30 @@
+ This data set is to test interval censoring. It has 2 left censored, 14
+right censored, 2 exact and 8 interval censored observations, grafted onto
+covariates from the ovarian data set.
+"ltime","rtime","age","resid.ds","rx","ecog.ps"
+"1",NA,150,72.3315,2,1,1
+"2",NA,150,74.4932,2,1,1
+"3",146,166,66.4658,2,1,2
+"4",421,NA,53.3644,2,2,1
+"5",421,421,50.3397,2,1,1
+"6",448,NA,56.4301,1,1,2
+"7",454,474,56.937,2,2,2
+"8",465,485,59.8548,2,2,2
+"9",477,NA,64.1753,2,1,1
+"10",553,573,55.1781,1,2,2
+"11",628,648,56.7562,1,1,2
+"12",744,NA,50.1096,1,2,1
+"13",769,NA,59.6301,2,2,2
+"14",770,NA,57.0521,2,2,1
+"15",803,NA,39.2712,1,1,1
+"16",855,NA,43.1233,1,1,2
+"17",1040,NA,38.8932,2,1,2
+"18",1106,NA,44.6,1,1,1
+"19",1129,NA,53.9068,1,2,1
+"20",1206,NA,44.2055,2,2,1
+"21",1227,NA,59.589,1,2,2
+"22",258,278,74.5041,2,1,2
+"23",319,339,43.137,2,1,1
+"24",343,363,63.2192,1,2,2
+"25",375,375,64.4247,2,2,1
+"26",377,NA,58.3096,1,2,1
diff --git a/win32/deps/library/survival/tests/data.motor b/win32/deps/library/survival/tests/data.motor
new file mode 100644
index 0000000..420752c
--- /dev/null
+++ b/win32/deps/library/survival/tests/data.motor
@@ -0,0 +1,40 @@
+150 8064 0
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diff --git a/win32/deps/library/survival/tests/data.peterson b/win32/deps/library/survival/tests/data.peterson
new file mode 100644
index 0000000..220f218
--- /dev/null
+++ b/win32/deps/library/survival/tests/data.peterson
@@ -0,0 +1,20 @@
+1 4 1
+1 7 1
+1 12 1
+2 3 0
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+2 22 1
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+2 11 0
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+6 18 1
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+3 16 0
+3 5 0
+3 14 0
+3 20 1
+4 2 1
+5 6 1
+
diff --git a/win32/deps/library/survival/tests/data.rat2 b/win32/deps/library/survival/tests/data.rat2
new file mode 100644
index 0000000..90ef33e
--- /dev/null
+++ b/win32/deps/library/survival/tests/data.rat2
@@ -0,0 +1,253 @@
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diff --git a/win32/deps/library/survival/tests/data.smoke b/win32/deps/library/survival/tests/data.smoke
new file mode 100644
index 0000000..edbc16b
--- /dev/null
+++ b/win32/deps/library/survival/tests/data.smoke
@@ -0,0 +1,33 @@
+ 186.0 439.2 234.4 365.8 159.6 216.9 167.4 159.5
+ 255.6 702.7 544.7 431.0 454.8 349.7 214.0 250.4
+ 448.9 1132.4 945.2 728.8 729.4 590.2 447.3 436.6
+ 733.7 1981.1 1177.7 1589.2 1316.5 1266.9 875.6 703.0
+1119.4 3003.0 2244.9 3380.3 2374.9 1820.2 1669.1 1159.2
+2070.5 4697.5 4255.3 5083.0 4485.0 3888.7 3184.3 2194.9
+3675.3 7340.6 5882.4 6597.2 7707.5 4945.1 5618.0 4128.9
+
+ 186.0 610.0 497.5 251.7 417.5 122.6 198.3 193.4
+ 255.6 915.6 482.8 500.7 488.9 402.9 393.9 354.3
+ 448.9 1391.0 1757.1 953.5 1025.8 744.0 668.5 537.8
+ 733.7 2393.4 1578.4 1847.2 1790.1 1220.7 1100.0 993.3
+1119.4 3497.9 2301.8 3776.6 2081.0 2766.4 2268.1 1230.7
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+3675.3 6250.0 4000.0 4424.8 7329.8 6383.0 7666.1 5048.1
+
+
+ 125.7 225.6 0 433.9 212.0 107.2 135.9 91.0
+ 177.3 353.8 116.8 92.1 289.5 200.9 121.3 172.1
+ 244.8 542.8 287.4 259.5 375.9 165.8 202.2 247.2
+ 397.7 858.0 1016.3 365.0 650.9 470.8 570.6 319.7
+ 692.1 1496.2 1108.0 1348.5 1263.2 864.8 586.6 618.0
+1160.0 2084.8 645.2 1483.1 1250.0 1126.3 1070.5 1272.1
+2070.8 3319.5 0 2580.6 2590.7 3960.4 1666.7 1861.5
+
+ 125.7 277.9 266.7 102.7 178.6 224.7 142.1 138.8
+ 177.3 517.9 138.7 466.8 270.1 190.2 116.8 83.0
+ 244.8 823.5 473.6 602.0 361.0 454.5 412.2 182.1
+ 397.7 1302.9 1114.8 862.1 699.6 541.7 373.1 356.4
+ 692.1 1934.9 2319.6 1250.0 1688.0 828.7 797.9 581.5
+1160.0 2827.0 4635.8 2517.2 1687.3 2848.7 1621.2 1363.4
+2070.8 4273.1 2409.6 5769.2 3125.0 2978.7 2803.7 2195.4
+
diff --git a/win32/deps/library/survival/tests/data.turbine b/win32/deps/library/survival/tests/data.turbine
new file mode 100644
index 0000000..0b24b6a
--- /dev/null
+++ b/win32/deps/library/survival/tests/data.turbine
@@ -0,0 +1,23 @@
+NA 4 0
+4 NA 39
+NA 10 4
+10 NA 49
+NA 14 2
+14 NA 31
+NA 18 7
+18 NA 66
+NA 22 5
+22 NA 25
+NA 26 9
+26 NA 30
+NA 30 9
+30 NA 33
+NA 34 6
+34 NA 7
+NA 38 22
+38 NA 12
+NA 42 21
+42 NA 19
+NA 46 21
+46 NA 15
+
diff --git a/win32/deps/library/survival/tests/data.valve b/win32/deps/library/survival/tests/data.valve
new file mode 100644
index 0000000..40c1ded
--- /dev/null
+++ b/win32/deps/library/survival/tests/data.valve
@@ -0,0 +1,89 @@
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diff --git a/win32/deps/library/survival/tests/detail.R b/win32/deps/library/survival/tests/detail.R
new file mode 100644
index 0000000..3b1f6b7
--- /dev/null
+++ b/win32/deps/library/survival/tests/detail.R
@@ -0,0 +1,69 @@
+# A short test on coxph.detail, to ensure that the computed hazard is
+# equal to the theoretical value
+library(survival)
+aeq <- function(a,b) all.equal(as.vector(a), as.vector(b))
+
+# taken from book4.R
+test2 <- data.frame(start=c(1, 2, 5, 2, 1, 7, 3, 4, 8, 8),
+ stop =c(2, 3, 6, 7, 8, 9, 9, 9,14,17),
+ event=c(1, 1, 1, 1, 1, 1, 1, 0, 0, 0),
+ x =c(1, 0, 0, 1, 0, 1, 1, 1, 0, 0) )
+
+byhand <- function(beta, newx=0) {
+ r <- exp(beta)
+ loglik <- 4*beta - (log(r+1) + log(r+2) + 2*log(3*r+2) + 2*log(3*r+1) +
+ log(2*r +2))
+ u <- 1/(r+1) + 1/(3*r+1) + 2*(1/(3*r+2) + 1/(2*r+2)) -
+ ( r/(r+2) +3*r/(3*r+2) + 3*r/(3*r+1))
+ imat <- r*(1/(r+1)^2 + 2/(r+2)^2 + 6/(3*r+2)^2 +
+ 6/(3*r+1)^2 + 6/(3*r+2)^2 + 4/(2*r +2)^2)
+
+ hazard <-c( 1/(r+1), 1/(r+2), 1/(3*r+2), 1/(3*r+1), 1/(3*r+1),
+ 1/(3*r+2), 1/(2*r +2) )
+
+
+ # The matrix of weights, one row per obs, one col per time
+ # deaths at 2,3,6,7,8,9
+ wtmat <- matrix(c(1,0,0,0,1, 0, 0,0,0,0,
+ 0,1,0,1,1, 0, 0,0,0,0,
+ 0,0,1,1,1, 0, 1,1,0,0,
+ 0,0,0,1,1, 0, 1,1,0,0,
+ 0,0,0,0,1, 1, 1,1,0,0,
+ 0,0,0,0,0, 1, 1,1,1,1,
+ 0,0,0,0,0,.5,.5,1,1,1), ncol=7)
+ wtmat <- diag(c(r,1,1,r,1,r,r,r,1,1)) %*% wtmat
+
+ x <- c(1,0,0,1,0,1,1,1,0,0)
+ status <- c(1,1,1,1,1,1,1,0,0,0)
+ xbar <- colSums(wtmat*x)/ colSums(wtmat)
+ n <- length(x)
+
+ # Table of sums for score and Schoenfeld resids
+ hazmat <- wtmat %*% diag(hazard) #each subject's hazard over time
+ dM <- -hazmat #Expected part
+ for (i in 1:5) dM[i,i] <- dM[i,i] +1 #observed
+ dM[6:7,6:7] <- dM[6:7,6:7] +.5 # observed
+ mart <- rowSums(dM)
+
+ # Table of sums for score and Schoenfeld resids
+ # Looks like the last table of appendix E.2.1 of the book
+ resid <- dM * outer(x, xbar, '-')
+ score <- rowSums(resid)
+ scho <- colSums(resid)
+
+ # We need to add the ties back up (they are symmetric)
+ scho[6:7] <- rep(mean(scho[6:7]), 2)
+
+ list(loglik=loglik, u=u, imat=imat, xbar=xbar, haz=hazard* exp(beta*newx),
+ mart=mart, score=score, rmat=resid,
+ scho=scho)
+ }
+
+# The actual coefficient of the fit is close to zero. Using a larger
+# number pushes the test harder, but it should still work without
+# the init and iter arguments, i.e., for any coefficient.
+fit1 <- coxph(Surv(start, stop, event) ~x, test2,init=-1, iter=0)
+temp <- coxph.detail(fit1)
+temp2 <- byhand(fit1$coef, fit1$means)
+aeq(temp$haz, c(temp2$haz[1:5], sum(temp2$haz[6:7])))
+
diff --git a/win32/deps/library/survival/tests/detail.Rout.save b/win32/deps/library/survival/tests/detail.Rout.save
new file mode 100644
index 0000000..068e63f
--- /dev/null
+++ b/win32/deps/library/survival/tests/detail.Rout.save
@@ -0,0 +1,89 @@
+
+R version 2.11.0 (2010-04-22)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> # A short test on coxph.detail, to ensure that the computed hazard is
+> # equal to the theoretical value
+> library(survival)
+Loading required package: splines
+> aeq <- function(a,b) all.equal(as.vector(a), as.vector(b))
+>
+> # taken from book4.R
+> test2 <- data.frame(start=c(1, 2, 5, 2, 1, 7, 3, 4, 8, 8),
++ stop =c(2, 3, 6, 7, 8, 9, 9, 9,14,17),
++ event=c(1, 1, 1, 1, 1, 1, 1, 0, 0, 0),
++ x =c(1, 0, 0, 1, 0, 1, 1, 1, 0, 0) )
+>
+> byhand <- function(beta, newx=0) {
++ r <- exp(beta)
++ loglik <- 4*beta - (log(r+1) + log(r+2) + 2*log(3*r+2) + 2*log(3*r+1) +
++ log(2*r +2))
++ u <- 1/(r+1) + 1/(3*r+1) + 2*(1/(3*r+2) + 1/(2*r+2)) -
++ ( r/(r+2) +3*r/(3*r+2) + 3*r/(3*r+1))
++ imat <- r*(1/(r+1)^2 + 2/(r+2)^2 + 6/(3*r+2)^2 +
++ 6/(3*r+1)^2 + 6/(3*r+2)^2 + 4/(2*r +2)^2)
++
++ hazard <-c( 1/(r+1), 1/(r+2), 1/(3*r+2), 1/(3*r+1), 1/(3*r+1),
++ 1/(3*r+2), 1/(2*r +2) )
++
++
++ # The matrix of weights, one row per obs, one col per time
++ # deaths at 2,3,6,7,8,9
++ wtmat <- matrix(c(1,0,0,0,1, 0, 0,0,0,0,
++ 0,1,0,1,1, 0, 0,0,0,0,
++ 0,0,1,1,1, 0, 1,1,0,0,
++ 0,0,0,1,1, 0, 1,1,0,0,
++ 0,0,0,0,1, 1, 1,1,0,0,
++ 0,0,0,0,0, 1, 1,1,1,1,
++ 0,0,0,0,0,.5,.5,1,1,1), ncol=7)
++ wtmat <- diag(c(r,1,1,r,1,r,r,r,1,1)) %*% wtmat
++
++ x <- c(1,0,0,1,0,1,1,1,0,0)
++ status <- c(1,1,1,1,1,1,1,0,0,0)
++ xbar <- colSums(wtmat*x)/ colSums(wtmat)
++ n <- length(x)
++
++ # Table of sums for score and Schoenfeld resids
++ hazmat <- wtmat %*% diag(hazard) #each subject's hazard over time
++ dM <- -hazmat #Expected part
++ for (i in 1:5) dM[i,i] <- dM[i,i] +1 #observed
++ dM[6:7,6:7] <- dM[6:7,6:7] +.5 # observed
++ mart <- rowSums(dM)
++
++ # Table of sums for score and Schoenfeld resids
++ # Looks like the last table of appendix E.2.1 of the book
++ resid <- dM * outer(x, xbar, '-')
++ score <- rowSums(resid)
++ scho <- colSums(resid)
++
++ # We need to add the ties back up (they are symmetric)
++ scho[6:7] <- rep(mean(scho[6:7]), 2)
++
++ list(loglik=loglik, u=u, imat=imat, xbar=xbar, haz=hazard* exp(beta*newx),
++ mart=mart, score=score, rmat=resid,
++ scho=scho)
++ }
+>
+> # The actual coefficient of the fit is close to zero. Using a larger
+> # number pushes the test harder, but it should still work without
+> # the init and iter arguments, i.e., for any coefficient.
+> fit1 <- coxph(Surv(start, stop, event) ~x, test2,init=-1, iter=0)
+> temp <- coxph.detail(fit1)
+> temp2 <- byhand(fit1$coef, fit1$means)
+> aeq(temp$haz, c(temp2$haz[1:5], sum(temp2$haz[6:7])))
+[1] TRUE
+>
+>
diff --git a/win32/deps/library/survival/tests/difftest.R b/win32/deps/library/survival/tests/difftest.R
new file mode 100644
index 0000000..51e8631
--- /dev/null
+++ b/win32/deps/library/survival/tests/difftest.R
@@ -0,0 +1,56 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Test some more features of surv.diff
+#
+# First, what happens when one group is a dummy
+#
+
+
+#
+# The AML data, with a third group of early censorings "tacked on"
+#
+aml3 <- list(time= c( 9, 13, 13, 18, 23, 28, 31, 34, 45, 48, 161,
+ 5, 5, 8, 8, 12, 16, 23, 27, 30, 33, 43, 45,
+ 1, 2, 2, 3, 3, 3, 4),
+ status= c( 1,1,0,1,1,0,1,1,0,1,0, 1,1,1,1,1,0,1,1,1,1,1,1,
+ 0,0,0,0,0,0,0),
+ x = as.factor(c(rep("Maintained", 11),
+ rep("Nonmaintained", 12), rep("Dummy",7) )))
+
+aml3 <- data.frame(aml3)
+
+# These should give the same result (chisq, df), but the second has an
+# extra group
+survdiff(Surv(time, status) ~x, aml)
+survdiff(Surv(time, status) ~x, aml3)
+
+
+#
+# Now a test of the stratified log-rank
+# There are no tied times within institution, so the coxph program
+# can be used to give a complete test
+#
+fit <- survdiff(Surv(time, status) ~ pat.karno + strata(inst), cancer)
+
+cfit <- coxph(Surv(time, status) ~ factor(pat.karno) + strata(inst),
+ cancer, iter=0)
+
+tdata <- na.omit(cancer[,c('time', 'status', 'pat.karno', 'inst')])
+
+temp1 <- tapply(tdata$status-1, list(tdata$pat.karno, tdata$inst), sum)
+temp1 <- ifelse(is.na(temp1), 0, temp1)
+temp2 <- tapply(cfit$resid, list(tdata$pat.karno, tdata$inst), sum)
+temp2 <- ifelse(is.na(temp2), 0, temp2)
+
+temp2 <- temp1 - temp2
+
+#Now temp1=observed, temp2=expected
+all.equal(c(temp1), c(fit$obs))
+all.equal(c(temp2), c(fit$exp))
+
+all.equal(fit$var[-1,-1], solve(cfit$var))
+
+rm(tdata, temp1, temp2)
diff --git a/win32/deps/library/survival/tests/difftest.Rout.save b/win32/deps/library/survival/tests/difftest.Rout.save
new file mode 100644
index 0000000..e9e4fee
--- /dev/null
+++ b/win32/deps/library/survival/tests/difftest.Rout.save
@@ -0,0 +1,96 @@
+
+R version 2.14.0 Under development (unstable) (2011-04-10 r55401)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Test some more features of surv.diff
+> #
+> # First, what happens when one group is a dummy
+> #
+>
+>
+> #
+> # The AML data, with a third group of early censorings "tacked on"
+> #
+> aml3 <- list(time= c( 9, 13, 13, 18, 23, 28, 31, 34, 45, 48, 161,
++ 5, 5, 8, 8, 12, 16, 23, 27, 30, 33, 43, 45,
++ 1, 2, 2, 3, 3, 3, 4),
++ status= c( 1,1,0,1,1,0,1,1,0,1,0, 1,1,1,1,1,0,1,1,1,1,1,1,
++ 0,0,0,0,0,0,0),
++ x = as.factor(c(rep("Maintained", 11),
++ rep("Nonmaintained", 12), rep("Dummy",7) )))
+>
+> aml3 <- data.frame(aml3)
+>
+> # These should give the same result (chisq, df), but the second has an
+> # extra group
+> survdiff(Surv(time, status) ~x, aml)
+Call:
+survdiff(formula = Surv(time, status) ~ x, data = aml)
+
+ N Observed Expected (O-E)^2/E (O-E)^2/V
+x=Maintained 11 7 10.69 1.27 3.4
+x=Nonmaintained 12 11 7.31 1.86 3.4
+
+ Chisq= 3.4 on 1 degrees of freedom, p= 0.0653
+> survdiff(Surv(time, status) ~x, aml3)
+Call:
+survdiff(formula = Surv(time, status) ~ x, data = aml3)
+
+ N Observed Expected (O-E)^2/E (O-E)^2/V
+x=Dummy 7 0 0.00 NaN NaN
+x=Maintained 11 7 10.69 1.27 3.4
+x=Nonmaintained 12 11 7.31 1.86 3.4
+
+ Chisq= 3.4 on 1 degrees of freedom, p= 0.0653
+>
+>
+> #
+> # Now a test of the stratified log-rank
+> # There are no tied times within institution, so the coxph program
+> # can be used to give a complete test
+> #
+> fit <- survdiff(Surv(time, status) ~ pat.karno + strata(inst), cancer)
+>
+> cfit <- coxph(Surv(time, status) ~ factor(pat.karno) + strata(inst),
++ cancer, iter=0)
+>
+> tdata <- na.omit(cancer[,c('time', 'status', 'pat.karno', 'inst')])
+>
+> temp1 <- tapply(tdata$status-1, list(tdata$pat.karno, tdata$inst), sum)
+> temp1 <- ifelse(is.na(temp1), 0, temp1)
+> temp2 <- tapply(cfit$resid, list(tdata$pat.karno, tdata$inst), sum)
+> temp2 <- ifelse(is.na(temp2), 0, temp2)
+>
+> temp2 <- temp1 - temp2
+>
+> #Now temp1=observed, temp2=expected
+> all.equal(c(temp1), c(fit$obs))
+[1] TRUE
+> all.equal(c(temp2), c(fit$exp))
+[1] TRUE
+>
+> all.equal(fit$var[-1,-1], solve(cfit$var))
+[1] TRUE
+>
+> rm(tdata, temp1, temp2)
+>
diff --git a/win32/deps/library/survival/tests/doaml.R b/win32/deps/library/survival/tests/doaml.R
new file mode 100644
index 0000000..4673f16
--- /dev/null
+++ b/win32/deps/library/survival/tests/doaml.R
@@ -0,0 +1,64 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+#
+# These results can be found in Miller
+#
+fit <- coxph(Surv(aml$time, aml$status) ~ aml$x, method='breslow')
+fit
+resid(fit, type='mart')
+resid(fit, type='score')
+resid(fit, type='scho')
+
+# Test the drop of an itercept: should have no effect
+fit2 <- coxph(Surv(time, status) ~ x -1, method='breslow',
+ data=aml)
+aeq(fit$loglik, fit2$loglik)
+aeq(coef(fit), coef(fit2))
+aeq(fit$var, fit2$var)
+
+fit <- survfit(Surv(aml$time, aml$status) ~ aml$x)
+fit
+summary(fit)
+survdiff(Surv(aml$time, aml$status)~ aml$x)
+
+#
+# Test out the weighted K-M
+#
+# First, equal case weights- shouldn't change the survival, but will
+# halve the variance
+temp2 <-survfit(Surv(aml$time, aml$status)~1, type='kaplan', weight=rep(2,23))
+temp <-survfit(Surv(time, status)~1, aml)
+aeq(temp$surv, temp2$surv)
+aeq(temp$std.err^2, 2*temp2$std.err^2)
+
+# Risk weights-- use a null Cox model
+tfit <- coxph(Surv(aml$time, aml$status) ~ offset(log(1:23)))
+sfit <- survfit(tfit, type='aalen', censor=FALSE)
+
+# Now compute it by hand. The survfit program will produce a curve
+# corresponding to the mean offset. This is a change on 7/2010,
+# which caused S(new) = S(old)^exp(mean(log(1:23))).
+# Ties are a nuisance
+rscore <- exp(log(1:23) - mean(log(1:23)))[order(aml$time)]
+atime <- sort(aml$time)
+denom <- rev(cumsum(rev(rscore)))
+denom <- denom[match(unique(atime), atime)]
+deaths <- tapply(aml$status, aml$time, sum)
+chaz <- cumsum(deaths/denom)
+all.equal(sfit$surv, as.vector(exp(-chaz[deaths>0])))
+cvar <- cumsum(deaths/denom^2)
+all.equal(sfit$std^2, as.vector(cvar[deaths>0]))
+
+# And the Efron result
+summary(survfit(tfit))
+
+# Lots of ties, so its a good test case
+x1 <- coxph(Surv(time, status)~x, aml, method='efron')
+x1
+x2 <- coxph(Surv(rep(0,23),time, status) ~x, aml, method='efron')
+aeq(x1$coef, x2$coef)
+
+
+rm(x1, x2, atime, denom, deaths, chaz,cvar, tfit, sfit, temp, temp2, fit)
diff --git a/win32/deps/library/survival/tests/doaml.Rout.save b/win32/deps/library/survival/tests/doaml.Rout.save
new file mode 100644
index 0000000..3e02ad8
--- /dev/null
+++ b/win32/deps/library/survival/tests/doaml.Rout.save
@@ -0,0 +1,185 @@
+
+R version 2.13.0 RC (2011-04-11 r55409)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+> #
+> # These results can be found in Miller
+> #
+> fit <- coxph(Surv(aml$time, aml$status) ~ aml$x, method='breslow')
+> fit
+Call:
+coxph(formula = Surv(aml$time, aml$status) ~ aml$x, method = "breslow")
+
+
+ coef exp(coef) se(coef) z p
+aml$xNonmaintained 0.904 2.47 0.512 1.77 0.078
+
+Likelihood ratio test=3.3 on 1 df, p=0.0694 n= 23, number of events= 18
+> resid(fit, type='mart')
+ 1 2 3 4 5 6
+ 0.86225539 0.79200985 -0.20799015 0.74818869 0.65652976 -0.39796610
+ 7 8 9 10 11 12
+ 0.45424957 0.25475051 -1.05400917 -0.55400917 -1.55400917 0.87844483
+ 13 14 15 16 17 18
+ 0.87844483 0.74006941 0.74006941 0.57677292 -0.51373647 0.15162716
+ 19 20 21 22 23
+ 0.01702219 -0.14897252 -0.56448258 -1.15185244 -1.60340676
+> resid(fit, type='score')
+ 1 2 3 4 5 6
+-0.546856248 -0.492501830 0.141063944 -0.479907930 -0.447416819 0.268453990
+ 7 8 9 10 11 12
+-0.235908976 -0.072655945 0.640826596 0.640826596 0.640826596 0.237767767
+ 13 14 15 16 17 18
+ 0.237767767 0.232585063 0.232585063 0.203878910 -0.165307985 0.044923326
+ 19 20 21 22 23
+ 0.007079721 -0.039651990 -0.181184547 -0.395076175 -0.472116894
+> resid(fit, type='scho')
+ 5 5 8 8 9 12 13
+ 0.2706690 0.2706690 0.3081229 0.3081229 -0.6423931 0.3360212 -0.6335658
+ 18 23 23 27 30 31 33
+-0.6494307 -0.6791937 0.3208063 0.3269751 0.3360212 -0.5970995 0.3505693
+ 34 43 45 48
+-0.5525731 0.3778334 0.5484457 0.0000000
+>
+> # Test the drop of an itercept: should have no effect
+> fit2 <- coxph(Surv(time, status) ~ x -1, method='breslow',
++ data=aml)
+> aeq(fit$loglik, fit2$loglik)
+[1] TRUE
+> aeq(coef(fit), coef(fit2))
+[1] TRUE
+> aeq(fit$var, fit2$var)
+[1] TRUE
+>
+> fit <- survfit(Surv(aml$time, aml$status) ~ aml$x)
+> fit
+Call: survfit(formula = Surv(aml$time, aml$status) ~ aml$x)
+
+ records n.max n.start events median 0.95LCL 0.95UCL
+aml$x=Maintained 11 11 11 7 31 18 NA
+aml$x=Nonmaintained 12 12 12 11 23 8 NA
+> summary(fit)
+Call: survfit(formula = Surv(aml$time, aml$status) ~ aml$x)
+
+ aml$x=Maintained
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 9 11 1 0.909 0.0867 0.7541 1.000
+ 13 10 1 0.818 0.1163 0.6192 1.000
+ 18 8 1 0.716 0.1397 0.4884 1.000
+ 23 7 1 0.614 0.1526 0.3769 0.999
+ 31 5 1 0.491 0.1642 0.2549 0.946
+ 34 4 1 0.368 0.1627 0.1549 0.875
+ 48 2 1 0.184 0.1535 0.0359 0.944
+
+ aml$x=Nonmaintained
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 5 12 2 0.8333 0.1076 0.6470 1.000
+ 8 10 2 0.6667 0.1361 0.4468 0.995
+ 12 8 1 0.5833 0.1423 0.3616 0.941
+ 23 6 1 0.4861 0.1481 0.2675 0.883
+ 27 5 1 0.3889 0.1470 0.1854 0.816
+ 30 4 1 0.2917 0.1387 0.1148 0.741
+ 33 3 1 0.1944 0.1219 0.0569 0.664
+ 43 2 1 0.0972 0.0919 0.0153 0.620
+ 45 1 1 0.0000 NaN NA NA
+
+> survdiff(Surv(aml$time, aml$status)~ aml$x)
+Call:
+survdiff(formula = Surv(aml$time, aml$status) ~ aml$x)
+
+ N Observed Expected (O-E)^2/E (O-E)^2/V
+aml$x=Maintained 11 7 10.69 1.27 3.4
+aml$x=Nonmaintained 12 11 7.31 1.86 3.4
+
+ Chisq= 3.4 on 1 degrees of freedom, p= 0.0653
+>
+> #
+> # Test out the weighted K-M
+> #
+> # First, equal case weights- shouldn't change the survival, but will
+> # halve the variance
+> temp2 <-survfit(Surv(aml$time, aml$status)~1, type='kaplan', weight=rep(2,23))
+> temp <-survfit(Surv(time, status)~1, aml)
+> aeq(temp$surv, temp2$surv)
+[1] TRUE
+> aeq(temp$std.err^2, 2*temp2$std.err^2)
+[1] TRUE
+>
+> # Risk weights-- use a null Cox model
+> tfit <- coxph(Surv(aml$time, aml$status) ~ offset(log(1:23)))
+> sfit <- survfit(tfit, type='aalen', censor=FALSE)
+>
+> # Now compute it by hand. The survfit program will produce a curve
+> # corresponding to the mean offset. This is a change on 7/2010,
+> # which caused S(new) = S(old)^exp(mean(log(1:23))).
+> # Ties are a nuisance
+> rscore <- exp(log(1:23) - mean(log(1:23)))[order(aml$time)]
+> atime <- sort(aml$time)
+> denom <- rev(cumsum(rev(rscore)))
+> denom <- denom[match(unique(atime), atime)]
+> deaths <- tapply(aml$status, aml$time, sum)
+> chaz <- cumsum(deaths/denom)
+> all.equal(sfit$surv, as.vector(exp(-chaz[deaths>0])))
+[1] TRUE
+> cvar <- cumsum(deaths/denom^2)
+> all.equal(sfit$std^2, as.vector(cvar[deaths>0]))
+[1] TRUE
+>
+> # And the Efron result
+> summary(survfit(tfit))
+Call: survfit(formula = tfit)
+
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 5 23 2 0.932 0.0461 0.8463 1.000
+ 8 21 2 0.863 0.0637 0.7467 0.997
+ 9 19 1 0.827 0.0704 0.6999 0.977
+ 12 18 1 0.793 0.0755 0.6576 0.955
+ 13 17 1 0.757 0.0801 0.6152 0.931
+ 18 14 1 0.719 0.0846 0.5709 0.905
+ 23 13 2 0.645 0.0907 0.4893 0.849
+ 27 11 1 0.607 0.0929 0.4496 0.819
+ 30 9 1 0.565 0.0955 0.4054 0.787
+ 31 8 1 0.519 0.0982 0.3579 0.752
+ 33 7 1 0.474 0.0994 0.3140 0.715
+ 34 6 1 0.423 0.1009 0.2649 0.675
+ 43 5 1 0.373 0.1006 0.2198 0.633
+ 45 4 1 0.312 0.1009 0.1657 0.588
+ 48 2 1 0.199 0.1102 0.0674 0.589
+>
+> # Lots of ties, so its a good test case
+> x1 <- coxph(Surv(time, status)~x, aml, method='efron')
+> x1
+Call:
+coxph(formula = Surv(time, status) ~ x, data = aml, method = "efron")
+
+
+ coef exp(coef) se(coef) z p
+xNonmaintained 0.916 2.5 0.512 1.79 0.074
+
+Likelihood ratio test=3.38 on 1 df, p=0.0658 n= 23, number of events= 18
+> x2 <- coxph(Surv(rep(0,23),time, status) ~x, aml, method='efron')
+> aeq(x1$coef, x2$coef)
+[1] TRUE
+>
+>
+> rm(x1, x2, atime, denom, deaths, chaz,cvar, tfit, sfit, temp, temp2, fit)
+>
diff --git a/win32/deps/library/survival/tests/doweight.R b/win32/deps/library/survival/tests/doweight.R
new file mode 100644
index 0000000..b8ff0cd
--- /dev/null
+++ b/win32/deps/library/survival/tests/doweight.R
@@ -0,0 +1,240 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+# Tests of the weighted Cox model
+#
+# Similar data set to test1, but add weights,
+# a double-death/censor tied time
+# a censored last subject
+# The latter two are cases covered only feebly elsewhere.
+#
+# The data set testw2 has the same data, but done via replication
+#
+aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+
+testw1 <- data.frame(time= c(1,1,2,2,2,2,3,4,5),
+ status= c(1,0,1,1,1,0,0,1,0),
+ x= c(2,0,1,1,0,1,0,1,0),
+ wt = c(1,2,3,4,3,2,1,2,1))
+xx <- c(1,2,3,4,3,2,1,2,1)
+testw2 <- data.frame(time= rep(c(1,1,2,2,2,2,3,4,5), xx),
+ status= rep(c(1,0,1,1,1,0,0,1,0), xx),
+ x= rep(c(2,0,1,1,0,1,0,1,0), xx),
+ id= rep(1:9, xx))
+indx <- match(1:9, testw2$id)
+testw2 <- data.frame(time= rep(c(1,1,2,2,2,2,3,4,5), xx),
+ status= rep(c(1,0,1,1,1,0,0,1,0), xx),
+ x= rep(c(2,0,1,1,0,1,0,1,0), xx),
+ id= rep(1:9, xx))
+indx <- match(1:9, testw2$id)
+
+fit0 <- coxph(Surv(time, status) ~x, testw1, weights=wt,
+ method='breslow', iter=0)
+fit0b <- coxph(Surv(time, status) ~x, testw2, method='breslow', iter=0)
+fit <- coxph(Surv(time, status) ~x, testw1, weights=wt, method='breslow')
+fitb <- coxph(Surv(time, status) ~x, testw2, method='breslow')
+
+texp <- function(beta) { # expected, Breslow estimate
+ r <- exp(beta)
+ temp <- cumsum(c(1/(r^2 + 11*r +7), 10/(11*r +5), 2/(2*r+1)))
+ c(r^2, 1,r,r,1,r,1,r,1)* temp[c(1,1,2,2,2,2,2,3,3)]
+ }
+aeq(texp(0), c(1/19, 1/19, rep(103/152, 5), rep(613/456,2))) #verify texp()
+
+xbar <- function(beta) { # xbar, Breslow estimate
+ r <- exp(beta)
+ temp <- r* rep(c(2*r + 11, 11/10, 1), c(2, 5, 2))
+ temp * texp(beta)
+ }
+
+fit0
+summary(fit)
+aeq(resid(fit0), testw1$status - texp(0))
+resid(fit0, type='score')
+resid(fit0, type='scho')
+
+aeq(resid(fit0, type='mart'), (resid(fit0b, type='mart'))[indx])
+aeq(resid(fit0, type='scor'), (resid(fit0b, type='scor'))[indx])
+aeq(unique(resid(fit0, type='scho')), unique(resid(fit0b, type='scho')))
+
+
+aeq(resid(fit, type='mart'), testw1$status - texp(fit$coef))
+resid(fit, type='score')
+resid(fit, type='scho')
+aeq(resid(fit, type='mart'), (resid(fitb, type='mart'))[indx])
+aeq(resid(fit, type='scor'), (resid(fitb, type='scor'))[indx])
+aeq(unique(resid(fit, type='scho')), unique(resid(fitb, type='scho')))
+rr1 <- resid(fit, type='mart')
+rr2 <- resid(fit, type='mart', weighted=T)
+aeq(rr2/rr1, testw1$wt)
+
+rr1 <- resid(fit, type='score')
+rr2 <- resid(fit, type='score', weighted=T)
+aeq(rr2/rr1, testw1$wt)
+
+fit <- coxph(Surv(time, status) ~x, testw1, weights=wt, method='efron')
+fit
+resid(fit, type='mart')
+resid(fit, type='score')
+resid(fit, type='scho')
+
+# Tests of the weighted Cox model, AG form of the data
+# Same solution as doweight1.s
+#
+testw3 <- data.frame(id = c( 1, 1, 2, 3, 3, 3, 4, 5, 5, 6, 7, 8, 8, 9),
+ begin= c( 0, 5, 0, 0,10,15, 0, 0,14, 0, 0, 0,23, 0),
+ time= c( 5,10,10,10,15,20,20,14,20,20,30,23,40,50),
+ status= c( 0, 1, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 1, 0),
+ x= c( 2, 2, 0, 1, 1, 1, 1, 0, 0, 1, 0, 1, 1, 0),
+ wt = c( 1, 1, 2, 3, 3, 3, 4, 3, 3, 2, 1, 2, 2, 1))
+
+fit0 <- coxph(Surv(begin,time, status) ~x, testw3, weights=wt,
+ method='breslow', iter=0)
+fit <- coxph(Surv(begin,time, status) ~x, testw3, weights=wt, method='breslow')
+fit0
+summary(fit)
+resid(fit0, type='mart', collapse=testw3$id)
+resid(fit0, type='score', collapse=testw3$id)
+resid(fit0, type='scho')
+
+resid(fit, type='mart', collapse=testw3$id)
+resid(fit, type='score', collapse=testw3$id)
+resid(fit, type='scho')
+fit0 <- coxph(Surv(begin, time, status) ~x,testw3, weights=wt, iter=0)
+resid(fit0, 'mart', collapse=testw3$id)
+resid(coxph(Surv(begin, time, status) ~1, testw3, weights=wt)
+ , collapse=testw3$id) #Null model
+
+fit <- coxph(Surv(begin,time, status) ~x, testw3, weights=wt, method='efron')
+fit
+resid(fit, type='mart', collapse=testw3$id)
+resid(fit, type='score', collapse=testw3$id)
+resid(fit, type='scho')
+#
+# Check out the impact of weights on the dfbetas
+# Am I computing them correctly?
+#
+wtemp <- rep(1,26)
+wtemp[c(5,10,15)] <- 2:4
+fit <- coxph(Surv(futime, fustat) ~ age + ecog.ps, ovarian, weights=wtemp)
+rr <- resid(fit, 'dfbeta')
+
+fit1 <- coxph(Surv(futime, fustat) ~ age + ecog.ps, ovarian, weights=wtemp,
+ subset=(-5))
+fit2 <- coxph(Surv(futime, fustat) ~ age + ecog.ps, ovarian, weights=wtemp,
+ subset=(-10))
+fit3 <- coxph(Surv(futime, fustat) ~ age + ecog.ps, ovarian, weights=wtemp,
+ subset=(-15))
+
+#
+# Effect of case weights on expected survival curves post Cox model
+#
+fit0 <- coxph(Surv(time, status) ~x, testw1, weights=wt, method='breslow',
+ iter=0)
+fit0b <- coxph(Surv(time, status) ~x, testw2, method='breslow', iter=0)
+
+surv1 <- survfit(fit0, newdata=list(x=0))
+surv2 <- survfit(fit0b, newdata=list(x=0))
+aeq(surv1$surv, surv2$surv)
+#
+# Check out the Efron approx.
+#
+
+fit0 <- coxph(Surv(time, status) ~x,testw1, weights=wt, iter=0)
+fit <- coxph(Surv(time, status) ~x,testw1, weights=wt)
+resid(fit0, 'mart')
+resid(coxph(Surv(time, status) ~1, testw1, weights=wt)) #Null model
+
+# lfun is the known log-likelihood for this data set, worked out in the
+# appendix of Therneau and Grambsch
+# ufun is the score vector and ifun the information matrix
+lfun <- function(beta) {
+ r <- exp(beta)
+ a <- 7*r +3
+ b <- 4*r +2
+ 11*beta - ( log(r^2 + 11*r +7) +
+ (10/3)*(log(a+b) + log(2*a/3 +b) + log(a/3 +b)) + 2*log(2*r +1))
+ }
+aeq(fit0$log[1], lfun(0))
+aeq(fit$log[2], lfun(fit$coef))
+
+ufun <- function(beta, efron=T) { #score statistic
+ r <- exp(beta)
+ xbar1 <- (2*r^2+11*r)/(r^2+11*r +7)
+ xbar2 <- 11*r/(11*r +5)
+ xbar3 <- 2*r/(2*r +1)
+ xbar2b<- 26*r/(26*r+12)
+ xbar2c<- 19*r/(19*r + 9)
+ temp <- 11 - (xbar1 + 2*xbar3)
+ if (efron) temp - (10/3)*(xbar2 + xbar2b + xbar2c)
+ else temp - 10*xbar2
+ }
+print(ufun(fit$coef) < 1e-4) # Should be true
+
+ifun <- function(beta, efron=T) { # information matrix
+ r <- exp(beta)
+ xbar1 <- (2*r^2+11*r)/(r^2+11*r +7)
+ xbar2 <- 11*r/(11*r +5)
+ xbar3 <- 2*r/(2*r +1)
+ xbar2b<- 26*r/(26*r+12)
+ xbar2c<- 19*r/(19*r + 9)
+ temp <- ((4*r^2 + 11*r)/(r^2+11*r +7) - xbar1^2) +
+ 2*(xbar3 - xbar3^2)
+ if (efron) temp + (10/3)*((xbar2- xbar2^2) + (xbar2b - xbar2b^2) +
+ (xbar2c -xbar2c^2))
+ else temp + 10 * (xbar2- xbar2^2)
+ }
+
+aeq(fit0$var, 1/ifun(0))
+aeq(fit$var, 1/ifun(fit$coef))
+
+
+
+# Make sure that the weights pass through the residuals correctly
+rr1 <- resid(fit, type='mart')
+rr2 <- resid(fit, type='mart', weighted=T)
+aeq(rr2/rr1, testw1$wt)
+rr1 <- resid(fit, type='score')
+rr2 <- resid(fit, type='score', weighted=T)
+aeq(rr2/rr1, testw1$wt)
+
+#
+# Look at the individual components
+#
+dt0 <- coxph.detail(fit0)
+dt <- coxph.detail(fit)
+aeq(sum(dt$score), ufun(fit$coef)) #score statistic
+aeq(sum(dt0$score), ufun(0))
+aeq(dt0$hazard, c(1/19, (10/3)*(1/16 + 1/(6+20/3) + 1/(6+10/3)), 2/3))
+
+
+
+rm(fit, fit0, rr1, rr2, dt, dt0)
+#
+# Effect of weights on the robust variance
+#
+test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
+ status=c(1,NA,1,0,1,1,0),
+ x= c(0, 2,1,1,1,0,0),
+ wt= c(3,0,1,1,1,1,1),
+ id= 1:7)
+testx <- data.frame(time= c(4,4,4,1,1,2,2,3),
+ status=c(1,1,1,1,0,1,1,0),
+ x= c(0,0,0,1,1,1,0,0),
+ wt= c(1,1,1,1,1,1,1,1),
+ id= 1:8)
+
+fit1 <- coxph(Surv(time, status) ~x + cluster(id), test1, method='breslow',
+ weights=wt)
+fit2 <- coxph(Surv(time, status) ~x + cluster(id), testx, method='breslow')
+
+db1 <- resid(fit1, 'dfbeta', weighted=F)
+db1 <- db1[-2] #toss the missing
+db2 <- resid(fit2, 'dfbeta')
+aeq(db1, db2[3:8])
+
+W <- c(3,1,1,1,1,1) #Weights, after removal of the missing value
+aeq(fit2$var, sum(db1*db1*W))
+aeq(fit1$var, sum(db1*db1*W*W))
+
diff --git a/win32/deps/library/survival/tests/doweight.Rout.save b/win32/deps/library/survival/tests/doweight.Rout.save
new file mode 100644
index 0000000..2a30311
--- /dev/null
+++ b/win32/deps/library/survival/tests/doweight.Rout.save
@@ -0,0 +1,429 @@
+
+R version 2.15.0 (2012-03-30)
+Copyright (C) 2012 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: i686-pc-linux-gnu (32-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> # Tests of the weighted Cox model
+> #
+> # Similar data set to test1, but add weights,
+> # a double-death/censor tied time
+> # a censored last subject
+> # The latter two are cases covered only feebly elsewhere.
+> #
+> # The data set testw2 has the same data, but done via replication
+> #
+> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+>
+> testw1 <- data.frame(time= c(1,1,2,2,2,2,3,4,5),
++ status= c(1,0,1,1,1,0,0,1,0),
++ x= c(2,0,1,1,0,1,0,1,0),
++ wt = c(1,2,3,4,3,2,1,2,1))
+> xx <- c(1,2,3,4,3,2,1,2,1)
+> testw2 <- data.frame(time= rep(c(1,1,2,2,2,2,3,4,5), xx),
++ status= rep(c(1,0,1,1,1,0,0,1,0), xx),
++ x= rep(c(2,0,1,1,0,1,0,1,0), xx),
++ id= rep(1:9, xx))
+> indx <- match(1:9, testw2$id)
+> testw2 <- data.frame(time= rep(c(1,1,2,2,2,2,3,4,5), xx),
++ status= rep(c(1,0,1,1,1,0,0,1,0), xx),
++ x= rep(c(2,0,1,1,0,1,0,1,0), xx),
++ id= rep(1:9, xx))
+> indx <- match(1:9, testw2$id)
+>
+> fit0 <- coxph(Surv(time, status) ~x, testw1, weights=wt,
++ method='breslow', iter=0)
+> fit0b <- coxph(Surv(time, status) ~x, testw2, method='breslow', iter=0)
+> fit <- coxph(Surv(time, status) ~x, testw1, weights=wt, method='breslow')
+> fitb <- coxph(Surv(time, status) ~x, testw2, method='breslow')
+>
+> texp <- function(beta) { # expected, Breslow estimate
++ r <- exp(beta)
++ temp <- cumsum(c(1/(r^2 + 11*r +7), 10/(11*r +5), 2/(2*r+1)))
++ c(r^2, 1,r,r,1,r,1,r,1)* temp[c(1,1,2,2,2,2,2,3,3)]
++ }
+> aeq(texp(0), c(1/19, 1/19, rep(103/152, 5), rep(613/456,2))) #verify texp()
+[1] TRUE
+>
+> xbar <- function(beta) { # xbar, Breslow estimate
++ r <- exp(beta)
++ temp <- r* rep(c(2*r + 11, 11/10, 1), c(2, 5, 2))
++ temp * texp(beta)
++ }
+>
+> fit0
+Call:
+coxph(formula = Surv(time, status) ~ x, data = testw1, weights = wt,
+ method = "breslow", iter = 0)
+
+
+ coef exp(coef) se(coef) z p
+x 0 1 0.586 0 1
+
+Likelihood ratio test=0 on 1 df, p=1 n= 9, number of events= 5
+> summary(fit)
+Call:
+coxph(formula = Surv(time, status) ~ x, data = testw1, weights = wt,
+ method = "breslow")
+
+ n= 9, number of events= 5
+
+ coef exp(coef) se(coef) z Pr(>|z|)
+x 0.8596 2.3621 0.7131 1.205 0.228
+
+ exp(coef) exp(-coef) lower .95 upper .95
+x 2.362 0.4233 0.5839 9.556
+
+Concordance= 0.638 (se = 0.159 )
+Rsquare= 0.171 (max possible= 0.999 )
+Likelihood ratio test= 1.69 on 1 df, p=0.1932
+Wald test = 1.45 on 1 df, p=0.2281
+Score (logrank) test = 1.52 on 1 df, p=0.217
+
+> aeq(resid(fit0), testw1$status - texp(0))
+[1] TRUE
+> resid(fit0, type='score')
+ 1 2 3 4 5 6
+ 1.24653740 0.03601108 0.10056700 0.10056700 -0.22180142 -0.21193300
+ 7 8 9
+ 0.46569858 -0.10082189 0.91014302
+> resid(fit0, type='scho')
+ 1 2 2 2 4
+ 1.3157895 0.3125000 0.3125000 -0.6875000 0.3333333
+>
+> aeq(resid(fit0, type='mart'), (resid(fit0b, type='mart'))[indx])
+[1] TRUE
+> aeq(resid(fit0, type='scor'), (resid(fit0b, type='scor'))[indx])
+[1] TRUE
+> aeq(unique(resid(fit0, type='scho')), unique(resid(fit0b, type='scho')))
+[1] TRUE
+>
+>
+> aeq(resid(fit, type='mart'), testw1$status - texp(fit$coef))
+[1] TRUE
+> resid(fit, type='score')
+ 1 2 3 4 5 6
+ 0.88681615 0.02497653 0.03608964 0.03608964 -0.54297652 -0.12528780
+ 7 8 9
+ 0.29564605 -0.09476911 0.58400064
+> resid(fit, type='scho')
+ 1 2 2 2 4
+ 1.0368337 0.1613774 0.1613774 -0.8386226 0.1746960
+> aeq(resid(fit, type='mart'), (resid(fitb, type='mart'))[indx])
+[1] TRUE
+> aeq(resid(fit, type='scor'), (resid(fitb, type='scor'))[indx])
+[1] TRUE
+> aeq(unique(resid(fit, type='scho')), unique(resid(fitb, type='scho')))
+[1] TRUE
+> rr1 <- resid(fit, type='mart')
+> rr2 <- resid(fit, type='mart', weighted=T)
+> aeq(rr2/rr1, testw1$wt)
+[1] TRUE
+>
+> rr1 <- resid(fit, type='score')
+> rr2 <- resid(fit, type='score', weighted=T)
+> aeq(rr2/rr1, testw1$wt)
+[1] TRUE
+>
+> fit <- coxph(Surv(time, status) ~x, testw1, weights=wt, method='efron')
+> fit
+Call:
+coxph(formula = Surv(time, status) ~ x, data = testw1, weights = wt,
+ method = "efron")
+
+
+ coef exp(coef) se(coef) z p
+x 0.873 2.39 0.713 1.22 0.22
+
+Likelihood ratio test=1.75 on 1 df, p=0.186 n= 9, number of events= 5
+> resid(fit, type='mart')
+ 1 2 3 4 5 6
+ 0.85334536 -0.02560716 0.32265266 0.32265266 0.71696234 -1.07772629
+ 7 8 9
+-0.45034077 -0.90490339 -0.79598658
+> resid(fit, type='score')
+ 1 2 3 4 5 6
+ 0.88116056 0.02477248 0.06057806 0.06057806 -0.59724033 -0.16737066
+ 7 8 9
+ 0.38040295 -0.13750290 0.66631324
+> resid(fit, type='scho')
+ 1 2 2 2 4
+ 1.0325955 0.1621759 0.1621759 -0.8378241 0.1728229
+>
+> # Tests of the weighted Cox model, AG form of the data
+> # Same solution as doweight1.s
+> #
+> testw3 <- data.frame(id = c( 1, 1, 2, 3, 3, 3, 4, 5, 5, 6, 7, 8, 8, 9),
++ begin= c( 0, 5, 0, 0,10,15, 0, 0,14, 0, 0, 0,23, 0),
++ time= c( 5,10,10,10,15,20,20,14,20,20,30,23,40,50),
++ status= c( 0, 1, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 1, 0),
++ x= c( 2, 2, 0, 1, 1, 1, 1, 0, 0, 1, 0, 1, 1, 0),
++ wt = c( 1, 1, 2, 3, 3, 3, 4, 3, 3, 2, 1, 2, 2, 1))
+>
+> fit0 <- coxph(Surv(begin,time, status) ~x, testw3, weights=wt,
++ method='breslow', iter=0)
+> fit <- coxph(Surv(begin,time, status) ~x, testw3, weights=wt, method='breslow')
+> fit0
+Call:
+coxph(formula = Surv(begin, time, status) ~ x, data = testw3,
+ weights = wt, method = "breslow", iter = 0)
+
+
+ coef exp(coef) se(coef) z p
+x 0 1 0.586 0 1
+
+Likelihood ratio test=0 on 1 df, p=1 n= 14, number of events= 5
+> summary(fit)
+Call:
+coxph(formula = Surv(begin, time, status) ~ x, data = testw3,
+ weights = wt, method = "breslow")
+
+ n= 14, number of events= 5
+
+ coef exp(coef) se(coef) z Pr(>|z|)
+x 0.8596 2.3621 0.7131 1.205 0.228
+
+ exp(coef) exp(-coef) lower .95 upper .95
+x 2.362 0.4233 0.5839 9.556
+
+Concordance= 0.638 (se = 0.159 )
+Rsquare= 0.114 (max possible= 0.991 )
+Likelihood ratio test= 1.69 on 1 df, p=0.1932
+Wald test = 1.45 on 1 df, p=0.2281
+Score (logrank) test = 1.52 on 1 df, p=0.217
+
+> resid(fit0, type='mart', collapse=testw3$id)
+ 1 2 3 4 5 6
+ 0.94736842 -0.05263158 0.32236842 0.32236842 0.32236842 -0.67763158
+ 7 8 9
+-0.67763158 -0.34429825 -1.34429825
+> resid(fit0, type='score', collapse=testw3$id)
+ 1 2 3 4 5 6
+ 1.24653740 0.03601108 0.10056700 0.10056700 -0.22180142 -0.21193300
+ 7 8 9
+ 0.46569858 -0.10082189 0.91014302
+> resid(fit0, type='scho')
+ 10 20 20 20 40
+ 1.3157895 0.3125000 0.3125000 -0.6875000 0.3333333
+>
+> resid(fit, type='mart', collapse=testw3$id)
+ 1 2 3 4 5 6
+ 0.85531186 -0.02593169 0.17636221 0.17636221 0.65131344 -0.82363779
+ 7 8 9
+-0.34868656 -0.64894181 -0.69807852
+> resid(fit, type='score', collapse=testw3$id)
+ 1 2 3 4 5 6
+ 0.88681615 0.02497653 0.03608964 0.03608964 -0.54297652 -0.12528780
+ 7 8 9
+ 0.29564605 -0.09476911 0.58400064
+> resid(fit, type='scho')
+ 10 20 20 20 40
+ 1.0368337 0.1613774 0.1613774 -0.8386226 0.1746960
+> fit0 <- coxph(Surv(begin, time, status) ~x,testw3, weights=wt, iter=0)
+> resid(fit0, 'mart', collapse=testw3$id)
+ 1 2 3 4 5 6
+ 0.94736842 -0.05263158 0.44454887 0.44454887 0.44454887 -0.88126566
+ 7 8 9
+-0.88126566 -0.54793233 -1.54793233
+> resid(coxph(Surv(begin, time, status) ~1, testw3, weights=wt)
++ , collapse=testw3$id) #Null model
+ 1 2 3 4 5 6
+ 0.94736842 -0.05263158 0.44454887 0.44454887 0.44454887 -0.88126566
+ 7 8 9
+-0.88126566 -0.54793233 -1.54793233
+>
+> fit <- coxph(Surv(begin,time, status) ~x, testw3, weights=wt, method='efron')
+> fit
+Call:
+coxph(formula = Surv(begin, time, status) ~ x, data = testw3,
+ weights = wt, method = "efron")
+
+
+ coef exp(coef) se(coef) z p
+x 0.873 2.39 0.713 1.22 0.22
+
+Likelihood ratio test=1.75 on 1 df, p=0.186 n= 14, number of events= 5
+> resid(fit, type='mart', collapse=testw3$id)
+ 1 2 3 4 5 6
+ 0.85334536 -0.02560716 0.32265266 0.32265266 0.71696234 -1.07772629
+ 7 8 9
+-0.45034077 -0.90490339 -0.79598658
+> resid(fit, type='score', collapse=testw3$id)
+ 1 2 3 4 5 6
+ 0.88116056 0.02477248 0.06057806 0.06057806 -0.59724033 -0.16737066
+ 7 8 9
+ 0.38040295 -0.13750290 0.66631324
+> resid(fit, type='scho')
+ 10 20 20 20 40
+ 1.0325955 0.1621759 0.1621759 -0.8378241 0.1728229
+> #
+> # Check out the impact of weights on the dfbetas
+> # Am I computing them correctly?
+> #
+> wtemp <- rep(1,26)
+> wtemp[c(5,10,15)] <- 2:4
+> fit <- coxph(Surv(futime, fustat) ~ age + ecog.ps, ovarian, weights=wtemp)
+> rr <- resid(fit, 'dfbeta')
+>
+> fit1 <- coxph(Surv(futime, fustat) ~ age + ecog.ps, ovarian, weights=wtemp,
++ subset=(-5))
+> fit2 <- coxph(Surv(futime, fustat) ~ age + ecog.ps, ovarian, weights=wtemp,
++ subset=(-10))
+> fit3 <- coxph(Surv(futime, fustat) ~ age + ecog.ps, ovarian, weights=wtemp,
++ subset=(-15))
+>
+> #
+> # Effect of case weights on expected survival curves post Cox model
+> #
+> fit0 <- coxph(Surv(time, status) ~x, testw1, weights=wt, method='breslow',
++ iter=0)
+> fit0b <- coxph(Surv(time, status) ~x, testw2, method='breslow', iter=0)
+>
+> surv1 <- survfit(fit0, newdata=list(x=0))
+> surv2 <- survfit(fit0b, newdata=list(x=0))
+> aeq(surv1$surv, surv2$surv)
+[1] TRUE
+> #
+> # Check out the Efron approx.
+> #
+>
+> fit0 <- coxph(Surv(time, status) ~x,testw1, weights=wt, iter=0)
+> fit <- coxph(Surv(time, status) ~x,testw1, weights=wt)
+> resid(fit0, 'mart')
+ 1 2 3 4 5 6
+ 0.94736842 -0.05263158 0.44454887 0.44454887 0.44454887 -0.88126566
+ 7 8 9
+-0.88126566 -0.54793233 -1.54793233
+> resid(coxph(Surv(time, status) ~1, testw1, weights=wt)) #Null model
+ 1 2 3 4 5 6
+ 0.94736842 -0.05263158 0.44454887 0.44454887 0.44454887 -0.88126566
+ 7 8 9
+-0.88126566 -0.54793233 -1.54793233
+>
+> # lfun is the known log-likelihood for this data set, worked out in the
+> # appendix of Therneau and Grambsch
+> # ufun is the score vector and ifun the information matrix
+> lfun <- function(beta) {
++ r <- exp(beta)
++ a <- 7*r +3
++ b <- 4*r +2
++ 11*beta - ( log(r^2 + 11*r +7) +
++ (10/3)*(log(a+b) + log(2*a/3 +b) + log(a/3 +b)) + 2*log(2*r +1))
++ }
+> aeq(fit0$log[1], lfun(0))
+[1] TRUE
+> aeq(fit$log[2], lfun(fit$coef))
+[1] TRUE
+>
+> ufun <- function(beta, efron=T) { #score statistic
++ r <- exp(beta)
++ xbar1 <- (2*r^2+11*r)/(r^2+11*r +7)
++ xbar2 <- 11*r/(11*r +5)
++ xbar3 <- 2*r/(2*r +1)
++ xbar2b<- 26*r/(26*r+12)
++ xbar2c<- 19*r/(19*r + 9)
++ temp <- 11 - (xbar1 + 2*xbar3)
++ if (efron) temp - (10/3)*(xbar2 + xbar2b + xbar2c)
++ else temp - 10*xbar2
++ }
+> print(ufun(fit$coef) < 1e-4) # Should be true
+ x
+TRUE
+>
+> ifun <- function(beta, efron=T) { # information matrix
++ r <- exp(beta)
++ xbar1 <- (2*r^2+11*r)/(r^2+11*r +7)
++ xbar2 <- 11*r/(11*r +5)
++ xbar3 <- 2*r/(2*r +1)
++ xbar2b<- 26*r/(26*r+12)
++ xbar2c<- 19*r/(19*r + 9)
++ temp <- ((4*r^2 + 11*r)/(r^2+11*r +7) - xbar1^2) +
++ 2*(xbar3 - xbar3^2)
++ if (efron) temp + (10/3)*((xbar2- xbar2^2) + (xbar2b - xbar2b^2) +
++ (xbar2c -xbar2c^2))
++ else temp + 10 * (xbar2- xbar2^2)
++ }
+>
+> aeq(fit0$var, 1/ifun(0))
+[1] TRUE
+> aeq(fit$var, 1/ifun(fit$coef))
+[1] TRUE
+>
+>
+>
+> # Make sure that the weights pass through the residuals correctly
+> rr1 <- resid(fit, type='mart')
+> rr2 <- resid(fit, type='mart', weighted=T)
+> aeq(rr2/rr1, testw1$wt)
+[1] TRUE
+> rr1 <- resid(fit, type='score')
+> rr2 <- resid(fit, type='score', weighted=T)
+> aeq(rr2/rr1, testw1$wt)
+[1] TRUE
+>
+> #
+> # Look at the individual components
+> #
+> dt0 <- coxph.detail(fit0)
+> dt <- coxph.detail(fit)
+> aeq(sum(dt$score), ufun(fit$coef)) #score statistic
+[1] TRUE
+> aeq(sum(dt0$score), ufun(0))
+[1] TRUE
+> aeq(dt0$hazard, c(1/19, (10/3)*(1/16 + 1/(6+20/3) + 1/(6+10/3)), 2/3))
+[1] TRUE
+>
+>
+>
+> rm(fit, fit0, rr1, rr2, dt, dt0)
+> #
+> # Effect of weights on the robust variance
+> #
+> test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
++ status=c(1,NA,1,0,1,1,0),
++ x= c(0, 2,1,1,1,0,0),
++ wt= c(3,0,1,1,1,1,1),
++ id= 1:7)
+> testx <- data.frame(time= c(4,4,4,1,1,2,2,3),
++ status=c(1,1,1,1,0,1,1,0),
++ x= c(0,0,0,1,1,1,0,0),
++ wt= c(1,1,1,1,1,1,1,1),
++ id= 1:8)
+>
+> fit1 <- coxph(Surv(time, status) ~x + cluster(id), test1, method='breslow',
++ weights=wt)
+> fit2 <- coxph(Surv(time, status) ~x + cluster(id), testx, method='breslow')
+>
+> db1 <- resid(fit1, 'dfbeta', weighted=F)
+> db1 <- db1[-2] #toss the missing
+> db2 <- resid(fit2, 'dfbeta')
+> aeq(db1, db2[3:8])
+[1] TRUE
+>
+> W <- c(3,1,1,1,1,1) #Weights, after removal of the missing value
+> aeq(fit2$var, sum(db1*db1*W))
+[1] TRUE
+> aeq(fit1$var, sum(db1*db1*W*W))
+[1] TRUE
+>
+>
+> proc.time()
+ user system elapsed
+ 0.292 0.036 0.325
diff --git a/win32/deps/library/survival/tests/expected.R b/win32/deps/library/survival/tests/expected.R
new file mode 100644
index 0000000..d82a3c4
--- /dev/null
+++ b/win32/deps/library/survival/tests/expected.R
@@ -0,0 +1,286 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+# Tests of expected survival
+aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+#
+# This makes several scripts easier
+# Certain tests depended in the now-depreciated date library
+{if (is.R()) mdy.date <- function(m, d, y) {
+ y <- ifelse(y<100, y+1900, y)
+ as.Date(paste(m,d,y, sep='/'), "%m/%d/%Y")
+ }
+else mdy.date <- function(m,d,y) {
+ y <- ifelse(y<100, y+1900, y)
+ timeDate(paste(y, m, d, sep='/'), in.format="%Y/%m/%d")
+ }
+ }
+
+# This function takes a single subject and walks down the rate table
+# Input: the vector of starting points, futime, and a ratetable
+# Output: the full history of walking through said table. Let n= #unique
+# rates that were used
+# cell = n by #dims of the table: index of the table cell
+# days = time spent in cell
+# hazard= accumulated hazard = days * rate
+# This does not do date or factor conversions -- start has to be numeric
+#
+ratewalk <- function(start, futime, ratetable=survexp.us) {
+ if (!is.ratetable(ratetable)) stop("Bad rate table")
+ ratedim <- dim(ratetable)
+ nvar <- length(ratedim)
+ if (length(start) != nvar) stop("Wrong length for start")
+ if (futime <=0) stop("Invalid futime")
+
+ attR <- attributes(ratetable)
+ discrete <- (attR$type ==1) #discrete categories
+
+ maxn <- sum(!discrete)*prod(ratedim[!discrete]) #most cells you can hit
+ cell <- matrix(0, nrow=maxn, ncol=nvar)
+ days <- hazard <- double(maxn)
+
+ eps <- 1e-8 #Avoid round off error
+ n <- 0
+ while (futime >0) {
+ n <- n+1
+ #what cell am I in?
+ # Note that at the edges of the rate table, we use the edge: if
+ # it only goes up the the year 2000, year 2000 is used for any
+ # dates beyond. This effectively eliminates one boundary
+ cell[n,discrete] <- start[discrete]
+ edge <- futime #time to nearest edge, or finish
+ for (j in which(!discrete)) {
+ indx <- sum(start[j] >= attR$cutpoints[[j]]-eps)
+ cell[n, j] <- max(1, indx)
+ if (indx < ratedim[j])
+ edge <- min(edge, (attR$cutpoints[[j]])[indx+1] - start[j])
+ }
+ days[n] <- edge #this many days in the cell
+ # using a matrix as a subscript is so handy sometimes
+ hazard[n] <- edge * (as.matrix(ratetable))[cell[n,,drop=F]]
+ futime <- futime - edge #amount of time yet to account for
+ start[!discrete] <- start[!discrete] + edge #walk forward in time
+ }
+ list(cell=cell[1:n,], days=days[1:n], hazard=hazard[1:n])
+ }
+
+# Simple test of ratewalk: 20 years old, start on 7Sep 1960 (day 250)
+# 116 days at the 1960, 20 year old male rate, through the end of the day
+# on 12/31/1960, then 84 days at the 1961 rate.
+# The decennial q for 1960 males is .00169.
+zz <- ratewalk(c(20.4*365.25, 1, 250), 200)
+all.equal(zz$hazard[1], -(116/365.25)*log(1-.00169))
+all.equal(zz$days, c(116,84))
+
+
+#
+# Simple case 1: a single male subject, born 1/1/36 and entered on study 1/2/55
+#
+# Compute the 1, 5, 10 and 12 year expected survival
+
+temp1 <- mdy.date(1,1,36)
+temp2 <- mdy.date(1,2,55)
+exp1 <- survexp(~ratetable(year=temp2, age=(temp2-temp1), sex=1, race='white'),
+ ratetable=survexp.usr,times=c(366, 1827, 3653, 4383))
+
+tyear <- as.numeric(temp2 - mdy.date(1,1,1960))
+h1 <- ratewalk(c(temp2-temp1, 1, 1, tyear), 366, survexp.usr)
+h2 <- ratewalk(c(temp2-temp1, 1, 1, tyear), 1827, survexp.usr)
+h3 <- ratewalk(c(temp2-temp1, 1, 1, tyear), 3653, survexp.usr)
+h4 <- ratewalk(c(temp2-temp1, 1, 1, tyear), 4383, survexp.usr)
+
+aeq(-log(exp1$surv), c(sum(h1$hazard), sum(h2$hazard), sum(h3$hazard),
+ sum(h4$hazard)))
+
+
+# Just a little harder:
+# Born 3/1/25 and entered the study on 6/10/55. The code creates shifted
+# dates to align with US rate tables - entry is 59 days earlier (days from
+# 1/1/25 to 3/1/25).
+#
+temp1 <- mdy.date(3,1,25)
+temp2 <- mdy.date(6,10,55)
+exp1 <- survexp(~ratetable(year=temp2, age=(temp2-temp1), sex=2, race='black'),
+ ratetable=survexp.usr,times=c(366, 1827, 3653, 4383))
+
+tyear <- as.numeric(temp2 - mdy.date(1,1,1960)) - 59
+h1 <- ratewalk(c(temp2-temp1, 2, 2, tyear), 366, survexp.usr)
+h2 <- ratewalk(c(temp2-temp1, 2, 2, tyear), 1827, survexp.usr)
+h3 <- ratewalk(c(temp2-temp1, 2, 2, tyear), 3653, survexp.usr)
+h4 <- ratewalk(c(temp2-temp1, 2, 2, tyear), 4383, survexp.usr)
+
+aeq(-log(exp1$surv), c(sum(h1$hazard), sum(h2$hazard), sum(h3$hazard),
+ sum(h4$hazard)))
+
+rm(temp1, temp2, zz, exp1, h1, h2, h3, h4 )
+
+#
+# Simple case 2: make sure that the averages are correct, for Ederer method
+#
+# Compute the 1, 5, 10 and 12 year expected survival
+
+temp1 <- mdy.date(1:6,6:11,1890:1895)
+temp2 <- mdy.date(6:1,11:6,c(55:50))
+temp3 <- c(1,2,1,2,1,2)
+age <- temp2 - temp1
+
+exp1 <- survexp(~ratetable(year=temp2, age=(temp2-temp1), sex=temp3),
+ times=c(366, 1827, 3653, 4383))
+exp2 <- survexp(~ratetable(year=temp2, age=(temp2-temp1), sex=temp3) + I(1:6),
+ times=c(366, 1827, 3653, 4383))
+exp3 <- exp2$surv
+for (i in 1:length(temp1)){
+ exp3[,i] <- survexp(~ratetable(year=temp2, age=(temp2-temp1), sex=temp3),
+ times=c(366, 1827, 3653, 4383), subset=i)$surv
+ }
+
+
+print(aeq(exp2$surv, exp3))
+print(all.equal(exp1$surv, apply(exp2$surv, 1, mean)))
+
+# They agree, but are they right?
+#
+for (i in 1:length(temp1)) {
+ offset <- as.numeric(temp1[i] - mdy.date(1,1, 1889+i))
+ tyear = (as.numeric(temp2[i] - mdy.date(1,1,1960))) - offset
+ haz1 <- ratewalk(c((temp2-temp1)[i], temp3[i], tyear), 366)
+ haz2 <- ratewalk(c((temp2-temp1)[i], temp3[i], tyear), 1827)
+ haz3 <- ratewalk(c((temp2-temp1)[i], temp3[i], tyear), 3653)
+ haz4 <- ratewalk(c((temp2-temp1)[i], temp3[i], tyear), 4383)
+ print(aeq(-log(exp2$surv[,i]), c(sum(haz1$hazard), sum(haz2$hazard),
+ sum(haz3$hazard), sum(haz4$hazard))))
+ }
+
+#
+# Check that adding more time points doesn't change things
+#
+exp4 <- survexp(~ratetable(year=temp2, age=(temp2-temp1), sex=temp3) + I(1:6),
+ times=sort(c(366, 1827, 3653, 4383, 30*(1:100))))
+aeq(exp4$surv[match(exp2$time, exp4$time),], exp2$surv)
+
+exp4 <- survexp(~ratetable(year=temp2, age=(temp2-temp1), sex=temp3),
+ times=sort(c(366, 1827, 3653, 4383, 30*(1:100))))
+aeq(exp1$surv, exp4$surv[match(exp1$time, exp4$time, nomatch=0)])
+
+
+#
+# Now test Hakulinen's method, assuming an analysis date of 3/1/57
+#
+futime <- mdy.date(3,1,57) - temp2
+xtime <- sort(c(futime, 30, 60, 185, 365))
+
+exp1 <- survexp(futime ~ ratetable(year=temp2, age=(temp2-temp1), sex=1),
+ times=xtime, conditional=F)
+exp2 <- survexp(~ratetable(year=temp2, age=(temp2-temp1), sex=1) + I(1:6),
+ times=futime)
+
+wt <- rep(1,6)
+con <- double(6)
+for (i in 1:6) {
+ con[i] <- sum(exp2$surv[i,i:6])/sum(wt[i:6])
+ wt <- exp2$surv[i,]
+ }
+
+exp1$surv[match(futime, xtime)]
+aeq(exp1$surv[match(futime, xtime)], cumprod(con))
+
+
+#
+# Now for the conditional method
+#
+exp1 <- survexp(futime ~ ratetable(year=temp2, age=(temp2-temp1), sex=1),
+ times=xtime, conditional=T)
+
+cond <- exp2$surv
+for (i in 6:2) cond[i,] <- (cond[i,]/cond[i-1,]) #conditional survival
+for (i in 1:6) con[i] <- exp(mean(log(cond[i, i:6])))
+
+all.equal(exp1$surv[match(futime, xtime)], cumprod(con))
+cumprod(con)
+
+rm(con, cond, exp1, exp2, wt, temp1, temp2, age)
+rm(exp3, exp4, futime, xtime)
+
+#
+# Test out expected survival, when the parent pop is another Cox model
+#
+test1 <- data.frame(time= c(4, 3,1,1,2,2,3),
+ status=c(1,NA,1,0,1,1,0),
+ x= c(0, 2,1,1,1,0,0))
+
+fit <- coxph(Surv(time, status) ~x, test1, method='breslow')
+
+dummy <- data.frame(time=c(.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5),
+ status=c(1,0,1,0,1,0,1,1,1), x=(-4:4)/2)
+
+efit <- survexp(time ~ ratetable(x=x), dummy, ratetable=fit, cohort=F)
+
+#
+# Now, compare to the true answer, which is known to us
+#
+ss <- exp(fit$coef)
+haz <- c( 1/(3*ss+3), 2/(ss+3), 1) #truth at time 0,1,2,4+
+chaz <- cumsum(c(0,haz))
+chaz2 <- chaz[c(1,2,2,3,3,3,3,4,4)]
+
+risk <- exp(fit$coef*dummy$x)
+efit2 <- exp(-risk*chaz2)
+
+all.equal(as.vector(efit), as.vector(efit2)) #ignore mismatched name attrib
+
+#
+# Now test the direct-adjusted curve (Ederer)
+#
+efit <- survexp( ~ ratetable(x=x), dummy, ratetable=fit, se=F)
+direct <- survfit(fit, newdata=dummy, censor=FALSE)$surv
+
+chaz <- chaz[-1] #drop time 0
+d2 <- exp(outer(-chaz, risk))
+all.equal(as.vector(direct), as.vector(d2)) #this tests survfit
+
+all.equal(as.vector(efit$surv), as.vector(apply(direct,1,mean))) #direct
+
+# Check out the "times" arg of survexp
+efit2 <- survexp( ~ ratetable(x=x), dummy, ratetable=fit, se=F,
+ times=c(.5, 2, 3.5,6))
+aeq(efit2$surv, c(1, efit$surv[c(2,2,3)]))
+
+#
+# Now test out the Hakulinen method (Bonsel's method)
+# By construction, we have a large correlation between x and censoring
+#
+# In theory, hak1 and hak2 would be the same. In practice, like a KM and
+# F-H, they differ when n is small.
+#
+efit <- survexp( time ~ ratetable(x=x), dummy, ratetable=fit, se=F)
+
+surv <- wt <- rep(1,9)
+tt <- c(1,2,4)
+hak1 <- hak2 <- NULL
+for (i in 1:3) {
+ wt[dummy$time < tt[i]] <- 0
+ hak1 <- c(hak1, exp(-sum(haz[i]*risk*surv*wt)/sum(surv*wt)))
+ hak2 <- c(hak2, sum(exp(-haz[i]*risk)*surv*wt)/sum(surv*wt))
+ surv <- surv * exp(-haz[i]*risk)
+ }
+
+all.equal(as.vector(efit$surv), as.vector(cumprod(hak2)))
+
+#
+# Now do the conditional estimate
+#
+efit <- survexp( time ~ ratetable(x=x), dummy, ratetable=fit, se=F,
+ conditional=T)
+wt <- rep(1,9)
+cond <- NULL
+for (i in 1:3) {
+ wt[dummy$time < tt[i]] <- 0
+ cond <- c(cond, exp(-sum(haz[i]*risk*wt)/sum(wt)))
+ }
+
+all.equal(as.vector(efit$surv), as.vector(cumprod(cond)))
+
+rm(wt, cond, efit, tt, surv, hak1, hak2)
+rm(fit, dummy, ss, efit2, chaz, chaz2, risk)
+rm(d2, direct)
diff --git a/win32/deps/library/survival/tests/expected.Rout.save b/win32/deps/library/survival/tests/expected.Rout.save
new file mode 100644
index 0000000..67a8b0d
--- /dev/null
+++ b/win32/deps/library/survival/tests/expected.Rout.save
@@ -0,0 +1,329 @@
+
+R version 2.11.1 (2010-05-31)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> # Tests of expected survival
+> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+> #
+> # This makes several scripts easier
+> # Certain tests depended in the now-depreciated date library
+> {if (is.R()) mdy.date <- function(m, d, y) {
++ y <- ifelse(y<100, y+1900, y)
++ as.Date(paste(m,d,y, sep='/'), "%m/%d/%Y")
++ }
++ else mdy.date <- function(m,d,y) {
++ y <- ifelse(y<100, y+1900, y)
++ timeDate(paste(y, m, d, sep='/'), in.format="%Y/%m/%d")
++ }
++ }
+>
+> # This function takes a single subject and walks down the rate table
+> # Input: the vector of starting points, futime, and a ratetable
+> # Output: the full history of walking through said table. Let n= #unique
+> # rates that were used
+> # cell = n by #dims of the table: index of the table cell
+> # days = time spent in cell
+> # hazard= accumulated hazard = days * rate
+> # This does not do date or factor conversions -- start has to be numeric
+> #
+> ratewalk <- function(start, futime, ratetable=survexp.us) {
++ if (!is.ratetable(ratetable)) stop("Bad rate table")
++ ratedim <- dim(ratetable)
++ nvar <- length(ratedim)
++ if (length(start) != nvar) stop("Wrong length for start")
++ if (futime <=0) stop("Invalid futime")
++
++ attR <- attributes(ratetable)
++ discrete <- (attR$type ==1) #discrete categories
++
++ maxn <- sum(!discrete)*prod(ratedim[!discrete]) #most cells you can hit
++ cell <- matrix(0, nrow=maxn, ncol=nvar)
++ days <- hazard <- double(maxn)
++
++ eps <- 1e-8 #Avoid round off error
++ n <- 0
++ while (futime >0) {
++ n <- n+1
++ #what cell am I in?
++ # Note that at the edges of the rate table, we use the edge: if
++ # it only goes up the the year 2000, year 2000 is used for any
++ # dates beyond. This effectively eliminates one boundary
++ cell[n,discrete] <- start[discrete]
++ edge <- futime #time to nearest edge, or finish
++ for (j in which(!discrete)) {
++ indx <- sum(start[j] >= attR$cutpoints[[j]]-eps)
++ cell[n, j] <- max(1, indx)
++ if (indx < ratedim[j])
++ edge <- min(edge, (attR$cutpoints[[j]])[indx+1] - start[j])
++ }
++ days[n] <- edge #this many days in the cell
++ # using a matrix as a subscript is so handy sometimes
++ hazard[n] <- edge * (as.matrix(ratetable))[cell[n,,drop=F]]
++ futime <- futime - edge #amount of time yet to account for
++ start[!discrete] <- start[!discrete] + edge #walk forward in time
++ }
++ list(cell=cell[1:n,], days=days[1:n], hazard=hazard[1:n])
++ }
+>
+> # Simple test of ratewalk: 20 years old, start on 7Sep 1960 (day 250)
+> # 116 days at the 1960, 20 year old male rate, through the end of the day
+> # on 12/31/1960, then 84 days at the 1961 rate.
+> # The decennial q for 1960 males is .00169.
+> zz <- ratewalk(c(20.4*365.25, 1, 250), 200)
+> all.equal(zz$hazard[1], -(116/365.25)*log(1-.00169))
+[1] TRUE
+> all.equal(zz$days, c(116,84))
+[1] TRUE
+>
+>
+> #
+> # Simple case 1: a single male subject, born 1/1/36 and entered on study 1/2/55
+> #
+> # Compute the 1, 5, 10 and 12 year expected survival
+>
+> temp1 <- mdy.date(1,1,36)
+> temp2 <- mdy.date(1,2,55)
+> exp1 <- survexp(~ratetable(year=temp2, age=(temp2-temp1), sex=1, race='white'),
++ ratetable=survexp.usr,times=c(366, 1827, 3653, 4383))
+>
+> tyear <- as.numeric(temp2 - mdy.date(1,1,1960))
+> h1 <- ratewalk(c(temp2-temp1, 1, 1, tyear), 366, survexp.usr)
+> h2 <- ratewalk(c(temp2-temp1, 1, 1, tyear), 1827, survexp.usr)
+> h3 <- ratewalk(c(temp2-temp1, 1, 1, tyear), 3653, survexp.usr)
+> h4 <- ratewalk(c(temp2-temp1, 1, 1, tyear), 4383, survexp.usr)
+>
+> aeq(-log(exp1$surv), c(sum(h1$hazard), sum(h2$hazard), sum(h3$hazard),
++ sum(h4$hazard)))
+[1] TRUE
+>
+>
+> # Just a little harder:
+> # Born 3/1/25 and entered the study on 6/10/55. The code creates shifted
+> # dates to align with US rate tables - entry is 59 days earlier (days from
+> # 1/1/25 to 3/1/25).
+> #
+> temp1 <- mdy.date(3,1,25)
+> temp2 <- mdy.date(6,10,55)
+> exp1 <- survexp(~ratetable(year=temp2, age=(temp2-temp1), sex=2, race='black'),
++ ratetable=survexp.usr,times=c(366, 1827, 3653, 4383))
+>
+> tyear <- as.numeric(temp2 - mdy.date(1,1,1960)) - 59
+> h1 <- ratewalk(c(temp2-temp1, 2, 2, tyear), 366, survexp.usr)
+> h2 <- ratewalk(c(temp2-temp1, 2, 2, tyear), 1827, survexp.usr)
+> h3 <- ratewalk(c(temp2-temp1, 2, 2, tyear), 3653, survexp.usr)
+> h4 <- ratewalk(c(temp2-temp1, 2, 2, tyear), 4383, survexp.usr)
+>
+> aeq(-log(exp1$surv), c(sum(h1$hazard), sum(h2$hazard), sum(h3$hazard),
++ sum(h4$hazard)))
+[1] TRUE
+>
+> rm(temp1, temp2, zz, exp1, h1, h2, h3, h4 )
+>
+> #
+> # Simple case 2: make sure that the averages are correct, for Ederer method
+> #
+> # Compute the 1, 5, 10 and 12 year expected survival
+>
+> temp1 <- mdy.date(1:6,6:11,1890:1895)
+> temp2 <- mdy.date(6:1,11:6,c(55:50))
+> temp3 <- c(1,2,1,2,1,2)
+> age <- temp2 - temp1
+>
+> exp1 <- survexp(~ratetable(year=temp2, age=(temp2-temp1), sex=temp3),
++ times=c(366, 1827, 3653, 4383))
+> exp2 <- survexp(~ratetable(year=temp2, age=(temp2-temp1), sex=temp3) + I(1:6),
++ times=c(366, 1827, 3653, 4383))
+> exp3 <- exp2$surv
+> for (i in 1:length(temp1)){
++ exp3[,i] <- survexp(~ratetable(year=temp2, age=(temp2-temp1), sex=temp3),
++ times=c(366, 1827, 3653, 4383), subset=i)$surv
++ }
+>
+>
+> print(aeq(exp2$surv, exp3))
+[1] TRUE
+> print(all.equal(exp1$surv, apply(exp2$surv, 1, mean)))
+[1] TRUE
+>
+> # They agree, but are they right?
