[rkward-cvs] SF.net SVN: rkward:[3371] branches/jss_dec_10
tfry at users.sourceforge.net
tfry at users.sourceforge.net
Thu Jan 20 17:01:10 UTC 2011
Revision: 3371
http://rkward.svn.sourceforge.net/rkward/?rev=3371&view=rev
Author: tfry
Date: 2011-01-20 17:01:10 +0000 (Thu, 20 Jan 2011)
Log Message:
-----------
Add plugin example
Modified Paths:
--------------
branches/jss_dec_10/FINAL_JSS_TEX/example_plugin.tex
branches/jss_dec_10/FINAL_JSS_TEX/revision_notes.txt
Added Paths:
-----------
branches/jss_dec_10/examples/plugin_demo/demo.pluginmap
branches/jss_dec_10/examples/plugin_demo/demo_t_test_two_vars.js
branches/jss_dec_10/examples/plugin_demo/demo_t_test_two_vars.rkh
branches/jss_dec_10/examples/plugin_demo/demo_t_test_two_vars.xml
Modified: branches/jss_dec_10/FINAL_JSS_TEX/example_plugin.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/example_plugin.tex 2011-01-20 16:47:03 UTC (rev 3370)
+++ branches/jss_dec_10/FINAL_JSS_TEX/example_plugin.tex 2011-01-20 17:01:10 UTC (rev 3371)
@@ -24,7 +24,7 @@
<document base_prefix="" namespace="rkward">
<components>
<component type="standard" id="t_test_two_vars"
- file="analysis/t_test_two_vars.xml" label="Two Variable t-test" />
+ file="demo_t_test_two_vars.xml" label="Two Variable t-test" />
</components>
<hierarchy>
@@ -67,8 +67,8 @@
\begin{Code}
<!DOCTYPE rkplugin>
<document>
- <code file="t_test_two_vars.js"/>
- <help file="t_test_two_vars.rkh"/>
+ <code file="demo_t_test_two_vars.js"/>
+ <help file="demo_t_test_two_vars.rkh"/>
<logic>
<connect client="varequal.enabled" governor="paired.not"/>
Modified: branches/jss_dec_10/FINAL_JSS_TEX/revision_notes.txt
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/revision_notes.txt 2011-01-20 16:47:03 UTC (rev 3370)
+++ branches/jss_dec_10/FINAL_JSS_TEX/revision_notes.txt 2011-01-20 17:01:10 UTC (rev 3371)
@@ -5,6 +5,32 @@
o In itemized/bullet lists please capitalize the first word of the item.
+o All code comments (#) should be removed and incorporated within the text
+of the manuscript.
+
+--- Notes from JSS that we have addressed, but which we are not entirely sure about ---
+
+Code:
+Please include a standalone replication script of all code/examples
+used within the manuscript
+
+We now provide
+- An R script to be run inside an RKWard session, which will replicate the
+examples from Sections 3, 4, and 5. Note that since most of these examples
+are concerned with interactive GUI elements, the script itself is interactive,
+and will prompt the user to perform certain actions, manually.
+- A sample data file used in Section 5. Since one example is concerned with
+importing this data file, the data cannot simply be inlined in the R script.
+- A set of files to replicate the plugin example in Section 6. These files
+cannot meaningfully be integrated into a standalone script.
+- A file README.txt with further instructions on using the examples.
+
+The scripts and files are only meaningful when used inside an RKWard session,
+not in a plain R session.
+
+Source code for RKWard 0.5.4 can be obtained from
+http://sourceforge.net/projects/rkward/files/Current_Stable_Releases/rkward-0.5.4.tar.gz/download .
+
--- Notes from JSS that we have not addressed, yet ---
Manuscript:
@@ -30,10 +56,6 @@
o please check all abbreviations
- see our notes below
-o All code comments (#) should be removed and incorporated within the text
-of the manuscript.
-
-
o Figure placement (i.e. placement of floating objects):
The {figure} or {table} environment should be close to the first
reference in the manuscript. It should first use the "t!" option for
@@ -43,11 +65,7 @@
References
- Java (not: JAVA, java)
-Code:
-Please include a standalone replication script of all code/examples
-used within the manuscript
-
--- Items that we are not sure about ---
---- Use of the \proglang macro ----
In several cases, we are not entirely sure, whether the use of the \proglang macro is called for or not.
