gnumeric r16966 - in trunk: . src/dialogs src/tools
- From: guelzow svn gnome org
- To: svn-commits-list gnome org
- Subject: gnumeric r16966 - in trunk: . src/dialogs src/tools
- Date: Sat, 15 Nov 2008 23:02:53 +0000 (UTC)
Author: guelzow
Date: Sat Nov 15 23:02:53 2008
New Revision: 16966
URL: http://svn.gnome.org/viewvc/gnumeric?rev=16966&view=rev
Log:
2008-11-15 Andreas J. Guelzow <aguelzow pyrshep ca>
* kaplan-meier.glade: add logrank checkbox
* dialog-analysis-tool-kaplan-meier.c (kaplan_meier_tool_ok_clicked_cb):
handle logrank checkbox
(dialog_kaplan_meier_tool): ditto
(KaplanMeierToolState): add new field
2008-11-15 Andreas J. Guelzow <aguelzow pyrshep ca>
* analysis-kaplan-meier.c (analysis_tool_kaplan_meier_engine_run):
calculate log-rank statistics if requested
(analysis_tool_kaplan_meier_engine): adjust dao size for test output
* analysis-kaplan-meier.h (analysis_tools_data_kaplan_meier_t): add
new field
Modified:
trunk/NEWS
trunk/src/dialogs/ChangeLog
trunk/src/dialogs/dialog-analysis-tool-kaplan-meier.c
trunk/src/dialogs/kaplan-meier.glade
trunk/src/tools/ChangeLog
trunk/src/tools/analysis-kaplan-meier.c
trunk/src/tools/analysis-kaplan-meier.h
Modified: trunk/NEWS
==============================================================================
--- trunk/NEWS (original)
+++ trunk/NEWS Sat Nov 15 23:02:53 2008
@@ -9,6 +9,7 @@
* Add functional seealso links in the function browser
* Allow ranges of censor marks in Kaplan-Meier tool and
multiple groups. Output median survival times. [#558582]
+ * Add Log-Rank Test to Kaplan-Meier tool. [#558582]
Hib Eris:
* Fix problems with toolbars when no handle bar present. [#559249]
Modified: trunk/src/dialogs/dialog-analysis-tool-kaplan-meier.c
==============================================================================
--- trunk/src/dialogs/dialog-analysis-tool-kaplan-meier.c (original)
+++ trunk/src/dialogs/dialog-analysis-tool-kaplan-meier.c Sat Nov 15 23:02:53 2008
@@ -62,6 +62,7 @@
GtkWidget *censor_spin_from;
GtkWidget *censor_spin_to;
GtkWidget *graph_button;
+ GtkWidget *logrank_button;
GtkWidget *tick_button;
GtkWidget *add_group_button;
GtkWidget *remove_group_button;
@@ -271,8 +272,15 @@
data->censor_mark_to = gtk_spin_button_get_value_as_int (GTK_SPIN_BUTTON (state->censor_spin_to));
data->group_list = kaplan_meier_tool_get_groups (state);
- data->range_3 = ((data->group_list == NULL) ? NULL : gnm_expr_entry_parse_as_value
- (GNM_EXPR_ENTRY (state->groups_input), state->base.sheet));
+ if (data->group_list == NULL) {
+ data->range_3 = NULL;
+ data->logrank_test = FALSE;
+ } else {
+ data->range_3 = gnm_expr_entry_parse_as_value
+ (GNM_EXPR_ENTRY (state->groups_input), state->base.sheet);
+ data->logrank_test = gtk_toggle_button_get_active (
+ GTK_TOGGLE_BUTTON (state->logrank_button));
+ }
data->median = gtk_toggle_button_get_active (
GTK_TOGGLE_BUTTON (glade_xml_get_widget
@@ -454,11 +462,13 @@
gtk_widget_set_sensitive (state->add_group_button, groups);
gtk_widget_set_sensitive (GTK_WIDGET (state->groups_treeview), groups);
- if (groups)
+ if (groups) {
cb_selection_changed (selection, state);
- else {
+ gtk_widget_set_sensitive (state->logrank_button, TRUE);
+ } else {
gtk_tree_selection_unselect_all (selection);
gtk_widget_set_sensitive (state->remove_group_button, FALSE);
+ gtk_widget_set_sensitive (state->logrank_button, FALSE);
}
}
@@ -637,6 +647,9 @@
state->std_error_button = GTK_WIDGET (glade_xml_get_widget
(state->base.gui,
"std-error-button"));
+ state->logrank_button = GTK_WIDGET (glade_xml_get_widget
+ (state->base.gui,
+ "logrank-button"));
state->groups_check = GTK_WIDGET (glade_xml_get_widget
(state->base.gui,
Modified: trunk/src/dialogs/kaplan-meier.glade
==============================================================================
--- trunk/src/dialogs/kaplan-meier.glade (original)
+++ trunk/src/dialogs/kaplan-meier.glade Sat Nov 15 23:02:53 2008
