[rkward-cvs] SF.net SVN: rkward:[2621] trunk/rkward/tests
tfry at users.sourceforge.net
tfry at users.sourceforge.net
Sat Aug 22 20:29:20 UTC 2009
Revision: 2621
http://rkward.svn.sourceforge.net/rkward/?rev=2621&view=rev
Author: tfry
Date: 2009-08-22 20:29:19 +0000 (Sat, 22 Aug 2009)
Log Message:
-----------
Add test for wilcoxon_exact_test, and fix the existing standards (which erroneously contained rerun-links)
Modified Paths:
--------------
trunk/rkward/tests/analysis_plugins/RKTestStandard.basic_statistics_a.rkout
trunk/rkward/tests/analysis_plugins/RKTestStandard.basic_statistics_b.rkout
trunk/rkward/tests/analysis_plugins/RKTestStandard.correlation_matrix.rkout
trunk/rkward/tests/analysis_plugins/RKTestStandard.correlation_matrix_plot.rkout
trunk/rkward/tests/analysis_plugins/RKTestStandard.descriptive_stats.rkout
trunk/rkward/tests/analysis_plugins/RKTestStandard.t_test_two_vars.rkout
trunk/rkward/tests/analysis_plugins/RKTestStandard.wilcoxon_test.rkout
trunk/rkward/tests/analysis_plugins.R
Added Paths:
-----------
trunk/rkward/tests/analysis_plugins/RKTestStandard.wilcoxon_exact_test.rkcommands.R
trunk/rkward/tests/analysis_plugins/RKTestStandard.wilcoxon_exact_test.rkout
Modified: trunk/rkward/tests/analysis_plugins/RKTestStandard.basic_statistics_a.rkout
===================================================================
--- trunk/rkward/tests/analysis_plugins/RKTestStandard.basic_statistics_a.rkout 2009-08-22 20:27:25 UTC (rev 2620)
+++ trunk/rkward/tests/analysis_plugins/RKTestStandard.basic_statistics_a.rkout 2009-08-22 20:29:19 UTC (rev 2621)
@@ -15,4 +15,3 @@
<tr><td>weight</td><td>15</td><td>0</td><td>136.73</td><td>240.21</td><td>15.499</td><td>115</td><td>164</td><td>135</td><td>23.5</td><td>0%: 115 25%: 124.5 50%: 135 75%: 148 100%: 164</td><td>0%: 115 20%: 122.4 40%: 130.8 60%: 140.2 80%: 150.8 100%: 164</td><td>136.73</td><td>17.554</td><td>3: 143.017677999144</td></tr>
<tr><td>test50x</td><td>50</td><td>0</td><td>125.5</td><td>212.5</td><td>14.577</td><td>101</td><td>150</td><td>125.5</td><td>24.5</td><td>0%: 101 25%: 113.25 50%: 125.5 75%: 137.75 100%: 150</td><td>0%: 101 20%: 110.8 40%: 120.6 60%: 130.4 80%: 140.2 100%: 150</td><td>125.5</td><td>18.285</td><td>3: 138.260549866364</td></tr>
</table>
-<a href="rkward://runplugin/rkward::basic_statistics/autre.real=6.000000%0aconstMad.real=1.46280000%0acustomMu.state=1%0acustomS.state=1%0ahuber.state=1%0ainitmu.string=median%0airq.state=1%0alength.state=1%0amad.state=1%0amaximum.state=1%0amean.state=1%0amedian.state=1%0aminimum.state=1%0amu.text=3%0anarm.state=1%0anbmaximum.real=0.000000%0anbminimum.real=0.000000%0anom.selection=my.data%0apourcent.real=0.05000000%0aquartile.state=1%0aresult.state=1%0as.text=%0asd.state=1%0atol.real=0.070000%0atrim.state=1%0avari.state=1%0awinsor.real=1.50000000%0az.available=women%5b%5b%5c%22weight%5c%22%5d%5d%5cntest50x">Run again</a>
\ No newline at end of file
Modified: trunk/rkward/tests/analysis_plugins/RKTestStandard.basic_statistics_b.rkout
===================================================================
--- trunk/rkward/tests/analysis_plugins/RKTestStandard.basic_statistics_b.rkout 2009-08-22 20:27:25 UTC (rev 2620)
