[rkward-cvs] SF.net SVN: rkward: [1620] trunk/rkward/rkward/plugins

tfry at users.sourceforge.net tfry at users.sourceforge.net
Sun Mar 18 20:10:42 UTC 2007


Revision: 1620
          http://svn.sourceforge.net/rkward/?rev=1620&view=rev
Author:   tfry
Date:     2007-03-18 13:10:42 -0700 (Sun, 18 Mar 2007)

Log Message:
-----------
I assume, talking about two 'samples' is not technically correct for a paired test, so rename to two 'variables' (step 2)

Modified Paths:
--------------
    trunk/rkward/rkward/plugins/analysis.pluginmap

Added Paths:
-----------
    trunk/rkward/rkward/plugins/analysis/t_test_two_vars.php
    trunk/rkward/rkward/plugins/analysis/t_test_two_vars.rkh
    trunk/rkward/rkward/plugins/analysis/t_test_two_vars.xml

Removed Paths:
-------------
    trunk/rkward/rkward/plugins/analysis/t_test_two_samples.php
    trunk/rkward/rkward/plugins/analysis/t_test_two_samples.rkh
    trunk/rkward/rkward/plugins/analysis/t_test_two_samples.xml

Deleted: trunk/rkward/rkward/plugins/analysis/t_test_two_samples.php
===================================================================
--- trunk/rkward/rkward/plugins/analysis/t_test_two_samples.php	2007-03-18 20:09:42 UTC (rev 1619)
+++ trunk/rkward/rkward/plugins/analysis/t_test_two_samples.php	2007-03-18 20:10:42 UTC (rev 1620)
@@ -1,57 +0,0 @@
-<?
-function preprocess () {
-	global $x;
-	global $y;
-
-	$x = getRK_val ("x");
-	$y = getRK_val ("y");
-?>
-names <- rk.get.description (<? echo ($x . ", " . $y); ?>)
-<?
-}
-
-function calculate () {
-	global $x;
-	global $y;
-	global $varequal;
-	global $paired;
-
-	$conflevel = getRK_val ("conflevel");
-	$varequal = getRK_val ("varequal");
-	$paired = getRK_val ("paired");
-	$hypothesis = getRK_val ("hypothesis");
-
-	$options = ", alternative=\"" . $hypothesis . "\"";
-	if ($paired) $options .= ", paired=TRUE";
-	if ((!$paired) && $varequal) $options .= ", var.equal=TRUE";
-	if ($conflevel != "0.95") $options .= ", conf.level=" . $conflevel;
-?>
-result <- t.test (<? echo ($x . ", " . $y . $options); ?>)
-<?
-}
-
-function printout () {
-	global $varequal;
-	global $paired;
-?>
-rk.header (result$method, 
-	parameters=list ("Comparing", paste (names[1], "against", names[2]),
-	"H1", rk.describe.alternative (result)<?
-	if (!$paired) { ?>
-,
-	"Equal variances", "<? if (!$varequal) echo ("not"); ?> assumed"<?
-	} ?>))
-
-rk.results (list (
-	'Variable Name'=names,
-	'estimated mean'=result$estimate,
-	'degrees of freedom'=result$parameter,
-	t=result$statistic,
-	p=result$p.value<?
-	if (getRK_val ("confint")) { ?>,
-	'confidence interval percent'=(100 * attr(result$conf.int, "conf.level")),
-	'confidence interval of difference'=result$conf.int <? } ?>))
-<?
-}
-
-?>