+> #
+> for (i in 1:length(temp1)) {
++ offset <- as.numeric(temp1[i] - mdy.date(1,1, 1889+i))
++ tyear = (as.numeric(temp2[i] - mdy.date(1,1,1960))) - offset
++ haz1 <- ratewalk(c((temp2-temp1)[i], temp3[i], tyear), 366)
++ haz2 <- ratewalk(c((temp2-temp1)[i], temp3[i], tyear), 1827)
++ haz3 <- ratewalk(c((temp2-temp1)[i], temp3[i], tyear), 3653)
++ haz4 <- ratewalk(c((temp2-temp1)[i], temp3[i], tyear), 4383)
++ print(aeq(-log(exp2$surv[,i]), c(sum(haz1$hazard), sum(haz2$hazard),
++ sum(haz3$hazard), sum(haz4$hazard))))
++ }
+[1] TRUE
+[1] TRUE
+[1] TRUE
+[1] TRUE
+[1] TRUE
+[1] TRUE
+>
+> #
+> # Check that adding more time points doesn't change things
+> #
+> exp4 <- survexp(~ratetable(year=temp2, age=(temp2-temp1), sex=temp3) + I(1:6),
++ times=sort(c(366, 1827, 3653, 4383, 30*(1:100))))
+> aeq(exp4$surv[match(exp2$time, exp4$time),], exp2$surv)
+[1] TRUE
+>
+> exp4 <- survexp(~ratetable(year=temp2, age=(temp2-temp1), sex=temp3),
++ times=sort(c(366, 1827, 3653, 4383, 30*(1:100))))
+> aeq(exp1$surv, exp4$surv[match(exp1$time, exp4$time, nomatch=0)])
+[1] TRUE
+>
+>
+> #
+> # Now test Hakulinen's method, assuming an analysis date of 3/1/57
+> #
+> futime <- mdy.date(3,1,57) - temp2
+> xtime <- sort(c(futime, 30, 60, 185, 365))
+>
+> exp1 <- survexp(futime ~ ratetable(year=temp2, age=(temp2-temp1), sex=1),
++ times=xtime, conditional=F)
+> exp2 <- survexp(~ratetable(year=temp2, age=(temp2-temp1), sex=1) + I(1:6),
++ times=futime)
+>
+> wt <- rep(1,6)
+> con <- double(6)
+> for (i in 1:6) {
++ con[i] <- sum(exp2$surv[i,i:6])/sum(wt[i:6])
++ wt <- exp2$surv[i,]
++ }
+>
+> exp1$surv[match(futime, xtime)]
+[1] 0.9557362 0.9285840 0.9025661 0.8774220 0.8532489 0.8297416
+> aeq(exp1$surv[match(futime, xtime)], cumprod(con))
+[1] TRUE
+>
+>
+> #
+> # Now for the conditional method
+> #
+> exp1 <- survexp(futime ~ ratetable(year=temp2, age=(temp2-temp1), sex=1),
++ times=xtime, conditional=T)
+>
+> cond <- exp2$surv
+> for (i in 6:2) cond[i,] <- (cond[i,]/cond[i-1,]) #conditional survival
+> for (i in 1:6) con[i] <- exp(mean(log(cond[i, i:6])))
+>
+> all.equal(exp1$surv[match(futime, xtime)], cumprod(con))
+[1] TRUE
+> cumprod(con)
+[1] 0.9556656 0.9284398 0.9023612 0.8771798 0.8529944 0.8294940
+>
+> rm(con, cond, exp1, exp2, wt, temp1, temp2, age)
+> rm(exp3, exp4, futime, xtime)
+>
+> #
+> # Test out expected survival, when the parent pop is another Cox model
+> #
+> test1 <- data.frame(time= c(4, 3,1,1,2,2,3),
++ status=c(1,NA,1,0,1,1,0),
++ x= c(0, 2,1,1,1,0,0))
+>
+> fit <- coxph(Surv(time, status) ~x, test1, method='breslow')
+>
+> dummy <- data.frame(time=c(.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5),
++ status=c(1,0,1,0,1,0,1,1,1), x=(-4:4)/2)
+>
+> efit <- survexp(time ~ ratetable(x=x), dummy, ratetable=fit, cohort=F)
+>
+> #
+> # Now, compare to the true answer, which is known to us
+> #
+> ss <- exp(fit$coef)
+> haz <- c( 1/(3*ss+3), 2/(ss+3), 1) #truth at time 0,1,2,4+
+> chaz <- cumsum(c(0,haz))
+> chaz2 <- chaz[c(1,2,2,3,3,3,3,4,4)]
+>
+> risk <- exp(fit$coef*dummy$x)
+> efit2 <- exp(-risk*chaz2)
+>
+> all.equal(as.vector(efit), as.vector(efit2)) #ignore mismatched name attrib
+[1] TRUE
+>
+> #
+> # Now test the direct-adjusted curve (Ederer)
+> #
+> efit <- survexp( ~ ratetable(x=x), dummy, ratetable=fit, se=F)
+> direct <- survfit(fit, newdata=dummy, censor=FALSE)$surv
+>
+> chaz <- chaz[-1] #drop time 0
+> d2 <- exp(outer(-chaz, risk))
+> all.equal(as.vector(direct), as.vector(d2)) #this tests survfit
+[1] TRUE
+>
+> all.equal(as.vector(efit$surv), as.vector(apply(direct,1,mean))) #direct
+[1] TRUE
+>
+> # Check out the "times" arg of survexp
+> efit2 <- survexp( ~ ratetable(x=x), dummy, ratetable=fit, se=F,
++ times=c(.5, 2, 3.5,6))
+> aeq(efit2$surv, c(1, efit$surv[c(2,2,3)]))
+[1] TRUE
+>
+> #
+> # Now test out the Hakulinen method (Bonsel's method)
+> # By construction, we have a large correlation between x and censoring
+> #
+> # In theory, hak1 and hak2 would be the same. In practice, like a KM and
+> # F-H, they differ when n is small.
+> #
+> efit <- survexp( time ~ ratetable(x=x), dummy, ratetable=fit, se=F)
+>
+> surv <- wt <- rep(1,9)
+> tt <- c(1,2,4)
+> hak1 <- hak2 <- NULL
+> for (i in 1:3) {
++ wt[dummy$time < tt[i]] <- 0
++ hak1 <- c(hak1, exp(-sum(haz[i]*risk*surv*wt)/sum(surv*wt)))
++ hak2 <- c(hak2, sum(exp(-haz[i]*risk)*surv*wt)/sum(surv*wt))
++ surv <- surv * exp(-haz[i]*risk)
++ }
+>
+> all.equal(as.vector(efit$surv), as.vector(cumprod(hak2)))
+[1] TRUE
+>
+> #
+> # Now do the conditional estimate
+> #
+> efit <- survexp( time ~ ratetable(x=x), dummy, ratetable=fit, se=F,
++ conditional=T)
+> wt <- rep(1,9)
+> cond <- NULL
+> for (i in 1:3) {
++ wt[dummy$time < tt[i]] <- 0
++ cond <- c(cond, exp(-sum(haz[i]*risk*wt)/sum(wt)))
++ }
+>
+> all.equal(as.vector(efit$surv), as.vector(cumprod(cond)))
+[1] TRUE
+>
+> rm(wt, cond, efit, tt, surv, hak1, hak2)
+> rm(fit, dummy, ss, efit2, chaz, chaz2, risk)
+> rm(d2, direct)
+>
diff --git a/win32/deps/library/survival/tests/expected2.R b/win32/deps/library/survival/tests/expected2.R
new file mode 100644
index 0000000..3c14410
--- /dev/null
+++ b/win32/deps/library/survival/tests/expected2.R
@@ -0,0 +1,16 @@
+library(survival)
+#
+# A Cox model with a factor, followed by survexp.
+#
+pfit2 <- coxph(Surv(time, status > 0) ~ trt + log(bili) +
+ log(protime) + age + platelet + sex, data = pbc)
+esurv <- survexp(~ trt, ratetable = pfit2, data = pbc)
+
+temp <- pbc
+temp$sex2 <- factor(as.numeric(pbc$sex), levels=2:0,
+ labels=c("f", "m", "unknown"))
+esurv2 <- survexp(~ trt, ratetable = pfit2, data = temp,
+ rmap=list(sex=sex2))
+
+# The call components won't match, which happen to be first
+all.equal(unclass(esurv)[-1], unclass(esurv2)[-1])
diff --git a/win32/deps/library/survival/tests/expected2.Rout.save b/win32/deps/library/survival/tests/expected2.Rout.save
new file mode 100644
index 0000000..deee9ee
--- /dev/null
+++ b/win32/deps/library/survival/tests/expected2.Rout.save
@@ -0,0 +1,36 @@
+
+R version 2.11.1 (2010-05-31)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+> #
+> # A Cox model with a factor, followed by survexp.
+> #
+> pfit2 <- coxph(Surv(time, status > 0) ~ trt + log(bili) +
++ log(protime) + age + platelet + sex, data = pbc)
+> esurv <- survexp(~ trt, ratetable = pfit2, data = pbc)
+>
+> temp <- pbc
+> temp$sex2 <- factor(as.numeric(pbc$sex), levels=2:0,
++ labels=c("f", "m", "unknown"))
+> esurv2 <- survexp(~ trt, ratetable = pfit2, data = temp,
++ rmap=list(sex=sex2))
+>
+> # The call components won't match, which happen to be first
+> all.equal(unclass(esurv)[-1], unclass(esurv2)[-1])
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/factor.R b/win32/deps/library/survival/tests/factor.R
new file mode 100644
index 0000000..60070cb
--- /dev/null
+++ b/win32/deps/library/survival/tests/factor.R
@@ -0,0 +1,33 @@
+#
+# Ensure that factors work in prediction
+#
+library(survival)
+
+options(na.action="na.exclude") # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+
+tfit <- coxph(Surv(time, status) ~ age + factor(ph.ecog), lung)
+p1 <- predict(tfit, type='risk')
+
+# Testing NA handling is important too
+keep <- (is.na(lung$ph.ecog) | lung$ph.ecog !=1)
+lung2 <- lung[keep,]
+p2 <- predict(tfit, type='risk', newdata=lung[keep,])
+aeq(p1[keep], p2)
+
+# Same, for survreg
+tfit <- survreg(Surv(time, status) ~ age + factor(ph.ecog), lung)
+p1 <- predict(tfit, type='response')
+p2 <- predict(tfit, type='response', newdata=lung2)
+aeq(p1[keep], p2)
+
+
+# Now repeat it tossing the missings
+options(na.action=na.omit)
+keep2 <- (lung$ph.ecog[!is.na(lung$ph.ecog)] !=1)
+
+tfit2 <- survreg(Surv(time, status) ~ age + factor(ph.ecog), lung)
+p3 <- predict(tfit2, type='response')
+p4 <- predict(tfit2, type='response', newdata=lung2, na.action=na.omit)
+aeq(p3[keep2] , p4)
diff --git a/win32/deps/library/survival/tests/factor.Rout.save b/win32/deps/library/survival/tests/factor.Rout.save
new file mode 100644
index 0000000..77db11d
--- /dev/null
+++ b/win32/deps/library/survival/tests/factor.Rout.save
@@ -0,0 +1,56 @@
+
+R version 2.14.0 (2011-10-31)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: i686-pc-linux-gnu (32-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> #
+> # Ensure that factors work in prediction
+> #
+> library(survival)
+Loading required package: splines
+>
+> options(na.action="na.exclude") # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+>
+> tfit <- coxph(Surv(time, status) ~ age + factor(ph.ecog), lung)
+> p1 <- predict(tfit, type='risk')
+>
+> # Testing NA handling is important too
+> keep <- (is.na(lung$ph.ecog) | lung$ph.ecog !=1)
+> lung2 <- lung[keep,]
+> p2 <- predict(tfit, type='risk', newdata=lung[keep,])
+> aeq(p1[keep], p2)
+[1] TRUE
+>
+> # Same, for survreg
+> tfit <- survreg(Surv(time, status) ~ age + factor(ph.ecog), lung)
+> p1 <- predict(tfit, type='response')
+> p2 <- predict(tfit, type='response', newdata=lung2)
+> aeq(p1[keep], p2)
+[1] TRUE
+>
+>
+> # Now repeat it tossing the missings
+> options(na.action=na.omit)
+> keep2 <- (lung$ph.ecog[!is.na(lung$ph.ecog)] !=1)
+>
+> tfit2 <- survreg(Surv(time, status) ~ age + factor(ph.ecog), lung)
+> p3 <- predict(tfit2, type='response')
+> p4 <- predict(tfit2, type='response', newdata=lung2, na.action=na.omit)
+> aeq(p3[keep2] , p4)
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/factor2.R b/win32/deps/library/survival/tests/factor2.R
new file mode 100644
index 0000000..07dca32
--- /dev/null
+++ b/win32/deps/library/survival/tests/factor2.R
@@ -0,0 +1,26 @@
+library(survival)
+aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+options(na.action=na.exclude)
+#
+# More tests of factors in prediction, using a new data set
+#
+fit <- coxph(Surv(time, status) ~ factor(ph.ecog), lung)
+
+tdata <- data.frame(ph.ecog = factor(0:3))
+p1 <- predict(fit, newdata=tdata, type='lp')
+p2 <- predict(fit, type='lp')
+aeq(p1, p2[match(0:3, lung$ph.ecog)])
+
+fit2 <- coxph(Surv(time, status) ~ factor(ph.ecog) + factor(sex), lung)
+tdata <- expand.grid(ph.ecog = factor(0:3), sex=factor(1:2))
+p1 <- predict(fit2, newdata=tdata, type='risk')
+
+xdata <- expand.grid(ph.ecog=factor(1:3), sex=factor(1:2))
+p2 <- predict(fit2, newdata=xdata, type='risk')
+all.equal(p2, p1[c(2:4, 6:8)], check.attributes=FALSE)
+
+
+fit3 <- survreg(Surv(time, status) ~ factor(ph.ecog) + age, lung)
+tdata <- data.frame(ph.ecog=factor(0:3), age=50)
+predict(fit, type='lp', newdata=tdata)
+predict(fit3, type='lp', newdata=tdata)
diff --git a/win32/deps/library/survival/tests/factor2.Rout.save b/win32/deps/library/survival/tests/factor2.Rout.save
new file mode 100644
index 0000000..60342b8
--- /dev/null
+++ b/win32/deps/library/survival/tests/factor2.Rout.save
@@ -0,0 +1,52 @@
+
+R version 2.14.0 (2011-10-31)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: i686-pc-linux-gnu (32-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+> options(na.action=na.exclude)
+> #
+> # More tests of factors in prediction, using a new data set
+> #
+> fit <- coxph(Surv(time, status) ~ factor(ph.ecog), lung)
+>
+> tdata <- data.frame(ph.ecog = factor(0:3))
+> p1 <- predict(fit, newdata=tdata, type='lp')
+> p2 <- predict(fit, type='lp')
+> aeq(p1, p2[match(0:3, lung$ph.ecog)])
+[1] TRUE
+>
+> fit2 <- coxph(Surv(time, status) ~ factor(ph.ecog) + factor(sex), lung)
+> tdata <- expand.grid(ph.ecog = factor(0:3), sex=factor(1:2))
+> p1 <- predict(fit2, newdata=tdata, type='risk')
+>
+> xdata <- expand.grid(ph.ecog=factor(1:3), sex=factor(1:2))
+> p2 <- predict(fit2, newdata=xdata, type='risk')
+> all.equal(p2, p1[c(2:4, 6:8)], check.attributes=FALSE)
+[1] TRUE
+>
+>
+> fit3 <- survreg(Surv(time, status) ~ factor(ph.ecog) + age, lung)
+> tdata <- data.frame(ph.ecog=factor(0:3), age=50)
+> predict(fit, type='lp', newdata=tdata)
+ 1 2 3 4
+-0.39518177 -0.02634168 0.52120527 1.81279848
+> predict(fit3, type='lp', newdata=tdata)
+ 1 2 3 4
+6.399571 6.142938 5.770523 4.916993
+>
diff --git a/win32/deps/library/survival/tests/fr_cancer.R b/win32/deps/library/survival/tests/fr_cancer.R
new file mode 100644
index 0000000..6813c69
--- /dev/null
+++ b/win32/deps/library/survival/tests/fr_cancer.R
@@ -0,0 +1,27 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Here is a test case with multiple smoothing terms
+#
+
+fit0 <- coxph(Surv(time, status) ~ ph.ecog + age, lung)
+fit1 <- coxph(Surv(time, status) ~ ph.ecog + pspline(age,3), lung)
+fit2 <- coxph(Surv(time, status) ~ ph.ecog + pspline(age,4), lung)
+fit3 <- coxph(Surv(time, status) ~ ph.ecog + pspline(age,8), lung)
+
+
+
+fit4 <- coxph(Surv(time, status) ~ ph.ecog + pspline(wt.loss,3), lung)
+
+fit5 <-coxph(Surv(time, status) ~ ph.ecog + pspline(age,3) +
+ pspline(wt.loss,3), lung)
+
+fit1
+fit2
+fit3
+fit4
+fit5
+
+rm(fit1, fit2, fit3, fit4, fit5)
diff --git a/win32/deps/library/survival/tests/fr_cancer.Rout.save b/win32/deps/library/survival/tests/fr_cancer.Rout.save
new file mode 100644
index 0000000..a6fc30e
--- /dev/null
+++ b/win32/deps/library/survival/tests/fr_cancer.Rout.save
@@ -0,0 +1,120 @@
+
+R version 2.14.0 Under development (unstable) (2011-04-10 r55401)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Here is a test case with multiple smoothing terms
+> #
+>
+> fit0 <- coxph(Surv(time, status) ~ ph.ecog + age, lung)
+> fit1 <- coxph(Surv(time, status) ~ ph.ecog + pspline(age,3), lung)
+> fit2 <- coxph(Surv(time, status) ~ ph.ecog + pspline(age,4), lung)
+> fit3 <- coxph(Surv(time, status) ~ ph.ecog + pspline(age,8), lung)
+>
+>
+>
+> fit4 <- coxph(Surv(time, status) ~ ph.ecog + pspline(wt.loss,3), lung)
+>
+> fit5 <-coxph(Surv(time, status) ~ ph.ecog + pspline(age,3) +
++ pspline(wt.loss,3), lung)
+>
+> fit1
+Call:
+coxph(formula = Surv(time, status) ~ ph.ecog + pspline(age, 3),
+ data = lung)
+
+ coef se(coef) se2 Chisq DF p
+ph.ecog 0.4480 0.11707 0.11678 14.64 1.00 0.00013
+pspline(age, 3), linear 0.0113 0.00928 0.00928 1.47 1.00 0.22000
+pspline(age, 3), nonlin 2.08 2.08 0.37000
+
+Iterations: 4 outer, 12 Newton-Raphson
+ Theta= 0.861
+Degrees of freedom for terms= 1.0 3.1
+Likelihood ratio test=21.9 on 4.08 df, p=0.000227
+ n=227 (1 observation deleted due to missingness)
+> fit2
+Call:
+coxph(formula = Surv(time, status) ~ ph.ecog + pspline(age, 4),
+ data = lung)
+
+ coef se(coef) se2 Chisq DF p
+ph.ecog 0.4505 0.11766 0.11723 14.66 1.00 0.00013
+pspline(age, 4), linear 0.0112 0.00927 0.00927 1.45 1.00 0.23000
+pspline(age, 4), nonlin 2.96 3.08 0.41000
+
+Iterations: 4 outer, 11 Newton-Raphson
+ Theta= 0.797
+Degrees of freedom for terms= 1.0 4.1
+Likelihood ratio test=22.7 on 5.07 df, p=0.000412
+ n=227 (1 observation deleted due to missingness)
+> fit3
+Call:
+coxph(formula = Surv(time, status) ~ ph.ecog + pspline(age, 8),
+ data = lung)
+
+ coef se(coef) se2 Chisq DF p
+ph.ecog 0.4764 0.12024 0.11925 15.70 1.00 7.4e-05
+pspline(age, 8), linear 0.0117 0.00923 0.00923 1.61 1.00 2.0e-01
+pspline(age, 8), nonlin 6.93 6.99 4.3e-01
+
+Iterations: 5 outer, 15 Newton-Raphson
+ Theta= 0.691
+Degrees of freedom for terms= 1 8
+Likelihood ratio test=27.6 on 8.97 df, p=0.00108
+ n=227 (1 observation deleted due to missingness)
+> fit4
+Call:
+coxph(formula = Surv(time, status) ~ ph.ecog + pspline(wt.loss,
+ 3), data = lung)
+
+ coef se(coef) se2 Chisq DF p
+ph.ecog 0.51545 0.12960 0.12737 15.82 1.00 0.00007
+pspline(wt.loss, 3), line -0.00702 0.00655 0.00655 1.15 1.00 0.28000
+pspline(wt.loss, 3), nonl 2.45 2.09 0.31000
+
+Iterations: 3 outer, 10 Newton-Raphson
+ Theta= 0.776
+Degrees of freedom for terms= 1.0 3.1
+Likelihood ratio test=21.1 on 4.06 df, p=0.000326
+ n=213 (15 observations deleted due to missingness)
+> fit5
+Call:
+coxph(formula = Surv(time, status) ~ ph.ecog + pspline(age, 3) +
+ pspline(wt.loss, 3), data = lung)
+
+ coef se(coef) se2 Chisq DF p
+ph.ecog 0.47422 0.13495 0.13206 12.35 1.00 0.00044
+pspline(age, 3), linear 0.01368 0.00976 0.00974 1.96 1.00 0.16000
+pspline(age, 3), nonlin 1.90 2.07 0.40000
+pspline(wt.loss, 3), line -0.00717 0.00661 0.00660 1.18 1.00 0.28000
+pspline(wt.loss, 3), nonl 2.08 2.03 0.36000
+
+Iterations: 4 outer, 12 Newton-Raphson
+ Theta= 0.85
+ Theta= 0.779
+Degrees of freedom for terms= 1.0 3.1 3.0
+Likelihood ratio test=25.2 on 7.06 df, p=0.000726
+ n=213 (15 observations deleted due to missingness)
+>
+> rm(fit1, fit2, fit3, fit4, fit5)
+>
diff --git a/win32/deps/library/survival/tests/fr_colon.R b/win32/deps/library/survival/tests/fr_colon.R
new file mode 100644
index 0000000..909be6f
--- /dev/null
+++ b/win32/deps/library/survival/tests/fr_colon.R
@@ -0,0 +1,58 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Fit models to the Colon cancer data used in Lin
+#
+fitc1 <- coxph(Surv(time, status) ~ rx + extent + node4 + cluster(id)
+ + strata(etype), colon)
+fitc1
+
+fitc2 <- coxph(Surv(time, status) ~ rx + extent + node4 +
+ frailty(id, dist='gauss', trace=T)
+ + strata(etype), colon)
+fitc2
+
+fitc3 <- coxph(Surv(time, status) ~ rx + extent + node4 + frailty(id, trace=T)
+ + strata(etype), colon)
+fitc3
+
+fitc4 <- coxph(Surv(time, status) ~ rx + extent + node4 + frailty(id, df=30)
+ + strata(etype), colon)
+fitc4
+
+# Do a fit, removing the no-event people
+temp <- tapply(colon$status, colon$id, sum)
+keep <- !(is.na(match(colon$id, names(temp[temp>0]))))
+fitc5 <- coxph(Surv(time, status) ~ rx + extent + node4 +cluster(id)
+ + strata(etype), colon, subset=keep)
+fitc5
+
+#
+# Do the factor fit, but first remove the no-event people
+#
+# Ha! This routine has a factor with 506 levels. It uses all available
+# memory, and can't finish in my patience window. Commented out.
+
+#fitc6 <- coxph(Surv(time, status) ~ rx + extent + node4 + factor(id), colon,
+# subset=keep)
+
+# Try the AIC
+fitc7 <- coxph(Surv(time, status) ~ rx + extent + node4 +
+ frailty(id, method='aic', caic=T), colon)
+fitc7
+
+if (FALSE) {
+ # This fails to converge, with different bad paths in different
+ # releases (due to changes in eps parameters). It's not a bug per
+ # se, just too unstable a solution for the code to find.
+ # Remove it from the tests 2/2/09
+ fitc8 <- coxph(Surv(time, status) ~ rx + extent + node4 +
+ frailty(id, method='aic', dist='t', caic=T), colon)
+
+ fitc8
+ }
+
+
+
diff --git a/win32/deps/library/survival/tests/fr_colon.Rout.save b/win32/deps/library/survival/tests/fr_colon.Rout.save
new file mode 100644
index 0000000..648069a
--- /dev/null
+++ b/win32/deps/library/survival/tests/fr_colon.Rout.save
@@ -0,0 +1,317 @@
+
+R version 2.14.0 Under development (unstable) (2011-04-10 r55401)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Fit models to the Colon cancer data used in Lin
+> #
+> fitc1 <- coxph(Surv(time, status) ~ rx + extent + node4 + cluster(id)
++ + strata(etype), colon)
+> fitc1
+Call:
+coxph(formula = Surv(time, status) ~ rx + extent + node4 + cluster(id) +
+ strata(etype), data = colon)
+
+
+ coef exp(coef) se(coef) robust se z p
+rxLev -0.0362 0.964 0.0768 0.1056 -0.343 7.3e-01
+rxLev+5FU -0.4488 0.638 0.0840 0.1168 -3.842 1.2e-04
+extent 0.5155 1.674 0.0796 0.1097 4.701 2.6e-06
+node4 0.8799 2.411 0.0681 0.0961 9.160 0.0e+00
+
+Likelihood ratio test=248 on 4 df, p=0 n= 1858, number of events= 920
+>
+> fitc2 <- coxph(Surv(time, status) ~ rx + extent + node4 +
++ frailty(id, dist='gauss', trace=T)
++ + strata(etype), colon)
+ theta resid fsum trace
+[1,] 1 0.5720661 677.1944 498.2329
+[2,] 3 0.8263010 2431.5386 880.5594
+ new theta= 6
+
+ theta resid fsum trace
+[1,] 1 0.5720661 677.1944 498.2329
+[2,] 3 0.8263010 2431.5386 880.5594
+[3,] 6 0.3191860 4522.8358 1279.6154
+ new theta= 12
+
+ theta resid fsum trace
+[1,] 1 0.5720661 677.1944 498.2329
+[2,] 3 0.8263010 2431.5386 880.5594
+[3,] 6 0.3191860 4522.8358 1279.6154
+[4,] 12 -2.1485959 7550.5833 1950.6309
+ new theta= 7.579324
+
+ theta resid fsum trace
+[1,] 1.000000 0.5720661 677.1944 498.2329
+[2,] 3.000000 0.8263010 2431.5386 880.5594
+[3,] 6.000000 0.3191860 4522.8358 1279.6154
+[4,] 12.000000 -2.1485959 7550.5833 1950.6309
+[5,] 7.579324 -0.1853733 5438.8102 1466.0258
+ new theta= 7.020146
+
+ theta resid fsum trace
+[1,] 1.000000 0.572066075 677.1944 498.2329
+[2,] 3.000000 0.826301016 2431.5386 880.5594
+[3,] 6.000000 0.319185976 4522.8358 1279.6154
+[4,] 12.000000 -2.148595876 7550.5833 1950.6309
+[5,] 7.579324 -0.185373320 5438.8102 1466.0258
+[6,] 7.020146 0.008957243 5127.0057 1401.2432
+ new theta= 7.047272
+
+ theta resid fsum trace
+[1,] 1.000000 0.572066075 677.1944 498.2329
+[2,] 3.000000 0.826301016 2431.5386 880.5594
+[3,] 6.000000 0.319185976 4522.8358 1279.6154
+[4,] 12.000000 -2.148595876 7550.5833 1950.6309
+[5,] 7.579324 -0.185373320 5438.8102 1466.0258
+[6,] 7.020146 0.008957243 5127.0057 1401.2432
+[7,] 7.047272 -0.001444564 5141.4462 1404.4156
+ new theta= 7.043486
+
+ theta resid fsum trace
+[1,] 1.000000 0.572066075 677.1944 498.2329
+[2,] 3.000000 0.826301016 2431.5386 880.5594
+[3,] 6.000000 0.319185976 4522.8358 1279.6154
+[4,] 12.000000 -2.148595876 7550.5833 1950.6309
+[5,] 7.579324 -0.185373320 5438.8102 1466.0258
+[6,] 7.020146 0.008957243 5127.0057 1401.2432
+[7,] 7.047272 -0.001444564 5141.4462 1404.4156
+[8,] 7.043486 0.000960198 5140.1195 1403.9797
+ new theta= 7.045177
+
+ theta resid fsum trace
+ [1,] 1.000000 0.5720660750 677.1944 498.2329
+ [2,] 3.000000 0.8263010161 2431.5386 880.5594
+ [3,] 6.000000 0.3191859764 4522.8358 1279.6154
+ [4,] 12.000000 -2.1485958763 7550.5833 1950.6309
+ [5,] 7.579324 -0.1853733197 5438.8102 1466.0258
+ [6,] 7.020146 0.0089572430 5127.0057 1401.2432
+ [7,] 7.047272 -0.0014445644 5141.4462 1404.4156
+ [8,] 7.043486 0.0009601980 5140.1195 1403.9797
+ [9,] 7.045177 -0.0002391451 5140.6313 1404.1637
+ new theta= 7.044809
+
+ theta resid fsum trace
+ [1,] 1.000000 5.720661e-01 677.1944 498.2329
+ [2,] 3.000000 8.263010e-01 2431.5386 880.5594
+ [3,] 6.000000 3.191860e-01 4522.8358 1279.6154
+ [4,] 12.000000 -2.148596e+00 7550.5833 1950.6309
+ [5,] 7.579324 -1.853733e-01 5438.8102 1466.0258
+ [6,] 7.020146 8.957243e-03 5127.0057 1401.2432
+ [7,] 7.047272 -1.444564e-03 5141.4462 1404.4156
+ [8,] 7.043486 9.601980e-04 5140.1195 1403.9797
+ [9,] 7.045177 -2.391451e-04 5140.6313 1404.1637
+[10,] 7.044809 8.359535e-05 5140.5615 1404.1267
+ new theta= 7.04491
+
+Warning message:
+In coxpenal.fit(X, Y, strats, offset, init = init, control, weights = weights, :
+ Inner loop failed to coverge for iterations 4 5
+> fitc2
+Call:
+coxph(formula = Surv(time, status) ~ rx + extent + node4 + frailty(id,
+ dist = "gauss", trace = T) + strata(etype), data = colon)
+
+ coef se(coef) se2 Chisq DF p
+rxLev -0.0267 0.241 0.0824 0.01 1 9.1e-01
+rxLev+5FU -0.7880 0.243 0.1071 10.50 1 1.2e-03
+extent 1.1305 0.218 0.1068 26.81 1 2.2e-07
+node4 2.1266 0.210 0.0984 102.58 1 0.0e+00
+frailty(id, dist = "gauss 5463.66 730 0.0e+00
+
+Iterations: 10 outer, 104 Newton-Raphson
+ Variance of random effect= 7.04
+Degrees of freedom for terms= 0.3 0.2 0.2 729.7
+Likelihood ratio test=3544 on 730 df, p=0 n= 1858
+>
+> fitc3 <- coxph(Surv(time, status) ~ rx + extent + node4 + frailty(id, trace=T)
++ + strata(etype), colon)
+ theta loglik c.loglik
+[1,] 0 -5846.216 -5846.216
+[2,] 1 -5305.049 -5590.102
+ new theta= 2
+
+ theta loglik c.loglik
+[1,] 0 -5846.216 -5846.216
+[2,] 1 -5305.049 -5590.102
+[3,] 2 -5036.927 -5479.479
+ new theta= 4
+
+ theta loglik c.loglik
+[1,] 0 -5846.216 -5846.216
+[2,] 1 -5305.049 -5590.102
+[3,] 2 -5036.927 -5479.479
+[4,] 4 -4740.394 -5385.886
+ new theta= 8
+
+ theta loglik c.loglik
+[1,] 0 -5846.216 -5846.216
+[2,] 1 -5305.049 -5590.102
+[3,] 2 -5036.927 -5479.479
+[4,] 4 -4740.394 -5385.886
+[5,] 8 -4457.094 -5347.375
+ new theta= 16
+
+ theta loglik c.loglik
+[1,] 0 -5846.216 -5846.216
+[2,] 1 -5305.049 -5590.102
+[3,] 2 -5036.927 -5479.479
+[4,] 4 -4740.394 -5385.886
+[5,] 8 -4457.094 -5347.375
+[6,] 16 -4223.785 -5393.362
+ new theta= 8.740334
+
+ theta loglik c.loglik
+[1,] 0.000000 -5846.216 -5846.216
+[2,] 1.000000 -5305.049 -5590.102
+[3,] 2.000000 -5036.927 -5479.479
+[4,] 4.000000 -4740.394 -5385.886
+[5,] 8.000000 -4457.094 -5347.375
+[6,] 16.000000 -4223.785 -5393.362
+[7,] 8.740334 -4423.925 -5348.128
+ new theta= 8.058156
+
+ theta loglik c.loglik
+[1,] 0.000000 -5846.216 -5846.216
+[2,] 1.000000 -5305.049 -5590.102
+[3,] 2.000000 -5036.927 -5479.479
+[4,] 4.000000 -4740.394 -5385.886
+[5,] 8.000000 -4457.094 -5347.375
+[6,] 16.000000 -4223.785 -5393.362
+[7,] 8.740334 -4423.925 -5348.128
+[8,] 8.058156 -4454.338 -5347.375
+ new theta= 8.02886
+
+ theta loglik c.loglik
+ [1,] 0.000000 -5846.216 -5846.216
+ [2,] 1.000000 -5305.049 -5590.102
+ [3,] 2.000000 -5036.927 -5479.479
+ [4,] 4.000000 -4740.394 -5385.886
+ [5,] 8.000000 -4457.094 -5347.375
+ [6,] 16.000000 -4223.785 -5393.362
+ [7,] 8.740334 -4423.925 -5348.128
+ [8,] 8.058156 -4454.338 -5347.375
+ [9,] 8.028860 -4455.719 -5347.369
+ new theta= 8.029002
+
+Warning message:
+In coxpenal.fit(X, Y, strats, offset, init = init, control, weights = weights, :
+ Inner loop failed to coverge for iterations 4 5 6 7 8
+> fitc3
+Call:
+coxph(formula = Surv(time, status) ~ rx + extent + node4 + frailty(id,
+ trace = T) + strata(etype), data = colon)
+
+ coef se(coef) se2 Chisq DF p
+rxLev 0.0433 0.305 0.140 0.02 1 8.9e-01
+rxLev+5FU -0.5117 0.310 0.170 2.72 1 9.9e-02
+extent 1.3360 0.251 0.137 28.36 1 1.0e-07
+node4 2.3345 0.233 0.156 100.45 1 0.0e+00
+frailty(id, trace = T) 5947.15 867 0.0e+00
+
+Iterations: 9 outer, 145 Newton-Raphson
+ Variance of random effect= 8.03 I-likelihood = -5347.4
+Degrees of freedom for terms= 0.5 0.3 0.4 866.8
+Likelihood ratio test=3788 on 868 df, p=0 n= 1858
+>
+> fitc4 <- coxph(Surv(time, status) ~ rx + extent + node4 + frailty(id, df=30)
++ + strata(etype), colon)
+> fitc4
+Call:
+coxph(formula = Surv(time, status) ~ rx + extent + node4 + frailty(id,
+ df = 30) + strata(etype), data = colon)
+
+ coef se(coef) se2 Chisq DF p
+rxLev -0.0374 0.0789 0.0769 0.22 1 6.4e-01
+rxLev+5FU -0.4565 0.0859 0.0840 28.27 1 1.1e-07
+extent 0.5289 0.0815 0.0798 42.13 1 8.5e-11
+node4 0.9078 0.0701 0.0681 167.85 1 0.0e+00
+frailty(id, df = 30) 58.56 30 1.4e-03
+
+Iterations: 3 outer, 9 Newton-Raphson
+ Variance of random effect= 0.0337 I-likelihood = -5832.4
+Degrees of freedom for terms= 1.9 1.0 0.9 30.0
+Likelihood ratio test=363 on 33.8 df, p=0 n= 1858
+>
+> # Do a fit, removing the no-event people
+> temp <- tapply(colon$status, colon$id, sum)
+> keep <- !(is.na(match(colon$id, names(temp[temp>0]))))
+> fitc5 <- coxph(Surv(time, status) ~ rx + extent + node4 +cluster(id)
++ + strata(etype), colon, subset=keep)
+> fitc5
+Call:
+coxph(formula = Surv(time, status) ~ rx + extent + node4 + cluster(id) +
+ strata(etype), data = colon, subset = keep)
+
+
+ coef exp(coef) se(coef) robust se z p
+rxLev 0.0832 1.087 0.0771 0.0989 0.841 4.0e-01
+rxLev+5FU -0.0277 0.973 0.0848 0.1090 -0.255 8.0e-01
+extent 0.1797 1.197 0.0785 0.1036 1.735 8.3e-02
+node4 0.5219 1.685 0.0684 0.0912 5.720 1.1e-08
+
+Likelihood ratio test=63.7 on 4 df, p=4.8e-13 n= 1012, number of events= 920
+>
+> #
+> # Do the factor fit, but first remove the no-event people
+> #
+> # Ha! This routine has a factor with 506 levels. It uses all available
+> # memory, and can't finish in my patience window. Commented out.
+>
+> #fitc6 <- coxph(Surv(time, status) ~ rx + extent + node4 + factor(id), colon,
+> # subset=keep)
+>
+> # Try the AIC
+> fitc7 <- coxph(Surv(time, status) ~ rx + extent + node4 +
++ frailty(id, method='aic', caic=T), colon)
+> fitc7
+Call:
+coxph(formula = Surv(time, status) ~ rx + extent + node4 + frailty(id,
+ method = "aic", caic = T), data = colon)
+
+ coef se(coef) se2 Chisq DF p
+rxLev -0.0409 0.0915 0.0781 0.2 1 6.6e-01
+rxLev+5FU -0.4832 0.0979 0.0852 24.4 1 7.9e-07
+extent 0.6037 0.0918 0.0816 43.2 1 4.8e-11
+node4 1.0463 0.0825 0.0700 160.9 1 0.0e+00
+frailty(id, method = "aic 416.3 205 1.1e-16
+
+Iterations: 8 outer, 38 Newton-Raphson
+ Variance of random effect= 0.271 I-likelihood = -6393
+Degrees of freedom for terms= 1.5 0.8 0.7 204.8
+Likelihood ratio test=964 on 208 df, p=0 n= 1858
+>
+> if (FALSE) {
++ # This fails to converge, with different bad paths in different
++ # releases (due to changes in eps parameters). It's not a bug per
++ # se, just too unstable a solution for the code to find.
++ # Remove it from the tests 2/2/09
++ fitc8 <- coxph(Surv(time, status) ~ rx + extent + node4 +
++ frailty(id, method='aic', dist='t', caic=T), colon)
++
++ fitc8
++ }
+>
+>
+>
+>
diff --git a/win32/deps/library/survival/tests/fr_kidney.R b/win32/deps/library/survival/tests/fr_kidney.R
new file mode 100644
index 0000000..e4a9183
--- /dev/null
+++ b/win32/deps/library/survival/tests/fr_kidney.R
@@ -0,0 +1,70 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+# From: McGilchrist and Aisbett, Biometrics 47, 461-66, 1991
+# Data on the recurrence times to infection, at the point of insertion of
+# the catheter, for kidney patients using portable dialysis equipment.
+# Catheters may be removed for reasons other than infection, in which case
+# the observation is censored. Each patient has exactly 2 observations.
+
+# Variables: patient, time, status, age,
+# sex (1=male, 2=female),
+# disease type (0=GN, 1=AN, 2=PKD, 3=Other)
+# author's estimate of the frailty
+aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+
+# I don't match their answers, and I think that I'm right
+kfit <- coxph(Surv(time, status)~ age + sex + disease + frailty(id), kidney)
+kfit1<- coxph(Surv(time, status) ~age + sex + disease +
+ frailty(id, theta=1), kidney, iter=20)
+kfit0 <- coxph(Surv(time, status)~ age + sex + disease, kidney)
+temp <- coxph(Surv(time, status) ~age + sex + disease +
+ frailty(id, theta=1, sparse=F), kidney)
+
+
+# Check out the EM based score equations
+# temp1 and kfit1 should have essentially the same coefficients
+# temp2 should equal kfit1$frail
+# equality won't be exact because of the different iteration paths
+temp1 <- coxph(Surv(time, status) ~ age + sex + disease +
+ offset(kfit1$frail[id]), kidney)
+rr <- tapply(resid(temp1), kidney$id, sum)
+temp2 <- log(rr/1 +1)
+aeq(temp1$coef, kfit1$coef, tolerance=.005)
+aeq(temp2, kfit1$frail, tolerance=.005)
+
+
+
+kfit
+kfit1
+kfit0
+temp
+
+#
+# Now fit the data using REML
+#
+kfitm1 <- coxph(Surv(time,status) ~ age + sex + disease +
+ frailty(id, dist='gauss'), kidney)
+kfitm2 <- coxph(Surv(time,status) ~ age + sex + disease +
+ frailty(id, dist='gauss', sparse=F), kidney)
+kfitm1
+summary(kfitm2)
+#
+# Fit the kidney data using AIC
+#
+
+# gamma, corrected aic
+coxph(Surv(time, status) ~ age + sex + frailty(id, method='aic', caic=T),
+ kidney)
+
+coxph(Surv(time, status) ~ age + sex + frailty(id, dist='t'), kidney)
+coxph(Surv(time, status) ~ age + sex + frailty(id, dist='gauss', method='aic',
+ caic=T), kidney)
+
+
+# uncorrected aic
+coxph(Surv(time, status) ~ age + sex + frailty(id, method='aic', caic=F),
+ kidney)
+
+coxph(Surv(time, status) ~ age + sex + frailty(id, dist='t', caic=F), kidney)
diff --git a/win32/deps/library/survival/tests/fr_kidney.Rout.save b/win32/deps/library/survival/tests/fr_kidney.Rout.save
new file mode 100644
index 0000000..7b22f98
--- /dev/null
+++ b/win32/deps/library/survival/tests/fr_kidney.Rout.save
@@ -0,0 +1,302 @@
+
+R version 2.13.0 (2011-04-13)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> # From: McGilchrist and Aisbett, Biometrics 47, 461-66, 1991
+> # Data on the recurrence times to infection, at the point of insertion of
+> # the catheter, for kidney patients using portable dialysis equipment.
+> # Catheters may be removed for reasons other than infection, in which case
+> # the observation is censored. Each patient has exactly 2 observations.
+>
+> # Variables: patient, time, status, age,
+> # sex (1=male, 2=female),
+> # disease type (0=GN, 1=AN, 2=PKD, 3=Other)
+> # author's estimate of the frailty
+> aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+>
+> # I don't match their answers, and I think that I'm right
+> kfit <- coxph(Surv(time, status)~ age + sex + disease + frailty(id), kidney)
+> kfit1<- coxph(Surv(time, status) ~age + sex + disease +
++ frailty(id, theta=1), kidney, iter=20)
+> kfit0 <- coxph(Surv(time, status)~ age + sex + disease, kidney)
+> temp <- coxph(Surv(time, status) ~age + sex + disease +
++ frailty(id, theta=1, sparse=F), kidney)
+>
+>
+> # Check out the EM based score equations
+> # temp1 and kfit1 should have essentially the same coefficients
+> # temp2 should equal kfit1$frail
+> # equality won't be exact because of the different iteration paths
+> temp1 <- coxph(Surv(time, status) ~ age + sex + disease +
++ offset(kfit1$frail[id]), kidney)
+> rr <- tapply(resid(temp1), kidney$id, sum)
+> temp2 <- log(rr/1 +1)
+> aeq(temp1$coef, kfit1$coef, tolerance=.005)
+[1] TRUE
+> aeq(temp2, kfit1$frail, tolerance=.005)
+[1] TRUE
+>
+>
+>
+> kfit
+Call:
+coxph(formula = Surv(time, status) ~ age + sex + disease + frailty(id),
+ data = kidney)
+
+ coef se(coef) se2 Chisq DF p
+age 0.00318 0.0111 0.0111 0.08 1 7.8e-01
+sex -1.48314 0.3582 0.3582 17.14 1 3.5e-05
+diseaseGN 0.08796 0.4064 0.4064 0.05 1 8.3e-01
+diseaseAN 0.35079 0.3997 0.3997 0.77 1 3.8e-01
+diseasePKD -1.43111 0.6311 0.6311 5.14 1 2.3e-02
+frailty(id) 0.00 0 9.3e-01
+
+Iterations: 6 outer, 35 Newton-Raphson
+ Variance of random effect= 5e-07 I-likelihood = -179.1
+Degrees of freedom for terms= 1 1 3 0
+Likelihood ratio test=17.6 on 5 df, p=0.00342 n= 76
+> kfit1
+Call:
+coxph(formula = Surv(time, status) ~ age + sex + disease + frailty(id,
+ theta = 1), data = kidney, iter = 20)
+
+ coef se(coef) se2 Chisq DF p
+age 0.00389 0.0196 0.00943 0.04 1.0 0.84000
+sex -2.00764 0.5910 0.41061 11.54 1.0 0.00068
+diseaseGN 0.35335 0.7165 0.38015 0.24 1.0 0.62000
+diseaseAN 0.52341 0.7230 0.40463 0.52 1.0 0.47000
+diseasePKD -0.45938 1.0898 0.66088 0.18 1.0 0.67000
+frailty(id, theta = 1) 28.51 18.8 0.06900
+
+Iterations: 1 outer, 14 Newton-Raphson
+ Variance of random effect= 1 I-likelihood = -182.5
+Degrees of freedom for terms= 0.2 0.5 1.1 18.8
+Likelihood ratio test=63.8 on 20.6 df, p=2.53e-06 n= 76
+> kfit0
+Call:
+coxph(formula = Surv(time, status) ~ age + sex + disease, data = kidney)
+
+
+ coef exp(coef) se(coef) z p
+age 0.00318 1.003 0.0111 0.285 7.8e-01
+sex -1.48314 0.227 0.3582 -4.140 3.5e-05
+diseaseGN 0.08796 1.092 0.4064 0.216 8.3e-01
+diseaseAN 0.35079 1.420 0.3997 0.878 3.8e-01
+diseasePKD -1.43111 0.239 0.6311 -2.268 2.3e-02
+
+Likelihood ratio test=17.6 on 5 df, p=0.00342 n= 76, number of events= 58
+> temp
+Call:
+coxph(formula = Surv(time, status) ~ age + sex + disease + frailty(id,
+ theta = 1, sparse = F), data = kidney)
+
+ coef se(coef) se2 Chisq DF p
+age 0.00389 0.0186 0.0112 0.04 1.0 0.83000
+sex -2.00763 0.5762 0.4080 12.14 1.0 0.00049
+diseaseGN 0.35335 0.6786 0.4315 0.27 1.0 0.60000
+diseaseAN 0.52340 0.6891 0.4404 0.58 1.0 0.45000
+diseasePKD -0.45934 1.0139 0.7130 0.21 1.0 0.65000
+frailty(id, theta = 1, sp 26.23 18.7 0.12000
+
+Iterations: 1 outer, 5 Newton-Raphson
+ Variance of random effect= 1 I-likelihood = -182.5
+Degrees of freedom for terms= 0.4 0.5 1.4 18.7
+Likelihood ratio test=63.8 on 21 df, p=3.27e-06 n= 76
+>
+> #
+> # Now fit the data using REML
+> #
+> kfitm1 <- coxph(Surv(time,status) ~ age + sex + disease +
++ frailty(id, dist='gauss'), kidney)
+> kfitm2 <- coxph(Surv(time,status) ~ age + sex + disease +
++ frailty(id, dist='gauss', sparse=F), kidney)
+> kfitm1
+Call:
+coxph(formula = Surv(time, status) ~ age + sex + disease + frailty(id,
+ dist = "gauss"), data = kidney)
+
+ coef se(coef) se2 Chisq DF p
+age 0.00489 0.015 0.0106 0.11 1.0 0.74000
+sex -1.69728 0.461 0.3617 13.55 1.0 0.00023
+diseaseGN 0.17986 0.545 0.3927 0.11 1.0 0.74000
+diseaseAN 0.39294 0.545 0.3982 0.52 1.0 0.47000
+diseasePKD -1.13631 0.825 0.6173 1.90 1.0 0.17000
+frailty(id, dist = "gauss 17.89 12.1 0.12000
+
+Iterations: 7 outer, 42 Newton-Raphson
+ Variance of random effect= 0.493
+Degrees of freedom for terms= 0.5 0.6 1.7 12.1
+Likelihood ratio test=47.5 on 14.9 df, p=2.82e-05 n= 76
+> summary(kfitm2)
+Call:
+coxph(formula = Surv(time, status) ~ age + sex + disease + frailty(id,
+ dist = "gauss", sparse = F), data = kidney)
+
+ n= 76, number of events= 58
+
+ coef se(coef) se2 Chisq DF p
+age 0.00492 0.0149 0.0108 0.11 1.0 0.74000
+sex -1.70204 0.4631 0.3613 13.51 1.0 0.00024
+diseaseGN 0.18173 0.5413 0.4017 0.11 1.0 0.74000
+diseaseAN 0.39442 0.5428 0.4052 0.53 1.0 0.47000
+diseasePKD -1.13160 0.8175 0.6298 1.92 1.0 0.17000
+frailty(id, dist = "gauss 18.13 12.3 0.12000
+
+ exp(coef) exp(-coef) lower .95 upper .95
+age 1.005 0.995 0.9760 1.035
+sex 0.182 5.485 0.0736 0.452
+diseaseGN 1.199 0.834 0.4151 3.465
+diseaseAN 1.484 0.674 0.5120 4.299
+diseasePKD 0.323 3.101 0.0650 1.601
+gauss:1 1.701 0.588 0.5181 5.586
+gauss:2 1.424 0.702 0.3851 5.266
+gauss:3 1.159 0.863 0.3828 3.511
+gauss:4 0.623 1.606 0.2340 1.657
+gauss:5 1.254 0.797 0.3981 3.953
+gauss:6 1.135 0.881 0.3834 3.360
+gauss:7 1.973 0.507 0.5694 6.834
+gauss:8 0.620 1.614 0.2166 1.772
+gauss:9 0.823 1.215 0.2888 2.346
+gauss:10 0.503 1.988 0.1747 1.448
+gauss:11 0.757 1.322 0.2708 2.113
+gauss:12 1.105 0.905 0.3343 3.651
+gauss:13 1.302 0.768 0.4275 3.967
+gauss:14 0.591 1.691 0.1854 1.885
+gauss:15 0.545 1.835 0.1858 1.598
+gauss:16 1.044 0.958 0.3142 3.470
+gauss:17 0.914 1.095 0.3000 2.782
+gauss:18 0.918 1.089 0.3248 2.597
+gauss:19 0.643 1.556 0.1951 2.117
+gauss:20 1.170 0.855 0.3453 3.963
+gauss:21 0.334 2.997 0.1020 1.091
+gauss:22 0.687 1.455 0.2353 2.006
+gauss:23 1.478 0.677 0.4756 4.592
+gauss:24 1.017 0.983 0.3156 3.278
+gauss:25 0.810 1.235 0.2749 2.384
+gauss:26 0.614 1.627 0.2149 1.757
+gauss:27 1.088 0.919 0.3282 3.610
+gauss:28 1.542 0.649 0.4923 4.829
+gauss:29 1.379 0.725 0.4377 4.342
+gauss:30 1.375 0.727 0.4444 4.253
+gauss:31 1.445 0.692 0.4703 4.438
+gauss:32 1.199 0.834 0.3521 4.085
+gauss:33 1.945 0.514 0.5523 6.849
+gauss:34 0.862 1.161 0.2769 2.682
+gauss:35 1.703 0.587 0.5266 5.508
+gauss:36 0.827 1.209 0.2281 3.002
+gauss:37 1.471 0.680 0.3894 5.555
+gauss:38 1.048 0.954 0.3068 3.579
+
+Iterations: 6 outer, 21 Newton-Raphson
+ Variance of random effect= 0.509
+Degrees of freedom for terms= 0.5 0.6 1.7 12.3
+Concordance= 0.796 (se = 0.046 )
+Rsquare= 0.788 (max possible= 0.997 )
+Likelihood ratio test= 118 on 15.1 df, p=0
+Wald test = 37.4 on 15.1 df, p=0.00119
+> #
+> # Fit the kidney data using AIC
+> #
+>
+> # gamma, corrected aic
+> coxph(Surv(time, status) ~ age + sex + frailty(id, method='aic', caic=T),
++ kidney)
+Call:
+coxph(formula = Surv(time, status) ~ age + sex + frailty(id,
+ method = "aic", caic = T), data = kidney)
+
+ coef se(coef) se2 Chisq DF p
+age 0.00364 0.0105 0.00891 0.12 1.00 0.73000
+sex -1.31953 0.3956 0.32497 11.13 1.00 0.00085
+frailty(id, method = "aic 13.55 7.81 0.08700
+
+Iterations: 9 outer, 63 Newton-Raphson
+ Variance of random effect= 0.203 I-likelihood = -182.1
+Degrees of freedom for terms= 0.7 0.7 7.8
+Likelihood ratio test=33.3 on 9.21 df, p=0.000137 n= 76
+>
+> coxph(Surv(time, status) ~ age + sex + frailty(id, dist='t'), kidney)
+Call:
+coxph(formula = Surv(time, status) ~ age + sex + frailty(id,
+ dist = "t"), data = kidney)
+
+ coef se(coef) se2 Chisq DF p
+age 0.00561 0.012 0.00872 0.22 1.0 0.64000
+sex -1.65487 0.483 0.38527 11.74 1.0 0.00061
+frailty(id, dist = "t") 20.33 13.9 0.12000
+
+Iterations: 8 outer, 58 Newton-Raphson
+ Variance of random effect= 0.825
+Degrees of freedom for terms= 0.5 0.6 13.9
+Likelihood ratio test=48.6 on 15.1 df, p=2.18e-05 n= 76
+> coxph(Surv(time, status) ~ age + sex + frailty(id, dist='gauss', method='aic',
++ caic=T), kidney)
+Call:
+coxph(formula = Surv(time, status) ~ age + sex + frailty(id,
+ dist = "gauss", method = "aic", caic = T), data = kidney)
+
+ coef se(coef) se2 Chisq DF p
+age 0.00303 0.0103 0.00895 0.09 1.00 0.7700
+sex -1.15152 0.3637 0.30556 10.03 1.00 0.0015
+frailty(id, dist = "gauss 12.35 6.76 0.0800
+
+Iterations: 7 outer, 41 Newton-Raphson
+ Variance of random effect= 0.185
+Degrees of freedom for terms= 0.8 0.7 6.8
+Likelihood ratio test=28.4 on 8.22 df, p=0.000476 n= 76
+>
+>
+> # uncorrected aic
+> coxph(Surv(time, status) ~ age + sex + frailty(id, method='aic', caic=F),
++ kidney)
+Call:
+coxph(formula = Surv(time, status) ~ age + sex + frailty(id,
+ method = "aic", caic = F), data = kidney)
+
+ coef se(coef) se2 Chisq DF p
+age 0.00785 0.015 0.00823 0.27 1.0 0.60000
+sex -1.88990 0.561 0.39941 11.34 1.0 0.00076
+frailty(id, method = "aic 37.46 19.7 0.00920
+
+Iterations: 8 outer, 87 Newton-Raphson
+ Variance of random effect= 0.886 I-likelihood = -182.8
+Degrees of freedom for terms= 0.3 0.5 19.7
+Likelihood ratio test=61.2 on 20.5 df, p=6.25e-06 n= 76
+Warning message:
+In coxpenal.fit(X, Y, strats, offset, init = init, control, weights = weights, :
+ Inner loop failed to coverge for iterations 4
+>
+> coxph(Surv(time, status) ~ age + sex + frailty(id, dist='t', caic=F), kidney)
+Call:
+coxph(formula = Surv(time, status) ~ age + sex + frailty(id,
+ dist = "t", caic = F), data = kidney)
+
+ coef se(coef) se2 Chisq DF p
+age 0.00561 0.012 0.00872 0.22 1.0 0.64000
+sex -1.65487 0.483 0.38527 11.74 1.0 0.00061
+frailty(id, dist = "t", c 20.33 13.9 0.12000
+
+Iterations: 8 outer, 58 Newton-Raphson
+ Variance of random effect= 0.825
+Degrees of freedom for terms= 0.5 0.6 13.9
+Likelihood ratio test=48.6 on 15.1 df, p=2.18e-05 n= 76
+>
diff --git a/win32/deps/library/survival/tests/fr_lung.R b/win32/deps/library/survival/tests/fr_lung.R
new file mode 100644
index 0000000..d0a4fbf
--- /dev/null
+++ b/win32/deps/library/survival/tests/fr_lung.R
@@ -0,0 +1,29 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# A test with the lung data
+# This caused problems in one release
+
+#
+# First, get rid of some missings
+#
+lung2 <- na.omit(lung[c('time', 'status', 'wt.loss')])
+
+#
+# Test the logliklihoods
+#
+fit <- coxph(Surv(time, status) ~ pspline(wt.loss,3), lung2, x=T)
+fit0<- coxph(Surv(time, status) ~ 1, lung2)
+fit1<- coxph(Surv(time, status) ~ fit$x, lung2, iter=0, init=fit$coef)
+
+all.equal(fit$loglik[1], fit0$loglik)
+all.equal(fit$loglik[2], fit1$loglik[2])
+
+#
+# Check variances
+#
+imat <- solve(fit1$var)
+var2 <- fit$var %*% imat %*% fit$var
+all.equal(fit$var2, var2)
diff --git a/win32/deps/library/survival/tests/fr_lung.Rout.save b/win32/deps/library/survival/tests/fr_lung.Rout.save
new file mode 100644
index 0000000..d79a420
--- /dev/null
+++ b/win32/deps/library/survival/tests/fr_lung.Rout.save
@@ -0,0 +1,51 @@
+
+R version 2.11.1 (2010-05-31)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # A test with the lung data
+> # This caused problems in one release
+>
+> #
+> # First, get rid of some missings
+> #
+> lung2 <- na.omit(lung[c('time', 'status', 'wt.loss')])
+>
+> #
+> # Test the logliklihoods
+> #
+> fit <- coxph(Surv(time, status) ~ pspline(wt.loss,3), lung2, x=T)
+> fit0<- coxph(Surv(time, status) ~ 1, lung2)
+> fit1<- coxph(Surv(time, status) ~ fit$x, lung2, iter=0, init=fit$coef)
+>
+> all.equal(fit$loglik[1], fit0$loglik)
+[1] TRUE
+> all.equal(fit$loglik[2], fit1$loglik[2])
+[1] TRUE
+>
+> #
+> # Check variances
+> #
+> imat <- solve(fit1$var)
+> var2 <- fit$var %*% imat %*% fit$var
+> all.equal(fit$var2, var2)
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/fr_ovarian.R b/win32/deps/library/survival/tests/fr_ovarian.R
new file mode 100644
index 0000000..0102006
--- /dev/null
+++ b/win32/deps/library/survival/tests/fr_ovarian.R
@@ -0,0 +1,21 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Test on the ovarian data
+
+fit1 <- coxph(Surv(futime, fustat) ~ rx + age, ovarian)
+fit2 <- coxph(Surv(futime, fustat) ~ rx + pspline(age, df=2),
+ data=ovarian)
+fit2$iter
+
+fit2$df
+
+fit2$history
+
+fit4 <- coxph(Surv(futime, fustat) ~ rx + pspline(age, df=4),
+ data=ovarian)
+fit4
+
+
diff --git a/win32/deps/library/survival/tests/fr_ovarian.Rout.save b/win32/deps/library/survival/tests/fr_ovarian.Rout.save
new file mode 100644
index 0000000..70b05e4
--- /dev/null
+++ b/win32/deps/library/survival/tests/fr_ovarian.Rout.save
@@ -0,0 +1,74 @@
+
+R version 2.14.0 Under development (unstable) (2011-04-10 r55401)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Test on the ovarian data
+>
+> fit1 <- coxph(Surv(futime, fustat) ~ rx + age, ovarian)
+> fit2 <- coxph(Surv(futime, fustat) ~ rx + pspline(age, df=2),
++ data=ovarian)
+> fit2$iter
+[1] 2 8
+>
+> fit2$df
+[1] 0.9426611 1.9293051
+>
+> fit2$history
+$`pspline(age, df = 2)`
+$`pspline(age, df = 2)`$theta
+[1] 0.4468868
+
+$`pspline(age, df = 2)`$done
+[1] TRUE
+
+$`pspline(age, df = 2)`$history
+ thetas dfs
+[1,] 1.0000000 1.000000
+[2,] 0.0000000 5.000000
+[3,] 0.6000000 1.734267
+[4,] 0.4845205 1.929305
+
+$`pspline(age, df = 2)`$half
+[1] 0
+
+
+>
+> fit4 <- coxph(Surv(futime, fustat) ~ rx + pspline(age, df=4),
++ data=ovarian)
+> fit4
+Call:
+coxph(formula = Surv(futime, fustat) ~ rx + pspline(age, df = 4),
+ data = ovarian)
+
+ coef se(coef) se2 Chisq DF p
+rx -0.373 0.761 0.749 0.24 1.00 0.6200
+pspline(age, df = 4), lin 0.139 0.044 0.044 9.98 1.00 0.0016
+pspline(age, df = 4), non 2.59 2.93 0.4500
+
+Iterations: 3 outer, 14 Newton-Raphson
+ Theta= 0.242
+Degrees of freedom for terms= 1.0 3.9
+Likelihood ratio test=19.4 on 4.9 df, p=0.00149 n= 26
+>
+>
+>
diff --git a/win32/deps/library/survival/tests/fr_rat1.R b/win32/deps/library/survival/tests/fr_rat1.R
new file mode 100644
index 0000000..5a3ddae
--- /dev/null
+++ b/win32/deps/library/survival/tests/fr_rat1.R
@@ -0,0 +1,24 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+# Tests using the rats data
+#
+# (Female rats, from Mantel et al, Cancer Research 37,
+# 3863-3868, November 77)
+
+rfit <- coxph(Surv(time,status) ~ rx + frailty(litter), rats,
+ method='breslow')
+names(rfit)
+rfit
+
+rfit$iter
+rfit$df
+rfit$history[[1]]
+
+rfit1 <- coxph(Surv(time,status) ~ rx + frailty(litter, theta=1), rats,
+ method='breslow')
+rfit1
+
+rfit2 <- coxph(Surv(time,status) ~ frailty(litter), rats)
+rfit2
diff --git a/win32/deps/library/survival/tests/fr_rat1.Rout.save b/win32/deps/library/survival/tests/fr_rat1.Rout.save
new file mode 100644
index 0000000..27c2123
--- /dev/null
+++ b/win32/deps/library/survival/tests/fr_rat1.Rout.save
@@ -0,0 +1,109 @@
+
+R version 2.13.0 (2011-04-13)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> # Tests using the rats data
+> #
+> # (Female rats, from Mantel et al, Cancer Research 37,
+> # 3863-3868, November 77)
+>
+> rfit <- coxph(Surv(time,status) ~ rx + frailty(litter), rats,
++ method='breslow')
+> names(rfit)
+ [1] "coefficients" "var" "var2"
+ [4] "loglik" "iter" "linear.predictors"
+ [7] "residuals" "means" "concordance"
+[10] "method" "frail" "fvar"
+[13] "df" "df2" "penalty"
+[16] "pterms" "assign2" "history"
+[19] "coxlist1" "printfun" "n"
+[22] "nevent" "terms" "assign"
+[25] "wald.test" "y" "formula"
+[28] "call"
+> rfit
+Call:
+coxph(formula = Surv(time, status) ~ rx + frailty(litter), data = rats,
+ method = "breslow")
+
+ coef se(coef) se2 Chisq DF p
+rx 0.906 0.323 0.319 7.88 1.0 0.005
+frailty(litter) 16.89 13.8 0.250
+
+Iterations: 6 outer, 25 Newton-Raphson
+ Variance of random effect= 0.474 I-likelihood = -181.1
+Degrees of freedom for terms= 1.0 13.9
+Likelihood ratio test=36.3 on 14.8 df, p=0.00144 n= 150
+>
+> rfit$iter
+[1] 6 25
+> rfit$df
+[1] 0.975943 13.854864
+> rfit$history[[1]]
+$theta
+[1] 0.4742849
+
+$done
+c.loglik
+ TRUE
+
+$history
+ theta loglik c.loglik
+[1,] 0.0000000 -181.8451 -181.8451
+[2,] 1.0000000 -168.3683 -181.5458
+[3,] 0.5000000 -173.3117 -181.0788
+[4,] 0.3090061 -175.9446 -181.1490
+[5,] 0.4645720 -173.7590 -181.0775
+[6,] 0.4736210 -173.6431 -181.0773
+
+$c.loglik
+[1] -181.0773
+
+>
+> rfit1 <- coxph(Surv(time,status) ~ rx + frailty(litter, theta=1), rats,
++ method='breslow')
+> rfit1
+Call:
+coxph(formula = Surv(time, status) ~ rx + frailty(litter, theta = 1),
+ data = rats, method = "breslow")
+
+ coef se(coef) se2 Chisq DF p
+rx 0.918 0.327 0.321 7.85 1.0 0.0051
+frailty(litter, theta = 1 27.25 22.7 0.2300
+
+Iterations: 1 outer, 6 Newton-Raphson
+ Variance of random effect= 1 I-likelihood = -181.5
+Degrees of freedom for terms= 1.0 22.7
+Likelihood ratio test=50.7 on 23.7 df, p=0.001 n= 150
+>
+> rfit2 <- coxph(Surv(time,status) ~ frailty(litter), rats)
+> rfit2
+Call:
+coxph(formula = Surv(time, status) ~ frailty(litter), data = rats)
+
+ coef se(coef) se2 Chisq DF p
+frailty(litter) 18 14.6 0.24
+
+Iterations: 6 outer, 22 Newton-Raphson
+ Variance of random effect= 0.504 I-likelihood = -184.8
+Degrees of freedom for terms= 14.6
+Likelihood ratio test=30 on 14.6 df, p=0.0101 n= 150
+>
diff --git a/win32/deps/library/survival/tests/fr_rat2.R b/win32/deps/library/survival/tests/fr_rat2.R
new file mode 100644
index 0000000..4edd1be
--- /dev/null
+++ b/win32/deps/library/survival/tests/fr_rat2.R
@@ -0,0 +1,65 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+# From Gail, Sautner and Brown, Biometrics 36, 255-66, 1980
+
+# 48 rats were injected with a carcinogen, and then randomized to either
+# drug or placebo. The number of tumors ranges from 0 to 13; all rats were
+# censored at 6 months after randomization.
+
+# Variables: rat, treatment (1=drug, 0=control), o
+# observation # within rat,
+# (start, stop] status
+# The raw data has some intervals of zero length, i.e., start==stop.
+# We add .1 to these times as an approximate solution
+#
+rat2 <- read.table('data.rat2', col.names=c('id', 'rx', 'enum', 'start',
+ 'stop', 'status'))
+temp1 <- rat2$start
+temp2 <- rat2$stop
+for (i in 1:nrow(rat2)) {
+ if (temp1[i] == temp2[i]) {
+ temp2[i] <- temp2[i] + .1
+ if (i < nrow(rat2) && rat2$id[i] == rat2$id[i+1]) {
+ temp1[i+1] <- temp1[i+1] + .1
+ if (temp2[i+1] <= temp1[i+1]) temp2[i+1] <- temp1[i+1]
+ }
+ }
+ }
+rat2$start <- temp1
+rat2$stop <- temp2
+
+r2fit0 <- coxph(Surv(start, stop, status) ~ rx + cluster(id), rat2)
+
+r2fitg <- coxph(Surv(start, stop, status) ~ rx + frailty(id), rat2)
+r2fitm <- coxph(Surv(start, stop, status) ~ rx + frailty.gaussian(id), rat2)
+
+r2fit0
+r2fitg
+r2fitm
+
+#This example is unusual: the frailties variances end up about the same,
+# but the effect on rx differs. Double check it
+# Because of different iteration paths, the coef won't be exactly the
+# same, but darn close.
+
+temp <- coxph(Surv(start, stop, status) ~ rx + offset(r2fitm$frail[id]), rat2)
+all.equal(temp$coef, r2fitm$coef[1], tolerance=1e-7)
+
+temp <- coxph(Surv(start, stop, status) ~ rx + offset(r2fitg$frail[id]), rat2)
+all.equal(temp$coef, r2fitg$coef[1], tolerance=1e-7)
+
+#
+# What do I get with AIC
+#
+r2fita1 <- coxph(Surv(start, stop, status) ~ rx + frailty(id, method='aic'),
+ rat2)
+r2fita2 <- coxph(Surv(start, stop, status) ~ rx + frailty(id, method='aic',
+ dist='gauss'), rat2)
+r2fita3 <- coxph(Surv(start, stop, status) ~ rx + frailty(id, dist='t'),
+ rat2)
+
+r2fita1
+r2fita2
+r2fita3
diff --git a/win32/deps/library/survival/tests/fr_rat2.Rout.save b/win32/deps/library/survival/tests/fr_rat2.Rout.save
new file mode 100644
index 0000000..aa32eba
--- /dev/null
+++ b/win32/deps/library/survival/tests/fr_rat2.Rout.save
@@ -0,0 +1,156 @@
+
+R version 2.14.0 Under development (unstable) (2011-04-10 r55401)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> # From Gail, Sautner and Brown, Biometrics 36, 255-66, 1980
+>
+> # 48 rats were injected with a carcinogen, and then randomized to either
+> # drug or placebo. The number of tumors ranges from 0 to 13; all rats were
+> # censored at 6 months after randomization.
+>
+> # Variables: rat, treatment (1=drug, 0=control), o
+> # observation # within rat,
+> # (start, stop] status
+> # The raw data has some intervals of zero length, i.e., start==stop.
+> # We add .1 to these times as an approximate solution
+> #
+> rat2 <- read.table('data.rat2', col.names=c('id', 'rx', 'enum', 'start',
++ 'stop', 'status'))
+> temp1 <- rat2$start
+> temp2 <- rat2$stop
+> for (i in 1:nrow(rat2)) {
++ if (temp1[i] == temp2[i]) {
++ temp2[i] <- temp2[i] + .1
++ if (i < nrow(rat2) && rat2$id[i] == rat2$id[i+1]) {
++ temp1[i+1] <- temp1[i+1] + .1
++ if (temp2[i+1] <= temp1[i+1]) temp2[i+1] <- temp1[i+1]
++ }
++ }
++ }
+> rat2$start <- temp1
+> rat2$stop <- temp2
+>
+> r2fit0 <- coxph(Surv(start, stop, status) ~ rx + cluster(id), rat2)
+>
+> r2fitg <- coxph(Surv(start, stop, status) ~ rx + frailty(id), rat2)
+> r2fitm <- coxph(Surv(start, stop, status) ~ rx + frailty.gaussian(id), rat2)
+>
+> r2fit0
+Call:
+coxph(formula = Surv(start, stop, status) ~ rx + cluster(id),
+ data = rat2)
+
+
+ coef exp(coef) se(coef) robust se z p
+rx -0.827 0.438 0.151 0.204 -4.05 5.2e-05
+
+Likelihood ratio test=32.9 on 1 df, p=9.89e-09 n= 253, number of events= 212
+> r2fitg
+Call:
+coxph(formula = Surv(start, stop, status) ~ rx + frailty(id),
+ data = rat2)
+
+ coef se(coef) se2 Chisq DF p
+rx -0.838 0.219 0.152 14.6 1.0 0.00013
+frailty(id) 57.3 26.4 0.00045
+
+Iterations: 7 outer, 26 Newton-Raphson
+ Variance of random effect= 0.317 I-likelihood = -779.1
+Degrees of freedom for terms= 0.5 26.3
+Likelihood ratio test=120 on 26.8 df, p=8.43e-14 n= 253
+> r2fitm
+Call:
+coxph(formula = Surv(start, stop, status) ~ rx + frailty.gaussian(id),
+ data = rat2)
+
+ coef se(coef) se2 Chisq DF p
+rx -0.79 0.22 0.154 12.9 1.0 3.2e-04
+frailty.gaussian(id) 60.9 24.9 7.3e-05
+
+Iterations: 6 outer, 23 Newton-Raphson
+ Variance of random effect= 0.303
+Degrees of freedom for terms= 0.5 24.9
+Likelihood ratio test=118 on 25.4 df, p=6.99e-14 n= 253
+>
+> #This example is unusual: the frailties variances end up about the same,
+> # but the effect on rx differs. Double check it
+> # Because of different iteration paths, the coef won't be exactly the
+> # same, but darn close.
+>
+> temp <- coxph(Surv(start, stop, status) ~ rx + offset(r2fitm$frail[id]), rat2)
+> all.equal(temp$coef, r2fitm$coef[1], tolerance=1e-7)
+[1] TRUE
+>
+> temp <- coxph(Surv(start, stop, status) ~ rx + offset(r2fitg$frail[id]), rat2)
+> all.equal(temp$coef, r2fitg$coef[1], tolerance=1e-7)
+[1] TRUE
+>
+> #
+> # What do I get with AIC
+> #
+> r2fita1 <- coxph(Surv(start, stop, status) ~ rx + frailty(id, method='aic'),
++ rat2)
+> r2fita2 <- coxph(Surv(start, stop, status) ~ rx + frailty(id, method='aic',
++ dist='gauss'), rat2)
+> r2fita3 <- coxph(Surv(start, stop, status) ~ rx + frailty(id, dist='t'),
++ rat2)
+>
+> r2fita1
+Call:
+coxph(formula = Surv(start, stop, status) ~ rx + frailty(id,
+ method = "aic"), data = rat2)
+
+ coef se(coef) se2 Chisq DF p
+rx -0.838 0.23 0.151 13.3 1.0 0.00026
+frailty(id, method = "aic 60.4 28.2 0.00039
+
+Iterations: 10 outer, 34 Newton-Raphson
+ Variance of random effect= 0.375 I-likelihood = -779.2
+Degrees of freedom for terms= 0.4 28.2
+Likelihood ratio test=124 on 28.6 df, p=7.92e-14 n= 253
+> r2fita2
+Call:
+coxph(formula = Surv(start, stop, status) ~ rx + frailty(id,
+ method = "aic", dist = "gauss"), data = rat2)
+
+ coef se(coef) se2 Chisq DF p
+rx -0.785 0.245 0.154 10.3 1.0 1.3e-03
+frailty(id, method = "aic 70.4 28.5 2.1e-05
+
+Iterations: 9 outer, 33 Newton-Raphson
+ Variance of random effect= 0.436
+Degrees of freedom for terms= 0.4 28.5
+Likelihood ratio test=125 on 28.9 df, p=5.93e-14 n= 253
+> r2fita3
+Call:
+coxph(formula = Surv(start, stop, status) ~ rx + frailty(id,
+ dist = "t"), data = rat2)
+
+ coef se(coef) se2 Chisq DF p
+rx -0.79 0.254 0.157 9.67 1 0.00190
+frailty(id, dist = "t") 64.72 30 0.00024
+
+Iterations: 7 outer, 29 Newton-Raphson
+ Variance of random effect= 0.78
+Degrees of freedom for terms= 0.4 30.0
+Likelihood ratio test=126 on 30.4 df, p=1.39e-13 n= 253
+>
diff --git a/win32/deps/library/survival/tests/fr_resid.R b/win32/deps/library/survival/tests/fr_resid.R
new file mode 100644
index 0000000..dde6c15
--- /dev/null
+++ b/win32/deps/library/survival/tests/fr_resid.R
@@ -0,0 +1,94 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# The residual methods treat a sparse frailty as a fixed offset with
+# no variance
+#
+aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+
+kfit1 <- coxph(Surv(time, status) ~ age + sex +
+ frailty(id, dist='gauss'), kidney)
+tempf <- predict(kfit1, type='terms')[,3]
+temp <- kfit1$frail[match(kidney$id, sort(unique(kidney$id)))]
+#all.equal(unclass(tempf), unclass(temp))
+all.equal(as.vector(tempf), as.vector(temp))
+
+# Now fit a model with explicit offset
+kfitx <- coxph(Surv(time, status) ~ age + sex + offset(tempf),kidney,
+ eps=1e-7)
+
+# These are not precisely the same, due to different iteration paths
+aeq(kfitx$coef, kfit1$coef)
+
+# This will make them identical
+kfitx <- coxph(Surv(time, status) ~ age + sex + offset(temp),kidney,
+ iter=0, init=kfit1$coef)
+aeq(resid(kfit1), resid(kfitx))
+aeq(resid(kfit1, type='score'), resid(kfitx, type='score'))
+aeq(resid(kfit1, type='schoe'), resid(kfitx, type='schoe'))
+
+# These are not the same, due to a different variance matrix
+# The frailty model's variance is about 2x the naive "assume an offset" var
+# The score residuals are equal, however.
+aeq(resid(kfit1, type='dfbeta'), resid(kfitx, type='dfbeta'))
+zed <- kfitx
+zed$var <- kfit1$var
+aeq(resid(kfit1, type='dfbeta'), resid(zed, type='dfbeta'))
+
+
+temp1 <- resid(kfit1, type='score')
+temp2 <- resid(kfitx, type='score')
+aeq(temp1, temp2)
+
+#
+# Now for some tests of predicted values
+#
+aeq(predict(kfit1, type='expected'), predict(kfitx, type='expected'))
+aeq(predict(kfit1, type='lp'), predict(kfitx, type='lp'))
+
+temp1 <- predict(kfit1, type='terms', se.fit=T)
+temp2 <- predict(kfitx, type='terms', se.fit=T)
+aeq(temp1$fit[,1:2], temp2$fit)
+aeq(temp1$se.fit[,1:2], temp2$se.fit) #should be false
+mean(temp1$se.fit[,1:2]/ temp2$se.fit)
+aeq(as.vector(temp1$se.fit[,3])^2,
+ as.vector(kfit1$fvar[match(kidney$id, sort(unique(kidney$id)))]))
+
+print(temp1)
+kfit1
+kfitx
+
+rm(temp1, temp2, kfitx, zed, tempf)
+#
+# The special case of a single sparse frailty
+#
+
+kfit1 <- coxph(Surv(time, status) ~ frailty(id, dist='gauss'), kidney)
+tempf <- predict(kfit1, type='terms')
+temp <- kfit1$frail[match(kidney$id, sort(unique(kidney$id)))]
+all.equal(as.vector(tempf), as.vector(temp))
+
+# Now fit a model with explicit offset
+kfitx <- coxph(Surv(time, status) ~ offset(tempf),kidney, eps=1e-7)
+
+aeq(resid(kfit1), resid(kfitx))
+aeq(resid(kfit1, type='deviance'), resid(kfitx, type='deviance'))
+
+#
+# Some tests of predicted values
+#
+aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+aeq(predict(kfit1, type='expected'), predict(kfitx, type='expected'))
+aeq(predict(kfit1, type='lp'), predict(kfitx, type='lp'))
+
+temp1 <- predict(kfit1, type='terms', se.fit=T)
+aeq(temp1$fit, kfitx$linear)
+aeq(temp1$se.fit^2,
+ kfit1$fvar[match(kidney$id, sort(unique(kidney$id)))])
+
+temp1
+kfit1
+
+
diff --git a/win32/deps/library/survival/tests/fr_resid.Rout.save b/win32/deps/library/survival/tests/fr_resid.Rout.save
new file mode 100644
index 0000000..8392ccd
--- /dev/null
+++ b/win32/deps/library/survival/tests/fr_resid.Rout.save
@@ -0,0 +1,358 @@
+
+R version 2.14.0 Under development (unstable) (2011-04-10 r55401)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # The residual methods treat a sparse frailty as a fixed offset with
+> # no variance
+> #
+> aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+>
+> kfit1 <- coxph(Surv(time, status) ~ age + sex +
++ frailty(id, dist='gauss'), kidney)
+> tempf <- predict(kfit1, type='terms')[,3]
+> temp <- kfit1$frail[match(kidney$id, sort(unique(kidney$id)))]
+> #all.equal(unclass(tempf), unclass(temp))
+> all.equal(as.vector(tempf), as.vector(temp))
+[1] TRUE
+>
+> # Now fit a model with explicit offset
+> kfitx <- coxph(Surv(time, status) ~ age + sex + offset(tempf),kidney,
++ eps=1e-7)
+>
+> # These are not precisely the same, due to different iteration paths
+> aeq(kfitx$coef, kfit1$coef)
+[1] TRUE
+>
+> # This will make them identical
+> kfitx <- coxph(Surv(time, status) ~ age + sex + offset(temp),kidney,
++ iter=0, init=kfit1$coef)
+> aeq(resid(kfit1), resid(kfitx))
+[1] TRUE
+> aeq(resid(kfit1, type='score'), resid(kfitx, type='score'))
+[1] TRUE
+> aeq(resid(kfit1, type='schoe'), resid(kfitx, type='schoe'))
+[1] TRUE
+>
+> # These are not the same, due to a different variance matrix
+> # The frailty model's variance is about 2x the naive "assume an offset" var
+> # The score residuals are equal, however.
