[chronojump] R EMD package for R 2.9.2
- From: Xavier de Blas <xaviblas src gnome org>
- To: commits-list gnome org
- Cc:
- Subject: [chronojump] R EMD package for R 2.9.2
- Date: Wed, 30 Jan 2013 23:22:30 +0000 (UTC)
commit fdebf10330b05ebe0e0b7061bd46aa50853de5f5
Author: Xavier de Blas <xaviblas gmail com>
Date: Thu Jan 31 00:20:45 2013 +0100
R EMD package for R 2.9.2
win32/deps/library/EMD/DESCRIPTION | 25 +-
win32/deps/library/EMD/INDEX | 12 +-
win32/deps/library/EMD/MD5 | 118 +++--
win32/deps/library/EMD/Meta/Rd.rds | Bin 961 -> 879 bytes
win32/deps/library/EMD/Meta/data.rds | Bin 214 -> 217 bytes
win32/deps/library/EMD/Meta/hsearch.rds | Bin 910 -> 835 bytes
win32/deps/library/EMD/Meta/links.rds | Bin 405 -> 0 bytes
win32/deps/library/EMD/Meta/nsInfo.rds | Bin 215 -> 0 bytes
win32/deps/library/EMD/Meta/package.rds | Bin 849 -> 746 bytes
win32/deps/library/EMD/NAMESPACE | 10 -
win32/deps/library/EMD/R/EMD | 27 +-
win32/deps/library/EMD/R/EMD.rdb | Bin 21138 -> 14649 bytes
win32/deps/library/EMD/R/EMD.rdx | Bin 499 -> 374 bytes
win32/deps/library/EMD/data/beryllium.rda | Bin 1765 -> 0 bytes
win32/deps/library/EMD/data/datalist | 7 -
win32/deps/library/EMD/data/kospi200.rda | Bin 5036 -> 0 bytes
win32/deps/library/EMD/data/lena.rda | Bin 188871 -> 0 bytes
win32/deps/library/EMD/data/lennon.rda | Bin 38130 -> 0 bytes
win32/deps/library/EMD/data/solar.hs.rda | Bin 1436 -> 0 bytes
win32/deps/library/EMD/data/solar.lean.rda | Bin 2346 -> 0 bytes
win32/deps/library/EMD/data/sunspot.rda | Bin 1850 -> 0 bytes
win32/deps/library/EMD/help/AnIndex | 3 -
win32/deps/library/EMD/help/EMD.rdb | Bin 51544 -> 0 bytes
win32/deps/library/EMD/help/EMD.rdx | Bin 586 -> 0 bytes
win32/deps/library/EMD/help/aliases.rds | Bin 304 -> 0 bytes
win32/deps/library/EMD/help/paths.rds | Bin 260 -> 0 bytes
win32/deps/library/EMD/html/00Index.html | 32 +-
win32/deps/library/EMD/html/R.css | 57 --
win32/deps/library/EMD/libs/i386/EMD.dll | Bin 20992 -> 0 bytes
win32/deps/library/EMD/libs/i386/symbols.rds | Bin 286 -> 0 bytes
win32/deps/library/EMD/libs/x64/EMD.dll | Bin 23040 -> 0 bytes
win32/deps/library/EMD/libs/x64/symbols.rds | Bin 284 -> 0 bytes
win32/deps/library/fields/DESCRIPTION | 38 +-
win32/deps/library/fields/INDEX | 247 +++++-----
win32/deps/library/fields/LICENSE | 11 -
win32/deps/library/fields/MD5 | 152 ++++--
win32/deps/library/fields/Meta/Rd.rds | Bin 4959 -> 5215 bytes
win32/deps/library/fields/Meta/data.rds | Bin 639 -> 580 bytes
win32/deps/library/fields/Meta/hsearch.rds | Bin 4834 -> 5056 bytes
win32/deps/library/fields/Meta/links.rds | Bin 2476 -> 0 bytes
win32/deps/library/fields/Meta/nsInfo.rds | Bin 367 -> 0 bytes
win32/deps/library/fields/Meta/package.rds | Bin 1267 -> 997 bytes
win32/deps/library/fields/NAMESPACE | 12 -
win32/deps/library/fields/R/fields | 27 +-
win32/deps/library/fields/R/fields.rdb | Bin 131217 -> 155455 bytes
win32/deps/library/fields/R/fields.rdx | Bin 2972 -> 3561 bytes
win32/deps/library/fields/data/CO2.rda | Bin 455372 -> 206014 bytes
win32/deps/library/fields/data/COmonthlyMet.rda | Bin 681966 -> 1206004 bytes
.../library/fields/data/NorthAmericanRainfall.rda | Bin 74279 -> 0 bytes
win32/deps/library/fields/data/PRISMelevation.rda | Bin 667593 -> 1451127 bytes
win32/deps/library/fields/data/RCMexample.rda | Bin 161424 -> 197751 bytes
win32/deps/library/fields/data/RMelevation.rda | Bin 94458 -> 180721 bytes
win32/deps/library/fields/data/US.dat.rda | Bin 44988 -> 66120 bytes
win32/deps/library/fields/data/WorldBankCO2.rda | Bin 3214 -> 0 bytes
win32/deps/library/fields/data/datalist | 11 -
win32/deps/library/fields/data/lennon.rda | Bin 38012 -> 72602 bytes
win32/deps/library/fields/data/ozone2.rda | Bin 22876 -> 31891 bytes
win32/deps/library/fields/data/rat.diet.rda | Bin 579 -> 0 bytes
win32/deps/library/fields/data/world.dat.rda | Bin 15254 -> 25231 bytes
win32/deps/library/fields/help/AnIndex | 93 +++--
win32/deps/library/fields/help/aliases.rds | Bin 2255 -> 0 bytes
win32/deps/library/fields/help/fields.rdb | Bin 356112 -> 0 bytes
win32/deps/library/fields/help/fields.rdx | Bin 1911 -> 0 bytes
win32/deps/library/fields/help/paths.rds | Bin 734 -> 0 bytes
win32/deps/library/fields/html/00Index.html | 133 +++---
win32/deps/library/fields/html/R.css | 57 --
win32/deps/library/fields/libs/i386/fields.dll | Bin 39424 -> 0 bytes
win32/deps/library/fields/libs/i386/symbols.rds | Bin 878 -> 0 bytes
win32/deps/library/fields/libs/x64/fields.dll | Bin 46592 -> 0 bytes
win32/deps/library/fields/libs/x64/symbols.rds | Bin 867 -> 0 bytes
win32/deps/library/spam/0NEWS | 404 --------------
win32/deps/library/spam/CITATION | 19 -
win32/deps/library/spam/DESCRIPTION | 15 +-
win32/deps/library/spam/INDEX | 23 +-
win32/deps/library/spam/MD5 | 107 +++--
win32/deps/library/spam/Meta/Rd.rds | Bin 3971 -> 3378 bytes
win32/deps/library/spam/Meta/data.rds | Bin 229 -> 230 bytes
win32/deps/library/spam/Meta/demo.rds | Bin 295 -> 304 bytes
win32/deps/library/spam/Meta/hsearch.rds | Bin 4073 -> 3452 bytes
win32/deps/library/spam/Meta/links.rds | Bin 2709 -> 0 bytes
win32/deps/library/spam/Meta/nsInfo.rds | Bin 1090 -> 834 bytes
win32/deps/library/spam/Meta/package.rds | Bin 924 -> 926 bytes
win32/deps/library/spam/NAMESPACE | 87 +---
win32/deps/library/spam/NEWS | 399 ++++++++++-----
win32/deps/library/spam/R/spam | 2 +-
win32/deps/library/spam/R/spam.rdb | Bin 369813 -> 378055 bytes
win32/deps/library/spam/R/spam.rdx | Bin 4730 -> 5960 bytes
win32/deps/library/spam/data/Rdata.rdb | Bin 319762 -> 319804 bytes
win32/deps/library/spam/data/Rdata.rds | Bin 127 -> 126 bytes
win32/deps/library/spam/data/Rdata.rdx | Bin 209 -> 210 bytes
.../deps/library/spam/demo/article-jss-example1.R | 73 ++--
.../deps/library/spam/demo/article-jss-example2.R | 49 +--
win32/deps/library/spam/demo/article-jss.R | 73 +--
