[rkward-cvs] SF.net SVN: rkward:[4214] branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted
sjar at users.sourceforge.net
sjar at users.sourceforge.net
Fri Apr 27 17:07:17 UTC 2012
Revision: 4214
http://rkward.svn.sourceforge.net/rkward/?rev=4214&view=rev
Author: sjar
Date: 2012-04-27 17:07:17 +0000 (Fri, 27 Apr 2012)
Log Message:
-----------
Changes to final request of the editor
Modified Paths:
--------------
branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/GUI_elements.tex
branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/RKWard_annex.tex
branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/RKWard_paper.tex
branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/annex_figures_extended.tex
branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/background.tex
branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/example_plugin.tex
branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/example_session.tex
branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/installing_starting_RKWard.tex
branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/sources.bib
branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/technical.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 2012-04-26 12:58:17 UTC (rev 4213)
+++ branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/GUI_elements.tex 2012-04-27 17:07:17 UTC (rev 4214)
@@ -9,7 +9,7 @@
} of the main application window is divided into five
parts, as depicted in Figure~\ref{fig:main_window}. The top of the window is occupied by menu bar and toolbar
(Figure~\ref{fig:main_window}A). The content of both bars is partially context
-sensitive, e.\,g., the ``Edit'' menu will offer
+sensitive, e.\,g., the \texttt{Edit} menu will offer
one set of actions when the current document window is a data editor,
and another set of actions for a \proglang{R} script
editor window. To ease orientation, all top level menus remain
@@ -20,7 +20,7 @@
interface.
A status bar is shown at the bottom of the window (Figure~\ref{fig:main_window}E). It displays (from
-right to left) a ``Stop''-button to interrupt the current computations,
+right to left) a \texttt{Stop}-button to interrupt the current computations,
the status of the \proglang{R} engine (busy or idle), the
current working directory, and a multi purpose region for additional
information on some menu items and other GUI elements, visible when
@@ -57,7 +57,7 @@
click, as well as using a series of keyboard shortcuts (defined by
default) for activating specific tool windows, or for cycling through all windows
in the order of most recent usage\footnote{
- This uses the shortcut ``Ctrl+Tab'' by default, and behaves similar to the ``Alt+Tab''
+ This uses the shortcut \texttt{Ctrl+Tab} by default, and behaves similar to the \texttt{Alt+Tab}
feature of common window managers. The difference is that this cycles through \pkg{RKWard} windows,
only, including both detached windows, and windows which are attached inside the main application
window.
@@ -67,29 +67,29 @@
\centering
\includegraphics[width=15.450cm]{./figures/main_window.png}
\caption{Default \pkg{RKWard} main window after start up.
-A) Menu bar and toolbar, B) tool panel showing workspace browser, C) document view area, showing
+(A) Menu bar and toolbar, (B) tool panel showing workspace browser, (C) document view area, showing
different documents (welcome message, \code{data.frame} ``my.data'', ``mean'' help page, \proglang{R}
-script ``demo.R''), D) tool panel showing embedded \proglang{R} console, and E) status bar with an option to
+script \code{demo.R}), (D) tool panel showing embedded \proglang{R} console, and (E) status bar with an option to
stop running processes. 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}
-All key bindings can be configured from the GUI via ``Settings$\rightarrow$Configure Shortcuts''.
+All key bindings can be configured from the GUI via \texttt{Settings$\rightarrow$Configure Shortcuts}.
However, for technical reasons only the shortcuts of currently active components
will be listed. Thus, for example, to
configure data editor shortcuts, one has to open a data editor first and
-then to select ``Settings$\rightarrow$Configure Shortcuts''. Since \pkg{RKWard} relies on the
+then to select \texttt{Settings$\rightarrow$Configure Shortcuts}. Since \pkg{RKWard} relies on the
\pkg{RKWard} editor component,
shortcuts for the script editor (Section~\ref{sec:code_editor}) are managed separately via
-``Settings$\rightarrow$Configure Editor$\rightarrow$Shortcuts''. On most systems, it is also
+\texttt{Settings$\rightarrow$Configure Editor$\rightarrow$Shortcuts}. On most systems, it is also
possible to configure shortcuts by right-clicking on the respective
menu item.