+++ trunk/rkward/tests/analysis_plugins/RKTestStandard.basic_statistics_b.rkout 2009-08-22 20:29:19 UTC (rev 2621)
@@ -8,4 +8,3 @@
<tr><td>test10x</td><td>101 102</td><td>110 109 108</td></tr>
<tr><td>height</td><td>58 59</td><td>72 71 70</td></tr>
</table>
-<a href="rkward://runplugin/rkward::basic_statistics/autre.real=0.000000%0ahuber.state=%0airq.state=0%0alength.state=0%0amad.state=%0amaximum.state=0%0amean.state=0%0amedian.state=0%0aminimum.state=0%0anarm.state=1%0anbmaximum.real=3.000000%0anbminimum.real=2.000000%0aquartile.state=0%0aresult.state=%0asd.state=0%0atrim.state=%0avari.state=0%0az.available=test10x%5cnwomen%5b%5b%5c%22height%5c%22%5d%5d">Run again</a>
\ No newline at end of file
Modified: trunk/rkward/tests/analysis_plugins/RKTestStandard.correlation_matrix.rkout
===================================================================
--- trunk/rkward/tests/analysis_plugins/RKTestStandard.correlation_matrix.rkout 2009-08-22 20:27:25 UTC (rev 2620)
+++ trunk/rkward/tests/analysis_plugins/RKTestStandard.correlation_matrix.rkout 2009-08-22 20:29:19 UTC (rev 2621)
@@ -16,7 +16,7 @@
<tr><td>test50y</td><td>50</td><td>NA</td><td>0</td></tr>
<tr><td>test50z</td><td>50</td><td>50</td><td>NA</td></tr>
</table>
-<a href="rkward://runplugin/rkward::corr_matrix/do_p.state=1%0amethod.string=pearson%0ause.string=pairwise%0ax.available=test50x%5cntest50y%5cntest50z">Run again</a><h1>Correlation Matrix</h1>
+<h1>Correlation Matrix</h1>
<h2>Parameters</h2>
<ul><li>Method: pearson</li>
<li>Exclusion: pairwise.complete.obs</li>
@@ -27,4 +27,3 @@
<tr><td>weight</td><td>1</td><td>0.9955</td></tr>
<tr><td>height</td><td>0.9955</td><td>1</td></tr>
</table>
-<a href="rkward://runplugin/rkward::corr_matrix/do_p.state=%0amethod.string=pearson%0ause.string=pairwise%0ax.available=women%5b%5b%5c%22weight%5c%22%5d%5d%5cnwomen%5b%5b%5c%22height%5c%22%5d%5d">Run again</a>
\ No newline at end of file
Modified: trunk/rkward/tests/analysis_plugins/RKTestStandard.correlation_matrix_plot.rkout
===================================================================
--- trunk/rkward/tests/analysis_plugins/RKTestStandard.correlation_matrix_plot.rkout 2009-08-22 20:27:25 UTC (rev 2620)
+++ trunk/rkward/tests/analysis_plugins/RKTestStandard.correlation_matrix_plot.rkout 2009-08-22 20:29:19 UTC (rev 2621)
@@ -7,4 +7,4 @@
</ul>
DATE<br>
<img src="graph.png" width="480" height="480"><br>
-<p class='character'>Legend: '***': p < 0.001 -- '**': p < 0.01 -- '*': p < 0.05 -- '.'': p < 0.1</p><a href="rkward://runplugin/rkward::cor_graph/digits.real=3.000000%0amethod.string=pearson%0ascale.state=TRUE%0ause.string=pairwise.complete.obs%0ax.available=rock">Run again</a>
\ No newline at end of file
+<p class='character'>Legend: '***': p < 0.001 -- '**': p < 0.01 -- '*': p < 0.05 -- '.'': p < 0.1</p>
\ No newline at end of file
Modified: trunk/rkward/tests/analysis_plugins/RKTestStandard.descriptive_stats.rkout
===================================================================
--- trunk/rkward/tests/analysis_plugins/RKTestStandard.descriptive_stats.rkout 2009-08-22 20:27:25 UTC (rev 2620)
