[rkward-cvs] SF.net SVN: rkward:[3344] branches/jss_dec_10/FINAL_JSS_TEX
tfry at users.sourceforge.net
tfry at users.sourceforge.net
Tue Dec 28 12:57:17 UTC 2010
Revision: 3344
http://rkward.svn.sourceforge.net/rkward/?rev=3344&view=rev
Author: tfry
Date: 2010-12-28 12:57:16 +0000 (Tue, 28 Dec 2010)
Log Message:
-----------
More editing esp. in the second half of the paper.
Largest change is to remove the text-version of the generated code for the t-test.
Modified Paths:
--------------
branches/jss_dec_10/FINAL_JSS_TEX/GUI_elements.tex
branches/jss_dec_10/FINAL_JSS_TEX/conclusion_summary_acknowledgments.tex
branches/jss_dec_10/FINAL_JSS_TEX/example_plugin.tex
branches/jss_dec_10/FINAL_JSS_TEX/installing_starting_RKWard.tex
branches/jss_dec_10/FINAL_JSS_TEX/technical.tex
Modified: branches/jss_dec_10/FINAL_JSS_TEX/GUI_elements.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/GUI_elements.tex 2010-12-28 07:55:56 UTC (rev 3343)
+++ branches/jss_dec_10/FINAL_JSS_TEX/GUI_elements.tex 2010-12-28 12:57:16 UTC (rev 3344)
@@ -25,7 +25,7 @@
\caption{Default RKWard main window after start up.
A) Menubar and toolbar, B) tool panel showing workspace browser, C) main view area, showing
a help page D) tool panel showing embedded \proglang{R} console E) tool buttons, and status bar.
-Panels B) and D) can be resized or collapsed. Note the red square (B) indicates the active interface element.}
+Panels B) and D) can be resized or collapsed. The red border around (B) indicates that the workspace browser is the active interface element.}
\label{fig:main_window}
\end{figure}
Modified: branches/jss_dec_10/FINAL_JSS_TEX/conclusion_summary_acknowledgments.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/conclusion_summary_acknowledgments.tex 2010-12-28 07:55:56 UTC (rev 3343)
+++ branches/jss_dec_10/FINAL_JSS_TEX/conclusion_summary_acknowledgments.tex 2010-12-28 12:57:16 UTC (rev 3344)
@@ -4,7 +4,7 @@
from easy to use dialogs for common statistical procedures targeted at \proglang{R} novices, to advanced
IDE features targeted at \proglang{R} experts.
-RKWard tries to empower users of all knowledge levels to make more efficient use of the
+RKWard aims to empower users of all knowledge levels to make more efficient use of the
\proglang{R} programming language, while carefully avoiding to lock in users to a specific
GUI solution. In particular, RKWard
\begin{itemize}
@@ -17,14 +17,14 @@
Future versions of RKWard will continue to add value for both groups of users. Planned features include
an enhanced interface for debugging \proglang{R} code, support for editing more types of data, and the
ability to connect the RKWard GUI to a remote \proglang{R} engine. Perhaps most importantly, RKWard will
-gain many new User Interface dialogs for manipulation, analysis, and visualization of data. The ability to
+gain many new graphical dialogs for manipulation, analysis, and visualization of data. The ability to
develop these dialogs as plugins allows to develop and distribute GUI dialogs
independently of the RKWard core application, allowing any user to help in enhancing RKWard, without in-depth
programming knowledge.
\section{Acknowledgments}
\label{sec:acknowledgments}
-The software RKWard, described in this paper, is currently developed by Thomas Friedrichsmeier (lead developer), Prasenjit Kapat, Meik Michalke,
+The software RKWard, presented in this paper, is currently developed by Thomas Friedrichsmeier (lead developer), Prasenjit Kapat, Meik Michalke,
and Stefan R\"odiger. Many more people have contributed, or are still contributing to the project in various forms. We would like to
thank (in alphabetical order) Adrien d'Hardemare, Daniele Medri, David Sibai, Detlef Steuer, Germ\'an M\'arquez Mej\'ia,
Ilias Soumpasis, Jannis Vajen, Marco Martin, Philippe Grosjean, Pierre Ecochard, Ralf Tautenhahn, Roland Vollgraf, Roy Qu,
Modified: branches/jss_dec_10/FINAL_JSS_TEX/example_plugin.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/example_plugin.tex 2010-12-28 07:55:56 UTC (rev 3343)
+++ branches/jss_dec_10/FINAL_JSS_TEX/example_plugin.tex 2010-12-28 12:57:16 UTC (rev 3344)
@@ -1,5 +1,5 @@
% !TEX root = RKWard_paper.tex
-\section{Extending RKWard - an example of creating a plugin}
+\section{Extending RKWard -- an example of creating a plugin}
\label{sec:example_plugin}
As discussed in Section~\ref{sec:technical_plugins}, plugins in RKWard are
defined by four separate files (Figure~\ref{fig:plugin_structure}). To give an impression of the technique,
@@ -9,10 +9,10 @@
\subsection{Defining the menu hierarchy}
\label{sec:defining_menu_hierarchy}
A so called ``.pluginmap'' file declares each plugin, and, if appropriate, defines where it should
-be placed in the menu hierarchy. Usually each .pluginmap-file declares many plugins. In this example
-we only show one, namely, the definition entry for a two variable t-test (see Figure~\ref{fig:ttest-gui-example}).
