[rkward-cvs] SF.net SVN: rkward:[3313] branches/jss_dec_10/FINAL_JSS_TEX

kapatp at users.sourceforge.net kapatp at users.sourceforge.net
Fri Dec 24 06:32:29 UTC 2010

Revision: 3313
http://rkward.svn.sourceforge.net/rkward/?rev=3313&view=rev
Author:   kapatp
Date:     2010-12-24 06:32:29 +0000 (Fri, 24 Dec 2010)

Log Message:
-----------

Modified Paths:
--------------
branches/jss_dec_10/FINAL_JSS_TEX/RKWard_paper.tex
branches/jss_dec_10/FINAL_JSS_TEX/example_session.tex

Modified: branches/jss_dec_10/FINAL_JSS_TEX/RKWard_paper.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/RKWard_paper.tex	2010-12-24 04:41:58 UTC (rev 3312)
+++ branches/jss_dec_10/FINAL_JSS_TEX/RKWard_paper.tex	2010-12-24 06:32:29 UTC (rev 3313)
@@ -3,6 +3,8 @@
%% declarations for jss.cls %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

+\usepackage{amssymb}
+
%% almost as usual
\author{Stefan R\"odiger$^{\ddag,\S}$\\L.U.A.S. \& Charit\'e
\And ~	% HACK to avoid over-printing of names

Modified: branches/jss_dec_10/FINAL_JSS_TEX/example_session.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/example_session.tex	2010-12-24 04:41:58 UTC (rev 3312)
+++ branches/jss_dec_10/FINAL_JSS_TEX/example_session.tex	2010-12-24 06:32:29 UTC (rev 3313)
@@ -1,31 +1,32 @@
+% !TEX root = RKWard_paper.tex
\section{Using RKWard - an example RKWard session}
\label{sec:using_RKWard}
This section describes an example RKWard session, in order to give an idea
-what working with RKWard is like in practice.
+of what working with RKWard is like in practice.
The session is organized along the routine tasks of importing,
-analyzing, and visualizing data. In this example, we assume that an experimental
-treatment was given to 20 test subjects and the values of the dependent
-variable before and after the treatment should be compared.
+analyzing, and visualizing data. In this example, it is assumed that an experimental
+treatment was given to 20 test subjects and the objective is to compare the responses
+before and after the treatment.

\subsection{Importing data}
\label{sec:importing_data}
-Data which was saved as or exported to CSV format for example from a
-spread sheet application. RKWard's import plugin can
+Suppose that the data was saved as or exported to CSV format, for example, from a
+spreadsheet application. RKWard's import plugin can
comfortably read it into a new \proglang{R} object.
-The import dialog (File->Import->Import
-format->Import Text / CSV data'') assists during the
-selection of the data by a common point and click interface (Figure~\ref{fig:import_data}A). Within our
-example comma'' and period'' were chosen via Quick mode'' as field
-separator character and decimal point character respectively.
+The import dialog (File$\rightarrow$Import$\rightarrow$Import
+format$\rightarrow$Import Text / CSV data'') assists in reading the
+data by a common point and click interface (Figure~\ref{fig:import_data}A). In this
+example, comma'' and period'' were chosen via Quick mode'' as the field
+separator and decimal point characters respectively.

-The corresponding \proglang{R} code would read as:
+The generated \proglang{R} code can be revealed by clicking on the Code'' button:

-na.strings = NA, nrows = -1, skip = 0,
-check.names = TRUE, strip.white = FALSE, blank.lines.skip = TRUE)}
+\code{read.csv(file=/media/software/experiment.txt',
+na.strings = NA', nrows = -1, skip = 0,
+check.names = TRUE, strip.white = FALSE, blank.lines.skip = TRUE)\\}

-Checking the Edit Object'' box will automatically open a data editor tab
+Checking the Edit Object'' box automatically opens a data editor tab
showing the imported data (Figure~\ref{fig:import_data}B).