+++ trunk/rkward/tests/analysis_plugins/RKTestStandard.descriptive_stats.rkout 2009-08-22 20:29:19 UTC (rev 2621)
@@ -9,4 +9,3 @@
<tr><td>height</td><td>65</td><td>65</td><td>58</td><td>72</td><td>4.4721</td><td>975</td><td>1.5110e+27</td><td>5.8512</td><td>15</td><td>0</td></tr>
<tr><td>test10z</td><td>22</td><td>22</td><td>4</td><td>40</td><td>12.111</td><td>220</td><td>3.8051e+12</td><td>14.628</td><td>11</td><td>1</td></tr>
</table>
-<a href="rkward://runplugin/rkward::descriptive/constMad.real=1.46280000%0alength.state=1%0amad.state=1%0amad_type.string=average%0amean.state=1%0amedian.state=1%0aprod.state=1%0arange.state=1%0asd.state=1%0asum.state=1%0atrim.real=0.00000000%0ax.available=women%5b%5b%5c%22height%5c%22%5d%5d%5cntest10z">Run again</a>
\ No newline at end of file
Modified: trunk/rkward/tests/analysis_plugins/RKTestStandard.t_test_two_vars.rkout
===================================================================
--- trunk/rkward/tests/analysis_plugins/RKTestStandard.t_test_two_vars.rkout 2009-08-22 20:27:25 UTC (rev 2620)
+++ trunk/rkward/tests/analysis_plugins/RKTestStandard.t_test_two_vars.rkout 2009-08-22 20:29:19 UTC (rev 2621)
@@ -12,7 +12,7 @@
<br/>225.5</td><td>98</td><td>-34.3</td><td>2.1436e-56</td><td>95</td><td>-105.79
<br/>-94.214</td></tr>
</table>
-<a href="rkward://runplugin/rkward::t_test_two_vars/confint.state=1%0aconflevel.real=0.95000000%0ahypothesis.string=two.sided%0apaired.state=0%0avarequal.state=0%0ax.available=test50x%0ay.available=test50y">Run again</a><h1>Paired t-test</h1>
+<h1>Paired t-test</h1>
<h2>Parameters</h2>
<ul><li>Comparing: test10y against test10z</li>
<li>H1: true difference in means is less than 0</li>
@@ -24,4 +24,3 @@
<br/>test10z</td><td>183.5</td><td>9</td><td>63.886</td><td>1</td><td>99</td><td>-Inf
<br/>191.60</td></tr>
</table>
-<a href="rkward://runplugin/rkward::t_test_two_vars/confint.state=1%0aconflevel.real=0.99000000%0ahypothesis.string=less%0apaired.state=1%0ax.available=test10y%0ay.available=test10z">Run again</a>
\ No newline at end of file
Added: trunk/rkward/tests/analysis_plugins/RKTestStandard.wilcoxon_exact_test.rkcommands.R
===================================================================
--- trunk/rkward/tests/analysis_plugins/RKTestStandard.wilcoxon_exact_test.rkcommands.R (rev 0)
+++ trunk/rkward/tests/analysis_plugins/RKTestStandard.wilcoxon_exact_test.rkcommands.R 2009-08-22 20:29:19 UTC (rev 2621)
@@ -0,0 +1,53 @@
+local({
+## Prepare
+require(exactRankTests)
+
+names = rk.get.description (test50x)
+## Compute
+result <- wilcox.exact (test50x, alternative = "two.sided", mu = 0.00000000, exact=TRUE, correct = FALSE, conf.int = TRUE)
+
+## Print result
+rk.header (result$method,
+ parameters=list ("Comparing", paste (names, collapse=" against "),
+ "H1", rk.describe.alternative (result),
+ "Continuity correction in normal approximation for p-value", "FALSE",
+ "Compute exact p-value", "yes", "Paired test", "FALSE",
+ "mu", "0.00000000"))
+
+rk.results (list (
+ 'Variable Names'=names,
+ 'statistic'=result$statistic,
+ 'Location Shift'=result$null.value,
+ 'Hypothesis'=result$alternative,
+ p=result$p.value,