+> aeq(resid(kfit1, type='dfbeta'), resid(kfitx, type='dfbeta'))
+[1] "Mean relative difference: 0.5216263"
+> zed <- kfitx
+> zed$var <- kfit1$var
+> aeq(resid(kfit1, type='dfbeta'), resid(zed, type='dfbeta'))
+[1] TRUE
+>
+>
+> temp1 <- resid(kfit1, type='score')
+> temp2 <- resid(kfitx, type='score')
+> aeq(temp1, temp2)
+[1] TRUE
+>
+> #
+> # Now for some tests of predicted values
+> #
+> aeq(predict(kfit1, type='expected'), predict(kfitx, type='expected'))
+[1] TRUE
+> aeq(predict(kfit1, type='lp'), predict(kfitx, type='lp'))
+[1] TRUE
+>
+> temp1 <- predict(kfit1, type='terms', se.fit=T)
+> temp2 <- predict(kfitx, type='terms', se.fit=T)
+> aeq(temp1$fit[,1:2], temp2$fit)
+[1] TRUE
+> aeq(temp1$se.fit[,1:2], temp2$se.fit) #should be false
+[1] "Mean relative difference: 0.3024526"
+> mean(temp1$se.fit[,1:2]/ temp2$se.fit)
+[1] 1.433017
+> aeq(as.vector(temp1$se.fit[,3])^2,
++ as.vector(kfit1$fvar[match(kidney$id, sort(unique(kidney$id)))]))
+[1] TRUE
+>
+> print(temp1)
+$fit
+ age sex frailty(id, dist = "gauss")
+1 -0.073981042 1.039553 0.59814468
+2 -0.073981042 1.039553 0.59814468
+3 0.020278123 -0.371269 0.38512389
+4 0.020278123 -0.371269 0.38512389
+5 -0.055129209 1.039553 0.20210998
+6 -0.055129209 1.039553 0.20210998
+7 -0.059842167 -0.371269 -0.55932015
+8 -0.055129209 -0.371269 -0.55932015
+9 -0.158814289 1.039553 0.28558387
+10 -0.158814289 1.039553 0.28558387
+11 -0.130536540 -0.371269 0.06628942
+12 -0.125823582 -0.371269 0.06628942
+13 0.034416998 1.039553 0.80505119
+14 0.034416998 1.039553 0.80505119
+15 0.053268830 -0.371269 -0.43834241
+16 0.057981789 -0.371269 -0.43834241
+17 0.119250245 -0.371269 -0.05631649
+18 0.119250245 -0.371269 -0.05631649
+19 0.034416998 1.039553 -0.49980572
+20 0.039129956 1.039553 -0.49980572
+21 0.001426290 -0.371269 -0.13028264
+22 0.001426290 -0.371269 -0.13028264
+23 -0.045703292 -0.371269 0.06377401
+24 -0.045703292 -0.371269 0.06377401
+25 -0.040990334 -0.371269 0.38815296
+26 -0.040990334 -0.371269 0.38815296
+27 -0.007999626 -0.371269 -0.47650510
+28 -0.007999626 -0.371269 -0.47650510
+29 -0.125823582 -0.371269 -0.66986830
+30 -0.125823582 -0.371269 -0.66986830
+31 0.076833621 1.039553 0.19359678
+32 0.076833621 1.039553 0.19359678
+33 0.076833621 -0.371269 -0.16483200
+34 0.076833621 -0.371269 -0.16483200
+35 -0.003286668 -0.371269 -0.15794998
+36 0.001426290 -0.371269 -0.15794998
+37 0.043842914 -0.371269 -0.46236014
+38 0.043842914 -0.371269 -0.46236014
+39 0.001426290 -0.371269 0.12603308
+40 0.001426290 -0.371269 0.12603308
+41 0.010852206 1.039553 -1.74303142
+42 0.015565165 1.039553 -1.74303142
+43 -0.064555125 -0.371269 -0.45211210
+44 -0.064555125 -0.371269 -0.45211210
+45 0.086259538 -0.371269 0.51574106
+46 0.090972496 -0.371269 0.51574106
+47 -0.007999626 -0.371269 0.09475123
+48 -0.003286668 -0.371269 0.09475123
+49 -0.003286668 1.039553 0.05790354
+50 -0.003286668 1.039553 0.05790354
+51 0.062694747 -0.371269 -0.37933234
+52 0.067407705 -0.371269 -0.37933234
+53 -0.158814289 -0.371269 0.11248891
+54 -0.158814289 -0.371269 0.11248891
+55 0.039129956 -0.371269 0.54791210
+56 0.039129956 -0.371269 0.54791210
+57 0.043842914 1.039553 0.45873482
+58 0.043842914 1.039553 0.45873482
+59 0.048555872 -0.371269 0.35639797
+60 0.048555872 -0.371269 0.35639797
+61 0.057981789 -0.371269 0.48803342
+62 0.057981789 -0.371269 0.48803342
+63 0.029704039 -0.371269 0.25597325
+64 0.034416998 -0.371269 0.25597325
+65 0.062694747 -0.371269 0.23054948
+66 0.062694747 -0.371269 0.23054948
+67 0.001426290 -0.371269 -0.13680005
+68 0.006139248 -0.371269 -0.13680005
+69 -0.102258791 -0.371269 0.51977995
+70 -0.102258791 -0.371269 0.51977995
+71 -0.007999626 -0.371269 -0.23878154
+72 -0.007999626 -0.371269 -0.23878154
+73 0.039129956 -0.371269 0.17174306
+74 0.039129956 -0.371269 0.17174306
+75 0.076833621 1.039553 -0.35822829
+76 0.076833621 1.039553 -0.35822829
+
+$se.fit
+ age sex frailty(id, dist = "gauss")
+1 0.195861829 0.3280279 0.6246430
+2 0.195861829 0.3280279 0.6246430
+3 0.053685514 0.1171528 0.6954922
+4 0.053685514 0.1171528 0.6954922
+5 0.145952360 0.3280279 0.5705340
+6 0.145952360 0.3280279 0.5705340
+7 0.158429727 0.1171528 0.4894541
+8 0.145952360 0.1171528 0.4894541
+9 0.420454437 0.3280279 0.6071455
+10 0.420454437 0.3280279 0.6071455
+11 0.345590234 0.1171528 0.5633997
+12 0.333112867 0.1171528 0.5633997
+13 0.091117615 0.3280279 0.6641707
+14 0.091117615 0.3280279 0.6641707
+15 0.141027084 0.1171528 0.5101890
+16 0.153504451 0.1171528 0.5101890
+17 0.315710223 0.1171528 0.5491569
+18 0.315710223 0.1171528 0.5491569
+19 0.091117615 0.3280279 0.5264083
+20 0.103594982 0.3280279 0.5264083
+21 0.003776045 0.1171528 0.5180953
+22 0.003776045 0.1171528 0.5180953
+23 0.120997626 0.1171528 0.6208806
+24 0.120997626 0.1171528 0.6208806
+25 0.108520259 0.1171528 0.5811421
+26 0.108520259 0.1171528 0.5811421
+27 0.021178689 0.1171528 0.6247779
+28 0.021178689 0.1171528 0.6247779
+29 0.333112867 0.1171528 0.5615987
+30 0.333112867 0.1171528 0.5615987
+31 0.203413919 0.3280279 0.6532405
+32 0.203413919 0.3280279 0.6532405
+33 0.203413919 0.1171528 0.5247227
+34 0.203413919 0.1171528 0.5247227
+35 0.008701322 0.1171528 0.5106606
+36 0.003776045 0.1171528 0.5106606
+37 0.116072349 0.1171528 0.6284328
+38 0.116072349 0.1171528 0.6284328
+39 0.003776045 0.1171528 0.6320009
+40 0.003776045 0.1171528 0.6320009
+41 0.028730780 0.3280279 0.5235228
+42 0.041208147 0.3280279 0.5235228
+43 0.170907094 0.1171528 0.5492095
+44 0.170907094 0.1171528 0.5492095
+45 0.228368654 0.1171528 0.6058686
+46 0.240846021 0.1171528 0.6058686
+47 0.021178689 0.1171528 0.6267998
+48 0.008701322 0.1171528 0.6267998
+49 0.008701322 0.3280279 0.5526664
+50 0.008701322 0.3280279 0.5526664
+51 0.165981818 0.1171528 0.5556706
+52 0.178459185 0.1171528 0.5556706
+53 0.420454437 0.1171528 0.5849825
+54 0.420454437 0.1171528 0.5849825
+55 0.103594982 0.1171528 0.6081780
+56 0.103594982 0.1171528 0.6081780
+57 0.116072349 0.3280279 0.6010279
+58 0.116072349 0.3280279 0.6010279
+59 0.128549717 0.1171528 0.5762113
+60 0.128549717 0.1171528 0.5762113
+61 0.153504451 0.1171528 0.5982501
+62 0.153504451 0.1171528 0.5982501
+63 0.078640248 0.1171528 0.6614053
+64 0.091117615 0.1171528 0.6614053
+65 0.165981818 0.1171528 0.5609510
+66 0.165981818 0.1171528 0.5609510
+67 0.003776045 0.1171528 0.5844921
+68 0.016253412 0.1171528 0.5844921
+69 0.270726031 0.1171528 0.6089631
+70 0.270726031 0.1171528 0.6089631
+71 0.021178689 0.1171528 0.6795741
+72 0.021178689 0.1171528 0.6795741
+73 0.103594982 0.1171528 0.6421784
+74 0.103594982 0.1171528 0.6421784
+75 0.203413919 0.3280279 0.5779661
+76 0.203413919 0.3280279 0.5779661
+
+> kfit1
+Call:
+coxph(formula = Surv(time, status) ~ age + sex + frailty(id,
+ dist = "gauss"), data = kidney)
+
+ coef se(coef) se2 Chisq DF p
+age 0.00471 0.0125 0.00856 0.14 1.0 0.7100
+sex -1.41082 0.4452 0.31504 10.04 1.0 0.0015
+frailty(id, dist = "gauss 26.54 14.7 0.0290
+
+Iterations: 6 outer, 39 Newton-Raphson
+ Variance of random effect= 0.569
+Degrees of freedom for terms= 0.5 0.5 14.7
+Likelihood ratio test=47.5 on 15.7 df, p=4.65e-05 n= 76
+> kfitx
+Call:
+coxph(formula = Surv(time, status) ~ age + sex + offset(temp),
+ data = kidney, init = kfit1$coef, iter = 0)
+
+
+ coef exp(coef) se(coef) z p
+age 0.00471 1.005 0.00875 0.539 5.9e-01
+sex -1.41082 0.244 0.30916 -4.563 5.0e-06
+
+Likelihood ratio test=0 on 2 df, p=1 n= 76, number of events= 58
+>
+> rm(temp1, temp2, kfitx, zed, tempf)
+> #
+> # The special case of a single sparse frailty
+> #
+>
+> kfit1 <- coxph(Surv(time, status) ~ frailty(id, dist='gauss'), kidney)
+> tempf <- predict(kfit1, type='terms')
+> temp <- kfit1$frail[match(kidney$id, sort(unique(kidney$id)))]
+> all.equal(as.vector(tempf), as.vector(temp))
+[1] TRUE
+>
+> # Now fit a model with explicit offset
+> kfitx <- coxph(Surv(time, status) ~ offset(tempf),kidney, eps=1e-7)
+>
+> aeq(resid(kfit1), resid(kfitx))
+[1] TRUE
+> aeq(resid(kfit1, type='deviance'), resid(kfitx, type='deviance'))
+[1] TRUE
+>
+> #
+> # Some tests of predicted values
+> #
+> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+> aeq(predict(kfit1, type='expected'), predict(kfitx, type='expected'))
+[1] TRUE
+> aeq(predict(kfit1, type='lp'), predict(kfitx, type='lp'))
+[1] TRUE
+>
+> temp1 <- predict(kfit1, type='terms', se.fit=T)
+> aeq(temp1$fit, kfitx$linear)
+[1] TRUE
+> aeq(temp1$se.fit^2,
++ kfit1$fvar[match(kidney$id, sort(unique(kidney$id)))])
+[1] TRUE
+>
+> temp1
+$fit
+ [1] 0.696003729 0.696003729 0.244575316 0.244575316 0.494175549
+ [6] 0.494175549 -0.659248798 -0.659248798 0.521423106 0.521423106
+[11] -0.114492938 -0.114492938 0.800127481 0.800127481 -0.488101282
+[16] -0.488101282 -0.120396647 -0.120396647 0.131121515 0.131121515
+[21] -0.214987009 -0.214987009 -0.054872789 -0.054872789 0.184657295
+[26] 0.184657295 -0.510007747 -0.510007747 -0.790746805 -0.790746805
+[31] 0.324674289 0.324674289 -0.239374060 -0.239374060 -0.264428564
+[36] -0.264428564 -0.472698773 -0.472698773 0.006304049 0.006304049
+[41] -0.873434085 -0.873434085 -0.530880840 -0.530880840 0.351411783
+[46] 0.351411783 -0.037212138 -0.037212138 0.442049266 0.442049266
+[51] -0.419206550 -0.419206550 -0.108012854 -0.108012854 0.346332076
+[56] 0.346332076 0.659300205 0.659300205 0.197278585 0.197278585
+[61] 0.304868889 0.304868889 0.139712997 0.139712997 0.093574024
+[66] 0.093574024 -0.209690355 -0.209690355 0.302070834 0.302070834
+[71] -0.278962288 -0.278962288 0.068599919 0.068599919 0.078493616
+[76] 0.078493616
+
+$se.fit
+ [1] 0.6150025 0.6150025 0.6160184 0.6160184 0.5715622 0.5715622 0.4393615
+ [8] 0.4393615 0.5761369 0.5761369 0.4834244 0.4834244 0.6421184 0.6421184
+[15] 0.4574824 0.4574824 0.4813578 0.4813578 0.5119792 0.5119792 0.4764145
+[22] 0.4764145 0.5532477 0.5532477 0.5195437 0.5195437 0.5534327 0.5534327
+[29] 0.4775572 0.4775572 0.6364522 0.6364522 0.4708988 0.4708988 0.4670896
+[36] 0.4670896 0.5600672 0.5600672 0.5641880 0.5641880 0.4650576 0.4650576
+[43] 0.4904715 0.4904715 0.5448430 0.5448430 0.5570120 0.5570120 0.5608187
+[50] 0.5608187 0.4996021 0.4996021 0.4831697 0.4831697 0.5452255 0.5452255
+[57] 0.6057428 0.6057428 0.5209402 0.5209402 0.5376594 0.5376594 0.5911350
+[64] 0.5911350 0.5065368 0.5065368 0.5290283 0.5290283 0.5368433 0.5368433
+[71] 0.5996077 0.5996077 0.5762814 0.5762814 0.5782753 0.5782753
+
+> kfit1
+Call:
+coxph(formula = Surv(time, status) ~ frailty(id, dist = "gauss"),
+ data = kidney)
+
+ coef se(coef) se2 Chisq DF p
+frailty(id, dist = "gauss 23 13.8 0.057
+
+Iterations: 7 outer, 39 Newton-Raphson
+ Variance of random effect= 0.458
+Degrees of freedom for terms= 13.8
+Likelihood ratio test=33.4 on 13.8 df, p=0.00234 n= 76
+>
+>
+>
diff --git a/win32/deps/library/survival/tests/fr_simple.R b/win32/deps/library/survival/tests/fr_simple.R
new file mode 100644
index 0000000..583d545
--- /dev/null
+++ b/win32/deps/library/survival/tests/fr_simple.R
@@ -0,0 +1,62 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Test the logic of the penalized code by fitting some no-frailty models
+# (theta=0). It should give exactly the same answers as 'ordinary' coxph.
+#
+test1 <- data.frame(time= c(4, 3,1,1,2,2,3),
+ status=c(1,NA,1,0,1,1,0),
+ x= c(0, 2,1,1,1,0,0))
+
+test2 <- data.frame(start=c(1, 2, 5, 2, 1, 7, 3, 4, 8, 8),
+ stop =c(2, 3, 6, 7, 8, 9, 9, 9,14,17),
+ event=c(1, 1, 1, 1, 1, 1, 1, 0, 0, 0),
+ x =c(1, 0, 0, 1, 0, 1, 1, 1, 0, 0) )
+
+zz <- rep(0, nrow(test1))
+tfit1 <- coxph(Surv(time,status) ~x, test1, eps=1e-7)
+tfit2 <- coxph(Surv(time,status) ~x + frailty(zz, theta=0, sparse=T), test1)
+tfit3 <- coxph(Surv(zz,time,status) ~x + frailty(zz, theta=0, sparse=T), test1)
+
+temp <- c('coefficients', 'var', 'loglik', 'linear.predictors',
+ 'means', 'n')
+
+all.equal(tfit1[temp], tfit2[temp])
+all.equal(tfit2[temp], tfit3[temp])
+
+zz <- rep(0, nrow(test2))
+tfit1 <- coxph(Surv(start, stop, event) ~x, test2, eps=1e-7)
+tfit2 <- coxph(Surv(start, stop, event) ~ x + frailty(zz, theta=0, sparse=T),
+ test2)
+all.equal(tfit1[temp], tfit2[temp])
+
+
+#
+# Repeat the above tests, but with a strata added
+# Because the data set is simply doubled, the loglik will double,
+# beta is the same, variance is halved.
+#
+test3 <- rbind(test1, test1)
+test3$x2 <- rep(1:2, rep(nrow(test1),2))
+zz <- rep(0, nrow(test3))
+tfit1 <- coxph(Surv(time,status) ~x + strata(x2), test3, eps=1e-7)
+tfit2 <- coxph(Surv(time,status) ~x + frailty(zz, theta=0, sparse=T)
+ + strata(x2), test3)
+tfit3 <- coxph(Surv(zz,time,status) ~x + frailty(zz, theta=0, sparse=T)
+ + strata(x2), test3)
+
+all.equal(tfit1[temp], tfit2[temp])
+all.equal(tfit2[temp], tfit3[temp])
+
+
+test4 <- rbind(test2, test2)
+test4$x2 <- rep(1:2, rep(nrow(test2),2))
+zz <- rep(0, nrow(test4))
+tfit1 <- coxph(Surv(start, stop, event) ~x, test4, eps=1e-7)
+tfit2 <- coxph(Surv(start, stop, event) ~ x + frailty(zz, theta=0, sparse=T),
+ test4)
+all.equal(tfit1[temp], tfit2[temp])
+
+rm(test3, test4, tfit1, tfit2, tfit3, temp, zz)
diff --git a/win32/deps/library/survival/tests/fr_simple.Rout.save b/win32/deps/library/survival/tests/fr_simple.Rout.save
new file mode 100644
index 0000000..ab69134
--- /dev/null
+++ b/win32/deps/library/survival/tests/fr_simple.Rout.save
@@ -0,0 +1,87 @@
+
+R version 2.7.1 (2008-06-23)
+Copyright (C) 2008 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Test the logic of the penalized code by fitting some no-frailty models
+> # (theta=0). It should give exactly the same answers as 'ordinary' coxph.
+> #
+> test1 <- data.frame(time= c(4, 3,1,1,2,2,3),
++ status=c(1,NA,1,0,1,1,0),
++ x= c(0, 2,1,1,1,0,0))
+>
+> test2 <- data.frame(start=c(1, 2, 5, 2, 1, 7, 3, 4, 8, 8),
++ stop =c(2, 3, 6, 7, 8, 9, 9, 9,14,17),
++ event=c(1, 1, 1, 1, 1, 1, 1, 0, 0, 0),
++ x =c(1, 0, 0, 1, 0, 1, 1, 1, 0, 0) )
+>
+> zz <- rep(0, nrow(test1))
+> tfit1 <- coxph(Surv(time,status) ~x, test1, eps=1e-7)
+> tfit2 <- coxph(Surv(time,status) ~x + frailty(zz, theta=0, sparse=T), test1)
+> tfit3 <- coxph(Surv(zz,time,status) ~x + frailty(zz, theta=0, sparse=T), test1)
+>
+> temp <- c('coefficients', 'var', 'loglik', 'linear.predictors',
++ 'means', 'n')
+>
+> all.equal(tfit1[temp], tfit2[temp])
+[1] TRUE
+> all.equal(tfit2[temp], tfit3[temp])
+[1] TRUE
+>
+> zz <- rep(0, nrow(test2))
+> tfit1 <- coxph(Surv(start, stop, event) ~x, test2, eps=1e-7)
+> tfit2 <- coxph(Surv(start, stop, event) ~ x + frailty(zz, theta=0, sparse=T),
++ test2)
+> all.equal(tfit1[temp], tfit2[temp])
+[1] TRUE
+>
+>
+> #
+> # Repeat the above tests, but with a strata added
+> # Because the data set is simply doubled, the loglik will double,
+> # beta is the same, variance is halved.
+> #
+> test3 <- rbind(test1, test1)
+> test3$x2 <- rep(1:2, rep(nrow(test1),2))
+> zz <- rep(0, nrow(test3))
+> tfit1 <- coxph(Surv(time,status) ~x + strata(x2), test3, eps=1e-7)
+> tfit2 <- coxph(Surv(time,status) ~x + frailty(zz, theta=0, sparse=T)
++ + strata(x2), test3)
+> tfit3 <- coxph(Surv(zz,time,status) ~x + frailty(zz, theta=0, sparse=T)
++ + strata(x2), test3)
+>
+> all.equal(tfit1[temp], tfit2[temp])
+[1] TRUE
+> all.equal(tfit2[temp], tfit3[temp])
+[1] TRUE
+>
+>
+> test4 <- rbind(test2, test2)
+> test4$x2 <- rep(1:2, rep(nrow(test2),2))
+> zz <- rep(0, nrow(test4))
+> tfit1 <- coxph(Surv(start, stop, event) ~x, test4, eps=1e-7)
+> tfit2 <- coxph(Surv(start, stop, event) ~ x + frailty(zz, theta=0, sparse=T),
++ test4)
+> all.equal(tfit1[temp], tfit2[temp])
+[1] TRUE
+>
+> rm(test3, test4, tfit1, tfit2, tfit3, temp, zz)
+>
diff --git a/win32/deps/library/survival/tests/frailty.R b/win32/deps/library/survival/tests/frailty.R
new file mode 100644
index 0000000..b1de713
--- /dev/null
+++ b/win32/deps/library/survival/tests/frailty.R
@@ -0,0 +1,22 @@
+library(survival)
+#
+# The constuction of a survival curve with sparse frailties
+#
+# In this case the coefficient vector is kept in two parts, the
+# fixed coefs and the (often very large) random effects coefficients
+# The survfit function treats the second set of coefficients as fixed
+# values, to avoid an unmanagable variance matrix, and behaves like
+# the second fit below.
+
+fit1 <- coxph(Surv(time, status) ~ age + frailty(inst), lung)
+sfit1 <- survfit(fit1)
+
+# A parallel model with the frailties treated as fixed offsets
+offvar <- fit1$frail[as.numeric(factor(lung$inst))]
+fit2 <- coxph(Surv(time, status) ~ age + offset(offvar),lung)
+fit2$var <- fit1$var #force variances to match
+
+all.equal(fit1$coef, fit2$coef)
+sfit2 <- survfit(fit2, newdata=list(age=fit1$means, offvar=0))
+all.equal(sfit1$surv, sfit2$surv)
+all.equal(sfit1$var, sfit2$var)
diff --git a/win32/deps/library/survival/tests/frailty.Rout.save b/win32/deps/library/survival/tests/frailty.Rout.save
new file mode 100644
index 0000000..807c287
--- /dev/null
+++ b/win32/deps/library/survival/tests/frailty.Rout.save
@@ -0,0 +1,44 @@
+
+R version 2.11.1 (2010-05-31)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+> #
+> # The constuction of a survival curve with sparse frailties
+> #
+> # In this case the coefficient vector is kept in two parts, the
+> # fixed coefs and the (often very large) random effects coefficients
+> # The survfit function treats the second set of coefficients as fixed
+> # values, to avoid an unmanagable variance matrix, and behaves like
+> # the second fit below.
+>
+> fit1 <- coxph(Surv(time, status) ~ age + frailty(inst), lung)
+> sfit1 <- survfit(fit1)
+>
+> # A parallel model with the frailties treated as fixed offsets
+> offvar <- fit1$frail[as.numeric(factor(lung$inst))]
+> fit2 <- coxph(Surv(time, status) ~ age + offset(offvar),lung)
+> fit2$var <- fit1$var #force variances to match
+>
+> all.equal(fit1$coef, fit2$coef)
+[1] TRUE
+> sfit2 <- survfit(fit2, newdata=list(age=fit1$means, offvar=0))
+> all.equal(sfit1$surv, sfit2$surv)
+[1] TRUE
+> all.equal(sfit1$var, sfit2$var)
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/frank.R b/win32/deps/library/survival/tests/frank.R
new file mode 100644
index 0000000..030cf39
--- /dev/null
+++ b/win32/deps/library/survival/tests/frank.R
@@ -0,0 +1,23 @@
+library(survival)
+#
+# Check out intercept/interaction for Frank H
+#
+age2 <- lung$age - 50
+fit1 <- coxph(Surv(time, status) ~ age * strata(sex), lung)
+fit2 <- coxph(Surv(time, status) ~ age2*strata(sex), lung)
+
+surv1 <- survfit(fit1)
+surv2 <- survfit(fit2)
+# The call won't match, but the rest should
+icall <- match("call", names(surv1))
+all.equal(unclass(surv1)[-icall], unclass(surv2)[-icall])
+
+
+# It should match what I get with a single strata fit
+
+fit3 <- coxph(Surv(time, status) ~ age, data=lung,
+ init=fit1$coef[1], subset=(sex==1), iter=0)
+surv1b <- survfit(fit3, newdata=fit1$means[1])
+icall <- match("call", surv1b)
+all.equal(unlist(surv1[1])[-icall], unlist(surv1b)[-icall])
+
diff --git a/win32/deps/library/survival/tests/frank.Rout.save b/win32/deps/library/survival/tests/frank.Rout.save
new file mode 100644
index 0000000..22e885f
--- /dev/null
+++ b/win32/deps/library/survival/tests/frank.Rout.save
@@ -0,0 +1,45 @@
+
+R version 2.12.1 (2010-12-16)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: i686-pc-linux-gnu (32-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+> #
+> # Check out intercept/interaction for Frank H
+> #
+> age2 <- lung$age - 50
+> fit1 <- coxph(Surv(time, status) ~ age * strata(sex), lung)
+> fit2 <- coxph(Surv(time, status) ~ age2*strata(sex), lung)
+>
+> surv1 <- survfit(fit1)
+> surv2 <- survfit(fit2)
+> # The call won't match, but the rest should
+> icall <- match("call", names(surv1))
+> all.equal(unclass(surv1)[-icall], unclass(surv2)[-icall])
+[1] TRUE
+>
+>
+> # It should match what I get with a single strata fit
+>
+> fit3 <- coxph(Surv(time, status) ~ age, data=lung,
++ init=fit1$coef[1], subset=(sex==1), iter=0)
+> surv1b <- survfit(fit3, newdata=fit1$means[1])
+> icall <- match("call", surv1b)
+> all.equal(unlist(surv1[1])[-icall], unlist(surv1b)[-icall])
+[1] TRUE
+>
+>
diff --git a/win32/deps/library/survival/tests/gray1.rda b/win32/deps/library/survival/tests/gray1.rda
new file mode 100644
index 0000000..ad4d80b
Binary files /dev/null and b/win32/deps/library/survival/tests/gray1.rda differ
diff --git a/win32/deps/library/survival/tests/infcox.R b/win32/deps/library/survival/tests/infcox.R
new file mode 100644
index 0000000..56efef7
--- /dev/null
+++ b/win32/deps/library/survival/tests/infcox.R
@@ -0,0 +1,35 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# A test to exercise the "infinity" check on 2 variables
+#
+test3 <- data.frame(futime=1:12, fustat=c(1,0,1,0,1,0,0,0,0,0,0,0),
+ x1=rep(0:1,6), x2=c(rep(0,6), rep(1,6)))
+
+# This will produce a warning message, which is the point of the test.
+# The variance is close to singular and gives different answers
+# on different machines
+fit3 <- coxph(Surv(futime, fustat) ~ x1 + x2, test3, iter=25)
+
+all.equal(round(fit3$coef,1), c(-22.2, -22.9), check.attributes=FALSE)
+all.equal(round(fit3$log, 4),c(-6.8669, -1.7918))
+
+#
+# Actual solution
+# time 1, 12 at risk, 3 each of x1/x2 = 00, 01, 10, 11
+# time 2, 10 at risk, 2, 3, 2 , 3
+# time 5, 8 at risk, 1, 3, 1, 3
+# Let r1 = exp(beta1), r2= exp(beta2)
+# loglik = -log(3 + 3r1 + 3r2 + 3 r1*r2) - log(2 + 2r1 + 3r2 + 3 r1*r2) -
+# log(1 + r1 + 3r2 + 3 r1*r2)
+true <- function(beta) {
+ r1 <- exp(beta[1])
+ r2 <- exp(beta[2])
+ loglik <- -log(3*(1+ r1+ r2+ r1*r2)) - log(2+ 2*r1 + 3*r2 + 3*r1*r2) -
+ log(1 + r1 + 3*r2 + 3*r1*r2)
+ loglik
+}
+
+all.equal(fit3$loglik[2], true(fit3$coef), check.attributes=FALSE)
diff --git a/win32/deps/library/survival/tests/infcox.Rout.save b/win32/deps/library/survival/tests/infcox.Rout.save
new file mode 100644
index 0000000..613dc05
--- /dev/null
+++ b/win32/deps/library/survival/tests/infcox.Rout.save
@@ -0,0 +1,61 @@
+
+R version 2.14.0 (2011-10-31)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # A test to exercise the "infinity" check on 2 variables
+> #
+> test3 <- data.frame(futime=1:12, fustat=c(1,0,1,0,1,0,0,0,0,0,0,0),
++ x1=rep(0:1,6), x2=c(rep(0,6), rep(1,6)))
+>
+> # This will produce a warning message, which is the point of the test.
+> # The variance is close to singular and gives different answers
+> # on different machines
+> fit3 <- coxph(Surv(futime, fustat) ~ x1 + x2, test3, iter=25)
+Warning message:
+In fitter(X, Y, strats, offset, init, control, weights = weights, :
+ Loglik converged before variable 1,2 ; beta may be infinite.
+>
+> all.equal(round(fit3$coef,1), c(-22.2, -22.9), check.attributes=FALSE)
+[1] TRUE
+> all.equal(round(fit3$log, 4),c(-6.8669, -1.7918))
+[1] TRUE
+>
+> #
+> # Actual solution
+> # time 1, 12 at risk, 3 each of x1/x2 = 00, 01, 10, 11
+> # time 2, 10 at risk, 2, 3, 2 , 3
+> # time 5, 8 at risk, 1, 3, 1, 3
+> # Let r1 = exp(beta1), r2= exp(beta2)
+> # loglik = -log(3 + 3r1 + 3r2 + 3 r1*r2) - log(2 + 2r1 + 3r2 + 3 r1*r2) -
+> # log(1 + r1 + 3r2 + 3 r1*r2)
+> true <- function(beta) {
++ r1 <- exp(beta[1])
++ r2 <- exp(beta[2])
++ loglik <- -log(3*(1+ r1+ r2+ r1*r2)) - log(2+ 2*r1 + 3*r2 + 3*r1*r2) -
++ log(1 + r1 + 3*r2 + 3*r1*r2)
++ loglik
++ }
+>
+> all.equal(fit3$loglik[2], true(fit3$coef), check.attributes=FALSE)
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/jasa.R b/win32/deps/library/survival/tests/jasa.R
new file mode 100644
index 0000000..5ab3481
--- /dev/null
+++ b/win32/deps/library/survival/tests/jasa.R
@@ -0,0 +1,89 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+expect <- survexp(futime ~ ratetable(age=(accept.dt - birth.dt), sex=1,
+ year=accept.dt, race='white'), jasa, cohort=F,
+ ratetable=survexp.usr)
+
+survdiff(Surv(jasa$futime, jasa$fustat) ~ offset(expect))
+# Now fit the 6 models found in Kalbfleisch and Prentice, p139
+sfit.1 <- coxph(Surv(start, stop, event)~ (age + surgery)*transplant,
+ jasa1, method='breslow')
+sfit.2 <- coxph(Surv(start, stop, event)~ year*transplant,
+ jasa1, method='breslow')
+sfit.3 <- coxph(Surv(start, stop, event)~ (age + year)*transplant,
+ jasa1, method='breslow')
+sfit.4 <- coxph(Surv(start, stop, event)~ (year +surgery) *transplant,
+ jasa1, method='breslow')
+sfit.5 <- coxph(Surv(start, stop, event)~ (age + surgery)*transplant + year ,
+ jasa1, method='breslow')
+sfit.6 <- coxph(Surv(start, stop, event)~ age*transplant + surgery + year,
+ jasa1, method='breslow')
+
+summary(sfit.1)
+sfit.2
+summary(sfit.3)
+sfit.4
+sfit.5
+sfit.6
+
+# Survival curve for an "average" subject,
+# done once as overall, once via individual method
+surv1 <- survfit(sfit.1, newdata=list(age=-2, surgery=0, transplant=0))
+newdata <- data.frame(start=c(0,50,100), stop=c(50,100, max(jasa1$stop)),
+ event=c(1,1,1), age=rep(-2,3), surgery=rep(0,3),
+ transplant=rep(0,3))
+surv2 <- survfit(sfit.1, newdata, individual=T)
+# Have to use unclass to avoid [.survfit trying to pick curves,
+# remove the final element "call" because it won't match
+all.equal(unclass(surv1)[-length(surv1)],
+ unclass(surv2)[-length(surv2)])
+
+
+# Survival curve for a subject of age 50, with prior surgery, tx at 6 months
+# Remember that 'age' in jasa 1 was centered at 48
+data <- data.frame(start=c(0,183), stop=c(183,3*365), event=c(1,1),
+ age=c(2,2), surgery=c(1,1), transplant=c(0,1))
+summary(survfit(sfit.1, data, individual=T))
+
+# These should all give the same answer
+# When there are offsets, the default curve is always for someone with
+# the mean offset.
+j.age <- jasa$age -48
+fit1 <- coxph(Surv(futime, fustat) ~ j.age, data=jasa)
+fit2 <- coxph(Surv(futime, fustat) ~ j.age, jasa, init=fit1$coef, iter=0)
+fit3 <- coxph(Surv(start, stop, event) ~ age, jasa1)
+fit4 <- coxph(Surv(start, stop, event) ~ offset(age*fit1$coef), jasa1)
+
+s1 <- survfit(fit1, fit3$means, censor=FALSE)
+s2 <- survfit(fit2, list(j.age=fit3$means), censor=FALSE)
+s3 <- survfit(fit3, censor=FALSE)
+s4 <- survfit(fit4, censor=FALSE)
+
+all.equal(s1$surv, s2$surv)
+all.equal(s1$surv, s3$surv)
+all.equal(s1$surv, s4$surv)
+
+# Still the same answer, fit multiple strata at once
+# Strata 1 has independent coefs of strata 2, so putting in
+# the other data should not affect it
+attach(jasa1)
+ll <- length(start)
+ss <- rep(0:1, c(ll,ll))
+tdata <- data.frame(start=rep(start,2), stop=rep(stop,2),
+ event=rep(event,2), ss=ss, age=rep(age,2),
+ age2 = (rep(age,2))^2 * ss)
+fit <- coxph(Surv(start, stop, event) ~ age*strata(ss) + age2, tdata)
+# Above replaced these 2 lines, which kill Splus5 as of 8/98
+# Something with data frames, I expect.
+#fit <- coxph(Surv(rep(start,2), rep(stop,2), rep(event,2)) ~
+# rep(age,2)*strata(ss) + I(rep(age,2)^2*ss) )
+all.equal(fit$coef[1], fit3$coef)
+s5 <- survfit(fit, data.frame(age=fit3$means, age2=0, ss=0), censor=FALSE)
+all.equal(s5$surv[1:(s5$strata[1])], s3$surv)
+detach("jasa1")
+
+rm(s1, s2, s3, s4, s5, tdata, ll, ss, data)
+rm(fit1, fit2, fit3, fit4, fit, j.age)
+rm(sfit.1, sfit.2, sfit.3, sfit.4, sfit.5, sfit.6)
diff --git a/win32/deps/library/survival/tests/jasa.Rout.save b/win32/deps/library/survival/tests/jasa.Rout.save
new file mode 100644
index 0000000..2fd0a7c
--- /dev/null
+++ b/win32/deps/library/survival/tests/jasa.Rout.save
@@ -0,0 +1,289 @@
+
+R version 2.12.2 (2011-02-25)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> expect <- survexp(futime ~ ratetable(age=(accept.dt - birth.dt), sex=1,
++ year=accept.dt, race='white'), jasa, cohort=F,
++ ratetable=survexp.usr)
+>
+> survdiff(Surv(jasa$futime, jasa$fustat) ~ offset(expect))
+Call:
+survdiff(formula = Surv(jasa$futime, jasa$fustat) ~ offset(expect))
+
+Observed Expected Z p
+ 75.000 0.587 -97.119 0.000
+> # Now fit the 6 models found in Kalbfleisch and Prentice, p139
+> sfit.1 <- coxph(Surv(start, stop, event)~ (age + surgery)*transplant,
++ jasa1, method='breslow')
+> sfit.2 <- coxph(Surv(start, stop, event)~ year*transplant,
++ jasa1, method='breslow')
+> sfit.3 <- coxph(Surv(start, stop, event)~ (age + year)*transplant,
++ jasa1, method='breslow')
+> sfit.4 <- coxph(Surv(start, stop, event)~ (year +surgery) *transplant,
++ jasa1, method='breslow')
+> sfit.5 <- coxph(Surv(start, stop, event)~ (age + surgery)*transplant + year ,
++ jasa1, method='breslow')
+> sfit.6 <- coxph(Surv(start, stop, event)~ age*transplant + surgery + year,
++ jasa1, method='breslow')
+>
+> summary(sfit.1)
+Call:
+coxph(formula = Surv(start, stop, event) ~ (age + surgery) *
+ transplant, data = jasa1, method = "breslow")
+
+ n= 170, number of events= 75
+
+ coef exp(coef) se(coef) z Pr(>|z|)
+age 0.01386 1.01395 0.01813 0.765 0.445
+surgery -0.54652 0.57896 0.61091 -0.895 0.371
+transplant 0.11572 1.12268 0.32729 0.354 0.724
+age:transplant 0.03473 1.03534 0.02725 1.274 0.202
+surgery:transplant -0.29037 0.74799 0.75819 -0.383 0.702
+
+ exp(coef) exp(-coef) lower .95 upper .95
+age 1.014 0.9862 0.9786 1.051
+surgery 0.579 1.7272 0.1748 1.917
+transplant 1.123 0.8907 0.5911 2.132
+age:transplant 1.035 0.9659 0.9815 1.092
+surgery:transplant 0.748 1.3369 0.1692 3.306
+
+Concordance= 0.595 (se = 0.037 )
+Rsquare= 0.071 (max possible= 0.97 )
+Likelihood ratio test= 12.45 on 5 df, p=0.02915
+Wald test = 11.62 on 5 df, p=0.04031
+Score (logrank) test = 12.02 on 5 df, p=0.03457
+
+> sfit.2
+Call:
+coxph(formula = Surv(start, stop, event) ~ year * transplant,
+ data = jasa1, method = "breslow")
+
+
+ coef exp(coef) se(coef) z p
+year -0.265 0.767 0.105 -2.522 0.012
+transplant -0.287 0.750 0.514 -0.559 0.580
+year:transplant 0.137 1.147 0.141 0.973 0.330
+
+Likelihood ratio test=8.61 on 3 df, p=0.0349 n= 170, number of events= 75
+> summary(sfit.3)
+Call:
+coxph(formula = Surv(start, stop, event) ~ (age + year) * transplant,
+ data = jasa1, method = "breslow")
+
+ n= 170, number of events= 75
+
+ coef exp(coef) se(coef) z Pr(>|z|)
+age 0.01558 1.01571 0.01734 0.899 0.36887
+year -0.27413 0.76023 0.10588 -2.589 0.00962 **
+transplant -0.59388 0.55218 0.54222 -1.095 0.27339
+age:transplant 0.03380 1.03438 0.02795 1.209 0.22653
+year:transplant 0.20228 1.22419 0.14247 1.420 0.15566
+---
+Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
+
+ exp(coef) exp(-coef) lower .95 upper .95
+age 1.0157 0.9845 0.9818 1.0508
+year 0.7602 1.3154 0.6178 0.9356
+transplant 0.5522 1.8110 0.1908 1.5981
+age:transplant 1.0344 0.9668 0.9792 1.0926
+year:transplant 1.2242 0.8169 0.9259 1.6185
+
+Concordance= 0.63 (se = 0.037 )
+Rsquare= 0.084 (max possible= 0.97 )
+Likelihood ratio test= 14.85 on 5 df, p=0.01102
+Wald test = 13.77 on 5 df, p=0.01716
+Score (logrank) test = 14.06 on 5 df, p=0.01525
+
+> sfit.4
+Call:
+coxph(formula = Surv(start, stop, event) ~ (year + surgery) *
+ transplant, data = jasa1, method = "breslow")
+
+
+ coef exp(coef) se(coef) z p
+year -0.254 0.776 0.108 -2.360 0.018
+surgery -0.237 0.789 0.628 -0.377 0.710
+transplant -0.297 0.743 0.505 -0.588 0.560
+year:transplant 0.165 1.180 0.142 1.167 0.240
+surgery:transplant -0.550 0.577 0.776 -0.709 0.480
+
+Likelihood ratio test=12.4 on 5 df, p=0.0302 n= 170, number of events= 75
+> sfit.5
+Call:
+coxph(formula = Surv(start, stop, event) ~ (age + surgery) *
+ transplant + year, data = jasa1, method = "breslow")
+
+
+ coef exp(coef) se(coef) z p
+age 0.0150 1.015 0.0176 0.855 0.390
+surgery -0.4202 0.657 0.6156 -0.683 0.490
+transplant 0.0741 1.077 0.3311 0.224 0.820
+year -0.1363 0.873 0.0710 -1.921 0.055
+age:transplant 0.0269 1.027 0.0271 0.992 0.320
+surgery:transplant -0.2966 0.743 0.7580 -0.391 0.700
+
+Likelihood ratio test=16.2 on 6 df, p=0.0127 n= 170, number of events= 75
+> sfit.6
+Call:
+coxph(formula = Surv(start, stop, event) ~ age * transplant +
+ surgery + year, data = jasa1, method = "breslow")
+
+
+ coef exp(coef) se(coef) z p
+age 0.0153 1.015 0.0175 0.873 0.380
+transplant 0.0446 1.046 0.3217 0.139 0.890
+surgery -0.6211 0.537 0.3679 -1.688 0.091
+year -0.1361 0.873 0.0709 -1.919 0.055
+age:transplant 0.0270 1.027 0.0271 0.996 0.320
+
+Likelihood ratio test=16.1 on 5 df, p=0.00669 n= 170, number of events= 75
+>
+> # Survival curve for an "average" subject,
+> # done once as overall, once via individual method
+> surv1 <- survfit(sfit.1, newdata=list(age=-2, surgery=0, transplant=0))
+> newdata <- data.frame(start=c(0,50,100), stop=c(50,100, max(jasa1$stop)),
++ event=c(1,1,1), age=rep(-2,3), surgery=rep(0,3),
++ transplant=rep(0,3))
+> surv2 <- survfit(sfit.1, newdata, individual=T)
+> # Have to use unclass to avoid [.survfit trying to pick curves,
+> # remove the final element "call" because it won't match
+> all.equal(unclass(surv1)[-length(surv1)],
++ unclass(surv2)[-length(surv2)])
+[1] TRUE
+>
+>
+> # Survival curve for a subject of age 50, with prior surgery, tx at 6 months
+> # Remember that 'age' in jasa 1 was centered at 48
+> data <- data.frame(start=c(0,183), stop=c(183,3*365), event=c(1,1),
++ age=c(2,2), surgery=c(1,1), transplant=c(0,1))
+> summary(survfit(sfit.1, data, individual=T))
+Call: survfit(formula = sfit.1, newdata = data, individual = T)
+
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 0.5 103 1 0.994 0.00722 0.980 1.000
+ 1.0 102 3 0.975 0.01860 0.939 1.000
+ 2.0 99 3 0.956 0.02914 0.900 1.000
+ 4.0 96 2 0.943 0.03605 0.875 1.000
+ 5.0 94 2 0.930 0.04286 0.849 1.000
+ 7.0 92 1 0.923 0.04623 0.837 1.000
+ 8.0 91 1 0.917 0.04959 0.824 1.000
+ 11.0 89 1 0.910 0.05294 0.812 1.000
+ 15.0 88 3 0.890 0.06278 0.775 1.000
+ 16.0 85 1 0.883 0.06608 0.763 1.000
+ 17.0 84 1 0.877 0.06928 0.751 1.000
+ 20.0 83 2 0.864 0.07538 0.728 1.000
+ 27.0 81 1 0.857 0.07849 0.716 1.000
+ 29.0 80 1 0.850 0.08160 0.705 1.000
+ 31.0 78 1 0.844 0.08473 0.693 1.000
+ 34.0 77 1 0.837 0.08786 0.681 1.000
+ 35.0 76 1 0.830 0.09098 0.669 1.000
+ 36.0 75 1 0.823 0.09412 0.658 1.000
+ 38.0 74 1 0.816 0.09727 0.646 1.000
+ 39.0 72 2 0.802 0.10349 0.623 1.000
+ 42.0 70 1 0.795 0.10664 0.611 1.000
+ 44.0 69 1 0.788 0.10982 0.600 1.000
+ 49.0 68 1 0.781 0.11300 0.588 1.000
+ 50.0 67 1 0.774 0.11614 0.577 1.000
+ 52.0 66 1 0.767 0.11925 0.565 1.000
+ 57.0 65 1 0.760 0.12238 0.554 1.000
+ 60.0 64 1 0.752 0.12552 0.542 1.000
+ 65.0 63 1 0.745 0.12866 0.531 1.000
+ 67.0 62 2 0.730 0.13494 0.508 1.000
+ 68.0 60 1 0.722 0.13809 0.497 1.000
+ 71.0 59 2 0.707 0.14420 0.474 1.000
+ 76.0 57 1 0.699 0.14729 0.463 1.000
+ 77.0 56 1 0.691 0.15043 0.451 1.000
+ 79.0 55 1 0.683 0.15362 0.439 1.000
+ 80.0 54 1 0.674 0.15680 0.428 1.000
+ 84.0 53 1 0.666 0.16005 0.416 1.000
+ 89.0 52 1 0.657 0.16326 0.404 1.000
+ 95.0 51 1 0.648 0.16648 0.392 1.000
+ 99.0 50 1 0.639 0.16972 0.380 1.000
+ 101.0 49 1 0.630 0.17293 0.368 1.000
+ 109.0 47 1 0.621 0.17611 0.356 1.000
+ 148.0 45 1 0.611 0.17927 0.344 1.000
+ 152.0 44 1 0.601 0.18236 0.332 1.000
+ 164.0 43 1 0.592 0.18551 0.320 1.000
+ 185.0 41 1 0.583 0.12737 0.380 0.894
+ 187.0 40 1 0.574 0.12889 0.370 0.891
+ 206.0 39 1 0.565 0.13036 0.359 0.888
+ 218.0 38 1 0.556 0.13180 0.349 0.885
+ 262.0 37 1 0.546 0.13320 0.339 0.881
+ 284.0 35 2 0.527 0.13585 0.318 0.874
+ 307.0 33 1 0.517 0.13707 0.308 0.869
+ 333.0 32 1 0.507 0.13823 0.297 0.865
+ 339.0 31 1 0.497 0.13930 0.287 0.861
+ 342.0 29 1 0.486 0.14029 0.276 0.856
+ 583.0 21 1 0.471 0.14187 0.261 0.850
+ 674.0 17 1 0.452 0.14361 0.243 0.843
+ 732.0 16 1 0.433 0.14506 0.225 0.835
+ 851.0 14 1 0.410 0.14622 0.204 0.825
+ 979.0 11 1 0.383 0.14698 0.180 0.813
+ 995.0 10 1 0.356 0.14735 0.158 0.801
+ 1031.0 9 1 0.330 0.14743 0.137 0.792
+>
+> # These should all give the same answer
+> # When there are offsets, the default curve is always for someone with
+> # the mean offset.
+> j.age <- jasa$age -48
+> fit1 <- coxph(Surv(futime, fustat) ~ j.age, data=jasa)
+> fit2 <- coxph(Surv(futime, fustat) ~ j.age, jasa, init=fit1$coef, iter=0)
+> fit3 <- coxph(Surv(start, stop, event) ~ age, jasa1)
+> fit4 <- coxph(Surv(start, stop, event) ~ offset(age*fit1$coef), jasa1)
+>
+> s1 <- survfit(fit1, fit3$means, censor=FALSE)
+> s2 <- survfit(fit2, list(j.age=fit3$means), censor=FALSE)
+> s3 <- survfit(fit3, censor=FALSE)
+> s4 <- survfit(fit4, censor=FALSE)
+>
+> all.equal(s1$surv, s2$surv)
+[1] TRUE
+> all.equal(s1$surv, s3$surv)
+[1] TRUE
+> all.equal(s1$surv, s4$surv)
+[1] TRUE
+>
+> # Still the same answer, fit multiple strata at once
+> # Strata 1 has independent coefs of strata 2, so putting in
+> # the other data should not affect it
+> attach(jasa1)
+> ll <- length(start)
+> ss <- rep(0:1, c(ll,ll))
+> tdata <- data.frame(start=rep(start,2), stop=rep(stop,2),
++ event=rep(event,2), ss=ss, age=rep(age,2),
++ age2 = (rep(age,2))^2 * ss)
+> fit <- coxph(Surv(start, stop, event) ~ age*strata(ss) + age2, tdata)
+> # Above replaced these 2 lines, which kill Splus5 as of 8/98
+> # Something with data frames, I expect.
+> #fit <- coxph(Surv(rep(start,2), rep(stop,2), rep(event,2)) ~
+> # rep(age,2)*strata(ss) + I(rep(age,2)^2*ss) )
+> all.equal(fit$coef[1], fit3$coef)
+[1] TRUE
+> s5 <- survfit(fit, data.frame(age=fit3$means, age2=0, ss=0), censor=FALSE)
+> all.equal(s5$surv[1:(s5$strata[1])], s3$surv)
+[1] TRUE
+> detach("jasa1")
+>
+> rm(s1, s2, s3, s4, s5, tdata, ll, ss, data)
+> rm(fit1, fit2, fit3, fit4, fit, j.age)
+> rm(sfit.1, sfit.2, sfit.3, sfit.4, sfit.5, sfit.6)
+>
diff --git a/win32/deps/library/survival/tests/model.matrix.R b/win32/deps/library/survival/tests/model.matrix.R
new file mode 100644
index 0000000..6cf768a
--- /dev/null
+++ b/win32/deps/library/survival/tests/model.matrix.R
@@ -0,0 +1,31 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Test out the revised model.matrix code
+#
+test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
+ status=c(1,NA,1,0,1,1,0),
+ x= c(0, 2,1,1,1,0,0),
+ z= factor(c('a', 'a', 'b', 'b', 'c', 'c', 'a')))
+
+fit1 <- coxph(Surv(time, status) ~ z, test1, iter=1)
+fit2 <- coxph(Surv(time, status) ~z, test1, x=T, iter=1)
+all.equal(model.matrix(fit1), fit2$x)
+
+# This has no level 'b', make sure dummies recode properly
+test2 <- data.frame(time= c(9, 3,1,1,6,6,8),
+ status=c(1,NA,1,0,1,1,0),
+ x= c(0, 2,1,1,1,0,0),
+ z= factor(c('a', 'a', 'a', 'a', 'c', 'c', 'a')))
+
+ftest <- model.frame(fit1, data=test2)
+all.equal(levels(ftest$z), levels(test1$z))
+
+# xtest will have one more row than the others, since it does not delete
+# the observation with a missing value for status
+xtest <- model.matrix(fit1, data=test2)
+dummy <- fit2$x
+dummy[,1] <- 0
+all.equal(xtest[-2,], dummy, check.attributes=FALSE)
diff --git a/win32/deps/library/survival/tests/model.matrix.Rout.save b/win32/deps/library/survival/tests/model.matrix.Rout.save
new file mode 100644
index 0000000..18f61ed
--- /dev/null
+++ b/win32/deps/library/survival/tests/model.matrix.Rout.save
@@ -0,0 +1,53 @@
+
+R version 2.11.1 (2010-05-31)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Test out the revised model.matrix code
+> #
+> test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
++ status=c(1,NA,1,0,1,1,0),
++ x= c(0, 2,1,1,1,0,0),
++ z= factor(c('a', 'a', 'b', 'b', 'c', 'c', 'a')))
+>
+> fit1 <- coxph(Surv(time, status) ~ z, test1, iter=1)
+> fit2 <- coxph(Surv(time, status) ~z, test1, x=T, iter=1)
+> all.equal(model.matrix(fit1), fit2$x)
+[1] TRUE
+>
+> # This has no level 'b', make sure dummies recode properly
+> test2 <- data.frame(time= c(9, 3,1,1,6,6,8),
++ status=c(1,NA,1,0,1,1,0),
++ x= c(0, 2,1,1,1,0,0),
++ z= factor(c('a', 'a', 'a', 'a', 'c', 'c', 'a')))
+>
+> ftest <- model.frame(fit1, data=test2)
+> all.equal(levels(ftest$z), levels(test1$z))
+[1] TRUE
+>
+> # xtest will have one more row than the others, since it does not delete
+> # the observation with a missing value for status
+> xtest <- model.matrix(fit1, data=test2)
+> dummy <- fit2$x
+> dummy[,1] <- 0
+> all.equal(xtest[-2,], dummy, check.attributes=FALSE)
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/mrtest.R b/win32/deps/library/survival/tests/mrtest.R
new file mode 100644
index 0000000..d5e7fa2
--- /dev/null
+++ b/win32/deps/library/survival/tests/mrtest.R
@@ -0,0 +1,28 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+{if (is.R()) mdy.date <- function(m, d, y) {
+ y <- ifelse(y<100, y+1900, y)
+ as.Date(paste(m,d,y, sep='/'), "%m/%d/%Y")
+ }
+else mdy.date <- function(m,d,y) {
+ y <- ifelse(y<100, y+1900, y)
+ timeDate(paste(y, m, d, sep='/'), in.format="%Y/%m/%d")
+ }
+ }
+
+#
+# A test of the match.ratetable function, specifically the
+# change to allow partial matching of strings
+# Note that 10,000 days old is 27.4 years
+#
+aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+
+temp1 <- data.frame(year=mdy.date(2,2,1960:1964),
+ age = 10000 + 1:5,
+ sex = c('M', 'fema', 'f', 'ma', 'F'))
+
+temp2 <- ratetable(year=temp1$year, age=temp1$age, sex=temp1$sex)
+temp3 <- match.ratetable(temp2, survexp.us)
+aeq(temp3$R[,2], c(1,2,2,1,2))
diff --git a/win32/deps/library/survival/tests/mrtest.Rout.save b/win32/deps/library/survival/tests/mrtest.Rout.save
new file mode 100644
index 0000000..6c3eb8f
--- /dev/null
+++ b/win32/deps/library/survival/tests/mrtest.Rout.save
@@ -0,0 +1,48 @@
+
+R version 2.7.1 (2008-06-23)
+Copyright (C) 2008 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> {if (is.R()) mdy.date <- function(m, d, y) {
++ y <- ifelse(y<100, y+1900, y)
++ as.Date(paste(m,d,y, sep='/'), "%m/%d/%Y")
++ }
++ else mdy.date <- function(m,d,y) {
++ y <- ifelse(y<100, y+1900, y)
++ timeDate(paste(y, m, d, sep='/'), in.format="%Y/%m/%d")
++ }
++ }
+>
+> #
+> # A test of the match.ratetable function, specifically the
+> # change to allow partial matching of strings
+> # Note that 10,000 days old is 27.4 years
+> #
+> aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+>
+> temp1 <- data.frame(year=mdy.date(2,2,1960:1964),
++ age = 10000 + 1:5,
++ sex = c('M', 'fema', 'f', 'ma', 'F'))
+>
+> temp2 <- ratetable(year=temp1$year, age=temp1$age, sex=temp1$sex)
+> temp3 <- match.ratetable(temp2, survexp.us)
+> aeq(temp3$R[,2], c(1,2,2,1,2))
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/nested.R b/win32/deps/library/survival/tests/nested.R
new file mode 100644
index 0000000..215b748
--- /dev/null
+++ b/win32/deps/library/survival/tests/nested.R
@@ -0,0 +1,16 @@
+library(survival)
+#
+# A test of nesting. It makes sure tha model.frame is built correctly
+#
+tfun <- function(fit, mydata) {
+ survfit(fit, newdata=mydata)
+ }
+
+myfit <- coxph(Surv(time, status) ~ age + factor(sex), lung)
+
+temp1 <- tfun(myfit, lung[1:5,])
+temp2 <- survfit(myfit, lung[1:5,])
+indx <- match('call', names(temp1)) #the call components won't match
+
+all.equal(unclass(temp1)[-indx], unclass(temp2)[-indx])
+
diff --git a/win32/deps/library/survival/tests/nested.Rout.save b/win32/deps/library/survival/tests/nested.Rout.save
new file mode 100644
index 0000000..0086204
--- /dev/null
+++ b/win32/deps/library/survival/tests/nested.Rout.save
@@ -0,0 +1,37 @@
+
+R version 2.12.0 (2010-10-15)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+> #
+> # A test of nesting. It makes sure tha model.frame is built correctly
+> #
+> tfun <- function(fit, mydata) {
++ survfit(fit, newdata=mydata)
++ }
+>
+> myfit <- coxph(Surv(time, status) ~ age + factor(sex), lung)
+>
+> temp1 <- tfun(myfit, lung[1:5,])
+> temp2 <- survfit(myfit, lung[1:5,])
+> indx <- match('call', names(temp1)) #the call components won't match
+>
+> all.equal(unclass(temp1)[-indx], unclass(temp2)[-indx])
+[1] TRUE
+>
+>
diff --git a/win32/deps/library/survival/tests/ovarian.R b/win32/deps/library/survival/tests/ovarian.R
new file mode 100644
index 0000000..6f9d574
--- /dev/null
+++ b/win32/deps/library/survival/tests/ovarian.R
@@ -0,0 +1,61 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Test the coxph program on the Ovarian data
+#
+
+attach(ovarian)
+
+summary(survfit(Surv(futime, fustat)~1), censor=TRUE)
+
+# Various models
+coxph(Surv(futime, fustat)~ age)
+coxph(Surv(futime, fustat)~ resid.ds)
+coxph(Surv(futime, fustat)~ rx)
+coxph(Surv(futime, fustat)~ ecog.ps)
+
+coxph(Surv(futime, fustat)~ resid.ds + rx + ecog.ps)
+coxph(Surv(futime, fustat)~ age + rx + ecog.ps)
+coxph(Surv(futime, fustat)~ age + resid.ds + ecog.ps)
+coxph(Surv(futime, fustat)~ age + resid.ds + rx)
+
+# Residuals
+fit <- coxph(Surv(futime, fustat)~ age + resid.ds + rx + ecog.ps )
+resid(fit)
+resid(fit, 'dev')
+resid(fit, 'scor')
+resid(fit, 'scho')
+
+fit <- coxph(Surv(futime, fustat) ~ age + ecog.ps + strata(rx))
+summary(fit)
+summary(survfit(fit))
+sfit <- survfit(fit, list(age=c(30,70), ecog.ps=c(2,3))) #two columns
+sfit
+summary(sfit)
+detach()
+
+
+# Check of offset + surv, added 7/2000
+fit1 <- coxph(Surv(futime, fustat) ~ age + rx, ovarian,
+ control=coxph.control(eps=1e-8))
+fit2 <- coxph(Surv(futime, fustat) ~ age + offset(rx*fit1$coef[2]), ovarian,
+ control=coxph.control(eps=1e-8))
+all.equal(fit1$coef[1], fit2$coef[1])
+
+fit <- coxph(Surv(futime, fustat) ~ age + offset(rx), ovarian)
+survfit(fit, censor=FALSE)$surv^exp(-1.5)
+
+# Check it by hand -- there are no tied times
+# Remember that offsets from survfit are centered, which is 1.5 for
+# this data set.
+eta <- fit$coef*(ovarian$age - fit$mean) + (ovarian$rx - 1.5)
+ord <- order(ovarian$futime)
+risk <- exp(eta[ord])
+rsum <- rev(cumsum(rev(risk))) # cumulative risk at each time point
+dead <- (ovarian$fustat[ord]==1)
+baseline <- cumsum(1/rsum[dead])
+all.equal(survfit(fit, censor=FALSE)$surv, exp(-baseline))
+
+rm(fit, fit1, fit2, ord, eta, risk, rsum, dead, baseline, sfit)
diff --git a/win32/deps/library/survival/tests/ovarian.Rout.save b/win32/deps/library/survival/tests/ovarian.Rout.save
new file mode 100644
index 0000000..a078c7f
--- /dev/null
+++ b/win32/deps/library/survival/tests/ovarian.Rout.save
@@ -0,0 +1,319 @@
+
+R version 2.15.0 (2012-03-30)
+Copyright (C) 2012 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: i686-pc-linux-gnu (32-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Test the coxph program on the Ovarian data
+> #
+>
+> attach(ovarian)
+>
+> summary(survfit(Surv(futime, fustat)~1), censor=TRUE)
+Call: survfit(formula = Surv(futime, fustat) ~ 1)
+
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 59 26 1 0.962 0.0377 0.890 1.000
+ 115 25 1 0.923 0.0523 0.826 1.000
+ 156 24 1 0.885 0.0627 0.770 1.000
+ 268 23 1 0.846 0.0708 0.718 0.997
+ 329 22 1 0.808 0.0773 0.670 0.974
+ 353 21 1 0.769 0.0826 0.623 0.949
+ 365 20 1 0.731 0.0870 0.579 0.923
+ 377 19 0 0.731 0.0870 0.579 0.923
+ 421 18 0 0.731 0.0870 0.579 0.923
+ 431 17 1 0.688 0.0919 0.529 0.894
+ 448 16 0 0.688 0.0919 0.529 0.894
+ 464 15 1 0.642 0.0965 0.478 0.862
+ 475 14 1 0.596 0.0999 0.429 0.828
+ 477 13 0 0.596 0.0999 0.429 0.828
+ 563 12 1 0.546 0.1032 0.377 0.791
+ 638 11 1 0.497 0.1051 0.328 0.752
+ 744 10 0 0.497 0.1051 0.328 0.752
+ 769 9 0 0.497 0.1051 0.328 0.752
+ 770 8 0 0.497 0.1051 0.328 0.752
+ 803 7 0 0.497 0.1051 0.328 0.752
+ 855 6 0 0.497 0.1051 0.328 0.752
+ 1040 5 0 0.497 0.1051 0.328 0.752
+ 1106 4 0 0.497 0.1051 0.328 0.752
+ 1129 3 0 0.497 0.1051 0.328 0.752
+ 1206 2 0 0.497 0.1051 0.328 0.752
+ 1227 1 0 0.497 0.1051 0.328 0.752
+>
+> # Various models
+> coxph(Surv(futime, fustat)~ age)
+Call:
+coxph(formula = Surv(futime, fustat) ~ age)
+
+
+ coef exp(coef) se(coef) z p
+age 0.162 1.18 0.0497 3.25 0.0012
+
+Likelihood ratio test=14.3 on 1 df, p=0.000156 n= 26, number of events= 12
+> coxph(Surv(futime, fustat)~ resid.ds)
+Call:
+coxph(formula = Surv(futime, fustat) ~ resid.ds)
+
+
+ coef exp(coef) se(coef) z p
+resid.ds 1.21 3.35 0.672 1.8 0.072
+
+Likelihood ratio test=3.76 on 1 df, p=0.0525 n= 26, number of events= 12
+> coxph(Surv(futime, fustat)~ rx)
+Call:
+coxph(formula = Surv(futime, fustat) ~ rx)
+
+
+ coef exp(coef) se(coef) z p
+rx -0.596 0.551 0.587 -1.02 0.31
+
+Likelihood ratio test=1.05 on 1 df, p=0.305 n= 26, number of events= 12
+> coxph(Surv(futime, fustat)~ ecog.ps)
+Call:
+coxph(formula = Surv(futime, fustat) ~ ecog.ps)
+
+
+ coef exp(coef) se(coef) z p
+ecog.ps 0.398 1.49 0.586 0.679 0.5
+
+Likelihood ratio test=0.47 on 1 df, p=0.494 n= 26, number of events= 12
+>
+> coxph(Surv(futime, fustat)~ resid.ds + rx + ecog.ps)
+Call:
+coxph(formula = Surv(futime, fustat) ~ resid.ds + rx + ecog.ps)
+
+
+ coef exp(coef) se(coef) z p
+resid.ds 1.347 3.844 0.680 1.980 0.048
+rx -0.749 0.473 0.595 -1.260 0.210
+ecog.ps 0.453 1.573 0.590 0.767 0.440
+
+Likelihood ratio test=6.03 on 3 df, p=0.11 n= 26, number of events= 12
+> coxph(Surv(futime, fustat)~ age + rx + ecog.ps)
+Call:
+coxph(formula = Surv(futime, fustat) ~ age + rx + ecog.ps)
+
+
+ coef exp(coef) se(coef) z p
+age 0.147 1.158 0.0463 3.17 0.0015
+rx -0.815 0.443 0.6342 -1.28 0.2000
+ecog.ps 0.103 1.109 0.6064 0.17 0.8600
+
+Likelihood ratio test=15.9 on 3 df, p=0.00118 n= 26, number of events= 12
+> coxph(Surv(futime, fustat)~ age + resid.ds + ecog.ps)
+Call:
+coxph(formula = Surv(futime, fustat) ~ age + resid.ds + ecog.ps)
+
+
+ coef exp(coef) se(coef) z p
+age 0.142 1.15 0.052 2.740 0.0061
+resid.ds 0.663 1.94 0.750 0.883 0.3800
+ecog.ps 0.166 1.18 0.615 0.271 0.7900
+
+Likelihood ratio test=15.1 on 3 df, p=0.00173 n= 26, number of events= 12
+> coxph(Surv(futime, fustat)~ age + resid.ds + rx)
+Call:
+coxph(formula = Surv(futime, fustat) ~ age + resid.ds + rx)
+
+
+ coef exp(coef) se(coef) z p
+age 0.129 1.137 0.0473 2.718 0.0066
+resid.ds 0.696 2.006 0.7585 0.918 0.3600
+rx -0.849 0.428 0.6392 -1.328 0.1800
+
+Likelihood ratio test=16.8 on 3 df, p=0.000789 n= 26, number of events= 12
+>
+> # Residuals
+> fit <- coxph(Surv(futime, fustat)~ age + resid.ds + rx + ecog.ps )
+> resid(fit)
+ 1 2 3 4 5 6
+ 0.84103277 0.54424388 0.59670824 -0.11281376 0.75111588 -0.32609026
+ 7 8 9 10 11 12
+ 0.59998927 0.29570718 -2.15325805 0.76243469 0.06474272 -0.11680752
+ 13 14 15 16 17 18
+-1.22562781 -0.63474839 -0.07535824 -0.17058905 -0.22986038 -0.14654862
+ 19 20 21 22 23 24
+-0.18762920 -0.12771548 -0.53373114 -0.65480022 0.95866131 0.82111675
+ 25 26
+ 0.55136554 -0.09154014
+> resid(fit, 'dev')
+ 1 2 3 4 5 6
+ 1.41281595 0.69505907 0.78916003 -0.47500266 1.13106322 -0.80757694
+ 7 8 9 10 11 12
+ 0.79532966 0.33122166 -2.07521471 1.16179002 0.06619519 -0.48333740
+ 13 14 15 16 17 18
+-1.56564862 -1.12671948 -0.38822221 -0.58410453 -0.67802711 -0.54138455
+ 19 20 21 22 23 24
+-0.61258338 -0.50540178 -1.03318066 -0.54976346 2.11059000 1.34157009
+ 25 26
+ 0.70736314 -0.42787881
+> resid(fit, 'scor')
+ age resid.ds rx ecog.ps
+1 2.26503249 0.05686357 -0.10565379 -0.42661688
+2 3.02525428 0.04641312 -0.08623662 -0.34821275
+3 -0.06851355 0.07131430 -0.13250357 0.06167527
+4 0.94597623 -0.02541510 -0.06423496 0.05971729
+5 -5.41507168 0.21605962 -0.32258092 -0.39333909
+6 1.48999552 0.24899474 0.14035143 -0.15380664
+7 -0.68612431 0.13740891 0.28392482 0.29196506
+8 0.93116906 0.08428957 0.16040160 0.18430641
+9 -8.20092595 -0.51356176 0.95647608 1.11337112
+10 0.95287510 -0.31078224 0.21463992 0.17363388
+11 2.85526159 0.09417730 -0.14186603 -0.07586086
+12 0.92721107 0.07495002 -0.05400751 0.07061578
+13 -1.93962967 -0.43919871 -0.56668535 -0.48467672
+14 0.63185387 -0.22745949 -0.29348437 0.38373600
+15 1.41495195 0.04835392 0.04051535 0.04555769
+16 2.54591188 0.10945916 0.09171493 -0.06745975
+17 4.40282381 -0.08236953 0.12358137 -0.09089870
+18 1.97071836 0.09403352 0.07878991 0.08859570
+19 0.77692371 0.12039304 -0.08675286 0.11343089
+20 1.76784279 -0.04576632 -0.05905095 0.07721016
+21 -0.82272526 0.34247077 -0.24677770 -0.21106494
+22 -3.48057998 -0.03965965 0.07368852 -0.26669335
+23 -14.86623758 0.28137017 -0.52279208 -0.43881151
+24 3.96084273 -0.56566921 0.34648950 0.44907410
+25 4.30025715 0.15241262 0.22417527 -0.20390438
+26 0.31490641 0.07091764 -0.05212198 0.04845623
+> resid(fit, 'scho')
+ age resid.ds rx ecog.ps
+59 2.69315603 0.06761160 -0.1256239 -0.5072536
+115 5.36390105 0.08039116 -0.1493686 -0.6031318
+156 -0.89877512 0.10683985 -0.1985108 0.1984379
+268 6.95664326 0.12857949 -0.2389036 0.2388157
+329 -15.73656605 0.28889883 -0.5367805 -0.4634169
+353 4.06104389 -0.70587654 0.4535120 0.5282024
+365 5.50035833 0.25348264 0.4796230 -0.4413864
+431 -8.06809505 0.27490176 -0.4297023 -0.5248323
+464 -2.15471559 0.23158421 0.5066040 0.4814387
+475 0.57065051 0.25226659 0.5518479 0.5244351
+563 0.06487219 -0.47274522 0.3319974 0.2747028
+638 1.64752655 -0.50593437 -0.6446947 0.2939883
+>
+> fit <- coxph(Surv(futime, fustat) ~ age + ecog.ps + strata(rx))
+> summary(fit)
+Call:
+coxph(formula = Surv(futime, fustat) ~ age + ecog.ps + strata(rx))
+
+ n= 26, number of events= 12
+
+ coef exp(coef) se(coef) z Pr(>|z|)
+age 0.13853 1.14858 0.04801 2.885 0.00391 **
+ecog.ps -0.09670 0.90783 0.62994 -0.154 0.87800
+---
+Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
+
+ exp(coef) exp(-coef) lower .95 upper .95
+age 1.1486 0.8706 1.0454 1.262
+ecog.ps 0.9078 1.1015 0.2641 3.120
+
+Concordance= 0.819 (se = 0.134 )
+Rsquare= 0.387 (max possible= 0.874 )
+Likelihood ratio test= 12.71 on 2 df, p=0.001736
+Wald test = 8.43 on 2 df, p=0.01476
+Score (logrank) test = 12.24 on 2 df, p=0.002195
+
+> summary(survfit(fit))
+Call: survfit(formula = fit)
+
+ rx=1
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 59 13 1 0.978 0.0266 0.9275 1
+ 115 12 1 0.951 0.0478 0.8620 1
+ 156 11 1 0.910 0.0760 0.7722 1
+ 268 10 1 0.862 0.1055 0.6776 1
+ 329 9 1 0.737 0.1525 0.4909 1
+ 431 8 1 0.627 0.1704 0.3680 1
+ 638 5 1 0.333 0.2296 0.0865 1
+
+ rx=2
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 353 13 1 0.943 0.0560 0.839 1.000
+ 365 12 1 0.880 0.0812 0.735 1.000
+ 464 9 1 0.789 0.1143 0.594 1.000
+ 475 8 1 0.697 0.1349 0.477 1.000
+ 563 7 1 0.597 0.1494 0.366 0.975
+
+> sfit <- survfit(fit, list(age=c(30,70), ecog.ps=c(2,3))) #two columns
+> sfit
+Call: survfit(formula = fit, newdata = list(age = c(30, 70), ecog.ps = c(2,
+ 3)))
+
+ records n.max n.start events median 0.95LCL 0.95UCL
+rx=1 13 13 13 7 NA NA NA
+rx=1 13 13 13 7 268 115 NA
+rx=2 13 13 13 5 NA NA NA
+rx=2 13 13 13 5 365 353 NA
+> summary(sfit)
+Call: survfit(formula = fit, newdata = list(age = c(30, 70), ecog.ps = c(2,
+ 3)))
+
+ rx=1
+ time n.risk n.event survival1 survival2
+ 59 13 1 0.999 0.87905
+ 115 12 1 0.999 0.74575
+ 156 11 1 0.998 0.57398
+ 268 10 1 0.996 0.41764
+ 329 9 1 0.992 0.16673
+ 431 8 1 0.988 0.06489
+ 638 5 1 0.973 0.00161
+
+ rx=2
+ time n.risk n.event survival1 survival2
+ 353 13 1 0.999 0.7092
+ 365 12 1 0.997 0.4738
+ 464 9 1 0.994 0.2494
+ 475 8 1 0.991 0.1207
+ 563 7 1 0.987 0.0489
+
+> detach()
+>
+>
+> # Check of offset + surv, added 7/2000
+> fit1 <- coxph(Surv(futime, fustat) ~ age + rx, ovarian,
++ control=coxph.control(eps=1e-8))
+> fit2 <- coxph(Surv(futime, fustat) ~ age + offset(rx*fit1$coef[2]), ovarian,
++ control=coxph.control(eps=1e-8))
+> all.equal(fit1$coef[1], fit2$coef[1])
+[1] TRUE
+>
+> fit <- coxph(Surv(futime, fustat) ~ age + offset(rx), ovarian)
+> survfit(fit, censor=FALSE)$surv^exp(-1.5)
+ [1] 0.9977751 0.9951975 0.9917927 0.9881504 0.9825769 0.9770280 0.9704304
+ [8] 0.9603196 0.9499085 0.9385539 0.9217097 0.9031334
+>
+> # Check it by hand -- there are no tied times
+> # Remember that offsets from survfit are centered, which is 1.5 for
+> # this data set.
+> eta <- fit$coef*(ovarian$age - fit$mean) + (ovarian$rx - 1.5)
+> ord <- order(ovarian$futime)
+> risk <- exp(eta[ord])
+> rsum <- rev(cumsum(rev(risk))) # cumulative risk at each time point
+> dead <- (ovarian$fustat[ord]==1)
+> baseline <- cumsum(1/rsum[dead])
+> all.equal(survfit(fit, censor=FALSE)$surv, exp(-baseline))
+[1] TRUE
+>
+> rm(fit, fit1, fit2, ord, eta, risk, rsum, dead, baseline, sfit)
+>
+> proc.time()
+ user system elapsed
+ 0.264 0.028 0.288
diff --git a/win32/deps/library/survival/tests/prednew.R b/win32/deps/library/survival/tests/prednew.R
new file mode 100644
index 0000000..7a4a104
--- /dev/null
+++ b/win32/deps/library/survival/tests/prednew.R
@@ -0,0 +1,73 @@
+#
+# Make sure that the newdata argument works for various
+# predictions
+# We purposely use a subset of the lung data that has only some
+# of the levels of the ph.ecog
+library(survival)
+options(na.action=na.exclude, contrasts=c('contr.treatment', 'contr.poly'))
+aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+
+myfit <- coxph(Surv(time, status) ~ age + factor(ph.ecog) + strata(sex), lung)
+
+keep <- which(lung$sex==1 & (lung$ph.ecog==1 | lung$ph.ecog==2))
+p1 <- predict(myfit, type='lp')
+p2 <- predict(myfit, type="lp", newdata=lung[keep,])
+p3 <- predict(myfit, type='lp', se.fit=TRUE)
+p4 <- predict(myfit, type="lp", newdata=lung[keep,], se.fit=TRUE)
+aeq(p1[keep], p2)
+aeq(p1, p3$fit)
+aeq(p1[keep], p4$fit)
+aeq(p3$se.fit[keep], p4$se.fit)
+
+p1 <- predict(myfit, type='risk')
+p2 <- predict(myfit, type="risk", newdata=lung[keep,])
+p3 <- predict(myfit, type='risk', se.fit=TRUE)
+p4 <- predict(myfit, type="risk", newdata=lung[keep,], se.fit=TRUE)
+aeq(p1[keep], p2)
+aeq(p1, p3$fit)
+aeq(p1[keep], p4$fit)
+aeq(p3$se.fit[keep], p4$se.fit)
+
+# The all.equal fails for type=expected, Efron approx, and tied death
+# times due to use of an approximation. See comments in the source code.
+myfit <- coxph(Surv(time, status) ~ age + factor(ph.ecog) + strata(sex),
+ data=lung, method='breslow')
+p1 <- predict(myfit, type='expected')
+p2 <- predict(myfit, type="expected", newdata=lung[keep,])
+p3 <- predict(myfit, type='expected', se.fit=TRUE)
+p4 <- predict(myfit, type="expected", newdata=lung[keep,], se.fit=TRUE)
+aeq(p1[keep], p2)
+aeq(p1, p3$fit)
+aeq(p1[keep], p4$fit)
+aeq(p3$se.fit[keep], p4$se.fit)
+
+p1 <- predict(myfit, type='terms')
+p2 <- predict(myfit, type="terms",newdata=lung[keep,])
+p3 <- predict(myfit, type='terms', se.fit=T)
+p4 <- predict(myfit, type="terms",newdata=lung[keep,], se.fit=T)
+aeq(p1[keep,], p2)
+aeq(p1, p3$fit)
+aeq(p1[keep,], p4$fit)
+aeq(p3$se.fit[keep,], p4$se.fit)
+
+#
+# Check out the logic whereby predict does not need to
+# recover the model frame. The first call should not
+# need to do so, the second should in each case.
+#
+myfit <- coxph(Surv(time, status) ~ age + factor(sex), lung, x=T)
+p1 <- predict(myfit, type='risk', se=T)
+myfit2 <- coxph(Surv(time, status) ~ age + factor(sex), lung)
+p2 <- predict(myfit2, type='risk', se=T)
+aeq(p1$fit, p2$fit)
+aeq(p1$se, p2$se)
+
+p1 <- predict(myfit, type='expected', se=T)
+p2 <- predict(myfit2, type='expected', se=T)
+aeq(p1$fit, p2$fit)
+aeq(p1$se.fit, p2$se.fit)
+
+p1 <- predict(myfit, type='terms', se=T)
+p2 <- predict(myfit2, type='terms', se=T)
+aeq(p1$fit, p2$fit)
+aeq(p1$se.fit, p2$se.fit)
diff --git a/win32/deps/library/survival/tests/prednew.Rout.save b/win32/deps/library/survival/tests/prednew.Rout.save
new file mode 100644
index 0000000..e60ca6b
--- /dev/null
+++ b/win32/deps/library/survival/tests/prednew.Rout.save
@@ -0,0 +1,115 @@
+
+R version 2.12.2 (2011-02-25)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> #
+> # Make sure that the newdata argument works for various
+> # predictions
+> # We purposely use a subset of the lung data that has only some
+> # of the levels of the ph.ecog
+> library(survival)
+Loading required package: splines
+> options(na.action=na.exclude, contrasts=c('contr.treatment', 'contr.poly'))
+> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+>
+> myfit <- coxph(Surv(time, status) ~ age + factor(ph.ecog) + strata(sex), lung)
+>
+> keep <- which(lung$sex==1 & (lung$ph.ecog==1 | lung$ph.ecog==2))
+> p1 <- predict(myfit, type='lp')
+> p2 <- predict(myfit, type="lp", newdata=lung[keep,])
+> p3 <- predict(myfit, type='lp', se.fit=TRUE)
+> p4 <- predict(myfit, type="lp", newdata=lung[keep,], se.fit=TRUE)
+> aeq(p1[keep], p2)
+[1] TRUE
+> aeq(p1, p3$fit)
+[1] TRUE
+> aeq(p1[keep], p4$fit)
+[1] TRUE
+> aeq(p3$se.fit[keep], p4$se.fit)
+[1] TRUE
+>
+> p1 <- predict(myfit, type='risk')
+> p2 <- predict(myfit, type="risk", newdata=lung[keep,])
+> p3 <- predict(myfit, type='risk', se.fit=TRUE)
+> p4 <- predict(myfit, type="risk", newdata=lung[keep,], se.fit=TRUE)
+> aeq(p1[keep], p2)
+[1] TRUE
+> aeq(p1, p3$fit)
+[1] TRUE
+> aeq(p1[keep], p4$fit)
+[1] TRUE
+> aeq(p3$se.fit[keep], p4$se.fit)
+[1] TRUE
+>
+> # The all.equal fails for type=expected, Efron approx, and tied death
+> # times due to use of an approximation. See comments in the source code.
+> myfit <- coxph(Surv(time, status) ~ age + factor(ph.ecog) + strata(sex),
++ data=lung, method='breslow')
+> p1 <- predict(myfit, type='expected')
+> p2 <- predict(myfit, type="expected", newdata=lung[keep,])
+> p3 <- predict(myfit, type='expected', se.fit=TRUE)
+> p4 <- predict(myfit, type="expected", newdata=lung[keep,], se.fit=TRUE)
+> aeq(p1[keep], p2)
+[1] TRUE
+> aeq(p1, p3$fit)
+[1] TRUE
+> aeq(p1[keep], p4$fit)
+[1] TRUE
+> aeq(p3$se.fit[keep], p4$se.fit)
+[1] TRUE
+>
+> p1 <- predict(myfit, type='terms')
+> p2 <- predict(myfit, type="terms",newdata=lung[keep,])
+> p3 <- predict(myfit, type='terms', se.fit=T)
+> p4 <- predict(myfit, type="terms",newdata=lung[keep,], se.fit=T)
+> aeq(p1[keep,], p2)
+[1] TRUE
+> aeq(p1, p3$fit)
+[1] TRUE
+> aeq(p1[keep,], p4$fit)
+[1] TRUE
+> aeq(p3$se.fit[keep,], p4$se.fit)
+[1] TRUE
+>
+> #
+> # Check out the logic whereby predict does not need to
+> # recover the model frame. The first call should not
+> # need to do so, the second should in each case.