@@ -43,45 +43,52 @@
<placeholder/>
</child>
<child>
- <widget class="GtkSpinButton" id="censored-spinbutton2">
+ <widget class="GtkCheckButton" id="censor-button">
<property name="visible">True</property>
<property name="can_focus">True</property>
- <property name="adjustment">0 0 1000 1 10 10</property>
- <property name="climb_rate">1</property>
+ <property name="label" translatable="yes">Permit censorship</property>
+ <property name="response_id">0</property>
+ <property name="active">True</property>
+ <property name="draw_indicator">True</property>
</widget>
<packing>
- <property name="left_attach">2</property>
<property name="right_attach">3</property>
- <property name="top_attach">4</property>
- <property name="bottom_attach">5</property>
+ <property name="top_attach">1</property>
+ <property name="bottom_attach">2</property>
+ <property name="x_options">GTK_FILL</property>
+ <property name="y_options">GTK_FILL</property>
</packing>
</child>
<child>
- <widget class="GtkSpinButton" id="censored-spinbutton1">
+ <widget class="GtkLabel" id="var2-label">
<property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="adjustment">0 0 1000 1 10 10</property>
- <property name="climb_rate">1</property>
+ <property name="xalign">0</property>
+ <property name="label" translatable="yes">Censor co_lumn:</property>
+ <property name="use_underline">True</property>
+ <property name="justify">GTK_JUSTIFY_RIGHT</property>
</widget>
<packing>
- <property name="left_attach">2</property>
- <property name="right_attach">3</property>
- <property name="top_attach">3</property>
- <property name="bottom_attach">4</property>
+ <property name="left_attach">1</property>
+ <property name="right_attach">2</property>
+ <property name="top_attach">2</property>
+ <property name="bottom_attach">3</property>
+ <property name="x_options">GTK_FILL</property>
+ <property name="y_options">GTK_FILL</property>
</packing>
</child>
<child>
- <widget class="GtkLabel" id="label5">
+ <widget class="GtkLabel" id="var1-label">
<property name="visible">True</property>
- <property name="xalign">1</property>
- <property name="label" translatable="yes">to:</property>
+ <property name="xalign">0</property>
+ <property name="xpad">5</property>
+ <property name="label" translatable="yes">_Time column:</property>
+ <property name="use_underline">True</property>
<property name="justify">GTK_JUSTIFY_RIGHT</property>
</widget>
<packing>
- <property name="left_attach">1</property>
<property name="right_attach">2</property>
- <property name="top_attach">4</property>
- <property name="bottom_attach">5</property>
+ <property name="x_options">GTK_FILL</property>
+ <property name="y_options">GTK_FILL</property>
</packing>
</child>
<child>
@@ -99,52 +106,45 @@
</packing>
</child>
<child>
- <widget class="GtkLabel" id="var1-label">
+ <widget class="GtkLabel" id="label5">
<property name="visible">True</property>
- <property name="xalign">0</property>
- <property name="xpad">5</property>
- <property name="label" translatable="yes">_Time column:</property>
- <property name="use_underline">True</property>
+ <property name="xalign">1</property>
+ <property name="label" translatable="yes">to:</property>
<property name="justify">GTK_JUSTIFY_RIGHT</property>
</widget>
<packing>
+ <property name="left_attach">1</property>
<property name="right_attach">2</property>
- <property name="x_options">GTK_FILL</property>
- <property name="y_options">GTK_FILL</property>
+ <property name="top_attach">4</property>
+ <property name="bottom_attach">5</property>
</packing>
</child>
<child>
- <widget class="GtkLabel" id="var2-label">
+ <widget class="GtkSpinButton" id="censored-spinbutton1">
<property name="visible">True</property>
- <property name="xalign">0</property>
- <property name="label" translatable="yes">Censor co_lumn:</property>
- <property name="use_underline">True</property>