win32/deps/library/spam/demo/cholesky.R | 2 +-
win32/deps/library/spam/demo/spam.R | 5 +-
win32/deps/library/spam/demo/timing.R | 2 +-
win32/deps/library/spam/help/AnIndex | 117 +----
win32/deps/library/spam/help/aliases.rds | Bin 2688 -> 0 bytes
win32/deps/library/spam/help/paths.rds | Bin 491 -> 0 bytes
win32/deps/library/spam/help/spam.rdb | Bin 159575 -> 0 bytes
win32/deps/library/spam/help/spam.rdx | Bin 1263 -> 0 bytes
win32/deps/library/spam/html/00Index.html | 548 +++++++++++---------
win32/deps/library/spam/html/R.css | 57 --
win32/deps/library/spam/libs/i386/spam.dll | Bin 69632 -> 0 bytes
win32/deps/library/spam/libs/i386/symbols.rds | Bin 1557 -> 0 bytes
win32/deps/library/spam/libs/x64/spam.dll | Bin 81408 -> 0 bytes
win32/deps/library/spam/libs/x64/symbols.rds | Bin 1551 -> 0 bytes
107 files changed, 1322 insertions(+), 1732 deletions(-)
---
diff --git a/win32/deps/library/EMD/DESCRIPTION b/win32/deps/library/EMD/DESCRIPTION
index f4f778b..fbb73ac 100644
--- a/win32/deps/library/EMD/DESCRIPTION
+++ b/win32/deps/library/EMD/DESCRIPTION
@@ -1,19 +1,14 @@
Package: EMD
-Version: 1.5.2
-Date: 2013-01-18
Title: Empirical Mode Decomposition and Hilbert Spectral Analysis
-Author: Donghoh Kim and Hee-Seok Oh
+Version: 1.2.0
+Date: 2008-11-08
+Author: Donghoh Kim <donghoh kim gmail com>, Hee-Seok Oh
+ <heeseok stats snu ac kr>
Maintainer: Donghoh Kim <donghoh kim gmail com>
-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)
+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
URL: http://dasan.sejong.ac.kr/~dhkim/software_emd.html
-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; 2013-01-24 20:25:30 UTC; windows
-Archs: i386, x64
+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
diff --git a/win32/deps/library/EMD/INDEX b/win32/deps/library/EMD/INDEX
index 0425bf6..699dfea 100644
--- a/win32/deps/library/EMD/INDEX
+++ b/win32/deps/library/EMD/INDEX
@@ -1,22 +1,18 @@
-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 Bidimenasional Empirical Mode Decomposition
-emddenoise Denoising by EMD and Thresholding
+emd2d Two dimensional Empirical Mode Decomposition
+emddenoise Denoising by EMD and Cross-Validation
extractimf Intrinsic Mode Function
-extractimf2d Bidimensional Intrinsic Mode Function
+extractimf2d Two dimensional Intrinsic Mode Function
extrema Finding Local Extrema and Zero-crossings
extrema2dC Finding Local Extrema
hilbertspec Hilbert Transform and Instantaneous Frequency
-imageEMD Plot of Bidimenasional Empirical Mode
- Decomposition Result
+imageEMD Plot of Two Dimensional 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 2219bd8..175aec5 100644
--- a/win32/deps/library/EMD/MD5
+++ b/win32/deps/library/EMD/MD5
@@ -1,31 +1,87 @@
-2bb1dbc2c82f61c55d27b4709fdff6cb *DESCRIPTION
-7cab3c6c0ec40e33a8e29db791dd7493 *INDEX
-9be851006daf880d243e72d9cb39c3bd *Meta/Rd.rds
-327a89d516fd51104a644d60e4d37e5c *Meta/data.rds
-9694c9e5938d5f8b6dff227f22e81319 *Meta/hsearch.rds
-5e78d512a47833f316a6f6beea4cebaa *Meta/links.rds
-e4480eec10ea860f496723208e300ba1 *Meta/nsInfo.rds
-b519fb3613d1c478caf434b079ef44ce *Meta/package.rds
-613324507c35b15519284127f38458d6 *NAMESPACE
-240d28d145138a75831809e31a480bad *R/EMD
-6ce426beb884abcff567512a7a48fc87 *R/EMD.rdb
-5e94892b2d1179e2c4f0ff8e300f4913 *R/EMD.rdx
-a101e733a90cbb1bbf82848273f91983 *data/beryllium.rda
-e9c9b986a1fcdbaad60575b7b8fd866b *data/datalist
-79d30ac997b95721113cdeed4764159c *data/kospi200.rda
-bcff9b4539ef195ca6af5f08fc34a21a *data/lena.rda
-40b3bf402353b781f06c8723acc59e09 *data/lennon.rda
-5a0d9d469dd564fd81e8c6f595213ce0 *data/solar.hs.rda
-f588d89cb0247e7592c955545be5bbab *data/solar.lean.rda
-c8e09219747bd132c5d706d69a2b795f *data/sunspot.rda
-4f46211dbfe73e7d13b6d4fa282c583c *help/AnIndex
-289c7c7c619a19c5eb751c761a53b230 *help/EMD.rdb
-646238596231937957860c7170d1b111 *help/EMD.rdx
-fffddfd179844861217ca3958304c206 *help/aliases.rds
-af2ab59afc3090d2ab5aeef6543e571a *help/paths.rds
-01ab19d3abd89cf4dbfc891974a995ef *html/00Index.html
-444535b9cb76ddff1bab1e1865a3fb14 *html/R.css
-9ca12b7b1fa6c2e301de13c6f843b81a *libs/i386/EMD.dll
-5c7b3d7a2ea9cb26c8dee58a1949fb8f *libs/i386/symbols.rds
-c7069ef298ef4bfcda367aeeb8886bc6 *libs/x64/EMD.dll
-deac506ea59db7390aa2669973654906 *libs/x64/symbols.rds
+607fe7c20cc6198d4769db1077b5f775 *CONTENTS
+4579c9a462f562c374ade65ee2d5ec90 *DESCRIPTION
+5f0f71033eb3046f27405bd7bb4217e6 *INDEX
+24c76ae3e75f992390bfae63b2105699 *Meta/Rd.rds
+f0124119ac488612606672d4fc50a7a6 *Meta/data.rds
+4494a1b7dfb36ee260776b7b5f3bc111 *Meta/hsearch.rds
+b5d136ef6ad10c2f783510373a367076 *Meta/package.rds
+eaad6298bae7cef17bc1f1d9e08a628c *R-ex/cvtype.R
+40c9a3f0f3e9b73396429898758c42f9 *R-ex/emd.R
+70d67a33d59c671b6087ad407ffb726a *R-ex/emd2d.R
+b9a944848f99bcbd5df8cbf732d37b52 *R-ex/emddenoise.R
+fe686fb4eef8b49fa81f9a0e8285c773 *R-ex/extractimf.R
+8e4e68ce272c4b4a44d79172c66b518f *R-ex/extractimf2d.R
+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
+ff567676bbf791e2bcfe5be12f69bdab *R/EMD.rdx
+b892a0cce7aeaf1cea70fa4b6cd39745 *chtml/EMD.chm
+a81e6d2e48afa4f265b5504978233942 *data/Rdata.zip
+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
+9e3f4fc933caffaa19108dc7b25df821 *help/extractimf2d
+4d1b7fb063259823fd8f8c9f47dfc6f4 *help/extrema
+81a93670f71f9cd9e24d498718f5e525 *help/extrema2dC
+f4876ed36bfbeb06603cba0889470e1b *help/hilbertspec
+f2e464ceec84659dc9fde2ce960c1436 *help/imageEMD
+dc1a34c082ad9d4c56af8429c0a9d2f6 *help/kospi200
+240a83af052a91f078e890ff57c816f2 *help/lena
+a3af05fd46524eb62ee787576bc3a311 *help/lennon
+bb001b996d6451f8d3a2667d65c81aa1 *help/solar
+f6a7fe4a6090e950a9b4f3f5f79b94fc *help/spectrogram
+1e160762f17eab3d7c97e9e13e22db11 *help/sunspot
+5bab497447d0adec13d449d4f1844d6a *html/00Index.html
+e66aeb5082a04be1a85fe81d2c28da81 *html/EMD-internal.html