Deleted: trunk/rkward/rkward/plugins/analysis/t_test_two_samples.rkh
===================================================================
--- trunk/rkward/rkward/plugins/analysis/t_test_two_samples.rkh	2007-03-18 20:09:42 UTC (rev 1619)
+++ trunk/rkward/rkward/plugins/analysis/t_test_two_samples.rkh	2007-03-18 20:10:42 UTC (rev 1620)
@@ -1,28 +0,0 @@
-<!DOCTYPE rkhelp>
-<document>
-	<summary>
-Two variable t-test (paired or independent samples).
-	</summary>
-
-	<usage>
-Chose two numeric vectors to compare against each other. Specify, whether the variables are paired or independent samples. For details, see below.
-	</usage>
-
-	<settings>
-		<caption id="tab_variables"/>
-		<setting id="x">A numeric vector for the first variable</setting>
-		<setting id="y">A numeric vector for the second variable</setting>
-		<setting id="hypothesis">Alternative hypothesis (H1) of the test.</setting>
-		<setting id="paired">Whether the samples are paired (repeated measurements on the same subject) or independent. For a paired test, if the two vectors are not of equal length, there will be an error.</setting>
-		<caption id="tab_options"/>
-		<setting id="varequal">Whether to assume equal variances for the two samples. This option is implied for a paired test.</setting>
-		<setting id="conflevel">Confidence level to use.</setting>
-		<setting id="confint">Whether to print the confidence interval of the estimated mean.</setting>
-	</settings>
-	<related>
-		<ul>
-			<li><link href="rkward://rhelp/cor"/></li>
-			<li><link href="rkward://rhelp/cor.test"/></li>
-		</ul>
-	</related>
-</document>

Deleted: trunk/rkward/rkward/plugins/analysis/t_test_two_samples.xml
===================================================================
--- trunk/rkward/rkward/plugins/analysis/t_test_two_samples.xml	2007-03-18 20:09:42 UTC (rev 1619)
+++ trunk/rkward/rkward/plugins/analysis/t_test_two_samples.xml	2007-03-18 20:10:42 UTC (rev 1620)
@@ -1,52 +0,0 @@
-<!DOCTYPE rkplugin>
-<document>
-	<code file="t_test_two_vars.php"/>
-	<help file="t_test_two_vars.rkh"/>
-
-	<logic>
-		<convert id="notpaired" mode="equals" sources="paired.state" standard="0"/>
-		<connect client="varequal.enabled" governor="notpaired"/>
-	</logic>
-
-	<dialog label="Two Variable t-Test">
-		<tabbook>
-			<tab label="Basic settings">
-				<row id="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="true" label="against"/>
-						<radio id="hypothesis" label="using test hypothesis">
-							<option value="two.sided" label="Two-sided"/>
-							<option value="greater" label="First is greater"/>
-							<option value="less" label="Second is greater"/>
-						</radio>
-						<checkbox id="paired" label="Paired sample" value="1" value_unchecked="0" />
-					</column>
-				</row>
-			</tab>
-			<tab label="Options">
-				<checkbox id="varequal" label="assume equal variances" value="1" value_unchecked="0"/>
-				<frame label="Confidence Interval" id="confint_frame">
-					<spinbox type="real" id="conflevel" label="confidence level" min="0" max="1" initial="0.95"/>
-					<checkbox id="confint" label="print confidence interval" value="1" checked="true"/>
-				</frame>
-				<stretch/>
-			</tab>
-		</tabbook>
-	</dialog>
-	<wizard label="Two Variable t-Test">
-		<page>
-			<text>As a first step, select the two variables you want to compare against each other. And specify, which one you theorize to be greater. Select two-sided, if your theory does not tell you, which variable is greater.</text>
-			<copy id="basic_settings_row"/>
-		</page>
-		<page>
-			<text>Below are some advanced options. It's generally safe not to assume the variables have equal variances. An appropriate correction will be applied then. Chosing "assume equal variances" may increase test-strength, however.</text>
-			<copy id="varequal"/>
-			<text>Sometimes it's helpful to get an estimate of the confidence interval of the difference in means. Below you can specify whether one should be shown, and which confidence-level should be applied (95% corresponds to a 5% level of significance).</text>
-			<copy id="confint_frame"/>
-			<stretch/>
-		</page>
-	</wizard>
-	
-</document>