- <property name="justify">GTK_JUSTIFY_RIGHT</property>
+ <property name="can_focus">True</property>
+ <property name="adjustment">0 0 1000 1 10 10</property>
+ <property name="climb_rate">1</property>
</widget>
<packing>
- <property name="left_attach">1</property>
- <property name="right_attach">2</property>
- <property name="top_attach">2</property>
- <property name="bottom_attach">3</property>
- <property name="x_options">GTK_FILL</property>
- <property name="y_options">GTK_FILL</property>
+ <property name="left_attach">2</property>
+ <property name="right_attach">3</property>
+ <property name="top_attach">3</property>
+ <property name="bottom_attach">4</property>
</packing>
</child>
<child>
- <widget class="GtkCheckButton" id="censor-button">
+ <widget class="GtkSpinButton" id="censored-spinbutton2">
<property name="visible">True</property>
<property name="can_focus">True</property>
- <property name="label" translatable="yes">Permit censorship</property>
- <property name="response_id">0</property>
- <property name="active">True</property>
- <property name="draw_indicator">True</property>
+ <property name="adjustment">0 0 1000 1 10 10</property>
+ <property name="climb_rate">1</property>
</widget>
<packing>
+ <property name="left_attach">2</property>
<property name="right_attach">3</property>
- <property name="top_attach">1</property>
- <property name="bottom_attach">2</property>
- <property name="x_options">GTK_FILL</property>
- <property name="y_options">GTK_FILL</property>
+ <property name="top_attach">4</property>
+ <property name="bottom_attach">5</property>
</packing>
</child>
</widget>
@@ -212,66 +212,66 @@
<placeholder/>
</child>
<child>
- <widget class="GtkScrolledWindow" id="groups-scrolled">
+ <widget class="GtkLabel" id="groups-label">
<property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="hscrollbar_policy">GTK_POLICY_AUTOMATIC</property>
- <property name="vscrollbar_policy">GTK_POLICY_AUTOMATIC</property>
- <property name="shadow_type">GTK_SHADOW_IN</property>
- <child>
- <placeholder/>
- </child>
+ <property name="xalign">0</property>
+ <property name="label" translatable="yes">Groups column:</property>
</widget>
<packing>
- <property name="right_attach">2</property>
- <property name="top_attach">1</property>
- <property name="bottom_attach">7</property>
+ <property name="y_options">GTK_FILL</property>
</packing>
</child>
<child>
- <widget class="GtkButton" id="remove-button">
+ <widget class="GtkButton" id="add-button">
<property name="visible">True</property>
<property name="can_focus">True</property>
<property name="receives_default">True</property>
- <property name="label" translatable="yes">gtk-remove</property>
+ <property name="label" translatable="yes">gtk-add</property>
<property name="use_stock">True</property>
<property name="response_id">0</property>
</widget>
<packing>
<property name="left_attach">2</property>
<property name="right_attach">3</property>
- <property name="top_attach">2</property>
- <property name="bottom_attach">3</property>
+ <property name="top_attach">1</property>
+ <property name="bottom_attach">2</property>
<property name="x_options">GTK_FILL</property>
<property name="y_options">GTK_SHRINK | GTK_FILL</property>
</packing>
</child>
<child>
- <widget class="GtkButton" id="add-button">
+ <widget class="GtkButton" id="remove-button">
<property name="visible">True</property>
<property name="can_focus">True</property>
<property name="receives_default">True</property>
- <property name="label" translatable="yes">gtk-add</property>
+ <property name="label" translatable="yes">gtk-remove</property>
<property name="use_stock">True</property>
<property name="response_id">0</property>
</widget>
<packing>
<property name="left_attach">2</property>
<property name="right_attach">3</property>
- <property name="top_attach">1</property>
- <property name="bottom_attach">2</property>