+816e2299b334bf787956f393b946bd5f *html/cvtype.html
+247fe3830f89852dc3aa46f15bfa52d3 *html/emd.html
+36b0bef014e96f8d39991bf3b35dfd78 *html/emd.pred.html
+52806933e19ea5f7f4aa8781b8bbc177 *html/emd2d.html
+1f41747469dbd56bf8865266b808efc4 *html/emddenoise.html
+6e1c55cd76995fdf9f94f8eb9da53de9 *html/extractimf.html
+8cf7bb09ef2164a7f12c633e29cc7a9e *html/extractimf2d.html
+b20c3f19a312fc0a3b8aacef4f4bb2a1 *html/extrema.html
+7454d3c8f3ba97956c5ff5a4e97868bd *html/extrema2dC.html
+00a7cabd351db292f907680c4b2b91a4 *html/hilbertspec.html
+610bd1dd475364ef860a1d65dcc0618c *html/imageEMD.html
+7f869850215826f53632570e82ac98c5 *html/kospi200.html
+a79f84a86511e40883172118d7167d51 *html/lena.html
+2761943895506250ab70b51144684eab *html/lennon.html
+feae1cf110786a5895d53013b2e5d61e *html/solar.html
+f620863be19e709830542e639909c2e4 *html/spectrogram.html
+486f919fd81b7f163eb386e45477b65a *html/sunspot.html
+a5876616e4850e095266e6792db37fa0 *latex/EMD-internal.tex
+f353848a0cc1406d2bc31d5463e088fe *latex/cvtype.tex
+47b98414562326e5def01ae5ee040fdf *latex/emd.pred.tex
+def06758d11448453433b4f1bcd260a7 *latex/emd.tex
+80ebc837a3a74ffeea25cbd898ecc11a *latex/emd2d.tex
+1076d8147587b2002ee60d46669c0913 *latex/emddenoise.tex
+24609b0e1c80963d9fa2149ec1dde9c6 *latex/extractimf.tex
+f000d5ede0ba17544a04b1337507ad86 *latex/extractimf2d.tex
+bd1080b9334a7281e960dc2f8edbc1eb *latex/extrema.tex
+067deee2072ab2f0c580c3d76d6c59bf *latex/extrema2dC.tex
+cea7e577ac1871b2e1436544a86feaea *latex/hilbertspec.tex
+58cfb363936a78bb46eefd19b4e482c5 *latex/imageEMD.tex
+e20472aec00fd6bf02d31d701ecaf9e9 *latex/kospi200.tex
+d911335bdbe2d08d2eb05c5457ca9a0e *latex/lena.tex
+98a99cb9656af9c39d8fa3d2c1474ea0 *latex/lennon.tex
+33da893b24594022be3016106899ded4 *latex/solar.tex
+f022d4406e7363855521a27880a58254 *latex/spectrogram.tex
+1994b554962ed5a28a9a47cf8550c845 *latex/sunspot.tex
+1d8088e0e2cbb72a9eaea539530f85d8 *libs/EMD.dll
+ebdea9070fe291a3164c1465e3011260 *man/EMD.Rd.gz
diff --git a/win32/deps/library/EMD/Meta/Rd.rds b/win32/deps/library/EMD/Meta/Rd.rds
index eb64c90..2e9759c 100644
Binary files a/win32/deps/library/EMD/Meta/Rd.rds and b/win32/deps/library/EMD/Meta/Rd.rds differ
diff --git a/win32/deps/library/EMD/Meta/data.rds b/win32/deps/library/EMD/Meta/data.rds
index 8b8c979..f7965d6 100644
Binary files a/win32/deps/library/EMD/Meta/data.rds and b/win32/deps/library/EMD/Meta/data.rds differ
diff --git a/win32/deps/library/EMD/Meta/hsearch.rds b/win32/deps/library/EMD/Meta/hsearch.rds
index aedd14b..2841564 100644
Binary files a/win32/deps/library/EMD/Meta/hsearch.rds and b/win32/deps/library/EMD/Meta/hsearch.rds differ
diff --git a/win32/deps/library/EMD/Meta/package.rds b/win32/deps/library/EMD/Meta/package.rds
index c2489c8..41179ae 100644
Binary files a/win32/deps/library/EMD/Meta/package.rds and b/win32/deps/library/EMD/Meta/package.rds differ
diff --git a/win32/deps/library/EMD/R/EMD b/win32/deps/library/EMD/R/EMD
index ac8cebe..be99e29 100644
--- a/win32/deps/library/EMD/R/EMD
+++ b/win32/deps/library/EMD/R/EMD
@@ -1,9 +1,18 @@
-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__.")
-})
+.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)
+ }
+}
diff --git a/win32/deps/library/EMD/R/EMD.rdb b/win32/deps/library/EMD/R/EMD.rdb
index 54b4a28..e992a9d 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 4b1669a..92e1d10 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/help/AnIndex b/win32/deps/library/EMD/help/AnIndex
index 0c1bfb6..706911e 100644
--- a/win32/deps/library/EMD/help/AnIndex
+++ b/win32/deps/library/EMD/help/AnIndex
@@ -1,5 +1,4 @@
beryllium solar
-cvimpute.by.mean cvimpute.by.mean
cvtype cvtype
emd emd
EMD-internal EMD-internal
@@ -10,7 +9,6 @@ extractimf extractimf
extractimf2d extractimf2d
extrema extrema
extrema2dC extrema2dC
-extrema2dVC EMD-internal
hilbert EMD-internal
hilbertspec hilbertspec
image.plot.ts EMD-internal
@@ -18,7 +16,6 @@ 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/html/00Index.html b/win32/deps/library/EMD/html/00Index.html
index 203c874..ac35dcc 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=utf-8">
-<link rel="stylesheet" type="text/css" href="R.css">
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><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="[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>
+<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>
-<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
-</ul>
+<h2>Documentation for package ‘EMD’ version 1.2.0</h2>
<h2>Help Pages</h2>
@@ -21,8 +21,6 @@
<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>
@@ -30,13 +28,13 @@
<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>Bidimenasional Empirical Mode Decomposition</td></tr>
+<td>Two dimensional Empirical Mode Decomposition</td></tr>
<tr><td width="25%"><a href="emddenoise.html">emddenoise</a></td>
-<td>Denoising by EMD and Thresholding</td></tr>
+<td>Denoising by EMD and Cross-Validation</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>Bidimensional Intrinsic Mode Function</td></tr>
+<td>Two dimensional 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>
@@ -44,15 +42,13 @@
<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 Bidimenasional Empirical Mode Decomposition Result</td></tr>
+<td>Plot of Two Dimensional 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/fields/DESCRIPTION b/win32/deps/library/fields/DESCRIPTION
index 9a71d62..a796ae3 100644
--- a/win32/deps/library/fields/DESCRIPTION
+++ b/win32/deps/library/fields/DESCRIPTION
@@ -1,33 +1,25 @@
Package: fields
-Version: 6.7
-Date: October 13, 2012
+Version: 6.01
+Date: September 4, 2009
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,
- 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.
+ 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.
