# [rkward-cvs] SF.net SVN: rkward:[4042] branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted

tfry at users.sourceforge.net tfry at users.sourceforge.net
Tue Nov 22 15:34:17 UTC 2011

Revision: 4042
http://rkward.svn.sourceforge.net/rkward/?rev=4042&view=rev
Author:   tfry
Date:     2011-11-22 15:34:16 +0000 (Tue, 22 Nov 2011)
Log Message:
-----------
More work on figure placement. NOTE: JSS does not allow 'h' placement, as far as I understand. NOTE: example_session.tex still needs adjustment.

For reference, here are the instructions we received during the pre-screening phase:
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
placement. If a figure then ends up before the start of its (sub)section,
"t!" should be changed to "b!".  e.g., {figure}[b!].

Modified Paths:
--------------
branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/GUI_elements.tex
branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/background.tex

Modified: branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/GUI_elements.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/GUI_elements.tex	2011-11-22 12:57:51 UTC (rev 4041)
+++ branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/GUI_elements.tex	2011-11-22 15:34:16 UTC (rev 4042)
@@ -63,7 +63,7 @@
window.
}.

-\begin{figure}[hb!]
+\begin{figure}[t!]
\centering
\includegraphics[width=15.450cm]{./figures/main_window.png}
\caption{Default \pkg{RKWard} main window after start up.
@@ -153,7 +153,7 @@
The editor automatically saves snapshots of the
currently edited files at configurable intervals.

-\begin{figure}[ht!]
+\begin{figure}[b!]
\centering
\includegraphics[width=15.5cm]{./figures/code_hinting.png}
\caption{Code hinting features of the script editor. The script editor is able to hint A) \proglang{R} object names
@@ -180,9 +180,9 @@
for inclusion in an \proglang{R} script, optionally

-\begin{figure}[hb]
+\begin{figure}[b!]
\centering
- \includegraphics[width=9.0cm]{./figures/special_paste.png}
+ \includegraphics[width=7.5cm]{./figures/special_paste.png}
\caption{Paste special dialog. This tool allows to paste data (e.\,g., tabular, text) from the clipboard, directly to an
\proglang{R} script and therefore accelerates the work process with data from different sources
@@ -190,7 +190,6 @@
\label{fig:special_paste}
\end{figure}

-\newpage
Script editor windows can be created by opening an existing
\proglang{R} script file from the file browser, the
File'' menu, or by creating a new empty script. It can
@@ -236,6 +235,19 @@
\proglang{R} code, the function \code{rk.edit()} can be used.
Figure~\ref{fig:data_editors} shows multiple \code{data.frame}s open for editing.

+\begin{figure}[t!]
+ \centering
+ \includegraphics[width=15.5cm]{./figures/data_editors.png}
+ \caption{\pkg{RKWard} with several \code{data.frame}s in use at the same time. A)
+  One \code{data.frame} (\code{CO2} data of the \pkg{datasets} package) is opened for editing in the main window. Two further \code{data.frame}s
+  are opened in the background in tabs.
+  B) Another \code{data.frame} (\code{ChickWeight}) is opened in a detached window.
+  C) \proglang{R}'s standard data editing features (e.\,g., \code{fix()}, \code{edit()})
+  are also usable in \pkg{RKWard}. In this example \code{fix(DNase)}
+  was invoked from the console (arrow).}
+ \label{fig:data_editors}
+\end{figure}
+
Metadata on each column of a \code{data.frame} (i.\,e., name of the column, data
type, and potentially data labels) is shown in the upper portion of
the data editor, and can be manipulated there, while the data itself is
@@ -263,19 +275,6 @@
user can manually convert the storage mode of a column by simply
selecting a different data type in the Type'' row of the meta information.