+ <property name="top_attach">2</property>
+ <property name="bottom_attach">3</property>
<property name="x_options">GTK_FILL</property>
<property name="y_options">GTK_SHRINK | GTK_FILL</property>
</packing>
</child>
<child>
- <widget class="GtkLabel" id="groups-label">
+ <widget class="GtkScrolledWindow" id="groups-scrolled">
<property name="visible">True</property>
- <property name="xalign">0</property>
- <property name="label" translatable="yes">Groups column:</property>
+ <property name="can_focus">True</property>
+ <property name="hscrollbar_policy">GTK_POLICY_AUTOMATIC</property>
+ <property name="vscrollbar_policy">GTK_POLICY_AUTOMATIC</property>
+ <property name="shadow_type">GTK_SHADOW_IN</property>
+ <child>
+ <placeholder/>
+ </child>
</widget>
<packing>
- <property name="y_options">GTK_FILL</property>
+ <property name="right_attach">2</property>
+ <property name="top_attach">1</property>
+ <property name="bottom_attach">7</property>
</packing>
</child>
</widget>
@@ -310,34 +310,34 @@
<placeholder/>
</child>
<child>
- <widget class="GtkCheckButton" id="graph-button">
+ <widget class="GtkCheckButton" id="tick-button">
<property name="visible">True</property>
<property name="can_focus">True</property>
- <property name="label" translatable="yes">Show graph </property>
+ <property name="label" translatable="yes">Include censorship ticks</property>
<property name="response_id">0</property>
<property name="active">True</property>
<property name="draw_indicator">True</property>
</widget>
<packing>
+ <property name="left_attach">1</property>
<property name="right_attach">2</property>
+ <property name="top_attach">1</property>
+ <property name="bottom_attach">2</property>
<property name="x_options">GTK_FILL</property>
<property name="y_options">GTK_FILL</property>
</packing>
</child>
<child>
- <widget class="GtkCheckButton" id="tick-button">
+ <widget class="GtkCheckButton" id="graph-button">
<property name="visible">True</property>
<property name="can_focus">True</property>
- <property name="label" translatable="yes">Include censorship ticks</property>
+ <property name="label" translatable="yes">Show graph </property>
<property name="response_id">0</property>
<property name="active">True</property>
<property name="draw_indicator">True</property>
</widget>
<packing>
- <property name="left_attach">1</property>
<property name="right_attach">2</property>
- <property name="top_attach">1</property>
- <property name="bottom_attach">2</property>
<property name="x_options">GTK_FILL</property>
<property name="y_options">GTK_FILL</property>
</packing>
@@ -377,6 +377,21 @@
<property name="position">2</property>
</packing>
</child>
+ <child>
+ <widget class="GtkCheckButton" id="logrank-button">
+ <property name="visible">True</property>
+ <property name="can_focus">True</property>
+ <property name="label" translatable="yes">Perform Log-Rank (Mantel-Haenszel) Test</property>
+ <property name="response_id">0</property>
+ <property name="active">True</property>
+ <property name="draw_indicator">True</property>
+ </widget>
+ <packing>
+ <property name="expand">False</property>
+ <property name="fill">False</property>
+ <property name="position">3</property>
+ </packing>
+ </child>
</widget>
<packing>
<property name="position">2</property>
Modified: trunk/src/tools/analysis-kaplan-meier.c
==============================================================================
--- trunk/src/tools/analysis-kaplan-meier.c (original)
+++ trunk/src/tools/analysis-kaplan-meier.c Sat Nov 15 23:02:53 2008
@@ -57,6 +57,7 @@
: g_slist_length (info->group_list));
int colspan = ((info->std_err ? 4 : 3) + (info->censored ? 1 : 0));
int i;
+ int logrank_test_y_offset = 0;
GnmExpr const *expr_data;
GnmExpr const *expr_group_data = NULL;
@@ -478,6 +479,7 @@
gl = info->group_list;
for (i = 0; i < repetitions; i++) {