License: GPL (>= 2)
URL: http://www.image.ucar.edu/Software/Fields
-Depends: R (>= 2.13), methods, spam
-Packaged: 2012-10-16 17:40:42 UTC; nychka
+Depends: methods, spam
+Packaged: 2009-09-22 19:37:06 UTC; nychka
Repository: CRAN
-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
+Date/Publication: 2009-09-22 20:23:49
+Built: R 2.9.2; i386-pc-mingw32; 2010-01-13 23:29:00 UTC; windows
diff --git a/win32/deps/library/fields/INDEX b/win32/deps/library/fields/INDEX
index 1e4246d..3d561f5 100644
--- a/win32/deps/library/fields/INDEX
+++ b/win32/deps/library/fields/INDEX
@@ -1,122 +1,125 @@
-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
+%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
diff --git a/win32/deps/library/fields/MD5 b/win32/deps/library/fields/MD5
index 8a4f8e9..6935c71 100644
--- a/win32/deps/library/fields/MD5
+++ b/win32/deps/library/fields/MD5
@@ -1,37 +1,115 @@
-0f6cd40458aafe676451ba8ad7498977 *DESCRIPTION
-ad2be08a47ce2d189e1a518366a86832 *INDEX
-9fdcee37301b4808ab63d8f9dbcd9bd9 *LICENSE
-996b82515235ee8add680c4930c74433 *Meta/Rd.rds
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-6def3359456254864ee60211eda810f9 *R/fields.rdx
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-74f28573008f6b64fae8e5b724bd36a3 *data/COmonthlyMet.rda
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-0c0be8a07fa347d68fc36fc6a117c759 *data/PRISMelevation.rda
-d5ae9ea8fb3cff4c92c686e2b8e2a669 *data/RCMexample.rda
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-3abfd104c2c387a4ebb62742932ca0a6 *data/ozone2.rda
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-933ffb5b8362960f5e294ebc9733dd49 *help/paths.rds
-7b8a0d5a1e9e9878731fa6bb280e2ee9 *html/00Index.html
-444535b9cb76ddff1bab1e1865a3fb14 *html/R.css
-3226ccc98c3cfed7f5f63e52706b06c3 *libs/i386/fields.dll
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-f6f22ef869a6f42581b8d1d3980529bf *libs/x64/symbols.rds
+0560fb103dec40ad9a3dbb2848cc31d4 *CONTENTS
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+16a5a45b82d87be951f5455e0e237d04 *html/00Index.html
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+ff037ed492d500001b248b2c695ee6fe *html/Krig.engine.default.html
+41fda5f275c9666f038370107a965c49 *html/Krig.html
+51b3854a9296f84313644965051acfe1 *html/Krig.null.function.html
+7edcacc9cc125431bd5b42502a89725e *html/RCMexample.html
+af32b656eec18d6d5e421fd5ddd070e4 *html/RMprecip.html
+4701aa3a35651c3b0d8ae23e0e2108a9 *html/Tps.html
+f92472af31f4de44d27d0740c5b74d30 *html/US.dat.html
+5fac681787961a744e51b293c71bfc4e *html/US.html
+5e9ebab5b915dfe8116b07b3193920f6 *html/W.info.html
+749e570c2aae646b88894ec9b0bcb7df *html/Wendland.html
+835aa091cff060699127bbe1bb519a78 *html/Wimage.cov.html
+51b6af9c0388287cf17387f22d40cfcf *html/Wimage.info.html
+d6a66171cf32adb961407425b65e446a *html/Wimage.info.plot.html
+bf8a347ee4b0bae0b70a65c2509b986c *html/Wtransform.html
+08993413c1104ae891ac2e1f32295348 *html/add.image.html
+a9ac8dce1d01453269532db29a1ca2fd *html/arrow.plot.html
+98509a2b945a0b8659015cd621fb2451 *html/as.image.html
+08c3e9be83875df321b73df7fc88d032 *html/as.surface.html
+8ef8cf28d3a2f653906ac51d34b268fe *html/bplot.html
+a1ccfc31e782f75f38f744fedd708453 *html/bplot.xy.html
+62de599904bb75a404261d39cfded822 *html/colorbar.plot.html
+067ec6b0b07d7bc3848935cbc3ed9413 *html/cover.design.html
+d615b53768d7ad4b1cad24aaa72db8a4 *html/diag_mult.html
+2e57998a47d4e8522b1554341034049c *html/drape.plot.html
+d6b06f6984ecf710a832043444624f7a *html/exp.cov.html
+2847102aae2e3244a621ded421fb4f0f *html/fields-internal.html
+9be6e5d1573e2750f76fba1912e5265f *html/fields-stuff.html
+86bc28b6a8e094b213009f7f78305d6d *html/fields.grid.html
+a56902bb1a8205eb86bd3b18b2455542 *html/fields.hints.html
+0be9f4831e7a978ac988cbfe3633d679 *html/fields.html
+b132b940dbf24b579f4e996cb1047350 *html/fields.tests.html
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+8444480ea2fdbf324a6a09f752a488c1 *html/krig.image.html
+1dd50fde3643cdc5302fc3c4947c4c97 *html/lennon.html
+d4a8ba78aed1c5b2630957a5ec9b169d *html/mKrig.html
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+3218935fc6e4d875613c367328bd67d3 *html/set.panel.html
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+cf477d9d3d0af3f7de7b6141f92695d8 *html/smooth.2d.html
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+0602a05b7f0ba1bd9a360a61c0ee2efd *html/stats.html
+d221d465fc2ce97ff569b5bc2a26b55e *html/summary.Krig.html
+ba9c9d4e57152ed901591cb4f493dbf5 *html/summary.ncdf.html
+a6a800ac638770103a4eee30ee190fa0 *html/surface.Krig.html
+cf9dc0a542cbb2cf1bccb3790e198338 *html/tim.colors.html
+c4bf77d60255642e705ab0112623f990 *html/transformx.html
+8ea39e69842673b29d93067773e1b3f8 *html/vgram.html
+ed498e29228de74a00dc85c641389142 *html/vgram.matrix.html
+777cfe3ea410021344f29cc7220e92b8 *html/world.html
+6a8ee8bacaaf06ee03019548640cf873 *html/xline.html
+0641d44d05dc98c01281781ffd88d718 *html/yline.html
+5697232ca82b8873560f29e65a5b8c32 *latex/Rhelp.zip
+97b306efd6b89771023e321be8ea6893 *libs/fields.dll
+0e7d9deae29c5babdd00755eaef91e9b *man/fields.Rd.gz
diff --git a/win32/deps/library/fields/Meta/Rd.rds b/win32/deps/library/fields/Meta/Rd.rds
index a2a0c98..05148cd 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 493df35..251b5cf 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 6e1f973..1dd5d90 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/package.rds b/win32/deps/library/fields/Meta/package.rds
index 5f60b15..03617f1 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/R/fields b/win32/deps/library/fields/R/fields
index ac8cebe..be99e29 100644
--- a/win32/deps/library/fields/R/fields
+++ b/win32/deps/library/fields/R/fields
@@ -1,9 +1,18 @@
-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__.")
-})
+.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)
+ }
+}
diff --git a/win32/deps/library/fields/R/fields.rdb b/win32/deps/library/fields/R/fields.rdb
index e569313..3e11efb 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 73bce55..ab4fe1c 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 949589d..df4e593 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 69fa997..a8255aa 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/PRISMelevation.rda b/win32/deps/library/fields/data/PRISMelevation.rda
index 4005686..902d4f0 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 9c45a50..bf4c2f3 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 ad90f87..4771db9 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 48393aa..0268828 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/lennon.rda b/win32/deps/library/fields/data/lennon.rda
index 11f395c..7a21eb4 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 fd08710..bf33a0d 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/world.dat.rda b/win32/deps/library/fields/data/world.dat.rda
index be48ea0..8eefba5 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 2f6370a..1c20dae 100644
--- a/win32/deps/library/fields/help/AnIndex
+++ b/win32/deps/library/fields/help/AnIndex
@@ -1,5 +1,9 @@
-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
@@ -8,6 +12,7 @@ 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
@@ -28,29 +33,26 @@ 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
@@ -64,7 +66,6 @@ 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
@@ -84,19 +85,17 @@ 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
@@ -117,6 +116,7 @@ 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
@@ -129,58 +129,53 @@ 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
@@ -191,19 +186,22 @@ 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
-REML.test REML.test
+replace.args.function fields-internal
resid.Krig Krig
ribbon.plot ribbon.plot
RMelevation RMprecip
@@ -234,13 +232,14 @@ 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
@@ -259,16 +258,46 @@ 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
-world.land world
-WorldBankCO2 WorldBank
+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
xline xline
yline yline
[.spatial.design fields-internal
diff --git a/win32/deps/library/fields/html/00Index.html b/win32/deps/library/fields/html/00Index.html
index fba3d26..747967c 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=utf-8">
-<link rel="stylesheet" type="text/css" href="R.css">
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><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="[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>
+<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>
-<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
-</ul>
+<h2>Documentation for package ‘fields’ version 6.01</h2>
<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>
@@ -32,7 +32,6 @@
<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>
@@ -44,12 +43,24 @@
<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="fields.html">fields-package</a></td>
-<td>fields - tools for spatial data</td></tr>
+<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>
</table>
<h2><a name="A">-- A --</a></h2>
@@ -113,12 +124,8 @@
<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>
@@ -135,7 +142,7 @@
<table width="100%">
<tr><td width="25%"><a href="tim.colors.html">designer.colors</a></td>
-<td>Some useful color tables for images and tools to handle them.</td></tr>
+<td>Some useful color tables for images.</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>
@@ -174,8 +181,6 @@
<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>
@@ -235,8 +240,6 @@
<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>
@@ -266,6 +269,8 @@
<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>
@@ -296,14 +301,6 @@
<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>
@@ -312,23 +309,8 @@
<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>
@@ -353,14 +335,14 @@
<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>
@@ -377,8 +359,6 @@
<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>
@@ -394,6 +374,8 @@
<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>
@@ -417,8 +399,6 @@
<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>
@@ -468,8 +448,6 @@
<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>
@@ -484,13 +462,13 @@
<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 and tools to handle them.</td></tr>
+<td>Some useful color tables for images.</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 and tools to handle them.</td></tr>
+<td>Some useful color tables for images.</td></tr>
</table>
<h2><a name="U">-- U --</a></h2>
@@ -514,6 +492,12 @@
<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>
@@ -524,14 +508,30 @@
<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="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>
+<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>
</table>
<h2><a name="X">-- X --</a></h2>
@@ -547,11 +547,4 @@
<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/spam/DESCRIPTION b/win32/deps/library/spam/DESCRIPTION
index 8662c00..a91bffd 100644
--- a/win32/deps/library/spam/DESCRIPTION
+++ b/win32/deps/library/spam/DESCRIPTION
@@ -1,11 +1,11 @@
Package: spam
-Version: 0.29-2
-Date: 2012-08-17
+Version: 0.20-3
+Date: 2010-01-13
Author: Reinhard Furrer
Maintainer: Reinhard Furrer <reinhard furrer math uzh ch>
-Depends: R (>= 2.11), methods
+Depends: R (>= 2.4), 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.