Added: branches/jss_dec_10/examples/plugin_demo/demo.pluginmap
===================================================================
--- branches/jss_dec_10/examples/plugin_demo/demo.pluginmap (rev 0)
+++ branches/jss_dec_10/examples/plugin_demo/demo.pluginmap 2011-01-20 17:01:10 UTC (rev 3371)
@@ -0,0 +1,18 @@
+<!DOCTYPE rkpluginmap>
+
+<document base_prefix="" namespace="rkward">
+ <components>
+ <component type="standard" id="t_test_two_vars"
+ file="demo_t_test_two_vars.xml" label="Two Variable t-test" />
+ </components>
+
+ <hierarchy>
+ <menu id="analysis" label="Analysis" index="4">
+ <menu id="means" label="Means" index="4">
+ <menu id="ttests" label="t-Tests">
+ <entry component="t_test_two_vars" />
+ </menu>
+ </menu>
+ </menu>
+ </hierarchy>
+</document>
Added: branches/jss_dec_10/examples/plugin_demo/demo_t_test_two_vars.js
===================================================================
--- branches/jss_dec_10/examples/plugin_demo/demo_t_test_two_vars.js (rev 0)
+++ branches/jss_dec_10/examples/plugin_demo/demo_t_test_two_vars.js 2011-01-20 17:01:10 UTC (rev 3371)
@@ -0,0 +1,53 @@
+// globals
+var x;
+var y;
+var varequal;
+var paired;
+
+function preprocess () {
+ x = getValue ("x");
+ y = getValue ("y");
+
+ echo ('names <- rk.get.description (' + x + ", " + y + ')\n');
+}
+
+function calculate () {
+ varequal = getValue ("varequal");
+ paired = getValue ("paired");
+
+ var conflevel = getValue ("conflevel");
+ var hypothesis = getValue ("hypothesis");
+
+ var options = ", alternative=\"" + hypothesis + "\"";
+ if (paired) options += ", paired=TRUE";
+ if ((!paired) && varequal) options += ", var.equal=TRUE";
+ if (conflevel != "0.95") options += ", conf.level=" + conflevel;
+
+ echo ('result <- t.test (' + x + ", " + y + options + ')\n');
+}
+
+function printout () {
+ echo ('rk.header (result\$method, \n');
+ echo (' parameters=list ("Comparing", paste (names[1], "against", names[2]),\n');
+ echo (' "H1", rk.describe.alternative (result)');
+ if (!paired) {
+ echo (',\n');
+ echo (' "Equal variances", "');
+ if (!varequal) echo ("not");
+ echo (' assumed"');
+ }
+ echo ('))\n');
+ echo ('\n');
+ echo ('rk.results (list (\n');
+ echo (' \'Variable Name\'=names,\n');
+ echo (' \'estimated mean\'=result\$estimate,\n');
+ echo (' \'degrees of freedom\'=result\$parameter,\n');
+ echo (' t=result\$statistic,\n');
+ echo (' p=result\$p.value');
+ if (getValue ("confint")) {
+ echo (',\n');
+ echo (' \'confidence interval percent\'=(100 * attr(result\$conf.int, "conf.level")),\n');
+ echo (' \'confidence interval of difference\'=result\$conf.int ');
+ }
+ echo ('))\n');
+}
Added: branches/jss_dec_10/examples/plugin_demo/demo_t_test_two_vars.rkh
===================================================================
--- branches/jss_dec_10/examples/plugin_demo/demo_t_test_two_vars.rkh (rev 0)
+++ branches/jss_dec_10/examples/plugin_demo/demo_t_test_two_vars.rkh 2011-01-20 17:01:10 UTC (rev 3371)
@@ -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 variables are paired (repeated measurements on the same subject) or independent samples. 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://component/F_test"/></li>
+ <li><link href="rkward://rhelp/t.test"/></li>
+ </ul>
+ </related>
+</document>
Added: branches/jss_dec_10/examples/plugin_demo/demo_t_test_two_vars.xml
===================================================================
--- branches/jss_dec_10/examples/plugin_demo/demo_t_test_two_vars.xml (rev 0)
+++ branches/jss_dec_10/examples/plugin_demo/demo_t_test_two_vars.xml 2011-01-20 17:01:10 UTC (rev 3371)
@@ -0,0 +1,42 @@
+<!DOCTYPE rkplugin>
+<document>
+ <code file="demo_t_test_two_vars.js"/>
+ <help file="demo_t_test_two_vars.rkh"/>
+
+ <logic>
+ <connect client="varequal.enabled" governor="paired.not"/>
+ </logic>
+
+ <dialog label="Two Variable t-Test">
+ <tabbook>
+ <tab label="Basic settings" id="tab_variables">
+ <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" id="tab_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>
+</document>
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