[rkward-cvs] SF.net SVN: rkward:[4303] trunk/rkward/rkward/plugins
m-eik at users.sourceforge.net
m-eik at users.sourceforge.net
Fri Sep 21 17:06:18 UTC 2012
Revision: 4303
http://rkward.svn.sourceforge.net/rkward/?rev=4303&view=rev
Author: m-eik
Date: 2012-09-21 17:06:18 +0000 (Fri, 21 Sep 2012)
Log Message:
-----------
removed separated wilcoxon dialogs (both are combined in the new one)
Modified Paths:
--------------
trunk/rkward/rkward/plugins/analysis.pluginmap
Removed Paths:
-------------
trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_exact_test.js
trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_exact_test.rkh
trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_exact_test.xml
trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_test.js
trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_test.rkh
trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_test.xml
Deleted: trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_exact_test.js
===================================================================
--- trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_exact_test.js 2012-09-21 17:01:17 UTC (rev 4302)
+++ trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_exact_test.js 2012-09-21 17:06:18 UTC (rev 4303)
@@ -1,55 +0,0 @@
-// globals
-var y;
-
-function preprocess () {
- y = getValue ("y");
- if (y != "") y = ", " + y;
-
- echo ('require(exactRankTests)\n');
- echo ('\n');
- echo ('names = rk.get.description (' + getValue ("x") + y + ')\n');
-}
-
-function calculate () {
- var exact_setting = getValue ("exact");
- var exact_opt = "";
- if (exact_setting == "yes") {
- exact_opt = ", exact=TRUE";
- } else if (exact_setting == "no") {
- exact_opt = ", exact=FALSE";
- }
- var paired_opt = "";
- if (y != "") paired_opt = ", paired = " + getValue ("paired");
- var conflevel = "";
- var conflevel_opt = "";
- if (getValue ("confint") == "TRUE") {
- if ((conflevel = getValue("conflevel")) != "0.95") conflevel_opt = ", conf.level=" + conflevel;
- }
-
- echo ('result <- wilcox.exact (' + getValue ("x") + y + ', alternative = "' + getValue ("alternative") + '", mu = ' + getValue ("mu") + paired_opt + exact_opt + ', correct = ' + getValue ("correct") + ', conf.int = ' + getValue ("confint") + conflevel_opt + ')\n');
- echo ('\n');
-}
-
-function printout () {
- echo ('rk.header (result$method,\n');
- echo (' parameters=list ("Comparing", paste (names, collapse=" against "),\n');
- echo (' "H1", rk.describe.alternative (result),\n');
- echo (' "Continuity correction in normal approximation for p-value", "' + getValue ("correct") + '",\n');
- echo (' "Compute exact p-value", "' + getValue ("exact") + '", "Paired test", "' + getValue ("paired") + '",\n');
- echo (' "mu", "' + getValue ("mu") + '"))\n');
- echo ('\n');
- echo ('rk.results (list (\n');
- echo (' \'Variable Names\'=names,\n');
- echo (' \'statistic\'=result$statistic,\n');
- echo (' \'Location Shift\'=result$null.value,\n');
- echo (' \'Hypothesis\'=result$alternative,\n');
- echo (' p=result$p.value');
- if (getValue ("confint") == "TRUE") {
- echo (',\n');
- echo (' \'confidence interval percent\'=(100 * attr(result$conf.int, "conf.level")),\n');
- echo (' \'confidence interval of difference\'=result$conf.int,\n');
- echo (' \'Difference in Location\' = result$estimate');
- }
- echo ('))\n');
-}
-
Deleted: trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_exact_test.rkh
===================================================================
--- trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_exact_test.rkh 2012-09-21 17:01:17 UTC (rev 4302)
+++ trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_exact_test.rkh 2012-09-21 17:06:18 UTC (rev 4303)
@@ -1,8 +0,0 @@
-<!DOCTYPE rkhelp>
-<document>
- <summary>
- This test differs from <link href="rkward://component/wilcoxon_test"/> in that it uses a different algorithm and supports the exact test even for tied samples. Please note: The package 'exactRankTests' which was previously used in RKWard is no longer under development. Thus the function wilcox_test from the 'coin' package will be used.
-
- For details of the implementation see <link href="rkward://rhelp/wilcox_test"/>. For documentation of the dialog settings, see <link href="rkward://component/wilcoxon_test"/>.