+> #
+> myfit <- coxph(Surv(time, status) ~ age + factor(sex), lung, x=T)
+> p1 <- predict(myfit, type='risk', se=T)
+> myfit2 <- coxph(Surv(time, status) ~ age + factor(sex), lung)
+> p2 <- predict(myfit2, type='risk', se=T)
+> aeq(p1$fit, p2$fit)
+[1] TRUE
+> aeq(p1$se, p2$se)
+[1] TRUE
+>
+> p1 <- predict(myfit, type='expected', se=T)
+> p2 <- predict(myfit2, type='expected', se=T)
+> aeq(p1$fit, p2$fit)
+[1] TRUE
+> aeq(p1$se.fit, p2$se.fit)
+[1] TRUE
+>
+> p1 <- predict(myfit, type='terms', se=T)
+> p2 <- predict(myfit2, type='terms', se=T)
+> aeq(p1$fit, p2$fit)
+[1] TRUE
+> aeq(p1$se.fit, p2$se.fit)
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/pspline.R b/win32/deps/library/survival/tests/pspline.R
new file mode 100644
index 0000000..8e7f5ec
--- /dev/null
+++ b/win32/deps/library/survival/tests/pspline.R
@@ -0,0 +1,34 @@
+library(survival)
+#
+# Tests with the pspline function, to verify the prediction aspects
+#
+options(na.action=na.exclude)
+aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+
+spfit <- coxph(Surv(time, status) ~ pspline(age) + ph.ecog, lung)
+
+spfit2 <- coxph(Surv(time, status) ~ pspline(age) + ph.ecog, lung, x=TRUE)
+x2 <- model.matrix(spfit)
+all.equal(spfit2$x, x2)
+
+keep <- (lung$age < 60)
+x3 <- model.matrix(spfit, data=lung[keep,])
+attr(x3, 'assign') <- NULL #subscripting loses the assign attr below
+all.equal(napredict(spfit$na.action,x2)[keep,], x3)
+
+p2 <- predict(spfit, newdata=lung[keep,])
+aeq(p2, predict(spfit)[keep])
+
+
+p3 <- survfit(spfit)
+p4 <- survfit(spfit, newdata=lung[1:2,])
+temp <- scale(x2[1:2,], center=spfit$means, scale=FALSE)%*% coef(spfit)
+aeq(p3$time, p4$time)
+aeq(outer(-log(p3$surv), exp(temp), '*'), -log(p4$surv))
+
+# Check out model.frame
+spfit3 <- coxph(Surv(time, status) ~ pspline(age) + sex, lung,
+ model=TRUE) #avoid the missing value
+m2 <- model.frame(spfit3, data=lung[keep,])
+all.equal(m2, spfit3$model[keep,])
+
diff --git a/win32/deps/library/survival/tests/pspline.Rout.save b/win32/deps/library/survival/tests/pspline.Rout.save
new file mode 100644
index 0000000..1b3a3ec
--- /dev/null
+++ b/win32/deps/library/survival/tests/pspline.Rout.save
@@ -0,0 +1,60 @@
+
+R version 2.14.0 (2011-10-31)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+> #
+> # Tests with the pspline function, to verify the prediction aspects
+> #
+> options(na.action=na.exclude)
+> aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+>
+> spfit <- coxph(Surv(time, status) ~ pspline(age) + ph.ecog, lung)
+>
+> spfit2 <- coxph(Surv(time, status) ~ pspline(age) + ph.ecog, lung, x=TRUE)
+> x2 <- model.matrix(spfit)
+> all.equal(spfit2$x, x2)
+[1] TRUE
+>
+> keep <- (lung$age < 60)
+> x3 <- model.matrix(spfit, data=lung[keep,])
+> attr(x3, 'assign') <- NULL #subscripting loses the assign attr below
+> all.equal(napredict(spfit$na.action,x2)[keep,], x3)
+[1] TRUE
+>
+> p2 <- predict(spfit, newdata=lung[keep,])
+> aeq(p2, predict(spfit)[keep])
+[1] TRUE
+>
+>
+> p3 <- survfit(spfit)
+> p4 <- survfit(spfit, newdata=lung[1:2,])
+> temp <- scale(x2[1:2,], center=spfit$means, scale=FALSE)%*% coef(spfit)
+> aeq(p3$time, p4$time)
+[1] TRUE
+> aeq(outer(-log(p3$surv), exp(temp), '*'), -log(p4$surv))
+[1] TRUE
+>
+> # Check out model.frame
+> spfit3 <- coxph(Surv(time, status) ~ pspline(age) + sex, lung,
++ model=TRUE) #avoid the missing value
+> m2 <- model.frame(spfit3, data=lung[keep,])
+> all.equal(m2, spfit3$model[keep,])
+[1] TRUE
+>
+>
diff --git a/win32/deps/library/survival/tests/pyear.R b/win32/deps/library/survival/tests/pyear.R
new file mode 100644
index 0000000..8e56350
--- /dev/null
+++ b/win32/deps/library/survival/tests/pyear.R
@@ -0,0 +1,211 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+{if (is.R()) mdy.date <- function(m, d, y) {
+ y <- ifelse(y<100, y+1900, y)
+ as.Date(paste(m,d,y, sep='/'), "%m/%d/%Y")
+ }
+else mdy.date <- function(m,d,y) {
+ y <- ifelse(y<100, y+1900, y)
+ timeDate(paste(y, m, d, sep='/'), in.format="%Y/%m/%d")
+ }
+ }
+
+#
+# Simple case: a single male subject, born 6/6/36 and entered on study 6/6/55.
+#
+
+temp1 <- mdy.date(6,6,36)
+temp2 <- mdy.date(6,6,55)# Now compare the results from person-years
+#
+temp.age <- tcut(temp2-temp1, floor(c(-1, (18:31 * 365.24))),
+ labels=c('0-18', paste(18:30, 19:31, sep='-')))
+temp.yr <- tcut(temp2, mdy.date(1,1,1954:1965), labels=1954:1964)
+temp.time <- 3700 #total days of fu
+py1 <- pyears(temp.time ~ temp.age + temp.yr, scale=1) #output in days
+
+# The subject should appear in 20 cells
+# 6/6/55 - 12/31/55, 209 days, age 19-20, 1955
+# 1/1/56 - 6/ 4/56, 156 days, age 19-20, 1956
+# 6/5/56 - 12/31/56, 210 days, age 20-21, 1956 (a leap year, and his
+# birthday computes one day earlier)
+# 1/1/57 - 6/ 5/57, 156 days, age 20-21, 1957
+# 6/6/57 - 12/31/57, 209 days, age 21-22, 1957
+# and etc
+# with 203 days "off table", ie, beyond the last cell of the table
+#
+# It is a nuisance, but tcut follows 'cut' in that we give the ENDS of
+# the intervals, whereas the survival tables use the starts of intervals.
+# Thus this breakdown does not match that in doexpect.s
+#
+xx <- matrix(0, nrow=14, ncol=11)
+xx[cbind(3:11, 3:11)] <- 156
+xx[cbind(3:12, 2:11)] <- c(209, 210, rep(c(209, 209, 209, 210),2))
+dimnames(xx) <- list(c('0-18', paste(18:30, 19:31, sep='-')), 1954:1964)
+all.equal(xx, py1$pyears)
+all.equal(203, py1$offtable)
+all.equal(1*(xx>0), py1$n)
+
+#
+# Now with expecteds
+#
+py2 <- pyears(temp.time ~ temp.age + temp.yr
+ + ratetable(age=temp2-temp1, year=temp2, sex=1),
+ scale=1, ratetable=survexp.us ) #output in days
+all.equal(xx, py2$pyears)
+all.equal(203, py2$offtable)
+all.equal(1*(xx>0), py2$n)
+
+py2b <- pyears(temp.time ~ temp.age + temp.yr,
+ rmap = list(age=temp2-temp1, year=temp2, sex=1),
+ scale=1, ratetable=survexp.us ) #output in days
+all.equal(xx, py2b$pyears)
+all.equal(203, py2b$offtable)
+all.equal(1*(xx>0), py2b$n)
+all.equal(py2$expected, py2b$expected)
+
+
+
+py3 <- pyears(temp.time ~ temp.age + temp.yr,
+ rmap=list(age=temp2-temp1, year=temp2, sex=1),
+ scale=1, ratetable=survexp.us , expect='pyears')
+all.equal(py2$n, py3$n)
+all.equal(py2$pyear, py3$pyear)
+all.equal(py3$n, 1*(py3$expect>0))
+
+# Now, compute the py3 result "by hand". Since there is only one person
+# it can be derived from py2.
+#
+xx1 <- py2$expect[py2$n>0] # the hazard over each interval
+cumhaz <- cumsum(c(0, xx1[-length(xx1)])) # the cumulative hazard
+xx2 <- py3$expect[py3$n>0] # the expected number of person days
+xx3 <- py3$pyears[py3$n>0] # the potential number of person days
+
+# This is the integral of the curve "exp(-haz *t)" over the interval
+integral <- xx3 * exp(-cumhaz)* (1- exp(-xx1))/ xx1
+# They might not be exactly equal, since the C code tracks changes in the
+# rate tables that occur -within- an interval. So try for 6 digits
+all.equal(round(integral,3), round(xx2,3))
+
+# Cut off the bottom of the table, instead of the side
+temp.age <- tcut(temp2-temp1, floor(c(-1, (18:27 * 365.24))),
+ labels=c('0-18', paste(18:26, 19:27, sep='-')))
+
+py4 <- eval(py3$call)
+all.equal(py4$pyear, py3$pyear[1:10,])
+all.equal(py4$expect, py3$expect[1:10,])
+
+
+rm(temp.age, integral, xx1, xx2, xx3, cumhaz, py1, py2, py3, py4)
+rm(temp1, temp2, temp.yr, temp.time, xx)
+
+
+
+
+#
+# Simple case: a single male subject, born 6/6/36 and entered on study 6/6/55.
+#
+
+temp1 <- mdy.date(6,6,36)
+temp2 <- mdy.date(6,6,55)# Now compare the results from person-years
+#
+temp.age <- tcut(temp2-temp1, floor(c(-1, (18:31 * 365.24))),
+ labels=c('0-18', paste(18:30, 19:31, sep='-')))
+temp.yr <- tcut(temp2, mdy.date(1,1,1954:1965), labels=1954:1964)
+temp.time <- 3700 #total days of fu
+py1 <- pyears(temp.time ~ temp.age + temp.yr, scale=1) #output in days
+
+# The subject should appear in 20 cells
+# 6/6/55 - 12/31/55, 209 days, age 19-20, 1955
+# 1/1/56 - 6/ 4/56, 156 days, age 19-20, 1956
+# 6/5/56 - 12/31/56, 210 days, age 20-21, 1956 (a leap year, and his
+# birthday computes one day earlier)
+# 1/1/57 - 6/ 5/57, 156 days, age 20-21, 1957
+# 6/6/57 - 12/31/57, 209 days, age 21-22, 1957
+# and etc
+# with 203 days "off table", ie, beyond the last cell of the table
+#
+# It is a nuisance, but tcut follows 'cut' in that we give the ENDS of
+# the intervals, whereas the survival tables use the starts of intervals.
+#
+xx <- matrix(0, nrow=14, ncol=11)
+xx[cbind(3:11, 3:11)] <- 156
+xx[cbind(3:12, 2:11)] <- c(209, 210, rep(c(209, 209, 209, 210),2))
+dimnames(xx) <- list(c('0-18', paste(18:30, 19:31, sep='-')), 1954:1964)
+all.equal(xx, py1$pyears)
+all.equal(203, py1$offtable)
+all.equal(1*(xx>0), py1$n)
+
+#
+# Now with expecteds
+#
+py2 <- pyears(temp.time ~ temp.age + temp.yr
+ + ratetable(age=temp2-temp1, year=temp2, sex=1),
+ scale=1, ratetable=survexp.us ) #output in days
+all.equal(xx, py2$pyears)
+all.equal(203, py2$offtable)
+all.equal(1*(xx>0), py2$n)
+
+
+py3 <- pyears(temp.time ~ temp.age + temp.yr
+ + ratetable(age=temp2-temp1, year=temp2, sex=1),
+ scale=1, ratetable=survexp.us , expect='pyears')
+all.equal(py2$n, py3$n)
+all.equal(py2$pyear, py3$pyear)
+all.equal(py3$n, 1*(py3$expect>0))
+
+# Now, compute the py3 result "by hand". Since there is only one person
+# it can be derived from py2.
+#
+xx1 <- py2$expect[py2$n>0] # the hazard over each interval
+cumhaz <- cumsum(c(0, xx1[-length(xx1)])) # the cumulative hazard
+xx2 <- py3$expect[py3$n>0] # the expected number of person days
+xx3 <- py3$pyears[py3$n>0] # the potential number of person days
+
+# This is the integral of the curve "exp(-haz *t)" over the interval
+integral <- xx3 * exp(-cumhaz)* (1- exp(-xx1))/ xx1
+# They might not be exactly equal, since the C code tracks changes in the
+# rate tables that occur -within- an interval. So try for 6 digits
+all.equal(round(integral,3), round(xx2,3))
+
+# Cut off the bottom of the table, instead of the side
+temp.age <- tcut(temp2-temp1, floor(c(-1, (18:27 * 365.24))),
+ labels=c('0-18', paste(18:26, 19:27, sep='-')))
+
+py4 <- eval(py3$call)
+all.equal(py4$pyear, py3$pyear[1:10,])
+all.equal(py4$expect, py3$expect[1:10,])
+
+
+rm(temp.age, integral, xx1, xx2, xx3, cumhaz, py1, py2, py3, py4)
+rm(temp1, temp2, temp.yr, temp.time, xx)
+
+
+
+
+#
+# Create a "user defined" rate table, using the smoking data
+#
+temp <- scan("data.smoke")/100000
+temp <- matrix(temp, ncol=8, byrow=T)
+smoke.rate <- c(rep(temp[,1],6), rep(temp[,2],6), temp[,3:8])
+attributes(smoke.rate) <- list(
+ dim=c(7,2,2,6,3),
+ dimnames=list(c("45-49","50-54","55-59","60-64","65-69","70-74","75-79"),
+ c("1-20", "21+"),
+ c("Male","Female"),
+ c("<1", "1-2", "3-5", "6-10", "11-15", ">=16"),
+ c("Never", "Current", "Former")),
+ dimid=c("age", "amount", "sex", "duration", "status"),
+ factor=c(0,1,1,0,1),
+ cutpoints=list(c(45,50,55,60,65,70,75),NULL, NULL,
+ c(0,1,3,6,11,16),NULL),
+ class='ratetable'
+ )
+rm(temp)
+
+is.ratetable(smoke.rate)
+summary(smoke.rate)
+print(smoke.rate)
+
+summary(smoke.rate[1:3,,1,,]) #test subscripting
diff --git a/win32/deps/library/survival/tests/pyear.Rout.save b/win32/deps/library/survival/tests/pyear.Rout.save
new file mode 100644
index 0000000..6eb671b
--- /dev/null
+++ b/win32/deps/library/survival/tests/pyear.Rout.save
@@ -0,0 +1,669 @@
+
+R version 2.12.1 (2010-12-16)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: i686-pc-linux-gnu (32-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+> {if (is.R()) mdy.date <- function(m, d, y) {
++ y <- ifelse(y<100, y+1900, y)
++ as.Date(paste(m,d,y, sep='/'), "%m/%d/%Y")
++ }
++ else mdy.date <- function(m,d,y) {
++ y <- ifelse(y<100, y+1900, y)
++ timeDate(paste(y, m, d, sep='/'), in.format="%Y/%m/%d")
++ }
++ }
+>
+> #
+> # Simple case: a single male subject, born 6/6/36 and entered on study 6/6/55.
+> #
+>
+> temp1 <- mdy.date(6,6,36)
+> temp2 <- mdy.date(6,6,55)# Now compare the results from person-years
+> #
+> temp.age <- tcut(temp2-temp1, floor(c(-1, (18:31 * 365.24))),
++ labels=c('0-18', paste(18:30, 19:31, sep='-')))
+> temp.yr <- tcut(temp2, mdy.date(1,1,1954:1965), labels=1954:1964)
+> temp.time <- 3700 #total days of fu
+> py1 <- pyears(temp.time ~ temp.age + temp.yr, scale=1) #output in days
+>
+> # The subject should appear in 20 cells
+> # 6/6/55 - 12/31/55, 209 days, age 19-20, 1955
+> # 1/1/56 - 6/ 4/56, 156 days, age 19-20, 1956
+> # 6/5/56 - 12/31/56, 210 days, age 20-21, 1956 (a leap year, and his
+> # birthday computes one day earlier)
+> # 1/1/57 - 6/ 5/57, 156 days, age 20-21, 1957
+> # 6/6/57 - 12/31/57, 209 days, age 21-22, 1957
+> # and etc
+> # with 203 days "off table", ie, beyond the last cell of the table
+> #
+> # It is a nuisance, but tcut follows 'cut' in that we give the ENDS of
+> # the intervals, whereas the survival tables use the starts of intervals.
+> # Thus this breakdown does not match that in doexpect.s
+> #
+> xx <- matrix(0, nrow=14, ncol=11)
+> xx[cbind(3:11, 3:11)] <- 156
+> xx[cbind(3:12, 2:11)] <- c(209, 210, rep(c(209, 209, 209, 210),2))
+> dimnames(xx) <- list(c('0-18', paste(18:30, 19:31, sep='-')), 1954:1964)
+> all.equal(xx, py1$pyears)
+[1] TRUE
+> all.equal(203, py1$offtable)
+[1] TRUE
+> all.equal(1*(xx>0), py1$n)
+[1] TRUE
+>
+> #
+> # Now with expecteds
+> #
+> py2 <- pyears(temp.time ~ temp.age + temp.yr
++ + ratetable(age=temp2-temp1, year=temp2, sex=1),
++ scale=1, ratetable=survexp.us ) #output in days
+> all.equal(xx, py2$pyears)
+[1] TRUE
+> all.equal(203, py2$offtable)
+[1] TRUE
+> all.equal(1*(xx>0), py2$n)
+[1] TRUE
+>
+> py2b <- pyears(temp.time ~ temp.age + temp.yr,
++ rmap = list(age=temp2-temp1, year=temp2, sex=1),
++ scale=1, ratetable=survexp.us ) #output in days
+> all.equal(xx, py2b$pyears)
+[1] TRUE
+> all.equal(203, py2b$offtable)
+[1] TRUE
+> all.equal(1*(xx>0), py2b$n)
+[1] TRUE
+> all.equal(py2$expected, py2b$expected)
+[1] TRUE
+>
+>
+>
+> py3 <- pyears(temp.time ~ temp.age + temp.yr,
++ rmap=list(age=temp2-temp1, year=temp2, sex=1),
++ scale=1, ratetable=survexp.us , expect='pyears')
+> all.equal(py2$n, py3$n)
+[1] TRUE
+> all.equal(py2$pyear, py3$pyear)
+[1] TRUE
+> all.equal(py3$n, 1*(py3$expect>0))
+[1] TRUE
+>
+> # Now, compute the py3 result "by hand". Since there is only one person
+> # it can be derived from py2.
+> #
+> xx1 <- py2$expect[py2$n>0] # the hazard over each interval
+> cumhaz <- cumsum(c(0, xx1[-length(xx1)])) # the cumulative hazard
+> xx2 <- py3$expect[py3$n>0] # the expected number of person days
+> xx3 <- py3$pyears[py3$n>0] # the potential number of person days
+>
+> # This is the integral of the curve "exp(-haz *t)" over the interval
+> integral <- xx3 * exp(-cumhaz)* (1- exp(-xx1))/ xx1
+> # They might not be exactly equal, since the C code tracks changes in the
+> # rate tables that occur -within- an interval. So try for 6 digits
+> all.equal(round(integral,3), round(xx2,3))
+[1] TRUE
+>
+> # Cut off the bottom of the table, instead of the side
+> temp.age <- tcut(temp2-temp1, floor(c(-1, (18:27 * 365.24))),
++ labels=c('0-18', paste(18:26, 19:27, sep='-')))
+>
+> py4 <- eval(py3$call)
+> all.equal(py4$pyear, py3$pyear[1:10,])
+[1] TRUE
+> all.equal(py4$expect, py3$expect[1:10,])
+[1] TRUE
+>
+>
+> rm(temp.age, integral, xx1, xx2, xx3, cumhaz, py1, py2, py3, py4)
+> rm(temp1, temp2, temp.yr, temp.time, xx)
+>
+>
+>
+>
+> #
+> # Simple case: a single male subject, born 6/6/36 and entered on study 6/6/55.
+> #
+>
+> temp1 <- mdy.date(6,6,36)
+> temp2 <- mdy.date(6,6,55)# Now compare the results from person-years
+> #
+> temp.age <- tcut(temp2-temp1, floor(c(-1, (18:31 * 365.24))),
++ labels=c('0-18', paste(18:30, 19:31, sep='-')))
+> temp.yr <- tcut(temp2, mdy.date(1,1,1954:1965), labels=1954:1964)
+> temp.time <- 3700 #total days of fu
+> py1 <- pyears(temp.time ~ temp.age + temp.yr, scale=1) #output in days
+>
+> # The subject should appear in 20 cells
+> # 6/6/55 - 12/31/55, 209 days, age 19-20, 1955
+> # 1/1/56 - 6/ 4/56, 156 days, age 19-20, 1956
+> # 6/5/56 - 12/31/56, 210 days, age 20-21, 1956 (a leap year, and his
+> # birthday computes one day earlier)
+> # 1/1/57 - 6/ 5/57, 156 days, age 20-21, 1957
+> # 6/6/57 - 12/31/57, 209 days, age 21-22, 1957
+> # and etc
+> # with 203 days "off table", ie, beyond the last cell of the table
+> #
+> # It is a nuisance, but tcut follows 'cut' in that we give the ENDS of
+> # the intervals, whereas the survival tables use the starts of intervals.
+> #
+> xx <- matrix(0, nrow=14, ncol=11)
+> xx[cbind(3:11, 3:11)] <- 156
+> xx[cbind(3:12, 2:11)] <- c(209, 210, rep(c(209, 209, 209, 210),2))
+> dimnames(xx) <- list(c('0-18', paste(18:30, 19:31, sep='-')), 1954:1964)
+> all.equal(xx, py1$pyears)
+[1] TRUE
+> all.equal(203, py1$offtable)
+[1] TRUE
+> all.equal(1*(xx>0), py1$n)
+[1] TRUE
+>
+> #
+> # Now with expecteds
+> #
+> py2 <- pyears(temp.time ~ temp.age + temp.yr
++ + ratetable(age=temp2-temp1, year=temp2, sex=1),
++ scale=1, ratetable=survexp.us ) #output in days
+> all.equal(xx, py2$pyears)
+[1] TRUE
+> all.equal(203, py2$offtable)
+[1] TRUE
+> all.equal(1*(xx>0), py2$n)
+[1] TRUE
+>
+>
+> py3 <- pyears(temp.time ~ temp.age + temp.yr
++ + ratetable(age=temp2-temp1, year=temp2, sex=1),
++ scale=1, ratetable=survexp.us , expect='pyears')
+> all.equal(py2$n, py3$n)
+[1] TRUE
+> all.equal(py2$pyear, py3$pyear)
+[1] TRUE
+> all.equal(py3$n, 1*(py3$expect>0))
+[1] TRUE
+>
+> # Now, compute the py3 result "by hand". Since there is only one person
+> # it can be derived from py2.
+> #
+> xx1 <- py2$expect[py2$n>0] # the hazard over each interval
+> cumhaz <- cumsum(c(0, xx1[-length(xx1)])) # the cumulative hazard
+> xx2 <- py3$expect[py3$n>0] # the expected number of person days
+> xx3 <- py3$pyears[py3$n>0] # the potential number of person days
+>
+> # This is the integral of the curve "exp(-haz *t)" over the interval
+> integral <- xx3 * exp(-cumhaz)* (1- exp(-xx1))/ xx1
+> # They might not be exactly equal, since the C code tracks changes in the
+> # rate tables that occur -within- an interval. So try for 6 digits
+> all.equal(round(integral,3), round(xx2,3))
+[1] TRUE
+>
+> # Cut off the bottom of the table, instead of the side
+> temp.age <- tcut(temp2-temp1, floor(c(-1, (18:27 * 365.24))),
++ labels=c('0-18', paste(18:26, 19:27, sep='-')))
+>
+> py4 <- eval(py3$call)
+> all.equal(py4$pyear, py3$pyear[1:10,])
+[1] TRUE
+> all.equal(py4$expect, py3$expect[1:10,])
+[1] TRUE
+>
+>
+> rm(temp.age, integral, xx1, xx2, xx3, cumhaz, py1, py2, py3, py4)
+> rm(temp1, temp2, temp.yr, temp.time, xx)
+>
+>
+>
+>
+> #
+> # Create a "user defined" rate table, using the smoking data
+> #
+> temp <- scan("data.smoke")/100000
+Read 224 items
+> temp <- matrix(temp, ncol=8, byrow=T)
+> smoke.rate <- c(rep(temp[,1],6), rep(temp[,2],6), temp[,3:8])
+> attributes(smoke.rate) <- list(
++ dim=c(7,2,2,6,3),
++ dimnames=list(c("45-49","50-54","55-59","60-64","65-69","70-74","75-79"),
++ c("1-20", "21+"),
++ c("Male","Female"),
++ c("<1", "1-2", "3-5", "6-10", "11-15", ">=16"),
++ c("Never", "Current", "Former")),
++ dimid=c("age", "amount", "sex", "duration", "status"),
++ factor=c(0,1,1,0,1),
++ cutpoints=list(c(45,50,55,60,65,70,75),NULL, NULL,
++ c(0,1,3,6,11,16),NULL),
++ class='ratetable'
++ )
+> rm(temp)
+>
+> is.ratetable(smoke.rate)
+[1] TRUE
+> summary(smoke.rate)
+ Rate table with 5 dimensions:
+ age ranges from 45 to 75; with 7 categories
+ amount has levels of: 1-20 21+
+ sex has levels of: Male Female
+ duration ranges from 0 to 16; with 6 categories
+ status has levels of: Never Current Former
+> print(smoke.rate)
+Rate table with dimension(s): age amount sex duration status
+, , Male, <1, Never
+
+ 1-20 21+
+45-49 0.001860 0.001860
+50-54 0.002556 0.002556
+55-59 0.004489 0.004489
+60-64 0.007337 0.007337
+65-69 0.011194 0.011194
+70-74 0.020705 0.020705
+75-79 0.036753 0.036753
+
+, , Female, <1, Never
+
+ 1-20 21+
+45-49 0.001257 0.001257
+50-54 0.001773 0.001773
+55-59 0.002448 0.002448
+60-64 0.003977 0.003977
+65-69 0.006921 0.006921
+70-74 0.011600 0.011600
+75-79 0.020708 0.020708
+
+, , Male, 1-2, Never
+
+ 1-20 21+
+45-49 0.001860 0.001860
+50-54 0.002556 0.002556
+55-59 0.004489 0.004489
+60-64 0.007337 0.007337
+65-69 0.011194 0.011194
+70-74 0.020705 0.020705
+75-79 0.036753 0.036753
+
+, , Female, 1-2, Never
+
+ 1-20 21+
+45-49 0.001257 0.001257
+50-54 0.001773 0.001773
+55-59 0.002448 0.002448
+60-64 0.003977 0.003977
+65-69 0.006921 0.006921
+70-74 0.011600 0.011600
+75-79 0.020708 0.020708
+
+, , Male, 3-5, Never
+
+ 1-20 21+
+45-49 0.001860 0.001860
+50-54 0.002556 0.002556
+55-59 0.004489 0.004489
+60-64 0.007337 0.007337
+65-69 0.011194 0.011194
+70-74 0.020705 0.020705
+75-79 0.036753 0.036753
+
+, , Female, 3-5, Never
+
+ 1-20 21+
+45-49 0.001257 0.001257
+50-54 0.001773 0.001773
+55-59 0.002448 0.002448
+60-64 0.003977 0.003977
+65-69 0.006921 0.006921
+70-74 0.011600 0.011600
+75-79 0.020708 0.020708
+
+, , Male, 6-10, Never
+
+ 1-20 21+
+45-49 0.001860 0.001860
+50-54 0.002556 0.002556
+55-59 0.004489 0.004489
+60-64 0.007337 0.007337
+65-69 0.011194 0.011194
+70-74 0.020705 0.020705
+75-79 0.036753 0.036753
+
+, , Female, 6-10, Never
+
+ 1-20 21+
+45-49 0.001257 0.001257
+50-54 0.001773 0.001773
+55-59 0.002448 0.002448
+60-64 0.003977 0.003977
+65-69 0.006921 0.006921
+70-74 0.011600 0.011600
+75-79 0.020708 0.020708
+
+, , Male, 11-15, Never
+
+ 1-20 21+
+45-49 0.001860 0.001860
+50-54 0.002556 0.002556
+55-59 0.004489 0.004489
+60-64 0.007337 0.007337
+65-69 0.011194 0.011194
+70-74 0.020705 0.020705
+75-79 0.036753 0.036753
+
+, , Female, 11-15, Never
+
+ 1-20 21+
+45-49 0.001257 0.001257
+50-54 0.001773 0.001773
+55-59 0.002448 0.002448
+60-64 0.003977 0.003977
+65-69 0.006921 0.006921
+70-74 0.011600 0.011600
+75-79 0.020708 0.020708
+
+, , Male, >=16, Never
+
+ 1-20 21+
+45-49 0.001860 0.001860
+50-54 0.002556 0.002556
+55-59 0.004489 0.004489
+60-64 0.007337 0.007337
+65-69 0.011194 0.011194
+70-74 0.020705 0.020705
+75-79 0.036753 0.036753
+
+, , Female, >=16, Never
+
+ 1-20 21+
+45-49 0.001257 0.001257
+50-54 0.001773 0.001773
+55-59 0.002448 0.002448
+60-64 0.003977 0.003977
+65-69 0.006921 0.006921
+70-74 0.011600 0.011600
+75-79 0.020708 0.020708
+
+, , Male, <1, Current
+
+ 1-20 21+
+45-49 0.004392 0.006100
+50-54 0.007027 0.009156
+55-59 0.011324 0.013910
+60-64 0.019811 0.023934
+65-69 0.030030 0.034979
+70-74 0.046975 0.058613
+75-79 0.073406 0.062500
+
+, , Female, <1, Current
+
+ 1-20 21+
+45-49 0.002256 0.002779
+50-54 0.003538 0.005179
+55-59 0.005428 0.008235
+60-64 0.008580 0.013029
+65-69 0.014962 0.019349
+70-74 0.020848 0.028270
+75-79 0.033195 0.042731
+
+, , Male, 1-2, Current
+
+ 1-20 21+
+45-49 0.004392 0.006100
+50-54 0.007027 0.009156
+55-59 0.011324 0.013910
+60-64 0.019811 0.023934
+65-69 0.030030 0.034979
+70-74 0.046975 0.058613
+75-79 0.073406 0.062500
+
+, , Female, 1-2, Current
+
+ 1-20 21+
+45-49 0.002256 0.002779
+50-54 0.003538 0.005179
+55-59 0.005428 0.008235
+60-64 0.008580 0.013029
+65-69 0.014962 0.019349
+70-74 0.020848 0.028270
+75-79 0.033195 0.042731
+
+, , Male, 3-5, Current
+
+ 1-20 21+
+45-49 0.004392 0.006100
+50-54 0.007027 0.009156
+55-59 0.011324 0.013910
+60-64 0.019811 0.023934
+65-69 0.030030 0.034979
+70-74 0.046975 0.058613
+75-79 0.073406 0.062500
+
+, , Female, 3-5, Current
+
+ 1-20 21+
+45-49 0.002256 0.002779
+50-54 0.003538 0.005179
+55-59 0.005428 0.008235
+60-64 0.008580 0.013029
+65-69 0.014962 0.019349
+70-74 0.020848 0.028270
+75-79 0.033195 0.042731
+
+, , Male, 6-10, Current
+
+ 1-20 21+
+45-49 0.004392 0.006100
+50-54 0.007027 0.009156
+55-59 0.011324 0.013910
+60-64 0.019811 0.023934
+65-69 0.030030 0.034979
+70-74 0.046975 0.058613
+75-79 0.073406 0.062500
+
+, , Female, 6-10, Current
+
+ 1-20 21+
+45-49 0.002256 0.002779
+50-54 0.003538 0.005179
+55-59 0.005428 0.008235
+60-64 0.008580 0.013029
+65-69 0.014962 0.019349
+70-74 0.020848 0.028270
+75-79 0.033195 0.042731
+
+, , Male, 11-15, Current
+
+ 1-20 21+
+45-49 0.004392 0.006100
+50-54 0.007027 0.009156
+55-59 0.011324 0.013910
+60-64 0.019811 0.023934
+65-69 0.030030 0.034979
+70-74 0.046975 0.058613
+75-79 0.073406 0.062500
+
+, , Female, 11-15, Current
+
+ 1-20 21+
+45-49 0.002256 0.002779
+50-54 0.003538 0.005179
+55-59 0.005428 0.008235
+60-64 0.008580 0.013029
+65-69 0.014962 0.019349
+70-74 0.020848 0.028270
+75-79 0.033195 0.042731
+
+, , Male, >=16, Current
+
+ 1-20 21+
+45-49 0.004392 0.006100
+50-54 0.007027 0.009156
+55-59 0.011324 0.013910
+60-64 0.019811 0.023934
+65-69 0.030030 0.034979
+70-74 0.046975 0.058613
+75-79 0.073406 0.062500
+
+, , Female, >=16, Current
+
+ 1-20 21+
+45-49 0.002256 0.002779
+50-54 0.003538 0.005179
+55-59 0.005428 0.008235
+60-64 0.008580 0.013029
+65-69 0.014962 0.019349
+70-74 0.020848 0.028270
+75-79 0.033195 0.042731
+
+, , Male, <1, Former
+
+ 1-20 21+
+45-49 0.002344 0.004975
+50-54 0.005447 0.004828
+55-59 0.009452 0.017571
+60-64 0.011777 0.015784
+65-69 0.022449 0.023018
+70-74 0.042553 0.031746
+75-79 0.058824 0.040000
+
+, , Female, <1, Former
+
+ 1-20 21+
+45-49 0.000000 0.002667
+50-54 0.001168 0.001387
+55-59 0.002874 0.004736
+60-64 0.010163 0.011148
+65-69 0.011080 0.023196
+70-74 0.006452 0.046358
+75-79 0.000000 0.024096
+
+, , Male, 1-2, Former
+
+ 1-20 21+
+45-49 0.003658 0.002517
+50-54 0.004310 0.005007
+55-59 0.007288 0.009535
+60-64 0.015892 0.018472
+65-69 0.033803 0.037766
+70-74 0.050830 0.029740
+75-79 0.065972 0.044248
+
+, , Female, 1-2, Former
+
+ 1-20 21+
+45-49 0.004339 0.001027
+50-54 0.000921 0.004668
+55-59 0.002595 0.006020
+60-64 0.003650 0.008621
+65-69 0.013485 0.012500
+70-74 0.014831 0.025172
+75-79 0.025806 0.057692
+
+, , Male, 3-5, Former
+
+ 1-20 21+
+45-49 0.001596 0.004175
+50-54 0.004548 0.004889
+55-59 0.007294 0.010258
+60-64 0.013165 0.017901
+65-69 0.023749 0.020810
+70-74 0.044850 0.037129
+75-79 0.077075 0.073298
+
+, , Female, 3-5, Former
+
+ 1-20 21+
+45-49 0.002120 0.001786
+50-54 0.002895 0.002701
+55-59 0.003759 0.003610
+60-64 0.006509 0.006996
+65-69 0.012632 0.016880
+70-74 0.012500 0.016873
+75-79 0.025907 0.031250
+
+, , Male, 6-10, Former
+
+ 1-20 21+
+45-49 0.002169 0.001226
+50-54 0.003497 0.004029
+55-59 0.005902 0.007440
+60-64 0.012669 0.012207
+65-69 0.018202 0.027664
+70-74 0.038887 0.039888
+75-79 0.049451 0.063830
+
+, , Female, 6-10, Former
+
+ 1-20 21+
+45-49 0.001072 0.002247
+50-54 0.002009 0.001902
+55-59 0.001658 0.004545
+60-64 0.004708 0.005417
+65-69 0.008648 0.008287
+70-74 0.011263 0.028487
+75-79 0.039604 0.029787
+
+, , Male, 11-15, Former
+
+ 1-20 21+
+45-49 0.001674 0.001983
+50-54 0.002140 0.003939
+55-59 0.004473 0.006685
+60-64 0.008756 0.011000
+65-69 0.016691 0.022681
+70-74 0.031843 0.032686
+75-79 0.056180 0.076661
+
+, , Female, 11-15, Former
+
+ 1-20 21+
+45-49 0.001359 0.001421
+50-54 0.001213 0.001168
+55-59 0.002022 0.004122
+60-64 0.005706 0.003731
+65-69 0.005866 0.007979
+70-74 0.010705 0.016212
+75-79 0.016667 0.028037
+
+, , Male, >=16, Former
+
+ 1-20 21+
+45-49 0.001595 0.001934
+50-54 0.002504 0.003543
+55-59 0.004366 0.005378
+60-64 0.007030 0.009933
+65-69 0.011592 0.012307
+70-74 0.021949 0.024689
+75-79 0.041289 0.050481
+
+, , Female, >=16, Former
+
+ 1-20 21+
+45-49 0.000910 0.001388
+50-54 0.001721 0.000830
+55-59 0.002472 0.001821
+60-64 0.003197 0.003564
+65-69 0.006180 0.005815
+70-74 0.012721 0.013634
+75-79 0.018615 0.021954
+
+>
+> summary(smoke.rate[1:3,,1,,]) #test subscripting
+ Rate table with 4 dimensions:
+ age ranges from 45 to 55; with 3 categories
+ amount has levels of: 1-20 21+
+ duration ranges from 0 to 16; with 6 categories
+ status has levels of: Never Current Former
+>
diff --git a/win32/deps/library/survival/tests/r_capacitor.R b/win32/deps/library/survival/tests/r_capacitor.R
new file mode 100644
index 0000000..b0d9597
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_capacitor.R
@@ -0,0 +1,18 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+capacitor <- read.table('data.capacitor', row.names=1,
+ col.names=c('', 'days', 'event', 'voltage'))
+
+fitig <- survreg(Surv(days, event)~voltage,
+ dist = "gaussian", data = capacitor)
+summary(fitig)
+
+fitix <- survreg(Surv(days, event)~voltage,
+ dist = "extreme", data = capacitor)
+summary(fitix)
+
+fitil <- survreg(Surv(days, event)~voltage,
+ dist = "logistic", data = capacitor)
+summary(fitil)
diff --git a/win32/deps/library/survival/tests/r_capacitor.Rout.save b/win32/deps/library/survival/tests/r_capacitor.Rout.save
new file mode 100644
index 0000000..0e1aeca
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_capacitor.Rout.save
@@ -0,0 +1,88 @@
+
+R version 2.7.1 (2008-06-23)
+Copyright (C) 2008 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> capacitor <- read.table('data.capacitor', row.names=1,
++ col.names=c('', 'days', 'event', 'voltage'))
+>
+> fitig <- survreg(Surv(days, event)~voltage,
++ dist = "gaussian", data = capacitor)
+> summary(fitig)
+
+Call:
+survreg(formula = Surv(days, event) ~ voltage, data = capacitor,
+ dist = "gaussian")
+ Value Std. Error z p
+(Intercept) 1764.9 163.387 10.80 3.36e-27
+voltage -53.9 5.545 -9.72 2.56e-22
+Log(scale) 4.8 0.105 45.56 0.00e+00
+
+Scale= 121
+
+Gaussian distribution
+Loglik(model)= -361.9 Loglik(intercept only)= -420.1
+ Chisq= 116.33 on 1 degrees of freedom, p= 0
+Number of Newton-Raphson Iterations: 6
+n= 125
+
+>
+> fitix <- survreg(Surv(days, event)~voltage,
++ dist = "extreme", data = capacitor)
+> summary(fitix)
+
+Call:
+survreg(formula = Surv(days, event) ~ voltage, data = capacitor,
+ dist = "extreme")
+ Value Std. Error z p
+(Intercept) 2055.59 180.349 11.4 4.28e-30
+voltage -62.21 5.967 -10.4 1.88e-25
+Log(scale) 4.53 0.108 41.9 0.00e+00
+
+Scale= 92.9
+
+Extreme value distribution
+Loglik(model)= -360 Loglik(intercept only)= -427.1
+ Chisq= 134.25 on 1 degrees of freedom, p= 0
+Number of Newton-Raphson Iterations: 7
+n= 125
+
+>
+> fitil <- survreg(Surv(days, event)~voltage,
++ dist = "logistic", data = capacitor)
+> summary(fitil)
+
+Call:
+survreg(formula = Surv(days, event) ~ voltage, data = capacitor,
+ dist = "logistic")
+ Value Std. Error z p
+(Intercept) 1811.56 148.853 12.2 4.48e-34
+voltage -55.48 4.986 -11.1 9.39e-29
+Log(scale) 4.19 0.117 35.8 2.03e-280
+
+Scale= 66.3
+
+Logistic distribution
+Loglik(model)= -360.4 Loglik(intercept only)= -423.7
+ Chisq= 126.5 on 1 degrees of freedom, p= 0
+Number of Newton-Raphson Iterations: 6
+n= 125
+
+>
diff --git a/win32/deps/library/survival/tests/r_donnell.R b/win32/deps/library/survival/tests/r_donnell.R
new file mode 100644
index 0000000..6d91b8b
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_donnell.R
@@ -0,0 +1,60 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Good initial values are key to this data set
+# It killed v4 of survreg;
+# data courtesy of Deborah Donnell, Fred Hutchinson Cancer Center
+#
+
+donnell <- scan("data.donnell", what=list(time1=0, time2=0, status=0))
+donnell <- data.frame(donnell)
+
+dfit <- survreg(Surv(time1, time2, status, type='interval') ~1, donnell)
+summary(dfit)
+
+#
+# Fit the Donnell data using Statsci's code - should get the same coefs
+#
+if (exists('censorReg')) {
+ dfitc <- censorReg(censor(time1, time2, status, type='interval') ~1,
+ donnell)
+ summary(dfitc)
+ }
+#
+# Do a contour plot of the donnell data
+#
+npt <- 20
+beta0 <- seq(.4, 3.4, length=npt)
+logsig <- seq(-1.4, 0.41, length=npt)
+donlog <- matrix(0,npt, npt)
+
+for (i in 1:npt) {
+ for (j in 1:npt) {
+ fit <- survreg(Surv(time1, time2, status, type='interval') ~1,
+ donnell, init=c(beta0[i],logsig[j]),
+ maxiter=0)
+ donlog[i,j] <- fit$log[1]
+ }
+ }
+
+clev <- -c(51, 51.5, 52:60, 65, 75, 85, 100, 150)
+#clev <- seq(-51, -50, length=10)
+
+contour(beta0, logsig, pmax(donlog, -200), levels=clev, xlab="Intercept",
+ ylab="Log(sigma)")
+points(2.39, log(.7885), pch=1, col=2)
+title("Donnell data")
+#
+# Compute the path of the iteration
+#
+niter <- 14
+donpath <- matrix(0,niter+1,2)
+for (i in 0:niter){
+ fit <- survreg(Surv(time1, time2, status, type='interval') ~1,
+ donnell, maxiter=i)
+ donpath[i+1,] <- c(fit$coef, log(fit$scale))
+ }
+points(donpath[,1], donpath[,2])
+lines(donpath[,1], donpath[,2], col=4)
diff --git a/win32/deps/library/survival/tests/r_donnell.Rout.save b/win32/deps/library/survival/tests/r_donnell.Rout.save
new file mode 100644
index 0000000..b3c8fe3
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_donnell.Rout.save
@@ -0,0 +1,114 @@
+
+R version 2.7.1 (2008-06-23)
+Copyright (C) 2008 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Good initial values are key to this data set
+> # It killed v4 of survreg;
+> # data courtesy of Deborah Donnell, Fred Hutchinson Cancer Center
+> #
+>
+> donnell <- scan("data.donnell", what=list(time1=0, time2=0, status=0))
+Read 210 records
+> donnell <- data.frame(donnell)
+>
+> dfit <- survreg(Surv(time1, time2, status, type='interval') ~1, donnell)
+> summary(dfit)
+
+Call:
+survreg(formula = Surv(time1, time2, status, type = "interval") ~
+ 1, data = donnell)
+ Value Std. Error z p
+(Intercept) 2.390 0.804 2.972 0.00295
+Log(scale) -0.237 0.346 -0.687 0.49232
+
+Scale= 0.789
+
+Weibull distribution
+Loglik(model)= -51 Loglik(intercept only)= -51
+Number of Newton-Raphson Iterations: 11
+n= 210
+
+>
+> #
+> # Fit the Donnell data using Statsci's code - should get the same coefs
+> #
+> if (exists('censorReg')) {
++ dfitc <- censorReg(censor(time1, time2, status, type='interval') ~1,
++ donnell)
++ summary(dfitc)
++ }
+> #
+> # Do a contour plot of the donnell data
+> #
+> npt <- 20
+> beta0 <- seq(.4, 3.4, length=npt)
+> logsig <- seq(-1.4, 0.41, length=npt)
+> donlog <- matrix(0,npt, npt)
+>
+> for (i in 1:npt) {
++ for (j in 1:npt) {
++ fit <- survreg(Surv(time1, time2, status, type='interval') ~1,
++ donnell, init=c(beta0[i],logsig[j]),
++ maxiter=0)
++ donlog[i,j] <- fit$log[1]
++ }
++ }
+>
+> clev <- -c(51, 51.5, 52:60, 65, 75, 85, 100, 150)
+> #clev <- seq(-51, -50, length=10)
+>
+> contour(beta0, logsig, pmax(donlog, -200), levels=clev, xlab="Intercept",
++ ylab="Log(sigma)")
+> points(2.39, log(.7885), pch=1, col=2)
+> title("Donnell data")
+> #
+> # Compute the path of the iteration
+> #
+> niter <- 14
+> donpath <- matrix(0,niter+1,2)
+> for (i in 0:niter){
++ fit <- survreg(Surv(time1, time2, status, type='interval') ~1,
++ donnell, maxiter=i)
++ donpath[i+1,] <- c(fit$coef, log(fit$scale))
++ }
+Warning messages:
+1: In survreg.fit(X, Y, weights, offset, init = init, controlvals = control, :
+ Ran out of iterations and did not converge
+2: In survreg.fit(X, Y, weights, offset, init = init, controlvals = control, :
+ Ran out of iterations and did not converge
+3: In survreg.fit(X, Y, weights, offset, init = init, controlvals = control, :
+ Ran out of iterations and did not converge
+4: In survreg.fit(X, Y, weights, offset, init = init, controlvals = control, :
+ Ran out of iterations and did not converge
+5: In survreg.fit(X, Y, weights, offset, init = init, controlvals = control, :
+ Ran out of iterations and did not converge
+6: In survreg.fit(X, Y, weights, offset, init = init, controlvals = control, :
+ Ran out of iterations and did not converge
+7: In survreg.fit(X, Y, weights, offset, init = init, controlvals = control, :
+ Ran out of iterations and did not converge
+8: In survreg.fit(X, Y, weights, offset, init = init, controlvals = control, :
+ Ran out of iterations and did not converge
+9: In survreg.fit(X, Y, weights, offset, init = init, controlvals = control, :
+ Ran out of iterations and did not converge
+> points(donpath[,1], donpath[,2])
+> lines(donpath[,1], donpath[,2], col=4)
+>
diff --git a/win32/deps/library/survival/tests/r_lung.R b/win32/deps/library/survival/tests/r_lung.R
new file mode 100644
index 0000000..2e887d8
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_lung.R
@@ -0,0 +1,49 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+
+lfit2 <- survreg(Surv(time, status) ~ age + ph.ecog + strata(sex), lung)
+lfit3 <- survreg(Surv(time, status) ~ sex + (age+ph.ecog)*strata(sex), lung)
+
+lfit4 <- survreg(Surv(time, status) ~ age + ph.ecog , lung,
+ subset=(sex==1))
+lfit5 <- survreg(Surv(time, status) ~ age + ph.ecog , lung,
+ subset=(sex==2))
+
+if (exists('censorReg')) {
+ lfit1 <- censorReg(censor(time, status) ~ age + ph.ecog + strata(sex),lung)
+ aeq(lfit4$coef, lfit1[[1]]$coef)
+ aeq(lfit4$scale, lfit1[[1]]$scale)
+ aeq(c(lfit4$scale, lfit5$scale), sapply(lfit1, function(x) x$scale))
+ }
+aeq(c(lfit4$scale, lfit5$scale), lfit3$scale )
+
+#
+# Test out ridge regression and splines
+#
+lfit0 <- survreg(Surv(time, status) ~1, lung)
+lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, theta=5), lung)
+lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog, theta=1), lung)
+lfit3 <- survreg(Surv(time, status) ~ sex + age + ph.ecog, lung)
+
+lfit0
+lfit1
+lfit2
+lfit3
+
+
+xx <- pspline(lung$age, nterm=3, theta=.3)
+xx <- matrix(unclass(xx), ncol=ncol(xx)) # the raw matrix
+lfit4 <- survreg(Surv(time, status) ~xx, lung)
+lfit5 <- survreg(Surv(time, status) ~age, lung)
+
+lfit6 <- survreg(Surv(time, status)~pspline(age, df=2), lung)
+
+lfit7 <- survreg(Surv(time, status) ~ offset(lfit6$lin), lung)
+
+lfit4
+lfit5
+lfit6
+signif(lfit7$coef,6)
diff --git a/win32/deps/library/survival/tests/r_lung.Rout.save b/win32/deps/library/survival/tests/r_lung.Rout.save
new file mode 100644
index 0000000..afe217f
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_lung.Rout.save
@@ -0,0 +1,165 @@
+
+R version 2.14.0 (2011-10-31)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+>
+> lfit2 <- survreg(Surv(time, status) ~ age + ph.ecog + strata(sex), lung)
+> lfit3 <- survreg(Surv(time, status) ~ sex + (age+ph.ecog)*strata(sex), lung)
+>
+> lfit4 <- survreg(Surv(time, status) ~ age + ph.ecog , lung,
++ subset=(sex==1))
+> lfit5 <- survreg(Surv(time, status) ~ age + ph.ecog , lung,
++ subset=(sex==2))
+>
+> if (exists('censorReg')) {
++ lfit1 <- censorReg(censor(time, status) ~ age + ph.ecog + strata(sex),lung)
++ aeq(lfit4$coef, lfit1[[1]]$coef)
++ aeq(lfit4$scale, lfit1[[1]]$scale)
++ aeq(c(lfit4$scale, lfit5$scale), sapply(lfit1, function(x) x$scale))
++ }
+> aeq(c(lfit4$scale, lfit5$scale), lfit3$scale )
+[1] TRUE
+>
+> #
+> # Test out ridge regression and splines
+> #
+> lfit0 <- survreg(Surv(time, status) ~1, lung)
+> lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, theta=5), lung)
+> lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog, theta=1), lung)
+> lfit3 <- survreg(Surv(time, status) ~ sex + age + ph.ecog, lung)
+>
+> lfit0
+Call:
+survreg(formula = Surv(time, status) ~ 1, data = lung)
+
+Coefficients:
+(Intercept)
+ 6.034904
+
+Scale= 0.7593936
+
+Loglik(model)= -1153.9 Loglik(intercept only)= -1153.9
+n= 228
+> lfit1
+Call:
+survreg(formula = Surv(time, status) ~ age + ridge(ph.ecog, theta = 5),
+ data = lung)
+
+ coef se(coef) se2 Chisq DF p
+(Intercept) 6.83082 0.42860 0.42860 254.0 1 0.00000
+age -0.00783 0.00687 0.00687 1.3 1 0.25000
+ridge(ph.ecog) -0.32032 0.08484 0.08405 14.2 1 0.00016
+
+Scale= 0.738
+
+Iterations: 1 outer, 5 Newton-Raphson
+Degrees of freedom for terms= 1 1 1 1
+Likelihood ratio test=18.6 on 2 df, p=8.73e-05
+ n=227 (1 observation deleted due to missingness)
+> lfit2
+Call:
+survreg(formula = Surv(time, status) ~ sex + ridge(age, ph.ecog,
+ theta = 1), data = lung)
+
+ coef se(coef) se2 Chisq DF p
+(Intercept) 6.27163 0.45280 0.45210 191.84 1 0.0e+00
+sex 0.40096 0.12371 0.12371 10.50 1 1.2e-03
+ridge(age) -0.00746 0.00675 0.00674 1.22 1 2.7e-01
+ridge(ph.ecog) -0.33848 0.08329 0.08314 16.51 1 4.8e-05
+
+Scale= 0.731
+
+Iterations: 1 outer, 6 Newton-Raphson
+Degrees of freedom for terms= 1 1 2 1
+Likelihood ratio test=30 on 3 df, p=1.37e-06
+ n=227 (1 observation deleted due to missingness)
+> lfit3
+Call:
+survreg(formula = Surv(time, status) ~ sex + age + ph.ecog, data = lung)
+
+Coefficients:
+ (Intercept) sex age ph.ecog
+ 6.273435252 0.401090541 -0.007475439 -0.339638098
+
+Scale= 0.731109
+
+Loglik(model)= -1132.4 Loglik(intercept only)= -1147.4
+ Chisq= 29.98 on 3 degrees of freedom, p= 1.4e-06
+n=227 (1 observation deleted due to missingness)
+>
+>
+> xx <- pspline(lung$age, nterm=3, theta=.3)
+> xx <- matrix(unclass(xx), ncol=ncol(xx)) # the raw matrix
+> lfit4 <- survreg(Surv(time, status) ~xx, lung)
+> lfit5 <- survreg(Surv(time, status) ~age, lung)
+>
+> lfit6 <- survreg(Surv(time, status)~pspline(age, df=2), lung)
+>
+> lfit7 <- survreg(Surv(time, status) ~ offset(lfit6$lin), lung)
+>
+> lfit4
+Call:
+survreg(formula = Surv(time, status) ~ xx, data = lung)
+
+Coefficients:
+(Intercept) xx1 xx2 xx3 xx4 xx5
+ 13.551290 -7.615741 -7.424565 -7.533378 -7.571272 -14.527489
+
+Scale= 0.755741
+
+Loglik(model)= -1150.1 Loglik(intercept only)= -1153.9
+ Chisq= 7.52 on 5 degrees of freedom, p= 0.19
+n= 228
+> lfit5
+Call:
+survreg(formula = Surv(time, status) ~ age, data = lung)
+
+Coefficients:
+(Intercept) age
+ 6.88712062 -0.01360829
+
+Scale= 0.7587515
+
+Loglik(model)= -1151.9 Loglik(intercept only)= -1153.9
+ Chisq= 3.91 on 1 degrees of freedom, p= 0.048
+n= 228
+> lfit6
+Call:
+survreg(formula = Surv(time, status) ~ pspline(age, df = 2),
+ data = lung)
+
+ coef se(coef) se2 Chisq DF p
+(Intercept) 6.5918 0.63681 0.41853 107.15 1.00 0.000
+pspline(age, df = 2), lin -0.0136 0.00687 0.00687 3.94 1.00 0.047
+pspline(age, df = 2), non 0.78 1.06 0.400
+
+Scale= 0.756
+
+Iterations: 4 outer, 12 Newton-Raphson
+ Theta= 0.926
+Degrees of freedom for terms= 0.4 2.1 1.0
+Likelihood ratio test=5.2 on 1.5 df, p=0.0441 n= 228
+> signif(lfit7$coef,6)
+(Intercept)
+1.47899e-09
+>
diff --git a/win32/deps/library/survival/tests/r_peterson.R b/win32/deps/library/survival/tests/r_peterson.R
new file mode 100644
index 0000000..37c7039
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_peterson.R
@@ -0,0 +1,44 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Data courtesy of Bercedis Peterson, Duke University.
+# v4 of survreg fails due to 2 groups that have only 1 subject; the coef
+# for them easily gets out of hand. In fact, this data set is my toughest
+# test of the minimizer.
+#
+# A shrinkage model for this coefficient is therefore interesting
+
+
+peterson <- data.frame(
+ scan('data.peterson', what=list(grp=0, time=0, status=0)))
+
+fitp <- survreg(Surv(time, status) ~ factor(grp), peterson)
+summary(fitp)
+
+# Now a shrinkage model. Give the group coefficients
+# about 1/2 the scale parameter of the original model, i.e., .18.
+#
+ffit <- survreg(Surv(time, status) ~ frailty(grp, theta=.1), peterson)
+ffit
+
+#
+# Try 3 degrees of freedom, since there are 6 groups
+# compare them to the unconstrained ones. The frailty coefs are
+# on a "sum to constant" constraint rather than "first coef=0", so
+# some conversion is neccessary
+#
+ffit3 <- survreg(Surv(time, status) ~ frailty(grp, df=3), peterson)
+print(ffit3)
+
+temp <- mean(c(0, fitp$coef[-1])) - mean(ffit3$frail)
+temp2 <- c(fitp$coef[1] + temp, c(0,fitp$coef[-1]) - temp)
+xx <- rbind(c(nrow(peterson), table(peterson$grp)),
+ temp2,
+ c(ffit3$coef, ffit3$frail))
+dimnames(xx) <- list(c("N", "factor", "frailty"),
+ c("Intercept", paste("grp", 1:6)))
+signif(xx,3)
+
+rm(ffit, ffit3, temp, temp2, xx, fitp)
diff --git a/win32/deps/library/survival/tests/r_peterson.Rout.save b/win32/deps/library/survival/tests/r_peterson.Rout.save
new file mode 100644
index 0000000..f496b54
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_peterson.Rout.save
@@ -0,0 +1,117 @@
+
+R version 2.14.0 Under development (unstable) (2011-04-10 r55401)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Data courtesy of Bercedis Peterson, Duke University.
+> # v4 of survreg fails due to 2 groups that have only 1 subject; the coef
+> # for them easily gets out of hand. In fact, this data set is my toughest
+> # test of the minimizer.
+> #
+> # A shrinkage model for this coefficient is therefore interesting
+>
+>
+> peterson <- data.frame(
++ scan('data.peterson', what=list(grp=0, time=0, status=0)))
+Read 19 records
+>
+> fitp <- survreg(Surv(time, status) ~ factor(grp), peterson)
+> summary(fitp)
+
+Call:
+survreg(formula = Surv(time, status) ~ factor(grp), data = peterson)
+ Value Std. Error z p
+(Intercept) 2.291 0.115 19.92 2.93e-88
+factor(grp)2 0.786 0.177 4.44 8.79e-06
+factor(grp)3 0.728 0.183 3.97 7.09e-05
+factor(grp)4 -1.598 0.218 -7.32 2.48e-13
+factor(grp)5 -0.500 0.218 -2.29 2.21e-02
+factor(grp)6 0.475 0.170 2.79 5.23e-03
+Log(scale) -1.684 0.257 -6.54 6.09e-11
+
+Scale= 0.186
+
+Weibull distribution
+Loglik(model)= -26.7 Loglik(intercept only)= -40.7
+ Chisq= 28.18 on 5 degrees of freedom, p= 3.4e-05
+Number of Newton-Raphson Iterations: 9
+n= 19
+
+>
+> # Now a shrinkage model. Give the group coefficients
+> # about 1/2 the scale parameter of the original model, i.e., .18.
+> #
+> ffit <- survreg(Surv(time, status) ~ frailty(grp, theta=.1), peterson)
+> ffit
+Call:
+survreg(formula = Surv(time, status) ~ frailty(grp, theta = 0.1),
+ data = peterson)
+
+ coef se(coef) se2 Chisq DF p
+(Intercept) 2.62 0.172 0.0874 232.0 1.00 0.0000
+frailty(grp, theta = 0.1) 10.4 2.15 0.0067
+
+Scale= 0.301
+
+Iterations: 1 outer, 6 Newton-Raphson
+ Variance of random effect= 0.1 I-likelihood = -11.8
+Degrees of freedom for terms= 0.3 2.2 0.7
+Likelihood ratio test=13.8 on 1.1 df, p=0.00027 n= 19
+>
+> #
+> # Try 3 degrees of freedom, since there are 6 groups
+> # compare them to the unconstrained ones. The frailty coefs are
+> # on a "sum to constant" constraint rather than "first coef=0", so
+> # some conversion is neccessary
+> #
+> ffit3 <- survreg(Surv(time, status) ~ frailty(grp, df=3), peterson)
+> print(ffit3)
+Call:
+survreg(formula = Surv(time, status) ~ frailty(grp, df = 3),
+ data = peterson)
+
+ coef se(coef) se2 Chisq DF p
+(Intercept) 2.54 0.187 0.0685 184.1 1.00 0.00000
+frailty(grp, df = 3) 16.7 3.06 0.00088
+
+Scale= 0.227
+
+Iterations: 6 outer, 32 Newton-Raphson
+ Variance of random effect= 0.17 I-likelihood = -10.1
+Degrees of freedom for terms= 0.1 3.1 0.3
+Likelihood ratio test=22.9 on 1.5 df, p=4.58e-06 n= 19
+>
+> temp <- mean(c(0, fitp$coef[-1])) - mean(ffit3$frail)
+> temp2 <- c(fitp$coef[1] + temp, c(0,fitp$coef[-1]) - temp)
+> xx <- rbind(c(nrow(peterson), table(peterson$grp)),
++ temp2,
++ c(ffit3$coef, ffit3$frail))
+> dimnames(xx) <- list(c("N", "factor", "frailty"),
++ c("Intercept", paste("grp", 1:6)))
+> signif(xx,3)
+ Intercept grp 1 grp 2 grp 3 grp 4 grp 5 grp 6
+N 19.00 3.000 6.000 6.000 1.00 1.000 2.000
+factor 2.43 -0.137 0.649 0.591 -1.74 -0.636 0.338
+frailty 2.54 -0.255 0.474 0.438 -1.21 -0.554 0.180
+>
+> rm(ffit, ffit3, temp, temp2, xx, fitp)
+>
diff --git a/win32/deps/library/survival/tests/r_resid.R b/win32/deps/library/survival/tests/r_resid.R
new file mode 100644
index 0000000..ead044e
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_resid.R
@@ -0,0 +1,109 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+
+fit1 <- survreg(Surv(futime, fustat) ~ age + ecog.ps, ovarian)
+fit4 <- survreg(Surv(log(futime), fustat) ~age + ecog.ps, ovarian,
+ dist='extreme')
+
+print(fit1)
+summary(fit4)
+
+
+# Hypothesis (and I'm fairly sure): censorReg shares the fault of many
+# iterative codes -- it returns the loglik and variance for iteration k
+# but the coef vector of iteration k+1. Hence the "all.equal" tests
+# below don't come out perfect.
+#
+if (exists('censorReg')) { #true for Splus, not R
+ fit2 <- censorReg(censor(futime, fustat) ~ age + ecog.ps, ovarian)
+ fit3 <- survreg(Surv(futime, fustat) ~ age + ecog.ps, ovarian,
+ iter=0, init=c(fit2$coef, log(fit2$scale)))
+
+ aeq(resid(fit2, type='working')[,1], resid(fit3, type='working'))
+ aeq(resid(fit2, type='response')[,1], resid(fit3, type='response'))
+
+ temp <- sign(resid(fit3, type='working'))
+ aeq(resid(fit2, type='deviance')[,1],
+ temp*abs(resid(fit3, type='deviance')))
+ aeq(resid(fit2, type='deviance')[,1], resid(fit3, type='deviance'))
+ }
+#
+# Now check fit1 and fit4, which should follow identical iteration paths
+# These tests should all be true
+#
+aeq(fit1$coef, fit4$coef)
+
+resid(fit1, type='working')
+resid(fit1, type='response')
+resid(fit1, type='deviance')
+resid(fit1, type='dfbeta')
+resid(fit1, type='dfbetas')
+resid(fit1, type='ldcase')
+resid(fit1, type='ldresp')
+resid(fit1, type='ldshape')
+resid(fit1, type='matrix')
+
+aeq(resid(fit1, type='working'),resid(fit4, type='working'))
+#aeq(resid(fit1, type='response'), resid(fit4, type='response'))#should differ
+aeq(resid(fit1, type='deviance'), resid(fit4, type='deviance'))
+aeq(resid(fit1, type='dfbeta'), resid(fit4, type='dfbeta'))
+aeq(resid(fit1, type='dfbetas'), resid(fit4, type='dfbetas'))
+aeq(resid(fit1, type='ldcase'), resid(fit4, type='ldcase'))
+aeq(resid(fit1, type='ldresp'), resid(fit4, type='ldresp'))
+aeq(resid(fit1, type='ldshape'), resid(fit4, type='ldshape'))
+aeq(resid(fit1, type='matrix'), resid(fit4, type='matrix'))
+#
+# Some tests of the quantile residuals
+#
+motor <- read.table('data.motor', col.names=c('temp', 'time', 'status'))
+
+# These should agree exactly with Ripley and Venables' book
+fit1 <- survreg(Surv(time, status) ~ temp, data=motor)
+summary(fit1)
+
+#
+# The first prediction has the SE that I think is correct
+# The third is the se found in an early draft of Ripley; fit1 ignoring
+# the variation in scale estimate, except via it's impact on the
+# upper left corner of the inverse information matrix.
+# Numbers 1 and 3 differ little for this dataset
+#
+predict(fit1, data.frame(temp=130), type='uquantile', p=c(.5, .1), se=T)
+
+fit2 <- survreg(Surv(time, status) ~ temp, data=motor, scale=fit1$scale)
+predict(fit2, data.frame(temp=130), type='uquantile', p=c(.5, .1), se=T)
+
+fit3 <- fit2
+fit3$var <- fit1$var[1:2,1:2]
+predict(fit3, data.frame(temp=130), type='uquantile', p=c(.5, .1), se=T)
+
+pp <- seq(.05, .7, length=40)
+xx <- predict(fit1, data.frame(temp=130), type='uquantile', se=T,
+ p=pp)
+#matplot(pp, cbind(xx$fit, xx$fit+2*xx$se, xx$fit - 2*xx$se), type='l')
+
+
+#
+# Now try out the various combinations of strata, #predicted, and
+# number of quantiles desired
+#
+fit1 <- survreg(Surv(time, status) ~ inst + strata(inst) + age + sex, lung)
+qq1 <- predict(fit1, type='quantile', p=.3, se=T)
+qq2 <- predict(fit1, type='quantile', p=c(.2, .3, .4), se=T)
+aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+aeq(qq1$fit, qq2$fit[,2])
+aeq(qq1$se.fit, qq2$se.fit[,2])
+
+qq3 <- predict(fit1, type='quantile', p=c(.2, .3, .4), se=T,
+ newdata= lung[1:5,])
+aeq(qq3$fit, qq2$fit[1:5,])
+
+qq4 <- predict(fit1, type='quantile', p=c(.2, .3, .4), se=T, newdata=lung[7,])
+aeq(qq4$fit, qq2$fit[7,])
+
+qq5 <- predict(fit1, type='quantile', p=c(.2, .3, .4), se=T, newdata=lung)
+aeq(qq2$fit, qq5$fit)
+aeq(qq2$se.fit, qq5$se.fit)
diff --git a/win32/deps/library/survival/tests/r_resid.Rout.save b/win32/deps/library/survival/tests/r_resid.Rout.save
new file mode 100644
index 0000000..d223f90
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_resid.Rout.save
@@ -0,0 +1,348 @@
+
+R version 2.7.1 (2008-06-23)
+Copyright (C) 2008 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+>
+> fit1 <- survreg(Surv(futime, fustat) ~ age + ecog.ps, ovarian)
+> fit4 <- survreg(Surv(log(futime), fustat) ~age + ecog.ps, ovarian,
++ dist='extreme')
+>
+> print(fit1)
+Call:
+survreg(formula = Surv(futime, fustat) ~ age + ecog.ps, data = ovarian)
+
+Coefficients:
+(Intercept) age ecog.ps
+12.28496723 -0.09702669 0.09977342
+
+Scale= 0.6032744
+
+Loglik(model)= -90 Loglik(intercept only)= -98
+ Chisq= 15.98 on 2 degrees of freedom, p= 0.00034
+n= 26
+> summary(fit4)
+
+Call:
+survreg(formula = Surv(log(futime), fustat) ~ age + ecog.ps,
+ data = ovarian, dist = "extreme")
+ Value Std. Error z p
+(Intercept) 12.2850 1.5015 8.182 2.80e-16
+age -0.0970 0.0235 -4.127 3.67e-05
+ecog.ps 0.0998 0.3657 0.273 7.85e-01
+Log(scale) -0.5054 0.2351 -2.149 3.16e-02
+
+Scale= 0.603
+
+Extreme value distribution
+Loglik(model)= -21.8 Loglik(intercept only)= -29.8
+ Chisq= 15.98 on 2 degrees of freedom, p= 0.00034
+Number of Newton-Raphson Iterations: 5
+n= 26
+
+>
+>
+> # Hypothesis (and I'm fairly sure): censorReg shares the fault of many
+> # iterative codes -- it returns the loglik and variance for iteration k
+> # but the coef vector of iteration k+1. Hence the "all.equal" tests
+> # below don't come out perfect.
+> #
+> if (exists('censorReg')) { #true for Splus, not R
++ fit2 <- censorReg(censor(futime, fustat) ~ age + ecog.ps, ovarian)
++ fit3 <- survreg(Surv(futime, fustat) ~ age + ecog.ps, ovarian,
++ iter=0, init=c(fit2$coef, log(fit2$scale)))
++
++ aeq(resid(fit2, type='working')[,1], resid(fit3, type='working'))
++ aeq(resid(fit2, type='response')[,1], resid(fit3, type='response'))
++
++ temp <- sign(resid(fit3, type='working'))
++ aeq(resid(fit2, type='deviance')[,1],
++ temp*abs(resid(fit3, type='deviance')))
++ aeq(resid(fit2, type='deviance')[,1], resid(fit3, type='deviance'))
++ }
+> #
+> # Now check fit1 and fit4, which should follow identical iteration paths
+> # These tests should all be true
+> #
+> aeq(fit1$coef, fit4$coef)
+[1] TRUE
+>
+> resid(fit1, type='working')
+ 1 2 3 4 5 6
+ -4.5081778 -0.5909810 -2.4878519 0.6032744 -5.8993431 0.6032744
+ 7 8 9 10 11 12
+ -1.7462937 -0.8102883 0.6032744 -1.6593962 -0.8235265 0.6032744
+ 13 14 15 16 17 18
+ 0.6032744 0.6032744 0.6032744 0.6032744 0.6032744 0.6032744
+ 19 20 21 22 23 24
+ 0.6032744 0.6032744 0.6032744 0.2572623 -31.8006867 -0.7426277
+ 25 26
+ -0.2857597 0.6032744
+> resid(fit1, type='response')
+ 1 2 3 4 5 6
+ -155.14523 -58.62744 -262.03173 -927.79842 -1377.84908 -658.86626
+ 7 8 9 10 11 12
+ -589.74449 -318.93436 4.50671 -686.83338 -434.39281 -1105.68733
+ 13 14 15 16 17 18
+ -42.43371 -173.09223 -4491.29974 -3170.49394 -5028.31053 -2050.91373
+ 19 20 21 22 23 24
+ -150.65033 -2074.09345 412.32400 76.35826 -3309.40331 -219.81579
+ 25 26
+ -96.19691 -457.76731
+> resid(fit1, type='deviance')
+ 1 2 3 4 5 6 7
+-1.5842290 -0.6132746 -1.2876971 0.5387840 -1.7148539 0.6682580 -1.1102921
+ 8 9 10 11 12 13 14
+-0.7460191 1.4253843 -1.0849419 -0.7531720 0.6648130 1.3526380 1.1954382
+ 15 16 17 18 19 20 21
+ 0.2962391 0.3916044 0.3278067 0.5929057 1.2747643 0.6171130 1.9857606
+ 22 23 24 25 26
+ 0.6125492 -2.4504208 -0.7080652 -0.3642424 0.7317955
+> resid(fit1, type='dfbeta')
+ (Intercept) age ecog.ps Log(scale)
+1 0.43370970 -1.087867e-02 0.126322520 0.048379059
+2 0.14426449 -5.144770e-03 0.088768478 -0.033939677
+3 0.25768057 -3.066698e-03 -0.066578834 0.021817646
+4 0.05772598 -5.068044e-04 -0.013121427 -0.007762466
+5 -0.58773456 6.676156e-03 0.084189274 0.008064026
+6 0.01499533 -7.881949e-04 0.026570173 -0.013513160
+7 -0.17869321 4.126121e-03 -0.072760519 -0.015006956
+8 -0.11851540 2.520303e-03 -0.045549628 -0.035686269
+9 0.08327656 3.206404e-03 -0.141835350 0.024490806
+10 -0.25083921 5.321702e-03 -0.073986269 -0.020648720
+11 -0.21333934 4.155746e-03 -0.049832434 -0.040215681
+12 0.13889770 -1.586136e-03 -0.019701151 -0.004686340
+13 0.07892133 -2.706713e-03 0.085242459 0.007847879
+14 0.29690157 -1.987141e-03 -0.085553120 0.017447343
+15 0.04344618 -6.319243e-04 -0.001944285 -0.003533279
+16 0.04866809 -1.068317e-03 0.012398602 -0.006340983
+17 0.04368104 -9.248316e-04 0.009428718 -0.004869178
+18 0.15684611 -2.081485e-03 -0.013068320 -0.003265399
+19 0.48839511 -4.775829e-03 -0.093258090 0.032703354
+20 0.17598922 -2.349254e-03 -0.014202966 -0.002486428
+21 0.37869758 -8.442011e-03 0.163476417 0.100850775
+22 -0.59761427 8.803638e-03 0.052784598 -0.053085234
+23 -0.79017984 1.092304e-02 0.053690092 0.080780399
+24 -0.02348526 8.331002e-04 -0.039028433 -0.032765737
+25 -0.13948485 3.687927e-04 0.056781884 -0.055647859
+26 0.05778937 3.766350e-06 -0.029232389 -0.008927920
+> resid(fit1, type='dfbetas')
+ [,1] [,2] [,3] [,4]
+1 0.288846658 -0.4627232074 0.345395116 0.20574292
+2 0.096078819 -0.2188323823 0.242713641 -0.14433617
+3 0.171612884 -0.1304417700 -0.182041999 0.09278449
+4 0.038444974 -0.0215568869 -0.035877029 -0.03301165
+5 -0.391425795 0.2839697749 0.230193032 0.03429410
+6 0.009986751 -0.0335258093 0.072649027 -0.05746778
+7 -0.119008027 0.1755042532 -0.198944162 -0.06382048
+8 -0.078930164 0.1072008799 -0.124543264 -0.15176395
+9 0.055461420 0.1363841532 -0.387810796 0.10415271
+10 -0.167056601 0.2263581990 -0.202295647 -0.08781336
+11 -0.142082031 0.1767643342 -0.136253451 -0.17102630
+12 0.092504589 -0.0674661531 -0.053867524 -0.01992972
+13 0.052560878 -0.1151298322 0.233072686 0.03337488
+14 0.197733705 -0.0845228882 -0.233922105 0.07419878
+15 0.028934753 -0.0268788526 -0.005316126 -0.01502607
+16 0.032412497 -0.0454407662 0.033900659 -0.02696647
+17 0.029091172 -0.0393376416 0.025780305 -0.02070728
+18 0.104458066 -0.0885357994 -0.035731824 -0.01388685
+19 0.325266641 -0.2031395176 -0.254989284 0.13907843
+20 0.117207199 -0.0999253459 -0.038834208 -0.01057410
+21 0.252209096 -0.3590802699 0.446982501 0.42889079
+22 -0.398005596 0.3744620571 0.144325354 -0.22575700
+23 -0.526252483 0.4646108448 0.146801184 0.34353696
+24 -0.015640965 0.0354358527 -0.106712804 -0.13934372
+25 -0.092895624 0.0156865706 0.155254862 -0.23665514
+26 0.038487186 0.0001602014 -0.079928144 -0.03796800
+> resid(fit1, type='ldcase')
+ 1 2 3 4 5 6
+0.374432175 0.145690278 0.112678800 0.006399163 0.261176992 0.013280058
+ 7 8 9 10 11 12
+0.109842490 0.074103234 0.248285282 0.128482147 0.094038203 0.016111951
+ 13 14 15 16 17 18
+0.132812463 0.111857574 0.001698300 0.004730718 0.003131173 0.015840667
+ 19 20 21 22 23 24
+0.179925399 0.019071941 0.797119488 0.233096445 0.666613755 0.062959708
+ 25 26
+0.080117437 0.015922378
+> resid(fit1, type='ldresp')
+ 1 2 3 4 5 6
+0.076910173 0.173810883 0.078356928 0.005310644 0.060742612 0.010002154
+ 7 8 9 10 11 12
+0.067356838 0.067065693 0.355103899 0.067043195 0.068142828 0.016740944
+ 13 14 15 16 17 18
+0.193444572 0.165021262 0.001494685 0.004083386 0.002767560 0.016400993
+ 19 20 21 22 23 24
+0.269571809 0.020129806 1.409736499 1.040266083 0.058637282 0.071819025
+ 25 26
+0.112702844 0.015105534
+> resid(fit1, type='ldshape')
+ 1 2 3 4 5 6
+0.870628250 0.383362440 0.412503605 0.005534970 0.513991064 0.003310847
+ 7 8 9 10 11 12
+0.291860593 0.154910362 0.256160646 0.312329770 0.183191309 0.004184904
+ 13 14 15 16 17 18
+0.110215710 0.049299495 0.007678445 0.011633336 0.011588605 0.008641251
+ 19 20 21 22 23 24
+0.112967758 0.008271358 2.246729275 0.966929220 1.022043272 0.143857170
+ 25 26
+0.079754096 0.001606647
+> resid(fit1, type='matrix')
+ g dg ddg ds dds dsg
+1 -1.74950763 -1.46198129 -0.32429540 0.88466493 -2.42358635 1.8800360
+2 -0.68266980 -0.82027857 -1.38799493 -0.66206188 -0.57351872 1.3921043
+3 -1.32369884 -1.33411374 -0.53625126 0.31503768 -1.83606321 1.8626973
+4 -0.14514412 0.24059386 -0.39881329 -0.28013223 -0.26053084 0.2237590
+5 -1.96497889 -1.50383619 -0.25491587 1.15700933 -2.68145423 1.8694717
+6 -0.22328436 0.37012071 -0.61351964 -0.33477229 -0.16715487 0.1848047
+7 -1.11099124 -1.23201028 -0.70550005 0.01052036 -1.48515401 1.8106760
+8 -0.77288913 -0.95018808 -1.17265428 -0.51190170 -0.79753045 1.5525642
+9 -1.01586016 1.68391053 -2.79128447 0.01598527 -0.01623681 -1.7104080
+10 -1.08316634 -1.21566480 -0.73259465 -0.03052447 -1.43539383 1.7998987
+11 -0.77825093 -0.95675178 -1.16177415 -0.50314979 -0.81016011 1.5600720
+12 -0.22098818 0.36631452 -0.60721042 -0.33361394 -0.17002503 0.1866908
+13 -0.91481479 1.51641567 -2.51364157 -0.08144930 0.07419757 -1.3814037
+14 -0.71453621 1.18442981 -1.96333502 -0.24017106 0.15944438 -0.7863174
+15 -0.04387880 0.07273440 -0.12056602 -0.13717935 -0.29168773 0.1546569
+16 -0.07667699 0.12710134 -0.21068577 -0.19691828 -0.30879813 0.1993144
+17 -0.05372862 0.08906165 -0.14763041 -0.15709224 -0.30221555 0.1713377
+18 -0.17576861 0.29135764 -0.48296037 -0.30558900 -0.22570402 0.2151929
+19 -0.81251205 1.34683655 -2.23254376 -0.16869744 0.13367171 -1.0672002
+20 -0.19041424 0.31563454 -0.52320225 -0.31581218 -0.20797917 0.2078622
+21 -1.97162252 3.26820173 -5.41743790 1.33844939 -2.24706488 -5.4868428
+22 -0.68222519 1.23245193 -4.79064290 -0.58668577 -0.95209805 -2.8390386
+23 -3.49689798 -1.62675999 -0.05115487 2.90949868 -4.20494743 1.7496975
+24 -0.74529506 -0.91462436 -1.23160543 -0.55723389 -0.73139169 1.5108398
+25 -0.56095318 -0.53280415 -1.86451840 -0.87536233 -0.22666819 0.9689667
+26 -0.26776235 0.44384834 -0.73573207 -0.35281852 -0.11207472 0.1409908
+>
+> aeq(resid(fit1, type='working'),resid(fit4, type='working'))
+[1] TRUE
+> #aeq(resid(fit1, type='response'), resid(fit4, type='response'))#should differ
+> aeq(resid(fit1, type='deviance'), resid(fit4, type='deviance'))
+[1] TRUE
+> aeq(resid(fit1, type='dfbeta'), resid(fit4, type='dfbeta'))
+[1] TRUE
+> aeq(resid(fit1, type='dfbetas'), resid(fit4, type='dfbetas'))
+[1] TRUE
+> aeq(resid(fit1, type='ldcase'), resid(fit4, type='ldcase'))
+[1] TRUE
+> aeq(resid(fit1, type='ldresp'), resid(fit4, type='ldresp'))
+[1] TRUE
+> aeq(resid(fit1, type='ldshape'), resid(fit4, type='ldshape'))
+[1] TRUE
+> aeq(resid(fit1, type='matrix'), resid(fit4, type='matrix'))
+[1] TRUE
+> #
+> # Some tests of the quantile residuals
+> #
+> motor <- read.table('data.motor', col.names=c('temp', 'time', 'status'))
+>
+> # These should agree exactly with Ripley and Venables' book
+> fit1 <- survreg(Surv(time, status) ~ temp, data=motor)
+> summary(fit1)
+
+Call:
+survreg(formula = Surv(time, status) ~ temp, data = motor)
+ Value Std. Error z p
+(Intercept) 16.3185 0.62296 26.2 3.03e-151
+temp -0.0453 0.00319 -14.2 6.74e-46
+Log(scale) -1.0956 0.21480 -5.1 3.38e-07
+
+Scale= 0.334
+
+Weibull distribution
+Loglik(model)= -147.4 Loglik(intercept only)= -169.5
+ Chisq= 44.32 on 1 degrees of freedom, p= 2.8e-11
+Number of Newton-Raphson Iterations: 7
+n= 40
+
+>
+> #
+> # The first prediction has the SE that I think is correct
+> # The third is the se found in an early draft of Ripley; fit1 ignoring
+> # the variation in scale estimate, except via it's impact on the
+> # upper left corner of the inverse information matrix.