+be placed in the menu hierarchy. Usually each .pluginmap file declares many plugins. In this example
+we only show one, namely, a two variable t-test (see Figure~\ref{fig:ttest-gui-example}).
The pluginmap (\code{<!DOCTYPE rkpluginmap>}) gives a unique identifier (``id"), the location of the GUI description (``file"), and the window title (``label''). The menu
-is defined in a hierarchical structure (see code example below\footnote{Long lines are broken at ``$\ldots~\ldots$''.}). Moreover, the position within the menu can be explicitly defined.
+is defined in a hierarchical structure, as shown in the code example below\footnote{Long lines are broken at ``$\ldots~\ldots$''.}. Moreover, the position within the menu can be explicitly defined.
This might be required if the menu entries are to be ordered non-alphabetically.
\begin{footnotesize}
@@ -45,7 +45,7 @@
\begin{figure}[htp]
\centering
\includegraphics{../figures/ttest-gui-example.png}
- \caption{Generated menu GUI as defined by the plugin map.}
+ \caption{Generated menu structure as defined by the plugin map.}
\label{fig:ttest-gui-example}
\end{figure}
@@ -55,13 +55,13 @@
The main \proglang{XML} file of each plugin defines the layout and behavior of the GUI, and references the
\proglang{ECMAScript} file that is used for generating \proglang{R} code from UI settings and the help file (not included in this paper).
-Some GUI behavior can also be scripted in \proglang{ECMAScript}. In this example, the logic is defined in \proglang{XML} (the ``Assume equal variances'' checkbox
-is only enabled for paired sample tests).
+GUI logic can be defined directly in the \proglang{XML} file. In this example, the ``Assume equal variances'' checkbox
+is only enabled for paired sample tests. Optionally, GUI behavior can also be scripted in \proglang{ECMAScript}.
-The \proglang{XML} file defines the t-test plugin (\code{<!DOCTYPE rkplugin>}) to be organized in two tabs (Figure~\ref{fig:t_test}A) asking for the variables
-to analyze in the first tab and optionally in the second tab for specific settings like the confidence level (default 0.95). Note that this \proglang{XML} file
-also invokes the \proglang{XML} help file. Two variables can be selected (\code{<varslot .../>}). These are set to be ``required'', i.\,e.
-the ``Submit'' button will remain disabled until the user has made a valid selection for both.
+The \proglang{XML} file defines the t-test plugin (\code{<!DOCTYPE rkplugin>}) to be organized in two tabs (Figure~\ref{fig:t_test}A).
+On the first tab, two variables can be selected (\code{<varslot .../>}). These are set to be ``required'', i.\,e.
+the ``Submit'' button will remain disabled until the user has made a valid selection for both. The second tab includes some
+additional settings like the confidence level (default 0.95).
\begin{footnotesize}
\begin{Code}
@@ -113,8 +113,9 @@
\subsection{Generating R code from UI settings}
\label{sec:generating_r_code_from_ui_settings}
-A simple \proglang{ECMAScript} script is used to generate \proglang{R} code from UI settings (using \code{echo()} commands).
-Generated code for each plugin is divided into three sections: ``Preprocess'', ``Calculate'', and ``Printout'', although each
+A simple \proglang{ECMAScript} script is used to generate \proglang{R} code from UI settings (using \code{echo()} commands)\footnote{
+ See Figure~\ref{fig:t_test}) for code generated in this example.
+}. Generated code for each plugin is divided into three sections: ``Preprocess'', ``Calculate'', and ``Printout'', although each
may be empty.
\begin{footnotesize}
@@ -175,32 +176,34 @@
\end{Code}
\end{footnotesize}
-The generated code readable by the user is the following \proglang{R} code (code below and Figure~\ref{fig:t_test}).