+ /* the next involves (colspan-1) since the median field moves to the right. */
gint prob_dx = - (repetitions - i)* (colspan - 1) - 1;
gint times_dx = - colspan * repetitions - i - 3;
GnmExpr const *expr_median;
@@ -518,7 +520,104 @@
dao->offset_col += 1;
}
+ logrank_test_y_offset = 5;
+ dao->offset_col -= (2 + repetitions);
}
+
+ if (info->logrank_test) {
+ GnmFunc *fd_chidist;
+ GnmExpr const *expr_statistics = gnm_expr_new_constant (value_new_int (0));
+ GnmExpr const *expr_p;
+ GnmExpr const *expr_n_total = gnm_expr_new_constant (value_new_int (0));
+ GnmExpr const *expr_death_total = gnm_expr_new_constant (value_new_int (0));
+
+ fd_chidist = gnm_func_lookup ("CHIDIST", NULL);
+ gnm_func_ref (fd_chidist);
+
+ dao_set_italic (dao, 1, logrank_test_y_offset, 1, logrank_test_y_offset+3);
+ set_cell_text_col (dao, 1, logrank_test_y_offset,
+ _("/Log-Rank Test:"
+ "/Statistics:"
+ "/Degrees of Freedom:"
+ "/p-Value:"));
+
+ /* Test Statistics */
+ for (i = 0; i < repetitions; i++) {
+ gint atrisk_dx = - (repetitions - i)* colspan - 2;
+ expr_n_total = gnm_expr_new_binary
+ (expr_n_total, GNM_EXPR_OP_ADD,
+ make_rangeref ( atrisk_dx,
+ - logrank_test_y_offset + 1,
+ atrisk_dx,
+ - logrank_test_y_offset + rows));
+ expr_death_total = gnm_expr_new_binary
+ (expr_death_total, GNM_EXPR_OP_ADD,
+ make_rangeref ( atrisk_dx + 1,
+ - logrank_test_y_offset + 1,
+ atrisk_dx + 1,
+ - logrank_test_y_offset + rows));
+ }
+
+ for (i = 0; i < repetitions; i++) {
+ GnmExpr const *expr_expect;
+ gint atrisk_dx = - (repetitions - i)* colspan - 2;
+
+ expr_expect = gnm_expr_new_binary
+ (gnm_expr_new_binary
+ (gnm_expr_copy (expr_death_total),
+ GNM_EXPR_OP_MULT,
+ make_rangeref (atrisk_dx,
+ - logrank_test_y_offset + 1,
+ atrisk_dx,
+ - logrank_test_y_offset + rows)),
+ GNM_EXPR_OP_DIV,
+ gnm_expr_copy (expr_n_total));
+
+ expr_expect = gnm_expr_new_funcall3 (
+ fd_if,
+ gnm_expr_new_funcall1 (fd_iserror,
+ gnm_expr_copy (expr_expect)),
+ gnm_expr_new_constant (value_new_int (0)),
+ expr_expect);
+ expr_expect = gnm_expr_new_funcall1 (fd_sum,
+ expr_expect);
+ expr_expect = gnm_expr_new_binary (
+ gnm_expr_new_binary (
+ gnm_expr_new_binary (
+ gnm_expr_new_funcall1 (
+ fd_sum,
+ make_rangeref
+ (atrisk_dx + 1,
+ - logrank_test_y_offset + 1,
+ atrisk_dx + 1,
+ - logrank_test_y_offset + rows)),
+ GNM_EXPR_OP_SUB,
+ gnm_expr_copy (expr_expect)),
+ GNM_EXPR_OP_EXP,
+ gnm_expr_new_constant (value_new_int (2))),
+ GNM_EXPR_OP_DIV,
+ expr_expect);
+ expr_statistics = gnm_expr_new_binary (
+ expr_statistics, GNM_EXPR_OP_ADD, expr_expect);
+ }
+ gnm_expr_free (expr_n_total);
+ gnm_expr_free (expr_death_total);
+
+ dao_set_cell_array_expr (dao, 2, logrank_test_y_offset + 1, expr_statistics);
+
+ /* Degree of Freedoms */
+ dao_set_cell_int (dao, 2, logrank_test_y_offset + 2, repetitions - 1);
+
+ /* p Value */
+ expr_p = gnm_expr_new_funcall2 (fd_chidist,
+ make_cellref (0,-2),
+ make_cellref (0,-1));
+ dao_set_cell_expr (dao, 2, logrank_test_y_offset + 3, expr_p);
+
+ gnm_func_unref (fd_chidist);
+ }
+
+
@@ -568,6 +667,8 @@
case TOOL_ENGINE_UPDATE_DAO:
multiple = ((info->group_list == NULL) ? 1 : g_slist_length (info->group_list));
median = (info->median ? (2 + multiple) : 0);
+ if (median == 0 && info->logrank_test)
+ median = 3;
dao_adjust (dao, median + 1 + multiple * ((info->std_err ? 4 : 3) + (info->censored ? 1 : 0)),
info->base.range_1->v_range.cell.b.row
- info->base.range_1->v_range.cell.a.row + 3);
Modified: trunk/src/tools/analysis-kaplan-meier.h
==============================================================================
--- trunk/src/tools/analysis-kaplan-meier.h (original)
+++ trunk/src/tools/analysis-kaplan-meier.h Sat Nov 15 23:02:53 2008
@@ -52,6 +52,7 @@
gboolean ticks;
gboolean std_err;
gboolean median;
+ gboolean logrank_test;
GSList *group_list;
} analysis_tools_data_kaplan_meier_t;
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