The choice of available actions on the toolbar can be
-configured via ``Settings$\rightarrow$Configure Toolbars''. Further, it is possible to add and remove sets
+configured via \texttt{Settings$\rightarrow$Configure Toolbars}. Further, it is possible to add and remove sets
of data manipulation and analysis features from the GUI, using
-``Settings$\rightarrow$Configure RKWard$\rightarrow$Plugins''.
+\texttt{Settings$\rightarrow$Configure RKWard$\rightarrow$Plugins}.
\subsection{Workspace browser and object viewer}
\label{sec:workspace_browser_object_viewer}
@@ -119,7 +119,7 @@
copy it to \code{.GlobalEnv}. Further, the context menu allows to open
supported types of objects for editing (see Section~\ref{sec:spreadsheet}; currently, only
\code{data.frame}s can be edited, and only while they exist in \code{.GlobalEnv}).
-Selecting ``View'' from the
+Selecting \texttt{View} from the
context menu opens a new window in the
document area, containing basic information on the object as well as
tabs which show the output of
@@ -156,8 +156,8 @@
\begin{figure}[t!]
\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
-and B) function arguments.}
+ \caption{Code hinting features of the script editor. The script editor is able to hint (A) \proglang{R} object names
+and (B) function arguments.}
\label{fig:code_hinting}
\end{figure}
@@ -174,7 +174,7 @@
\proglang{R} distribution. For this reason, they are
technically based on different mechanisms.}. A further feature specific
to the \proglang{R} language is the
-``Paste Special'' action, which allows to
+\texttt{Paste Special} action, which allows to
paste the clipboard content (e.\,g., from a separate spreadsheet
application) as a single string, vector, or matrix, suitable
for inclusion in an \proglang{R} script, optionally
@@ -192,7 +192,7 @@
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
+\texttt{File} menu, . It can
also be invoked from \proglang{R}, e.\,g., using the
\code{file.edit()}, \code{file.show()}, or \code{fix()}
commands.
@@ -238,11 +238,11 @@
\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)
+ \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()})
+ (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}
@@ -257,7 +257,7 @@
can be shown or hidden separately from the data.
For columns of type \code{factor}, factor levels can be edited by double-clicking on the
-``Levels'' row of the meta information. Levels can also be assigned to other types of
+\texttt{Levels} row of the meta information. Levels can also be assigned to other types of
variables, but only for consecutive integer values. These levels will
be displayed instead of the underlying value, if applicable. Each
column can also be assigned an arbitrary descriptive
@@ -321,42 +321,42 @@
\proglang{Stata}, and ``delimited text'' data. Internally, \pkg{RKWard}
relies on standard \proglang{R} functions and the package \pkg{foreign}
\citep{Murdoch2002} for reading these data files. To import CSV data,
-select ``File$\rightarrow$Import format$\rightarrow$Import Text$\rightarrow$CSV''
+select \texttt{File$\rightarrow$Import format$\rightarrow$Import Text$\rightarrow$CSV}
data from the menu. This will open the dialog shown in
Figure~\ref{fig:CSV_import}. The central area of this dialog provides
options to control the import. The
-``File name'' field is highlighted, to indicate that
+\texttt{File name} field is highlighted, to indicate that
it is required to specify a file before the dialog can proceed.
Further options are available from the tabbed pages of the central area.
The right-side area is common to all data handling
-dialogs. Here the ``Submit'' button is used
+dialogs. Here the \texttt{Submit} button is used
to start the import action. It is enabled once all required
settings have been made, i.\,e., in this case, once a file name has been
-selected. The ``Close'' button will close the
+selected. The \texttt{Close} button will close the
dialog without taking any action.
\begin{figure}[t!]