-\begin{figure}[ht]
- \centering
- \includegraphics[width=15.5cm]{./figures/data_editors.png}
- \caption{\pkg{RKWard} with several \code{data.frame}s in use at the same time. A)
-  One \code{data.frame} (\code{CO2} data of the \pkg{datasets} package) is opened for editing in the main window. Two further \code{data.frame}s
-  are opened in the background in tabs.
-  B) Another \code{data.frame} (\code{ChickWeight}) is opened in a detached window.
-  C) \proglang{R}'s standard data editing features (e.\,g., \code{fix()}, \code{edit()})
-  are also usable in \pkg{RKWard}. In this example \code{fix(DNase)}
-  was invoked from the console (arrow).}
- \label{fig:data_editors}
-\end{figure}
-
The data editor supports insertion and deletion of rows or columns at
arbitrary positions. Rows (columns) can also be added at the bottom
(right) by simply entering data into the trailing row (column) shown in
@@ -337,7 +336,7 @@
selected. The Close'' button will close the
dialog without taking any action.

-\begin{figure}[hb!]
+\begin{figure}[b!]
\centering
\includegraphics[width=14.99cm]{./figures/CSV_import.png}
\caption{General data import dialog. Useful defaults for a variety of formats can
@@ -374,7 +373,7 @@
and adding a grid to an existing plot
(works on only certain types of plots).

-\begin{figure}[ht!]
+\begin{figure}[b!]
\centering
\includegraphics{./figures/plot_history_cropped.png}
\caption{On{}-screen graphics device window in \pkg{RKWard}. The plot history is
@@ -444,6 +443,21 @@
data, providing benefits similar to, for example, the automated report generation
available from \pkg{RreportGenerator} \citep{RaffelsbergerW2008}.

+\begin{figure}[t!]
+ \centering
+ \includegraphics[width=15.5cm]{./figures/results_output_cropped.png}
+ \caption{Sample contents of the output window. Upper portion: Result of analyzing sample data (from the
+\code{DNase} and \code{ChickWeight}
+  datasets of the \pkg{datasets} package) in the Descriptive Statistics'' plugin. Standard elements of
+  plugin output include a standardized header, and a  Run again''-link, which allows to repeat the
+  analysis with identical or similar parameters. Lower portion: A custom heading added using the
+  \code{rk.header()} function, and a short transcript of R code with corresponding output.}
+% TF: Stefan: I've removed the bit below. It was not really designed to allow this, and for the more complex plugins, this is fairly useless,
+% since only a fraction of the options will fit in the status bar:
+% (Details of the previous analysis are shown in the status bar when the mouse pointer hovers over the Run again''-link)
+ \label{fig:results_output}
+\end{figure}
+
The formatting of output is kept to a minimum. In particular,
\pkg{RKWard} is very reluctant to round numerical results for the sake of a
pretty output. Rather, the focus is on making the results easily
@@ -477,21 +491,6 @@
the \pkg{RKWard} output window, including syntax highlighting (see the lower portion of
Figure~\ref{fig:results_output}).

-\begin{figure}[hb!]
- \centering
- \includegraphics[width=15.5cm]{./figures/results_output_cropped.png}
- \caption{Sample contents of the output window. Upper portion: Result of analyzing sample data (from the
-\code{DNase} and \code{ChickWeight}
-  datasets of the \pkg{datasets} package) in the Descriptive Statistics'' plugin. Standard elements of
-  plugin output include a standardized header, and a  Run again''-link, which allows to repeat the
-  analysis with identical or similar parameters. Lower portion: A custom heading added using the
-  \code{rk.header()} function, and a short transcript of R code with corresponding output.}
-% TF: Stefan: I've removed the bit below. It was not really designed to allow this, and for the more complex plugins, this is fairly useless,
-% since only a fraction of the options will fit in the status bar:
-% (Details of the previous analysis are shown in the status bar when the mouse pointer hovers over the Run again''-link)
- \label{fig:results_output}
-\end{figure}
-
\subsection{Package management}
\label{sec:package_management}
The number of \proglang{R} packages available from the comprehensive \proglang{R} archive

Modified: branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/background.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/background.tex	2011-11-22 12:57:51 UTC (rev 4041)
+++ branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/background.tex	2011-11-22 15:34:16 UTC (rev 4042)
@@ -94,7 +94,7 @@
design, and reasons for certain design decisions, a technical supplement to this article
is available.

-\begin{figure}[hb!]
+\begin{figure}[b!]
\centering
\includegraphics[clip=true,trim=0cm 5.7cm 0cm 5.7cm,width=15.4cm]{./figures/timeline.pdf}
\caption{Timeline of important development milestones and changes in \pkg{RKWard}.

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