@@ -15,8 +15,7 @@ LazyData: Yes
License: GPL | file LICENSE
Title: SPArse Matrix
URL: http://www.math.uzh.ch/furrer/software/spam/
-Packaged: 2012-08-17 09:43:09 UTC; furrer
+Packaged: 2010-01-13 08:59:46 UTC; furrer
Repository: CRAN
-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
+Date/Publication: 2010-01-13 11:29:37
+Built: R 2.9.2; i386-pc-mingw32; 2010-01-13 23:20:15 UTC; windows
diff --git a/win32/deps/library/spam/INDEX b/win32/deps/library/spam/INDEX
index b8b6f92..08f8fa6 100644
--- a/win32/deps/library/spam/INDEX
+++ b/win32/deps/library/spam/INDEX
@@ -7,47 +7,36 @@ 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.spam Cholesky Factorization for Sparse Matrices
-circulant.spam Create Circulant Matrices
-cleanup Cleaning up sparse matrices
+chol Cholesky Factorization for Sparse Matrices
complexity Complexity for Sparse Matrices
det Calculate the determinant of a positive
definite Sparse Matrix
diag Sparse Matrix diagonals
-dim<-.spam Dimensions of an Object
-display Graphially Represent the Nonzero Entries
+dim 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.default Kronecker Products on Sparse Matrices
+kronecker 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 b7e5d8d..775dab7 100644
--- a/win32/deps/library/spam/MD5
+++ b/win32/deps/library/spam/MD5
@@ -1,38 +1,73 @@
-512c41e65e4afe45afa7c4e54e753367 *0NEWS
-9c84294096a034b8f22f473187ddac2f *CITATION
-41a5ba2ed83f451f9920d0dd92f74b2f *DESCRIPTION
-2084ca5f776d6eca0ad57615945081e1 *INDEX
+34428e5eaa439730735765db41b992b2 *CONTENTS
+5209247a5d8de7348c03af4d1197adf7 *DESCRIPTION
+872d3232bc4d1db97925711e6f003193 *INDEX
0981f20e64159b699b6f28b281905af8 *LICENSE
-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
+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
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diff --git a/win32/deps/library/spam/Meta/Rd.rds b/win32/deps/library/spam/Meta/Rd.rds
index 12d08a5..13020b6 100644
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diff --git a/win32/deps/library/spam/Meta/data.rds b/win32/deps/library/spam/Meta/data.rds
index 1cb5040..72a65b6 100644
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diff --git a/win32/deps/library/spam/Meta/demo.rds b/win32/deps/library/spam/Meta/demo.rds
index 6b7affa..86639c2 100644
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diff --git a/win32/deps/library/spam/Meta/hsearch.rds b/win32/deps/library/spam/Meta/hsearch.rds
index ca1a5ec..2f81d8d 100644
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diff --git a/win32/deps/library/spam/Meta/nsInfo.rds b/win32/deps/library/spam/Meta/nsInfo.rds
index c3c7ea7..42ccd0e 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 0891f2d..03b9731 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 eeaa9f5..0dcf2cf 100644
--- a/win32/deps/library/spam/NAMESPACE
+++ b/win32/deps/library/spam/NAMESPACE
@@ -3,12 +3,38 @@ 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",
@@ -53,13 +79,6 @@ export("dcheck",
"kronecker.default",
"kronecker.spam",
-
- "diff.spam",
-
- "circulant.spam",
- "toeplitz.spam",
-
- "make.prec",
"determinant.spam",
"determinant.spam.chol.NgPeyton",
@@ -85,45 +104,12 @@ 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",
- "bandwidth",
+ "adiag.spam",
# ".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",
@@ -135,15 +121,8 @@ export("dcheck",
"read.MM",
"read.HB",
- "powerboost",
-
- "permutation.spam",
-
"map.landkreis",
- "adjacency.landkreis",
-
- "cleanup",
- "backsolve"
+ "adjacency.landkreis"
)
@@ -187,24 +166,14 @@ 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 a1c9f19..6e62011 100644
--- a/win32/deps/library/spam/NEWS
+++ b/win32/deps/library/spam/NEWS
@@ -1,232 +1,385 @@
- CHANGES IN VERSION 0.29-0, 0.29-1, 0.29-2
+ Dear Emacs, please make this -*-Text-*- mode!
-SIGNIFICANT USER-VISIBLE CHANGES
+ **************************************************
+ * *
+ * SPAM VERSION 0.20 *
+ * *
+ **************************************************
- 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.
+ 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).
- Currently, this conflict is not properly solved. I propose
- to load 'spam' first then the other packages, followed by
- manually calling:
- setMethod("backsolve","spam.chol.NgPeyton",backsolve.spam)
- setMethod("backsolve","spam",backsolve.spam)
+ CHANGES IN R VERSION 0.15-5
- Stay tuned...
+ o New function adiag.spam, creation of block diagonal sparse
+ matrices. No method though.
- o Calls like:
-
- mat <- diag.spam(4)
- diag( mat[-1,]) <- 3
- diag.spam( mat[,-1]) <-2
+ o New functions rmvnorm.spam, rmvnorm.canonical and
+ rmvnorm.prec to draw multivariate normals.
- now work. They are, however, somewhat inefficient.
- 'toeplitz.spam' is to be prefered. Pointed out by
- Florian Gerber.
+ o New function apply.spam, similar functionality as apply.
- 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 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.
-NEW FEATURES
+ o Orders/complexities of major algorithms are now described
+ in the help 'complexity'.
- o New functions 'rmvnorm.const', 'rmvnorm.prec.const' and
- 'rmvnorm.canonical.const' to draw constrained multivariate
- normal variates.
+ o Using packageStartupMessage in .onAttach.
- o New functions 'precmat' (wrapper to), 'precmat.RW1', 'precmat.RW2',
- 'precmat.season', 'precmat.IGMRFreglat' and 'precmat.IGMRFirreglat'
- to create precision matrices for IGMRF.
+ o Code clean up and help improvements. Changes reflecting the
+ change to UZH.
- o New methods 'rowSums', 'colSums' and 'rowMeans', 'colMeans' for
- 'spam' objects.
+ o Bugfix in assinging via a nx2 matrix.
+
- o New methods 'head' and 'tail' for 'spam' and 'spam.chol.NgPeyton'
- objects.
+
+ CHANGES IN R VERSION 0.15-4
- o New method 'chol2inv' for 'spam' object.
+ 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 option 'inefficiencywarning': handling of warnings issued
- in case of an inefficient calculation.
+
- 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.
+ CHANGES IN R VERSION 0.15-3
+ o Several bug fixes in the demos due to the changes in
+ the previous versions.
-INTERNAL CHANGES
+ o Several minior changes in the help files to compile with
+ the new help parser and to correct for typos.
- o New much faster approach to extract rows. For not too sparse
- large matrices improvements over two orders of magnitudes are
- achieved.
+ o Added the demos into the tests directory. Additionally,
+ tests contains now the proper Rout.saves files.
- o Elininated '.Internal()' calls that induce a 'Note' on CRAN
- checks. This also implied a minor rewrite of 'image.spam'.
+ 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 Minor code improvements.
- o Eliminated non-API calls (29.1).
+ o Bug fix in spam.list(), negative values were not correctly
+ handled.
- o Rewritten .C("bincode",...) call as suggested by Brian Ripley
- (29.2).
-
+ o Bug fix in subsetting (occured when subsetting very
+ sparse matrices, memory allocation problem).
-BUG FIXES
- o Bug fix that occures when multiplying elementwise matrices
- that have non-intersecting structures (pointed out by
- Corentin Barbu).
+ CHANGES IN R VERSION 0.15-2
- o Bug fix in triangular backsolves involving 'spam' objects
- and rhs matrices.
+ o Method all.equal for matrix-spam signature.
- o Bug fix in triangular backsolve causing errors on some
- architectures.
+ 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
- CHANGES IN VERSION 0.28
+ o Improvements in the nearest.dist function. The diagonals
+ are now handled consistenly.
-NEW FEATURES
+ 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 New function 'cleanup' (suggested by Simon Barthelme).
+ o Methods isSymmetric and all.equal for spam.
+
+ o Methods image and display for spam.chol.NgPeyton.
- o Extending help files.
+ o Method as.spam for distance class implemented.
- o Improved functionality of 'isSymmetric'.
+ 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.
-INTERNAL CHANGES
+ o Bug fix: the Cholesky Fortran routine checks if diagonal
+ elements are available (and positive).
- o Proper storage of data files.
+ o Bug fix: in dim<-.spam
- o Cleaning up argument names within spam functions.
+ o Minor improvements in the help files as well as the following
+ R functions: norm, .spam.matmul.
- o Cleaning up old Fortran code, i.e., eliminating
- unnecessary subroutines and write calls.