+> # Numbers 1 and 3 differ little for this dataset
+> #
+> predict(fit1, data.frame(temp=130), type='uquantile', p=c(.5, .1), se=T)
+$fit
+[1] 10.306068 9.676248
+
+$se.fit
+[1] 0.2135247 0.2202088
+
+>
+> fit2 <- survreg(Surv(time, status) ~ temp, data=motor, scale=fit1$scale)
+> predict(fit2, data.frame(temp=130), type='uquantile', p=c(.5, .1), se=T)
+$fit
+[1] 10.306068 9.676248
+
+$se.fit
+ 1 1
+0.2057964 0.2057964
+
+>
+> fit3 <- fit2
+> fit3$var <- fit1$var[1:2,1:2]
+> predict(fit3, data.frame(temp=130), type='uquantile', p=c(.5, .1), se=T)
+$fit
+[1] 10.306068 9.676248
+
+$se.fit
+ 1 1
+0.2219959 0.2219959
+
+>
+> pp <- seq(.05, .7, length=40)
+> xx <- predict(fit1, data.frame(temp=130), type='uquantile', se=T,
++ p=pp)
+> #matplot(pp, cbind(xx$fit, xx$fit+2*xx$se, xx$fit - 2*xx$se), type='l')
+>
+>
+> #
+> # Now try out the various combinations of strata, #predicted, and
+> # number of quantiles desired
+> #
+> fit1 <- survreg(Surv(time, status) ~ inst + strata(inst) + age + sex, lung)
+> qq1 <- predict(fit1, type='quantile', p=.3, se=T)
+> qq2 <- predict(fit1, type='quantile', p=c(.2, .3, .4), se=T)
+> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+> aeq(qq1$fit, qq2$fit[,2])
+[1] TRUE
+> aeq(qq1$se.fit, qq2$se.fit[,2])
+[1] TRUE
+>
+> qq3 <- predict(fit1, type='quantile', p=c(.2, .3, .4), se=T,
++ newdata= lung[1:5,])
+> aeq(qq3$fit, qq2$fit[1:5,])
+[1] TRUE
+>
+> qq4 <- predict(fit1, type='quantile', p=c(.2, .3, .4), se=T, newdata=lung[7,])
+> aeq(qq4$fit, qq2$fit[7,])
+[1] TRUE
+>
+> qq5 <- predict(fit1, type='quantile', p=c(.2, .3, .4), se=T, newdata=lung)
+> aeq(qq2$fit, qq5$fit)
+[1] TRUE
+> aeq(qq2$se.fit, qq5$se.fit)
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/r_sas.R b/win32/deps/library/survival/tests/r_sas.R
new file mode 100644
index 0000000..b94e89f
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_sas.R
@@ -0,0 +1,259 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Reproduce example 1 in the SAS lifereg documentation
+#
+
+# this fit doesn't give the same log-lik that they claim
+motor <- read.table('data.motor', col.names=c('temp', 'time', 'status'))
+fit1 <- survreg(Surv(time, status) ~ I(1000/(273.2+temp)), motor,
+ subset=(temp>150), dist='lognormal')
+summary(fit1)
+
+# This one, with the loglik on the transformed scale (the inappropriate
+# scale, Ripley & Venables would argue) does agree.
+# All coefs are of course identical.
+fit2 <- survreg(Surv(log(time), status) ~ I(1000/(273.2+temp)), motor,
+ subset=(temp>150), dist='gaussian')
+
+
+# Give the quantile estimates, which is the lower half of "output 48.1.5"
+# in the SAS 9.2 manual
+
+pp1 <- predict(fit1, newdata=list(temp=c(130,150)), p=c(.1, .5, .9),
+ type='quantile', se=T)
+pp2 <- predict(fit1, newdata=list(temp=c(130,150)), p=c(.1, .5, .9),
+ type='uquantile', se=T)
+pp1
+
+temp130 <- matrix(0, nrow=3, ncol=6)
+temp130[,1] <- pp1$fit[1,]
+temp130[,2] <- pp1$se.fit[1,]
+temp130[,3] <- pp2$fit[1,]
+temp130[,4] <- pp2$se.fit[1,]
+temp130[,5] <- exp(pp2$fit[1,] - 1.64*pp2$se.fit[1,])
+temp130[,6] <- exp(pp2$fit[1,] + 1.64*pp2$se.fit[1,])
+dimnames(temp130) <- list(c("p=.1", "p=.2", "p=.3"),
+ c("Time", "se(time)", "log(time)", "se[log(time)]",
+ "lower 90", "upper 90"))
+print(temp130)
+
+# A set of examples, copied from the manual pages of SAS procedure
+# "reliability", which is part of their QC product.
+#
+
+color <- c("black", "red", "green", "blue", "magenta", "red4",
+ "orange", "DarkGreen", "cyan2", "DarkViolet")
+palette(color)
+pdf(file='reliability.pdf')
+
+#
+# Insulating fluids example
+#
+fluid <- read.table('data.fluid', col.names=c('time', 'voltage'))
+
+# Adding a -1 to the fit just causes the each group to have it's own
+# intercept, rather than a global intercept + constrasts. The strata
+# statement allows each to have a separate scale
+ffit <- survreg(Surv(time) ~ voltage + strata(voltage) -1, fluid)
+
+# Get predicted quantiles at each of the voltages
+# By default predict() would give a line of results for each observation,
+# I only want the unique set of x's, i.e., only 4 cases
+uvolt <- sort(unique(fluid$voltage)) #the unique levels
+plist <- c(1, 2, 5, 1:9 *10, 95, 99)/100
+pred <- predict(ffit, type='quantile', p=plist,
+ newdata=data.frame(voltage=factor(uvolt)))
+tfun <- function(x) log(-log(1-x))
+
+matplot(t(pred), tfun(plist), type='l', log='x', lty=1,
+ col=1:4, yaxt='n')
+axis(2, tfun(plist), format(100*plist), adj=1)
+
+kfit <- survfit(Surv(time) ~ voltage, fluid, type='fleming') #KM fit
+for (i in 1:4) {
+ temp <- kfit[i]
+ points(temp$time, tfun(1-temp$surv), col=i, pch=i)
+ }
+
+# Now a table
+temp <- array(0, dim=c(4,4,4)) #4 groups by 4 parameters by 4 stats
+temp[,1,1] <- ffit$coef # "EV Location" in SAS manual
+temp[,2,1] <- ffit$scale # "EV scale"
+temp[,3,1] <- exp(ffit$coef) # "Weibull Scale"
+temp[,4,1] <- 1/ffit$scale # "Weibull Shape"
+
+temp[,1,2] <- sqrt(diag(ffit$var))[1:4] #standard error
+temp[,2,2] <- sqrt(diag(ffit$var))[5:8] * ffit$scale
+temp[,3,2] <- temp[,1,2] * temp[,3,1]
+temp[,4,2] <- temp[,2,2] / (temp[,2,1])^2
+
+temp[,1,3] <- temp[,1,1] - 1.96*temp[,1,2] #lower conf limits
+temp[,1,4] <- temp[,1,1] + 1.96*temp[,1,2] # upper
+# log(scale) is the natural parameter, in which the routine did its fitting
+# and on which the std errors were computed
+temp[,2, 3] <- exp(log(ffit$scale) - 1.96*sqrt(diag(ffit$var))[5:8])
+temp[,2, 4] <- exp(log(ffit$scale) + 1.96*sqrt(diag(ffit$var))[5:8])
+
+temp[,3, 3:4] <- exp(temp[,1,3:4])
+temp[,4, 3:4] <- 1/temp[,2,4:3]
+
+dimnames(temp) <- list(uvolt, c("EV Location", "EV Scale", "Weibull scale",
+ "Weibull shape"),
+ c("Estimate", "SE", "lower 95% CI", "uppper 95% CI"))
+print(aperm(temp, c(2,3,1)), digits=5)
+
+rm(temp, uvolt, plist, pred, ffit, kfit)
+
+#####################################################################
+# Turbine cracks data
+cracks <- read.table('data.cracks', col.names=c('time1', 'time2', 'n'))
+cfit <- survreg(Surv(time1, time2, type='interval2') ~1,
+ dist='weibull', data=cracks, weight=n)
+
+summary(cfit)
+#Their output also has Wiebull scale = exp(cfit$coef), shape = 1/(cfit$scale)
+
+# Draw the SAS plot
+# The "type=fleming" argument reflects that they estimate hazards rather than
+# survival, and forces a Nelson-Aalen hazard estimate
+#
+plist <- c(1, 2, 5, 1:8 *10)/100
+plot(qsurvreg(plist, cfit$coef, cfit$scale), tfun(plist), log='x',
+ yaxt='n', type='l',
+ xlab="Weibull Plot for Time", ylab="Percent")
+axis(2, tfun(plist), format(100*plist), adj=1)
+
+kfit <- survfit(Surv(time1, time2, type='interval2') ~1, data=cracks,
+ weight=n, type='fleming')
+# Only plot point where n.event > 0
+# Why? I'm trying to match them. Personally, all should be plotted.
+who <- (kfit$n.event > 0)
+points(kfit$time[who], tfun(1-kfit$surv[who]), pch='+')
+points(kfit$time[who], tfun(1-kfit$upper[who]), pch='-')
+points(kfit$time[who], tfun(1-kfit$lower[who]), pch='-')
+
+text(rep(3,6), seq(.5, -1.0, length=6),
+ c("Scale", "Shape", "Right Censored", "Left Censored",
+ "Interval Censored", "Fit"), adj=0)
+text(rep(9,6), seq(.5, -1.0, length=6),
+ c(format(round(exp(cfit$coef), 2)),
+ format(round(1/cfit$scale, 2)),
+ format(tapply(cracks$n, cfit$y[,3], sum)), "ML"), adj=1)
+
+# Now a portion of his percentiles table
+# I don't get the same SE as SAS, I haven't checked out why. The
+# estimates and se for the underlying Weibull model are the same.
+temp <- predict(cfit, type='quantile', p=plist, se=T)
+tempse <- sqrt(temp$se[1,])
+mat <- cbind(temp$fit[1,], tempse,
+ temp$fit[1,] -1.96*tempse, temp$fit[1,] + 1.96*tempse)
+dimnames(mat) <- list(plist*100, c("Estimate", "SE", "Lower .95", "Upper .95"))
+print(mat)
+
+#
+# The cracks data has a particularly easy estimate, so use
+# it to double check code
+time <- c(cracks$time2[1], (cracks$time1 + cracks$time2)[2:8]/2,
+ cracks$time1[9])
+cdf <- cumsum(cracks$n)/sum(cracks$n)
+all.equal(kfit$time, time)
+all.equal(kfit$surv, 1-cdf[c(1:8,8)])
+rm(time, cdf, kfit)
+
+
+#######################################################
+#
+# Valve data
+# The input data has id, time, and an indicator of whether there was an
+# event at that time: -1=no, 1=yes. No one has an event at their last time.
+# Convert the data to (start, stop] form
+# The input data has two engines with dual failures: 328 loses 2 valves at
+# time 653, and number 402 loses 2 at time 139. For each, fudge the first
+# time to be .1 days earlier.
+#
+temp <- matrix(scan('data.valve'), byrow=T, ncol=3)
+
+n <- nrow(temp)
+valve <- data.frame(id=temp[,1],
+ time1 = c(0, ifelse(diff(temp[,1])==0, temp[-n,2],0)),
+ time2 = temp[,2],
+ status= as.numeric(temp[,3]==1))
+
+indx <- (1:nrow(valve))[valve$time1==valve$time2]
+valve$time1[indx] <- valve$time1[indx] - .1
+valve$time2[indx-1] <- valve$time2[indx-1] - .1
+
+kfit <- survfit(Surv(time1, time2, status) ~1, valve, type='fh2')
+
+plot(kfit, fun='cumhaz', ylab="Sample Mean Cumulative Failures", xlab='Time',
+ ylim=range(-log(kfit$lower)))
+title("Valve replacement data")
+
+# The summary.survfit function doesn't have an option for printing out
+# cumulative hazards instead of survival --- need to add that
+# so I just reprise the central code of print.summary.survfit
+xx <- summary(kfit)
+temp <- cbind(xx$time, xx$n.risk, xx$n.event, -log(xx$surv),
+ xx$std.err/xx$surv, -log(xx$upper), -log(xx$lower))
+dimnames(temp) <- list(rep("", nrow(temp)),
+ c("time", "n.risk", "n.event", "Cum haz", "std.err",
+ "lower 95%", "upper 95%"))
+print(temp, digits=2)
+
+# Note that I have the same estimates but different SE's. We are using a
+# different estimator. It's a statistical argument as to which is
+# better (one could defend both sides): do you favor JASA or Technometrics?
+rm(temp, kfit, indx, xx)
+
+######################################################
+# Turbine data, lognormal fit
+turbine <- read.table('data.turbine',
+ col.names=c("time1", "time2", "n"))
+
+tfit <- survreg(Surv(time1, time2, type='interval2') ~1, turbine,
+ dist='lognormal', weights=n, subset=(n>0))
+
+summary(tfit)
+
+# Now, do his plot, but put bootstrap confidence bands on it!
+# First, make a simple data set without weights
+tdata <- turbine[rep(1:nrow(turbine), turbine$n),]
+
+qstat <- function(data) {
+ temp <- survreg(Surv(time1, time2, type='interval2') ~1, data=data,
+ dist='lognormal')
+ qsurvreg(plist, temp$coef, temp$scale, dist='lognormal')
+ }
+
+{if (exists('bootstrap')) {
+ bfit <- bootstrap(tdata, qstat, B=1000)
+ bci <- limits.bca(bfit, probs=c(.025, .975))
+ }
+else {
+ values <- matrix(0, nrow=1000, ncol=length(plist))
+ n <- nrow(tdata)
+ for (i in 1:1000) {
+ subset <- sample(1:n, n, replace=T)
+ values[i,] <- qstat(tdata[subset,])
+ }
+ bci <- t(apply(values,2, quantile, c(.05, .95)))
+ }
+ }
+xmat <- cbind(qsurvreg(plist, tfit$coef, tfit$scale, dist='lognormal'),
+ bci)
+
+
+matplot(xmat, qnorm(plist),
+ type='l', lty=c(1,2,2), col=c(1,1,1),
+ log='x', yaxt='n', ylab='Percent',
+ xlab='Time of Cracking (Hours x 100)')
+axis(2, qnorm(plist), format(100*plist), adj=1)
+title("Turbine Data")
+kfit <- survfit(Surv(time1, time2, type='interval2') ~1, data=tdata)
+points(kfit$time, qnorm(1-kfit$surv), pch='+')
+
+dev.off() #close the plot file
+
diff --git a/win32/deps/library/survival/tests/r_sas.Rout.save b/win32/deps/library/survival/tests/r_sas.Rout.save
new file mode 100644
index 0000000..131c6b4
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_sas.Rout.save
@@ -0,0 +1,438 @@
+
+R version 2.12.2 (2011-02-25)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Reproduce example 1 in the SAS lifereg documentation
+> #
+>
+> # this fit doesn't give the same log-lik that they claim
+> motor <- read.table('data.motor', col.names=c('temp', 'time', 'status'))
+> fit1 <- survreg(Surv(time, status) ~ I(1000/(273.2+temp)), motor,
++ subset=(temp>150), dist='lognormal')
+> summary(fit1)
+
+Call:
+survreg(formula = Surv(time, status) ~ I(1000/(273.2 + temp)),
+ data = motor, subset = (temp > 150), dist = "lognormal")
+ Value Std. Error z p
+(Intercept) -10.471 2.772 -3.78 1.58e-04
+I(1000/(273.2 + temp)) 8.322 1.284 6.48 9.13e-11
+Log(scale) -0.504 0.183 -2.75 5.96e-03
+
+Scale= 0.604
+
+Log Normal distribution
+Loglik(model)= -145.9 Loglik(intercept only)= -155
+ Chisq= 18.3 on 1 degrees of freedom, p= 1.9e-05
+Number of Newton-Raphson Iterations: 6
+n= 30
+
+>
+> # This one, with the loglik on the transformed scale (the inappropriate
+> # scale, Ripley & Venables would argue) does agree.
+> # All coefs are of course identical.
+> fit2 <- survreg(Surv(log(time), status) ~ I(1000/(273.2+temp)), motor,
++ subset=(temp>150), dist='gaussian')
+>
+>
+> # Give the quantile estimates, which is the lower half of "output 48.1.5"
+> # in the SAS 9.2 manual
+>
+> pp1 <- predict(fit1, newdata=list(temp=c(130,150)), p=c(.1, .5, .9),
++ type='quantile', se=T)
+> pp2 <- predict(fit1, newdata=list(temp=c(130,150)), p=c(.1, .5, .9),
++ type='uquantile', se=T)
+> pp1
+$fit
+ [,1] [,2] [,3]
+[1,] 12033.185 26095.677 56592.20
+[2,] 4536.877 9838.864 21336.98
+
+$se.fit
+ [,1] [,2] [,3]
+[1,] 5482.338 11359.450 26036.917
+[2,] 1443.072 2901.155 7172.343
+
+>
+> temp130 <- matrix(0, nrow=3, ncol=6)
+> temp130[,1] <- pp1$fit[1,]
+> temp130[,2] <- pp1$se.fit[1,]
+> temp130[,3] <- pp2$fit[1,]
+> temp130[,4] <- pp2$se.fit[1,]
+> temp130[,5] <- exp(pp2$fit[1,] - 1.64*pp2$se.fit[1,])
+> temp130[,6] <- exp(pp2$fit[1,] + 1.64*pp2$se.fit[1,])
+> dimnames(temp130) <- list(c("p=.1", "p=.2", "p=.3"),
++ c("Time", "se(time)", "log(time)", "se[log(time)]",
++ "lower 90", "upper 90"))
+> print(temp130)
+ Time se(time) log(time) se[log(time)] lower 90 upper 90
+p=.1 12033.18 5482.338 9.395424 0.4556015 5700.089 25402.68
+p=.2 26095.68 11359.450 10.169525 0.4353001 12779.950 53285.37
+p=.3 56592.20 26036.917 10.943626 0.4600796 26611.422 120349.71
+>
+> # A set of examples, copied from the manual pages of SAS procedure
+> # "reliability", which is part of their QC product.
+> #
+>
+> color <- c("black", "red", "green", "blue", "magenta", "red4",
++ "orange", "DarkGreen", "cyan2", "DarkViolet")
+> palette(color)
+> pdf(file='reliability.pdf')
+>
+> #
+> # Insulating fluids example
+> #
+> fluid <- read.table('data.fluid', col.names=c('time', 'voltage'))
+>
+> # Adding a -1 to the fit just causes the each group to have it's own
+> # intercept, rather than a global intercept + constrasts. The strata
+> # statement allows each to have a separate scale
+> ffit <- survreg(Surv(time) ~ voltage + strata(voltage) -1, fluid)
+>
+> # Get predicted quantiles at each of the voltages
+> # By default predict() would give a line of results for each observation,
+> # I only want the unique set of x's, i.e., only 4 cases
+> uvolt <- sort(unique(fluid$voltage)) #the unique levels
+> plist <- c(1, 2, 5, 1:9 *10, 95, 99)/100
+> pred <- predict(ffit, type='quantile', p=plist,
++ newdata=data.frame(voltage=factor(uvolt)))
+> tfun <- function(x) log(-log(1-x))
+>
+> matplot(t(pred), tfun(plist), type='l', log='x', lty=1,
++ col=1:4, yaxt='n')
+> axis(2, tfun(plist), format(100*plist), adj=1)
+>
+> kfit <- survfit(Surv(time) ~ voltage, fluid, type='fleming') #KM fit
+> for (i in 1:4) {
++ temp <- kfit[i]
++ points(temp$time, tfun(1-temp$surv), col=i, pch=i)
++ }
+>
+> # Now a table
+> temp <- array(0, dim=c(4,4,4)) #4 groups by 4 parameters by 4 stats
+> temp[,1,1] <- ffit$coef # "EV Location" in SAS manual
+> temp[,2,1] <- ffit$scale # "EV scale"
+> temp[,3,1] <- exp(ffit$coef) # "Weibull Scale"
+> temp[,4,1] <- 1/ffit$scale # "Weibull Shape"
+>
+> temp[,1,2] <- sqrt(diag(ffit$var))[1:4] #standard error
+> temp[,2,2] <- sqrt(diag(ffit$var))[5:8] * ffit$scale
+> temp[,3,2] <- temp[,1,2] * temp[,3,1]
+> temp[,4,2] <- temp[,2,2] / (temp[,2,1])^2
+>
+> temp[,1,3] <- temp[,1,1] - 1.96*temp[,1,2] #lower conf limits
+> temp[,1,4] <- temp[,1,1] + 1.96*temp[,1,2] # upper
+> # log(scale) is the natural parameter, in which the routine did its fitting
+> # and on which the std errors were computed
+> temp[,2, 3] <- exp(log(ffit$scale) - 1.96*sqrt(diag(ffit$var))[5:8])
+> temp[,2, 4] <- exp(log(ffit$scale) + 1.96*sqrt(diag(ffit$var))[5:8])
+>
+> temp[,3, 3:4] <- exp(temp[,1,3:4])
+> temp[,4, 3:4] <- 1/temp[,2,4:3]
+>
+> dimnames(temp) <- list(uvolt, c("EV Location", "EV Scale", "Weibull scale",
++ "Weibull shape"),
++ c("Estimate", "SE", "lower 95% CI", "uppper 95% CI"))
+> print(aperm(temp, c(2,3,1)), digits=5)
+, , 26kV
+
+ Estimate SE lower 95% CI uppper 95% CI
+EV Location 6.86249 1.10404 4.69857 9.0264
+EV Scale 1.83423 0.96114 0.65677 5.1227
+Weibull scale 955.74665 1055.18620 109.78973 8320.0103
+Weibull shape 0.54519 0.28568 0.19521 1.5226
+
+, , 30kV
+
+ Estimate SE lower 95% CI uppper 95% CI
+EV Location 4.35133 0.30151 3.76037 4.9423
+EV Scale 0.94446 0.22544 0.59156 1.5079
+Weibull scale 77.58159 23.39176 42.96420 140.0911
+Weibull shape 1.05881 0.25274 0.66318 1.6904
+
+, , 34kV
+
+ Estimate SE lower 95% CI uppper 95% CI
+EV Location 2.50326 0.31476 1.88632 3.1202
+EV Scale 1.29732 0.22895 0.91796 1.8334
+Weibull scale 12.22222 3.84707 6.59509 22.6506
+Weibull shape 0.77082 0.13603 0.54542 1.0894
+
+, , 38kV
+
+ Estimate SE lower 95% CI uppper 95% CI
+EV Location 0.00092629 0.27318 -0.53450 0.53635
+EV Scale 0.73367610 0.20380 0.42565 1.26460
+Weibull scale 1.00092672 0.27343 0.58596 1.70976
+Weibull shape 1.36299929 0.37861 0.79077 2.34933
+
+>
+> rm(temp, uvolt, plist, pred, ffit, kfit)
+>
+> #####################################################################
+> # Turbine cracks data
+> cracks <- read.table('data.cracks', col.names=c('time1', 'time2', 'n'))
+> cfit <- survreg(Surv(time1, time2, type='interval2') ~1,
++ dist='weibull', data=cracks, weight=n)
+>
+> summary(cfit)
+
+Call:
+survreg(formula = Surv(time1, time2, type = "interval2") ~ 1,
+ data = cracks, weights = n, dist = "weibull")
+ Value Std. Error z p
+(Intercept) 4.272 0.0744 57.43 0.00e+00
+Log(scale) -0.396 0.0987 -4.01 6.06e-05
+
+Scale= 0.673
+
+Weibull distribution
+Loglik(model)= -309.7 Loglik(intercept only)= -309.7
+Number of Newton-Raphson Iterations: 5
+n= 9
+
+> #Their output also has Wiebull scale = exp(cfit$coef), shape = 1/(cfit$scale)
+>
+> # Draw the SAS plot
+> # The "type=fleming" argument reflects that they estimate hazards rather than
+> # survival, and forces a Nelson-Aalen hazard estimate
+> #
+> plist <- c(1, 2, 5, 1:8 *10)/100
+> plot(qsurvreg(plist, cfit$coef, cfit$scale), tfun(plist), log='x',
++ yaxt='n', type='l',
++ xlab="Weibull Plot for Time", ylab="Percent")
+> axis(2, tfun(plist), format(100*plist), adj=1)
+>
+> kfit <- survfit(Surv(time1, time2, type='interval2') ~1, data=cracks,
++ weight=n, type='fleming')
+> # Only plot point where n.event > 0
+> # Why? I'm trying to match them. Personally, all should be plotted.
+> who <- (kfit$n.event > 0)
+> points(kfit$time[who], tfun(1-kfit$surv[who]), pch='+')
+> points(kfit$time[who], tfun(1-kfit$upper[who]), pch='-')
+> points(kfit$time[who], tfun(1-kfit$lower[who]), pch='-')
+>
+> text(rep(3,6), seq(.5, -1.0, length=6),
++ c("Scale", "Shape", "Right Censored", "Left Censored",
++ "Interval Censored", "Fit"), adj=0)
+> text(rep(9,6), seq(.5, -1.0, length=6),
++ c(format(round(exp(cfit$coef), 2)),
++ format(round(1/cfit$scale, 2)),
++ format(tapply(cracks$n, cfit$y[,3], sum)), "ML"), adj=1)
+>
+> # Now a portion of his percentiles table
+> # I don't get the same SE as SAS, I haven't checked out why. The
+> # estimates and se for the underlying Weibull model are the same.
+> temp <- predict(cfit, type='quantile', p=plist, se=T)
+> tempse <- sqrt(temp$se[1,])
+> mat <- cbind(temp$fit[1,], tempse,
++ temp$fit[1,] -1.96*tempse, temp$fit[1,] + 1.96*tempse)
+> dimnames(mat) <- list(plist*100, c("Estimate", "SE", "Lower .95", "Upper .95"))
+> print(mat)
+ Estimate SE Lower .95 Upper .95
+1 3.239372 0.965006 1.347960 5.130784
+2 5.183283 1.121677 2.984796 7.381770
+5 9.705766 1.337420 7.084422 12.327109
+10 15.757758 1.491460 12.834497 18.681020
+20 26.115947 1.622573 22.935705 29.296190
+30 35.812585 1.704575 32.471618 39.153553
+40 45.610018 1.809448 42.063500 49.156536
+50 56.014351 1.973350 52.146585 59.882116
+60 67.592818 2.214072 63.253237 71.932400
+70 81.233457 2.543490 76.248217 86.218697
+80 98.764571 2.991889 92.900469 104.628673
+>
+> #
+> # The cracks data has a particularly easy estimate, so use
+> # it to double check code
+> time <- c(cracks$time2[1], (cracks$time1 + cracks$time2)[2:8]/2,
++ cracks$time1[9])
+> cdf <- cumsum(cracks$n)/sum(cracks$n)
+> all.equal(kfit$time, time)
+[1] TRUE
+> all.equal(kfit$surv, 1-cdf[c(1:8,8)])
+[1] TRUE
+> rm(time, cdf, kfit)
+>
+>
+> #######################################################
+> #
+> # Valve data
+> # The input data has id, time, and an indicator of whether there was an
+> # event at that time: -1=no, 1=yes. No one has an event at their last time.
+> # Convert the data to (start, stop] form
+> # The input data has two engines with dual failures: 328 loses 2 valves at
+> # time 653, and number 402 loses 2 at time 139. For each, fudge the first
+> # time to be .1 days earlier.
+> #
+> temp <- matrix(scan('data.valve'), byrow=T, ncol=3)
+Read 267 items
+>
+> n <- nrow(temp)
+> valve <- data.frame(id=temp[,1],
++ time1 = c(0, ifelse(diff(temp[,1])==0, temp[-n,2],0)),
++ time2 = temp[,2],
++ status= as.numeric(temp[,3]==1))
+>
+> indx <- (1:nrow(valve))[valve$time1==valve$time2]
+> valve$time1[indx] <- valve$time1[indx] - .1
+> valve$time2[indx-1] <- valve$time2[indx-1] - .1
+>
+> kfit <- survfit(Surv(time1, time2, status) ~1, valve, type='fh2')
+>
+> plot(kfit, fun='cumhaz', ylab="Sample Mean Cumulative Failures", xlab='Time',
++ ylim=range(-log(kfit$lower)))
+> title("Valve replacement data")
+>
+> # The summary.survfit function doesn't have an option for printing out
+> # cumulative hazards instead of survival --- need to add that
+> # so I just reprise the central code of print.summary.survfit
+> xx <- summary(kfit)
+> temp <- cbind(xx$time, xx$n.risk, xx$n.event, -log(xx$surv),
++ xx$std.err/xx$surv, -log(xx$upper), -log(xx$lower))
+> dimnames(temp) <- list(rep("", nrow(temp)),
++ c("time", "n.risk", "n.event", "Cum haz", "std.err",
++ "lower 95%", "upper 95%"))
+> print(temp, digits=2)
+ time n.risk n.event Cum haz std.err lower 95% upper 95%
+ 61 41 1 0.024 0.025 0.00000 0.073
+ 76 41 1 0.049 0.035 0.00000 0.117
+ 84 41 1 0.073 0.043 0.00000 0.157
+ 87 41 1 0.098 0.049 0.00077 0.194
+ 92 41 1 0.122 0.055 0.01373 0.230
+ 98 41 1 0.146 0.060 0.02779 0.265
+ 120 41 1 0.171 0.065 0.04268 0.299
+ 139 41 1 0.195 0.070 0.05823 0.332
+ 139 41 1 0.220 0.074 0.07432 0.365
+ 165 41 1 0.244 0.078 0.09085 0.397
+ 166 41 1 0.268 0.082 0.10778 0.429
+ 202 41 1 0.293 0.086 0.12503 0.460
+ 206 41 1 0.317 0.089 0.14257 0.492
+ 249 41 1 0.341 0.092 0.16038 0.523
+ 254 41 1 0.366 0.096 0.17841 0.553
+ 258 41 1 0.390 0.099 0.19665 0.584
+ 265 41 1 0.415 0.102 0.21508 0.614
+ 276 41 1 0.439 0.105 0.23369 0.644
+ 298 41 1 0.463 0.108 0.25245 0.674
+ 323 41 1 0.488 0.110 0.27136 0.704
+ 326 41 1 0.512 0.113 0.29041 0.734
+ 328 41 1 0.537 0.116 0.30958 0.764
+ 344 41 1 0.561 0.118 0.32887 0.793
+ 348 41 1 0.585 0.121 0.34827 0.822
+ 349 41 1 0.610 0.123 0.36777 0.852
+ 367 41 1 0.634 0.126 0.38736 0.881
+ 377 41 1 0.659 0.128 0.40705 0.910
+ 404 40 1 0.684 0.131 0.42720 0.940
+ 408 40 1 0.709 0.133 0.44745 0.970
+ 410 40 1 0.734 0.136 0.46777 0.999
+ 449 40 1 0.759 0.138 0.48818 1.029
+ 479 40 1 0.784 0.140 0.50866 1.058
+ 497 40 1 0.809 0.143 0.52922 1.088
+ 538 40 1 0.834 0.145 0.54985 1.117
+ 539 40 1 0.859 0.147 0.57054 1.147
+ 561 40 1 0.884 0.149 0.59129 1.176
+ 563 40 1 0.909 0.151 0.61211 1.205
+ 570 40 1 0.934 0.153 0.63299 1.234
+ 573 40 1 0.959 0.155 0.65392 1.263
+ 581 38 1 0.985 0.158 0.67578 1.294
+ 586 34 1 1.014 0.160 0.69970 1.329
+ 604 22 1 1.060 0.167 0.73221 1.387
+ 621 17 1 1.119 0.178 0.77014 1.467
+ 635 16 1 1.181 0.189 0.81038 1.552
+ 640 16 1 1.244 0.200 0.85188 1.635
+ 646 13 1 1.320 0.215 0.89854 1.742
+ 653 9 1 1.432 0.245 0.95056 1.913
+ 653 9 1 1.543 0.272 1.00909 2.076
+>
+> # Note that I have the same estimates but different SE's. We are using a
+> # different estimator. It's a statistical argument as to which is
+> # better (one could defend both sides): do you favor JASA or Technometrics?
+> rm(temp, kfit, indx, xx)
+>
+> ######################################################
+> # Turbine data, lognormal fit
+> turbine <- read.table('data.turbine',
++ col.names=c("time1", "time2", "n"))
+>
+> tfit <- survreg(Surv(time1, time2, type='interval2') ~1, turbine,
++ dist='lognormal', weights=n, subset=(n>0))
+>
+> summary(tfit)
+
+Call:
+survreg(formula = Surv(time1, time2, type = "interval2") ~ 1,
+ data = turbine, weights = n, subset = (n > 0), dist = "lognormal")
+ Value Std. Error z p
+(Intercept) 3.700 0.0708 52.23 0.00000
+Log(scale) -0.329 0.1232 -2.67 0.00763
+
+Scale= 0.72
+
+Log Normal distribution
+Loglik(model)= -190.7 Loglik(intercept only)= -190.7
+Number of Newton-Raphson Iterations: 6
+n= 21
+
+>
+> # Now, do his plot, but put bootstrap confidence bands on it!
+> # First, make a simple data set without weights
+> tdata <- turbine[rep(1:nrow(turbine), turbine$n),]
+>
+> qstat <- function(data) {
++ temp <- survreg(Surv(time1, time2, type='interval2') ~1, data=data,
++ dist='lognormal')
++ qsurvreg(plist, temp$coef, temp$scale, dist='lognormal')
++ }
+>
+> {if (exists('bootstrap')) {
++ bfit <- bootstrap(tdata, qstat, B=1000)
++ bci <- limits.bca(bfit, probs=c(.025, .975))
++ }
++ else {
++ values <- matrix(0, nrow=1000, ncol=length(plist))
++ n <- nrow(tdata)
++ for (i in 1:1000) {
++ subset <- sample(1:n, n, replace=T)
++ values[i,] <- qstat(tdata[subset,])
++ }
++ bci <- t(apply(values,2, quantile, c(.05, .95)))
++ }
++ }
+> xmat <- cbind(qsurvreg(plist, tfit$coef, tfit$scale, dist='lognormal'),
++ bci)
+>
+>
+> matplot(xmat, qnorm(plist),
++ type='l', lty=c(1,2,2), col=c(1,1,1),
++ log='x', yaxt='n', ylab='Percent',
++ xlab='Time of Cracking (Hours x 100)')
+> axis(2, qnorm(plist), format(100*plist), adj=1)
+> title("Turbine Data")
+> kfit <- survfit(Surv(time1, time2, type='interval2') ~1, data=tdata)
+> points(kfit$time, qnorm(1-kfit$surv), pch='+')
+>
+> dev.off() #close the plot file
+null device
+ 1
+>
+>
diff --git a/win32/deps/library/survival/tests/r_scale.R b/win32/deps/library/survival/tests/r_scale.R
new file mode 100644
index 0000000..26f02b7
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_scale.R
@@ -0,0 +1,30 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Verify that scale can be fixed at a value
+# coefs will differ slightly due to different iteration paths
+tol <- .001
+
+# Intercept only models
+fit1 <- survreg(Surv(time,status) ~ 1, lung)
+fit2 <- survreg(Surv(time,status) ~ 1, lung, scale=fit1$scale)
+all.equal(fit1$coef, fit2$coef, tolerance= tol)
+all.equal(fit1$loglik, fit2$loglik, tolerance= tol)
+
+# multiple covariates
+fit1 <- survreg(Surv(time,status) ~ age + ph.karno, lung)
+fit2 <- survreg(Surv(time,status) ~ age + ph.karno, lung,
+ scale=fit1$scale)
+all.equal(fit1$coef, fit2$coef, tolerance=tol)
+all.equal(fit1$loglik[2], fit2$loglik[2], tolerance=tol)
+
+# penalized models
+fit1 <- survreg(Surv(time, status) ~ pspline(age), lung)
+fit2 <- survreg(Surv(time, status) ~ pspline(age), lung, scale=fit1$scale)
+all.equal(fit1$coef, fit2$coef, tolerance=tol)
+all.equal(fit1$loglik[2], fit2$loglik[2], tolerance=tol)
+
+rm(fit1, fit2, tol)
+
diff --git a/win32/deps/library/survival/tests/r_scale.Rout.save b/win32/deps/library/survival/tests/r_scale.Rout.save
new file mode 100644
index 0000000..0f5f141
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_scale.Rout.save
@@ -0,0 +1,55 @@
+
+R version 2.7.1 (2008-06-23)
+Copyright (C) 2008 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Verify that scale can be fixed at a value
+> # coefs will differ slightly due to different iteration paths
+> tol <- .001
+>
+> # Intercept only models
+> fit1 <- survreg(Surv(time,status) ~ 1, lung)
+> fit2 <- survreg(Surv(time,status) ~ 1, lung, scale=fit1$scale)
+> all.equal(fit1$coef, fit2$coef, tolerance= tol)
+[1] TRUE
+> all.equal(fit1$loglik, fit2$loglik, tolerance= tol)
+[1] TRUE
+>
+> # multiple covariates
+> fit1 <- survreg(Surv(time,status) ~ age + ph.karno, lung)
+> fit2 <- survreg(Surv(time,status) ~ age + ph.karno, lung,
++ scale=fit1$scale)
+> all.equal(fit1$coef, fit2$coef, tolerance=tol)
+[1] TRUE
+> all.equal(fit1$loglik[2], fit2$loglik[2], tolerance=tol)
+[1] TRUE
+>
+> # penalized models
+> fit1 <- survreg(Surv(time, status) ~ pspline(age), lung)
+> fit2 <- survreg(Surv(time, status) ~ pspline(age), lung, scale=fit1$scale)
+> all.equal(fit1$coef, fit2$coef, tolerance=tol)
+[1] TRUE
+> all.equal(fit1$loglik[2], fit2$loglik[2], tolerance=tol)
+[1] TRUE
+>
+> rm(fit1, fit2, tol)
+>
+>
diff --git a/win32/deps/library/survival/tests/r_stanford.R b/win32/deps/library/survival/tests/r_stanford.R
new file mode 100644
index 0000000..c79e0a7
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_stanford.R
@@ -0,0 +1,71 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# The Stanford data from 1980 is used in Escobar and Meeker, Biometrics 1992.
+# t5 = T5 mismatch score
+# Their case numbers correspond to a data set sorted by age
+#
+aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+
+stanford2$t5 <- ifelse(stanford2$t5 <0, NA, stanford2$t5)
+stanford2 <- stanford2[order(stanford2$age, stanford2$time),]
+stanford2$time <- ifelse(stanford2$time==0, .5, stanford2$time)
+
+cage <- stanford2$age - mean(stanford2$age)
+fit1 <- survreg(Surv(time, status) ~ cage + I(cage^2), stanford2,
+ dist='lognormal')
+fit1
+ldcase <- resid(fit1, type='ldcase')
+ldresp <- resid(fit1, type='ldresp')
+# The ldcase and ldresp should be compared to table 1 in Escobar and
+# Meeker, Biometrics 1992, p519; the colums they label as (1/2) A_{ii}
+# They give data for selected cases, entered below as mdata
+mdata <- cbind(c(1,2,4,5,12,16,23,61,66,72,172,182,183,184),
+ c(.035, .244, .141, .159, .194, .402, 0,0, .143, .403,
+ .178, .033, .005, .015),
+ c(.138, .145, .073, .076, .104, .159, 0,0, .109, .184,
+ .116, .063, .103, .144))
+dimnames(mdata) <- list(NULL, c("case#", "ldcase", "ldresp"))
+aeq(round(ldcase[mdata[,1]],3), mdata[,2])
+aeq(round(ldresp[mdata[,1]],3), mdata[,3])
+
+plot1 <- function() {
+ # make their figure 1, 2, and 6
+ temp <- predict(fit1, type='quantile', p=c(.1, .5, .9))
+ plot(stanford2$age, stanford2$time, log='y', xlab="Age", ylab="Days",
+ ylim=range(stanford2$time, temp))
+ matlines(stanford2$age, temp, lty=c(1,2,2), col=1)
+
+ n <- length(ldcase)
+ plot(1:n, ldcase, xlab="Case Number", ylab="(1/2) A", type='l')
+ title (main="Case weight pertubations")
+ plot(1:n, ldresp, xlab="Case Number", ylab="(1/2) A",
+ ylim=c(0, .2), type='l')
+ title(main="Response pertubations")
+ indx <- which(ldresp > .07)
+ text(indx, ldresp[indx]+ .005, indx%%10, cex=.6)
+ }
+
+postscript('meekerplot.ps')
+plot1()
+dev.off()
+#
+# Stanford predictions in other ways
+#
+fit2 <- survreg(Surv(time, status) ~ poly(age,2), stanford2,
+ dist='lognormal')
+
+p1 <- predict(fit1, type='response')
+p2 <- predict(fit2, type='response')
+aeq(p1, p2)
+
+p3 <- predict(fit2, type='terms', se=T)
+p4 <- predict(fit2, type='lp', se=T)
+p5 <- predict(fit1, type='lp', se=T)
+# aeq(p3$fit + attr(p3$fit, 'constant'), p4$fit) #R is missing the attribute
+aeq(p4$fit, p5$fit)
+aeq(p3$se.fit, p4$se.fit) #this one should be false
+aeq(p4$se.fit, p5$se.fit) #this one true
+
diff --git a/win32/deps/library/survival/tests/r_stanford.Rout.save b/win32/deps/library/survival/tests/r_stanford.Rout.save
new file mode 100644
index 0000000..9d369f9
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_stanford.Rout.save
@@ -0,0 +1,111 @@
+
+R version 2.9.0 (2009-04-17)
+Copyright (C) 2009 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # The Stanford data from 1980 is used in Escobar and Meeker, Biometrics 1992.
+> # t5 = T5 mismatch score
+> # Their case numbers correspond to a data set sorted by age
+> #
+> aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+>
+> stanford2$t5 <- ifelse(stanford2$t5 <0, NA, stanford2$t5)
+> stanford2 <- stanford2[order(stanford2$age, stanford2$time),]
+> stanford2$time <- ifelse(stanford2$time==0, .5, stanford2$time)
+>
+> cage <- stanford2$age - mean(stanford2$age)
+> fit1 <- survreg(Surv(time, status) ~ cage + I(cage^2), stanford2,
++ dist='lognormal')
+> fit1
+Call:
+survreg(formula = Surv(time, status) ~ cage + I(cage^2), data = stanford2,
+ dist = "lognormal")
+
+Coefficients:
+ (Intercept) cage I(cage^2)
+ 6.717591081 -0.061908619 -0.003504315
+
+Scale= 2.362872
+
+Loglik(model)= -863.6 Loglik(intercept only)= -868.8
+ Chisq= 10.5 on 2 degrees of freedom, p= 0.0053
+n= 184
+> ldcase <- resid(fit1, type='ldcase')
+> ldresp <- resid(fit1, type='ldresp')
+> # The ldcase and ldresp should be compared to table 1 in Escobar and
+> # Meeker, Biometrics 1992, p519; the colums they label as (1/2) A_{ii}
+> # They give data for selected cases, entered below as mdata
+> mdata <- cbind(c(1,2,4,5,12,16,23,61,66,72,172,182,183,184),
++ c(.035, .244, .141, .159, .194, .402, 0,0, .143, .403,
++ .178, .033, .005, .015),
++ c(.138, .145, .073, .076, .104, .159, 0,0, .109, .184,
++ .116, .063, .103, .144))
+> dimnames(mdata) <- list(NULL, c("case#", "ldcase", "ldresp"))
+> aeq(round(ldcase[mdata[,1]],3), mdata[,2])
+[1] TRUE
+> aeq(round(ldresp[mdata[,1]],3), mdata[,3])
+[1] TRUE
+>
+> plot1 <- function() {
++ # make their figure 1, 2, and 6
++ temp <- predict(fit1, type='quantile', p=c(.1, .5, .9))
++ plot(stanford2$age, stanford2$time, log='y', xlab="Age", ylab="Days",
++ ylim=range(stanford2$time, temp))
++ matlines(stanford2$age, temp, lty=c(1,2,2), col=1)
++
++ n <- length(ldcase)
++ plot(1:n, ldcase, xlab="Case Number", ylab="(1/2) A", type='l')
++ title (main="Case weight pertubations")
++ plot(1:n, ldresp, xlab="Case Number", ylab="(1/2) A",
++ ylim=c(0, .2), type='l')
++ title(main="Response pertubations")
++ indx <- which(ldresp > .07)
++ text(indx, ldresp[indx]+ .005, indx%%10, cex=.6)
++ }
+>
+> postscript('meekerplot.ps')
+> plot1()
+> dev.off()
+null device
+ 1
+> #
+> # Stanford predictions in other ways
+> #
+> fit2 <- survreg(Surv(time, status) ~ poly(age,2), stanford2,
++ dist='lognormal')
+>
+> p1 <- predict(fit1, type='response')
+> p2 <- predict(fit2, type='response')
+> aeq(p1, p2)
+[1] TRUE
+>
+> p3 <- predict(fit2, type='terms', se=T)
+> p4 <- predict(fit2, type='lp', se=T)
+> p5 <- predict(fit1, type='lp', se=T)
+> # aeq(p3$fit + attr(p3$fit, 'constant'), p4$fit) #R is missing the attribute
+> aeq(p4$fit, p5$fit)
+[1] TRUE
+> aeq(p3$se.fit, p4$se.fit) #this one should be false
+[1] "Mean relative difference: 0.758395"
+> aeq(p4$se.fit, p5$se.fit) #this one true
+[1] TRUE
+>
+>
diff --git a/win32/deps/library/survival/tests/r_strata.R b/win32/deps/library/survival/tests/r_strata.R
new file mode 100644
index 0000000..35d9f47
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_strata.R
@@ -0,0 +1,60 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Test out the strata capabilities
+#
+tol <- survreg.control()$rel.tolerance
+aeq <- function(x,y,...) all.equal(as.vector(x), as.vector(y), ...)
+
+# intercept only models
+fit1 <- survreg(Surv(time, status) ~ strata(sex), lung)
+fit2 <- survreg(Surv(time, status) ~ strata(sex) + sex, lung)
+fit3a<- survreg(Surv(time,status) ~1, lung, subset=(sex==1))
+fit3b<- survreg(Surv(time,status) ~1, lung, subset=(sex==2))
+
+fit1
+fit2
+aeq(fit2$scale, c(fit3a$scale, fit3b$scale), tolerance=tol)
+aeq(fit2$loglik[2], (fit3a$loglik + fit3b$loglik)[2], tolerance=tol)
+aeq(fit2$coef[1] + 1:2*fit2$coef[2], c(fit3a$coef, fit3b$coef), tolerance=tol)
+
+#penalized models
+fit1 <- survreg(Surv(time, status) ~ pspline(age, theta=.92)+
+ strata(sex), lung)
+fit2 <- survreg(Surv(time, status) ~ pspline(age, theta=.92)+
+ strata(sex) + sex, lung)
+fit1
+fit2
+
+age1 <- ifelse(lung$sex==1, lung$age, mean(lung$age))
+age2 <- ifelse(lung$sex==2, lung$age, mean(lung$age))
+fit3 <- survreg(Surv(time,status) ~ pspline(age1, theta=.92) +
+ pspline(age2, theta=.95) + sex + strata(sex), lung)
+fit3a<- survreg(Surv(time,status) ~pspline(age, theta=.92), lung,
+ subset=(sex==1))
+fit3b<- survreg(Surv(time,status) ~pspline(age, theta=.95), lung,
+ subset=(sex==2))
+fit3b<- survreg(Surv(time,status) ~pspline(age, theta=.95),
+ lung[lung$sex==2,], x=T)
+#
+# The above line is tricky, and it took me a long time to realize
+# it's necessity. The range of age1 = range(age) = 39-82. That for
+# age2 = range of females = 41-77. The basis functions for pspline are
+# based on age. If I used data=lung, subset=(sex==2) in fit3b (earlier
+# form of the test, the pspline function is called before the subset
+# occurs, and fit3b has a different basis for the second spline than
+# fit3 does; leading to failure of the all.equal tests below. A theta
+# of .95 on one basis is not exactly the same as a theta of .95 on the
+# other. Coefficients were within 1%, but not the same.
+
+aeq(fit3$scale, c(fit3a$scale, fit3b$scale))
+aeq(fit3$loglik[2], (fit3a$loglik + fit3b$loglik)[2])
+pred <- predict(fit3)
+aeq(pred[lung$sex==1] , predict(fit3a))
+aeq(pred[lung$sex==2], predict(fit3b))
+
+
+
+
diff --git a/win32/deps/library/survival/tests/r_strata.Rout.save b/win32/deps/library/survival/tests/r_strata.Rout.save
new file mode 100644
index 0000000..617dad0
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_strata.Rout.save
@@ -0,0 +1,148 @@
+
+R version 2.11.1 (2010-05-31)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Test out the strata capabilities
+> #
+> tol <- survreg.control()$rel.tolerance
+> aeq <- function(x,y,...) all.equal(as.vector(x), as.vector(y), ...)
+>
+> # intercept only models
+> fit1 <- survreg(Surv(time, status) ~ strata(sex), lung)
+> fit2 <- survreg(Surv(time, status) ~ strata(sex) + sex, lung)
+> fit3a<- survreg(Surv(time,status) ~1, lung, subset=(sex==1))
+> fit3b<- survreg(Surv(time,status) ~1, lung, subset=(sex==2))
+>
+> fit1
+Call:
+survreg(formula = Surv(time, status) ~ strata(sex), data = lung)
+
+Coefficients:
+(Intercept)
+ 6.062171
+
+Scale:
+ sex=1 sex=2
+0.8167551 0.6533036
+
+Loglik(model)= -1152.5 Loglik(intercept only)= -1152.5
+n= 228
+> fit2
+Call:
+survreg(formula = Surv(time, status) ~ strata(sex) + sex, data = lung)
+
+Coefficients:
+(Intercept) sex
+ 5.494409 0.380171
+
+Scale:
+ sex=1 sex=2
+0.8084294 0.6355816
+
+Loglik(model)= -1147.1 Loglik(intercept only)= -1152.5
+ Chisq= 10.9 on 1 degrees of freedom, p= 0.00096
+n= 228
+> aeq(fit2$scale, c(fit3a$scale, fit3b$scale), tolerance=tol)
+[1] TRUE
+> aeq(fit2$loglik[2], (fit3a$loglik + fit3b$loglik)[2], tolerance=tol)
+[1] TRUE
+> aeq(fit2$coef[1] + 1:2*fit2$coef[2], c(fit3a$coef, fit3b$coef), tolerance=tol)
+[1] TRUE
+>
+> #penalized models
+> fit1 <- survreg(Surv(time, status) ~ pspline(age, theta=.92)+
++ strata(sex), lung)
+> fit2 <- survreg(Surv(time, status) ~ pspline(age, theta=.92)+
++ strata(sex) + sex, lung)
+> fit1
+Call:
+survreg(formula = Surv(time, status) ~ pspline(age, theta = 0.92) +
+ strata(sex), data = lung)
+
+ coef se(coef) se2 Chisq DF p
+(Intercept) 6.9036 0.8469 0.5688 66.45 1.00 3.3e-16
+pspline(age, theta = 0.92 -0.0124 0.0067 0.0067 3.45 1.00 6.3e-02
+pspline(age, theta = 0.92 2.53 2.65 4.0e-01
+
+Scale:
+sex=1 sex=2
+0.807 0.654
+
+Iterations: 1 outer, 4 Newton-Raphson
+ Theta= 0.92
+Degrees of freedom for terms= 0.5 3.6 2.0
+Likelihood ratio test=6.54 on 3.1 df, p=0.0937 n= 228
+> fit2
+Call:
+survreg(formula = Surv(time, status) ~ pspline(age, theta = 0.92) +
+ strata(sex) + sex, data = lung)
+
+ coef se(coef) se2 Chisq DF p
+(Intercept) 6.3729 0.84471 0.59118 56.92 1.00 4.5e-14
+pspline(age, theta = 0.92 -0.0111 0.00666 0.00666 2.77 1.00 9.6e-02
+pspline(age, theta = 0.92 2.46 2.68 4.2e-01
+sex 0.3686 0.11711 0.11685 9.91 1.00 1.6e-03
+
+Scale:
+sex=1 sex=2
+0.800 0.636
+
+Iterations: 1 outer, 5 Newton-Raphson
+ Theta= 0.92
+Degrees of freedom for terms= 0.5 3.7 1.0 2.0
+Likelihood ratio test=16.8 on 4.2 df, p=0.00245 n= 228
+>
+> age1 <- ifelse(lung$sex==1, lung$age, mean(lung$age))
+> age2 <- ifelse(lung$sex==2, lung$age, mean(lung$age))
+> fit3 <- survreg(Surv(time,status) ~ pspline(age1, theta=.92) +
++ pspline(age2, theta=.95) + sex + strata(sex), lung)
+> fit3a<- survreg(Surv(time,status) ~pspline(age, theta=.92), lung,
++ subset=(sex==1))
+> fit3b<- survreg(Surv(time,status) ~pspline(age, theta=.95), lung,
++ subset=(sex==2))
+> fit3b<- survreg(Surv(time,status) ~pspline(age, theta=.95),
++ lung[lung$sex==2,], x=T)
+> #
+> # The above line is tricky, and it took me a long time to realize
+> # it's necessity. The range of age1 = range(age) = 39-82. That for
+> # age2 = range of females = 41-77. The basis functions for pspline are
+> # based on age. If I used data=lung, subset=(sex==2) in fit3b (earlier
+> # form of the test, the pspline function is called before the subset
+> # occurs, and fit3b has a different basis for the second spline than
+> # fit3 does; leading to failure of the all.equal tests below. A theta
+> # of .95 on one basis is not exactly the same as a theta of .95 on the
+> # other. Coefficients were within 1%, but not the same.
+>
+> aeq(fit3$scale, c(fit3a$scale, fit3b$scale))
+[1] TRUE
+> aeq(fit3$loglik[2], (fit3a$loglik + fit3b$loglik)[2])
+[1] TRUE
+> pred <- predict(fit3)
+> aeq(pred[lung$sex==1] , predict(fit3a))
+[1] TRUE
+> aeq(pred[lung$sex==2], predict(fit3b))
+[1] TRUE
+>
+>
+>
+>
+>
diff --git a/win32/deps/library/survival/tests/r_tdist.R b/win32/deps/library/survival/tests/r_tdist.R
new file mode 100644
index 0000000..3e7d572
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_tdist.R
@@ -0,0 +1,41 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Test out the t-distribution
+#
+
+capacitor <- read.table('data.capacitor', row.names=1,
+ col.names=c('', 'days', 'event', 'voltage'))
+# First, a t-dist with 500 df should be nearly identical to the Gaussian
+
+fitig <- survreg(Surv(days, event)~voltage,
+ dist = "gaussian", data = capacitor)
+fit1 <- survreg(Surv(days, event) ~ voltage,
+ dist='t', parms=500, capacitor)
+fitig
+summary(fit1, corr=F)
+
+# A more realistic fit
+fit2 <- survreg(Surv(days, event) ~ voltage,
+ dist='t', parms=5, capacitor)
+print(fit2)
+
+xx <- seq(1,125, by=10)
+resid(fit2, type='response')[xx]
+resid(fit2, type='deviance')[xx]
+resid(fit2, type='working') [xx]
+resid(fit2, type='dfbeta')[xx,]
+resid(fit2, type='dfbetas')[xx,]
+resid(fit2, type='ldresp')[xx]
+resid(fit2, type='ldshape')[xx]
+resid(fit2, type='ldcase')[xx]
+resid(fit2, type='matrix')[xx,]
+
+predict(fit2, type='response')[xx]
+predict(fit2, type='link')[xx]
+predict(fit2, type='terms')[xx,]
+predict(fit2, type='quantile')[xx]
+
+rm(fitig, fit1, fit2, xx)
diff --git a/win32/deps/library/survival/tests/r_tdist.Rout.save b/win32/deps/library/survival/tests/r_tdist.Rout.save
new file mode 100644
index 0000000..24ab699
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_tdist.Rout.save
@@ -0,0 +1,200 @@
+
+R version 2.7.1 (2008-06-23)
+Copyright (C) 2008 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Test out the t-distribution
+> #
+>
+> capacitor <- read.table('data.capacitor', row.names=1,
++ col.names=c('', 'days', 'event', 'voltage'))
+> # First, a t-dist with 500 df should be nearly identical to the Gaussian
+>
+> fitig <- survreg(Surv(days, event)~voltage,
++ dist = "gaussian", data = capacitor)
+> fit1 <- survreg(Surv(days, event) ~ voltage,
++ dist='t', parms=500, capacitor)
+> fitig
+Call:
+survreg(formula = Surv(days, event) ~ voltage, data = capacitor,
+ dist = "gaussian")
+
+Coefficients:
+(Intercept) voltage
+ 1764.93485 -53.87917
+
+Scale= 121.4319
+
+Loglik(model)= -361.9 Loglik(intercept only)= -420.1
+ Chisq= 116.33 on 1 degrees of freedom, p= 0
+n= 125
+> summary(fit1, corr=F)
+
+Call:
+survreg(formula = Surv(days, event) ~ voltage, data = capacitor,
+ dist = "t", parms = 500)
+ Value Std. Error z p
+(Intercept) 1765.8 163.137 10.82 2.64e-27
+voltage -53.9 5.536 -9.74 2.06e-22
+Log(scale) 4.8 0.106 45.44 0.00e+00
+
+Scale= 121
+
+Student-t distribution: parmameters= 500
+Loglik(model)= -361.9 Loglik(intercept only)= -420.1
+ Chisq= 116.48 on 1 degrees of freedom, p= 0
+Number of Newton-Raphson Iterations: 6
+n= 125
+
+>
+> # A more realistic fit
+> fit2 <- survreg(Surv(days, event) ~ voltage,
++ dist='t', parms=5, capacitor)
+> print(fit2)
+Call:
+survreg(formula = Surv(days, event) ~ voltage, data = capacitor,
+ dist = "t", parms = 5)
+
+Coefficients:
+(Intercept) voltage
+ 1819.28554 -55.74915
+
+Scale= 96.84073
+
+Loglik(model)= -360.4 Loglik(intercept only)= -424.7
+ Chisq= 128.55 on 1 degrees of freedom, p= 0
+n= 125
+>
+> xx <- seq(1,125, by=10)
+> resid(fit2, type='response')[xx]
+ 1 11 21 31 41 51 61
+-404.30257 -404.30257 -404.30257 -98.07767 -69.80767 -69.80767 -69.80767
+ 71 81 91 101 111 121
+ -69.80767 -93.94023 97.43977 113.88722 -33.24278 -20.67278
+> resid(fit2, type='deviance')[xx]
+ 1 11 21 31 41 51 61
+ 0.0933622 0.0933622 0.0933622 -2.2347398 0.7614136 0.7614136 0.7614136
+ 71 81 91 101 111 121
+ 0.7614136 -2.2156512 1.8511554 2.3107823 -2.0035571 -1.9821491
+> resid(fit2, type='working') [xx]
+ 1 11 21 31 41 51 61
+ 86.38692 86.38692 86.38692 -148.70263 83.43717 83.43717 83.43717
+ 71 81 91 101 111 121
+ 83.43717 -137.49634 467.64123 200.98252 -34.84748 -21.05308
+> resid(fit2, type='dfbeta')[xx,]
+ (Intercept) voltage Log(scale)
+1 0.2105054 -0.00703909 -1.743331e-04
+11 0.2105054 -0.00703909 -1.743331e-04
+21 0.2105054 -0.00703909 -1.743331e-04
+31 -29.7982886 0.93975839 -1.076889e-02
+41 9.6554540 -0.30502561 3.507039e-05
+51 9.6554540 -0.30502561 3.507039e-05
+61 9.6554540 -0.30502561 3.507039e-05
+71 9.6554540 -0.30502561 3.507039e-05
+81 -7.9425298 0.20791541 -6.194989e-03
+91 16.3379622 -0.46035101 2.516742e-02
+101 -13.8131372 0.53202477 4.665894e-03
+111 0.7894992 -0.06147045 -1.308494e-02
+121 -1.7672591 0.03187567 -1.433810e-02
+> resid(fit2, type='dfbetas')[xx,]
+ [,1] [,2] [,3]
+1 0.001445482 -0.001447807 -0.0014173482
+11 0.001445482 -0.001447807 -0.0014173482
+21 0.001445482 -0.001447807 -0.0014173482
+31 -0.204616568 0.193290466 -0.0875522695
+41 0.066301320 -0.062737980 0.0002851263
+51 0.066301320 -0.062737980 0.0002851263
+61 0.066301320 -0.062737980 0.0002851263
+71 0.066301320 -0.062737980 0.0002851263
+81 -0.054539145 0.042764254 -0.0503659665
+91 0.112188247 -0.094685467 0.2046140370
+101 -0.094850975 0.109427398 0.0379342550
+111 0.005421271 -0.012643305 -0.1063820631
+121 -0.012135277 0.006556221 -0.1165704260
+> resid(fit2, type='ldresp')[xx]
+ 1 11 21 31 41 51
+6.303033e-06 6.303033e-06 6.303033e-06 4.198946e-02 1.121526e-02 1.121526e-02
+ 61 71 81 91 101 111
+1.121526e-02 1.121526e-02 3.796054e-02 3.773652e-02 5.409081e-02 4.663892e-02
+ 121
+4.455789e-02
+> resid(fit2, type='ldshape')[xx]
+ 1 11 21 31 41 51
+8.281125e-05 8.281125e-05 8.281125e-05 1.355729e-01 1.789400e-04 1.789400e-04
+ 61 71 81 91 101 111
+1.789400e-04 1.789400e-04 6.346182e-02 9.934752e-02 1.534546e-01 1.958545e-02
+ 121
+7.748320e-03
+> resid(fit2, type='ldcase')[xx]
+ 1 11 21 31 41 51
+6.114509e-06 6.114509e-06 6.114509e-06 5.563427e-02 6.706055e-03 6.706055e-03
+ 61 71 81 91 101 111
+6.706055e-03 6.706055e-03 1.966021e-02 6.803951e-02 3.806159e-02 1.617087e-02
+ 121
+1.551988e-02
+> resid(fit2, type='matrix')[xx,]
+ g dg ddg ds dds
+1 -0.00435825 4.361059e-05 -5.048286e-07 -0.01763187 -0.06488770
+11 -0.00435825 4.361059e-05 -5.048286e-07 -0.01763187 -0.06488770
+21 -0.00435825 4.361059e-05 -5.048286e-07 -0.01763187 -0.06488770
+31 -6.10147902 -1.041351e-02 -7.002908e-05 0.02133278 -1.69495867
+41 -0.28987533 3.893573e-03 -4.666473e-05 -0.27180126 0.04439884
+51 -0.28987533 3.893573e-03 -4.666473e-05 -0.27180126 0.04439884
+61 -0.28987533 3.893573e-03 -4.666473e-05 -0.27180126 0.04439884
+71 -0.28987533 3.893573e-03 -4.666473e-05 -0.27180126 0.04439884
+81 -6.05900320 -1.011644e-02 -7.357605e-05 -0.04965962 -1.59963182
+91 -1.71338808 1.250705e-02 -2.674498e-05 1.21868456 -1.47261500
+101 -6.27430559 1.141518e-02 -5.679687e-05 0.30004293 -2.03671532
+111 -5.61156875 -4.155718e-03 -1.192545e-04 -0.86185235 -0.26993370
+121 -5.56890563 -2.621343e-03 -1.245112e-04 -0.94580955 -0.10740203
+ dsg
+1 0.0001604929
+11 0.0001604929
+21 0.0001604929
+31 0.0172817991
+41 -0.0006360167
+51 -0.0006360167
+61 -0.0006360167
+71 -0.0006360167
+81 0.0170281873
+91 -0.0151130795
+101 -0.0178836167
+111 0.0081200691
+121 0.0051953348
+>
+> predict(fit2, type='response')[xx]
+ [1] 704.30257 704.30257 704.30257 369.80767 369.80767 369.80767 369.80767
+ [8] 369.80767 202.56023 202.56023 35.31278 35.31278 35.31278
+> predict(fit2, type='link')[xx]
+ [1] 704.30257 704.30257 704.30257 369.80767 369.80767 369.80767 369.80767
+ [8] 369.80767 202.56023 202.56023 35.31278 35.31278 35.31278
+> predict(fit2, type='terms')[xx,]
+ 1 11 21 31 41 51 61
+ 374.63428 374.63428 374.63428 40.13939 40.13939 40.13939 40.13939
+ 71 81 91 101 111 121
+ 40.13939 -127.10806 -127.10806 -294.35550 -294.35550 -294.35550
+> predict(fit2, type='quantile')[xx]
+ [1] 561.37687 561.37687 561.37687 226.88198 226.88198 226.88198
+ [7] 226.88198 226.88198 59.63453 59.63453 -107.61291 -107.61291
+[13] -107.61291
+>
+> rm(fitig, fit1, fit2, xx)
+>
diff --git a/win32/deps/library/survival/tests/r_user.R b/win32/deps/library/survival/tests/r_user.R
new file mode 100644
index 0000000..6b9580e
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_user.R
@@ -0,0 +1,29 @@
+options(na.action=na.exclude) #preserve length of missings
+library(survival)
+
+#
+# Check out using a "user specified" distribution
+#
+mydist <- c(survreg.distributions$extreme, survreg.distributions$weibull[-1])
+mydist$name <- "Weibull2"
+mydist$dist <- NULL
+
+fit1 <- survreg(Surv(time, status) ~ age + ph.ecog, lung)
+fit2 <- survreg(Surv(time, status) ~ age + ph.ecog, lung, dist=mydist)
+
+all.equal(fit1$coef, fit2$coef)
+all.equal(fit1$var, fit2$var)
+
+#
+# And with an data set containing interval censoring
+#
+idat <- read.table('data.interval', skip=3, header=T, sep=',')
+
+fit1 <- survreg(Surv(ltime, rtime, type='interval2') ~ age + ecog.ps, idat)
+fit2 <- survreg(Surv(ltime, rtime, type='interval2') ~ age + ecog.ps,
+ data=idat, dist=mydist)
+
+all.equal(fit1$coef, fit2$coef)
+all.equal(fit1$var, fit2$var)
+all.equal(fit1$log, fit2$log)
+
diff --git a/win32/deps/library/survival/tests/r_user.Rout.save b/win32/deps/library/survival/tests/r_user.Rout.save
new file mode 100644
index 0000000..84406e4
--- /dev/null
+++ b/win32/deps/library/survival/tests/r_user.Rout.save
@@ -0,0 +1,53 @@
+
+R version 2.9.0 (2009-04-17)
+Copyright (C) 2009 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) #preserve length of missings
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Check out using a "user specified" distribution
+> #
+> mydist <- c(survreg.distributions$extreme, survreg.distributions$weibull[-1])
+> mydist$name <- "Weibull2"
+> mydist$dist <- NULL
+>
+> fit1 <- survreg(Surv(time, status) ~ age + ph.ecog, lung)
+> fit2 <- survreg(Surv(time, status) ~ age + ph.ecog, lung, dist=mydist)
+>
+> all.equal(fit1$coef, fit2$coef)
+[1] TRUE
+> all.equal(fit1$var, fit2$var)
+[1] TRUE
+>
+> #
+> # And with an data set containing interval censoring
+> #
+> idat <- read.table('data.interval', skip=3, header=T, sep=',')
+>
+> fit1 <- survreg(Surv(ltime, rtime, type='interval2') ~ age + ecog.ps, idat)
+> fit2 <- survreg(Surv(ltime, rtime, type='interval2') ~ age + ecog.ps,
++ data=idat, dist=mydist)
+>
+> all.equal(fit1$coef, fit2$coef)
+[1] TRUE
+> all.equal(fit1$var, fit2$var)
+[1] TRUE
+> all.equal(fit1$log, fit2$log)
+[1] TRUE
+>
+>
diff --git a/win32/deps/library/survival/tests/ratetable.R b/win32/deps/library/survival/tests/ratetable.R
new file mode 100644
index 0000000..f841a9c
--- /dev/null
+++ b/win32/deps/library/survival/tests/ratetable.R
@@ -0,0 +1,63 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Generate each of the messages from is.ratetable
+#
+{if (is.R()) mdy.date <- function(m, d, y) {
+ y <- ifelse(y<100, y+1900, y)
+ as.Date(paste(m,d,y, sep='/'), "%m/%d/%Y")
+ }
+else mdy.date <- function(m,d,y) {
+ y <- ifelse(y<100, y+1900, y)
+ timeDate(paste(y, m, d, sep='/'), in.format="%Y/%m/%d")
+ }
+ }
+
+temp <- runif(21*2*4)
+
+# Good
+attributes(temp) <- list(dim=c(21,2,4),
+ dimnames=list(c(as.character(75:95)), c("male","female"),
+ c(as.character(2000:2003))),
+ dimid=c("age","sex","year"),
+ type=c(2,1,4),
+ cutpoints=list(c(75:95), NULL, mdy.date(1,1,2000) +c(0:3)*366.25),
+ class='ratetable')
+is.ratetable(temp)
+
+# Factor problem + cutpoints length
+attributes(temp) <- list(dim=c(21,2,4),
+ dimnames=list(c(as.character(75:95)), c("male","female"),
+ c(as.character(2000:2003))),
+ dimid=c("age","sex","year"),
+ type=c(1,1,2),
+ cutpoints=list(c(75:95), NULL, mdy.date(1,1,2000) +c(0:4)*366.25),
+ class='ratetable')
+is.ratetable(temp, verbose=T)
+
+
+# missing dimid attribute + unsorted cutpoint
+attributes(temp) <- list(dim=c(21,2,4),
+ dimnames=list(c(as.character(75:95)), c("male","female"),
+ c(as.character(2000:2003))),
+ type=c(2,1,3),
+ cutpoints=list(c(75:95), NULL, mdy.date(1,1,2000) +c(4:1)*366.25),
+ class='ratetable')
+is.ratetable(temp, verbose=T)
+
+# wrong length for dimid and type, illegal type
+attributes(temp) <- list(dim=c(21,2,4),
+ dimnames=list(c(as.character(75:95)), c("male","female"),
+ c(as.character(2000:2003))),
+ dimid=c("age","sex","year", "zed"),
+ type=c(2,1,3,6),
+ cutpoints=list(c(75:95), NULL, mdy.date(1,1,2000) +c(0:3)*366.25),
+ class='ratetable')
+is.ratetable(temp, verbose=T)
+
+
+# Print and summary
+print(survexp.us[1:30,,c('1953', '1985')] )
+summary(survexp.usr)
diff --git a/win32/deps/library/survival/tests/ratetable.Rout.save b/win32/deps/library/survival/tests/ratetable.Rout.save
new file mode 100644
index 0000000..89c28b9
--- /dev/null
+++ b/win32/deps/library/survival/tests/ratetable.Rout.save
@@ -0,0 +1,164 @@
+
+R version 2.11.1 (2010-05-31)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Generate each of the messages from is.ratetable
+> #
+> {if (is.R()) mdy.date <- function(m, d, y) {
++ y <- ifelse(y<100, y+1900, y)
++ as.Date(paste(m,d,y, sep='/'), "%m/%d/%Y")
++ }
++ else mdy.date <- function(m,d,y) {
++ y <- ifelse(y<100, y+1900, y)
++ timeDate(paste(y, m, d, sep='/'), in.format="%Y/%m/%d")
++ }
++ }
+>
+> temp <- runif(21*2*4)
+>
+> # Good
+> attributes(temp) <- list(dim=c(21,2,4),
++ dimnames=list(c(as.character(75:95)), c("male","female"),
++ c(as.character(2000:2003))),
++ dimid=c("age","sex","year"),
++ type=c(2,1,4),
++ cutpoints=list(c(75:95), NULL, mdy.date(1,1,2000) +c(0:3)*366.25),
++ class='ratetable')
+> is.ratetable(temp)
+[1] TRUE
+>
+> # Factor problem + cutpoints length
+> attributes(temp) <- list(dim=c(21,2,4),
++ dimnames=list(c(as.character(75:95)), c("male","female"),
++ c(as.character(2000:2003))),
++ dimid=c("age","sex","year"),
++ type=c(1,1,2),
++ cutpoints=list(c(75:95), NULL, mdy.date(1,1,2000) +c(0:4)*366.25),
++ class='ratetable')
+> is.ratetable(temp, verbose=T)
+[1] "type[ 1 ] is 1; cutpoint should be null"
+[2] "wrong length for cutpoints 3"
+>
+>
+> # missing dimid attribute + unsorted cutpoint
+> attributes(temp) <- list(dim=c(21,2,4),
++ dimnames=list(c(as.character(75:95)), c("male","female"),
++ c(as.character(2000:2003))),
++ type=c(2,1,3),
++ cutpoints=list(c(75:95), NULL, mdy.date(1,1,2000) +c(4:1)*366.25),
++ class='ratetable')
+> is.ratetable(temp, verbose=T)
+[1] "missing attribute: dimid" "wrong length for dimid"
+[3] "unsorted cutpoints for dimension 3"
+>
+> # wrong length for dimid and type, illegal type
+> attributes(temp) <- list(dim=c(21,2,4),
++ dimnames=list(c(as.character(75:95)), c("male","female"),
++ c(as.character(2000:2003))),
++ dimid=c("age","sex","year", "zed"),
++ type=c(2,1,3,6),
++ cutpoints=list(c(75:95), NULL, mdy.date(1,1,2000) +c(0:3)*366.25),
++ class='ratetable')
+> is.ratetable(temp, verbose=T)
+[1] "wrong length for dimid"
+[2] "type attribute must be 1, 2, 3, or 4"
+[3] "wrong length for type attribute"
+>
+>
+> # Print and summary
+> print(survexp.us[1:30,,c('1953', '1985')] )
+Rate table with dimension(s): age sex year
+, , 1953
+
+ male female
+0-1d 1.157372e-02 8.844000e-03
+1-7d 1.446302e-03 1.027012e-03
+7-28d 1.379175e-04 1.106070e-04
+28-365d 2.814865e-05 2.346732e-05
+1 6.169963e-06 5.423669e-06
+2 3.860391e-06 3.161334e-06
+3 2.909162e-06 2.424089e-06
+4 2.448747e-06 1.950051e-06
+5 2.210350e-06 1.692520e-06
+6 1.988411e-06 1.481583e-06
+7 1.813065e-06 1.298053e-06
+8 1.684303e-06 1.169315e-06
+9 1.593900e-06 1.087146e-06
+10 1.569249e-06 1.051541e-06
+11 1.626780e-06 1.043325e-06
+12 1.771975e-06 1.089887e-06
+13 2.062389e-06 1.199447e-06
+14 2.462443e-06 1.347361e-06
+15 2.944779e-06 1.550072e-06
+16 3.410754e-06 1.752797e-06
+17 3.819231e-06 1.928140e-06
+18 4.164702e-06 2.056914e-06
+19 4.504735e-06 2.169256e-06
+20 4.822866e-06 2.289823e-06
+21 5.086174e-06 2.410395e-06
+22 5.278187e-06 2.511789e-06
+23 5.335795e-06 2.613186e-06
+24 5.286423e-06 2.714587e-06
+25 5.198648e-06 2.815992e-06
+26 5.130079e-06 2.917400e-06
+
+, , 1985
+
+ male female
+0-1d 4.429985e-03 3.701977e-03
+1-7d 3.595869e-04 2.735770e-04
+7-28d 6.385309e-05 5.193376e-05
+28-365d 1.277308e-05 9.947467e-06
+1 2.451492e-06 2.108968e-06
+2 1.739100e-06 1.341882e-06
+3 1.369277e-06 1.013196e-06
+4 1.122754e-06 7.940941e-07
+5 9.995021e-07 7.530142e-07
+6 9.173378e-07 6.571643e-07
+7 8.488687e-07 5.887021e-07
+8 7.530153e-07 5.339338e-07
+9 6.297793e-07 4.791661e-07
+10 5.202416e-07 4.517830e-07
+11 5.202416e-07 4.517830e-07
+12 7.530134e-07 5.202412e-07
+13 1.232311e-06 6.571636e-07
+14 1.862374e-06 8.351727e-07
+15 2.533686e-06 1.026887e-06
+16 3.150341e-06 1.204921e-06
+17 3.657474e-06 1.341877e-06
+18 4.041315e-06 1.424054e-06
+19 4.315527e-06 1.465144e-06
+20 4.603481e-06 1.506233e-06
+21 4.864041e-06 1.561021e-06
+22 5.069759e-06 1.615810e-06
+23 5.138331e-06 1.643205e-06
+24 5.152035e-06 1.670600e-06
+25 5.110881e-06 1.697995e-06
+26 5.097158e-06 1.725391e-06
+
+> summary(survexp.usr)
+ Rate table with 4 dimensions:
+ age ranges from 0 to 39812.25; with 113 categories
+ sex has levels of: male female
+ race has levels of: white black
+ year ranges from 1940-01-01 to 2004-01-01; with 65 categories
+>
diff --git a/win32/deps/library/survival/tests/rounding.R b/win32/deps/library/survival/tests/rounding.R
new file mode 100644
index 0000000..4b94256
--- /dev/null
+++ b/win32/deps/library/survival/tests/rounding.R
@@ -0,0 +1,14 @@
+library(survival)
+#
+# Survival curves could fail with data that was almost exact.
+# The calculations use both unique() and table(), which don't
+# necessarily give the same number of values.
+# Check that the routine handles this properly
+#
+
+tdata <- data.frame(time=c(1,2, sqrt(2)^2, 2, sqrt(2)^2),
+ status=rep(1,5),
+ group=c(1,1,1,2,2))
+fit <- survfit(Surv(time, status) ~ group, data=tdata)
+
+all.equal(sum(fit$strata), length(fit$time))
diff --git a/win32/deps/library/survival/tests/rounding.Rout.save b/win32/deps/library/survival/tests/rounding.Rout.save
new file mode 100644
index 0000000..6d314cc
--- /dev/null
+++ b/win32/deps/library/survival/tests/rounding.Rout.save
@@ -0,0 +1,34 @@
+
+R version 2.11.0 (2010-04-22)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+> #
+> # Survival curves could fail with data that was almost exact.
+> # The calculations use both unique() and table(), which don't
+> # necessarily give the same number of values.
+> # Check that the routine handles this properly
+> #
+>
+> tdata <- data.frame(time=c(1,2, sqrt(2)^2, 2, sqrt(2)^2),
++ status=rep(1,5),
++ group=c(1,1,1,2,2))
+> fit <- survfit(Surv(time, status) ~ group, data=tdata)
+>
+> all.equal(sum(fit$strata), length(fit$time))
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/singtest.R b/win32/deps/library/survival/tests/singtest.R
new file mode 100644
index 0000000..5fd21d6
--- /dev/null
+++ b/win32/deps/library/survival/tests/singtest.R
@@ -0,0 +1,22 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# A simple test of the singular=ok option
+#
+test1 <- data.frame(time= c(4, 3,1,1,2,2,3),
+ status=c(1,NA,1,0,1,1,0),
+ x= c(0, 2,1,1,1,0,0))
+
+temp <- rep(0:3, rep(7,4))
+
+stest <- data.frame(start = 10*temp,
+ stop = 10*temp + test1$time,
+ status = rep(test1$status,4),
+ x = c(test1$x+ 1:7, rep(test1$x,3)),
+ epoch = rep(1:4, rep(7,4)))
+
+fit1 <- coxph(Surv(start, stop, status) ~ x * factor(epoch), stest)
+fit1$coef # elements 2:4 should be NA
+all.equal(is.na(fit1$coef), c(F,T,T,T,F,F,F), check.attributes=FALSE)
diff --git a/win32/deps/library/survival/tests/singtest.Rout.save b/win32/deps/library/survival/tests/singtest.Rout.save
new file mode 100644
index 0000000..8036046
--- /dev/null
+++ b/win32/deps/library/survival/tests/singtest.Rout.save
@@ -0,0 +1,50 @@
+
+R version 2.12.2 (2011-02-25)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # A simple test of the singular=ok option
+> #
+> test1 <- data.frame(time= c(4, 3,1,1,2,2,3),
++ status=c(1,NA,1,0,1,1,0),
++ x= c(0, 2,1,1,1,0,0))
+>
+> temp <- rep(0:3, rep(7,4))
+>
+> stest <- data.frame(start = 10*temp,
++ stop = 10*temp + test1$time,
++ status = rep(test1$status,4),
++ x = c(test1$x+ 1:7, rep(test1$x,3)),
++ epoch = rep(1:4, rep(7,4)))
+>
+> fit1 <- coxph(Surv(start, stop, status) ~ x * factor(epoch), stest)
+Warning message:
+In coxph(Surv(start, stop, status) ~ x * factor(epoch), stest) :
+ X matrix deemed to be singular; variable 2 3 4
+> fit1$coef # elements 2:4 should be NA
+ x factor(epoch)2 factor(epoch)3 factor(epoch)4
+ 0.1041579 NA NA NA
+x:factor(epoch)2 x:factor(epoch)3 x:factor(epoch)4
+ 1.5726996 1.5726996 1.5726996
+> all.equal(is.na(fit1$coef), c(F,T,T,T,F,F,F), check.attributes=FALSE)
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/strata2.R b/win32/deps/library/survival/tests/strata2.R
new file mode 100644
index 0000000..1436177
--- /dev/null
+++ b/win32/deps/library/survival/tests/strata2.R
@@ -0,0 +1,17 @@
+#
+# New tests 4/2010 to validate strata by covariate interactions
+#
+library(survival)
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+
+tdata <- lung
+tdata$sex <- lung$sex +3
+
+fit1 <- coxph(Surv(time, status) ~ age + sex:strata(ph.ecog), lung)
+fit2 <- coxph(Surv(time, status) ~ age + sex:strata(ph.ecog), tdata)
+
+aeq(fit1$coef, fit2$coef)
+aeq(fit1$var, fit2$var)
+aeq(predict(fit1), predict(fit2))
diff --git a/win32/deps/library/survival/tests/strata2.Rout.save b/win32/deps/library/survival/tests/strata2.Rout.save
new file mode 100644
index 0000000..3ed6108
--- /dev/null
+++ b/win32/deps/library/survival/tests/strata2.Rout.save
@@ -0,0 +1,45 @@
+
+R version 2.11.1 (2010-05-31)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> #
+> # New tests 4/2010 to validate strata by covariate interactions
+> #
+> library(survival)
+Loading required package: splines
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+>
+> tdata <- lung
+> tdata$sex <- lung$sex +3
+>
+> fit1 <- coxph(Surv(time, status) ~ age + sex:strata(ph.ecog), lung)
+Warning message:
+In coxph(Surv(time, status) ~ age + sex:strata(ph.ecog), lung) :
+ X matrix deemed to be singular; variable 5
+> fit2 <- coxph(Surv(time, status) ~ age + sex:strata(ph.ecog), tdata)
+Warning message:
+In coxph(Surv(time, status) ~ age + sex:strata(ph.ecog), tdata) :
+ X matrix deemed to be singular; variable 5
+>
+> aeq(fit1$coef, fit2$coef)
+[1] TRUE
+> aeq(fit1$var, fit2$var)
+[1] TRUE
+> aeq(predict(fit1), predict(fit2))
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/stratatest.R b/win32/deps/library/survival/tests/stratatest.R
new file mode 100644
index 0000000..c0dee39
--- /dev/null
+++ b/win32/deps/library/survival/tests/stratatest.R
@@ -0,0 +1,43 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Trivial test of stratified residuals
+# Make a second strata = replicate of the first, and I should get the
+# exact same answers
+test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
+ status=c(1,NA,1,0,1,1,0),
+ x= c(0, 2,1,1,1,0,0))
+test2 <- data.frame(start=c(1, 2, 5, 2, 1, 7, 3, 4, 8, 8),
+ stop =c(2, 3, 6, 7, 8, 9, 9, 9,14,17),
+ event=c(1, 1, 1, 1, 1, 1, 1, 0, 0, 0),
+ x =c(1, 0, 0, 1, 0, 1, 1, 1, 0, 0) )
+
+temp <- as.matrix(test1)
+n <- nrow(temp)
+ndead<- sum(test1$status[!is.na(test1$status)])
+temp <- data.frame(rbind(temp, temp)) #later releases of S have rbind.data.frame
+tstrat <- rep(1:2, c(n,n))
+
+fit1 <- coxph(Surv(time, status) ~x, test1)
+fit2 <- coxph(Surv(time, status) ~x + strata(tstrat), temp)
+
+all.equal(resid(fit1) , (resid(fit2))[1:n])
+all.equal(resid(fit1, type='score') , (resid(fit2, type='score'))[1:n])
+all.equal(resid(fit1, type='schoe') , (resid(fit2, type='schoe'))[1:ndead])
+
+
+#AG model
+temp <- as.matrix(test2)
+n <- nrow(temp)
+ndead<- sum(test2$event[!is.na(test2$event)])
+temp <- data.frame(rbind(temp, temp))
+tstrat <- rep(1:2, c(n,n))
+
+fit1 <- coxph(Surv(start, stop, event) ~x, test2)
+fit2 <- coxph(Surv(start, stop, event) ~x + strata(tstrat), temp)
+
+all.equal(resid(fit1) , (resid(fit2))[1:n])
+all.equal(resid(fit1, type='score') , (resid(fit2, type='score'))[1:n])
+all.equal(resid(fit1, type='schoe') , (resid(fit2, type='schoe'))[1:ndead])
diff --git a/win32/deps/library/survival/tests/stratatest.Rout.save b/win32/deps/library/survival/tests/stratatest.Rout.save
new file mode 100644
index 0000000..2e96f3a
--- /dev/null
+++ b/win32/deps/library/survival/tests/stratatest.Rout.save
@@ -0,0 +1,68 @@
+
+R version 2.7.1 (2008-06-23)
+Copyright (C) 2008 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Trivial test of stratified residuals
+> # Make a second strata = replicate of the first, and I should get the
+> # exact same answers
+> test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
++ status=c(1,NA,1,0,1,1,0),
++ x= c(0, 2,1,1,1,0,0))
+> test2 <- data.frame(start=c(1, 2, 5, 2, 1, 7, 3, 4, 8, 8),
++ stop =c(2, 3, 6, 7, 8, 9, 9, 9,14,17),
++ event=c(1, 1, 1, 1, 1, 1, 1, 0, 0, 0),
++ x =c(1, 0, 0, 1, 0, 1, 1, 1, 0, 0) )
+>
+> temp <- as.matrix(test1)
+> n <- nrow(temp)
+> ndead<- sum(test1$status[!is.na(test1$status)])
+> temp <- data.frame(rbind(temp, temp)) #later releases of S have rbind.data.frame
+> tstrat <- rep(1:2, c(n,n))
+>
+> fit1 <- coxph(Surv(time, status) ~x, test1)
+> fit2 <- coxph(Surv(time, status) ~x + strata(tstrat), temp)
+>
+> all.equal(resid(fit1) , (resid(fit2))[1:n])
+[1] TRUE
+> all.equal(resid(fit1, type='score') , (resid(fit2, type='score'))[1:n])
+[1] TRUE
+> all.equal(resid(fit1, type='schoe') , (resid(fit2, type='schoe'))[1:ndead])
+[1] TRUE
+>
+>
+> #AG model
+> temp <- as.matrix(test2)
+> n <- nrow(temp)
+> ndead<- sum(test2$event[!is.na(test2$event)])
+> temp <- data.frame(rbind(temp, temp))
+> tstrat <- rep(1:2, c(n,n))
+>
+> fit1 <- coxph(Surv(start, stop, event) ~x, test2)
+> fit2 <- coxph(Surv(start, stop, event) ~x + strata(tstrat), temp)
+>
+> all.equal(resid(fit1) , (resid(fit2))[1:n])
+[1] TRUE
+> all.equal(resid(fit1, type='score') , (resid(fit2, type='score'))[1:n])
+[1] TRUE
+> all.equal(resid(fit1, type='schoe') , (resid(fit2, type='schoe'))[1:ndead])
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/summary_survfit.R b/win32/deps/library/survival/tests/summary_survfit.R
new file mode 100644
index 0000000..9ccdd9e
--- /dev/null
+++ b/win32/deps/library/survival/tests/summary_survfit.R
@@ -0,0 +1,5 @@
+## check that the scale option to summary.survfit works
+## Marc Schwartz reported this as a bug in 2.35-3.