\centering
\includegraphics[width=14.99cm]{./figures/CSV_import.png}
\caption{General data import dialog. Useful defaults for a variety of formats can
- be set using the ``Quick Mode'' selector on the left. Further customizations can be done
- from the ``Rows and Columns'' and ''Further Options'' tabs. The
+ be set using the \texttt{Quick Mode} selector on the left. Further customizations can be done
+ from the \texttt{Rows and Columns} and \texttt{Further Options} tabs. The
code in the bottom area can be copied and used for other purposes.}
\label{fig:CSV_import}
\end{figure}
The bottom area optionally shows the \proglang{R}
code corresponding to the current settings which will be run
-upon pressing the ``Submit'' button (see Section~\ref{sec:importing_data} for generated \proglang{R} code).
+upon pressing the \texttt{Submit} button (see Section~\ref{sec:importing_data} for generated \proglang{R} code).
The code display is hidden by default and can be revealed using
-the ``Code'' button. This
+the \texttt{Code} button. This
generated code display is updated dynamically as the user changes settings, allowing
to see the effect of each change instantly.
Most data handling functions will produce some output, which is
sent to the output window. From there it is possible to repeat the
-action by clicking on the ``Run again''-link
+action by clicking on the \texttt{Run again}-link
(see Section~\ref{sec:results_output}).
\subsection{Graphics window and plot previews}
@@ -380,7 +380,7 @@
available as a drop-down list, allowing to jump directly to a previous
plot. In this example, five different plots were performed on the same data
set of a random sample (\code{rnorm()}). The plot can be
- exported via ``Device$\rightarrow$Export'' as described in Section~\ref{sec:create_plot}.
+ exported via \texttt{Device$\rightarrow$Export} as described in Section~\ref{sec:create_plot}.
}
\label{fig:plot_history}
\end{figure}
@@ -388,8 +388,8 @@
Further, a history mechanism is provided,
which stores created plots automatically and allows to navigate
back to earlier plots (Figure~\ref{fig:plot_history}).
-The history is available as a drop-down list of the plot calls as well as using typical ``back''
-and ``forward'' buttons on the toolbar.
+The history is available as a drop-down list of the plot calls as well as using typical \texttt{back}
+and \texttt{forward} buttons on the toolbar.
The maximum number
of plots to record, as well as the maximum size of each individual plot,
is configurable from the settings menu. This plot history is shared
@@ -401,15 +401,15 @@
window records any unsaved plots to the history.
Further, \pkg{RKWard} provides access to different plotting functions using GUI dialogs,
-available from the ``Plots'' menu. Wherever appropriate, \pkg{RKWard} supports a ``plot
-preview'' feature. When the ``Preview'' box of
+available from the \texttt{Plots} menu. Wherever appropriate, \pkg{RKWard} supports a ``plot
+preview'' feature. When the \texttt{Preview} box of
the respective dialog is checked, a device window is opened, which
shows the plot as it would be created with the current settings (see Section~\ref{sec:create_plot} for an example). The
preview is updated automatically as the user makes changes, allowing to
see the effect of each setting instantly\footnote{The preview is
updated asynchronously to keep the GUI responsive; see also the technical supplement to this article.}. For example, the
central limit theorem plugins
-under the ``Distributions'' menu can be very helpful to dynamically ``show''
+under the \texttt{Distributions} menu can be very helpful to dynamically ``show''
the convergence in distribution while teaching. For the sake of simplicity, such preview plots are not added to
the history.