+ 'confidence interval percent'=(100 * attr(result$conf.int, "conf.level")),
+ 'confidence interval of difference'=result$conf.int,
+ 'Difference in Location' = result$estimate))
+})
+.rk.rerun.plugin.link(plugin="rkward::wilcoxon_exact_test", settings="alternative.string=two.sided\nconfint.state=TRUE\nconflevel.real=0.95000000\ncorrect.state=FALSE\nexact.string=yes\nmu.real=0.00000000\nx.available=test50x\ny.available=", label="Run again")
+.rk.make.hr()
+local({
+## Prepare
+require(exactRankTests)
+
+names = rk.get.description (test50x, test50y)
+## Compute
+result <- wilcox.exact (test50x, test50y, alternative = "less", mu = 0.00000000, paired = TRUE, correct = TRUE, conf.int = FALSE)
+
+## Print result
+rk.header (result$method,
+ parameters=list ("Comparing", paste (names, collapse=" against "),
+ "H1", rk.describe.alternative (result),
+ "Continuity correction in normal approximation for p-value", "TRUE",
+ "Compute exact p-value", "automatic", "Paired test", "TRUE",
+ "mu", "0.00000000"))
+
+rk.results (list (
+ 'Variable Names'=names,
+ 'statistic'=result$statistic,
+ 'Location Shift'=result$null.value,
+ 'Hypothesis'=result$alternative,
+ p=result$p.value))
+})
+.rk.rerun.plugin.link(plugin="rkward::wilcoxon_exact_test", settings="alternative.string=less\nconfint.state=FALSE\ncorrect.state=TRUE\nexact.string=automatic\nmu.real=0.00000000\npaired.state=TRUE\nx.available=test50x\ny.available=test50y", label="Run again")
+.rk.make.hr()
Added: trunk/rkward/tests/analysis_plugins/RKTestStandard.wilcoxon_exact_test.rkout
===================================================================
--- trunk/rkward/tests/analysis_plugins/RKTestStandard.wilcoxon_exact_test.rkout (rev 0)
+++ trunk/rkward/tests/analysis_plugins/RKTestStandard.wilcoxon_exact_test.rkout 2009-08-22 20:29:19 UTC (rev 2621)
@@ -0,0 +1,30 @@
+<h1>Exact Wilcoxon signed rank test</h1>
+<h2>Parameters</h2>
+<ul><li>Comparing: test50x</li>
+<li>H1: true mu is not equal to 0</li>
+<li>Continuity correction in normal approximation for p-value: FALSE</li>
+<li>Compute exact p-value: yes</li>
+<li>Paired test: FALSE</li>
+<li>mu: 0.00000000</li>
+</ul>
+DATE<br>
+<table border="1">
+<tr><td>Variable Names</td><td>statistic</td><td>Location Shift</td><td>Hypothesis</td><td>p</td><td>confidence interval percent</td><td>confidence interval of difference</td><td>Difference in Location</td></tr>
+<tr><td>test50x</td><td>1275</td><td>0</td><td>two.sided</td><td>1.7764e-15</td><td>95</td><td>121
+<br/>130</td><td>125.5</td></tr>
+</table>
+<h1>Asymptotic Wilcoxon signed rank test</h1>
+<h2>Parameters</h2>
+<ul><li>Comparing: test50x against test50y</li>
+<li>H1: true mu is less than 0</li>
+<li>Continuity correction in normal approximation for p-value: TRUE</li>
+<li>Compute exact p-value: automatic</li>
+<li>Paired test: TRUE</li>
+<li>mu: 0.00000000</li>
+</ul>
+DATE<br>
+<table border="1">
+<tr><td>Variable Names</td><td>statistic</td><td>Location Shift</td><td>Hypothesis</td><td>p</td></tr>
+<tr><td>test50x
+<br/>test50y</td><td>0</td><td>0</td><td>less</td><td>7.6873e-13</td></tr>
+</table>
Modified: trunk/rkward/tests/analysis_plugins/RKTestStandard.wilcoxon_test.rkout