+library(survival)
+summary( survfit( Surv(futime, fustat)~1, data=ovarian))
+summary( survfit( Surv(futime, fustat)~1, data=ovarian), scale=365.25)
diff --git a/win32/deps/library/survival/tests/summary_survfit.Rout.save b/win32/deps/library/survival/tests/summary_survfit.Rout.save
new file mode 100644
index 0000000..2a2e81a
--- /dev/null
+++ b/win32/deps/library/survival/tests/summary_survfit.Rout.save
@@ -0,0 +1,54 @@
+
+R version 2.9.0 Under development (unstable) (2009-03-17 r48144)
+Copyright (C) 2009 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> ## check that the scale option to summary.survfit works
+> ## Marc Schwartz reported this as a bug in 2.35-3.
+> library(survival)
+Loading required package: splines
+> summary( survfit( Surv(futime, fustat)~1, data=ovarian))
+Call: survfit(formula = Surv(futime, fustat) ~ 1, data = ovarian)
+
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 59 26 1 0.962 0.0377 0.890 1.000
+ 115 25 1 0.923 0.0523 0.826 1.000
+ 156 24 1 0.885 0.0627 0.770 1.000
+ 268 23 1 0.846 0.0708 0.718 0.997
+ 329 22 1 0.808 0.0773 0.670 0.974
+ 353 21 1 0.769 0.0826 0.623 0.949
+ 365 20 1 0.731 0.0870 0.579 0.923
+ 431 17 1 0.688 0.0919 0.529 0.894
+ 464 15 1 0.642 0.0965 0.478 0.862
+ 475 14 1 0.596 0.0999 0.429 0.828
+ 563 12 1 0.546 0.1032 0.377 0.791
+ 638 11 1 0.497 0.1051 0.328 0.752
+> summary( survfit( Surv(futime, fustat)~1, data=ovarian), scale=365.25)
+Call: survfit(formula = Surv(futime, fustat) ~ 1, data = ovarian)
+
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 0.162 26 1 0.962 0.0377 0.890 1.000
+ 0.315 25 1 0.923 0.0523 0.826 1.000
+ 0.427 24 1 0.885 0.0627 0.770 1.000
+ 0.734 23 1 0.846 0.0708 0.718 0.997
+ 0.901 22 1 0.808 0.0773 0.670 0.974
+ 0.966 21 1 0.769 0.0826 0.623 0.949
+ 0.999 20 1 0.731 0.0870 0.579 0.923
+ 1.180 17 1 0.688 0.0919 0.529 0.894
+ 1.270 15 1 0.642 0.0965 0.478 0.862
+ 1.300 14 1 0.596 0.0999 0.429 0.828
+ 1.541 12 1 0.546 0.1032 0.377 0.791
+ 1.747 11 1 0.497 0.1051 0.328 0.752
+>
diff --git a/win32/deps/library/survival/tests/surv.R b/win32/deps/library/survival/tests/surv.R
new file mode 100644
index 0000000..ec5d6e9
--- /dev/null
+++ b/win32/deps/library/survival/tests/surv.R
@@ -0,0 +1,23 @@
+#
+library(survival)
+
+# Some simple tests of the Surv function
+# The first two are motivated by a bug, pointed out by Kevin Buhr,
+# where a mixture of NAs and invalid values didn't work right
+# Even for the simplest things a test case is good.
+#
+aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+temp <- Surv(c(1, 10, 20, 30), c(2, NA, 0, 40), c(1,1,1,1))
+aeq(temp, c(1,10,NA,30, 2,NA,0,40, 1,1,1,1))
+
+temp <- Surv(c(1, 10, 20, 30), c(2, NA, 0, 40), type='interval2')
+aeq(temp, c(1,10,NA,30, 2,1,0,40, 3,0,3,3))
+
+temp <- Surv(1:5)
+aeq(temp, c(1:5, 1,1,1,1,1))
+
+temp1 <- Surv(c(1,10,NA, 30, 30), c(1,NA,10,20, 40), type='interval2')
+temp2 <- Surv(c(1,10,10,30,30), c(9, NA, 5, 20,40), c(1, 0, 2,3,3),
+ type='interval')
+aeq(temp1, temp2)
+aeq(temp1, c(1,10,10,NA,30, 1,1,1,20, 40, 1,0,2,3,3))
diff --git a/win32/deps/library/survival/tests/surv.Rout.save b/win32/deps/library/survival/tests/surv.Rout.save
new file mode 100644
index 0000000..5c66f4a
--- /dev/null
+++ b/win32/deps/library/survival/tests/surv.Rout.save
@@ -0,0 +1,59 @@
+
+R version 2.9.0 (2009-04-17)
+Copyright (C) 2009 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> #
+> library(survival)
+Loading required package: splines
+>
+> # Some simple tests of the Surv function
+> # The first two are motivated by a bug, pointed out by Kevin Buhr,
+> # where a mixture of NAs and invalid values didn't work right
+> # Even for the simplest things a test case is good.
+> #
+> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+> temp <- Surv(c(1, 10, 20, 30), c(2, NA, 0, 40), c(1,1,1,1))
+Warning message:
+In Surv(c(1, 10, 20, 30), c(2, NA, 0, 40), c(1, 1, 1, 1)) :
+ Stop time must be > start time, NA created
+> aeq(temp, c(1,10,NA,30, 2,NA,0,40, 1,1,1,1))
+[1] TRUE
+>
+> temp <- Surv(c(1, 10, 20, 30), c(2, NA, 0, 40), type='interval2')
+Warning message:
+In Surv(c(1, 10, 20, 30), c(2, NA, 0, 40), type = "interval2") :
+ Invalid interval: start > stop, NA created
+> aeq(temp, c(1,10,NA,30, 2,1,0,40, 3,0,3,3))
+[1] TRUE
+>
+> temp <- Surv(1:5)
+> aeq(temp, c(1:5, 1,1,1,1,1))
+[1] TRUE
+>
+> temp1 <- Surv(c(1,10,NA, 30, 30), c(1,NA,10,20, 40), type='interval2')
+Warning message:
+In Surv(c(1, 10, NA, 30, 30), c(1, NA, 10, 20, 40), type = "interval2") :
+ Invalid interval: start > stop, NA created
+> temp2 <- Surv(c(1,10,10,30,30), c(9, NA, 5, 20,40), c(1, 0, 2,3,3),
++ type='interval')
+Warning message:
+In Surv(c(1, 10, 10, 30, 30), c(9, NA, 5, 20, 40), c(1, 0, 2, 3, :
+ Invalid interval: start > stop, NA created
+> aeq(temp1, temp2)
+[1] TRUE
+> aeq(temp1, c(1,10,10,NA,30, 1,1,1,20, 40, 1,0,2,3,3))
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/survfit2.R b/win32/deps/library/survival/tests/survfit2.R
new file mode 100644
index 0000000..04ead6d
--- /dev/null
+++ b/win32/deps/library/survival/tests/survfit2.R
@@ -0,0 +1,13 @@
+library(survival)
+#
+# Check out the Dory&Korn confidence interval option
+#
+tdata <- data.frame(time= 1:10,
+ status=c(1,0,1,0,1,0,0,0,1,0))
+
+fit1 <- survfit(Surv(time, status) ~1, tdata, conf.lower='modified')
+fit2 <- survfit(Surv(time, status) ~1, tdata)
+
+stdlow <- fit2$std * sqrt(c(1, 10/9, 1, 8/7, 1, 6/5, 6/4, 6/3, 1, 2/1))
+lower <- exp(log(fit2$surv) - qnorm(.975)*stdlow)
+all.equal(fit1$lower, lower, check.attributes=FALSE)
diff --git a/win32/deps/library/survival/tests/survfit2.Rout.save b/win32/deps/library/survival/tests/survfit2.Rout.save
new file mode 100644
index 0000000..8fef50d
--- /dev/null
+++ b/win32/deps/library/survival/tests/survfit2.Rout.save
@@ -0,0 +1,33 @@
+
+R version 2.11.0 (2010-04-22)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+> #
+> # Check out the Dory&Korn confidence interval option
+> #
+> tdata <- data.frame(time= 1:10,
++ status=c(1,0,1,0,1,0,0,0,1,0))
+>
+> fit1 <- survfit(Surv(time, status) ~1, tdata, conf.lower='modified')
+> fit2 <- survfit(Surv(time, status) ~1, tdata)
+>
+> stdlow <- fit2$std * sqrt(c(1, 10/9, 1, 8/7, 1, 6/5, 6/4, 6/3, 1, 2/1))
+> lower <- exp(log(fit2$surv) - qnorm(.975)*stdlow)
+> all.equal(fit1$lower, lower, check.attributes=FALSE)
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/survreg2.R b/win32/deps/library/survival/tests/survreg2.R
new file mode 100644
index 0000000..dd31368
--- /dev/null
+++ b/win32/deps/library/survival/tests/survreg2.R
@@ -0,0 +1,62 @@
+library(survival)
+options(na.action=na.exclude, contrasts=c('contr.treatment', 'contr.poly'))
+
+# Verify stratified fits in a simple way, but combining two data
+# sets and doing a single fit
+#
+aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+
+tdata <- data.frame(time=c(lung$time, ovarian$futime),
+ status=c(lung$status-1, ovarian$fustat),
+ group =rep(0:1, c(nrow(lung), nrow(ovarian))))
+fit1 <- survreg(Surv(time, status) ~ 1, lung)
+fit2 <- survreg(Surv(futime, fustat) ~ 1, ovarian)
+fit3 <- survreg(Surv(time, status) ~ group + strata(group), tdata)
+
+aeq(c(fit1$coef, fit2$coef-fit1$coef), fit3$coef)
+aeq(c(fit1$scale, fit2$scale), fit3$scale)
+aeq(fit1$loglik[2] + fit2$loglik[2], fit3$loglik[2])
+
+#
+# Test out the cluster term in survreg, which means first a test
+# of the dfbeta residuals
+# I also am checking that missing values propogate
+test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
+ status=c(1,NA,1,0,1,1,0),
+ x= c(0, 2,1,1,1,0,0))
+fit1 <- survreg(Surv(time, status) ~ x + cluster(1:7), test1)
+
+db1 <- resid(fit1, 'dfbeta')
+ijack <-db1
+eps <- 1e-7
+for (i in 1:7) {
+ temp <- rep(1.0,7)
+ temp[i] <- 1-eps
+ tfit <- survreg(Surv(time, status) ~ x, test1, weight=temp)
+ ijack[i,] <- c(tfit$coef, log(tfit$scale))
+ }
+ijack[2,] <- NA # stick the NA back in
+ijack <- (rep(c(fit1$coef, log(fit1$scale)), each=nrow(db1)) - ijack)/eps
+all.equal(db1, ijack, tol=eps)
+all.equal(t(db1[-2,])%*% db1[-2,], fit1$var)
+
+# This is a harder test since there are multiple strata and multiple
+# obs/subject. Use of enum + strata(enum) in essenence fits a different
+# baseline Weibull to each strata, with common coefficients for rx, size, and
+# number.
+fit1 <- survreg(Surv(stop-start, event) ~ rx + size + number +
+ factor(enum) + strata(enum), data=bladder2)
+
+db1 <- resid(fit1, type='dfbeta', collapse=bladder2$id)
+ijack <- db1 # a matrix of the same size
+for (i in 1:nrow(db1)) {
+ twt <- rep(1., nrow(bladder2))
+ twt[bladder2$id==i] <- 1-eps
+ tfit <- survreg(Surv(stop-start, event) ~ rx + size + number +
+ factor(enum) + strata(enum), data=bladder2,
+ weight=twt)
+ ijack[i,] <- c(coef(tfit), log(tfit$scale))
+ }
+ijack <- (rep(c(fit1$coef, log(fit1$scale)), each=nrow(db1)) - ijack)/eps
+all.equal(db1, ijack, tol=eps*2)
+
diff --git a/win32/deps/library/survival/tests/survreg2.Rout.save b/win32/deps/library/survival/tests/survreg2.Rout.save
new file mode 100644
index 0000000..f0c79bf
--- /dev/null
+++ b/win32/deps/library/survival/tests/survreg2.Rout.save
@@ -0,0 +1,87 @@
+
+R version 2.9.0 (2009-04-17)
+Copyright (C) 2009 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+> options(na.action=na.exclude, contrasts=c('contr.treatment', 'contr.poly'))
+>
+> # Verify stratified fits in a simple way, but combining two data
+> # sets and doing a single fit
+> #
+> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
+>
+> tdata <- data.frame(time=c(lung$time, ovarian$futime),
++ status=c(lung$status-1, ovarian$fustat),
++ group =rep(0:1, c(nrow(lung), nrow(ovarian))))
+> fit1 <- survreg(Surv(time, status) ~ 1, lung)
+> fit2 <- survreg(Surv(futime, fustat) ~ 1, ovarian)
+> fit3 <- survreg(Surv(time, status) ~ group + strata(group), tdata)
+>
+> aeq(c(fit1$coef, fit2$coef-fit1$coef), fit3$coef)
+[1] TRUE
+> aeq(c(fit1$scale, fit2$scale), fit3$scale)
+[1] TRUE
+> aeq(fit1$loglik[2] + fit2$loglik[2], fit3$loglik[2])
+[1] TRUE
+>
+> #
+> # Test out the cluster term in survreg, which means first a test
+> # of the dfbeta residuals
+> # I also am checking that missing values propogate
+> test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
++ status=c(1,NA,1,0,1,1,0),
++ x= c(0, 2,1,1,1,0,0))
+> fit1 <- survreg(Surv(time, status) ~ x + cluster(1:7), test1)
+>
+> db1 <- resid(fit1, 'dfbeta')
+> ijack <-db1
+> eps <- 1e-7
+> for (i in 1:7) {
++ temp <- rep(1.0,7)
++ temp[i] <- 1-eps
++ tfit <- survreg(Surv(time, status) ~ x, test1, weight=temp)
++ ijack[i,] <- c(tfit$coef, log(tfit$scale))
++ }
+> ijack[2,] <- NA # stick the NA back in
+> ijack <- (rep(c(fit1$coef, log(fit1$scale)), each=nrow(db1)) - ijack)/eps
+> all.equal(db1, ijack, tol=eps)
+[1] TRUE
+> all.equal(t(db1[-2,])%*% db1[-2,], fit1$var)
+[1] TRUE
+>
+> # This is a harder test since there are multiple strata and multiple
+> # obs/subject. Use of enum + strata(enum) in essenence fits a different
+> # baseline Weibull to each strata, with common coefficients for rx, size, and
+> # number.
+> fit1 <- survreg(Surv(stop-start, event) ~ rx + size + number +
++ factor(enum) + strata(enum), data=bladder2)
+>
+> db1 <- resid(fit1, type='dfbeta', collapse=bladder2$id)
+> ijack <- db1 # a matrix of the same size
+> for (i in 1:nrow(db1)) {
++ twt <- rep(1., nrow(bladder2))
++ twt[bladder2$id==i] <- 1-eps
++ tfit <- survreg(Surv(stop-start, event) ~ rx + size + number +
++ factor(enum) + strata(enum), data=bladder2,
++ weight=twt)
++ ijack[i,] <- c(coef(tfit), log(tfit$scale))
++ }
+> ijack <- (rep(c(fit1$coef, log(fit1$scale)), each=nrow(db1)) - ijack)/eps
+> all.equal(db1, ijack, tol=eps*2)
+[1] TRUE
+>
+>
diff --git a/win32/deps/library/survival/tests/survtest.R b/win32/deps/library/survival/tests/survtest.R
new file mode 100644
index 0000000..1715a8c
--- /dev/null
+++ b/win32/deps/library/survival/tests/survtest.R
@@ -0,0 +1,60 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Simple test of (start, stop] Kaplan-Meier curves, using the test2 data
+# set
+#
+test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
+ status=c(1,NA,1,0,1,1,0),
+ x= c(0, 2,1,1,1,0,0))
+test2 <- data.frame(start=c(1, 2, 5, 2, 1, 7, 3, 4, 8, 8),
+ stop =c(2, 3, 6, 7, 8, 9, 9, 9,14,17),
+ event=c(1, 1, 1, 1, 1, 1, 1, 0, 0, 0),
+ x =c(1, 0, 0, 1, 0, 1, 1, 1, 0, 0) )
+aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+
+fit1 <- survfit(Surv(start, stop, event) ~1, test2, type='fh2',
+ error='tsiatis')
+fit2 <- survfit(Surv(start, stop, event) ~x, test2, start.time=3,
+ type='fh2')
+
+cfit1<- survfit(coxph(Surv(start, stop, event)~1, test2))
+cfit2<- survfit(coxph(Surv(start, stop, event) ~ strata(x), test2, subset=-1))
+
+deaths <- (fit1$n.event + fit1$n.censor)>0
+aeq(fit1$time[deaths], cfit1$time)
+aeq(fit1$n.risk[deaths], cfit1$n.risk)
+aeq(fit1$n.event[deaths], cfit1$n.event)
+aeq(fit1$surv[deaths], cfit1$surv)
+aeq(fit1$std.err[deaths], cfit1$std.err)
+
+deaths <- (fit2$n.event + fit2$n.censor)>0
+aeq(fit2$time[deaths], cfit2$time)
+aeq(fit2$n.risk[deaths], cfit2$n.risk)
+aeq(fit2$n.event[deaths], cfit2$n.event)
+aeq(fit2$surv[deaths], cfit2$surv)
+
+fit3 <- survfit(Surv(start, stop, event) ~1, test2) #Kaplan-Meier
+aeq(fit3$n, 10)
+aeq(fit3$time, c(1:9,14,17))
+aeq(fit3$n.risk, c(0,2,3,3,4,5,4,4,5,2,1))
+aeq(fit3$n.event,c(0,1,1,0,0,1,1,1,2,0,0))
+aeq(fit3$surv[fit3$n.event>0], c(.5, 1/3, 4/15, 1/5, 3/20, 9/100))
+#
+# Verify that both surv AND n.risk are right between time points.
+#
+fit <- survfit(Surv(time, status) ~1, test1)
+temp <- summary(fit, time=c(.5,1, 1.5, 6, 7.5, 8, 8.9, 9, 10), extend=TRUE)
+
+aeq(temp$n.risk, c(6,6,4,4,2,2,1,1,0))
+aeq(temp$surv, c(1, fit$surv[c(1,1,2,2,3,3,4,4)]))
+aeq(temp$n.event, c(0,1,0,2,0,0,0,1,0))
+aeq(temp$std.err, c(0, (fit$surv*fit$std.err)[c(1,1,2,2,3,3,4,4)]))
+
+
+fit <- survfit(Surv(start, stop, event) ~1, test2)
+temp <- summary(fit, times=c(.5, 1.5, 2.5, 3, 6.5, 14.5, 16.5))
+aeq(temp$surv, c(1, fit$surv[c(1,2,3,6, 10,10)]))
+aeq(temp$n.risk, c(0, 2, 3, 3, 4, 1,1))
diff --git a/win32/deps/library/survival/tests/survtest.Rout.save b/win32/deps/library/survival/tests/survtest.Rout.save
new file mode 100644
index 0000000..d10c401
--- /dev/null
+++ b/win32/deps/library/survival/tests/survtest.Rout.save
@@ -0,0 +1,99 @@
+
+R version 2.11.1 (2010-05-31)
+Copyright (C) 2010 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Simple test of (start, stop] Kaplan-Meier curves, using the test2 data
+> # set
+> #
+> test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
++ status=c(1,NA,1,0,1,1,0),
++ x= c(0, 2,1,1,1,0,0))
+> test2 <- data.frame(start=c(1, 2, 5, 2, 1, 7, 3, 4, 8, 8),
++ stop =c(2, 3, 6, 7, 8, 9, 9, 9,14,17),
++ event=c(1, 1, 1, 1, 1, 1, 1, 0, 0, 0),
++ x =c(1, 0, 0, 1, 0, 1, 1, 1, 0, 0) )
+> aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+>
+> fit1 <- survfit(Surv(start, stop, event) ~1, test2, type='fh2',
++ error='tsiatis')
+> fit2 <- survfit(Surv(start, stop, event) ~x, test2, start.time=3,
++ type='fh2')
+>
+> cfit1<- survfit(coxph(Surv(start, stop, event)~1, test2))
+> cfit2<- survfit(coxph(Surv(start, stop, event) ~ strata(x), test2, subset=-1))
+>
+> deaths <- (fit1$n.event + fit1$n.censor)>0
+> aeq(fit1$time[deaths], cfit1$time)
+[1] TRUE
+> aeq(fit1$n.risk[deaths], cfit1$n.risk)
+[1] TRUE
+> aeq(fit1$n.event[deaths], cfit1$n.event)
+[1] TRUE
+> aeq(fit1$surv[deaths], cfit1$surv)
+[1] TRUE
+> aeq(fit1$std.err[deaths], cfit1$std.err)
+[1] TRUE
+>
+> deaths <- (fit2$n.event + fit2$n.censor)>0
+> aeq(fit2$time[deaths], cfit2$time)
+[1] TRUE
+> aeq(fit2$n.risk[deaths], cfit2$n.risk)
+[1] TRUE
+> aeq(fit2$n.event[deaths], cfit2$n.event)
+[1] TRUE
+> aeq(fit2$surv[deaths], cfit2$surv)
+[1] TRUE
+>
+> fit3 <- survfit(Surv(start, stop, event) ~1, test2) #Kaplan-Meier
+> aeq(fit3$n, 10)
+[1] TRUE
+> aeq(fit3$time, c(1:9,14,17))
+[1] TRUE
+> aeq(fit3$n.risk, c(0,2,3,3,4,5,4,4,5,2,1))
+[1] TRUE
+> aeq(fit3$n.event,c(0,1,1,0,0,1,1,1,2,0,0))
+[1] TRUE
+> aeq(fit3$surv[fit3$n.event>0], c(.5, 1/3, 4/15, 1/5, 3/20, 9/100))
+[1] TRUE
+> #
+> # Verify that both surv AND n.risk are right between time points.
+> #
+> fit <- survfit(Surv(time, status) ~1, test1)
+> temp <- summary(fit, time=c(.5,1, 1.5, 6, 7.5, 8, 8.9, 9, 10), extend=TRUE)
+>
+> aeq(temp$n.risk, c(6,6,4,4,2,2,1,1,0))
+[1] TRUE
+> aeq(temp$surv, c(1, fit$surv[c(1,1,2,2,3,3,4,4)]))
+[1] TRUE
+> aeq(temp$n.event, c(0,1,0,2,0,0,0,1,0))
+[1] TRUE
+> aeq(temp$std.err, c(0, (fit$surv*fit$std.err)[c(1,1,2,2,3,3,4,4)]))
+[1] TRUE
+>
+>
+> fit <- survfit(Surv(start, stop, event) ~1, test2)
+> temp <- summary(fit, times=c(.5, 1.5, 2.5, 3, 6.5, 14.5, 16.5))
+> aeq(temp$surv, c(1, fit$surv[c(1,2,3,6, 10,10)]))
+[1] TRUE
+> aeq(temp$n.risk, c(0, 2, 3, 3, 4, 1,1))
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/testci.R b/win32/deps/library/survival/tests/testci.R
new file mode 100644
index 0000000..4129b6c
--- /dev/null
+++ b/win32/deps/library/survival/tests/testci.R
@@ -0,0 +1,67 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# Test out the survfit.ci function, which does competing risk
+# estimates
+#
+# For this we need the sequential MGUS data set, using the first
+# obs for each subject
+#
+aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+
+tdata <- data.frame(time=mgus1$stop,
+ status=mgus1$status,
+ event=mgus1$event,
+ sex=mgus1$sex)[mgus1$start==0,]
+
+fit1 <- survfit(Surv(time, status) ~ 1, etype=event, tdata)
+
+# Now get the overall survival, and the hazard for progression
+fit2 <- survfit(Surv(time, status) ~1, tdata) #overall to "first bad thing"
+fit3 <- survfit(Surv(time, status*(event=='progression')) ~1, tdata,
+ type='fleming')
+
+# Classic CI formula
+# integral [hazard(t) S(t-0) dt], where S= "survival to first event"
+haz <- diff(c(0, -log(fit3$surv))) #Aalen hazard estimate
+tsurv <- c(1, fit2$surv[-length(fit2$surv)]) #lagged survival
+ci <- cumsum(haz *tsurv)
+aeq(1-ci, fit1$surv[,1])
+
+#
+# Now, make sure that it works for subgroups
+#
+fit1 <- survfit(Surv(time, status) ~ sex, etype=event, tdata)
+fit2 <- survfit(Surv(time, status) ~ 1, etype=event, tdata,
+ subset=(sex=='male'))
+fit3 <- survfit(Surv(time, status) ~ 1, etype=event, tdata,
+ subset=(sex=='female'))
+
+aeq(fit2$surv, fit1$surv[1:fit1$strata[1],])
+aeq(fit3$surv, fit1$surv[-(1:fit1$strata[1]),])
+
+# A second test of cumulative incidence
+# compare results to Bob Gray's functions
+# The file gray1 is the result of
+#
+# tstat <- ifelse(tdata$status==0, 0, 1+ (tdata$event=='death'))
+# gray1 <- cuminc(tdata$time, tstat)
+load("gray1.rda")
+plot(gray1[[1]]$time, gray1[[1]]$est, type='l',
+ ylim=range(c(gray1[[1]]$est, gray1[[2]]$est)),
+ xlab="Time")
+lines(gray1[[2]]$time, gray1[[2]]$est, lty=2)
+
+fit2 <- survfit(Surv(time, status) ~ 1, etype=event, tdata)
+matlines(fit2$time, 1-fit2$surv, col=2, lty=1:2, type='s')
+
+# To formally match these is a bit of a nuisance.
+# The cuminc function returns full step function, and survfit.ci only
+# the bottoms of the steps.
+# The survfit.ci function returns all time points, cuminc only the jumps.
+temp1 <- tapply(gray1[[1]]$est, gray1[[1]]$time, max)
+indx1 <- match(names(temp1), fit2$time)
+aeq(temp1, 1-fit2$surv[indx1,1])
+
diff --git a/win32/deps/library/survival/tests/testci.Rout.save b/win32/deps/library/survival/tests/testci.Rout.save
new file mode 100644
index 0000000..d650a44
--- /dev/null
+++ b/win32/deps/library/survival/tests/testci.Rout.save
@@ -0,0 +1,91 @@
+
+R version 2.13.0 RC (2011-04-12 r55424)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Test out the survfit.ci function, which does competing risk
+> # estimates
+> #
+> # For this we need the sequential MGUS data set, using the first
+> # obs for each subject
+> #
+> aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+>
+> tdata <- data.frame(time=mgus1$stop,
++ status=mgus1$status,
++ event=mgus1$event,
++ sex=mgus1$sex)[mgus1$start==0,]
+>
+> fit1 <- survfit(Surv(time, status) ~ 1, etype=event, tdata)
+>
+> # Now get the overall survival, and the hazard for progression
+> fit2 <- survfit(Surv(time, status) ~1, tdata) #overall to "first bad thing"
+> fit3 <- survfit(Surv(time, status*(event=='progression')) ~1, tdata,
++ type='fleming')
+>
+> # Classic CI formula
+> # integral [hazard(t) S(t-0) dt], where S= "survival to first event"
+> haz <- diff(c(0, -log(fit3$surv))) #Aalen hazard estimate
+> tsurv <- c(1, fit2$surv[-length(fit2$surv)]) #lagged survival
+> ci <- cumsum(haz *tsurv)
+> aeq(1-ci, fit1$surv[,1])
+[1] TRUE
+>
+> #
+> # Now, make sure that it works for subgroups
+> #
+> fit1 <- survfit(Surv(time, status) ~ sex, etype=event, tdata)
+> fit2 <- survfit(Surv(time, status) ~ 1, etype=event, tdata,
++ subset=(sex=='male'))
+> fit3 <- survfit(Surv(time, status) ~ 1, etype=event, tdata,
++ subset=(sex=='female'))
+>
+> aeq(fit2$surv, fit1$surv[1:fit1$strata[1],])
+[1] TRUE
+> aeq(fit3$surv, fit1$surv[-(1:fit1$strata[1]),])
+[1] TRUE
+>
+> # A second test of cumulative incidence
+> # compare results to Bob Gray's functions
+> # The file gray1 is the result of
+> #
+> # tstat <- ifelse(tdata$status==0, 0, 1+ (tdata$event=='death'))
+> # gray1 <- cuminc(tdata$time, tstat)
+> load("gray1.rda")
+> plot(gray1[[1]]$time, gray1[[1]]$est, type='l',
++ ylim=range(c(gray1[[1]]$est, gray1[[2]]$est)),
++ xlab="Time")
+> lines(gray1[[2]]$time, gray1[[2]]$est, lty=2)
+>
+> fit2 <- survfit(Surv(time, status) ~ 1, etype=event, tdata)
+> matlines(fit2$time, 1-fit2$surv, col=2, lty=1:2, type='s')
+>
+> # To formally match these is a bit of a nuisance.
+> # The cuminc function returns full step function, and survfit.ci only
+> # the bottoms of the steps.
+> # The survfit.ci function returns all time points, cuminc only the jumps.
+> temp1 <- tapply(gray1[[1]]$est, gray1[[1]]$time, max)
+> indx1 <- match(names(temp1), fit2$time)
+> aeq(temp1, 1-fit2$surv[indx1,1])
+[1] TRUE
+>
+>
diff --git a/win32/deps/library/survival/tests/testci2.R b/win32/deps/library/survival/tests/testci2.R
new file mode 100644
index 0000000..ced4d87
--- /dev/null
+++ b/win32/deps/library/survival/tests/testci2.R
@@ -0,0 +1,52 @@
+library(survival)
+
+#
+# Test the current prevalence version of the CI curve
+#
+tdata <- data.frame(id=c(1,1,1,1, 2,2,2, 3,3, 4,4,4,4, 5, 6, 6),
+ time=c(10,20,30,40, 5, 15,25, 20, 22, 6,18,34,50,10,15,20),
+ status=c(1,1,1,1, 1,1,1, 1,0, 1,1,1,0,0,1,0),
+ event= letters[c(1,2,3,4, 2,4,3, 2,2, 3,1,2,2,1, 1,1)],
+ wt = c(2,2,2,2, 1,1,1, 3,3, 1,1,1,1, 2, 1,1))
+
+fit <- survfit(Surv(time, status) ~1, etype=event, id=id, weight=wt, tdata)
+all.equal(as.vector(1-fit$surv),
+ as.vector(matrix(c(0,0,2,3.5, 4.5, 2.5, 2.5, 2.5, 2.5, 0,0,0,
+ 1,1,1,0,0, 6.5, 6.5, 6.5, 0, 2.5, 2.5, 2.5,
+ 0,1,1,1,0,0,0,1, 7.5, 7.5, 1,1,
+ 0,0,0,1,1,1,1,0,0,0, 6.5, 6.5)/10, ncol=4)))
+
+# The exact figures for testci2.
+
+# The subject data of id, weight, (transition time, transition)
+
+#1: 2 (10, 0->1) (20, 1->2) (30, 2->3) (40, 3->4)
+#2: 1 ( 5, 0->2) (15, 2->4) (25, 4->3)
+#3: 3 (20, 0->2) (22, censor)
+#4: 1 ( 6, 0->3) (18, 3->1) (34, 1->2) (50, censor)
+#5: 2 (10, censor)
+#6: 1 (15, 0->1) (20, censor)
+
+#Each line below follows a subject through time as a (state, weight) pair
+
+# | Time
+#Subject | 5 6 10 10+ 15 18 20 20+ 22+ 25
+#----------------------------------------------------------------------
+#1 0,2 0,2 1,2 1,2 1,2 1,2 2,2 2,2 2,6.5 2,6.5
+#2 2,1 2,1 2,1 2,1 4,1 4,1 4,1 4,1 4,1 3,1
+#3 0,3 0,3 0,3 0,4.5 0,4.5 0,4.5 2,4.5 2,4.5
+#4 0,1 3,1 3,1 3,1 3,1 1,1 1,1 1,2.5 1,2.5 1,2.5
+#5 0,2 0,2 0,2
+#6 0,1 0,1 0,1 0,1.5 1,1.5 1,1.5 1,1.5
+#
+#
+# 30 34 40 50
+#--------------------------------------
+#1 3,6.5 3,6.5 4,6.5 4,6.5
+#2 3,1 3,1 3,1 3,1
+#4 1,2,5 2,2.5 2,2.5
+
+
+# 1-fit$surv for time i and state j = total weight at that time/state in the
+# above table, divided by 10.
+
diff --git a/win32/deps/library/survival/tests/testci2.Rout.save b/win32/deps/library/survival/tests/testci2.Rout.save
new file mode 100644
index 0000000..0841b11
--- /dev/null
+++ b/win32/deps/library/survival/tests/testci2.Rout.save
@@ -0,0 +1,72 @@
+
+R version 2.9.0 (2009-04-17)
+Copyright (C) 2009 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Test the current prevalence version of the CI curve
+> #
+> tdata <- data.frame(id=c(1,1,1,1, 2,2,2, 3,3, 4,4,4,4, 5, 6, 6),
++ time=c(10,20,30,40, 5, 15,25, 20, 22, 6,18,34,50,10,15,20),
++ status=c(1,1,1,1, 1,1,1, 1,0, 1,1,1,0,0,1,0),
++ event= letters[c(1,2,3,4, 2,4,3, 2,2, 3,1,2,2,1, 1,1)],
++ wt = c(2,2,2,2, 1,1,1, 3,3, 1,1,1,1, 2, 1,1))
+>
+> fit <- survfit(Surv(time, status) ~1, etype=event, id=id, weight=wt, tdata)
+> all.equal(as.vector(1-fit$surv),
++ as.vector(matrix(c(0,0,2,3.5, 4.5, 2.5, 2.5, 2.5, 2.5, 0,0,0,
++ 1,1,1,0,0, 6.5, 6.5, 6.5, 0, 2.5, 2.5, 2.5,
++ 0,1,1,1,0,0,0,1, 7.5, 7.5, 1,1,
++ 0,0,0,1,1,1,1,0,0,0, 6.5, 6.5)/10, ncol=4)))
+[1] TRUE
+>
+> # The exact figures for testci2.
+>
+> # The subject data of id, weight, (transition time, transition)
+>
+> #1: 2 (10, 0->1) (20, 1->2) (30, 2->3) (40, 3->4)
+> #2: 1 ( 5, 0->2) (15, 2->4) (25, 4->3)
+> #3: 3 (20, 0->2) (22, censor)
+> #4: 1 ( 6, 0->3) (18, 3->1) (34, 1->2) (50, censor)
+> #5: 2 (10, censor)
+> #6: 1 (15, 0->1) (20, censor)
+>
+> #Each line below follows a subject through time as a (state, weight) pair
+>
+> # | Time
+> #Subject | 5 6 10 10+ 15 18 20 20+ 22+ 25
+> #----------------------------------------------------------------------
+> #1 0,2 0,2 1,2 1,2 1,2 1,2 2,2 2,2 2,6.5 2,6.5
+> #2 2,1 2,1 2,1 2,1 4,1 4,1 4,1 4,1 4,1 3,1
+> #3 0,3 0,3 0,3 0,4.5 0,4.5 0,4.5 2,4.5 2,4.5
+> #4 0,1 3,1 3,1 3,1 3,1 1,1 1,1 1,2.5 1,2.5 1,2.5
+> #5 0,2 0,2 0,2
+> #6 0,1 0,1 0,1 0,1.5 1,1.5 1,1.5 1,1.5
+> #
+> #
+> # 30 34 40 50
+> #--------------------------------------
+> #1 3,6.5 3,6.5 4,6.5 4,6.5
+> #2 3,1 3,1 3,1 3,1
+> #4 1,2,5 2,2.5 2,2.5
+>
+>
+> # 1-fit$surv for time i and state j = total weight at that time/state in the
+> # above table, divided by 10.
+>
+>
diff --git a/win32/deps/library/survival/tests/testnull.R b/win32/deps/library/survival/tests/testnull.R
new file mode 100644
index 0000000..bef18e7
--- /dev/null
+++ b/win32/deps/library/survival/tests/testnull.R
@@ -0,0 +1,19 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# A test of NULL models
+#
+fit1 <- coxph(Surv(stop, event) ~ rx + strata(number), bladder, iter=0)
+fit2 <- coxph(Surv(stop, event) ~ strata(number), bladder)
+
+all.equal(fit1$loglik[2], fit2$loglik)
+all.equal(fit1$resid, fit2$resid)
+
+
+fit1 <- coxph(Surv(start, stop, event) ~ rx + strata(number), bladder2, iter=0)
+fit2 <- coxph(Surv(start, stop, event) ~ strata(number), bladder2)
+
+all.equal(fit1$loglik[2], fit2$loglik)
+all.equal(fit1$resid, fit2$resid)
diff --git a/win32/deps/library/survival/tests/testnull.Rout.save b/win32/deps/library/survival/tests/testnull.Rout.save
new file mode 100644
index 0000000..30cd77a
--- /dev/null
+++ b/win32/deps/library/survival/tests/testnull.Rout.save
@@ -0,0 +1,42 @@
+
+R version 2.7.1 (2008-06-23)
+Copyright (C) 2008 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # A test of NULL models
+> #
+> fit1 <- coxph(Surv(stop, event) ~ rx + strata(number), bladder, iter=0)
+> fit2 <- coxph(Surv(stop, event) ~ strata(number), bladder)
+>
+> all.equal(fit1$loglik[2], fit2$loglik)
+[1] TRUE
+> all.equal(fit1$resid, fit2$resid)
+[1] TRUE
+>
+>
+> fit1 <- coxph(Surv(start, stop, event) ~ rx + strata(number), bladder2, iter=0)
+> fit2 <- coxph(Surv(start, stop, event) ~ strata(number), bladder2)
+>
+> all.equal(fit1$loglik[2], fit2$loglik)
+[1] TRUE
+> all.equal(fit1$resid, fit2$resid)
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/testreg.R b/win32/deps/library/survival/tests/testreg.R
new file mode 100644
index 0000000..3a9ad77
--- /dev/null
+++ b/win32/deps/library/survival/tests/testreg.R
@@ -0,0 +1,79 @@
+options(na.action=na.exclude) #preserve length of missings
+library(survival)
+
+#
+# Run a test that can be verified using other packages (we used SAS)
+#
+test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
+ status=c(1,NA,1,0,1,1,0),
+ x= c(0, 2,1,1,1,0,0))
+fit1w <- survreg(Surv(time, status) ~x, test1, dist='weibull')
+fit1w
+summary(fit1w)
+
+fit1e <- survreg(Surv(time, status) ~x, test1, dist='exponential')
+fit1e
+summary(fit1e)
+
+fit1l <- survreg(Surv(time, status) ~x, test1, dist='loglogistic')
+fit1l
+summary(fit1l)
+
+fit1g <- survreg(Surv(time, status) ~x, test1, dist='lognormal')
+summary(fit1g)
+#
+# Do a test with the ovarian data
+#
+fitfw <- survreg(Surv(futime, fustat) ~ age + ecog.ps, ovarian,
+ dist='weibull')
+fitfw
+
+fitfl <- survreg(Surv(futime, fustat) ~ age + ecog.ps, ovarian,
+ dist='loglogistic')
+fitfl
+
+#test out interval censoring, using some dummy time values
+
+idat <- read.table('data.interval', skip=3, header=T, sep=',')
+flsurv<- Surv(idat$ltime, idat$rtime, type='interval2')
+
+fitfw2 <- survreg(flsurv ~ age + ecog.ps, idat, dist='weibull')
+summary(fitfw2)
+
+fitfl2 <- survreg(flsurv ~ age + ecog.ps, idat, dist='loglogistic')
+summary(fitfl2)
+
+fitfg2 <- survreg(flsurv ~ age + ecog.ps, idat, dist='lognormal')
+summary(fitfg2)
+
+logt <- c(survreg.distributions$t,
+ survreg.distributions$weibull[c('trans', 'itrans', 'dtrans')])
+logt$name <- 'log(t)'
+
+fitft2 <- survreg(Surv(ltime, rtime, type='interval2') ~ age + ecog.ps,
+ idat, dist=logt, parm=100)
+summary(fitft2) #should be quite close to fitfg2
+
+#
+# Check out the survreg density and probability functions
+#
+
+# Gaussian
+x <- -10:10
+p <- seq(.1, .95, length=25)
+all.equal(dsurvreg(x, 1, 5, 'gaussian'), dnorm(x, 1, 5))
+all.equal(psurvreg(x, 1, 5, 'gaussian'), pnorm(x, 1, 5))
+all.equal(qsurvreg(p, 1, 5, 'gaussian'), qnorm(p, 1, 5))
+
+# Lognormal
+x <- 1:10
+all.equal(dsurvreg(x, 1, 5, 'lognormal'), dlnorm(x, 1, 5))
+all.equal(psurvreg(x, 1, 5, 'lognormal'), plnorm(x, 1, 5))
+all.equal(qsurvreg(p, 1, 5, 'lognormal'), qlnorm(p, 1, 5))
+
+# Weibull
+lambda <- exp(-2)
+rho <- 1/3
+temp <- (lambda*x)^rho
+all.equal(psurvreg(x, 2, 3), 1- exp(-temp))
+all.equal(dsurvreg(x, 2, 3), lambda*rho*(lambda*x)^(rho-1)*exp(-temp))
diff --git a/win32/deps/library/survival/tests/testreg.Rout.save b/win32/deps/library/survival/tests/testreg.Rout.save
new file mode 100644
index 0000000..9f6fa28
--- /dev/null
+++ b/win32/deps/library/survival/tests/testreg.Rout.save
@@ -0,0 +1,301 @@
+
+R version 2.14.0 Under development (unstable) (2011-04-10 r55401)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) #preserve length of missings
+> library(survival)
+Loading required package: splines
+>
+> #
+> # Run a test that can be verified using other packages (we used SAS)
+> #
+> test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
++ status=c(1,NA,1,0,1,1,0),
++ x= c(0, 2,1,1,1,0,0))
+> fit1w <- survreg(Surv(time, status) ~x, test1, dist='weibull')
+> fit1w
+Call:
+survreg(formula = Surv(time, status) ~ x, data = test1, dist = "weibull")
+
+Coefficients:
+(Intercept) x
+ 2.2373335 -0.7442249
+
+Scale= 0.4563163
+
+Loglik(model)= -10.3 Loglik(intercept only)= -11.4
+ Chisq= 2.22 on 1 degrees of freedom, p= 0.14
+n=6 (1 observation deleted due to missingness)
+> summary(fit1w)
+
+Call:
+survreg(formula = Surv(time, status) ~ x, data = test1, dist = "weibull")
+ Value Std. Error z p
+(Intercept) 2.237 0.330 6.78 1.18e-11
+x -0.744 0.486 -1.53 1.26e-01
+Log(scale) -0.785 0.433 -1.81 6.99e-02
+
+Scale= 0.456
+
+Weibull distribution
+Loglik(model)= -10.3 Loglik(intercept only)= -11.4
+ Chisq= 2.22 on 1 degrees of freedom, p= 0.14
+Number of Newton-Raphson Iterations: 8
+n=6 (1 observation deleted due to missingness)
+
+>
+> fit1e <- survreg(Surv(time, status) ~x, test1, dist='exponential')
+> fit1e
+Call:
+survreg(formula = Surv(time, status) ~ x, data = test1, dist = "exponential")
+
+Coefficients:
+(Intercept) x
+ 2.442347 -1.056053
+
+Scale fixed at 1
+
+Loglik(model)= -11.7 Loglik(intercept only)= -12.2
+ Chisq= 1.07 on 1 degrees of freedom, p= 0.3
+n=6 (1 observation deleted due to missingness)
+> summary(fit1e)
+
+Call:
+survreg(formula = Surv(time, status) ~ x, data = test1, dist = "exponential")
+ Value Std. Error z p
+(Intercept) 2.44 0.707 3.45 0.000552
+x -1.06 1.000 -1.06 0.290944
+
+Scale fixed at 1
+
+Exponential distribution
+Loglik(model)= -11.7 Loglik(intercept only)= -12.2
+ Chisq= 1.07 on 1 degrees of freedom, p= 0.3
+Number of Newton-Raphson Iterations: 4
+n=6 (1 observation deleted due to missingness)
+
+>
+> fit1l <- survreg(Surv(time, status) ~x, test1, dist='loglogistic')
+> fit1l
+Call:
+survreg(formula = Surv(time, status) ~ x, data = test1, dist = "loglogistic")
+
+Coefficients:
+(Intercept) x
+ 2.177208 -1.195672
+
+Scale= 0.3847582
+
+Loglik(model)= -10.7 Loglik(intercept only)= -12
+ Chisq= 2.7 on 1 degrees of freedom, p= 0.1
+n=6 (1 observation deleted due to missingness)
+> summary(fit1l)
+
+Call:
+survreg(formula = Surv(time, status) ~ x, data = test1, dist = "loglogistic")
+ Value Std. Error z p
+(Intercept) 2.177 0.365 5.96 2.48e-09
+x -1.196 0.711 -1.68 9.25e-02
+Log(scale) -0.955 0.396 -2.41 1.58e-02
+
+Scale= 0.385
+
+Log logistic distribution
+Loglik(model)= -10.7 Loglik(intercept only)= -12
+ Chisq= 2.7 on 1 degrees of freedom, p= 0.1
+Number of Newton-Raphson Iterations: 4
+n=6 (1 observation deleted due to missingness)
+
+>
+> fit1g <- survreg(Surv(time, status) ~x, test1, dist='lognormal')
+> summary(fit1g)
+
+Call:
+survreg(formula = Surv(time, status) ~ x, data = test1, dist = "lognormal")
+ Value Std. Error z p
+(Intercept) 2.210 0.404 5.48 4.35e-08
+x -1.268 0.585 -2.17 3.03e-02
+Log(scale) -0.446 0.342 -1.30 1.93e-01
+
+Scale= 0.64
+
+Log Normal distribution
+Loglik(model)= -10.5 Loglik(intercept only)= -12.1
+ Chisq= 3.26 on 1 degrees of freedom, p= 0.071
+Number of Newton-Raphson Iterations: 5
+n=6 (1 observation deleted due to missingness)
+
+> #
+> # Do a test with the ovarian data
+> #
+> fitfw <- survreg(Surv(futime, fustat) ~ age + ecog.ps, ovarian,
++ dist='weibull')
+> fitfw
+Call:
+survreg(formula = Surv(futime, fustat) ~ age + ecog.ps, data = ovarian,
+ dist = "weibull")
+
+Coefficients:
+(Intercept) age ecog.ps
+12.28496723 -0.09702669 0.09977342
+
+Scale= 0.6032744
+
+Loglik(model)= -90 Loglik(intercept only)= -98
+ Chisq= 15.98 on 2 degrees of freedom, p= 0.00034
+n= 26
+>
+> fitfl <- survreg(Surv(futime, fustat) ~ age + ecog.ps, ovarian,
++ dist='loglogistic')
+> fitfl
+Call:
+survreg(formula = Surv(futime, fustat) ~ age + ecog.ps, data = ovarian,
+ dist = "loglogistic")
+
+Coefficients:
+(Intercept) age ecog.ps
+11.50853384 -0.08876814 0.09033348
+
+Scale= 0.4464064
+
+Loglik(model)= -89.5 Loglik(intercept only)= -97.4
+ Chisq= 15.67 on 2 degrees of freedom, p= 4e-04
+n= 26
+>
+> #test out interval censoring, using some dummy time values
+>
+> idat <- read.table('data.interval', skip=3, header=T, sep=',')
+> flsurv<- Surv(idat$ltime, idat$rtime, type='interval2')
+>
+> fitfw2 <- survreg(flsurv ~ age + ecog.ps, idat, dist='weibull')
+> summary(fitfw2)
+
+Call:
+survreg(formula = flsurv ~ age + ecog.ps, data = idat, dist = "weibull")
+ Value Std. Error z p
+(Intercept) 12.3886 1.6027 7.730 1.08e-14
+age -0.0986 0.0254 -3.885 1.02e-04
+ecog.ps 0.0971 0.3776 0.257 7.97e-01
+Log(scale) -0.4773 0.2583 -1.848 6.47e-02
+
+Scale= 0.62
+
+Weibull distribution
+Loglik(model)= -56.2 Loglik(intercept only)= -64
+ Chisq= 15.57 on 2 degrees of freedom, p= 0.00042
+Number of Newton-Raphson Iterations: 6
+n= 26
+
+>
+> fitfl2 <- survreg(flsurv ~ age + ecog.ps, idat, dist='loglogistic')
+> summary(fitfl2)
+
+Call:
+survreg(formula = flsurv ~ age + ecog.ps, data = idat, dist = "loglogistic")
+ Value Std. Error z p
+(Intercept) 11.5268 1.528 7.542 4.62e-14
+age -0.0888 0.024 -3.703 2.13e-04
+ecog.ps 0.0818 0.364 0.225 8.22e-01
+Log(scale) -0.8023 0.271 -2.965 3.03e-03
+
+Scale= 0.448
+
+Log logistic distribution
+Loglik(model)= -55.9 Loglik(intercept only)= -63.5
+ Chisq= 15.35 on 2 degrees of freedom, p= 0.00046
+Number of Newton-Raphson Iterations: 5
+n= 26
+
+>
+> fitfg2 <- survreg(flsurv ~ age + ecog.ps, idat, dist='lognormal')
+> summary(fitfg2)
+
+Call:
+survreg(formula = flsurv ~ age + ecog.ps, data = idat, dist = "lognormal")
+ Value Std. Error z p
+(Intercept) 11.1548 1.4347 7.775 7.56e-15
+age -0.0855 0.0238 -3.598 3.20e-04
+ecog.ps 0.2066 0.3828 0.540 5.89e-01
+Log(scale) -0.2297 0.2508 -0.916 3.60e-01
+
+Scale= 0.795
+
+Log Normal distribution
+Loglik(model)= -56 Loglik(intercept only)= -63.5
+ Chisq= 14.94 on 2 degrees of freedom, p= 0.00057
+Number of Newton-Raphson Iterations: 5
+n= 26
+
+>
+> logt <- c(survreg.distributions$t,
++ survreg.distributions$weibull[c('trans', 'itrans', 'dtrans')])
+> logt$name <- 'log(t)'
+>
+> fitft2 <- survreg(Surv(ltime, rtime, type='interval2') ~ age + ecog.ps,
++ idat, dist=logt, parm=100)
+> summary(fitft2) #should be quite close to fitfg2
+
+Call:
+survreg(formula = Surv(ltime, rtime, type = "interval2") ~ age +
+ ecog.ps, data = idat, dist = logt, parms = 100)
+ Value Std. Error z p
+(Intercept) 11.1856 1.4419 7.758 8.66e-15
+age -0.0858 0.0238 -3.609 3.07e-04
+ecog.ps 0.1978 0.3814 0.519 6.04e-01
+Log(scale) -0.2394 0.2522 -0.949 3.43e-01
+
+Scale= 0.787
+
+log(t) distribution: parmameters= 100
+Loglik(model)= -56 Loglik(intercept only)= -63.5
+ Chisq= 14.97 on 2 degrees of freedom, p= 0.00056
+Number of Newton-Raphson Iterations: 5
+n= 26
+
+>
+> #
+> # Check out the survreg density and probability functions
+> #
+>
+> # Gaussian
+> x <- -10:10
+> p <- seq(.1, .95, length=25)
+> all.equal(dsurvreg(x, 1, 5, 'gaussian'), dnorm(x, 1, 5))
+[1] TRUE
+> all.equal(psurvreg(x, 1, 5, 'gaussian'), pnorm(x, 1, 5))
+[1] TRUE
+> all.equal(qsurvreg(p, 1, 5, 'gaussian'), qnorm(p, 1, 5))
+[1] TRUE
+>
+> # Lognormal
+> x <- 1:10
+> all.equal(dsurvreg(x, 1, 5, 'lognormal'), dlnorm(x, 1, 5))
+[1] TRUE
+> all.equal(psurvreg(x, 1, 5, 'lognormal'), plnorm(x, 1, 5))
+[1] TRUE
+> all.equal(qsurvreg(p, 1, 5, 'lognormal'), qlnorm(p, 1, 5))
+[1] TRUE
+>
+> # Weibull
+> lambda <- exp(-2)
+> rho <- 1/3
+> temp <- (lambda*x)^rho
+> all.equal(psurvreg(x, 2, 3), 1- exp(-temp))
+[1] TRUE
+> all.equal(dsurvreg(x, 2, 3), lambda*rho*(lambda*x)^(rho-1)*exp(-temp))
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/tiedtime.R b/win32/deps/library/survival/tests/tiedtime.R
new file mode 100644
index 0000000..647b996
--- /dev/null
+++ b/win32/deps/library/survival/tests/tiedtime.R
@@ -0,0 +1,23 @@
+library(survival)
+
+#
+# The survival code was failing for certain data sets when called as
+# survfit(Surv(time2-time1, status) ~ ......
+# The issue was how tied floating point numbers are handled, and the
+# fact that unique(x), factor(x) and tapply(x) are not guarranteed to
+# all be the same.
+# This test fails in survival 2.36-5, fixed in 2.36-6. Data sets that
+# can cause it are few and far between.
+#
+
+load('ties.rda')
+x <- time2 -time1
+
+# Here is the heart of the old problem
+# length(unique(x))== length(table(x))
+# And the prior fix which worked ALMOST always
+# x <- round(x, 15)
+# length(unique(round(x,15)))== length(table(round(x,15)))
+
+fit1 <- survfit(Surv(x) ~1)
+length(fit1$time) == length(fit1$surv)
diff --git a/win32/deps/library/survival/tests/tiedtime.Rout.save b/win32/deps/library/survival/tests/tiedtime.Rout.save
new file mode 100644
index 0000000..4a1d84b
--- /dev/null
+++ b/win32/deps/library/survival/tests/tiedtime.Rout.save
@@ -0,0 +1,44 @@
+
+R version 2.12.2 (2011-02-25)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(survival)
+Loading required package: splines
+>
+> #
+> # The survival code was failing for certain data sets when called as
+> # survfit(Surv(time2-time1, status) ~ ......
+> # The issue was how tied floating point numbers are handled, and the
+> # fact that unique(x), factor(x) and tapply(x) are not guarranteed to
+> # all be the same.
+> # This test fails in survival 2.36-5, fixed in 2.36-6. Data sets that
+> # can cause it are few and far between.
+> #
+>
+> load('ties.rda')
+> x <- time2 -time1
+>
+> # Here is the heart of the old problem
+> # length(unique(x))== length(table(x))
+> # And the prior fix which worked ALMOST always
+> # x <- round(x, 15)
+> # length(unique(round(x,15)))== length(table(round(x,15)))
+>
+> fit1 <- survfit(Surv(x) ~1)
+> length(fit1$time) == length(fit1$surv)
+[1] TRUE
+>
diff --git a/win32/deps/library/survival/tests/ties.rda b/win32/deps/library/survival/tests/ties.rda
new file mode 100644
index 0000000..f92af90
Binary files /dev/null and b/win32/deps/library/survival/tests/ties.rda differ
diff --git a/win32/deps/library/survival/tests/tt.R b/win32/deps/library/survival/tests/tt.R
new file mode 100644
index 0000000..e33f3ee
--- /dev/null
+++ b/win32/deps/library/survival/tests/tt.R
@@ -0,0 +1,38 @@
+library(survival)
+
+# A contrived example for the tt function
+#
+mkdata <- function(n, beta) {
+ age <- runif(n, 20, 60)
+ x <- rbinom(n, 1, .5)
+
+ futime <- rep(40, n) # everyone has 40 years of follow-up
+ status <- rep(0, n)
+ dtime <- runif(n/2, 1, 40) # 1/2 of them die
+ dtime <- sort(dtime)
+
+ # The risk is set to beta[1]*x + beta[2]* f(current_age)
+ # where f= 0 up to age 40, rises linear to age 70, flat after that
+ for (i in 1:length(dtime)) {
+ atrisk <- (futime >= dtime[i])
+ c.age <- age + dtime
+ age2 <- pmin(30, pmax(0, c.age-40))
+ xbeta <- beta[1]*x + beta[2]*age2
+
+ # Select a death according to risk
+ risk <- ifelse(atrisk, exp(xbeta), 0)
+ dead <- sample(1:n, 1, prob=risk/sum(risk))
+
+ futime[dead] <- dtime[i]
+ status[dead] <- 1
+ }
+ data.frame(futime=futime, status=status, age=age, x=x, risk=risk)
+}
+tdata <- mkdata(500, c(log(1.5), 2/30))
+
+fit1 <- coxph(Surv(futime, status) ~ x + pspline(age), tdata)
+fit2 <- coxph(Surv(futime, status) ~ x + tt(age), tdata,
+ tt= function(x, t, ...) pspline(x+t))
+
+dfit <- coxph(Surv(futime, status) ~ x + tt(age), tdata,
+ tt= function(x, t, ...) x+t, iter=0, x=T)
diff --git a/win32/deps/library/survival/tests/turnbull.R b/win32/deps/library/survival/tests/turnbull.R
new file mode 100644
index 0000000..9085298
--- /dev/null
+++ b/win32/deps/library/survival/tests/turnbull.R
@@ -0,0 +1,156 @@
+options(na.action=na.exclude) # preserve missings
+options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+library(survival)
+
+#
+# The test data set from Turnbull, JASA 1974, 169-73.
+#
+# status 0=right censored
+# 1=exact
+# 2=left censored
+#
+aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+
+
+turnbull <- data.frame( time =c( 1,1,1, 2,2,2, 3,3,3, 4,4,4),
+ status=c( 1,0,2, 1,0,2, 1,0,2, 1,0,2),
+ n =c(12,3,2, 6,2,4, 2,0,2, 3,3,5))
+#
+# Compute the K-M for the Turnbull data
+# via a slow EM calculation
+#
+
+emsurv <- function(time, status, wt, verbose=T) {
+ left.cen <- (status==2)
+ if (!any(left.cen)) stop("No left censored data!")
+ if (!any(status==1))stop("Must have some exact death times")
+
+ tempy <- Surv(time[!left.cen], status[!left.cen])
+ ww <- wt[!left.cen]
+ tempx <- factor(rep(1, sum(!left.cen)))
+ tfit <- survfit(tempy~tempx, weight=ww)
+ if (verbose)
+ cat("Iteration 0, survival=", format(round(tfit$surv[tfit$n.event>0],3)),
+ "\n")
+
+ stimes <- tfit$time[tfit$n.event>0]
+ ltime <- time[left.cen]
+ lwt <- wt[left.cen]
+ tempx <- factor(rep(1, length(stimes) + sum(!left.cen)))
+ tempy <- Surv(c(time[!left.cen], stimes),
+ c(status[!left.cen], rep(1, length(stimes))))
+ for (iter in 1:4) {
+ wt2 <- stimes*0
+ ssurv <- tfit$surv[tfit$n.event>0]
+ sjump <- diff(c(1, ssurv))
+ for (j in 1:(length(ltime))) {
+ k <- sum(ltime[j]>=stimes) #index of the death time
+ if (k==0)
+ stop("Left censored observation before the first death")
+ wt2[1:k] <- wt2[1:k] + lwt[j]*sjump[1:k] /(ssurv[k]-1)
+ }
+ tfit <- survfit(tempy~tempx, weight=c(ww, wt2))
+ if (verbose) {
+ cat("Iteration", iter, "survival=",
+ format(round(tfit$surv[tfit$n.event>0],3)), "\n")
+ cat(" weights=", format(round(wt2,3)), "\n")
+ }
+ }
+ survfit(tempy ~ tempx, weights=c(ww, wt2))
+ }
+
+temp <-emsurv(turnbull$time, turnbull$status, turnbull$n)
+print(summary(temp))
+# First check, use the data from Turnbull, JASA 1974, 169-173.
+
+tdata <- data.frame(time =c(1,1,1,2,2,2,3,3,3,4,4,4),
+ status=rep(c(1,0,2),4),
+ n =c(12,3,2,6,2,4,2,0,2,3,3,5))
+
+tfit <- survfit(Surv(time, time, status, type='interval') ~1, tdata, weight=n)
+all.equal(round(tfit$surv,3), c(.538, .295, .210, .095))
+
+
+# Second check, compare to a reversed survival curve
+# This is not as simple a test as one might think, because left and right
+# censored observations are not treated symmetrically by the routine:
+# time <= y for left and time> y for right (this is to make the routine
+# correct for the common situation of panel data).
+# To get equivalence, make the left censoreds happen just a little bit
+# earlier. The left-continuous/right-continuous shift is also a bother.
+#
+test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
+ status=c(1,NA,1,0,1,1,0),
+ x= c(0, 2,1,1,1,0,0))
+fit1 <- survfit(Surv(time, status) ~1, test1)
+temp <- ifelse(test1$status==0, 4.99,5) - test1$time
+fit2 <- survfit(Surv(temp, status, type='left') ~1, test1)
+
+all.equal(round(fit1$surv[1:2],5), round(1-fit2$surv[3:2],5))
+
+rm(tdata, tfit, fit1, temp, fit2)
+#
+# Create a data set similar to the one provided by Al Zinsmeister
+# It is a hard test case for survfit.turnbull
+#
+time1 <- c(rep(0,100), rep(1,200), 100, 200, 210, 220,
+ rep(365,100), rep(366,5), 731:741)
+
+time2 <- c((1:100)*3, 10+1:100, rep(365:366, c(60,40)), NA, 500, NA, 450,
+ rep(730,90), rep(NA,10), c(528,571,691,730,731),
+ NA, 1095:1099, NA, 1400, 1200, 772, 1461)
+
+zfit <- survfit(Surv(time1, time2, type='interval2') ~1)
+
+#
+# There are 100 intervals of the form (0,x) where x is from 3 to 300,
+# and 200 more of the form (1,x) where x is from 11 to 366. These
+# lead to a mass point in the interval (1,3), which is placed at 2.
+# The starting estimate has far too little mass placed here, and it takes
+# the EM a long time to realize that most of the weight for the first 300
+# subjects goes here. With acceleration, it takes 16 iterations, without
+# it takes >40. (On Al's orginal data, without accel still wasn't there after
+# 165 iters!)
+#
+# The next 4 obs give rise to potential jumps at 100.5, 200.5, 211.5, and
+# 221. However, the final estimate has no mass at all on any of these.
+# Assume mass of a,b, and c at 2, 100.5 and 365.5, and consider the
+# contributions:
+# 123 obs that overlap a only
+# 137 obs that overlap a and b
+# 40 obs that overlap a, b, c
+# 1 obs that overlap b, c
+# 108 obs that overlap c (200, 210,200, 365, and 366 starting points)
+# For some trial values of a,b,c, compare the loglik to that of (a+b),0,c
+# First one: a^123 (a+b)^137 (a+b+c)^40 (b+c) c^108
+# Second: (a+b)^123 (a+b)^137 (a+b+c)^40 c c^108
+# Likelhood improves if (1 + b/a)^123 > 1+ b/c, which is true for almost
+# all a and c. In particular, at the solution a and c are approx .7 and
+# .18, respectively.
+#
+# The program can't see this coming, of course, and so iterates towards a
+# KM with epsilon sized jumps at 100.5, 200.5, and 211.5. Whether these
+# intervals should be removed during iteration, as detected, is an open
+# question for me.
+#
+#
+# True solution: mass points at 2, 365.5, 408, and 756.5, of sizes a, b, c, d
+# Likelihood: a^260 (a+b)^40 (b+c)^92 (b+c+d)^12 c^5 d^11
+# Solution: a=0.6958, b=0.1674, c=0.1079, d=0.0289
+
+tfun <- function(x) {
+ if (length(x) ==3) x <- c(x, .03)
+ x <- x/sum(x) #make probabilities sum to 1
+ loglik <- 260*log(x[1]) + 40*log(x[1]+x[2]) + 92*log(x[2] + x[3]) +
+ 12*log(x[2]+x[3]+x[4]) + 5*log(x[3]) + 11*log(x[4])
+ -loglik #find the max, not the min
+ }
+
+nfit <- nlminb(start=c(.7,.15, .1), tfun, lower=0, upper=1)
+nparm <- c(nfit$par, .03)
+nparm <- nparm / sum(nparm)
+zparm <- -diff(c(1, zfit$surv[match(c(2, 365.5, 408, 756.5), zfit$time)]))
+aeq(round(tfun(nparm),4), round(tfun(zparm),4))
+# .0001 is the tolerance in survfit.turnbull
+
+rm(tfun, nfit, nparm, zparm, time1, time2, zfit)
diff --git a/win32/deps/library/survival/tests/turnbull.Rout.save b/win32/deps/library/survival/tests/turnbull.Rout.save
new file mode 100644
index 0000000..06c2c6c
--- /dev/null
+++ b/win32/deps/library/survival/tests/turnbull.Rout.save
@@ -0,0 +1,194 @@
+
+R version 2.7.1 (2008-06-23)
+Copyright (C) 2008 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> options(na.action=na.exclude) # preserve missings
+> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
+> library(survival)
+Loading required package: splines
+>
+> #
+> # The test data set from Turnbull, JASA 1974, 169-73.
+> #
+> # status 0=right censored
+> # 1=exact
+> # 2=left censored
+> #
+> aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
+>
+>
+> turnbull <- data.frame( time =c( 1,1,1, 2,2,2, 3,3,3, 4,4,4),
++ status=c( 1,0,2, 1,0,2, 1,0,2, 1,0,2),
++ n =c(12,3,2, 6,2,4, 2,0,2, 3,3,5))
+> #
+> # Compute the K-M for the Turnbull data
+> # via a slow EM calculation
+> #
+>
+> emsurv <- function(time, status, wt, verbose=T) {
++ left.cen <- (status==2)
++ if (!any(left.cen)) stop("No left censored data!")
++ if (!any(status==1))stop("Must have some exact death times")
++
++ tempy <- Surv(time[!left.cen], status[!left.cen])
++ ww <- wt[!left.cen]
++ tempx <- factor(rep(1, sum(!left.cen)))
++ tfit <- survfit(tempy~tempx, weight=ww)
++ if (verbose)
++ cat("Iteration 0, survival=", format(round(tfit$surv[tfit$n.event>0],3)),
++ "\n")
++
++ stimes <- tfit$time[tfit$n.event>0]
++ ltime <- time[left.cen]
++ lwt <- wt[left.cen]
++ tempx <- factor(rep(1, length(stimes) + sum(!left.cen)))
++ tempy <- Surv(c(time[!left.cen], stimes),
++ c(status[!left.cen], rep(1, length(stimes))))
++ for (iter in 1:4) {
++ wt2 <- stimes*0
++ ssurv <- tfit$surv[tfit$n.event>0]
++ sjump <- diff(c(1, ssurv))
++ for (j in 1:(length(ltime))) {
++ k <- sum(ltime[j]>=stimes) #index of the death time
++ if (k==0)
++ stop("Left censored observation before the first death")
++ wt2[1:k] <- wt2[1:k] + lwt[j]*sjump[1:k] /(ssurv[k]-1)
++ }
++ tfit <- survfit(tempy~tempx, weight=c(ww, wt2))
++ if (verbose) {
++ cat("Iteration", iter, "survival=",
++ format(round(tfit$surv[tfit$n.event>0],3)), "\n")
++ cat(" weights=", format(round(wt2,3)), "\n")
++ }
++ }
++ survfit(tempy ~ tempx, weights=c(ww, wt2))
++ }
+>
+> temp <-emsurv(turnbull$time, turnbull$status, turnbull$n)
+Iteration 0, survival= 0.613 0.383 0.287 0.144
+Iteration 1 survival= 0.549 0.303 0.214 0.094
+ weights= 7.856 3.477 0.828 0.839
+Iteration 2 survival= 0.540 0.296 0.210 0.095
+ weights= 8.228 3.394 0.714 0.664
+Iteration 3 survival= 0.538 0.295 0.210 0.095
+ weights= 8.315 3.356 0.690 0.638
+Iteration 4 survival= 0.538 0.295 0.210 0.095
+ weights= 8.338 3.342 0.685 0.635
+> print(summary(temp))
+Call: survfit(formula = tempy ~ tempx, weights = c(ww, wt2))
+
+ time n.risk n.event survival std.err lower 95% CI upper 95% CI
+ 1 44.00 20.34 0.5378 0.0752 0.4089 0.707
+ 2 20.66 9.34 0.2946 0.0719 0.1827 0.475
+ 3 9.32 2.68 0.2098 0.0673 0.1119 0.393
+ 4 6.64 3.64 0.0948 0.0507 0.0333 0.270
+> # First check, use the data from Turnbull, JASA 1974, 169-173.
+>
+> tdata <- data.frame(time =c(1,1,1,2,2,2,3,3,3,4,4,4),
++ status=rep(c(1,0,2),4),
++ n =c(12,3,2,6,2,4,2,0,2,3,3,5))
+>
+> tfit <- survfit(Surv(time, time, status, type='interval') ~1, tdata, weight=n)
+> all.equal(round(tfit$surv,3), c(.538, .295, .210, .095))
+[1] TRUE
+>
+>
+> # Second check, compare to a reversed survival curve
+> # This is not as simple a test as one might think, because left and right
+> # censored observations are not treated symmetrically by the routine:
+> # time <= y for left and time> y for right (this is to make the routine
+> # correct for the common situation of panel data).
+> # To get equivalence, make the left censoreds happen just a little bit
+> # earlier. The left-continuous/right-continuous shift is also a bother.
+> #
+> test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
++ status=c(1,NA,1,0,1,1,0),
++ x= c(0, 2,1,1,1,0,0))
+> fit1 <- survfit(Surv(time, status) ~1, test1)
+> temp <- ifelse(test1$status==0, 4.99,5) - test1$time
+> fit2 <- survfit(Surv(temp, status, type='left') ~1, test1)
+>
+> all.equal(round(fit1$surv[1:2],5), round(1-fit2$surv[3:2],5))
+[1] TRUE
+>
+> rm(tdata, tfit, fit1, temp, fit2)
+> #
+> # Create a data set similar to the one provided by Al Zinsmeister
+> # It is a hard test case for survfit.turnbull
+> #
+> time1 <- c(rep(0,100), rep(1,200), 100, 200, 210, 220,
++ rep(365,100), rep(366,5), 731:741)
+>
+> time2 <- c((1:100)*3, 10+1:100, rep(365:366, c(60,40)), NA, 500, NA, 450,
++ rep(730,90), rep(NA,10), c(528,571,691,730,731),
++ NA, 1095:1099, NA, 1400, 1200, 772, 1461)
+>
+> zfit <- survfit(Surv(time1, time2, type='interval2') ~1)
+>
+> #
+> # There are 100 intervals of the form (0,x) where x is from 3 to 300,
+> # and 200 more of the form (1,x) where x is from 11 to 366. These
+> # lead to a mass point in the interval (1,3), which is placed at 2.
+> # The starting estimate has far too little mass placed here, and it takes
+> # the EM a long time to realize that most of the weight for the first 300
+> # subjects goes here. With acceleration, it takes 16 iterations, without
+> # it takes >40. (On Al's orginal data, without accel still wasn't there after
+> # 165 iters!)
+> #
+> # The next 4 obs give rise to potential jumps at 100.5, 200.5, 211.5, and
+> # 221. However, the final estimate has no mass at all on any of these.
+> # Assume mass of a,b, and c at 2, 100.5 and 365.5, and consider the
+> # contributions:
+> # 123 obs that overlap a only
+> # 137 obs that overlap a and b
+> # 40 obs that overlap a, b, c
+> # 1 obs that overlap b, c
+> # 108 obs that overlap c (200, 210,200, 365, and 366 starting points)
+> # For some trial values of a,b,c, compare the loglik to that of (a+b),0,c
+> # First one: a^123 (a+b)^137 (a+b+c)^40 (b+c) c^108
+> # Second: (a+b)^123 (a+b)^137 (a+b+c)^40 c c^108
+> # Likelhood improves if (1 + b/a)^123 > 1+ b/c, which is true for almost
+> # all a and c. In particular, at the solution a and c are approx .7 and
+> # .18, respectively.
+> #
+> # The program can't see this coming, of course, and so iterates towards a
+> # KM with epsilon sized jumps at 100.5, 200.5, and 211.5. Whether these
+> # intervals should be removed during iteration, as detected, is an open
+> # question for me.