\begin{figure}[htp]
@@ -39,49 +40,50 @@

\subsection{Conducting a Student's t-test}
\label{sec:conducting_ttest}
-To test the hypothesis that the given treatment significantly increased
-the values of the dependent variable, a Student's
-t-test for a paired sample is applied. In the variable slot on the left
-side you select the variables from the unfolded
-\proglang{R} object containing the table of imported data (Figure~\ref{fig:t_test}A).
+To test the hypothesis that the given treatment significantly increased the response, a Student's
+t-test for a paired sample is conducted using the
+Analysis$\rightarrow$Means$\rightarrow$t-Tests$\rightarrow$Two variable t-test'' plugin.
+In the object browser on the left side the two variables from the expanded
+\proglang{R} object containing the table of imported data
+are selected (Figure~\ref{fig:t_test}A).
+Pressing the Submit'' button opens the output document tab
+showing the results (Figure~\ref{fig:t_test}B).

\begin{figure}[htp]
\centering
\includegraphics[width=15.5cm]{../figures/t-test.png}
- \caption{A) Student's t-test dialog for a two variables. B) Test results in tabular \proglang{HTML} format.
-Besides the result information like the date of analysis and relevant test parameters are reported.}
+ \caption{A) Student's t-test dialog for two variables. B) Test results in tabular \proglang{HTML} format.
+Besides the result, information such as the date of analysis and the relevant test parameters are also reported.}
\label{fig:t_test}
\end{figure}

-After the Submit'' button was pressed, RKWard opens the output document
-to show the results (Figure~\ref{fig:t_test}B).

+
\subsection{Creating a plot}
\label{sec:create_plot}
-To visualize the test data, Boxplot'' is chosen from the Plots'' menu
-and variables selected are as for the Student's t-test.
+To visualize the data, Boxplot'' is chosen from the Plots'' menu
+and the two variables, corresponding to the t-test above, are selected.
The dialog allows to define custom variable labels (Figure~\ref{fig:boxplot1}).
+Checking the Preview'' box opens a graphics window showing the boxplot as
+it is configured and updates the window, in real time, on any changes to plot parameters. From
+that window, the plot can then be exported to several image formats (Figure~\ref{fig:boxplot2}).

\begin{figure}[htp]
\centering
\includegraphics[width=15.5cm]{../figures/boxplot1.png}
- \caption{Boxplot dialog. The first tab (Variables) is used to select a set of data for analysis. It is possible to
-  combine any data present in the .GloabelEnv. The second tab (''Options'') allows further adjustments (e.g the addition
-  of mean and standard deviation) of the plot (not shown).}
+ \caption{Boxplot dialog. The first tab (Variables'') is used to select the variables for analysis. It is possible to
+  combine any data present in the .GlobalEnv. The second tab (Options'') allows further adjustments (e.g the addition
+  of mean and standard deviation) to the plot (not shown).}
\label{fig:boxplot1}
\end{figure}

-Checking the Preview'' box will open a graphics window, show the plot as
-it is configured and update the window on changes in real time. From
-that window it can be exported directly to several data formats as
-well (Figure~\ref{fig:boxplot2}).

\begin{figure}[htp]
\centering
\includegraphics[width=15.5cm]{../figures/boxplot2.png}
- \caption{Plotted data and plot export dialog. The export dialog provides numerous
+ \caption{Plotted data and plot export dialog. The export dialog (Device$\rightarrow$Export'') provides numerous
options like resolution and size for different vector formats (e.g. SVG, PDF) and
-  pixel formats (e.g. PNG, JPG). Note: The RKWard boxplot plugin was extended to present optionally
-  the mean (square) and standard deviation (cross) for all data.}
+  pixel formats (e.g. PNG, JPG). (Note: For the shown figure, the optional
+  mean ($\blacksquare$) and standard deviation ($+$) parameters were selected in the boxplot plugin.)}
\label{fig:boxplot2}
\end{figure}

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