+ CHANGES IN R VERSION 0.15-0
-BUG FIXES
+ 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.
- 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.
- CHANGES IN VERSION 0.27
+ o Functionality to read matrices stored in the Harwell-Boeing
+ or MatrixMarket formats.Read MatrixMarket.
-NEW FEATURES
+ 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 Requires now R2.10 and higher.
+ 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 Functions to create Toeplitz and circulant matrices.
+ o Implemented the function 'dim<-' for spam objects.
- o Function to create precision matrices for gridded GMRF.
+ o Method diag and as.matrix for spam.chol.NgPeyton.
- o Improvements in the mle.* functions.
+ 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 Method diff for sparse matrices (suggested by Paul Eilers).
+ o Eliminated bug in subsetting (occuring when subsetting
+ for an empty matrix). Clean out subsetting and assigning.
- o Improvement of help pages.
+ 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 Eliminated some help aliases to base functions
- (for which no 'usage' is given).
+ 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.
-INTERNAL CHANGES
+ o Similar changes as for 13-3. Additionally, considerable
+ improvements in help, file structure, tests, timing, etc.
- o Change to iL coding.
- o Start to using 'identical'.
+ CHANGES IN R VERSION 0.14-0
- o Code cleaning due to requirement of R2.10 and higher.
+ Major revision. Slight loss of backwards compatibility.
+ o New demo article-jss.
-BUG FIXES
+ 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 Bug fix in as.spam.list (thanks to Paul Eilers).
+ 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 demo(spam) (thanks to Thomas Gsponer).
+ 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).
- CHANGES IN VERSION 0.24, 0.25 and 0.26
+ o print and show now emphasize that the non-zero elements
+ are row-wise printed.
- o Devel versions, not released.
+ 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 VERSION 0.23
+ CHANGES IN R VERSION 0.13-3
-NEW FEATURES
+ o Minor changes in R and Fortran code to eliminate warnings.
- o Further improved versions of demos.
+ o In diag()'s argument list, drop the explicit default (' = n').
+ As is now in R-2.7.
- 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 VERSION 0.22
+ CHANGES IN R VERSION 0.13-1
-NEW FEATURES
+ o Minor Fortran Changes for g77 compatibility. Thanks to
+ Roger Bivand.
- o Improved versions of demos. Synchronized with the JSS article.
+ o Updated DESCRIPTION file.
- o Additional changes and improvements in the help files (thanks
- to Steve Geinitz).
+
+ 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.
- CHANGES IN VERSION 0.21
+ o Minor R code cleaning.
-
-NEW FEATURES
- o New NEWS file, to work better with news() command.
- The previous is available under ONEWS.
+ **************************************************
+ * *
+ * SPAM VERSION 0.12 *
+ * *
+ **************************************************
- o New functions bandwidth, permutation, mle[.nomean][.spam],
- neg2loglikelihood[.spam].
-
- o Renamed adiag.spam to bdiag.spam.
+ 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 Cleaned up argument naming with the rmvnorm.*
- suite.
+ o Introduced a prototype in the definition of spam
+ and spam.chol.*.
+ o .Spam$safemode also determines if a spam object is
+ tested for validity, as well as for NAOK.
-INTERNAL CHANGES
+ o In many functions sparse matrix construction is
+ done manually using slots (and check=FALSE, if
+ approprate).
- o Various Fortran code, R code and help file
- improvements.
+ o Increased the value of symmetry criteria to
+ (2+eps)*eps, as each element can be off by eps,
+ subtraction leads to a 2*eps offset and yet we are
+ symmetric.
+ o Major restructuration of chol/det with elimination
+ of auxiliarychol.
-BUG FIXES
+ o Methods chol/backsolve/forwarsolve now call the *.spam
+ functions.
- o Minor change in one of the demos (solves a 64bit issue).
+ o Many internal changes to favour speed and efficiency.
+ o Bug fix in .spam.elemul. occuring when the result is the
+ zero matrix.
diff --git a/win32/deps/library/spam/R/spam b/win32/deps/library/spam/R/spam
index ac8cebe..16b2ccb 100644
--- a/win32/deps/library/spam/R/spam
+++ b/win32/deps/library/spam/R/spam
@@ -2,7 +2,7 @@ local({
info <- loadingNamespaceInfo()
ns <- .Internal(getRegisteredNamespace(as.name(info$pkgname)))
if (is.null(ns))
- stop("cannot find namespace environment");
+ stop("cannot find name space 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 0ae3d0a..0a9fdf2 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 ef3854d..5589873 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 163ae99..a9f2263 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 ddd52e9..6ba072a 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 efc475b..fa46268 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 a4be16c..473156a 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 ../spam0.29-2/demo/article-jss-example1.R
+# This is file ../spam0.20-3/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.
@@ -6,22 +6,9 @@
-# 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
+library(spam)
-
-
-# SETUP:
-library("spam")
-
-data("UKDriverDeaths")
+data(UKDriverDeaths)
y <- sqrt(c(UKDriverDeaths)) # square root counts
@@ -30,7 +17,7 @@ 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
@@ -38,19 +25,19 @@ 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:
@@ -78,16 +65,12 @@ 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])
@@ -96,10 +79,9 @@ display(Qst_yk[P,P])
# k=( kappa_y, kappa_s, kappa_t)'
# Gibbs sampler
-ngibbs <- 500 # Is very fast!
+ngibbs <- 100 # In the original version is 500!
burnin <- 10 # > 0
totalg <- ngibbs+burnin
-set.seed(14)
# Initialize parameters:
spost <- tpost <- array(0, c(totalg, nm))
@@ -112,7 +94,7 @@ 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) {
@@ -142,7 +124,7 @@ for (ig in 2:totalg) {
kpost[ig,] <- rgamma(3, postshape, postinvscale)
- if( (ig%%10)==0) cat(".")
+ if( (ig%%10)==0) cat('.')
}
@@ -150,7 +132,7 @@ 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:
@@ -158,15 +140,11 @@ 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")
@@ -176,7 +154,7 @@ 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)
@@ -187,13 +165,13 @@ 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)
@@ -204,11 +182,20 @@ 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 d3f710e..84c0d0d 100644
--- a/win32/deps/library/spam/demo/article-jss-example2.R
+++ b/win32/deps/library/spam/demo/article-jss-example2.R
@@ -1,26 +1,12 @@
-# This is file ../spam0.29-2/demo/article-jss-example2.R
+# This is file ../spam0.20-3/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:
@@ -85,8 +71,8 @@ postshape <- ahyper + c(n-1,n)/2
accept <- numeric(totalg)
-struct <- chol(Q1 + Q2 + diag.spam(2*n),
- memory=list(nnzcolindices=5500))
+struct <- chol(Q1 + Q2,
+ memory=list(nnzcolindices=6467))
# struct <- NULL # If no update steps are wanted
@@ -113,7 +99,8 @@ for (ig in 2:totalg) {
b,
# Precision matrix
Q,
- Rstruct=struct)
+ Rstruct=struct,
+ memory=list(nnzcolindices=6467))
ustar <- xstar[1:n]
@@ -148,7 +135,7 @@ for (ig in 2:totalg) {
kpost[ig,] <- kpost[ig-1,]
}
- if( (ig%%10)==0) cat(".")
+ if( (ig%%10)==0) cat('.')
}
@@ -157,10 +144,10 @@ 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),]
@@ -184,32 +171,30 @@ vpostmedian <- apply(vpost,2,median)
######################################################################
-# Figure 8:
-
+# Figures
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=TRUE)
+hist(kpost[,1],main='',xlab=expression(kappa[u]),prob=T)
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=TRUE)
+hist(kpost[,2],main='',xlab=expression(kappa[y]),prob=T)
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:
@@ -223,9 +208,9 @@ 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 a4cbbaf..1eb542a 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 ../spam0.29-2/demo/article-jss.R
+# This is file ../spam0.20-3/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.