+> #
+> #
+> # True solution: mass points at 2, 365.5, 408, and 756.5, of sizes a, b, c, d
+> # Likelihood: a^260 (a+b)^40 (b+c)^92 (b+c+d)^12 c^5 d^11
+> # Solution: a=0.6958, b=0.1674, c=0.1079, d=0.0289
+>
+> tfun <- function(x) {
++ if (length(x) ==3) x <- c(x, .03)
++ x <- x/sum(x) #make probabilities sum to 1
++ loglik <- 260*log(x[1]) + 40*log(x[1]+x[2]) + 92*log(x[2] + x[3]) +
++ 12*log(x[2]+x[3]+x[4]) + 5*log(x[3]) + 11*log(x[4])
++ -loglik #find the max, not the min
++ }
+>
+> nfit <- nlminb(start=c(.7,.15, .1), tfun, lower=0, upper=1)
+> nparm <- c(nfit$par, .03)
+> nparm <- nparm / sum(nparm)
+> zparm <- -diff(c(1, zfit$surv[match(c(2, 365.5, 408, 756.5), zfit$time)]))
+> aeq(round(tfun(nparm),4), round(tfun(zparm),4))
+[1] TRUE
+> # .0001 is the tolerance in survfit.turnbull
+>
+> rm(tfun, nfit, nparm, zparm, time1, time2, zfit)
+>
diff --git a/win32/deps/library/tcltk/DESCRIPTION b/win32/deps/library/tcltk/DESCRIPTION
index e751aa4..f6775a6 100644
--- a/win32/deps/library/tcltk/DESCRIPTION
+++ b/win32/deps/library/tcltk/DESCRIPTION
@@ -1,9 +1,9 @@
Package: tcltk
-Version: 2.9.2
+Version: 2.15.2
Priority: base
Title: Tcl/Tk Interface
-Author: R Development Core Team
+Author: R Core Team
Maintainer: R Core Team <R-core r-project org>
Description: Interface and language bindings to Tcl/Tk GUI elements
-License: Part of R 2.9.2
-Built: R 2.9.2; i386-pc-mingw32; 2009-08-24 12:46:17 UTC; windows
+License: Part of R 2.15.2
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:07:59 UTC; windows
diff --git a/win32/deps/library/tcltk/Meta/Rd.rds b/win32/deps/library/tcltk/Meta/Rd.rds
index f6dcf06..8ba6f84 100644
Binary files a/win32/deps/library/tcltk/Meta/Rd.rds and b/win32/deps/library/tcltk/Meta/Rd.rds differ
diff --git a/win32/deps/library/tcltk/Meta/demo.rds b/win32/deps/library/tcltk/Meta/demo.rds
index cbee420..05fbae2 100644
Binary files a/win32/deps/library/tcltk/Meta/demo.rds and b/win32/deps/library/tcltk/Meta/demo.rds differ
diff --git a/win32/deps/library/tcltk/Meta/hsearch.rds b/win32/deps/library/tcltk/Meta/hsearch.rds
index 505542f..7d39ba5 100644
Binary files a/win32/deps/library/tcltk/Meta/hsearch.rds and b/win32/deps/library/tcltk/Meta/hsearch.rds differ
diff --git a/win32/deps/library/tcltk/Meta/links.rds b/win32/deps/library/tcltk/Meta/links.rds
new file mode 100644
index 0000000..6e932d4
Binary files /dev/null and b/win32/deps/library/tcltk/Meta/links.rds differ
diff --git a/win32/deps/library/tcltk/Meta/nsInfo.rds b/win32/deps/library/tcltk/Meta/nsInfo.rds
index 34b622b..e199a7d 100644
Binary files a/win32/deps/library/tcltk/Meta/nsInfo.rds and b/win32/deps/library/tcltk/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/tcltk/Meta/package.rds b/win32/deps/library/tcltk/Meta/package.rds
index a06ad86..78663cf 100644
Binary files a/win32/deps/library/tcltk/Meta/package.rds and b/win32/deps/library/tcltk/Meta/package.rds differ
diff --git a/win32/deps/library/tcltk/NAMESPACE b/win32/deps/library/tcltk/NAMESPACE
index a78c001..03cc88e 100644
--- a/win32/deps/library/tcltk/NAMESPACE
+++ b/win32/deps/library/tcltk/NAMESPACE
@@ -14,6 +14,7 @@ S3method(as.character, tclVar)
S3method(as.double, tclObj)
S3method(as.integer, tclObj)
S3method(as.logical, tclObj)
+S3method(as.raw, tclObj)
S3method(print, tclObj)
S3method("[[", tclArray)
S3method("[[<-", tclArray)
diff --git a/win32/deps/library/tcltk/R/tcltk b/win32/deps/library/tcltk/R/tcltk
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/tcltk/R/tcltk
+++ b/win32/deps/library/tcltk/R/tcltk
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/tcltk/R/tcltk.rdb b/win32/deps/library/tcltk/R/tcltk.rdb
index 332bdca..dc96e7c 100644
Binary files a/win32/deps/library/tcltk/R/tcltk.rdb and b/win32/deps/library/tcltk/R/tcltk.rdb differ
diff --git a/win32/deps/library/tcltk/R/tcltk.rdx b/win32/deps/library/tcltk/R/tcltk.rdx
index 43741c0..f49bb47 100644
Binary files a/win32/deps/library/tcltk/R/tcltk.rdx and b/win32/deps/library/tcltk/R/tcltk.rdx differ
diff --git a/win32/deps/library/tcltk/demo/tkcanvas.R b/win32/deps/library/tcltk/demo/tkcanvas.R
index 249ba2e..9783f4e 100644
--- a/win32/deps/library/tcltk/demo/tkcanvas.R
+++ b/win32/deps/library/tcltk/demo/tkcanvas.R
@@ -5,6 +5,8 @@
### It is a ripoff of the plot.tcl demo from the tk 8.0 distribution
### All I did was to add the code to plot the fitted regression line.
+# Copyright (C) 2000-2008 The R Core Team
+
require(tcltk) || stop("tcl/tk library not available")
require(graphics); require(stats)
local({
diff --git a/win32/deps/library/tcltk/demo/tkdensity.R b/win32/deps/library/tcltk/demo/tkdensity.R
index 6144ab5..1abf94f 100644
--- a/win32/deps/library/tcltk/demo/tkdensity.R
+++ b/win32/deps/library/tcltk/demo/tkdensity.R
@@ -1,4 +1,6 @@
-### Interactive density plots. Based on TCL version by Guido Masarotto
+### Interactive density plots. Based on Tcl version by Guido Masarotto
+
+# Copyright (C) 2000-2009 The R Core Team
require(tcltk) || stop("tcltk support is absent")
require(graphics); require(stats)
@@ -40,7 +42,7 @@ local({
replot()
}
-
+ grDevices::devAskNewPage(FALSE) # override setting in demo()
tclServiceMode(FALSE)
base <- tktoplevel()
tkwm.title(base, "Density")
diff --git a/win32/deps/library/tcltk/demo/tkfaq.R b/win32/deps/library/tcltk/demo/tkfaq.R
index 21c5bd0..a4556e8 100644
--- a/win32/deps/library/tcltk/demo/tkfaq.R
+++ b/win32/deps/library/tcltk/demo/tkfaq.R
@@ -1,3 +1,5 @@
+# Copyright (C) 2000-2008 The R Core Team
+
require(tcltk) || stop("tcltk support is absent")
local({
have_ttk <- as.character(tcl("info", "tclversion")) >= "8.5"
diff --git a/win32/deps/library/tcltk/demo/tkttest.R b/win32/deps/library/tcltk/demo/tkttest.R
index c2f8393..b0f37b9 100644
--- a/win32/deps/library/tcltk/demo/tkttest.R
+++ b/win32/deps/library/tcltk/demo/tkttest.R
@@ -1,3 +1,5 @@
+# Copyright (C) 2000-2008 The R Core Team
+
require(tcltk) || stop("tcltk support is absent")
require(stats)
diff --git a/win32/deps/library/tcltk/exec/Tk-frontend.R b/win32/deps/library/tcltk/exec/Tk-frontend.R
index e828e7b..93c0cbf 100644
--- a/win32/deps/library/tcltk/exec/Tk-frontend.R
+++ b/win32/deps/library/tcltk/exec/Tk-frontend.R
@@ -1,6 +1,24 @@
+# File src/library/tools/R/news.R
+# Part of the R package, http://www.R-project.org
+#
+# Copyright (C) 2003 The R Core Team
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# A copy of the GNU General Public License is available at
+# http://www.r-project.org/Licenses/
+
{
# NOTE: This file resides in the exec directory rather than the R
- # directory because it does not define functions but is intended to
+ # directory because it does not define functions but is intended to
# be sourced into a running R.
library(tcltk)
tkStartGUI()
diff --git a/win32/deps/library/tcltk/exec/console.tcl b/win32/deps/library/tcltk/exec/console.tcl
index f41924f..3c63022 100644
--- a/win32/deps/library/tcltk/exec/console.tcl
+++ b/win32/deps/library/tcltk/exec/console.tcl
@@ -2,7 +2,7 @@ menu .menu
toplevel .tk-R -menu .menu
wm protocol .tk-R WM_DELETE_WINDOW {}
pack [frame .tk-R.toolbar] -anchor n -fill x
-pack [text .tk-R.term -bg white -font 9x15]
+pack [text .tk-R.term -bg white -font [list Courier 14]] -expand true -fill both
## Implements a "stop button" which sends SIGINT to the R process.
## Unfortunately, SIGINTs are not handled gracefully...
diff --git a/win32/deps/library/tcltk/help/AnIndex b/win32/deps/library/tcltk/help/AnIndex
index 0943aaf..7f5e625 100644
--- a/win32/deps/library/tcltk/help/AnIndex
+++ b/win32/deps/library/tcltk/help/AnIndex
@@ -17,6 +17,8 @@ as.character.tclObj TclInterface
as.character.tclVar TclInterface
as.double.tclObj TclInterface
as.integer.tclObj TclInterface
+as.logical.tclObj TclInterface
+as.raw.tclObj TclInterface
as.tclObj TclInterface
close.tkProgressBar tkProgressBar
getTkProgressBar tkProgressBar
diff --git a/win32/deps/library/tcltk/help/aliases.rds b/win32/deps/library/tcltk/help/aliases.rds
new file mode 100644
index 0000000..e03797f
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@@ -0,0 +1,664 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Tcl/Tk Interface</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Tcl/Tk Interface
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘tcltk’ version 2.15.2</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+<li><a href="../demo">Code demos</a>. Use <a href="../../utils/help/demo">demo()</a> to run them.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<p align="center">
+<a href="# "> </a>
+<a href="#A">A</a>
+<a href="#C">C</a>
+<a href="#G">G</a>
+<a href="#I">I</a>
+<a href="#L">L</a>
+<a href="#N">N</a>
+<a href="#P">P</a>
+<a href="#S">S</a>
+<a href="#T">T</a>
+<a href="#misc">misc</a>
+</p>
+
+<table width="100%">
+<tr><td width="25%"><a href="tcltk-package.html">tcltk-package</a></td>
+<td>Tcl/Tk Interface</td></tr>
+</table>
+
+<h2><a name="A">-- A --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="TclInterface.html">addTclPath</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">as.character.tclObj</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">as.character.tclVar</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">as.double.tclObj</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">as.integer.tclObj</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">as.logical.tclObj</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">as.raw.tclObj</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">as.tclObj</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+</table>
+
+<h2><a name="C">-- C --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="tkProgressBar.html">close.tkProgressBar</a></td>
+<td>Progress Bars via Tk</td></tr>
+</table>
+
+<h2><a name="G">-- G --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="tkProgressBar.html">getTkProgressBar</a></td>
+<td>Progress Bars via Tk</td></tr>
+</table>
+
+<h2><a name="I">-- I --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="TclInterface.html">is.tclObj</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">is.tkwin</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+</table>
+
+<h2><a name="L">-- L --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="TclInterface.html">length.tclArray</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">length<-.tclArray</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+</table>
+
+<h2><a name="N">-- N --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="TclInterface.html">names.tclArray</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">names<-.tclArray</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+</table>
+
+<h2><a name="P">-- P --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="TclInterface.html">print.tclObj</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+</table>
+
+<h2><a name="S">-- S --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="tkProgressBar.html">setTkProgressBar</a></td>
+<td>Progress Bars via Tk</td></tr>
+</table>
+
+<h2><a name="T">-- T --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="TkCommands.html">tcl</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">tclArray</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tclclose</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tclfile.dir</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tclfile.tail</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">TclInterface</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">tclObj</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">tclObj.tclVar</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">tclObj<-</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">tclObj<-.tclVar</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tclopen</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tclputs</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tclread</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">tclRequire</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="tclServiceMode.html">tclServiceMode</a></td>
+<td>Allow Tcl events to be serviced or not</td></tr>
+<tr><td width="25%"><a href="tcltk-package.html">tcltk</a></td>
+<td>Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">tclvalue</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">tclvalue.default</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">tclvalue.tclObj</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">tclvalue.tclVar</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">tclvalue<-</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">tclvalue<-.default</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">tclvalue<-.tclVar</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">tclVar</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">tclvar</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkactivate</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkadd</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkaddtag</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkbbox</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkbell</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkbind</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkbindtags</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">tkbutton</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">tkcanvas</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkcanvasx</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkcanvasy</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkcget</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">tkcheckbutton</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkchooseDirectory</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkclipboard.append</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkclipboard.clear</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">TkCommands</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkcompare</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkconfigure</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkcoords</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkcreate</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkcurselection</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkdchars</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkdebug</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkdelete</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkdelta</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkdeselect</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">tkdestroy</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkdialog</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkdlineinfo</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkdtag</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkdump</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">tkentry</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkentrycget</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkentryconfigure</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkevent.add</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkevent.delete</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkevent.generate</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkevent.info</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkfind</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkflash</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkfocus</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkfont.actual</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkfont.configure</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkfont.create</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkfont.delete</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkfont.families</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkfont.measure</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkfont.metrics</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkfont.names</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkfraction</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">tkframe</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkget</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkgetOpenFile</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkgetSaveFile</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkgettags</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkgrab</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkgrab.current</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkgrab.release</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkgrab.set</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkgrab.status</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkgrid</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkgrid.bbox</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkgrid.columnconfigure</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkgrid.configure</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkgrid.forget</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkgrid.info</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkgrid.location</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkgrid.propagate</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkgrid.remove</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkgrid.rowconfigure</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkgrid.size</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkgrid.slaves</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkicursor</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkidentify</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkimage.cget</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkimage.configure</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkimage.create</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkimage.names</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkindex</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkinsert</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkinvoke</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkitembind</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkitemcget</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkitemconfigure</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkitemfocus</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkitemlower</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkitemraise</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkitemscale</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">tklabel</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">tklistbox</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tklower</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkmark.gravity</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkmark.names</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkmark.next</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkmark.previous</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkmark.set</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkmark.unset</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">tkmenu</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">tkmenubutton</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">tkmessage</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkmessageBox</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkmove</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tknearest</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkpack</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkpack.configure</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkpack.forget</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkpack.info</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkpack.propagate</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkpack.slaves</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="tkpager.html">tkpager</a></td>
+<td>Page file using Tk text widget</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkplace</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkplace.configure</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkplace.forget</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkplace.info</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkplace.slaves</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkpopup</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkpost</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkpostcascade</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkpostscript</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="tkProgressBar.html">tkProgressBar</a></td>
+<td>Progress Bars via Tk</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">tkradiobutton</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkraise</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">tkscale</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkscan.dragto</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkscan.mark</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">tkscrollbar</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tksearch</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tksee</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkselect</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkselection.adjust</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkselection.anchor</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkselection.clear</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkselection.from</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkselection.includes</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkselection.present</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkselection.range</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkselection.set</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkselection.to</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkset</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tksize</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="tkStartGUI.html">tkStartGUI</a></td>
+<td>Tcl/Tk GUI startup</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tktag.add</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tktag.bind</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tktag.cget</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tktag.configure</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tktag.delete</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tktag.lower</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tktag.names</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tktag.nextrange</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tktag.prevrange</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tktag.raise</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tktag.ranges</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tktag.remove</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">tktext</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tktitle</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tktitle<-</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tktoggle</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">tktoplevel</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tktype</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkunpost</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwait.variable</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwait.visibility</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwait.window</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">tkwidget</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">TkWidgetcmds</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">TkWidgets</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkwindow.cget</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkwindow.configure</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkwindow.create</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkwindow.names</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwinfo</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.aspect</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.client</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.colormapwindows</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.command</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.deiconify</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.focusmodel</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.frame</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.geometry</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.grid</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.group</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.iconbitmap</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.iconify</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.iconmask</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.iconname</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.iconposition</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.iconwindow</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.maxsize</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.minsize</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.overrideredirect</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.positionfrom</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.protocol</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.resizable</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.sizefrom</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.state</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.title</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.transient</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkwm.withdraw</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkXselection.clear</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkXselection.get</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkXselection.handle</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkCommands.html">tkXselection.own</a></td>
+<td>Tk non-widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkxview</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkxview.moveto</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkxview.scroll</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkyposition</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkyview</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkyview.moveto</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="TkWidgetcmds.html">tkyview.scroll</a></td>
+<td>Tk widget commands</td></tr>
+<tr><td width="25%"><a href="tk_choose.dir.html">tk_choose.dir</a></td>
+<td>Choose a Folder Interactively</td></tr>
+<tr><td width="25%"><a href="tk_choose.files.html">tk_choose.files</a></td>
+<td>Choose a List of Files Interactively</td></tr>
+<tr><td width="25%"><a href="tk_messageBox.html">tk_messageBox</a></td>
+<td>Tk Message Box</td></tr>
+<tr><td width="25%"><a href="tk_select.list.html">tk_select.list</a></td>
+<td>Select Items from a List</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">ttkbutton</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">ttkcheckbutton</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">ttkcombobox</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">ttkentry</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">ttkframe</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">ttkimage</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">ttklabel</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">ttklabelframe</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">ttkmenubutton</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">ttknotebook</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">ttkpanedwindow</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">ttkprogressbar</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">ttkradiobutton</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">ttkscrollbar</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">ttkseparator</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">ttksizegrip</a></td>
+<td>Tk widgets</td></tr>
+<tr><td width="25%"><a href="TkWidgets.html">ttktreeview</a></td>
+<td>Tk widgets</td></tr>
+</table>
+
+<h2><a name="misc">-- misc --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="TclInterface.html">$.tclArray</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">$<-.tclArray</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">.Tcl</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">.Tcl.args</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">.Tcl.args.objv</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">.Tcl.callback</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">.Tcl.objv</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">.Tk.ID</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">.Tk.newwin</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">.Tk.subwin</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">.TkRoot</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">[[.tclArray</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+<tr><td width="25%"><a href="TclInterface.html">[[<-.tclArray</a></td>
+<td>Low-level Tcl/Tk Interface</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/tcltk/html/R.css b/win32/deps/library/tcltk/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/tcltk/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/tcltk/libs/i386/tcltk.dll b/win32/deps/library/tcltk/libs/i386/tcltk.dll
new file mode 100644
index 0000000..8bb20d7
Binary files /dev/null and b/win32/deps/library/tcltk/libs/i386/tcltk.dll differ
diff --git a/win32/deps/library/tcltk/po/da/LC_MESSAGES/R-tcltk.mo b/win32/deps/library/tcltk/po/da/LC_MESSAGES/R-tcltk.mo
new file mode 100644
index 0000000..4a39272
Binary files /dev/null and b/win32/deps/library/tcltk/po/da/LC_MESSAGES/R-tcltk.mo differ
diff --git a/win32/deps/library/tcltk/po/da/LC_MESSAGES/tcltk.mo b/win32/deps/library/tcltk/po/da/LC_MESSAGES/tcltk.mo
new file mode 100644
index 0000000..19e8f4b
Binary files /dev/null and b/win32/deps/library/tcltk/po/da/LC_MESSAGES/tcltk.mo differ
diff --git a/win32/deps/library/tcltk/po/de/LC_MESSAGES/R-tcltk.mo b/win32/deps/library/tcltk/po/de/LC_MESSAGES/R-tcltk.mo
new file mode 100644
index 0000000..315550c
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diff --git a/win32/deps/library/tcltk/po/ru/LC_MESSAGES/R-tcltk.mo b/win32/deps/library/tcltk/po/ru/LC_MESSAGES/R-tcltk.mo
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index 0000000..5a424a5
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diff --git a/win32/deps/library/tcltk/po/zh_CN/LC_MESSAGES/R-tcltk.mo b/win32/deps/library/tcltk/po/zh_CN/LC_MESSAGES/R-tcltk.mo
new file mode 100644
index 0000000..0354ed0
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diff --git a/win32/deps/library/tcltk/po/zh_CN/LC_MESSAGES/tcltk.mo b/win32/deps/library/tcltk/po/zh_CN/LC_MESSAGES/tcltk.mo
new file mode 100644
index 0000000..b66c5e1
Binary files /dev/null and b/win32/deps/library/tcltk/po/zh_CN/LC_MESSAGES/tcltk.mo differ
diff --git a/win32/deps/library/tools/DESCRIPTION b/win32/deps/library/tools/DESCRIPTION
index 68a2ced..388c890 100644
--- a/win32/deps/library/tools/DESCRIPTION
+++ b/win32/deps/library/tools/DESCRIPTION
@@ -1,10 +1,9 @@
Package: tools
-Version: 2.9.2
+Version: 2.15.2
Priority: base
Title: Tools for Package Development
-Author: Kurt Hornik and Friedrich Leisch
+Author: R Core Team
Maintainer: R Core Team <R-core r-project org>
-Description: Tools for package development, administration and
- documentation
-License: Part of R 2.9.2
-Built: R 2.9.2; i386-pc-mingw32; 2009-08-24 12:43:32 UTC; windows
+Description: Tools for package development, administration and documentation
+License: Part of R 2.15.2
+Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-27 03:04:38 UTC; windows
diff --git a/win32/deps/library/tools/INDEX b/win32/deps/library/tools/INDEX
index 7ca09f1..c6f7937 100644
--- a/win32/deps/library/tools/INDEX
+++ b/win32/deps/library/tools/INDEX
@@ -1,31 +1,53 @@
Adobe_glyphs Conversion Tables between Character Sets
+HTMLheader Generate a standard HTML header for R help
QC QC Checks for R Code and/or Documentation
-Rd2HTML Work with an Rd object
+Rd2HTML Rd Converters
+Rd2txt_options Set formatting options for text help
+RdTextFilter Select text in an Rd file.
Rd_db Rd Utilities
-Rdiff Difference \R Output Files
+Rdiff Difference R Output Files
Rdindex Generate Index from Rd Files
+SweaveTeXFilter Strip R code out of Sweave file
+add_datalist Add a 'datalist' File to a Package
+bibstyle Select or define a bibliography style.
buildVignettes List and Build Package Vignettes
checkFF Check Foreign Function Calls
checkMD5sums Check and Create MD5 Checksum Files
+checkPoFiles Check translation files for inconsistent format
+ strings.
+checkRd Check an Rd Object
+checkRdaFiles Report on Details of Saved Images or Re-saves
+ them
checkTnF Check R Packages or Code for T/F
checkVignettes Check Package Vignettes
codoc Check Code/Documentation Consistency
+compactPDF Compact PDF Files
delimMatch Delimited Pattern Matching
dependsOnPkgs Find Reverse Dependencies
encoded_text_to_latex Translate non-ASCII Text to LaTeX Escapes
-file_path_as_absolute File Utilities
+file_ext File Utilities
+findHTMLlinks Collect HTML Links from Package Documentation
getDepList Functions to Retrieve Dependency Information
installFoundDepends A function to install unresolved dependencies
-makeLazyLoading Lazy Loading of Packages
md5sum Compute MD5 Checksums
package.dependencies Check Package Dependencies
+package_dependencies Computations on the Dependency Hierarchy of
+ Packages
+parseLatex These experimental functions work with a subset
+ of LaTeX code.
parse_Rd Parse an Rd file
+pskill Kill a Process
+psnice Get or Set the Priority (Niceness) of a Process
read.00Index Read 00Index-style Files
readNEWS Read R's NEWS file or a similar one
-showNonASCII Highlight non-ASCII characters
+showNonASCII Pick Out Non-ASCII Characters
+startDynamicHelp Start the Dynamic HTML Help System
testInstalledPackage Test Installed Packages
texi2dvi Compile LaTeX Files
-tools-deprecated Deprecated Objects in Package tools
+toHTML Display an object in HTML.
+toRd Generic function to convert object to a
+ fragment of Rd code.
+tools-deprecated Deprecated Objects in Package 'tools'
tools-package Tools for Package Development
undoc Find Undocumented Objects
vignetteDepends Retrieve Dependency Information for a Vignette
diff --git a/win32/deps/library/tools/Meta/Rd.rds b/win32/deps/library/tools/Meta/Rd.rds
index a5af79a..38fba28 100644
Binary files a/win32/deps/library/tools/Meta/Rd.rds and b/win32/deps/library/tools/Meta/Rd.rds differ
diff --git a/win32/deps/library/tools/Meta/hsearch.rds b/win32/deps/library/tools/Meta/hsearch.rds
index 3c2b59b..a40ec81 100644
Binary files a/win32/deps/library/tools/Meta/hsearch.rds and b/win32/deps/library/tools/Meta/hsearch.rds differ
diff --git a/win32/deps/library/tools/Meta/links.rds b/win32/deps/library/tools/Meta/links.rds
new file mode 100644
index 0000000..b60dbac
Binary files /dev/null and b/win32/deps/library/tools/Meta/links.rds differ
diff --git a/win32/deps/library/tools/Meta/nsInfo.rds b/win32/deps/library/tools/Meta/nsInfo.rds
index b65daa7..76a2b4e 100644
Binary files a/win32/deps/library/tools/Meta/nsInfo.rds and b/win32/deps/library/tools/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/tools/Meta/package.rds b/win32/deps/library/tools/Meta/package.rds
index afdea5e..fa975ea 100644
Binary files a/win32/deps/library/tools/Meta/package.rds and b/win32/deps/library/tools/Meta/package.rds differ
diff --git a/win32/deps/library/tools/NAMESPACE b/win32/deps/library/tools/NAMESPACE
index 83ae095..c18cbfb 100644
--- a/win32/deps/library/tools/NAMESPACE
+++ b/win32/deps/library/tools/NAMESPACE
@@ -1,26 +1,80 @@
useDynLib(tools, .registration = TRUE)
-export("Rd2HTML", "Rd2ex", "Rd2latex", "Rd2txt", "Rdindex",
- "checkDocFiles", "checkDocStyle", "checkFF", "checkMD5sums",
- "checkReplaceFuns", "checkS3methods", "checkTnF",
- "checkVignettes", "codoc", "codocClasses", "codocData",
- "md5sum", "undoc", "file_path_as_absolute",
- "file_path_sans_ext", "list_files_with_exts", "findHTMLlinks",
- "list_files_with_type", "showNonASCII", "delimMatch",
- "parse_Rd", "checkRd", "texi2dvi", "buildVignettes",
- "pkgVignettes", "pkgDepends", "getDepList",
- "installFoundDepends", "vignetteDepends", "write_PACKAGES",
- "xgettext", "xgettext2pot", "xngettext",
- "encoded_text_to_latex", "charset_to_Unicode", "Adobe_glyphs",
- "checkNEWS", "readNEWS", "dependsOnPkgs", "Rdiff",
- "testInstalledBasic", "testInstalledPackage",
- "testInstalledPackages")
-
-export("Rd_db", "Rd_parse", "package.dependencies", "read.00Index")
+export("Adobe_glyphs", "HTMLheader", "Rd2HTML", "Rd2ex", "Rd2latex",
+ "Rd2txt", "Rd2txt_options", "RdTextFilter", "Rd_db",
+ "Rd_parse", "Rdiff", "Rdindex", "SweaveTeXFilter",
+ "add_datalist", "bibstyle", "buildVignettes",
+ "charset_to_Unicode", "checkDocFiles", "checkDocStyle",
+ "checkFF", "checkMD5sums", "checkNEWS", "checkRd",
+ "checkPoFile", "checkPoFiles", "checkRdaFiles", "checkReplaceFuns",
+ "checkS3methods", "checkTnF", "checkVignettes", "codoc",
+ "codocClasses", "codocData", "compactPDF", "delimMatch",
+ "deparseLatex", "dependsOnPkgs", "encoded_text_to_latex",
+ "file_ext", "file_path_as_absolute", "file_path_sans_ext",
+ "findHTMLlinks", "getDepList", "installFoundDepends",
+ "latexToUtf8", "list_files_with_exts", "list_files_with_type",
+ "md5sum", "package.dependencies", "package_dependencies",
+ "parseLatex", "parse_Rd", "pkgDepends", "pkgVignettes",
+ "pskill", "psnice", "read.00Index", "readNEWS",
+ "resaveRdaFiles", "showNonASCII", "showNonASCIIfile",
+ "startDynamicHelp", "testInstalledBasic",
+ "testInstalledPackage", "testInstalledPackages", "texi2dvi",
+ "texi2pdf", "toHTML", "toRd", "undoc", "vignetteDepends",
+ "write_PACKAGES", "xgettext", "xgettext2pot", "xngettext")
+exportPattern("^SIG.+")
+
+S3method("[", "pdf_doc")
+S3method("[[", "pdf_doc")
+
+S3method("as.character", "Rd")
+
+S3method("format", "check_Rd_contents")
+S3method("format", "check_Rd_metadata")
+S3method("format", "check_Rd_xrefs")
+S3method("format", "check_T_and_F")
+S3method("format", "check_code_usage_in_package")
+S3method("format", "check_compiled_code")
+S3method("format", "check_dotInternal")
+S3method("format", "check_make_vars")
+S3method("format", "check_package_CRAN_incoming")
+S3method("format", "check_package_code_startup_functions")
+S3method("format", "check_package_datasets")
+S3method("format", "check_package_depends")
+S3method("format", "check_package_description_encoding")
+S3method("format", "check_package_license")
+S3method("format", "check_packages_used")
+S3method("format", "check_so_symbols")
+S3method("format", "checkDocFiles")
+S3method("format", "checkDocStyle")
+S3method("format", "checkFF")
+S3method("format", "checkReplaceFuns")
+S3method("format", "checkS3methods")
+S3method("format", "checkTnF")
+S3method("format", "codocClasses")
+S3method("format", "codocData")
+S3method("format", "compactPDF")
+S3method("format", "subdir_tests")
+S3method("format", "undoc")
+
+S3method("format", "pdf_fonts")
+S3method("format", "pdf_info")
+S3method("format", "PDF_Array")
+S3method("format", "PDF_Dictionary")
+S3method("format", "PDF_Indirect_Reference")
+S3method("format", "PDF_Stream")
+S3method("format", "PDF_String")
+
+S3method("length", "pdf_doc")
+
+S3method("names", "pdf_doc")
+
+S3method("print", "LaTeX")
+S3method("print", "Rd")
S3method("print", "checkDocFiles")
S3method("print", "checkDocStyle")
S3method("print", "checkFF")
+S3method("print", "checkRd")
S3method("print", "checkReplaceFuns")
S3method("print", "checkS3methods")
S3method("print", "checkTnF")
@@ -28,26 +82,51 @@ S3method("print", "checkVignettes")
S3method("print", "codoc")
S3method("print", "codocClasses")
S3method("print", "codocData")
-S3method("print", "Rd")
+S3method("print", "compactPDF")
S3method("print", "subdir_tests")
S3method("print", "undoc")
S3method("print", "xgettext")
S3method("print", "xngettext")
-S3method("print", "check_Rd_files_in_Rd_db")
+S3method("print", "pdf_doc")
+S3method("print", "pdf_fonts")
+S3method("print", "pdf_info")
+S3method("print", "PDF_Array")
+S3method("print", "PDF_Dictionary")
+S3method("print", "PDF_Indirect_Reference")
+S3method("print", "PDF_Keyword")
+S3method("print", "PDF_Name")
+S3method("print", "PDF_Stream")
+S3method("print", "PDF_String")
+
+S3method("print", "check_Rd_contents")
+S3method("print", "check_Rd_metadata")
S3method("print", "check_Rd_xrefs")
S3method("print", "check_T_and_F")
S3method("print", "check_code_usage_in_package")
+S3method("print", "check_compiled_code")
S3method("print", "check_demo_index")
S3method("print", "check_dotInternal")
S3method("print", "check_make_vars")
+S3method("print", "check_package_CRAN_incoming")
+S3method("print", "check_package_code_startup_functions")
S3method("print", "check_package_code_syntax")
S3method("print", "check_package_depends")
S3method("print", "check_package_description")
S3method("print", "check_package_description_encoding")
S3method("print", "check_package_license")
S3method("print", "check_package_datasets")
+S3method("print", "check_package_compact_datasets")
S3method("print", "check_packages_used")
+S3method("print", "check_po_files")
+S3method("print", "check_so_symbols")
S3method("print", "check_vignette_index")
-S3method("as.character", "Rd")
+S3method("summary", "PDF_Dictionary")
+S3method("summary", "PDF_Stream")
+
+S3method("toHTML", "news_db")
+S3method("toHTML", "packageIQR")
+
+S3method("toRd", "bibentry")
+S3method("toRd", "default")
diff --git a/win32/deps/library/tools/R/tools b/win32/deps/library/tools/R/tools
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/tools/R/tools
+++ b/win32/deps/library/tools/R/tools
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/tools/R/tools.rdb b/win32/deps/library/tools/R/tools.rdb
index 0efb6b9..b931957 100644
Binary files a/win32/deps/library/tools/R/tools.rdb and b/win32/deps/library/tools/R/tools.rdb differ
diff --git a/win32/deps/library/tools/R/tools.rdx b/win32/deps/library/tools/R/tools.rdx
index 3f93793..57e7927 100644
Binary files a/win32/deps/library/tools/R/tools.rdx and b/win32/deps/library/tools/R/tools.rdx differ
diff --git a/win32/deps/library/tools/help/AnIndex b/win32/deps/library/tools/help/AnIndex
index 7f8ee98..3397017 100644
--- a/win32/deps/library/tools/help/AnIndex
+++ b/win32/deps/library/tools/help/AnIndex
@@ -1,5 +1,8 @@
tools-package tools-package
+add_datalist add_datalist
Adobe_glyphs charsets
+as.character.Rd parse_Rd
+bibstyle bibstyle
buildVignettes buildVignettes
charset_to_Unicode charsets
checkDocFiles QC
@@ -7,7 +10,10 @@ checkDocStyle QC
checkFF checkFF
checkMD5sums checkMD5sums
checkNEWS readNEWS
-checkRd Rd2HTML
+checkPoFile checkPoFiles
+checkPoFiles checkPoFiles
+checkRd checkRd
+checkRdaFiles checkRdaFiles
checkReplaceFuns QC
checkS3methods QC
checkTnF checkTnF
@@ -15,19 +21,28 @@ checkVignettes checkVignettes
codoc codoc
codocClasses codoc
codocData codoc
+compactPDF compactPDF
delimMatch delimMatch
+deparseLatex parseLatex
dependsOnPkgs dependsOnPkgs
encoded_text_to_latex encoded
+file_ext fileutils
file_path_as_absolute fileutils
file_path_sans_ext fileutils
-findHTMLlinks Rd2HTML
+findHTMLlinks HTMLlinks
+format.compactPDF compactPDF
getDepList getDepList
+help.ports startDynamicHelp
+HTMLheader HTMLheader
installFoundDepends installFoundDepends
+latexToUtf8 parseLatex
list_files_with_exts fileutils
list_files_with_type fileutils
makeLazyLoading makeLazyLoading
md5sum md5sum
package.dependencies package.dependencies
+package_dependencies package_dependencies
+parseLatex parseLatex
parse_Rd parse_Rd
pkgDepends getDepList
pkgVignettes buildVignettes
@@ -41,26 +56,53 @@ print.checkVignettes checkVignettes
print.codoc codoc
print.codocClasses codoc
print.codocData codoc
+print.Rd parse_Rd
print.undoc undoc
+pskill pskill
+psnice psnice
QC QC
Rd2ex Rd2HTML
Rd2HTML Rd2HTML
Rd2latex Rd2HTML
Rd2txt Rd2HTML
+Rd2txt_options Rd2txt_options
Rdiff Rdiff
Rdindex Rdindex
+RdTextFilter RdTextFilter
Rd_db Rdutils
-Rd_parse Rdutils
+Rd_parse tools-defunct
read.00Index read.00Index
readNEWS readNEWS
+resaveRdaFiles checkRdaFiles
showNonASCII showNonASCII
+showNonASCIIfile showNonASCII
+SIGCHLD pskill
+SIGCONT pskill
+SIGHUP pskill
+SIGINT pskill
+SIGKILL pskill
+SIGQUIT pskill
+SIGSTOP pskill
+SIGTERM pskill
+SIGTSTP pskill
+SIGUSR1 pskill
+SIGUSR2 pskill
+startDynamicHelp startDynamicHelp
+SweaveTeXFilter SweaveTeXFilter
testInstalledBasic testInstalledPackage
testInstalledPackage testInstalledPackage
testInstalledPackages testInstalledPackage
texi2dvi texi2dvi
+texi2pdf texi2dvi
+toHTML toHTML
+toHTML.news_db toHTML
+toHTML.packageIQR toHTML
tools tools-package
tools-defunct tools-defunct
tools-deprecated tools-deprecated
+toRd toRd
+toRd.bibentry toRd
+toRd.default toRd
undoc undoc
vignetteDepends vignetteDepends
write_PACKAGES writePACKAGES
diff --git a/win32/deps/library/tools/help/aliases.rds b/win32/deps/library/tools/help/aliases.rds
new file mode 100644
index 0000000..f7b0104
Binary files /dev/null and b/win32/deps/library/tools/help/aliases.rds differ
diff --git a/win32/deps/library/tools/help/paths.rds b/win32/deps/library/tools/help/paths.rds
new file mode 100644
index 0000000..234dacf
Binary files /dev/null and b/win32/deps/library/tools/help/paths.rds differ
diff --git a/win32/deps/library/tools/help/tools.rdb b/win32/deps/library/tools/help/tools.rdb
new file mode 100644
index 0000000..fd9ac7e
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diff --git a/win32/deps/library/tools/help/tools.rdx b/win32/deps/library/tools/help/tools.rdx
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index 0000000..edee4e0
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diff --git a/win32/deps/library/tools/html/00Index.html b/win32/deps/library/tools/html/00Index.html
new file mode 100644
index 0000000..4997d09
--- /dev/null
+++ b/win32/deps/library/tools/html/00Index.html
@@ -0,0 +1,363 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Tools for Package Development</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Tools for Package Development
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘tools’ version 2.15.2</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<p align="center">
+<a href="# "> </a>
+<a href="#A">A</a>
+<a href="#B">B</a>
+<a href="#C">C</a>
+<a href="#D">D</a>
+<a href="#E">E</a>
+<a href="#F">F</a>
+<a href="#G">G</a>
+<a href="#H">H</a>
+<a href="#I">I</a>
+<a href="#L">L</a>
+<a href="#M">M</a>
+<a href="#P">P</a>
+<a href="#Q">Q</a>
+<a href="#R">R</a>
+<a href="#S">S</a>
+<a href="#T">T</a>
+<a href="#U">U</a>
+<a href="#V">V</a>
+<a href="#W">W</a>
+<a href="#X">X</a>
+</p>
+
+<table width="100%">
+<tr><td width="25%"><a href="tools-package.html">tools-package</a></td>
+<td>Tools for Package Development</td></tr>
+</table>
+
+<h2><a name="A">-- A --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="add_datalist.html">add_datalist</a></td>
+<td>Add a 'datalist' File to a Package</td></tr>
+<tr><td width="25%"><a href="charsets.html">Adobe_glyphs</a></td>
+<td>Conversion Tables between Character Sets</td></tr>
+<tr><td width="25%"><a href="parse_Rd.html">as.character.Rd</a></td>
+<td>Parse an Rd file</td></tr>
+</table>
+
+<h2><a name="B">-- B --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="bibstyle.html">bibstyle</a></td>
+<td>Select or define a bibliography style.</td></tr>
+<tr><td width="25%"><a href="buildVignettes.html">buildVignettes</a></td>
+<td>List and Build Package Vignettes</td></tr>
+</table>
+
+<h2><a name="C">-- C --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="charsets.html">charset_to_Unicode</a></td>
+<td>Conversion Tables between Character Sets</td></tr>
+<tr><td width="25%"><a href="QC.html">checkDocFiles</a></td>
+<td>QC Checks for R Code and/or Documentation</td></tr>
+<tr><td width="25%"><a href="QC.html">checkDocStyle</a></td>
+<td>QC Checks for R Code and/or Documentation</td></tr>
+<tr><td width="25%"><a href="checkFF.html">checkFF</a></td>
+<td>Check Foreign Function Calls</td></tr>
+<tr><td width="25%"><a href="checkMD5sums.html">checkMD5sums</a></td>
+<td>Check and Create MD5 Checksum Files</td></tr>
+<tr><td width="25%"><a href="readNEWS.html">checkNEWS</a></td>
+<td>Read R's NEWS file or a similar one</td></tr>
+<tr><td width="25%"><a href="checkPoFiles.html">checkPoFile</a></td>
+<td>Check translation files for inconsistent format strings.</td></tr>
+<tr><td width="25%"><a href="checkPoFiles.html">checkPoFiles</a></td>
+<td>Check translation files for inconsistent format strings.</td></tr>
+<tr><td width="25%"><a href="checkRd.html">checkRd</a></td>
+<td>Check an Rd Object</td></tr>
+<tr><td width="25%"><a href="checkRdaFiles.html">checkRdaFiles</a></td>
+<td>Report on Details of Saved Images or Re-saves them</td></tr>
+<tr><td width="25%"><a href="QC.html">checkReplaceFuns</a></td>
+<td>QC Checks for R Code and/or Documentation</td></tr>
+<tr><td width="25%"><a href="QC.html">checkS3methods</a></td>
+<td>QC Checks for R Code and/or Documentation</td></tr>
+<tr><td width="25%"><a href="checkTnF.html">checkTnF</a></td>
+<td>Check R Packages or Code for T/F</td></tr>
+<tr><td width="25%"><a href="checkVignettes.html">checkVignettes</a></td>
+<td>Check Package Vignettes</td></tr>
+<tr><td width="25%"><a href="codoc.html">codoc</a></td>
+<td>Check Code/Documentation Consistency</td></tr>
+<tr><td width="25%"><a href="codoc.html">codocClasses</a></td>
+<td>Check Code/Documentation Consistency</td></tr>
+<tr><td width="25%"><a href="codoc.html">codocData</a></td>
+<td>Check Code/Documentation Consistency</td></tr>
+<tr><td width="25%"><a href="compactPDF.html">compactPDF</a></td>
+<td>Compact PDF Files</td></tr>
+</table>
+
+<h2><a name="D">-- D --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="delimMatch.html">delimMatch</a></td>
+<td>Delimited Pattern Matching</td></tr>
+<tr><td width="25%"><a href="parseLatex.html">deparseLatex</a></td>
+<td>These experimental functions work with a subset of LaTeX code.</td></tr>
+<tr><td width="25%"><a href="dependsOnPkgs.html">dependsOnPkgs</a></td>
+<td>Find Reverse Dependencies</td></tr>
+</table>
+
+<h2><a name="E">-- E --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="encoded.html">encoded_text_to_latex</a></td>
+<td>Translate non-ASCII Text to LaTeX Escapes</td></tr>
+</table>
+
+<h2><a name="F">-- F --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="fileutils.html">file_ext</a></td>
+<td>File Utilities</td></tr>
+<tr><td width="25%"><a href="fileutils.html">file_path_as_absolute</a></td>
+<td>File Utilities</td></tr>
+<tr><td width="25%"><a href="fileutils.html">file_path_sans_ext</a></td>
+<td>File Utilities</td></tr>
+<tr><td width="25%"><a href="HTMLlinks.html">findHTMLlinks</a></td>
+<td>Collect HTML Links from Package Documentation</td></tr>
+<tr><td width="25%"><a href="compactPDF.html">format.compactPDF</a></td>
+<td>Compact PDF Files</td></tr>
+</table>
+
+<h2><a name="G">-- G --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="getDepList.html">getDepList</a></td>
+<td>Functions to Retrieve Dependency Information</td></tr>
+</table>
+
+<h2><a name="H">-- H --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="startDynamicHelp.html">help.ports</a></td>
+<td>Start the Dynamic HTML Help System</td></tr>
+<tr><td width="25%"><a href="HTMLheader.html">HTMLheader</a></td>
+<td>Generate a standard HTML header for R help</td></tr>
+</table>
+
+<h2><a name="I">-- I --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="installFoundDepends.html">installFoundDepends</a></td>
+<td>A function to install unresolved dependencies</td></tr>
+</table>
+
+<h2><a name="L">-- L --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="parseLatex.html">latexToUtf8</a></td>
+<td>These experimental functions work with a subset of LaTeX code.</td></tr>
+<tr><td width="25%"><a href="fileutils.html">list_files_with_exts</a></td>
+<td>File Utilities</td></tr>
+<tr><td width="25%"><a href="fileutils.html">list_files_with_type</a></td>
+<td>File Utilities</td></tr>
+</table>
+
+<h2><a name="M">-- M --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="md5sum.html">md5sum</a></td>
+<td>Compute MD5 Checksums</td></tr>
+</table>
+
+<h2><a name="P">-- P --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="package.dependencies.html">package.dependencies</a></td>
+<td>Check Package Dependencies</td></tr>
+<tr><td width="25%"><a href="package_dependencies.html">package_dependencies</a></td>
+<td>Computations on the Dependency Hierarchy of Packages</td></tr>
+<tr><td width="25%"><a href="parseLatex.html">parseLatex</a></td>
+<td>These experimental functions work with a subset of LaTeX code.</td></tr>
+<tr><td width="25%"><a href="parse_Rd.html">parse_Rd</a></td>
+<td>Parse an Rd file</td></tr>
+<tr><td width="25%"><a href="getDepList.html">pkgDepends</a></td>
+<td>Functions to Retrieve Dependency Information</td></tr>
+<tr><td width="25%"><a href="buildVignettes.html">pkgVignettes</a></td>
+<td>List and Build Package Vignettes</td></tr>
+<tr><td width="25%"><a href="QC.html">print.checkDocFiles</a></td>
+<td>QC Checks for R Code and/or Documentation</td></tr>
+<tr><td width="25%"><a href="QC.html">print.checkDocStyle</a></td>
+<td>QC Checks for R Code and/or Documentation</td></tr>
+<tr><td width="25%"><a href="checkFF.html">print.checkFF</a></td>
+<td>Check Foreign Function Calls</td></tr>
+<tr><td width="25%"><a href="QC.html">print.checkReplaceFuns</a></td>
+<td>QC Checks for R Code and/or Documentation</td></tr>
+<tr><td width="25%"><a href="QC.html">print.checkS3methods</a></td>
+<td>QC Checks for R Code and/or Documentation</td></tr>
+<tr><td width="25%"><a href="checkTnF.html">print.checkTnF</a></td>
+<td>Check R Packages or Code for T/F</td></tr>
+<tr><td width="25%"><a href="checkVignettes.html">print.checkVignettes</a></td>
+<td>Check Package Vignettes</td></tr>
+<tr><td width="25%"><a href="codoc.html">print.codoc</a></td>
+<td>Check Code/Documentation Consistency</td></tr>
+<tr><td width="25%"><a href="codoc.html">print.codocClasses</a></td>
+<td>Check Code/Documentation Consistency</td></tr>
+<tr><td width="25%"><a href="codoc.html">print.codocData</a></td>
+<td>Check Code/Documentation Consistency</td></tr>
+<tr><td width="25%"><a href="parse_Rd.html">print.Rd</a></td>
+<td>Parse an Rd file</td></tr>
+<tr><td width="25%"><a href="undoc.html">print.undoc</a></td>
+<td>Find Undocumented Objects</td></tr>
+<tr><td width="25%"><a href="pskill.html">pskill</a></td>
+<td>Kill a Process</td></tr>
+<tr><td width="25%"><a href="psnice.html">psnice</a></td>
+<td>Get or Set the Priority (Niceness) of a Process</td></tr>
+</table>
+
+<h2><a name="Q">-- Q --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="QC.html">QC</a></td>
+<td>QC Checks for R Code and/or Documentation</td></tr>
+</table>
+
+<h2><a name="R">-- R --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Rd2HTML.html">Rd2ex</a></td>
+<td>Rd Converters</td></tr>
+<tr><td width="25%"><a href="Rd2HTML.html">Rd2HTML</a></td>
+<td>Rd Converters</td></tr>
+<tr><td width="25%"><a href="Rd2HTML.html">Rd2latex</a></td>
+<td>Rd Converters</td></tr>
+<tr><td width="25%"><a href="Rd2HTML.html">Rd2txt</a></td>
+<td>Rd Converters</td></tr>
+<tr><td width="25%"><a href="Rd2txt_options.html">Rd2txt_options</a></td>
+<td>Set formatting options for text help</td></tr>
+<tr><td width="25%"><a href="Rdiff.html">Rdiff</a></td>
+<td>Difference R Output Files</td></tr>
+<tr><td width="25%"><a href="Rdindex.html">Rdindex</a></td>
+<td>Generate Index from Rd Files</td></tr>
+<tr><td width="25%"><a href="RdTextFilter.html">RdTextFilter</a></td>
+<td>Select text in an Rd file.</td></tr>
+<tr><td width="25%"><a href="Rdutils.html">Rd_db</a></td>
+<td>Rd Utilities</td></tr>
+<tr><td width="25%"><a href="read.00Index.html">read.00Index</a></td>
+<td>Read 00Index-style Files</td></tr>
+<tr><td width="25%"><a href="readNEWS.html">readNEWS</a></td>
+<td>Read R's NEWS file or a similar one</td></tr>
+<tr><td width="25%"><a href="checkRdaFiles.html">resaveRdaFiles</a></td>
+<td>Report on Details of Saved Images or Re-saves them</td></tr>
+</table>
+
+<h2><a name="S">-- S --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="showNonASCII.html">showNonASCII</a></td>
+<td>Pick Out Non-ASCII Characters</td></tr>
+<tr><td width="25%"><a href="showNonASCII.html">showNonASCIIfile</a></td>
+<td>Pick Out Non-ASCII Characters</td></tr>
+<tr><td width="25%"><a href="pskill.html">SIGCHLD</a></td>
+<td>Kill a Process</td></tr>
+<tr><td width="25%"><a href="pskill.html">SIGCONT</a></td>
+<td>Kill a Process</td></tr>
+<tr><td width="25%"><a href="pskill.html">SIGHUP</a></td>
+<td>Kill a Process</td></tr>
+<tr><td width="25%"><a href="pskill.html">SIGINT</a></td>
+<td>Kill a Process</td></tr>
+<tr><td width="25%"><a href="pskill.html">SIGKILL</a></td>
+<td>Kill a Process</td></tr>
+<tr><td width="25%"><a href="pskill.html">SIGQUIT</a></td>
+<td>Kill a Process</td></tr>
+<tr><td width="25%"><a href="pskill.html">SIGSTOP</a></td>
+<td>Kill a Process</td></tr>
+<tr><td width="25%"><a href="pskill.html">SIGTERM</a></td>
+<td>Kill a Process</td></tr>
+<tr><td width="25%"><a href="pskill.html">SIGTSTP</a></td>
+<td>Kill a Process</td></tr>
+<tr><td width="25%"><a href="pskill.html">SIGUSR1</a></td>
+<td>Kill a Process</td></tr>
+<tr><td width="25%"><a href="pskill.html">SIGUSR2</a></td>
+<td>Kill a Process</td></tr>
+<tr><td width="25%"><a href="startDynamicHelp.html">startDynamicHelp</a></td>
+<td>Start the Dynamic HTML Help System</td></tr>
+<tr><td width="25%"><a href="SweaveTeXFilter.html">SweaveTeXFilter</a></td>
+<td>Strip R code out of Sweave file</td></tr>
+</table>
+
+<h2><a name="T">-- T --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="testInstalledPackage.html">testInstalledBasic</a></td>
+<td>Test Installed Packages</td></tr>
+<tr><td width="25%"><a href="testInstalledPackage.html">testInstalledPackage</a></td>
+<td>Test Installed Packages</td></tr>
+<tr><td width="25%"><a href="testInstalledPackage.html">testInstalledPackages</a></td>
+<td>Test Installed Packages</td></tr>
+<tr><td width="25%"><a href="texi2dvi.html">texi2dvi</a></td>
+<td>Compile LaTeX Files</td></tr>
+<tr><td width="25%"><a href="texi2dvi.html">texi2pdf</a></td>
+<td>Compile LaTeX Files</td></tr>
+<tr><td width="25%"><a href="toHTML.html">toHTML</a></td>
+<td>Display an object in HTML.</td></tr>
+<tr><td width="25%"><a href="toHTML.html">toHTML.news_db</a></td>
+<td>Display an object in HTML.</td></tr>
+<tr><td width="25%"><a href="toHTML.html">toHTML.packageIQR</a></td>
+<td>Display an object in HTML.</td></tr>
+<tr><td width="25%"><a href="tools-package.html">tools</a></td>
+<td>Tools for Package Development</td></tr>
+<tr><td width="25%"><a href="tools-deprecated.html">tools-deprecated</a></td>
+<td>Deprecated Objects in Package 'tools'</td></tr>
+<tr><td width="25%"><a href="toRd.html">toRd</a></td>
+<td>Generic function to convert object to a fragment of Rd code.</td></tr>
+<tr><td width="25%"><a href="toRd.html">toRd.bibentry</a></td>
+<td>Generic function to convert object to a fragment of Rd code.</td></tr>
+<tr><td width="25%"><a href="toRd.html">toRd.default</a></td>
+<td>Generic function to convert object to a fragment of Rd code.</td></tr>
+</table>
+
+<h2><a name="U">-- U --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="undoc.html">undoc</a></td>
+<td>Find Undocumented Objects</td></tr>
+</table>
+
+<h2><a name="V">-- V --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="vignetteDepends.html">vignetteDepends</a></td>
+<td>Retrieve Dependency Information for a Vignette</td></tr>
+</table>
+
+<h2><a name="W">-- W --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="writePACKAGES.html">write_PACKAGES</a></td>
+<td>Generate PACKAGES files</td></tr>
+</table>
+
+<h2><a name="X">-- X --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="xgettext.html">xgettext</a></td>
+<td>Extract Translatable Messages from R Files in a Package</td></tr>
+<tr><td width="25%"><a href="xgettext.html">xgettext2pot</a></td>
+<td>Extract Translatable Messages from R Files in a Package</td></tr>
+<tr><td width="25%"><a href="xgettext.html">xngettext</a></td>
+<td>Extract Translatable Messages from R Files in a Package</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/tools/html/R.css b/win32/deps/library/tools/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/tools/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/tools/libs/i386/tools.dll b/win32/deps/library/tools/libs/i386/tools.dll
new file mode 100644
index 0000000..b192243
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diff --git a/win32/deps/library/tools/po/da/LC_MESSAGES/R-tools.mo b/win32/deps/library/tools/po/da/LC_MESSAGES/R-tools.mo
new file mode 100644
index 0000000..4859111
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diff --git a/win32/deps/library/tools/po/da/LC_MESSAGES/tools.mo b/win32/deps/library/tools/po/da/LC_MESSAGES/tools.mo
new file mode 100644
index 0000000..998bd7b
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diff --git a/win32/deps/library/tools/po/de/LC_MESSAGES/R-tools.mo b/win32/deps/library/tools/po/de/LC_MESSAGES/R-tools.mo
new file mode 100644
index 0000000..3c8f8b4
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diff --git a/win32/deps/library/tools/po/de/LC_MESSAGES/tools.mo b/win32/deps/library/tools/po/de/LC_MESSAGES/tools.mo
new file mode 100644
index 0000000..343a2f3
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diff --git a/win32/deps/library/tools/po/en quot/LC_MESSAGES/R-tools.mo b/win32/deps/library/tools/po/en quot/LC_MESSAGES/R-tools.mo
new file mode 100644
index 0000000..f5e4b6b
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diff --git a/win32/deps/library/tools/po/en quot/LC_MESSAGES/tools.mo b/win32/deps/library/tools/po/en quot/LC_MESSAGES/tools.mo
new file mode 100644
index 0000000..3104bbe
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diff --git a/win32/deps/library/tools/po/fr/LC_MESSAGES/R-tools.mo b/win32/deps/library/tools/po/fr/LC_MESSAGES/R-tools.mo
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diff --git a/win32/deps/library/tools/po/it/LC_MESSAGES/R-tools.mo b/win32/deps/library/tools/po/it/LC_MESSAGES/R-tools.mo
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diff --git a/win32/deps/library/tools/po/ja/LC_MESSAGES/R-tools.mo b/win32/deps/library/tools/po/ja/LC_MESSAGES/R-tools.mo
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diff --git a/win32/deps/library/tools/po/ko/LC_MESSAGES/R-tools.mo b/win32/deps/library/tools/po/ko/LC_MESSAGES/R-tools.mo
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diff --git a/win32/deps/library/tools/po/pl/LC_MESSAGES/R-tools.mo b/win32/deps/library/tools/po/pl/LC_MESSAGES/R-tools.mo
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diff --git a/win32/deps/library/tools/po/pt_BR/LC_MESSAGES/R-tools.mo b/win32/deps/library/tools/po/pt_BR/LC_MESSAGES/R-tools.mo
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diff --git a/win32/deps/library/tools/po/ru/LC_MESSAGES/R-tools.mo b/win32/deps/library/tools/po/ru/LC_MESSAGES/R-tools.mo
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diff --git a/win32/deps/library/tools/po/tr/LC_MESSAGES/R-tools.mo b/win32/deps/library/tools/po/tr/LC_MESSAGES/R-tools.mo
new file mode 100644
index 0000000..4e5942e
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diff --git a/win32/deps/library/tools/po/zh_CN/LC_MESSAGES/R-tools.mo b/win32/deps/library/tools/po/zh_CN/LC_MESSAGES/R-tools.mo
new file mode 100644
index 0000000..7a9a6b1
Binary files /dev/null and b/win32/deps/library/tools/po/zh_CN/LC_MESSAGES/R-tools.mo differ
diff --git a/win32/deps/library/tools/po/zh_CN/LC_MESSAGES/tools.mo b/win32/deps/library/tools/po/zh_CN/LC_MESSAGES/tools.mo
new file mode 100644
index 0000000..3f3f03f
Binary files /dev/null and b/win32/deps/library/tools/po/zh_CN/LC_MESSAGES/tools.mo differ
diff --git a/win32/deps/library/tools/tests/undoc.R b/win32/deps/library/tools/tests/undoc.R
new file mode 100644
index 0000000..9773008
--- /dev/null
+++ b/win32/deps/library/tools/tests/undoc.R
@@ -0,0 +1,4 @@
+require("tools")
+
+(ud4 <- undoc("stats4"))
+stopifnot(sapply(ud4, length) == 0)
diff --git a/win32/deps/library/utils/DESCRIPTION b/win32/deps/library/utils/DESCRIPTION
index 922f894..79abb38 100644
--- a/win32/deps/library/utils/DESCRIPTION
+++ b/win32/deps/library/utils/DESCRIPTION
@@ -1,9 +1,9 @@
Package: utils
-Version: 2.9.2
+Version: 2.15.2
Priority: base
Title: The R Utils Package
-Author: R Development Core Team and contributors worldwide
+Author: R Core Team and contributors worldwide
Maintainer: R Core Team <R-core r-project org>
Description: R utility functions
-License: Part of R 2.9.2
-Built: R 2.9.2; ; 2009-08-24 12:43:33 UTC; windows
+License: Part of R 2.15.2
+Built: R 2.15.2; ; 2012-10-27 03:05:31 UTC; windows
diff --git a/win32/deps/library/utils/INDEX b/win32/deps/library/utils/INDEX
index 995bde3..fe97ffc 100644
--- a/win32/deps/library/utils/INDEX
+++ b/win32/deps/library/utils/INDEX
@@ -1,10 +1,11 @@
BATCH Batch Execution of R
DLL.version DLL Version Information
INSTALL Install Add-on Packages
+Question Documentation Shortcuts
REMOVE Remove Add-on Packages
RShowDoc Show R Manuals and Other Documentation
-RSiteSearch Search for Key Words or Phrases in the R-help
- Mailing List Archives or Documentation
+RSiteSearch Search for Key Words or Phrases in
+ Documentation
Rconsole R for Windows Configuration
Rprof Enable Profiling of R's Execution
Rprofmem Enable Profiling of R's Memory Use
@@ -12,63 +13,84 @@ Rscript Scripting Front-End for R
Rtangle R Driver for Stangle
RweaveLatex R/LaTeX Driver for Sweave
SHLIB Build Shared Object/DLL for Dynamic Loading
-SHLIB Build a DLL for Dynamic Loading
Sweave Automatic Generation of Reports
SweaveSyntConv Convert Sweave Syntax
URLencode Encode or Decode a (partial) URL
View Invoke a Data Viewer
-alarm Alert the user
+adist Approximate String Distances
+alarm Alert the User
apropos Find Objects by (Partial) Name
+aregexec Approximate String Match Positions
+arrangeWindows Rearrange windows in the R GUI.
as.roman Roman Numerals
+aspell Spell Check Interface
+aspell-utils Spell Check Utilities
+available.packages List Available Packages at CRAN-like
+ Repositories
+bibentry Bibliography Entries
browseEnv Browse Objects in Environment
browseURL Load URL into a WWW Browser
browseVignettes List Vignettes in an HTML Browser
bug.report Send a Bug Report
build Utilities for Building and Checking Add-on
Packages
-capture.output Send output to a character string or file
+capture.output Send Output to a Character String or File
choose.dir Choose a Folder Interactively
choose.files Choose a List of Files Interactively
+chooseBioCmirror Select a Bioconductor Mirror
chooseCRANmirror Select a CRAN Mirror
-citEntry Writing Package CITATION Files
+citEntry Bibliography Entries (Older Interface)
citation Citing R and R Packages in Publications
clipboard Read/Write to/from the Windows Clipboard
close.socket Close a Socket
combn Generate All Combinations of n Elements, Taken
m at a Time
compareVersion Compare Two Package Version Numbers
+contrib.url Find Appropriate Paths in CRAN-like
+ Repositories
count.fields Count the Number of Fields per Line
+create.post Ancillary Function for Preparing Emails and
+ Postings
data Data Sets
dataentry Spreadsheet Interface for Entering Data
debugger Post-Mortem Debugging
demo Demonstrations of R Functionality
download.file Download File from the Internet
+download.packages Download Packages from CRAN-like Repositories
edit Invoke a Text Editor
edit.data.frame Edit Data Frames and Matrices
example Run an Examples Section from the Online Help
file.edit Edit One or More Files
file_test Shell-style Tests on Files
+findLineNum Find the Location of a Line of Source Code, or
+ Set a Breakpoint There.
fix Fix an Object
flush.console Flush Output to A Console
formatUL Format Unordered and Ordered Lists
-getAnywhere Retrieve an R Object, Including from a Name
- Space
+getAnywhere Retrieve an R Object, Including from a
+ Namespace
getFromNamespace Utility functions for Developing Namespaces
getS3method Get An S3 Method
+getSrcFilename Source Reference Utilities
getWindowsHandle Get a Windows Handle
+getWindowsHandles Get handles of windows.
glob2rx Change Wildcard or Globbing Pattern into
Regular Expression
+globalVariables Declare Variables to be Treated as Global in
+ Checking a Package
head Return the First or Last Part of an Object
help Documentation
help.request Send a Post to R-help
help.search Search the Help System
help.start Hypertext Documentation
-index.search Search Indices for Help Files
+install.packages Install Packages from Repositories or Local
+ Files
installed.packages Find Installed Packages
-link.html.help Update HTML documentation files
localeToCharset Select a Suitable Encoding Name from a Locale
Name
ls.str List Objects and their Structure
+maintainer Show Package Maintainer
+make.packages.html Update HTML Package List
make.socket Create a Socket Connection
memory.size Report on Memory Allocation
menu Menu Interaction Function
@@ -76,19 +98,19 @@ methods List Methods for S3 Generic Functions or
Classes
mirrorAdmin Managing Repository Mirrors
modifyList Recursively Modify Elements of a List
-normalizePath Express File Paths in Canonical Form
+news Build and Query R or Package News Information
object.size Report the Space Allocated for an Object
package.skeleton Create a Skeleton for a New Source Package
packageDescription Package Description
packageStatus Package Management Tools
page Invoke a Pager on an R Object
-person Person Names and Contact Information
+person Persons
prompt Produce Prototype of an R Documentation File
-promptData Generate a Shell for Documentation of Data Sets
+promptData Generate Outline Documentation for a Data Set
promptPackage Generate a Shell for Documentation of a Package
rcompgen A Completion Generator for R
read.DIF Data Input from Spreadsheet
-read.fortran Read fixed-format data
+read.fortran Read Fixed-Format Data
read.fwf Read Fixed Width Format Files
read.socket Read from or Write to a Socket
read.table Data Input
@@ -96,7 +118,8 @@ readRegistry Read a Windows Registy Hive
recover Browsing after an Error
relist Allow Re-Listing an unlist()ed Object
remove.packages Remove Installed Packages
-rtags An etags-like a tagging utility for R
+removeSource Remove Stored Source from a Function.
+rtags An Etags-like Tagging Utility for R
savehistory Load or Save or Display the Commands History
select.list Select Items from a List
sessionInfo Collect Information About the Current R Session
@@ -111,13 +134,16 @@ stack Stack or Unstack Vectors from a Data Frame or
str Compactly Display the Structure of an Arbitrary
R Object
summaryRprof Summarise Output of R Sampling Profiler
+tar Create a Tar Archive
toLatex Converting R Objects to BibTeX or LaTeX
txtProgressBar Text Progress Bar
type.convert Type Conversion on Character Variables
-unzip Extract or List Zip archives
-update.packages Download Packages from CRAN-like repositories
+untar Extract or List Tar Archives
+unzip Extract or List Zip Archives
+update.packages Compare Installed Packages with CRAN-like
+ Repositories
url.show Display a text URL
-utils-deprecated Deprecated Functions in Package utils
+utils-deprecated Deprecated Functions in Package 'utils'
utils-package The R Utils Package
vignette View or List Vignettes
win.version Auxiliary Functions for the Windows Port
@@ -125,4 +151,4 @@ winDialog Dialog Boxes under Windows
winMenuAdd User Menus under Windows
winProgressBar Progress Bars under Windows
write.table Data Output
-zip.file.extract Extract File from a Zip Archive
+zip Create Zip archives
diff --git a/win32/deps/library/utils/Meta/Rd.rds b/win32/deps/library/utils/Meta/Rd.rds
index 061318f..2c4c9c5 100644
Binary files a/win32/deps/library/utils/Meta/Rd.rds and b/win32/deps/library/utils/Meta/Rd.rds differ
diff --git a/win32/deps/library/utils/Meta/hsearch.rds b/win32/deps/library/utils/Meta/hsearch.rds
index 1f4beb6..2dff7d3 100644
Binary files a/win32/deps/library/utils/Meta/hsearch.rds and b/win32/deps/library/utils/Meta/hsearch.rds differ
diff --git a/win32/deps/library/utils/Meta/links.rds b/win32/deps/library/utils/Meta/links.rds
new file mode 100644
index 0000000..171c0df
Binary files /dev/null and b/win32/deps/library/utils/Meta/links.rds differ
diff --git a/win32/deps/library/utils/Meta/nsInfo.rds b/win32/deps/library/utils/Meta/nsInfo.rds
index 801872b..ff1b17c 100644
Binary files a/win32/deps/library/utils/Meta/nsInfo.rds and b/win32/deps/library/utils/Meta/nsInfo.rds differ
diff --git a/win32/deps/library/utils/Meta/package.rds b/win32/deps/library/utils/Meta/package.rds
index dc7f97a..ee96422 100644
Binary files a/win32/deps/library/utils/Meta/package.rds and b/win32/deps/library/utils/Meta/package.rds differ
diff --git a/win32/deps/library/utils/Meta/vignette.rds b/win32/deps/library/utils/Meta/vignette.rds
new file mode 100644
index 0000000..1b3038c
Binary files /dev/null and b/win32/deps/library/utils/Meta/vignette.rds differ
diff --git a/win32/deps/library/utils/NAMESPACE b/win32/deps/library/utils/NAMESPACE
index 444807f..c4344c8 100644
--- a/win32/deps/library/utils/NAMESPACE
+++ b/win32/deps/library/utils/NAMESPACE
@@ -1,40 +1,44 @@
-export("?", CRAN.packages, Rprof,Rprofmem, RShowDoc, RSiteSearch,
- URLdecode, URLencode, View, alarm, apropos, argsAnywhere,
- assignInNamespace, as.roman, as.person, as.personList,
- as.relistable, available.packages, browseEnv, browseURL,
- browseVignettes, bug.report, capture.output, checkCRAN,
- chooseCRANmirror, citation, citEntry, citHeader, citFooter,
- close.socket, combn, compareVersion, contrib.url, count.fields,
- data, data.entry, dataentry, de, de.ncols, de.restore, de.setup,
+export("?", .DollarNames, CRAN.packages, Rprof, Rprofmem, RShowDoc,
+ RSiteSearch, URLdecode, URLencode, View, adist, alarm, apropos,
+ aregexec, argsAnywhere, assignInMyNamespace, assignInNamespace,
+ as.roman, as.person, as.personList, as.relistable, aspell,
+ aspell_package_Rd_files, aspell_package_vignettes,
+ aspell_write_personal_dictionary_file, available.packages,
+ browseEnv, browseURL, browseVignettes, bug.report,
+ capture.output, checkCRAN, chooseBioCmirror, chooseCRANmirror,
+ citation, citEntry, citHeader, citFooter, close.socket, combn,
+ compareVersion, contrib.url, count.fields, create.post, data,
+ data.entry, dataentry, de, de.ncols, de.restore, de.setup,
debugger, demo, download.file, download.packages, dump.frames,
edit, emacs, example, file_test, file.edit, find, fix,
- fixInNamespace, flush.console, formatOL, formatUL, getAnywhere,
- getCRANmirrors, getFromNamespace, getS3method, glob2rx, head,
- head.matrix, help, help.request, help.search, help.start,
- history, index.search, install.packages, installed.packages,
+ fixInNamespace, findLineNum, flush.console, formatOL, formatUL,
+ getAnywhere, getCRANmirrors, getFromNamespace, getS3method,
+ getSrcDirectory, getSrcFilename, getSrcLocation, getSrcref,
+ glob2rx, globalVariables, head, head.matrix, help, help.request, help.search,
+ help.start, history, install.packages, installed.packages,
is.relistable, limitedLabels, loadhistory, localeToCharset,
- ls.str, lsf.str, make.packages.html, make.socket, memory.limit,
- memory.size, menu, methods, mirror2html, modifyList,
- new.packages, normalizePath, object.size, old.packages,
+ ls.str, lsf.str, maintainer, make.packages.html, make.socket,
+ memory.limit, memory.size, menu, methods, mirror2html,
+ modifyList, new.packages, news, object.size, old.packages,
package.contents, package.skeleton, packageDescription,
- packageStatus, page, person, personList, pico, prompt,
- promptData, promptPackage, rc.getOption, rc.options, rc.settings,
- rc.status, readCitationFile, read.DIF, read.csv, read.csv2,
- read.delim, read.delim2, read.fwf, read.fortran, read.socket,
- read.table, recover, relist, remove.packages, savehistory,
- select.list, sessionInfo, setRepositories, stack, str,
- strOptions, summaryRprof, tail, tail.matrix, timestamp, toBibtex,
- toLatex, type.convert, unstack, unzip, update.packageStatus,
- update.packages, upgrade, url.show, vi, vignette, write.csv,
- write.csv2, write.socket, write.table, wsbrowser, xedit, xemacs,
- zip.file.extract, rtags)
+ packageVersion, packageStatus, page, person, personList, pico,
+ prompt, promptData, promptPackage, rc.getOption, rc.options,
+ rc.settings, rc.status, readCitationFile, read.DIF, read.csv,
+ read.csv2, read.delim, read.delim2, read.fwf, read.fortran,
+ read.socket, read.table, recover, relist, remove.packages,
+ removeSource, rtags, savehistory, select.list, sessionInfo,
+ setBreakpoint, setRepositories, stack, str, strOptions,
+ summaryRprof, tail, tail.matrix, tar, timestamp, toBibtex,
+ toLatex, type.convert, unstack, untar, unzip,
+ update.packageStatus, update.packages, upgrade, url.show, vi,
+ vignette, write.csv, write.csv2, write.socket, write.table,
+ wsbrowser, xedit, xemacs, zip, zip.file.extract)
export(txtProgressBar, getTxtProgressBar, setTxtProgressBar)
S3method("[", getAnywhere)
S3method("[", roman)
S3method(as.character, person)
-S3method(as.character, personList)
S3method(as.character, roman)
S3method(as.person, default)
S3method(as.personList, default)
@@ -44,22 +48,24 @@ S3method(edit, data.frame)
S3method(edit, default)
S3method(edit, matrix)
S3method(edit, vignette)
-S3method(format, roman)
+S3method(format, "roman")
S3method(head, data.frame)
S3method(head, default)
S3method(head, "function")
S3method(head, matrix)
S3method(head, ftable)
S3method(head, table)
-S3method(print, citation)
+S3method(print, "aspell")
+S3method(print, "aspell_inspect_context")
S3method(print, Bibtex)
-S3method(print, citationList)
+S3method(print, findLineNumResult)
S3method(print, getAnywhere)
S3method(print, hsearch)
S3method(print, "help_files_with_topic")
S3method(print, Latex)
S3method(print, "ls_str")
S3method(print, MethodsFunction)
+S3method(print, "news_db")
S3method(print, "object_size")
S3method(print, packageDescription)
S3method(print, packageIQR)
@@ -67,6 +73,7 @@ S3method(print, packageStatus)
S3method(print, roman)
S3method(print, sessionInfo)
S3method(print, socket)
+S3method(print, summary.packageStatus)
S3method(print, vignette)
S3method(print, browseVignettes)
S3method(prompt, data.frame)
@@ -78,8 +85,10 @@ S3method(relist, matrix)
S3method(stack, data.frame)
S3method(stack, default)
S3method(str, POSIXt)
+S3method(str, Date)
S3method(str, data.frame)
S3method(str, default)
+S3method(summary, aspell)
S3method(summary, packageStatus)
S3method(tail, data.frame)
S3method(tail, default)
@@ -87,10 +96,7 @@ S3method(tail, "function")
S3method(tail, matrix)
S3method(tail, ftable)
S3method(tail, table)
-S3method(toBibtex, citation)
-S3method(toBibtex, citationList)
S3method(toBibtex, person)
-S3method(toBibtex, personList)
S3method(toLatex, sessionInfo)
S3method(unlist, relistable)
S3method(unstack, data.frame)
@@ -99,6 +105,28 @@ S3method(upgrade, packageStatus)
## can't register update.packageStatus as update is in stats
## and would create a cycle.
+export("bibentry")
+S3method("$", "bibentry")
+S3method("$", "person")
+S3method("$<-", "bibentry")
+S3method("$<-", "person")
+S3method("[", "bibentry")
+S3method("[", "person")
+S3method("[[", "bibentry")
+S3method("[[", "person")
+S3method("c", "bibentry")
+S3method("c", "person")
+S3method("format", "bibentry")
+S3method("format", "person")
+S3method("print", "bibentry")
+S3method("print", "citation")
+S3method("print", "person")
+S3method("toBibtex", "bibentry")
+
+S3method(.DollarNames, default)
+S3method(.DollarNames, list)
+S3method(.DollarNames, environment)
+
export(Rtangle, RtangleSetup, RweaveLatex, RweaveLatexSetup, Stangle,
Sweave, SweaveSyntConv, SweaveSyntaxLatex, SweaveSyntaxNoweb,
RtangleWritedoc, RweaveLatexOptions, RweaveChunkPrefix,
@@ -111,15 +139,14 @@ export(nsl)
}
if(tools:::.OStype() == "windows") {
-export(DLL.version, Filters, choose.dir, choose.files,
- fixup.libraries.URLs, fixup.package.URLs, getClipboardFormats,
- getIdentification, getWindowsHandle, getWindowTitle,
- link.html.help, loadRconsole, make.search.html, readClipboard,
+export(DLL.version, Filters, choose.dir, choose.files, getClipboardFormats,
+ getIdentification, getWindowsHandle, getWindowsHandles, getWindowTitle,
+ loadRconsole, readClipboard,
readRegistry, setStatusBar, setWindowTitle, shortPathName,
win.version, winDialog, winDialogString, winMenuAdd,
winMenuAddItem, winMenuDel, winMenuDelItem, winMenuNames,
winMenuItems, writeClipboard, zip.unpack,
winProgressBar, getWinProgressBar, setWinProgressBar,
- setInternet2)
+ setInternet2, arrangeWindows)
S3method(close, winProgressBar)
}
diff --git a/win32/deps/library/utils/R/utils b/win32/deps/library/utils/R/utils
index 16b2ccb..ac8cebe 100644
--- a/win32/deps/library/utils/R/utils
+++ b/win32/deps/library/utils/R/utils
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find name space environment");
+ stop("cannot find namespace environment");
barepackage <- sub("([^-]+)_.*", "\\1", info$pkgname)
dbbase <- file.path(info$libname, info$pkgname, "R", barepackage)
lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
diff --git a/win32/deps/library/utils/R/utils.rdb b/win32/deps/library/utils/R/utils.rdb
index bee2778..2c70044 100644
Binary files a/win32/deps/library/utils/R/utils.rdb and b/win32/deps/library/utils/R/utils.rdb differ
diff --git a/win32/deps/library/utils/R/utils.rdx b/win32/deps/library/utils/R/utils.rdx
index 0f2ef5c..e359e6f 100644
Binary files a/win32/deps/library/utils/R/utils.rdx and b/win32/deps/library/utils/R/utils.rdx differ
diff --git a/win32/deps/library/utils/Sweave/Sweave-test-1.Rnw b/win32/deps/library/utils/Sweave/Sweave-test-1.Rnw
index c67e527..ae5bd35 100644
--- a/win32/deps/library/utils/Sweave/Sweave-test-1.Rnw
+++ b/win32/deps/library/utils/Sweave/Sweave-test-1.Rnw
@@ -11,8 +11,7 @@
\maketitle
-A simple example that will run in any S engine: The integers from 1 to
-10 are
+A simple example: the integers from 1 to 10 are
<<print=TRUE>>=
1:10
<<results=hide>>=
@@ -38,14 +37,12 @@ Note that we can easily integrate some numbers into standard text: The
third element of vector \texttt{x} is \Sexpr{x[3]}, the
$p$-value of the test is \Sexpr{format.pval(t1$p.value)}. % $
-Now we look at a summary of the famous iris data set, and we want to
-see the commands in the code chunks:
+Now we look at a summary of the famous \texttt{iris} data set, and we
+want to see the commands in the code chunks:
\SweaveOpts{echo=true}
-% the following code is R-specific, as data(iris) will not run in Splus.
-% Hence, we mark it as R code.
-<<engine=R>>=
+<<>>=
data(iris)
summary(iris)
@ %def
@@ -57,7 +54,7 @@ summary(iris)
library(graphics)
pairs(iris)
@
- \caption{Pairs plot of the iris data.}
+ \caption{Pairs plot of the iris data.}
\end{center}
\end{figure}
@@ -69,13 +66,6 @@ boxplot(Sepal.Length~Species, data=iris)
\caption{Boxplot of sepal length grouped by species.}
\end{center}
\end{figure}
-
-
-% R is not S-PLUS, hence this chunk will be ignored:
-<<engine=S4>>=
-function.that.comes.only.with.Splus(x)
@
\end{document}
-
-
diff --git a/win32/deps/library/utils/Sweave/example-1.Rnw b/win32/deps/library/utils/Sweave/example-1.Rnw
new file mode 100644
index 0000000..f9c86cb
--- /dev/null
+++ b/win32/deps/library/utils/Sweave/example-1.Rnw
@@ -0,0 +1,29 @@
+\documentclass[a4paper]{article}
+
+\title{Sweave Example 1}
+\author{Friedrich Leisch}
+
+\begin{document}
+
+\maketitle
+
+In this example we embed parts of the examples from the
+\texttt{kruskal.test} help page into a \LaTeX{} document:
+
+<<>>=
+data(airquality, package="datasets")
+library("stats")
+kruskal.test(Ozone ~ Month, data = airquality)
+@
+which shows that the location parameter of the Ozone
+distribution varies significantly from month to month. Finally we
+include a boxplot of the data:
+
+\begin{center}
+<<fig=TRUE,echo=FALSE>>=
+library("graphics")
+boxplot(Ozone ~ Month, data = airquality)
+@
+\end{center}
+
+\end{document}
diff --git a/win32/deps/library/utils/doc/Sweave.R b/win32/deps/library/utils/doc/Sweave.R
new file mode 100644
index 0000000..3e84422
--- /dev/null
+++ b/win32/deps/library/utils/doc/Sweave.R
@@ -0,0 +1,39 @@
+### R code from vignette source 'Sweave.Rnw'
+
+###################################################
+### code chunk number 1: Sweave.Rnw:122-124
+###################################################
+rnwfile <- system.file("Sweave", "example-1.Rnw", package = "utils")
+Sweave(rnwfile)
+
+
+###################################################
+### code chunk number 2: Sweave.Rnw:129-130
+###################################################
+tools::texi2pdf("example-1.tex")
+
+
+###################################################
+### code chunk number 3: Sweave.Rnw:365-366
+###################################################
+SweaveSyntConv(rnwfile, SweaveSyntaxLatex)
+
+
+###################################################
+### code chunk number 4: Sweave.Rnw:468-469 (eval = FALSE)
+###################################################
+## help("Sweave")
+
+
+###################################################
+### code chunk number 5: Sweave.Rnw:478-479 (eval = FALSE)
+###################################################
+## help("RweaveLatex")
+
+
+###################################################
+### code chunk number 6: Sweave.Rnw:594-595 (eval = FALSE)
+###################################################
+## help("Rtangle")
+
+
diff --git a/win32/deps/library/utils/doc/Sweave.Rnw b/win32/deps/library/utils/doc/Sweave.Rnw
new file mode 100644
index 0000000..430aa47
--- /dev/null
+++ b/win32/deps/library/utils/doc/Sweave.Rnw
@@ -0,0 +1,814 @@
+\documentclass[a4paper]{article}
+
+%\VignetteIndexEntry{Sweave User Manual}
+%\VignettePackage{utils}
+%\VignetteDepends{tools}
+%\VignetteDepends{datasets}
+%\VignetteDepends{stats}
+
+\title{Sweave User Manual}
+\author{Friedrich Leisch and R-core}
+
+\usepackage[round]{natbib}
+\usepackage{graphicx, Rd}
+\usepackage{listings}
+
+\lstset{frame=trbl,basicstyle=\small\tt}
+\usepackage{hyperref}
+\usepackage{color}
+\definecolor{Blue}{rgb}{0,0,0.8}
+\hypersetup{%
+colorlinks,%
+plainpages=true,%
+linkcolor=black,%
+citecolor=black,%
+urlcolor=Blue,%
+%pdfstartview=FitH,% or Fit
+pdfstartview={XYZ null null 1},%
+pdfview={XYZ null null null},%
+pdfpagemode=UseNone,% for no outline
+pdfauthor={Friedrich Leisch and R-core},%
+pdftitle={Sweave User Manual},%
+pdfsubject={R vignette documentation system}%
+}
+
+\sloppy
+
+\begin{document}
+
+\maketitle
+
+\section{Introduction}
+\label{sec:intro}
+
+Sweave provides a flexible framework for mixing text and \R{} code for
+automatic document generation. A single source file contains both
+documentation text and \R{} code, which are then \emph{woven} into a
+final document containing
+\begin{itemize}
+ \item the documentation text together with
+ \item the \R{} code and/or
+ \item the output of the code (text, graphs)
+\end{itemize}
+This allows the re-generation of a report if the input data change and
+documents the code to reproduce the analysis in the same file that
+contains the report. The \R{} code of the complete analysis is embedded
+into a \LaTeX{} document\footnote{\url{http://www.ctan.org}} using the
+\texttt{noweb} syntax \citep{flm:Ramsey:1998} which is usually used
+for literate programming \cite{fla:Knuth:1984}. Hence, the full power
+of \LaTeX{} (for high-quality typesetting) and \R{} (for data analysis)
+can be used simultaneously. See \cite{e1071-papers:Leisch:2002} and
+references therein for more general thoughts on dynamic report
+generation and pointers to other systems.
+
+Sweave uses a modular concept using different drivers for the actual
+translations. Obviously different drivers are needed for different
+text markup languages (\LaTeX{}, HTML, \ldots). Several packages on
+CRAN provide support for other word processing systems (see
+Appendix~A).
+
+
+\section{Noweb files}
+\label{sec:noweb}
+
+\texttt{noweb} \citep{flm:Ramsey:1998} is a simple
+literate-programming tool which allows combining program source code
+and the corresponding documentation into a single file. A
+\texttt{noweb} file is a simple text file which consists of a sequence
+of code and documentation segments, called \emph{chunks}:
+\begin{description}
+\item[Documentation chunks] start with a line that has an at sign
+ (\verb|@|) as first character, followed by a space or newline
+ character. The rest of this line is a comment and ignored.
+ Typically documentation chunks will contain text in a markup
+ language like \LaTeX{}. The chunk continues until a new code or
+ documentation chunk is started: note that Sweave does not interpret
+ the contents of documentation chunks, and so will identify chunk
+ indicators even inside \LaTeX{} verbatim environments.
+
+\item[Code chunks] start with \verb|<<options>>=| at the beginning of
+ a line; again the rest of the line is a comment and ignored.
+\end{description}
+The default for the first chunk is documentation.
+
+In the simplest usage of \texttt{noweb}, the options (if present) of
+the code chunks give the names of source code files, and the tool
+\texttt{notangle} can be used to extract the code chunks from the
+\texttt{noweb} file. Multiple code chunks can have the same name, the
+corresponding code chunks are the concatenated when the source code is
+extracted. \texttt{noweb} has some additional mechanisms to
+cross-reference code chunks (the \verb|[[...]]| operator, etc.),
+Sweave does currently not use nor support these features, so they are
+not described here.
+
+
+\section{Sweave files}
+\label{sec:sweavefile}
+
+\subsection{A simple example}
+
+Sweave source files are \texttt{noweb} files with some additional
+syntax that allows some additional control over the final
+output. Traditional \texttt{noweb} files have the extension
+\file{.nw}, which is also fine for Sweave files (and fully supported
+by the software). Additionally, Sweave currently recognizes files with
+extensions \file{.rnw}, \file{.Rnw}, \file{.snw} and
+\file{.Snw} to directly indicate a \texttt{noweb} file with Sweave
+extensions. We will use \file{.Rnw} throughout this document.
+
+A minimal Sweave file is shown in Figure~\ref{fig:ex1.Rnw}, which
+contains two code chunks embedded in a simple \LaTeX{}
+document. Running
+<<>>=
+rnwfile <- system.file("Sweave", "example-1.Rnw", package = "utils")
+Sweave(rnwfile)
+@
+translates this into the \LaTeX{} document shown in
+Figures~\ref{fig:ex1.tex} and~\ref{fig:ex1.pdf}. The latter can also
+be created directly from within \R{} using
+<<>>=
+tools::texi2pdf("example-1.tex")
+@
+
+The first difference between \file{example-1.Rnw} and
+\file{example-1.tex} is that the \LaTeX{} style file
+\file{Sweave.sty} is automatically loaded, which provides
+environments for typesetting \R{} input and output (the \LaTeX{}
+environments \texttt{Sinput} and \texttt{Soutput}). Otherwise, the
+documentation chunks are copied without any modification from
+\file{example-1.Rnw} to \file{example-1.tex}.
+
+\begin{figure}[htbp]
+ \centering
+ \begin{minipage}{0.9\textwidth}
+ \lstinputlisting{\Sexpr{rnwfile}}
+ \end{minipage}
+ \caption{A minimal Sweave file: \file{example-1.Rnw}.}
+ \label{fig:ex1.Rnw}
+\end{figure}
+
+The real work of Sweave is done on the code chunks: The first code
+chunk has no name, hence the default behavior of Sweave is used, which
+transfers both the \R{} commands and their respective output to the \LaTeX{}
+file, embedded in \texttt{Sinput} and \texttt{Soutput} environments,
+respectively.
+
+The second code chunk shows one of the Sweave extension to the
+\texttt{noweb} syntax: Code chunk names can be used to pass options to
+Sweave which control the final output.
+\begin{itemize}
+\item The chunk is marked as a figure chunk (\texttt{fig=TRUE}) such
+ that Sweave creates (by default) a PDF file of the plot created by
+ the commands in the chunk. Furthermore, a
+ \verb|\includegraphics{example-1-002}| statement is inserted into
+ the \LaTeX{} file (details on the choice of file names for figures
+ follow later in this manual).