===================================================================
--- trunk/rkward/tests/analysis_plugins/RKTestStandard.wilcoxon_test.rkout 2009-08-22 20:27:25 UTC (rev 2620)
+++ trunk/rkward/tests/analysis_plugins/RKTestStandard.wilcoxon_test.rkout 2009-08-22 20:29:19 UTC (rev 2621)
@@ -13,7 +13,7 @@
<tr><td>test50x</td><td>1275</td><td>0</td><td>two.sided</td><td>1.7764e-15</td><td>95</td><td>121
<br/>130</td><td>125.5</td></tr>
</table>
-<a href="rkward://runplugin/rkward::wilcoxon_test/alternative.string=two.sided%0aconfint.state=TRUE%0aconflevel.real=0.95000000%0acorrect.state=FALSE%0aexact.string=yes%0amu.real=0.00000000%0ax.available=test50x%0ay.available=">Run again</a><h1>Wilcoxon signed rank test with continuity correction</h1>
+<h1>Wilcoxon signed rank test with continuity correction</h1>
<h2>Parameters</h2>
<ul><li>Comparing: test50x against test50y</li>
<li>H1: true location shift is less than 0</li>
@@ -28,4 +28,3 @@
<tr><td>test50x
<br/>test50y</td><td>0</td><td>0</td><td>less</td><td>8.0007e-13</td></tr>
</table>
-<a href="rkward://runplugin/rkward::wilcoxon_test/alternative.string=less%0aconfint.state=FALSE%0acorrect.state=TRUE%0aexact.string=automatic%0amu.real=0.00000000%0apaired.state=TRUE%0ax.available=test50x%0ay.available=test50y">Run again</a>
\ No newline at end of file
Modified: trunk/rkward/tests/analysis_plugins.R
===================================================================
--- trunk/rkward/tests/analysis_plugins.R 2009-08-22 20:27:25 UTC (rev 2620)
+++ trunk/rkward/tests/analysis_plugins.R 2009-08-22 20:29:19 UTC (rev 2621)
@@ -52,9 +52,12 @@
rk.call.plugin ("rkward::wilcoxon_test", alternative.string="two.sided", confint.state="TRUE", conflevel.real="0.95000000", correct.state="FALSE", exact.string="yes", mu.real="0.00000000", x.available="test50x", y.available="", submit.mode="submit")
rk.call.plugin ("rkward::wilcoxon_test", alternative.string="less", confint.state="FALSE", correct.state="TRUE", exact.string="automatic", mu.real="0.00000000", paired.state="TRUE", x.available="test50x", y.available="test50y", submit.mode="submit")
- })#,
-# new ("RKTest", id="wilcoxon_exact_test", call=function () {
-# }, libraries=c ("coin"))
+ }),
+ new ("RKTest", id="wilcoxon_exact_test", call=function () {
+ rk.call.plugin ("rkward::wilcoxon_exact_test", alternative.string="two.sided", confint.state="TRUE", conflevel.real="0.95000000", correct.state="FALSE", exact.string="yes", mu.real="0.00000000", x.available="test50x", y.available="", submit.mode="submit")
+
+ rk.call.plugin ("rkward::wilcoxon_exact_test", alternative.string="less", confint.state="FALSE", correct.state="TRUE", exact.string="automatic", mu.real="0.00000000", paired.state="TRUE", x.available="test50x", y.available="test50y", submit.mode="submit")
+ }, libraries=c ("exactRankTests"))
), postCalls = list ( # like initCalls: run after all tests to clean up.
function () {
suppressWarnings (rm (list=c ("women", "warpbreaks", "rock", "test50x", "test50y", "test50z", "test10x", "test10y", "test10z"), envir=globalenv()))
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