- </summary>
-</document>
Deleted: trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_exact_test.xml
===================================================================
--- trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_exact_test.xml 2012-09-21 17:01:17 UTC (rev 4302)
+++ trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_exact_test.xml 2012-09-21 17:06:18 UTC (rev 4303)
@@ -1,46 +0,0 @@
-<!DOCTYPE rkplugin>
-<document>
- <code file="wilcoxon_exact_test.js"/>
- <help file="wilcoxon_exact_test.rkh"/>
-
- <logic>
- <convert id="y_specified" mode="notequals" standard="" sources="y.available"/>
- <connect client="paired.enabled" governor="y_specified"/>
- <connect client="conflevel.enabled" governor="confint.state"/>
- </logic>
-
- <dialog label="Wilcoxon exact test">
- <tabbook>
- <tab label="Basic settings">
- <row>
- <varselector id="vars"/>
- <column>
- <varslot type="numeric" id="x" source="vars" required="true" label="compare"/>
- <varslot type="numeric" id="y" source="vars" required="false" label="against (optional)"/>
- <radio id="alternative" label="using test hypothesis">
- <option value="two.sided" label="Two-sided"/>
- <option value="greater" label="greater"/>
- <option value="less" label="less"/>
- </radio>
- <checkbox id="paired" label="paired test" checked="false" value="TRUE" value_unchecked="FALSE"/>
- <stretch/>
- </column>
- </row>
- </tab>
- <tab label="Options">
- <frame label="Confidence Interval">
- <checkbox id="confint" label="compute confidence interval" checked="false" value="TRUE" value_unchecked="FALSE" />
- <spinbox type="real" id="conflevel" label="confidence level" min="0" max="1" initial="0.95"/>
- </frame>
- <spinbox id="mu" label="location (shift) to test against (mu)" initial="0"/>
- <radio id="exact" label="compute exact p-value">
- <option label="Always" value="yes" />
- <option label="Automatic" value="automatic" checked="true" />
- <option label="Never" value="no" />
- </radio>
- <checkbox id="correct" label="apply continuity correction" checked="true" value="TRUE" value_unchecked="FALSE"/>
- </tab>
- </tabbook>
- </dialog>
-
-</document>
Deleted: trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_test.js
===================================================================
--- trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_test.js 2012-09-21 17:01:17 UTC (rev 4302)
+++ trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_test.js 2012-09-21 17:06:18 UTC (rev 4303)
@@ -1,53 +0,0 @@
-// globals
-var y;
-
-function preprocess () {
- y = getValue ("y");
- if (y != "") y = ", " + y;
-
- echo ('names = rk.get.description (' + getValue ("x") + y + ')\n');
-}
-
-function calculate () {
- var exact_setting = getValue ("exact");
- var exact_opt = "";
- if (exact_setting == "yes") {
- exact_opt = ", exact=TRUE";
- } else if (exact_setting == "no") {
- exact_opt = ", exact=FALSE";
- }
- var paired_opt = "";
- if (y != "") paired_opt = ", paired = " + getValue ("paired");
- var conflevel = "";
- var conflevel_opt = "";
- if (getValue ("confint") == "TRUE") {
- if ((conflevel = getValue("conflevel")) != "0.95") conflevel_opt = ", conf.level=" + conflevel;
- }
-
- echo ('result <- wilcox.test (' + getValue ("x") + y + ', alternative = "' + getValue ("alternative") + '", mu = ' + getValue ("mu") + paired_opt + exact_opt + ', correct = ' + getValue ("correct") + ', conf.int = ' + getValue ("confint") + conflevel_opt + ')\n');
- echo ('\n');
-}
-
-function printout () {
- echo ('rk.header (result$method,\n');
- echo (' parameters=list ("Comparing", paste (names, collapse=" against "),\n');
- echo (' "H1", rk.describe.alternative (result),\n');
- echo (' "Continuity correction in normal approximation for p-value", "' + getValue ("correct") + '",\n');
- echo (' "Compute exact p-value", "' + getValue ("exact") + '", "Paired test", "' + getValue ("paired") + '",\n');
- echo (' "mu", "' + getValue ("mu") + '"))\n');
- echo ('\n');
- echo ('rk.results (list (\n');
- echo (' \'Variable Names\'=names,\n');
- echo (' \'statistic\'=result$statistic,\n');
- echo (' \'Location Shift\'=result$null.value,\n');
- echo (' \'Hypothesis\'=result$alternative,\n');
- echo (' p=result$p.value');
- if (getValue ("confint") == "TRUE") {
- echo (',\n');
- echo (' \'confidence interval percent\'=(100 * attr(result$conf.int, "conf.level")),\n');
- echo (' \'confidence interval of difference\'=result$conf.int,\n');
- echo (' \'Difference in Location\' = result$estimate');
- }
- echo ('))\n');
-}
-
Deleted: trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_test.rkh
===================================================================
--- trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_test.rkh 2012-09-21 17:01:17 UTC (rev 4302)
+++ trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_test.rkh 2012-09-21 17:06:18 UTC (rev 4303)
@@ -1,31 +0,0 @@
-<!DOCTYPE rkhelp>
-<document>
- <summary>
- This test performs the Wilcoxon Rank Sum and Signed Rank Tests (the later is equivalent to the Mann-Whitney test).
- </summary>
-
- <usage>
- Select a single vector (or paired test) to perform a Wilcoxon signed rank test on the null that the true distribution of x (or the difference between the paired vectors) is symmetric about 0 (or the specified location).
-
- Select two vectors to perform a Wilcoxon rank sum test (equivalent to the Mann-Whitney test: see <link href="rkward://rhelp/wilcox.test"/> for details) on the null that the distributions of x and y differ (by 0 or the specified location shift).