+\item Option \texttt{echo=FALSE} indicates that the \R{} input should not
+ be included in the final document (no \texttt{Sinput} environment).
+\end{itemize}
+
+\begin{figure}[htbp]
+ \centering
+ \begin{minipage}{0.9\textwidth}
+ \lstinputlisting{example-1.tex}
+ \end{minipage}
+ \caption{Running \texttt{Sweave("example-1.Rnw")} produces the file
+ \file{example-1.tex}.}
+ \label{fig:ex1.tex}
+\end{figure}
+
+\begin{figure}[htbp]
+ \centering
+ \fbox{\begin{minipage}{0.8\textwidth}
+ \includegraphics[width=\textwidth]{example-1}
+ \end{minipage}}
+ \caption{The final document is created by running \texttt{pdflatex} on
+ \file{example-1.tex}.}
+ \label{fig:ex1.pdf}
+\end{figure}
+
+
+\subsection{Sweave options}
+
+Options control how code chunks and their output (text, figures) are
+transferred from the \file{.Rnw} file to the \file{.tex} file. All
+options have the form \texttt{key=value}, where \texttt{value} can be
+a number, string or logical value. Several options can be specified at
+once (separated by commas), all options must take a value (which must
+not contain a comma or equal sign). Logical options can take the
+values \texttt{TRUE}, \texttt{FALSE}, \texttt{T}, \texttt{F} as well
+as lower-case and capitalized versions of the first two.
+
+In the \file{.Rnw} file options can be specified either
+\begin{enumerate}
+ \item inside the angle brackets at the beginning of a code chunk,
+ modifying the behaviour \emph{only for this chunk}, or
+ \item anywhere in a documentation chunk using the command %
+ \begin{quote}
+ \verb|\SweaveOpts{opt1=value1, opt2=value2, ..., optN=valueN}|
+ \end{quote}
+ which modifies the defaults for the rest of the document, i.e.,
+ \emph{all code chunks after the statement}. Hence, an
+ \verb|\SweaveOpts| statement in the preamble of the document sets
+ defaults for all code chunks.
+\end{enumerate}
+Further, global options can be specified (as a comma-separated list of
+\texttt{key=value} items) in the environment variable
+\verb|SWEAVE_OPTIONS|, and via the \verb|--options=| flag of
+\verb|R CMD Sweave|.
+
+Which options are supported depends on the driver in use. All drivers
+should at least support the following options (all options appear
+together with their default value, if any):
+\begin{description}
+ \item[split=FALSE:] a logical value. If \texttt{TRUE}, then the output is
+ distributed over several files, if \texttt{FALSE} all output is
+ written to a single file. Details depend on the driver.
+
+ \item[label:] a text label for the code chunk, which is used for
+ file-name creation when \texttt{split=TRUE}. It is also used in
+ the comments added above the chunk when the file is processed by
+ \texttt{Rtangle} (provided the \texttt{annotate} option is true, as
+ it is by default), and as part of the file names for files
+ generated by figure chunks.
+\end{description}
+
+The first (and only the first) option in a code chunk name can be
+optionally without a name, then it is taken to be a label. I.e.,
+starting a code chunk with
+\begin{quote}
+ \verb|<<hello, split=FALSE>>|
+\end{quote}
+is the same as
+\begin{quote}
+ \verb|<<split=FALSE, label=hello>>|
+\end{quote}
+but
+\begin{quote}
+ \verb|<<split=FALSE, hello>>|
+\end{quote}
+gives a syntax error. Having an unnamed first argument for labels is
+needed for \texttt{noweb} compatibility. If only \verb|\SweaveOpts| is used for
+setting options, then Sweave files can be written to be fully
+compatible with \texttt{noweb} (as only file names appear in code chunk
+names).
+
+Note that \texttt{split=TRUE} should \textbf{not} be used in package
+vignettes.
+
+The help pages for \texttt{RweaveLatex} and \texttt{Rtangle} list the
+options supported by the default Sweave and Stangle drivers.
+
+Now for the promised details on the file names corresponding to
+figures. These are of the form \texttt{prefix-label.ext}. Here
+\texttt{prefix} can be set by the option \texttt{prefix.string},
+otherwise is the basename of the output file (which unless specified
+otherwise is the basename of the input file). \texttt{label} is the
+label of the code chunk if it has one, otherwise the number of the
+code chunk in the range \texttt{001} to \texttt{999}. \texttt{ext} is
+the appropriate extension for the type of graphics, e.g.{}
+\texttt{pdf}, \texttt{eps}, \ldots{}. So for the
+\file{example-1.Rnw} file, the PDF version of the boxplot is
+\file{example-1-002.pdf}, since it is the second code chunk in the
+document. Note that if \texttt{prefix.string} is used it can specify
+a directory as part of the prefix, so that for example if
+\verb|\SweaveOpts{prefix.string=figures/fig}|, the auto-generated
+figures will be placed in sub-directory \verb|figures|: the Sweave
+document should arrange to create this before use.
+
+\subsection{Using multiple input files}
+
+\LaTeX{} files can include others via \verb|\input{}| commands. These
+can also be used in Sweave files, but the included files will be
+included by \LaTeX{} and are not processed by Sweave. The equivalent
+if you want the included files to be processed is the
+\verb|\SweaveInput{}| command.
+
+Included files should use the same Sweave syntax (see below) and
+encoding as the main file.
+
+
+\subsection{Using scalars in text}
+
+There is limited support for using the values of \R{} objects in text
+chunks. Any occurrence of \verb|\Sexpr{|\texttt{\textit{expr}}\verb|}|
+is replaced by the string resulting from coercing the value of the
+expression \texttt{expr} to a character vector; only the first element
+of this vector is used. E.g., \verb|\Sexpr{sqrt(9)}| will be replaced
+by the string \texttt{'3'} (without any quotes).
+
+The expression is evaluated in the same environment as the code
+chunks, hence one can access all objects defined in the code chunks
+which have appeared before the expression and were evaluated. The
+expression may contain any valid \R{} code, only braces (\verb|{ }|) are
+not allowed. (This is not really a limitation because more complicated
+computations can be easily done in a hidden code chunk and the result
+then be used inside a \verb|\Sexpr|.)
+
+\subsection{Code chunk reuse}
+
+Named code chunks can be reused in other code chunks following later
+in the document. Consider the simple example
+\begin{quote}% NB: this is indented to avoid interpretation by Sweave.
+\begin{verbatim}
+ <<a>>=
+ x <- 10
+ @
+
+ <<b>>=
+ x + y
+ @
+
+ <<c>>=
+ <<a>>
+ y <- 20
+ <<b>>
+@
+\end{verbatim}
+\end{quote}
+which is equivalent to defining the last code chunk as
+\begin{quote}
+\begin{verbatim}
+ <<c>>=
+ x <- 10
+ y <- 20
+ x + y
+ @
+\end{verbatim}
+\end{quote}
+
+The chunk reference operator \verb|<<>>| takes only the name of the
+chunk as its argument: no additional Sweave options are allowed.
+It has to occur at the beginning of a line.
+
+References to unknown chunk names are omitted, with a warning.
+
+\subsection{Syntax definition}
+
+So far we have only talked about Sweave files using \texttt{noweb} syntax
+(which is the default). However, Sweave allows the user to redefine
+the syntax marking documentation and code chunks, using scalars in
+text or reuse code chunks.
+
+\begin{figure}[htbp]
+ \centering
+ \begin{minipage}{0.9\textwidth}
+ \lstinputlisting{example-1.Stex}
+ \end{minipage}
+ \caption{An Sweave file using \LaTeX{} syntax: \file{example-1.Stex}.}
+ \label{fig:ex1.Stex}
+\end{figure}
+
+Figure~\ref{fig:ex1.Stex} shows the example from
+Figure~\ref{fig:ex1.Rnw} using the \texttt{SweaveSyntaxLatex}
+definition. It can be created using
+<<>>=
+SweaveSyntConv(rnwfile, SweaveSyntaxLatex)
+@
+
+Code chunks are now enclosed in \texttt{Scode}
+environments, code chunk reuse is performed using
+\verb|\Scoderef{chunkname}|. All other operators are the same as in
+the noweb-style syntax.
+
+Which syntax is used for a document is determined by the extension of
+the input file, files with extension\footnote{or the lowercase
+ versions, for convenience on case-insensitive file systems.}
+\file{.Rtex} or \file{.Stex} are assumed to follow the
+\LaTeX-style syntax. Alternatively the syntax can be changed at any
+point within the document using the commands
+\begin{quote}
+ \verb|\SweaveSyntax{SweaveSyntaxLatex}|
+\end{quote}
+or
+\begin{quote}
+ \verb|\SweaveSyntax{SweaveSyntaxNoweb}|
+\end{quote}
+at the beginning of a line within a documentation chunk. Syntax
+definitions are simply lists of regular expression for several Sweave
+commands: see the two default definitions mentioned above for
+examples. (More detailed instructions will follow once the API has
+stabilized).
+
+\subsection{Encoding}
+
+\LaTeX{} documents are normally written entirely in ASCII, using
+\LaTeX{} escapes such as \verb|\'e| for accented characters. This
+can be inconvenient when writing a non-English document, and an
+alternative input encoding can be selected by using a statement such as
+\begin{quote}
+ \verb|\usepackage[latin1]{inputenc}|
+\end{quote}
+in the document's preamble, to tell \LaTeX{} to translate the input to
+its own escapes. There is a wide range of input encodings which are
+supported, at least partially, and the more recent \LaTeX{} package
+\texttt{inputenx} supports more. Other encodings commonly encountered
+in Sweave documents are \texttt{latin9}, \texttt{utf8} and
+\texttt{ansinew} (the CP1252 codepage on Windows). Greater
+coverage\footnote{including Eastern European, Greek and Hebrew
+ letters.} of UTF-8 can be obtained by
+\begin{quote}
+ \verb|\usepackage[utf8]{inputenx}|
+ \verb|\input{ix-utf8enc.dfu}|
+\end{quote}
+
+
+The previous paragraph covered the documentation sections, but what of
+the code sections where \LaTeX{} escapes cannot be used? The first
+piece of advice is to use only ASCII code sections as anything else
+will reduce the portability of your document. But \R{} code can be
+included if in the input encoding declared in the preamble.
+
+The next complication is inclusions: the final vignette may well
+include \R{} output, \LaTeX{} or other Sweave files \emph{via}
+\verb|\input{}| and \verb|\SweaveInput{}| lines, a bibliography and
+figures. It is the user's responsibility that the text inclusions are
+covered by the declared input encoding. \LaTeX{} allows the input
+encoding to be changed by
+\begin{quote}
+ \verb|\inputencoding{something}|
+\end{quote}
+statements: these may not work well in Sweave processing.
+
+It is all too easy for BiBTeX to pick up UTF-8-encoded references for
+a Latin-1 document, or \emph{vice versa}.
+
+R output is again to a large extent under the user's control. If a
+Latin-1 Sweave document is processed by \R{} running a Latin-1 locale or
+a UTF-8 document is processed in a UTF-8 locale, the only problems
+which are likely to arise are from handling data in another encoding,
+but it may be necessary to declare the document's encoding to cover
+the \R{} output which is generated even if the document is itself ASCII.
+One common problem is the quotes produced by \verb|\sQuote()| and
+\verb|\dQuote()|: these will be in UTF-8 when \R{} is run in a UTF-8
+locale, and will be in CP1252 when Sweave is run from \verb|Rgui.exe|
+on Windows. Two possible solutions are to suppress fancy quotes by
+\verb|options(useFancyQuotes=FALSE)| or to force UTF-8 by
+\verb|options(useFancyQuotes="UTF-8")|.
+
+The encoding of figures is not usually an issue as they are either
+bitmaps or include encoding information: it may be necessary to use
+the \texttt{pdf.encoding} Sweave option to set the \texttt{pdf()}
+device up appropriately.
+
+Handling non-ASCII vignettes is a work in progress: they do not work
+well before \R{} 2.13.0.
+
+
+\section{Tangling and weaving}
+
+The user front-ends of the Sweave system are the two \R{} functions
+\texttt{Stangle()} and \texttt{Sweave()}, both are contained in
+package~\pkg{utils}. \texttt{Stangle} can be used to extract only
+the code chunks from an \file{.Rnw} file and write to one or several
+files. \texttt{Sweave()} runs the code chunks through \R{} and replaces
+them with the respective input and/or output. \texttt{Stangle} is
+actually just a wrapper function for \texttt{Sweave}, which uses a
+tangling instead of a weaving driver by default. See
+<<eval=FALSE>>=
+help("Sweave")
+@
+for more details and arguments of the functions.
+
+\subsection{The \texttt{RweaveLatex} driver}
+
+This driver transforms \file{.Rnw} files with \LaTeX{} documentation
+chunks and \R{} code chunks to proper \LaTeX{} files (for typesetting both
+with standard \texttt{latex} or \texttt{pdflatex}), see
+<<eval=FALSE>>=
+help("RweaveLatex")
+@
+for details, including the supported options.
+
+\subsubsection{Writing to separate files}
+
+If \texttt{split} is set to \texttt{TRUE}, then all text corresponding
+to code chunks (the \texttt{Sinput} and \texttt{Soutput} environments)
+is written to separate files. The file names are of form
+\file{prefix.string-label.tex}, if several code chunks have the same
+label, their outputs are concatenated. If a code chunk has no label,
+then the number of the chunk is used instead. The same naming scheme
+applies to figures. You do need to ensure that the file names
+generated are valid and not so long that there are not regarded as the
+same by your OS (some file systems only recognize 13 characters).
+
+\subsubsection{\LaTeX{} style file}
+
+The driver automatically inserts a \verb|\usepackage{Sweave.sty}|
+command as last line before the \verb|\begin{document}| statement of
+ the final \LaTeX{} file if no \verb|\usepackage{Sweave}| is found in
+ the Sweave source file. This style file defines the environments
+ \texttt{Sinput} and \texttt{Soutput} for typesetting code chunks. If
+ you do not want to include the standard style file, e.g., because
+ you have your own definitions for \texttt{Sinput} and
+ \texttt{Soutput} environments in a different place, simply insert a
+ comment like
+\begin{verbatim}
+% \usepackage{Sweave}
+\end{verbatim}
+in the preamble of your latex file, this will prevent automatic
+insertion of the line.
+
+
+\subsubsection{Figure sizes}
+
+\file{Sweave.sty} sets the default \emph{\LaTeX{}} figure width (which
+is independent of the size of the generated EPS or PDF files). The
+current default is
+\begin{verbatim}
+\setkeys{Gin}{width=0.8\textwidth}
+\end{verbatim}
+if you want to use another width for the figures that are
+automatically generated and included by Sweave, simply add a line
+similar to the one above \emph{after} \verb|\begin{document}|. If you
+want no default width for figures insert a
+\verb|\usepackage[nogin]{Sweave}| in the header of your file. Note
+that a new graphics device is opened for each figure chunk (one with
+option \texttt{fig=TRUE}), hence all graphical parameters of the
+\texttt{par()} command must be set in each single figure chunk and
+are forgotten after the respective chunk (because the device is
+closed when leaving the chunk).
+
+Attention: One thing that gets easily confused are the width/height
+parameters of the \R{} graphics devices and the corresponding arguments
+to the \LaTeX{} \verb|\includegraphics| command. The Sweave options
+\texttt{width} and \texttt{height} are passed to the \R{} graphics
+devices, and hence affect the default size of the produced EPS and PDF
+files. They do not affect the size of figures in the document, by
+default they will always be 80\% of the current text width. Use
+\verb|\setkeys{Gin}| to modify figure sizes or use explicit
+\verb|\includegraphics| commands in combination with the Sweave option
+\texttt{include=FALSE}.
+
+\subsubsection{Prompts and text width}
+
+By default the driver gets the prompts used for input lines
+and continuation lines from R's \texttt{options()} settings. To set new
+prompts use something like
+\begin{verbatim}
+options(prompt = "MyR> ", continue = "...")
+\end{verbatim}
+see \texttt{help(options)} for details. Similarly the output text
+width is controlled by option \texttt{"width"}.
+
+
+\subsubsection{Graphics devices}
+
+The default graphics device for \texttt{fig=TRUE} chunks is
+\texttt{pdf()}: the standard options \texttt{pdf}, \texttt{eps},
+\texttt{png} and \texttt{jpg}\footnote{the latter two available only
+ from \R{} 2.13.0.} allow one or more of these to be selected for a
+particular chunk or (via \verb|\SweaveOpts|) for the whole document.
+It can be convenient to select PNG for a particular figure chunk by
+something like \verb|<<figN, fig=TRUE, pdf=FALSE, png=TRUE>>|:
+\texttt{pdflatex} should automatically include the PNG file for that
+chunk.
+
+You can define your own graphics devices\footnote{in \R{} 2.13.0 and
+ later.} and select one of them by the option
+\texttt{grdevice=my.Swd} where the device function (here
+\texttt{my.Swd}) is defined in a hidden code chunk. For example, we
+could make use of the \texttt{cairo\_pdf} device by
+\begin{verbatim}
+my.Swd <- function(name, width, height, ...)
+ grDevices::cairo_pdf(filename = paste(name, "pdf", sep = "."),
+ width = width, height = height)
+\end{verbatim}
+Specialized custom graphics devices may need a customized way to shut
+them down in place of \verb|graphics.off()|: this can be
+supplied\footnote{from \R{} 2.13.1} \emph{via} a companion function
+\verb|my.Swd.off|, which is called with no arguments.
+
+For a complete example see the file
+\file{src/library/utils/tests/customgraphics.Rnw} in the \R{} sources.
+
+\subsection{The \texttt{Rtangle} driver}
+
+This driver can be used to extract \R{} code chunks from a \file{.Rnw}
+file. Code chunks can either be written to one large file or separate
+files (one for each code chunk). The options \texttt{split},
+\texttt{prefix}, and \texttt{prefix.string} have the same defaults and
+interpretation as for the \texttt{RweaveLatex} driver. Use the
+standard \texttt{noweb} command line tool \texttt{notangle} if chunks
+other than \R{} code should be extracted. See
+<<eval=FALSE>>=
+help("Rtangle")
+@
+for details.
+
+Note that \texttt{split=TRUE} rarely makes much sense, as the files
+produced are often interdependent and need to be run in a particular
+order, an order which is often not the alphabetical order of the
+files.
+
+
+\section{Adding Sweave Drivers}
+
+Adding drivers is relatively simple by modelling them on\footnote{but
+ if you copy, \textbf{do} be careful not to infringe R-core's
+ copyright: the copyright notices in the \R{} sources \textbf{must} also
+ be copied.} the existing \texttt{RweaveLatex} and \texttt{Rtangle}
+drivers.
+
+An Sweave driver is a function of no arguments which should return a
+list of five functions:
+\begin{description}
+\item{\texttt{setup(file, syntax, \dots)}:} Set up the driver, e.g.{}
+ open the output file. Its return value is an object which is
+ passed to the next three functions, and can be updated by the next
+ two. The value should be a list, and contain a component
+ \texttt{options}, a named list of the default settings for the
+ options needed by \texttt{runcode}.
+\item{\texttt{runcode(object, chunk, options)}:} Process a code
+ chunk. Returns a possibly updated \texttt{object}. Argument
+ \texttt{chunk} is a character vector, and \texttt{options} is a
+ options list for this chunk.
+\item{\texttt{writedoc(object, chunk)}:} Write out a documentation
+ chunk. Returns a possibly updated \texttt{object}.
+\item{\texttt{finish(object, error)}:} Finish up, or clean up if
+ \texttt{error} is true.
+\item{\texttt{checkopts(options)}:} Converts/validates \texttt{options}
+ given as a named list of character strings.
+\end{description}
+
+Note that the \texttt{setup} function should have a \texttt{\ldots}
+argument. It will be passed additional arguments from a
+\texttt{Sweave()} call, but in future \texttt{Sweave} may itself set
+options and pass them on the setup function: one such may be the
+encoding used for the text to be processed.
+
+\bibliographystyle{jss}
+\bibliography{Sweave}
+
+\newpage
+\appendix
+
+
+\section{Frequently Asked Questions}
+\label{sec:faq}
+
+ \subsection{How can I get Emacs to automatically recognize files
+ in Sweave format?}
+
+ Recent versions of ESS (Emacs speaks statistics,
+ \url{http://ess.R-project.org}) automatically recognize files with
+ extension \file{.Rnw} as Sweave files and turn on the correct
+ modes. Please follow the instructions on the ESS homepage on how to
+ install ESS on your computer.
+
+ \subsection{Can I run Sweave directly from a shell?}
+
+ E.g., for writing makefiles it can be useful to run Sweave directly
+ from a shell rather than manually starting \R{} and then running
+ Sweave. This can easily be done using
+\begin{verbatim}
+R CMD Sweave file.Rnw
+\end{verbatim}
+
+ % A more elaborate solution which also includes automatically running
+ % \texttt{latex} has been written by Gregor Gorjanc and is available
+ % at \url{http://www.bfro.uni-lj.si/MR/ggorjan/software/shell/Sweave.sh}.
+
+ \subsection{Why does \LaTeX{} not find my EPS and PDF graphic files when
+ the file name contains a dot?}
+
+ Sweave uses the standard \LaTeX{} package \texttt{graphicx} to
+ handle graphic files, which automatically chooses the type of file,
+ provided the basename given in the \verb|\includegraphics{}|
+ statement has no extension. Hence, you may run into trouble with
+ graphics handling if the basename of your Sweave file contains
+ dots: \file{foo.Rnw} is OK, while \file{foo.bar.Rnw} is not.
+
+ \subsection{Empty figure chunks give \LaTeX{} errors.}
+
+ When a code chunk with \texttt{fig=TRUE} does not call any plotting
+ functions, invalid PDF (or EPS) files may be created. Sweave cannot
+ know if the code in a figure chunk actually plotted something or
+ not, so it will try to include the graphics, which is bound to
+ fail.
+
+ \subsection{Why do R lattice graphics not work?}
+
+ In recent versions of Sweave they do if they would when run at the
+ command line: some calls (e.g.{} those inside loops) need to be
+ explicitly \code{print()}-ed.
+
+ \subsection{How can I get Black \& White lattice graphics?}
+
+ What is the most elegant way to specify that strip panels are to have
+ transparent backgrounds and graphs are to be in black and white when
+ lattice is being used with Sweave? I would prefer a global option that
+ stays in effect for multiple plots.
+
+ Answer by Deepayan Sarkar: I'd do something like this as part of
+ the initialization:
+\begin{verbatim}
+ <<...>>
+ library(lattice)
+ ltheme <- canonical.theme(color = FALSE) ## in-built B&W theme
+ ltheme$strip.background$col <- "transparent" ## change strip bg
+ lattice.options(default.theme = ltheme) ## set as default
+ @
+\end{verbatim}
+
+ \subsection{Creating several figures from one figure chunk does
+ not work}
+
+ Consider that you want to create several graphs in a loop similar
+ to
+\begin{verbatim}
+ <<fig=TRUE>>
+ for (i in 1:4) plot(rnorm(100)+i)
+ @
+\end{verbatim}
+ This will currently \textbf{not} work, because Sweave allows
+ \textbf{only one graph} per figure chunk. The simple reason is that
+ Sweave opens a \texttt{pdf} device before executing the code and
+ closes it afterwards. If you need to plot in a loop, you have to
+ program it along the lines of
+\begin{verbatim}
+ <<results=tex,echo=FALSE>>=
+ for(i in 1:4){
+ fname <- paste("myfile", i, ".pdf", sep = "")
+ pdf(file = fname, width = 6, height = 6)
+ plot(rnorm(100)+i)
+ dev.off()
+ cat("\\includegraphics{", fname, "}\n\n", sep = "")
+ }
+ @
+\end{verbatim}
+
+
+ \subsection{How can I set default \texttt{par()} settings for figure
+ chunks?}
+
+ Because Sweave opens a new device for each graphics file in each
+ figure chunk, using \texttt{par()} has only an effect if it is used
+ inside a figure chunk. If you want to use the same settings for a
+ series of figures, it is easier to use a hook function than
+ repeating the same \texttt{par()} statement in each figure chunk.
+
+ The effect of
+\begin{verbatim}
+ options(SweaveHooks = list(fig = function() par(bg = "red", fg = "blue")))
+\end{verbatim}
+ should be easy to spot.
+
+ \subsection{How can I change the formatting of R input and output
+ chunks?}
+
+ Sweave uses the \texttt{fancyvrb} package for formatting all \R{} code
+ and text output. \texttt{fancyvrb} is a very powerful and flexible
+ package that allows fine control for layouting text in verbatim
+ environments. If you want to change the default layout, simply read
+ the \texttt{fancyvrb} documentation and modify the definitions of
+ the \texttt{Sinput} and \texttt{Soutput} environments in
+ \file{Sweave.sty}, respectively.
+
+
+ \subsection{How can I change the line length of R input and
+ output?}
+
+ Sweave respects the usual way of specifying the desired line length
+ in R, namely \texttt{options(width)}. E.g., after
+ \texttt{options(width = 40)} lines will be formatted to have at most 40
+ characters (if possible).
+
+
+ \subsection{Can I use Sweave for Word files?}
+
+ Not directly, but package~\pkg{SWord} provides similar
+ functionality for Microsoft Word on Windows platforms.
+
+ \subsection{Can I use Sweave for OpenOffice files?}
+
+ Yes, package \CRANpkg{odfWeave} provides functions for using Sweave in
+ combination with OpenOffice Writer rather than \LaTeX.
+
+ \subsection{Can I use Sweave for HTML files?}
+
+ Yes, package \CRANpkg{R2HTML} provides a driver for using Sweave in
+ combination with HTML rather than \LaTeX.
+
+ \subsection{After loading package \pkg{R2HTML} Sweave doesn't
+ work properly!}
+
+ Package \CRANpkg{R2HTML} registers an Sweave driver for HTML files
+ using the same file extensions as the default \texttt{noweb}
+ syntax, and after that its syntax is on the search list before the
+ default syntax. Using
+\begin{verbatim}
+ options(SweaveSyntax = "SweaveSyntaxNoweb")
+\end{verbatim}
+or calling Sweave like
+\begin{verbatim}
+ Sweave(..., syntax = "SweaveSyntaxNoweb")
+\end{verbatim}
+ensures the default syntax even after loading package \CRANpkg{R2HTML}.
+
+\end{document}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:
diff --git a/win32/deps/library/utils/doc/Sweave.pdf b/win32/deps/library/utils/doc/Sweave.pdf
new file mode 100644
index 0000000..01e307a
Binary files /dev/null and b/win32/deps/library/utils/doc/Sweave.pdf differ
diff --git a/win32/deps/library/utils/doc/index.html b/win32/deps/library/utils/doc/index.html
new file mode 100644
index 0000000..b23b063
--- /dev/null
+++ b/win32/deps/library/utils/doc/index.html
@@ -0,0 +1,27 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Vignettes</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="/doc/html/R.css">
+</head><body>
+<h1> Vignettes
+<img class="toplogo" src="/doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="/doc/html/index.html"><img src="/doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div>
+<h2>Vignettes from package 'utils'</h2>
+<table width="100%">
+<col width="22%">
+<col width="2%">
+<col width="50%">
+<col width="8%">
+<col width="8%">
+<col width="8%">
+<tr><td align="right" valign="top"><a href="../../../library/utils/doc/Sweave.pdf">utils::Sweave</a></td>
+<td></td><td valign="top">Sweave User Manual</td>
+<td valign="top"><a href="../../../library/utils/doc/Sweave.pdf">PDF</a></td>
+<td valign="top"><a href="../../../library/utils/doc/Sweave.Rnw">source</a></td>
+<td valign="top" nowrap><a href="../../../library/utils/doc/Sweave.R">R code</a></td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/utils/help/AnIndex b/win32/deps/library/utils/help/AnIndex
index 12402d4..13cd0ef 100644
--- a/win32/deps/library/utils/help/AnIndex
+++ b/win32/deps/library/utils/help/AnIndex
@@ -1,11 +1,18 @@
utils-package utils-package
-? help
+$.person person
+.DollarNames rcompgen
+.DollarNames.default rcompgen
+.DollarNames.environment rcompgen
+.DollarNames.list rcompgen
+? Question
?? help.search
+adist adist
alarm alarm
apropos apropos
+aregexec aregexec
argsAnywhere getAnywhere
+arrangeWindows arrangeWindows
as.character.person person
-as.character.personList person
as.person person
as.person.default person
as.personList person
@@ -13,21 +20,30 @@ as.personList.default person
as.personList.person person
as.relistable relist
as.roman roman
+aspell aspell
+aspell-utils aspell-utils
+aspell_package_Rd_files aspell-utils
+aspell_package_vignettes aspell-utils
+aspell_write_personal_dictionary_file aspell-utils
+assignInMyNamespace getFromNamespace
assignInNamespace getFromNamespace
-available.packages update.packages
+available.packages available.packages
BATCH BATCH
+bibentry bibentry
browseEnv browseEnv
browseURL browseURL
browseVignettes browseVignettes
bug.report bug.report
build PkgUtils
+c.person person
capture.output capture.output
check PkgUtils
checkCRAN mirrorAdmin
choose.dir choose.dir
choose.files choose.files
+chooseBioCmirror chooseBioCmirror
chooseCRANmirror chooseCRANmirror
-CITATION citEntry
+CITATION citation
citation citation
citEntry citEntry
citFooter citEntry
@@ -38,9 +54,11 @@ close.txtProgressBar txtProgressBar
close.winProgressBar winProgressBar
combn combn
compareVersion compareVersion
-contrib.url update.packages
+completion rcompgen
+contrib.url contrib.url
count.fields count.fields
CRAN.packages utils-deprecated
+create.post create.post
data data
data.entry dataentry
dataentry dataentry
@@ -52,7 +70,7 @@ debugger debugger
demo demo
DLL.version DLL.version
download.file download.file
-download.packages update.packages
+download.packages download.packages
dump.frames debugger
edit edit
edit.data.frame edit.data.frame
@@ -65,24 +83,31 @@ file.edit file.edit
file_test filetest
Filters choose.files
find apropos
+findLineNum findLineNum
fix fix
fixInNamespace getFromNamespace
-fixup.libraries.URLs linkhtml
-fixup.package.URLs linkhtml
flush.console flush.console
+format.person person
formatOL format
formatUL format
getAnywhere getAnywhere
+getBioCmirrors chooseBioCmirror
getClipboardFormats clipboard
getCRANmirrors chooseCRANmirror
getFromNamespace getFromNamespace
getIdentification setWindowTitle
getS3method getS3method
+getSrcDirectory sourceutils
+getSrcFilename sourceutils
+getSrcLocation sourceutils
+getSrcref sourceutils
getTxtProgressBar txtProgressBar
getWindowsHandle getWindowsHandle
+getWindowsHandles getWindowsHandles
getWindowTitle setWindowTitle
getWinProgressBar winProgressBar
glob2rx glob2rx
+globalVariables globalVariables
head head
head.data.frame head
head.default head
@@ -95,20 +120,18 @@ help.request help.request
help.search help.search
help.start help.start
history savehistory
-index.search index.search
INSTALL INSTALL
-install.packages update.packages
+install.packages install.packages
installed.packages installed.packages
is.relistable relist
limitedLabels recover
-link.html.help linkhtml
loadhistory savehistory
loadRconsole Rconsole
localeToCharset localeToCharset
ls.str ls_str
lsf.str ls_str
-make.packages.html linkhtml
-make.search.html linkhtml
+maintainer maintainer
+make.packages.html make.packages.html
make.socket make.socket
makeRweaveLatexCodeRunner SweaveUtils
memory.limit memory.size
@@ -119,17 +142,19 @@ mirror2html mirrorAdmin
mirrorAdmin mirrorAdmin
modifyList modifyList
new.packages update.packages
-normalizePath normalizePath
+news news
object.size object.size
old.packages update.packages
package.contents utils-defunct
package.skeleton package.skeleton
packageDescription packageDescription
packageStatus packageStatus
+packageVersion packageDescription
page page
person person
personList person
pico edit
+print.bibentry bibentry
print.Bibtex toLatex
print.browseVignettes browseVignettes
print.getAnywhere getAnywhere
@@ -141,6 +166,7 @@ print.object_size object.size
print.packageDescription packageDescription
print.packageIQR data
print.packageStatus packageStatus
+print.person person
print.sessionInfo sessionInfo
print.socket make.socket
print.vignette vignette
@@ -149,6 +175,7 @@ prompt.data.frame prompt
prompt.default prompt
promptData promptData
promptPackage promptPackage
+Question Question
rc.getOption rcompgen
rc.options rcompgen
rc.settings rcompgen
@@ -165,7 +192,7 @@ read.fortran read.fortran
read.fwf read.fwf
read.socket read.socket
read.table read.table
-readCitationFile citEntry
+readCitationFile citation
readClipboard clipboard
readRegistry readRegistry
recover recover
@@ -176,6 +203,7 @@ relist.list relist
relist.matrix relist
REMOVE REMOVE
remove.packages remove.packages
+removeSource removeSource
Rprof Rprof
Rprofmem Rprofmem
Rscript Rscript
@@ -196,6 +224,7 @@ RweaveTryStop SweaveUtils
savehistory savehistory
select.list select.list
sessionInfo sessionInfo
+setBreakpoint findLineNum
setInternet2 setInternet2
setRepositories setRepositories
setStatusBar setWindowTitle
@@ -203,7 +232,6 @@ setTxtProgressBar txtProgressBar
setWindowTitle setWindowTitle
setWinProgressBar winProgressBar
SHLIB SHLIB
-SHLIB SHLIB
shortPathName shortPathName
stack stack
stack.data.frame stack
@@ -228,12 +256,10 @@ tail.ftable head
tail.function head
tail.matrix head
tail.table head
+tar tar
timestamp savehistory
toBibtex toLatex
-toBibtex.citation citation
-toBibtex.citationList citation
toBibtex.person person
-toBibtex.personList person
toLatex toLatex
toLatex.sessionInfo sessionInfo
txtProgressBar txtProgressBar
@@ -242,6 +268,7 @@ unlist.relistable relist
unstack stack
unstack.data.frame stack
unstack.default stack
+untar untar
unzip unzip
update.packages update.packages
update.packageStatus packageStatus
@@ -275,6 +302,8 @@ writeClipboard clipboard
wsbrowser browseEnv
xedit edit
xemacs edit
-zip.file.extract zip.file.extract
-zip.unpack winextras
+zip zip
+zip.file.extract utils-defunct
+zip.unpack utils-defunct
[.getAnywhere getAnywhere
+[.person person
diff --git a/win32/deps/library/utils/help/aliases.rds b/win32/deps/library/utils/help/aliases.rds
new file mode 100644
index 0000000..96d4c85
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diff --git a/win32/deps/library/utils/help/paths.rds b/win32/deps/library/utils/help/paths.rds
new file mode 100644
index 0000000..9b15d15
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diff --git a/win32/deps/library/utils/help/utils.rdb b/win32/deps/library/utils/help/utils.rdb
new file mode 100644
index 0000000..e231592
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diff --git a/win32/deps/library/utils/help/utils.rdx b/win32/deps/library/utils/help/utils.rdx
new file mode 100644
index 0000000..317e835
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diff --git a/win32/deps/library/utils/html/00Index.html b/win32/deps/library/utils/html/00Index.html
new file mode 100644
index 0000000..904185e
--- /dev/null
+++ b/win32/deps/library/utils/html/00Index.html
@@ -0,0 +1,670 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: The R Utils Package</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> The R Utils Package
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘utils’ version 2.15.2</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+<li><a href="../doc/index.html">Overview of user guides and package vignettes</a>; browse <a href="../doc">directory</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<p align="center">
+<a href="# "> </a>
+<a href="#A">A</a>
+<a href="#B">B</a>
+<a href="#C">C</a>
+<a href="#D">D</a>
+<a href="#E">E</a>
+<a href="#F">F</a>
+<a href="#G">G</a>
+<a href="#H">H</a>
+<a href="#I">I</a>
+<a href="#L">L</a>
+<a href="#M">M</a>
+<a href="#N">N</a>
+<a href="#O">O</a>
+<a href="#P">P</a>
+<a href="#Q">Q</a>
+<a href="#R">R</a>
+<a href="#S">S</a>
+<a href="#T">T</a>
+<a href="#U">U</a>
+<a href="#V">V</a>
+<a href="#W">W</a>
+<a href="#X">X</a>
+<a href="#Z">Z</a>
+<a href="#misc">misc</a>
+</p>
+
+<table width="100%">
+<tr><td width="25%"><a href="utils-package.html">utils-package</a></td>
+<td>The R Utils Package</td></tr>
+</table>
+
+<h2><a name="A">-- A --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="adist.html">adist</a></td>
+<td>Approximate String Distances</td></tr>
+<tr><td width="25%"><a href="alarm.html">alarm</a></td>
+<td>Alert the User</td></tr>
+<tr><td width="25%"><a href="apropos.html">apropos</a></td>
+<td>Find Objects by (Partial) Name</td></tr>
+<tr><td width="25%"><a href="aregexec.html">aregexec</a></td>
+<td>Approximate String Match Positions</td></tr>
+<tr><td width="25%"><a href="getAnywhere.html">argsAnywhere</a></td>
+<td>Retrieve an R Object, Including from a Namespace</td></tr>
+<tr><td width="25%"><a href="arrangeWindows.html">arrangeWindows</a></td>
+<td>Rearrange windows in the R GUI.</td></tr>
+<tr><td width="25%"><a href="person.html">as.character.person</a></td>
+<td>Persons</td></tr>
+<tr><td width="25%"><a href="person.html">as.person</a></td>
+<td>Persons</td></tr>
+<tr><td width="25%"><a href="person.html">as.personList</a></td>
+<td>Persons</td></tr>
+<tr><td width="25%"><a href="relist.html">as.relistable</a></td>
+<td>Allow Re-Listing an unlist()ed Object</td></tr>
+<tr><td width="25%"><a href="roman.html">as.roman</a></td>
+<td>Roman Numerals</td></tr>
+<tr><td width="25%"><a href="aspell.html">aspell</a></td>
+<td>Spell Check Interface</td></tr>
+<tr><td width="25%"><a href="aspell-utils.html">aspell-utils</a></td>
+<td>Spell Check Utilities</td></tr>
+<tr><td width="25%"><a href="aspell-utils.html">aspell_package_Rd_files</a></td>
+<td>Spell Check Utilities</td></tr>
+<tr><td width="25%"><a href="aspell-utils.html">aspell_package_vignettes</a></td>
+<td>Spell Check Utilities</td></tr>
+<tr><td width="25%"><a href="aspell-utils.html">aspell_write_personal_dictionary_file</a></td>
+<td>Spell Check Utilities</td></tr>
+<tr><td width="25%"><a href="getFromNamespace.html">assignInMyNamespace</a></td>
+<td>Utility functions for Developing Namespaces</td></tr>
+<tr><td width="25%"><a href="getFromNamespace.html">assignInNamespace</a></td>
+<td>Utility functions for Developing Namespaces</td></tr>
+<tr><td width="25%"><a href="available.packages.html">available.packages</a></td>
+<td>List Available Packages at CRAN-like Repositories</td></tr>
+</table>
+
+<h2><a name="B">-- B --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="BATCH.html">BATCH</a></td>
+<td>Batch Execution of R</td></tr>
+<tr><td width="25%"><a href="bibentry.html">bibentry</a></td>
+<td>Bibliography Entries</td></tr>
+<tr><td width="25%"><a href="browseEnv.html">browseEnv</a></td>
+<td>Browse Objects in Environment</td></tr>
+<tr><td width="25%"><a href="browseURL.html">browseURL</a></td>
+<td>Load URL into a WWW Browser</td></tr>
+<tr><td width="25%"><a href="browseVignettes.html">browseVignettes</a></td>
+<td>List Vignettes in an HTML Browser</td></tr>
+<tr><td width="25%"><a href="bug.report.html">bug.report</a></td>
+<td>Send a Bug Report</td></tr>
+<tr><td width="25%"><a href="PkgUtils.html">build</a></td>
+<td>Utilities for Building and Checking Add-on Packages</td></tr>
+</table>
+
+<h2><a name="C">-- C --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="person.html">c.person</a></td>
+<td>Persons</td></tr>
+<tr><td width="25%"><a href="capture.output.html">capture.output</a></td>
+<td>Send Output to a Character String or File</td></tr>
+<tr><td width="25%"><a href="PkgUtils.html">check</a></td>
+<td>Utilities for Building and Checking Add-on Packages</td></tr>
+<tr><td width="25%"><a href="mirrorAdmin.html">checkCRAN</a></td>
+<td>Managing Repository Mirrors</td></tr>
+<tr><td width="25%"><a href="choose.dir.html">choose.dir</a></td>
+<td>Choose a Folder Interactively</td></tr>
+<tr><td width="25%"><a href="choose.files.html">choose.files</a></td>
+<td>Choose a List of Files Interactively</td></tr>
+<tr><td width="25%"><a href="chooseBioCmirror.html">chooseBioCmirror</a></td>
+<td>Select a Bioconductor Mirror</td></tr>
+<tr><td width="25%"><a href="chooseCRANmirror.html">chooseCRANmirror</a></td>
+<td>Select a CRAN Mirror</td></tr>
+<tr><td width="25%"><a href="citation.html">CITATION</a></td>
+<td>Citing R and R Packages in Publications</td></tr>
+<tr><td width="25%"><a href="citation.html">citation</a></td>
+<td>Citing R and R Packages in Publications</td></tr>
+<tr><td width="25%"><a href="citEntry.html">citEntry</a></td>
+<td>Bibliography Entries (Older Interface)</td></tr>
+<tr><td width="25%"><a href="citEntry.html">citFooter</a></td>
+<td>Bibliography Entries (Older Interface)</td></tr>
+<tr><td width="25%"><a href="citEntry.html">citHeader</a></td>
+<td>Bibliography Entries (Older Interface)</td></tr>
+<tr><td width="25%"><a href="clipboard.html">clipboard</a></td>
+<td>Read/Write to/from the Windows Clipboard</td></tr>
+<tr><td width="25%"><a href="close.socket.html">close.socket</a></td>
+<td>Close a Socket</td></tr>
+<tr><td width="25%"><a href="txtProgressBar.html">close.txtProgressBar</a></td>
+<td>Text Progress Bar</td></tr>
+<tr><td width="25%"><a href="winProgressBar.html">close.winProgressBar</a></td>
+<td>Progress Bars under Windows</td></tr>
+<tr><td width="25%"><a href="combn.html">combn</a></td>
+<td>Generate All Combinations of n Elements, Taken m at a Time</td></tr>
+<tr><td width="25%"><a href="compareVersion.html">compareVersion</a></td>
+<td>Compare Two Package Version Numbers</td></tr>
+<tr><td width="25%"><a href="rcompgen.html">completion</a></td>
+<td>A Completion Generator for R</td></tr>
+<tr><td width="25%"><a href="contrib.url.html">contrib.url</a></td>
+<td>Find Appropriate Paths in CRAN-like Repositories</td></tr>
+<tr><td width="25%"><a href="count.fields.html">count.fields</a></td>
+<td>Count the Number of Fields per Line</td></tr>
+<tr><td width="25%"><a href="utils-deprecated.html">CRAN.packages</a></td>
+<td>Deprecated Functions in Package 'utils'</td></tr>
+<tr><td width="25%"><a href="create.post.html">create.post</a></td>
+<td>Ancillary Function for Preparing Emails and Postings</td></tr>
+</table>
+
+<h2><a name="D">-- D --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="data.html">data</a></td>
+<td>Data Sets</td></tr>
+<tr><td width="25%"><a href="dataentry.html">data.entry</a></td>
+<td>Spreadsheet Interface for Entering Data</td></tr>
+<tr><td width="25%"><a href="dataentry.html">dataentry</a></td>
+<td>Spreadsheet Interface for Entering Data</td></tr>
+<tr><td width="25%"><a href="dataentry.html">de</a></td>
+<td>Spreadsheet Interface for Entering Data</td></tr>
+<tr><td width="25%"><a href="debugger.html">debugger</a></td>
+<td>Post-Mortem Debugging</td></tr>
+<tr><td width="25%"><a href="demo.html">demo</a></td>
+<td>Demonstrations of R Functionality</td></tr>
+<tr><td width="25%"><a href="DLL.version.html">DLL.version</a></td>
+<td>DLL Version Information</td></tr>
+<tr><td width="25%"><a href="download.file.html">download.file</a></td>
+<td>Download File from the Internet</td></tr>
+<tr><td width="25%"><a href="download.packages.html">download.packages</a></td>
+<td>Download Packages from CRAN-like Repositories</td></tr>
+<tr><td width="25%"><a href="debugger.html">dump.frames</a></td>
+<td>Post-Mortem Debugging</td></tr>
+</table>
+
+<h2><a name="E">-- E --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="edit.html">edit</a></td>
+<td>Invoke a Text Editor</td></tr>
+<tr><td width="25%"><a href="edit.data.frame.html">edit.data.frame</a></td>
+<td>Edit Data Frames and Matrices</td></tr>
+<tr><td width="25%"><a href="vignette.html">edit.vignette</a></td>
+<td>View or List Vignettes</td></tr>
+<tr><td width="25%"><a href="edit.html">emacs</a></td>
+<td>Invoke a Text Editor</td></tr>
+<tr><td width="25%"><a href="example.html">example</a></td>
+<td>Run an Examples Section from the Online Help</td></tr>
+</table>
+
+<h2><a name="F">-- F --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="file.edit.html">file.edit</a></td>
+<td>Edit One or More Files</td></tr>
+<tr><td width="25%"><a href="filetest.html">file_test</a></td>
+<td>Shell-style Tests on Files</td></tr>
+<tr><td width="25%"><a href="choose.files.html">Filters</a></td>
+<td>Choose a List of Files Interactively</td></tr>
+<tr><td width="25%"><a href="apropos.html">find</a></td>
+<td>Find Objects by (Partial) Name</td></tr>
+<tr><td width="25%"><a href="findLineNum.html">findLineNum</a></td>
+<td>Find the Location of a Line of Source Code, or Set a Breakpoint There.</td></tr>
+<tr><td width="25%"><a href="fix.html">fix</a></td>
+<td>Fix an Object</td></tr>
+<tr><td width="25%"><a href="getFromNamespace.html">fixInNamespace</a></td>
+<td>Utility functions for Developing Namespaces</td></tr>
+<tr><td width="25%"><a href="flush.console.html">flush.console</a></td>
+<td>Flush Output to A Console</td></tr>
+<tr><td width="25%"><a href="person.html">format.person</a></td>
+<td>Persons</td></tr>
+<tr><td width="25%"><a href="format.html">formatOL</a></td>
+<td>Format Unordered and Ordered Lists</td></tr>
+<tr><td width="25%"><a href="format.html">formatUL</a></td>
+<td>Format Unordered and Ordered Lists</td></tr>
+</table>
+
+<h2><a name="G">-- G --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="getAnywhere.html">getAnywhere</a></td>
+<td>Retrieve an R Object, Including from a Namespace</td></tr>
+<tr><td width="25%"><a href="chooseBioCmirror.html">getBioCmirrors</a></td>
+<td>Select a Bioconductor Mirror</td></tr>
+<tr><td width="25%"><a href="clipboard.html">getClipboardFormats</a></td>
+<td>Read/Write to/from the Windows Clipboard</td></tr>
+<tr><td width="25%"><a href="chooseCRANmirror.html">getCRANmirrors</a></td>
+<td>Select a CRAN Mirror</td></tr>
+<tr><td width="25%"><a href="getFromNamespace.html">getFromNamespace</a></td>
+<td>Utility functions for Developing Namespaces</td></tr>
+<tr><td width="25%"><a href="setWindowTitle.html">getIdentification</a></td>
+<td>Set or get the Window Title, or Set the Statusbar</td></tr>
+<tr><td width="25%"><a href="getS3method.html">getS3method</a></td>
+<td>Get An S3 Method</td></tr>
+<tr><td width="25%"><a href="sourceutils.html">getSrcDirectory</a></td>
+<td>Source Reference Utilities</td></tr>
+<tr><td width="25%"><a href="sourceutils.html">getSrcFilename</a></td>
+<td>Source Reference Utilities</td></tr>
+<tr><td width="25%"><a href="sourceutils.html">getSrcLocation</a></td>
+<td>Source Reference Utilities</td></tr>
+<tr><td width="25%"><a href="sourceutils.html">getSrcref</a></td>
+<td>Source Reference Utilities</td></tr>
+<tr><td width="25%"><a href="txtProgressBar.html">getTxtProgressBar</a></td>
+<td>Text Progress Bar</td></tr>
+<tr><td width="25%"><a href="getWindowsHandle.html">getWindowsHandle</a></td>
+<td>Get a Windows Handle</td></tr>
+<tr><td width="25%"><a href="getWindowsHandles.html">getWindowsHandles</a></td>
+<td>Get handles of windows.</td></tr>
+<tr><td width="25%"><a href="setWindowTitle.html">getWindowTitle</a></td>
+<td>Set or get the Window Title, or Set the Statusbar</td></tr>
+<tr><td width="25%"><a href="winProgressBar.html">getWinProgressBar</a></td>
+<td>Progress Bars under Windows</td></tr>
+<tr><td width="25%"><a href="glob2rx.html">glob2rx</a></td>
+<td>Change Wildcard or Globbing Pattern into Regular Expression</td></tr>
+<tr><td width="25%"><a href="globalVariables.html">globalVariables</a></td>
+<td>Declare Variables to be Treated as Global in Checking a Package</td></tr>
+</table>
+
+<h2><a name="H">-- H --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="head.html">head</a></td>
+<td>Return the First or Last Part of an Object</td></tr>
+<tr><td width="25%"><a href="help.html">help</a></td>
+<td>Documentation</td></tr>
+<tr><td width="25%"><a href="help.request.html">help.request</a></td>
+<td>Send a Post to R-help</td></tr>
+<tr><td width="25%"><a href="help.search.html">help.search</a></td>
+<td>Search the Help System</td></tr>
+<tr><td width="25%"><a href="help.start.html">help.start</a></td>
+<td>Hypertext Documentation</td></tr>
+<tr><td width="25%"><a href="savehistory.html">history</a></td>
+<td>Load or Save or Display the Commands History</td></tr>
+</table>
+
+<h2><a name="I">-- I --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="INSTALL.html">INSTALL</a></td>
+<td>Install Add-on Packages</td></tr>
+<tr><td width="25%"><a href="install.packages.html">install.packages</a></td>
+<td>Install Packages from Repositories or Local Files</td></tr>
+<tr><td width="25%"><a href="installed.packages.html">installed.packages</a></td>
+<td>Find Installed Packages</td></tr>
+<tr><td width="25%"><a href="relist.html">is.relistable</a></td>
+<td>Allow Re-Listing an unlist()ed Object</td></tr>
+</table>
+
+<h2><a name="L">-- L --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="recover.html">limitedLabels</a></td>
+<td>Browsing after an Error</td></tr>
+<tr><td width="25%"><a href="savehistory.html">loadhistory</a></td>
+<td>Load or Save or Display the Commands History</td></tr>
+<tr><td width="25%"><a href="Rconsole.html">loadRconsole</a></td>
+<td>R for Windows Configuration</td></tr>
+<tr><td width="25%"><a href="localeToCharset.html">localeToCharset</a></td>
+<td>Select a Suitable Encoding Name from a Locale Name</td></tr>
+<tr><td width="25%"><a href="ls_str.html">ls.str</a></td>
+<td>List Objects and their Structure</td></tr>
+<tr><td width="25%"><a href="ls_str.html">lsf.str</a></td>
+<td>List Objects and their Structure</td></tr>
+</table>
+
+<h2><a name="M">-- M --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="maintainer.html">maintainer</a></td>
+<td>Show Package Maintainer</td></tr>
+<tr><td width="25%"><a href="make.packages.html.html">make.packages.html</a></td>
+<td>Update HTML Package List</td></tr>
+<tr><td width="25%"><a href="make.socket.html">make.socket</a></td>
+<td>Create a Socket Connection</td></tr>
+<tr><td width="25%"><a href="memory.size.html">memory.size</a></td>
+<td>Report on Memory Allocation</td></tr>
+<tr><td width="25%"><a href="menu.html">menu</a></td>
+<td>Menu Interaction Function</td></tr>
+<tr><td width="25%"><a href="methods.html">methods</a></td>
+<td>List Methods for S3 Generic Functions or Classes</td></tr>
+<tr><td width="25%"><a href="mirrorAdmin.html">mirror2html</a></td>
+<td>Managing Repository Mirrors</td></tr>
+<tr><td width="25%"><a href="mirrorAdmin.html">mirrorAdmin</a></td>
+<td>Managing Repository Mirrors</td></tr>
+<tr><td width="25%"><a href="modifyList.html">modifyList</a></td>
+<td>Recursively Modify Elements of a List</td></tr>
+</table>
+
+<h2><a name="N">-- N --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="update.packages.html">new.packages</a></td>
+<td>Compare Installed Packages with CRAN-like Repositories</td></tr>
+<tr><td width="25%"><a href="news.html">news</a></td>
+<td>Build and Query R or Package News Information</td></tr>
+</table>
+
+<h2><a name="O">-- O --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="object.size.html">object.size</a></td>
+<td>Report the Space Allocated for an Object</td></tr>
+<tr><td width="25%"><a href="update.packages.html">old.packages</a></td>
+<td>Compare Installed Packages with CRAN-like Repositories</td></tr>
+</table>
+
+<h2><a name="P">-- P --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="package.skeleton.html">package.skeleton</a></td>
+<td>Create a Skeleton for a New Source Package</td></tr>
+<tr><td width="25%"><a href="packageDescription.html">packageDescription</a></td>
+<td>Package Description</td></tr>
+<tr><td width="25%"><a href="packageStatus.html">packageStatus</a></td>
+<td>Package Management Tools</td></tr>
+<tr><td width="25%"><a href="packageDescription.html">packageVersion</a></td>
+<td>Package Description</td></tr>
+<tr><td width="25%"><a href="page.html">page</a></td>
+<td>Invoke a Pager on an R Object</td></tr>
+<tr><td width="25%"><a href="person.html">person</a></td>
+<td>Persons</td></tr>
+<tr><td width="25%"><a href="person.html">personList</a></td>
+<td>Persons</td></tr>
+<tr><td width="25%"><a href="edit.html">pico</a></td>
+<td>Invoke a Text Editor</td></tr>
+<tr><td width="25%"><a href="bibentry.html">print.bibentry</a></td>
+<td>Bibliography Entries</td></tr>
+<tr><td width="25%"><a href="toLatex.html">print.Bibtex</a></td>
+<td>Converting R Objects to BibTeX or LaTeX</td></tr>
+<tr><td width="25%"><a href="browseVignettes.html">print.browseVignettes</a></td>
+<td>List Vignettes in an HTML Browser</td></tr>
+<tr><td width="25%"><a href="getAnywhere.html">print.getAnywhere</a></td>
+<td>Retrieve an R Object, Including from a Namespace</td></tr>
+<tr><td width="25%"><a href="help.search.html">print.hsearch</a></td>
+<td>Search the Help System</td></tr>
+<tr><td width="25%"><a href="toLatex.html">print.Latex</a></td>
+<td>Converting R Objects to BibTeX or LaTeX</td></tr>
+<tr><td width="25%"><a href="ls_str.html">print.ls_str</a></td>
+<td>List Objects and their Structure</td></tr>
+<tr><td width="25%"><a href="methods.html">print.MethodsFunction</a></td>
+<td>List Methods for S3 Generic Functions or Classes</td></tr>
+<tr><td width="25%"><a href="object.size.html">print.object_size</a></td>
+<td>Report the Space Allocated for an Object</td></tr>
+<tr><td width="25%"><a href="packageDescription.html">print.packageDescription</a></td>
+<td>Package Description</td></tr>
+<tr><td width="25%"><a href="data.html">print.packageIQR</a></td>
+<td>Data Sets</td></tr>
+<tr><td width="25%"><a href="packageStatus.html">print.packageStatus</a></td>
+<td>Package Management Tools</td></tr>
+<tr><td width="25%"><a href="person.html">print.person</a></td>
+<td>Persons</td></tr>
+<tr><td width="25%"><a href="sessionInfo.html">print.sessionInfo</a></td>
+<td>Collect Information About the Current R Session</td></tr>
+<tr><td width="25%"><a href="make.socket.html">print.socket</a></td>
+<td>Create a Socket Connection</td></tr>
+<tr><td width="25%"><a href="vignette.html">print.vignette</a></td>
+<td>View or List Vignettes</td></tr>
+<tr><td width="25%"><a href="prompt.html">prompt</a></td>
+<td>Produce Prototype of an R Documentation File</td></tr>
+<tr><td width="25%"><a href="promptData.html">promptData</a></td>
+<td>Generate Outline Documentation for a Data Set</td></tr>
+<tr><td width="25%"><a href="promptPackage.html">promptPackage</a></td>
+<td>Generate a Shell for Documentation of a Package</td></tr>
+</table>
+
+<h2><a name="Q">-- Q --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="Question.html">Question</a></td>
+<td>Documentation Shortcuts</td></tr>
+</table>
+
+<h2><a name="R">-- R --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="rcompgen.html">rc.settings</a></td>
+<td>A Completion Generator for R</td></tr>
+<tr><td width="25%"><a href="rcompgen.html">rcompgen</a></td>
+<td>A Completion Generator for R</td></tr>
+<tr><td width="25%"><a href="Rconsole.html">Rconsole</a></td>
+<td>R for Windows Configuration</td></tr>
+<tr><td width="25%"><a href="Rconsole.html">Rdevga</a></td>
+<td>R for Windows Configuration</td></tr>
+<tr><td width="25%"><a href="read.DIF.html">read.DIF</a></td>
+<td>Data Input from Spreadsheet</td></tr>
+<tr><td width="25%"><a href="read.fortran.html">read.fortran</a></td>
+<td>Read Fixed-Format Data</td></tr>
+<tr><td width="25%"><a href="read.fwf.html">read.fwf</a></td>
+<td>Read Fixed Width Format Files</td></tr>
+<tr><td width="25%"><a href="read.socket.html">read.socket</a></td>
+<td>Read from or Write to a Socket</td></tr>
+<tr><td width="25%"><a href="read.table.html">read.table</a></td>
+<td>Data Input</td></tr>
+<tr><td width="25%"><a href="citation.html">readCitationFile</a></td>
+<td>Citing R and R Packages in Publications</td></tr>
+<tr><td width="25%"><a href="clipboard.html">readClipboard</a></td>
+<td>Read/Write to/from the Windows Clipboard</td></tr>
+<tr><td width="25%"><a href="readRegistry.html">readRegistry</a></td>
+<td>Read a Windows Registy Hive</td></tr>
+<tr><td width="25%"><a href="recover.html">recover</a></td>
+<td>Browsing after an Error</td></tr>
+<tr><td width="25%"><a href="relist.html">relist</a></td>
+<td>Allow Re-Listing an unlist()ed Object</td></tr>
+<tr><td width="25%"><a href="REMOVE.html">REMOVE</a></td>
+<td>Remove Add-on Packages</td></tr>
+<tr><td width="25%"><a href="remove.packages.html">remove.packages</a></td>
+<td>Remove Installed Packages</td></tr>
+<tr><td width="25%"><a href="removeSource.html">removeSource</a></td>
+<td>Remove Stored Source from a Function.</td></tr>
+<tr><td width="25%"><a href="Rprof.html">Rprof</a></td>
+<td>Enable Profiling of R's Execution</td></tr>
+<tr><td width="25%"><a href="Rprofmem.html">Rprofmem</a></td>
+<td>Enable Profiling of R's Memory Use</td></tr>
+<tr><td width="25%"><a href="Rscript.html">Rscript</a></td>
+<td>Scripting Front-End for R</td></tr>
+<tr><td width="25%"><a href="RShowDoc.html">RShowDoc</a></td>
+<td>Show R Manuals and Other Documentation</td></tr>
+<tr><td width="25%"><a href="RSiteSearch.html">RSiteSearch</a></td>
+<td>Search for Key Words or Phrases in Documentation</td></tr>
+<tr><td width="25%"><a href="rtags.html">rtags</a></td>
+<td>An Etags-like Tagging Utility for R</td></tr>
+<tr><td width="25%"><a href="Rtangle.html">Rtangle</a></td>
+<td>R Driver for Stangle</td></tr>
+<tr><td width="25%"><a href="Rtangle.html">RtangleSetup</a></td>
+<td>R Driver for Stangle</td></tr>
+<tr><td width="25%"><a href="RweaveLatex.html">RweaveLatex</a></td>
+<td>R/LaTeX Driver for Sweave</td></tr>
+<tr><td width="25%"><a href="RweaveLatex.html">RweaveLatexSetup</a></td>
+<td>R/LaTeX Driver for Sweave</td></tr>
+</table>
+
+<h2><a name="S">-- S --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="savehistory.html">savehistory</a></td>
+<td>Load or Save or Display the Commands History</td></tr>
+<tr><td width="25%"><a href="select.list.html">select.list</a></td>
+<td>Select Items from a List</td></tr>
+<tr><td width="25%"><a href="sessionInfo.html">sessionInfo</a></td>
+<td>Collect Information About the Current R Session</td></tr>
+<tr><td width="25%"><a href="findLineNum.html">setBreakpoint</a></td>
+<td>Find the Location of a Line of Source Code, or Set a Breakpoint There.</td></tr>
+<tr><td width="25%"><a href="setInternet2.html">setInternet2</a></td>
+<td>Set or disable the use of Internet Explorer for Internet access.</td></tr>
+<tr><td width="25%"><a href="setRepositories.html">setRepositories</a></td>
+<td>Select Package Repositories</td></tr>
+<tr><td width="25%"><a href="setWindowTitle.html">setStatusBar</a></td>
+<td>Set or get the Window Title, or Set the Statusbar</td></tr>
+<tr><td width="25%"><a href="txtProgressBar.html">setTxtProgressBar</a></td>
+<td>Text Progress Bar</td></tr>
+<tr><td width="25%"><a href="setWindowTitle.html">setWindowTitle</a></td>
+<td>Set or get the Window Title, or Set the Statusbar</td></tr>
+<tr><td width="25%"><a href="winProgressBar.html">setWinProgressBar</a></td>
+<td>Progress Bars under Windows</td></tr>
+<tr><td width="25%"><a href="SHLIB.html">SHLIB</a></td>
+<td>Build Shared Object/DLL for Dynamic Loading</td></tr>
+<tr><td width="25%"><a href="shortPathName.html">shortPathName</a></td>
+<td>Express File Paths in Short Form</td></tr>
+<tr><td width="25%"><a href="stack.html">stack</a></td>
+<td>Stack or Unstack Vectors from a Data Frame or List</td></tr>
+<tr><td width="25%"><a href="Sweave.html">Stangle</a></td>
+<td>Automatic Generation of Reports</td></tr>
+<tr><td width="25%"><a href="str.html">str</a></td>
+<td>Compactly Display the Structure of an Arbitrary R Object</td></tr>
+<tr><td width="25%"><a href="str.html">strOptions</a></td>
+<td>Compactly Display the Structure of an Arbitrary R Object</td></tr>
+<tr><td width="25%"><a href="packageStatus.html">summary.packageStatus</a></td>
+<td>Package Management Tools</td></tr>
+<tr><td width="25%"><a href="summaryRprof.html">summaryRprof</a></td>
+<td>Summarise Output of R Sampling Profiler</td></tr>
+<tr><td width="25%"><a href="Sweave.html">Sweave</a></td>
+<td>Automatic Generation of Reports</td></tr>
+<tr><td width="25%"><a href="Sweave.html">SweaveSyntaxLatex</a></td>
+<td>Automatic Generation of Reports</td></tr>
+<tr><td width="25%"><a href="Sweave.html">SweaveSyntaxNoweb</a></td>
+<td>Automatic Generation of Reports</td></tr>
+<tr><td width="25%"><a href="SweaveSyntConv.html">SweaveSyntConv</a></td>
+<td>Convert Sweave Syntax</td></tr>
+</table>
+
+<h2><a name="T">-- T --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="head.html">tail</a></td>
+<td>Return the First or Last Part of an Object</td></tr>
+<tr><td width="25%"><a href="tar.html">tar</a></td>
+<td>Create a Tar Archive</td></tr>
+<tr><td width="25%"><a href="savehistory.html">timestamp</a></td>
+<td>Load or Save or Display the Commands History</td></tr>
+<tr><td width="25%"><a href="toLatex.html">toBibtex</a></td>
+<td>Converting R Objects to BibTeX or LaTeX</td></tr>
+<tr><td width="25%"><a href="person.html">toBibtex.person</a></td>
+<td>Persons</td></tr>
+<tr><td width="25%"><a href="toLatex.html">toLatex</a></td>
+<td>Converting R Objects to BibTeX or LaTeX</td></tr>
+<tr><td width="25%"><a href="sessionInfo.html">toLatex.sessionInfo</a></td>
+<td>Collect Information About the Current R Session</td></tr>
+<tr><td width="25%"><a href="txtProgressBar.html">txtProgressBar</a></td>
+<td>Text Progress Bar</td></tr>
+<tr><td width="25%"><a href="type.convert.html">type.convert</a></td>
+<td>Type Conversion on Character Variables</td></tr>
+</table>
+
+<h2><a name="U">-- U --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="relist.html">unlist.relistable</a></td>
+<td>Allow Re-Listing an unlist()ed Object</td></tr>
+<tr><td width="25%"><a href="stack.html">unstack</a></td>
+<td>Stack or Unstack Vectors from a Data Frame or List</td></tr>
+<tr><td width="25%"><a href="untar.html">untar</a></td>
+<td>Extract or List Tar Archives</td></tr>
+<tr><td width="25%"><a href="unzip.html">unzip</a></td>
+<td>Extract or List Zip Archives</td></tr>
+<tr><td width="25%"><a href="update.packages.html">update.packages</a></td>
+<td>Compare Installed Packages with CRAN-like Repositories</td></tr>
+<tr><td width="25%"><a href="packageStatus.html">update.packageStatus</a></td>
+<td>Package Management Tools</td></tr>
+<tr><td width="25%"><a href="packageStatus.html">upgrade.packageStatus</a></td>
+<td>Package Management Tools</td></tr>
+<tr><td width="25%"><a href="url.show.html">url.show</a></td>
+<td>Display a text URL</td></tr>
+<tr><td width="25%"><a href="URLencode.html">URLdecode</a></td>
+<td>Encode or Decode a (partial) URL</td></tr>
+<tr><td width="25%"><a href="URLencode.html">URLencode</a></td>
+<td>Encode or Decode a (partial) URL</td></tr>
+<tr><td width="25%"><a href="utils-package.html">utils</a></td>
+<td>The R Utils Package</td></tr>
+<tr><td width="25%"><a href="utils-deprecated.html">utils-deprecated</a></td>
+<td>Deprecated Functions in Package 'utils'</td></tr>
+</table>
+
+<h2><a name="V">-- V --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="edit.html">vi</a></td>
+<td>Invoke a Text Editor</td></tr>
+<tr><td width="25%"><a href="View.html">View</a></td>
+<td>Invoke a Data Viewer</td></tr>
+<tr><td width="25%"><a href="vignette.html">vignette</a></td>
+<td>View or List Vignettes</td></tr>
+<tr><td width="25%"><a href="vignette.html">vignettes</a></td>
+<td>View or List Vignettes</td></tr>
+</table>
+
+<h2><a name="W">-- W --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="winextras.html">win.version</a></td>
+<td>Auxiliary Functions for the Windows Port</td></tr>
+<tr><td width="25%"><a href="winDialog.html">winDialog</a></td>
+<td>Dialog Boxes under Windows</td></tr>
+<tr><td width="25%"><a href="winDialog.html">winDialogString</a></td>
+<td>Dialog Boxes under Windows</td></tr>
+<tr><td width="25%"><a href="winMenus.html">winMenuAdd</a></td>
+<td>User Menus under Windows</td></tr>
+<tr><td width="25%"><a href="winMenus.html">winMenuAddItem</a></td>
+<td>User Menus under Windows</td></tr>
+<tr><td width="25%"><a href="winMenus.html">winMenuDel</a></td>
+<td>User Menus under Windows</td></tr>
+<tr><td width="25%"><a href="winMenus.html">winMenuDelItem</a></td>
+<td>User Menus under Windows</td></tr>
+<tr><td width="25%"><a href="winMenus.html">winMenuItems</a></td>
+<td>User Menus under Windows</td></tr>
+<tr><td width="25%"><a href="winMenus.html">winMenuNames</a></td>
+<td>User Menus under Windows</td></tr>
+<tr><td width="25%"><a href="winProgressBar.html">winProgressBar</a></td>
+<td>Progress Bars under Windows</td></tr>
+<tr><td width="25%"><a href="read.socket.html">write.socket</a></td>
+<td>Read from or Write to a Socket</td></tr>
+<tr><td width="25%"><a href="write.table.html">write.table</a></td>
+<td>Data Output</td></tr>
+<tr><td width="25%"><a href="clipboard.html">writeClipboard</a></td>
+<td>Read/Write to/from the Windows Clipboard</td></tr>
+<tr><td width="25%"><a href="browseEnv.html">wsbrowser</a></td>
+<td>Browse Objects in Environment</td></tr>
+</table>
+
+<h2><a name="X">-- X --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="edit.html">xedit</a></td>
+<td>Invoke a Text Editor</td></tr>
+<tr><td width="25%"><a href="edit.html">xemacs</a></td>
+<td>Invoke a Text Editor</td></tr>
+</table>
+
+<h2><a name="Z">-- Z --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="zip.html">zip</a></td>
+<td>Create Zip archives</td></tr>
+</table>
+
+<h2><a name="misc">-- misc --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="person.html">$.person</a></td>
+<td>Persons</td></tr>
+<tr><td width="25%"><a href="rcompgen.html">.DollarNames</a></td>
+<td>A Completion Generator for R</td></tr>
+<tr><td width="25%"><a href="Question.html">?</a></td>
+<td>Documentation Shortcuts</td></tr>
+<tr><td width="25%"><a href="help.search.html">??</a></td>
+<td>Search the Help System</td></tr>
+<tr><td width="25%"><a href="getAnywhere.html">[.getAnywhere</a></td>
+<td>Retrieve an R Object, Including from a Namespace</td></tr>
+<tr><td width="25%"><a href="person.html">[.person</a></td>
+<td>Persons</td></tr>
+</table>
+</body></html>
diff --git a/win32/deps/library/utils/html/R.css b/win32/deps/library/utils/html/R.css
new file mode 100644
index 0000000..6f058f3
--- /dev/null
+++ b/win32/deps/library/utils/html/R.css
@@ -0,0 +1,57 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: x-large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-size: large }
+
+H4{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic;
+ font-size: large }
+
+H5{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+H6{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace;
+ font-style: italic }
+
+IMG.toplogo{ vertical-align: middle }
+
+IMG.arrow{ width: 30px;
+ height: 30px;
+ border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+ background: rgb(85%, 85%, 85%);
+}
+
diff --git a/win32/deps/library/utils/po/da/LC_MESSAGES/R-utils.mo b/win32/deps/library/utils/po/da/LC_MESSAGES/R-utils.mo
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diff --git a/win32/deps/library/utils/po/en quot/LC_MESSAGES/R-utils.mo b/win32/deps/library/utils/po/en quot/LC_MESSAGES/R-utils.mo
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diff --git a/win32/deps/library/utils/po/fr/LC_MESSAGES/R-utils.mo b/win32/deps/library/utils/po/fr/LC_MESSAGES/R-utils.mo
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index 0000000..ebd3ab1
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diff --git a/win32/deps/library/utils/po/ja/LC_MESSAGES/R-utils.mo b/win32/deps/library/utils/po/ja/LC_MESSAGES/R-utils.mo
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index 0000000..7aaeb64
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diff --git a/win32/deps/library/utils/po/ko/LC_MESSAGES/R-utils.mo b/win32/deps/library/utils/po/ko/LC_MESSAGES/R-utils.mo
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diff --git a/win32/deps/library/utils/po/pl/LC_MESSAGES/R-utils.mo b/win32/deps/library/utils/po/pl/LC_MESSAGES/R-utils.mo
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diff --git a/win32/deps/library/utils/po/pt_BR/LC_MESSAGES/R-utils.mo b/win32/deps/library/utils/po/pt_BR/LC_MESSAGES/R-utils.mo
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diff --git a/win32/deps/library/utils/po/ru/LC_MESSAGES/R-utils.mo b/win32/deps/library/utils/po/ru/LC_MESSAGES/R-utils.mo
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diff --git a/win32/deps/library/utils/po/tr/LC_MESSAGES/R-utils.mo b/win32/deps/library/utils/po/tr/LC_MESSAGES/R-utils.mo
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diff --git a/win32/deps/library/utils/po/zh_CN/LC_MESSAGES/R-utils.mo b/win32/deps/library/utils/po/zh_CN/LC_MESSAGES/R-utils.mo
new file mode 100644
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diff --git a/win32/deps/library/utils/tests/Sexpr-verb-ex.Rnw b/win32/deps/library/utils/tests/Sexpr-verb-ex.Rnw
new file mode 100644
index 0000000..f8acd06
--- /dev/null
+++ b/win32/deps/library/utils/tests/Sexpr-verb-ex.Rnw
@@ -0,0 +1,44 @@
+\documentclass[11pt,a4paper]{article}
+
+%% *** automatically switched by 'make' ( ./Makefile ) --- CARE!! in changing
+\SweaveOpts{echo=FALSE,eval=FALSE,results=hide} % Exercise mode
+%\SweaveOpts{echo=TRUE,eval=TRUE,results=verbatim} % Solution mode
+%% other Sweave options
+\SweaveOpts{engine=R, keep.source=TRUE, strip.white=true}
+
+\newif\ifSolution
+\Solutiontrue% if solution
+\Solutionfalse%if exercise
+%
+\ifSolution\newcommand{\commentSol}[1]{#1}
+\else \newcommand{\commentSol}[1]{}
+\fi
+\newcommand{\T}[1]{\texttt{#1}}
+
+\begin{document}
+
+<<preliminaries,echo=FALSE,results=hide>>=
+options(width = 75, digits = 5, str=list(vec.len=2))
+@
+
+We work with the data set \T{airquality} which is part of R....
+You can address it simply by \T{airquality}. Use \T{?airquality} to read about the
+meaning of the variables contained in the dataset.
+
+Get a summary of the data,
+<<s-air-2,echo=TRUE,eval=TRUE>>=
+summary(airquality)
+@
+
+\commentSol{The data set contains \Sexpr{nrow(airquality)} observations. The data is
+complete for all but the first two variables \T{Ozone}, \T{Solar.R},
+which contain \Sexpr{sum(is.na(airquality[,1]))} and
+\Sexpr{sum(is.na(airquality[,2]))} missing values, respectively.
+}
+
+The above works in solution mode,
+but in exercise mode, the $\backslash$Sexpr results are put out verbatim,
+unfortunately using $\backslash$\verb|verb{bla bla{| and the left brace
+\emph{really} messes up the $\backslash$commentSol\verb|{..}| command...
+
+\end{document}
diff --git a/win32/deps/library/utils/tests/Sweave-tst.R b/win32/deps/library/utils/tests/Sweave-tst.R
new file mode 100644
index 0000000..a943c7f
--- /dev/null
+++ b/win32/deps/library/utils/tests/Sweave-tst.R
@@ -0,0 +1,84 @@
+# File src/library/utils/tests/Sweave-tst.R
+# Part of the R package, http://www.R-project.org
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# A copy of the GNU General Public License is available at
+# http://www.r-project.org/Licenses/
+
+## Testing Sweave
+
+.proctime00 <- proc.time()
+library(utils)
+options(digits=5) # to avoid trivial printed differences
+options(show.signif.stars=FALSE) # avoid fancy quotes in o/p
+
+SweaveTeX <- function(file, ...) {
+ if(!file.exists(file))
+ stop("File", file, "does not exist in", getwd())
+ texF <- sub("\\.[RSrs]nw$", ".tex", file)
+ Sweave(file, ...)
+ if(!file.exists(texF))
+ stop("File", texF, "does not exist in", getwd())
+ readLines(texF)
+}
+
+p0 <- function(...) paste(..., sep="")
+latexEnv <- function(lines, name) {
+ stopifnot(is.character(lines), is.character(name),
+ length(lines) >= 2, length(name) == 1)
+ beg <- p0("\\begin{",name,"}")
+ end <- p0("\\end{",name,"}")
+ i <- grep(beg, lines, fixed=TRUE)
+ j <- grep(end, lines, fixed=TRUE)
+ if((n <- length(i)) != length(j))
+ stop(sprintf("different number of %s / %s", beg,end))
+ if(any(j-1 < i+1))
+ stop(sprintf("positionally mismatched %s / %s", beg,end))
+ lapply(mapply(seq, i+1,j-1, SIMPLIFY=FALSE),
+ function(ind) lines[ind])
+}
+
+## now, Sweave() and check *.Rnw examples :
+
+### ------------------------------------ 1 ----------------------------------
+t1 <- SweaveTeX("swv-keepSrc-1.Rnw")
+if(FALSE)## look at it
+writeLines(t1)
+
+inp <- latexEnv(t1, "Sinput")
+out <- latexEnv(t1, "Soutput")
+## This may have to be updated when the *.Rnw changes:
+stopifnot(length(inp) == 5,
+ grepl("#", inp[[2]]), length(inp[[3]]) == 1,
+ length(out) == 1,
+ any(grepl("\\includegraphics", t1)))
+
+### ------------------------------------ 2 ----------------------------------
+## Sweave() comments with keep.source=TRUE
+t2 <- SweaveTeX("keepsource.Rnw")
+comml <- grep("##", t2, value=TRUE)
+stopifnot(length(comml) == 2,
+ grepl("initial comment line", comml[1]),
+ grepl("last comment", comml[2]))
+## the first was lost in 2.12.0; the last in most/all previous versions of R
+
+### ------------------------------------ 3 ----------------------------------
+## custom graphics devices
+Sweave("customgraphics.Rnw")
+
+### ------------------------------------ 4 ----------------------------------
+## SweaveOpts + \Sexpr --> \verb... output
+Sweave(f <- "Sexpr-verb-ex.Rnw")
+tools::texi2pdf(sub("Rnw$","tex", f))# used to fail
+
+
+cat('Time elapsed: ', proc.time() - .proctime00,'\n')
diff --git a/win32/deps/library/utils/tests/completion.R b/win32/deps/library/utils/tests/completion.R
new file mode 100644
index 0000000..d608361
--- /dev/null
+++ b/win32/deps/library/utils/tests/completion.R
@@ -0,0 +1,29 @@
+
+## test some typical completion attempts
+
+testLine <- function(line, cursor = nchar(line))
+{
+ str(utils:::.win32consoleCompletion(line, cursor))
+}
+
+testLine("")
+
+testLine("lib")
+testLine("data(")
+testLine("data(US")
+testLine("data(US", 3)
+
+testLine("?INS")
+
+testLine("utils::data")
+testLine("utils:::.show_help_on_topic_")
+testLine("utils::.show_help_on_topic_")
+
+testLine("update(")
+
+testLine("version$m")
+testLine("nchar(version[")
+
+## testLine("")
+## testLine("")
+## testLine("")
diff --git a/win32/deps/library/utils/tests/customgraphics.Rnw b/win32/deps/library/utils/tests/customgraphics.Rnw
new file mode 100644
index 0000000..785afbc
--- /dev/null
+++ b/win32/deps/library/utils/tests/customgraphics.Rnw
@@ -0,0 +1,20 @@
+Test file for custom graphics devices
+<<results=hide>>=
+my.Swd <- function(name, width, height, ...) {
+ cat("running my.Swd\n")
+ grDevices::png(filename = paste(name, "png", sep = "."),
+ width = width, height = height, res = 100, units = "in",
+ bg = "transparent")
+}
+my.Swd.off <- function() {
+ cat("shutting down my.Swd\n")
+ grDevices::dev.off()
+}
+<<fig=TRUE, grdevice=my.Swd>>=
+plot(1:2)
+<<fig=TRUE, pdf=TRUE, grdevice=my.Swd>>=
+plot(1:3)
+<<fig=TRUE, grdevice=my.Swd, pdf=TRUE>>=
+plot(1:4)
+@
+Done!
diff --git a/win32/deps/library/utils/tests/keepsource.Rnw b/win32/deps/library/utils/tests/keepsource.Rnw
new file mode 100644
index 0000000..9622141
--- /dev/null
+++ b/win32/deps/library/utils/tests/keepsource.Rnw
@@ -0,0 +1,12 @@
+\SweaveOpts{keep.source=TRUE}
+
+Now a chunk starting with a comment, lost in R 2.12.0 patched:
+<<ex>>=
+## This is an initial comment line. Let's hope it's not being lost
+"Above there's a comment."
+1:10 # a comment here is preserved
+pi # also, there's one the next (last) line - which used to get lost
+## and a last comment here ... lost also in earlier R versions
+@
+
+and some more text.
diff --git a/win32/deps/library/utils/tests/swv-keepSrc-1.Rnw b/win32/deps/library/utils/tests/swv-keepSrc-1.Rnw
new file mode 100644
index 0000000..3cfcb48
--- /dev/null
+++ b/win32/deps/library/utils/tests/swv-keepSrc-1.Rnw
@@ -0,0 +1,47 @@
+\documentclass{article}
+\SweaveOpts{engine=R,eps=FALSE,pdf=TRUE,strip.white=true,keep.source=TRUE}
+
+\usepackage{Sweave}
+
+\begin{document}
+<<preliminaries, echo=FALSE, results=hide>>=
+options(width=70, useFancyQuotes = FALSE, prompt="R> ", continue="+ ")
+@
+\subsection*{Introduction}
+
+We generate 3D gaussian data,
+<<ex1-U3>>=
+set.seed(1)
+n <- 100
+x <- rnorm(n); y <- 2*x + rnorm(n)/2
+U3 <- cbind(x, y, z = -3*x + y + rnorm(n)/4)
+@
+look at its structure
+<<str>>=
+str(U3) # its structure ((comment kept))
+@
+and load package \texttt{lattice}
+<<req-lattice>>=
+require("lattice")
+@
+to visualize it by a simple scatter plot matrix
+\begin{figure}[h!]
+\centering
+<<splom-def, eval=false>>=
+splom(U3, xlab ="", cex = 0.4)
+<<splom, echo=FALSE, fig=TRUE, height=5>>=
+print(
+<<splom-def>>
+ )
+@
+\caption{\Sexpr{n} vectors of random variates ... ...}
+\label{fig:AC_Joe}
+\end{figure}
+
+\subsection*{Session Information}
+
+<<sessionInfo, results=tex>>=
+toLatex(sessionInfo())
+@
+
+\end{document}
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