Copied: trunk/rkward/rkward/plugins/analysis/t_test_two_vars.php (from rev 1618, trunk/rkward/rkward/plugins/analysis/t_test_two_samples.php)
===================================================================
--- trunk/rkward/rkward/plugins/analysis/t_test_two_vars.php	                        (rev 0)
+++ trunk/rkward/rkward/plugins/analysis/t_test_two_vars.php	2007-03-18 20:10:42 UTC (rev 1620)
@@ -0,0 +1,57 @@
+<?
+function preprocess () {
+	global $x;
+	global $y;
+
+	$x = getRK_val ("x");
+	$y = getRK_val ("y");
+?>
+names <- rk.get.description (<? echo ($x . ", " . $y); ?>)
+<?
+}
+
+function calculate () {
+	global $x;
+	global $y;
+	global $varequal;
+	global $paired;
+
+	$conflevel = getRK_val ("conflevel");
+	$varequal = getRK_val ("varequal");
+	$paired = getRK_val ("paired");
+	$hypothesis = getRK_val ("hypothesis");
+
+	$options = ", alternative=\"" . $hypothesis . "\"";
+	if ($paired) $options .= ", paired=TRUE";
+	if ((!$paired) && $varequal) $options .= ", var.equal=TRUE";
+	if ($conflevel != "0.95") $options .= ", conf.level=" . $conflevel;
+?>
+result <- t.test (<? echo ($x . ", " . $y . $options); ?>)
+<?
+}
+
+function printout () {
+	global $varequal;
+	global $paired;
+?>
+rk.header (result$method, 
+	parameters=list ("Comparing", paste (names[1], "against", names[2]),
+	"H1", rk.describe.alternative (result)<?
+	if (!$paired) { ?>
+,
+	"Equal variances", "<? if (!$varequal) echo ("not"); ?> assumed"<?
+	} ?>))
+
+rk.results (list (
+	'Variable Name'=names,
+	'estimated mean'=result$estimate,
+	'degrees of freedom'=result$parameter,
+	t=result$statistic,
+	p=result$p.value<?
+	if (getRK_val ("confint")) { ?>,
+	'confidence interval percent'=(100 * attr(result$conf.int, "conf.level")),
+	'confidence interval of difference'=result$conf.int <? } ?>))
+<?
+}
+
+?>

Copied: trunk/rkward/rkward/plugins/analysis/t_test_two_vars.rkh (from rev 1618, trunk/rkward/rkward/plugins/analysis/t_test_two_samples.rkh)
===================================================================
--- trunk/rkward/rkward/plugins/analysis/t_test_two_vars.rkh	                        (rev 0)
+++ trunk/rkward/rkward/plugins/analysis/t_test_two_vars.rkh	2007-03-18 20:10:42 UTC (rev 1620)
@@ -0,0 +1,28 @@
+<!DOCTYPE rkhelp>
+<document>
+	<summary>
+Two variable t-test (paired or independent samples).
+	</summary>
+
+	<usage>
+Chose two numeric vectors to compare against each other. Specify, whether the variables are paired or independent samples. For details, see below.
+	</usage>
+
+	<settings>
+		<caption id="tab_variables"/>
+		<setting id="x">A numeric vector for the first variable</setting>
+		<setting id="y">A numeric vector for the second variable</setting>
+		<setting id="hypothesis">Alternative hypothesis (H1) of the test.</setting>
+		<setting id="paired">Whether the samples are paired (repeated measurements on the same subject) or independent. For a paired test, if the two vectors are not of equal length, there will be an error.</setting>
+		<caption id="tab_options"/>
+		<setting id="varequal">Whether to assume equal variances for the two samples. This option is implied for a paired test.</setting>
+		<setting id="conflevel">Confidence level to use.</setting>
+		<setting id="confint">Whether to print the confidence interval of the estimated mean.</setting>
+	</settings>
+	<related>
+		<ul>
+			<li><link href="rkward://rhelp/cor"/></li>
+			<li><link href="rkward://rhelp/cor.test"/></li>
+		</ul>
+	</related>
+</document>