- </usage>
-
- <settings>
- <caption id="tab_variables"/>
- <setting id="x">Select the data to be computed. The vectors need to be numeric.</setting>
- <setting id="alternative">The alternative hypothesis. "greater" means that x is shifted to the right of y / of the location parameter.</setting>
- <setting id="paired">Check this for a paired test (Wilcoxon signed rank test of the difference between the two vectors).</setting>
- <caption id="tab_options"/>
- <setting id="confint">Check this if you want the confidence interval to be computed/printed.</setting>
- <setting id="conflevel">Confidence level of the printed confidence interval.</setting>
- <setting id="mu">The location / location shift to form the null hypothesis.</setting>
- <setting id="exact">Should an exact p-value be computed? By default ("Automatic") an asymptomatic p-value is calculated if and only if you have less than 50 cases per group without binding than an exact test should be performed. To compute an exact p-value in the presence of ties, use <link href="rkward://component/wilcoxon_exact_test"/></setting>
- <setting id="correct">If checked a continuity correction in the normal approximation for the p-value is applied.</setting>
- </settings>
- <related>
- <ul>
- <li><link href="rkward://rhelp/wilcox.test"/></li>
- <li><link href="rkward://component/wilcoxon_exact_test"/></li>
- </ul>
- </related>
-</document>
Deleted: trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_test.xml
===================================================================
--- trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_test.xml 2012-09-21 17:01:17 UTC (rev 4302)
+++ trunk/rkward/rkward/plugins/analysis/wilcoxon/wilcoxon_test.xml 2012-09-21 17:06:18 UTC (rev 4303)
@@ -1,46 +0,0 @@
-<!DOCTYPE rkplugin>
-<document>
- <code file="wilcoxon_test.js"/>
- <help file="wilcoxon_test.rkh"/>
-
- <logic>
- <convert id="y_specified" mode="notequals" standard="" sources="y.available"/>
- <connect client="paired.enabled" governor="y_specified"/>
- <connect client="conflevel.enabled" governor="confint.state"/>
- </logic>
-
- <dialog label="Wilcoxon test">
- <tabbook>
- <tab label="Basic settings" id="tab_variables">
- <row>
- <varselector id="vars"/>
- <column>
- <varslot type="numeric" id="x" source="vars" required="true" label="compare"/>
- <varslot type="numeric" id="y" source="vars" required="false" label="against (optional)"/>
- <radio id="alternative" label="using test hypothesis">
- <option value="two.sided" label="Two-sided"/>
- <option value="greater" label="greater"/>
- <option value="less" label="less"/>
- </radio>
- <checkbox id="paired" label="paired test" checked="false" value="TRUE" value_unchecked="FALSE"/>
- <stretch/>
- </column>
- </row>
- </tab>
- <tab label="Options" id="tab_options">
- <frame label="Confidence Interval">
- <checkbox id="confint" label="Compute confidence interval" checked="false" value="TRUE" value_unchecked="FALSE" />
- <spinbox type="real" id="conflevel" label="confidence level" min="0" max="1" initial="0.95"/>
- </frame>
- <spinbox id="mu" label="location (shift) to test against (mu)" initial="0"/>
- <radio id="exact" label="compute exact p-value">
- <option label="Always" value="yes" />
- <option label="Automatic" value="automatic" checked="true" />
- <option label="Never" value="no" />
- </radio>
- <checkbox id="correct" label="apply continuity correction" checked="true" value="TRUE" value_unchecked="FALSE"/>
- </tab>
- </tabbook>
- </dialog>
-
-</document>
Modified: trunk/rkward/rkward/plugins/analysis.pluginmap
===================================================================
--- trunk/rkward/rkward/plugins/analysis.pluginmap 2012-09-21 17:01:17 UTC (rev 4302)
+++ trunk/rkward/rkward/plugins/analysis.pluginmap 2012-09-21 17:06:18 UTC (rev 4303)
@@ -8,8 +8,6 @@
<component type="standard" id="descriptive" file="descriptive/descriptive_statistics.xml" label="Descriptive Statistics" />
<component type="standard" id="t_test" file="analysis/t_test.xml" label="t-Test" />
<component type="standard" id="wilcoxon_tests" file="analysis/wilcoxon/wilcoxon_tests.xml" label="Wilcoxon/Mann-Whitney Tests" />
- <component type="standard" id="wilcoxon_test" file="analysis/wilcoxon/wilcoxon_test.xml" label="Wilcoxon Test" />
- <component type="standard" id="wilcoxon_exact_test" file="analysis/wilcoxon/wilcoxon_exact_test.xml" label="Wilcoxon Exact Test" />
<!-- moments -->
<component type="standard" id="moment" file="analysis/moments/moment.xml" label="Moment" />
@@ -101,8 +99,6 @@
</menu>
<menu id="wilcoxon_test" label="Wilcoxon Tests" index="11">
<entry component="wilcoxon_tests" />
- <entry component="wilcoxon_test" />
- <entry component="wilcoxon_exact_test" />
</menu>
</menu>
</hierarchy>
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