@@ -12,21 +12,22 @@
# This demo contains the R code to construct the figures and the table of the
-# JSS article:
+# 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 (50+1) are performed here;
+# - Instead of (100+1) factorizations only (10+1) are performed here;
+# - The ratios in Fig 3 and 4 are not included 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)
@@ -57,7 +58,6 @@ display( as.spam(R))
abline( h=-U supernodes+ 5,col=3,lty=2)
-######################################################################
# Figure 2:
theta1 <- .1
theta2 <- .01
@@ -81,23 +81,19 @@ display( as.spam(U))
text(400,-2200,"no permutation\nz=689615\nw=96463\ns=711",adj=0)
-
-
-######################################################################
-# Figure 3:
-
-# general parameters for the following figures
-N <- 50 # would be 100 in the article
+# general parameters for the following
+N <- 25 # would be 100 in the article
stsel <- 1 # user.self
rPsx <- 1 # for function "system.time"
rPsy <- 3 # memory usage
rPint <- .0001 # small interval
-theta1 <- .1
+# Figure 3:
+theta1 <- .1
theta2 <- .05
-xseq <- ceiling(4 + exp(seq(0.5,to=5.5,by=.5))/2) # would be seq(0,to=6,by=.5) in the article
+xseq <- ceiling(4 + exp(seq(0,to=5,by=1))/2) # would be seq(0.5,to=6,by=.5) in the article
xseql <- length(xseq)
table <- array(NA,c(xseql,4))
@@ -130,30 +126,18 @@ 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:
-# 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
+x <- 30 # was 50 in article
maxnn <- 6 # was 6 in article
egdx <- expand.grid( 1:(maxnn+1), 1:(maxnn+1))
@@ -189,45 +173,20 @@ for (id in 1:dvall) {
}
-# If we have a small N, elements in table might be zero.
+# Since 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 26cfb3e..070a487 100644
--- a/win32/deps/library/spam/demo/cholesky.R
+++ b/win32/deps/library/spam/demo/cholesky.R
@@ -1,4 +1,4 @@
-# This is file ../spam0.29-2/demo/cholesky.R
+# This is file ../spam0.20-3/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 f2d01f7..dbbbd95 100644
--- a/win32/deps/library/spam/demo/spam.R
+++ b/win32/deps/library/spam/demo/spam.R
@@ -1,4 +1,4 @@
-# This is file ../spam0.29-2/demo/spam.R
+# This is file ../spam0.20-3/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.
@@ -67,7 +67,8 @@ par(ask=interactive() &&
display(smat, main="'scatterplot'-type display, very efficient")
-spam.options("imagesize"=prod(smat dimension)+1)
+
+.Spam$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 a90bb54..7b22ed5 100644
--- a/win32/deps/library/spam/demo/timing.R
+++ b/win32/deps/library/spam/demo/timing.R
@@ -1,4 +1,4 @@
-# This is file ../spam0.29-2/demo/timing.R
+# This is file ../spam0.20-3/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 e396669..5c60544 100644
--- a/win32/deps/library/spam/help/AnIndex
+++ b/win32/deps/library/spam/help/AnIndex
@@ -50,6 +50,8 @@
abs math
acos math
acosh math
+adiag adiag
+adiag.spam adiag
adjacency.landkreis germany
all summary
all.equal,matrix,spam-method allequal
@@ -72,7 +74,7 @@ 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.chol.NgPeyton-class
+as.spam,spam.chol.NgPeyton-method spam.creation
as.spam.chol.NgPeyton spam.creation
as.spam.dgCMatrix foreign
as.spam.dgRMatrix foreign
@@ -93,33 +95,19 @@ 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
@@ -134,9 +122,8 @@ det,spam.chol.NgPeyton-method det
det.spam det
determinant det
determinant,spam-method det
-determinant,spam.chol.NgPeyton-method spam.chol.NgPeyton-class
+determinant,spam.chol.NgPeyton-method det
determinant.spam det
-determinant.spam.chol det
determinant.spam.chol.NgPeyton det
diag diag
diag,ANY-method diag
@@ -150,7 +137,7 @@ diag<- diag
diag<-,ANY-method diag
diag<-,spam-method diag
diag<-.spam diag
-diff.spam methods
+dim dim
dim,ANY-method operations
dim,spam-method operations
dim,spam.chol.NgPeyton-method spam.chol.NgPeyton-class
@@ -159,7 +146,7 @@ dim<-,spam.chol.NgPeyton-method spam.chol.NgPeyton-class
dim<-.spam dim
display display
display,spam-method display
-display,spam.chol.NgPeyton-method spam.chol.NgPeyton-class
+display,spam.chol.NgPeyton-method display
display.spam display
dist.spam nearestdist
distance nearestdist
@@ -172,26 +159,24 @@ 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 spam.chol.NgPeyton-class
+image,spam.chol.NgPeyton-method image
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
@@ -207,7 +192,6 @@ 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
@@ -216,20 +200,10 @@ 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
@@ -239,30 +213,17 @@ Oral Oral
ordering ordering
ordering,matrix-method ordering
ordering,spam-method ordering
-ordering,spam.chol.NgPeyton-method spam.chol.NgPeyton-class
+ordering,spam.chol.NgPeyton-method ordering
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 spam.chol.NgPeyton-class
+print,spam.chol.NgPeyton-method print
print.spam print
-print.spam.chol print
print.spam.chol.NgPeyton print
prod summary
range summary
@@ -272,22 +233,14 @@ 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
@@ -309,29 +262,23 @@ 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 spam.chol.NgPeyton-class
+summary,spam.chol.NgPeyton-method print
Summary.spam summary
summary.spam print
-summary.spam.chol print
summary.spam.chol.NgPeyton print
-t,spam-method spam-class
+t,ANY-method operations
+t,spam-method operations
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
@@ -346,43 +293,31 @@ UScounties.storder UScounties
USprecip USprecip
validspamobject spam.creation
version version
-[,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,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 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/html/00Index.html b/win32/deps/library/spam/html/00Index.html
index 2e97600..6fc22f7 100644
--- a/win32/deps/library/spam/html/00Index.html
+++ b/win32/deps/library/spam/html/00Index.html
@@ -1,26 +1,25 @@
<!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=utf-8">
-<link rel="stylesheet" type="text/css" href="R.css">
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><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="[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>
+<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>
-<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>Documentation for package ‘spam’ version 0.20-3</h2>
<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>
@@ -28,7 +27,6 @@
<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>
@@ -45,6 +43,109 @@
</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%">
@@ -54,11 +155,17 @@
<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-method</a></td>
+<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>
<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>
@@ -66,15 +173,19 @@
<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-method</a></td>
+<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>
<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-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">as.matrix,spam-method</a></td>
<td>Class "spam"</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">as.matrix-method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">as.matrix,spam.chol.NgPeyton-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>
@@ -82,9 +193,17 @@
<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.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>
+<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>
<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>
@@ -121,66 +240,50 @@
<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-method</a></td>
+<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>
<td>Linear Equation Solving for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">backsolve-method</a></td>
+<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>
<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-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">c,spam-method</a></td>
<td>Class "spam"</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">c-method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">c,spam.chol.NgPeyton-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-method</a></td>
+<tr><td width="25%"><a href="xybind.html">cbind,spam-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-method</a></td>
+<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>
<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="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>
+<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>
<td>Class "spam"</td></tr>
<tr><td width="25%"><a href="complexity.html">complexities</a></td>
<td>Complexity for Sparse Matrices</td></tr>
@@ -199,29 +302,31 @@
<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-method</a></td>
+<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>
<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-method</a></td>
+<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="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>
+<tr><td width="25%"><a href="det.html">determinant,spam.chol.NgPeyton-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</a></td>
+<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.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-method</a></td>
+<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>
<td>Sparse Matrix diagonals</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">diag-method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">diag,spam.chol.NgPeyton-method</a></td>
<td>Class "spam.chol.NgPeyton"</td></tr>
-<tr><td width="25%"><a href="diag.html">diag.assign-method</a></td>
+<tr><td width="25%"><a href="diag.html">diag.assign,spam-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>
@@ -231,28 +336,34 @@
<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<--method</a></td>
+<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>
<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="operations.html">dim-method</a></td>
+<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>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">dim-method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">dim,spam.chol.NgPeyton-method</a></td>
<td>Class "spam.chol.NgPeyton"</td></tr>
-<tr><td width="25%"><a href="dim.html">dim<--method</a></td>
+<tr><td width="25%"><a href="dim.html">dim<-,spam-method</a></td>
<td>Dimensions of an Object</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">dim<--method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">dim<-,spam.chol.NgPeyton-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-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>
+<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>
<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>
@@ -275,12 +386,18 @@
<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-method</a></td>
+<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>
<td>Linear Equation Solving for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">forwardsolve-method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">forwardsolve,spam.chol.NgPeyton-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>
@@ -296,35 +413,24 @@
<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-method</a></td>
+<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>
<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-method</a></td>