-Here, \code{rk.header} and \code{rk.results}
-are RKWard functions provided by the package \pkg{rkward}. In case the package is installed the code below
-can be run from any \proglang{R} engine.
-
-\begin{footnotesize}
-\begin{Code}
-local({
-## Prepare
-names <- rk.get.description (my.csv.data[["before"]], my.csv.data[["after"]])
-## Compute
-result <- t.test (my.csv.data[["before"]], my.csv.data[["after"]], alternative="less", paired=TRUE)
-## Print result
-rk.header (result$method,
- parameters=list ("Comparing", paste (names[1], "against", names[2]),
- "H1", rk.describe.alternative (result)))
-
-rk.results (list (
- 'Variable Name'=names,
- 'estimated mean'=result$estimate,
- 'degrees of freedom'=result$parameter,
- t=result$statistic,
- p=result$p.value,
- 'confidence interval percent'=(100 * attr(result$conf.int, "conf.level")),
- 'confidence interval of difference'=result$conf.int ))
-})
-
-\end{Code}
-\end{footnotesize}
\ No newline at end of file
+%% TF: I think this part is redundant. Instead, for the curious, I've added a footnote above, referring to the t_test-figure.
+%% ----
+% The generated code readable by the user is the following \proglang{R} code (code below and Figure~\ref{fig:t_test}).
+% Here, \code{rk.header} and \code{rk.results}
+% are RKWard functions provided by the package \pkg{rkward}. In case the package is installed the code below
+% can be run from any \proglang{R} engine.
+%
+% \begin{footnotesize}
+% \begin{Code}
+% local({
+% ## Prepare
+% names <- rk.get.description (my.csv.data[["before"]], my.csv.data[["after"]])
+% ## Compute
+% result <- t.test (my.csv.data[["before"]], my.csv.data[["after"]], alternative="less", paired=TRUE)
+% ## Print result
+% rk.header (result\$method,
+% parameters=list ("Comparing", paste (names[1], "against", names[2]),
+% "H1", rk.describe.alternative (result)))
+%
+% rk.results (list (
+% 'Variable Name'=names,
+% 'estimated mean'=result\$estimate,
+% 'degrees of freedom'=result\$parameter,
+% t=result\$statistic,
+% p=result\$p.value,
+% 'confidence interval percent'=(100 * attr(result\$conf.int, "conf.level")),
+% 'confidence interval of difference'=result\$conf.int ))
+% })
+%
+% \end{Code}
+% \end{footnotesize}
Modified: branches/jss_dec_10/FINAL_JSS_TEX/installing_starting_RKWard.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/installing_starting_RKWard.tex 2010-12-28 07:55:56 UTC (rev 3343)
+++ branches/jss_dec_10/FINAL_JSS_TEX/installing_starting_RKWard.tex 2010-12-28 12:57:16 UTC (rev 3344)
@@ -8,7 +8,7 @@
\proglang{R} and \proglang{KDE}) and
as an installation bundle (including \proglang{R} and
essential parts of the \proglang{KDE} SC)\footnote{For detailed information please refer to the
-RKWard wiki \url{http://sourceforge.net/apps/mediawiki/rkward/index.php?title=Main_Page}.}. At the time of
+RKWard wiki \url{http://p.sf.net/rkward/windows}.}. At the time of
this writing, the developers lack the resources to support a Mac OS X
port, and especially to provide binaries for Mac OS X. However, RKWard
has been shown to be compilable and installable on the Mac, and appears
Modified: branches/jss_dec_10/FINAL_JSS_TEX/technical.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/technical.tex 2010-12-28 07:55:56 UTC (rev 3343)
+++ branches/jss_dec_10/FINAL_JSS_TEX/technical.tex 2010-12-28 12:57:16 UTC (rev 3344)
@@ -39,9 +39,8 @@
Specifically, objects which would usually be ``lazy loaded'' only when needed \citep[see][]{Ripley2004} are
accessed in order to fetch information on their properties. This means the data
has to be loaded from disk; however, the memory is freed immediately after fetching
-information on the object. Additionally, as an override switch, RKWard provides an option
-to list packages which will not be scanned pro-actively for object structures when loaded.
-%% PK: Thomas can you verify/modify/delete the above sentence?
+information on the object. Additionally, for packages with extremely many objects, RKWard
+provides an option to exclude specific packages from scanning the object structures.
A further side-effect of the asynchronous threaded design is that there is
inherently a rather clear separation between the GUI code and the code making direct use
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