Copied: trunk/rkward/rkward/plugins/analysis/t_test_two_vars.xml (from rev 1619, trunk/rkward/rkward/plugins/analysis/t_test_two_samples.xml)
===================================================================
--- trunk/rkward/rkward/plugins/analysis/t_test_two_vars.xml	                        (rev 0)
+++ trunk/rkward/rkward/plugins/analysis/t_test_two_vars.xml	2007-03-18 20:10:42 UTC (rev 1620)
@@ -0,0 +1,52 @@
+<!DOCTYPE rkplugin>
+<document>
+	<code file="t_test_two_vars.php"/>
+	<help file="t_test_two_vars.rkh"/>
+
+	<logic>
+		<convert id="notpaired" mode="equals" sources="paired.state" standard="0"/>
+		<connect client="varequal.enabled" governor="notpaired"/>
+	</logic>
+
+	<dialog label="Two Variable t-Test">
+		<tabbook>
+			<tab label="Basic settings">
+				<row id="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="true" label="against"/>
+						<radio id="hypothesis" label="using test hypothesis">
+							<option value="two.sided" label="Two-sided"/>
+							<option value="greater" label="First is greater"/>
+							<option value="less" label="Second is greater"/>
+						</radio>
+						<checkbox id="paired" label="Paired sample" value="1" value_unchecked="0" />
+					</column>
+				</row>
+			</tab>
+			<tab label="Options">
+				<checkbox id="varequal" label="assume equal variances" value="1" value_unchecked="0"/>
+				<frame label="Confidence Interval" id="confint_frame">
+					<spinbox type="real" id="conflevel" label="confidence level" min="0" max="1" initial="0.95"/>
+					<checkbox id="confint" label="print confidence interval" value="1" checked="true"/>
+				</frame>
+				<stretch/>
+			</tab>
+		</tabbook>
+	</dialog>
+	<wizard label="Two Variable t-Test">
+		<page>
+			<text>As a first step, select the two variables you want to compare against each other. And specify, which one you theorize to be greater. Select two-sided, if your theory does not tell you, which variable is greater.</text>
+			<copy id="basic_settings_row"/>
+		</page>
+		<page>
+			<text>Below are some advanced options. It's generally safe not to assume the variables have equal variances. An appropriate correction will be applied then. Chosing "assume equal variances" may increase test-strength, however.</text>
+			<copy id="varequal"/>
+			<text>Sometimes it's helpful to get an estimate of the confidence interval of the difference in means. Below you can specify whether one should be shown, and which confidence-level should be applied (95% corresponds to a 5% level of significance).</text>
+			<copy id="confint_frame"/>
+			<stretch/>
+		</page>
+	</wizard>
+	
+</document>

Modified: trunk/rkward/rkward/plugins/analysis.pluginmap
===================================================================
--- trunk/rkward/rkward/plugins/analysis.pluginmap	2007-03-18 20:09:42 UTC (rev 1619)
+++ trunk/rkward/rkward/plugins/analysis.pluginmap	2007-03-18 20:10:42 UTC (rev 1620)
@@ -6,7 +6,7 @@
 		<component type="standard" id="corr_matrix" file="analysis/corr_matrix.xml" label="Correlation Matrix" />
 		<component type="standard" id="cor_graph" file="plots/cor_graph.xml" label="Correlation Matrix Plot" />
 		<component type="standard" id="descriptive" file="descriptive/descriptive_statistics.xml" label="Descriptive Statistics" />
-		<component type="standard" id="t_test_two_samples" file="analysis/t_test_two_samples.xml" label="Two Sample t-test" />
+		<component type="standard" id="t_test_two_vars" file="analysis/t_test_two_vars.xml" label="Two Variable t-test" />
 		<component type="standard" id="simple_anova" file="simple_anova/description.xml" label="Simple Anova" />
 		<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" />
@@ -29,7 +29,7 @@
 			<entry component="descriptive" index="2"/>
 			<menu id="means" label="Means" index="3">
 				<menu id="ttests" label="t-Tests" index="0">
-					<entry component="t_test_two_samples" />
+					<entry component="t_test_two_vars" />
 				</menu>
 			</menu>
 			<entry component="simple_anova" index="6"/>


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