+<td>Read external matrix formats</td></tr>
+<tr><td width="25%"><a href="spam.creation.html">initialize,spam-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-method</a></td>
+<tr><td width="25%"><a href="isSymmetric.html">isSymmetric,spam-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>
@@ -333,24 +439,30 @@
<h2><a name="K">-- K --</a></h2>
<table width="100%">
-<tr><td width="25%"><a href="spam-class.html">kronecker-method</a></td>
+<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>
<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-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">length,spam-method</a></td>
<td>Class "spam"</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">length-method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">length,spam.chol.NgPeyton-method</a></td>
<td>Class "spam.chol.NgPeyton"</td></tr>
-<tr><td width="25%"><a href="spam-class.html">length<--method</a></td>
+<tr><td width="25%"><a href="spam-class.html">length<-,spam-method</a></td>
<td>Class "spam"</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">length<--method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">length<-,spam.chol.NgPeyton-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>
@@ -360,7 +472,7 @@
<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-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">lower.tri,spam-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>
@@ -369,50 +481,42 @@
<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-method</a></td>
+<tr><td width="25%"><a href="math.html">Math,spam-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-method</a></td>
+<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>
<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-method</a></td>
+<tr><td width="25%"><a href="operations.html">ncol,spam-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-method</a></td>
+<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>
<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-method</a></td>
+<tr><td width="25%"><a href="operations.html">nrow,spam-method</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
</table>
@@ -425,15 +529,13 @@
<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-method</a></td>
+<tr><td width="25%"><a href="ordering.html">ordering,matrix-method</a></td>
<td>Extract the permutation</td></tr>
-<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>
+<tr><td width="25%"><a href="ordering.html">ordering,spam-method</a></td>
<td>Extract the permutation</td></tr>
-<tr><td width="25%"><a href="ordering.html">ordering.spam.chol</a></td>
+<tr><td width="25%"><a href="ordering.html">ordering,spam.chol.NgPeyton-method</a></td>
<td>Extract the permutation</td></tr>
-<tr><td width="25%"><a href="ordering.html">ordering.spam.chol.NgPeyton</a></td>
+<tr><td width="25%"><a href="ordering.html">ordering-methods</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>
@@ -442,39 +544,21 @@
<h2><a name="P">-- P --</a></h2>
<table width="100%">
-<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>
+<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>
<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-method</a></td>
+<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="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>
+<tr><td width="25%"><a href="print.html">print,spam.chol.NgPeyton-method</a></td>
<td>Printing and summarizing sparse matrices</td></tr>
-<tr><td width="25%"><a href="print.html">print.spam.chol</a></td>
+<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.NgPeyton</a></td>
<td>Printing and summarizing sparse matrices</td></tr>
@@ -489,54 +573,40 @@
<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-method</a></td>
+<tr><td width="25%"><a href="xybind.html">rbind,spam-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-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">show,spam-method</a></td>
<td>Class "spam"</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">show-method</a></td>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">show,spam.chol.NgPeyton-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-method</a></td>
+<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>
<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>
@@ -546,10 +616,12 @@
<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>
@@ -572,8 +644,6 @@
<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>
@@ -582,18 +652,16 @@
<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-method</a></td>
+<tr><td width="25%"><a href="summary.html">Summary,spam-method</a></td>
<td>Rounding of Numbers</td></tr>
-<tr><td width="25%"><a href="print.html">summary-method</a></td>
+<tr><td width="25%"><a href="print.html">summary,spam-method</a></td>
+<td>Printing and summarizing sparse matrices</td></tr>
+<tr><td width="25%"><a href="print.html">summary,spam.chol.NgPeyton-method</a></td>
<td>Printing and summarizing sparse matrices</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">summary-method</a></td>
-<td>Class "spam.chol.NgPeyton"</td></tr>
<tr><td width="25%"><a href="summary.html">Summary.spam</a></td>
<td>Rounding of Numbers</td></tr>
<tr><td width="25%"><a href="print.html">summary.spam</a></td>
<td>Printing and summarizing sparse matrices</td></tr>
-<tr><td width="25%"><a href="print.html">summary.spam.chol</a></td>
-<td>Printing and summarizing sparse matrices</td></tr>
<tr><td width="25%"><a href="print.html">summary.spam.chol.NgPeyton</a></td>
<td>Printing and summarizing sparse matrices</td></tr>
</table>
@@ -601,22 +669,16 @@
<h2><a name="T">-- T --</a></h2>
<table width="100%">
-<tr><td width="25%"><a href="spam-class.html">t-method</a></td>
-<td>Class "spam"</td></tr>
-<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">t-method</a></td>
+<tr><td width="25%"><a href="operations.html">t,ANY-method</a></td>
+<td>Basic Linear Algebra for Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="operations.html">t,spam-method</a></td>
+<td>Basic Linear Algebra for Sparse Matrices</td></tr>
+<tr><td width="25%"><a href="spam.chol.NgPeyton-class.html">t,spam.chol.NgPeyton-method</a></td>
<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>
-<td>Return the First or Last Part of an Object</td></tr>
-<tr><td width="25%"><a href="headtail.html">tail-method</a></td>
-<td>Return the First or Last Part of an Object</td></tr>
-<tr><td width="25%"><a href="headtail.html">tail.spam</a></td>
-<td>Return the First or Last Part of an Object</td></tr>
<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>
-<td>Create Toeplitz Matrices</td></tr>
<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>
@@ -628,13 +690,13 @@
<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-method</a></td>
+<tr><td width="25%"><a href="chol.html">update,spam.chol.NgPeyton-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-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">upper.tri,spam-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>
@@ -660,59 +722,67 @@
<h2><a name="misc">-- misc --</a></h2>
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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">%*%-methods</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<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">%d*%</a></td>
-<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">%d*%-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+%-method</a></td>
+<tr><td width="25%"><a href="operations.html">[,spam,ANY,ANY-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>
-<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">--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">/-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">[,spam,ANY-method</a></td>
+<td>Class "spam"</td></tr>
+<tr><td width="25%"><a href="spam-class.html">[,spam,matrix,matrix-method</a></td>
+<td>Class "spam"</td></tr>
+<tr><td width="25%"><a href="spam-class.html">[,spam,matrix,missing-method</a></td>
+<td>Class "spam"</td></tr>
+<tr><td width="25%"><a href="spam-class.html">[,spam,missing,missing-method</a></td>
+<td>Class "spam"</td></tr>
+<tr><td width="25%"><a href="spam-class.html">[,spam,missing,vector-method</a></td>
+<td>Class "spam"</td></tr>
+<tr><td width="25%"><a href="spam-class.html">[,spam,spam,missing-method</a></td>
+<td>Class "spam"</td></tr>
+<tr><td width="25%"><a href="spam-class.html">[,spam,vector,missing-method</a></td>
+<td>Class "spam"</td></tr>
+<tr><td width="25%"><a href="spam-class.html">[,spam,vector,vector-method</a></td>
+<td>Class "spam"</td></tr>
+<tr><td width="25%"><a href="operations.html">[.spam</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html"><-method</a></td>
+<tr><td width="25%"><a href="operations.html">[<-,spam,ANY,ANY-method</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html"><=-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">[<-,spam,ANY-method</a></td>
+<td>Class "spam"</td></tr>
+<tr><td width="25%"><a href="spam-class.html">[<-,spam,matrix,matrix,numeric-method</a></td>
+<td>Class "spam"</td></tr>
+<tr><td width="25%"><a href="operations.html">[<-,spam,matrix,matrix-method</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">==-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">[<-,spam,matrix,missing,numeric-method</a></td>
+<td>Class "spam"</td></tr>
+<tr><td width="25%"><a href="operations.html">[<-,spam,matrix,missing-method</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">>-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">[<-,spam,missing,missing,numeric-method</a></td>
+<td>Class "spam"</td></tr>
+<tr><td width="25%"><a href="operations.html">[<-,spam,missing,missing-method</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">>=-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">[<-,spam,missing,vector,numeric-method</a></td>
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+<tr><td width="25%"><a href="operations.html">[<-,spam,missing,vector-method</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="spam-class.html">[-method</a></td>
+<tr><td width="25%"><a href="spam-class.html">[<-,spam,spam,missing,numeric-method</a></td>
<td>Class "spam"</td></tr>
-<tr><td width="25%"><a href="operations.html">[.spam</a></td>
+<tr><td width="25%"><a href="operations.html">[<-,spam,spam,missing-method</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">[<--method</a></td>
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+<td>Class "spam"</td></tr>
+<tr><td width="25%"><a href="operations.html">[<-,spam,vector,missing-method</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="spam-class.html">[<--method</a></td>
+<tr><td width="25%"><a href="spam-class.html">[<-,spam,vector,vector,numeric-method</a></td>
<td>Class "spam"</td></tr>
+<tr><td width="25%"><a href="operations.html">[<-,spam,vector,vector-method</a></td>
+<td>Basic Linear Algebra for Sparse Matrices</td></tr>
<tr><td width="25%"><a href="operations.html">[<-.spam</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
-<tr><td width="25%"><a href="operations.html">^-method</a></td>
+<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,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">|-method</a></td>
+<tr><td width="25%"><a href="operations.html">|,spam,spam-method</a></td>
<td>Basic Linear Algebra for Sparse Matrices</td></tr>
</table>
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