@@ -431,17 +431,17 @@
functions included in the \code{rkward} package. For the GUI-driven data handling functions, the output is
standardized to include the name of the feature, the date and time of
its execution, and other basic parameters, wherever
-applicable. Further, a clickable ``Run
-Again'' link is rendered below the output of each data
+applicable. Further, a clickable \texttt{Run
+again} link is rendered below the output of each data
handling feature, which allows to invoke the same feature again with
identical parameters\footnote{In case not all parameters could be
reused, e.\,g., because some of the objects in
question are no longer available, the user will be notified.} (see
-Figure~\ref{fig:results_output}). Thus, the ``Run
-Again'' feature combines the documentation of the result
+Figure~\ref{fig:results_output}). Thus, the \texttt{Run
+again} feature combines the documentation of the result
with an automated way to conduct the same analysis again on new
data, providing benefits similar to, for example, the automated report generation
-available from \pkg{RreportGenerator} \citep{RaffelsbergerW2008}.
+available from \pkg{RReportGenerator} \citep{RaffelsbergerW2008}.
\begin{figure}[t!]
\centering
@@ -449,12 +449,9 @@
\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
+ plugin output include a standardized header, and a \texttt{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)
+ \code{rk.header()} function, and a short transcript of \proglang{R} code with corresponding output.}
\label{fig:results_output}
\end{figure}
@@ -466,19 +463,19 @@
HTML, and the raw
HTML file and any images therein can be directly
retrieved from a dedicated folder
-(by default, this is a folder named ``.rkward'' inside the user's home folder). It is also
+(by default, this is a folder named \code{.rkward} inside the user's home folder). It is also
possible to select and copy sections of the output directly from the
output window, and to paste them into office applications as
richly formatted text; even images and tables can be easily copied by drag \& drop to many office applications. In future releases,
it is planned to integrate \pkg{RKWard}
with existing office suites. This
-will possibly also mean addition of different file formats such as Open Document Format and technologies such as \pkg{sweave} and \pkg{odfWeave}
+will possibly also mean addition of different file formats such as Open Document Format and technologies such as \code{sweave} and \pkg{odfWeave}
\citep{Leisch2002, Kuhn2006}.
Images contained in the output are stored as
-portable network graphics (PNG)\footnote{\url{http://www.libpng.org/pub/png/}} by
-default, but JPEG\footnote{\url{http://www.jpeg.org/jpeg/index.html}} and
-scalable vector graphics (SVG)\footnote{\url{http://www.w3.org/Graphics/SVG/}}
+portable network graphics (PNG)\footnote{http://www.libpng.org/pub/png/} by
+default, but JPEG\footnote{http://www.jpeg.org/jpeg/index.html} and
+scalable vector graphics (SVG)\footnote{http://www.w3.org/Graphics/SVG/}
can also be used. Similarly, the size of
images can be configured by the user. It is expected that SVG will
become the default output format eventually, but currently some SVG
@@ -487,14 +484,14 @@
\pkg{KDE} libraries.
Users can also add custom content to the output window using \code{rk.header()}, \code{rk.print()}, and some
-related functions. Further, custom R code as well as the corresponding R output can easily be documented in
+related functions. Further, custom \proglang{R} code as well as the corresponding \proglang{R} output can easily be documented in
the \pkg{RKWard} output window, including syntax highlighting (see the lower portion of
Figure~\ref{fig:results_output}).
\subsection{Package management}
\label{sec:package_management}
The number of \proglang{R} packages available from the comprehensive \proglang{R} archive
-network (CRAN), Omegahat\footnote{\url{http://www.omegahat.org/}} and Bioconductor \citep{Gentleman2004} has grown exponentially since \proglang{R}\, 1.3
+network (CRAN), Omegahat\footnote{http://www.omegahat.org/} and Bioconductor \citep{Gentleman2004} has grown exponentially since \proglang{R}\, 1.3
(2001) to \proglang{R}\, 2.7 (2008) \citep{Fox2008, Ligges2003, Visne2009}. \pkg{RKWard}
utilizes functionality from a growing number of these packages, but avoids
making the installation of all supported packages a pre-requirement to using
@@ -502,13 +499,13 @@
action, a package management dialog is invoked automatically, which allows to
download and install the package from a repository such as CRAN. The package
management dialog can also be invoked manually from the menu
-(``Settings$\rightarrow$Configure Packages'') for installing new or updating existing \proglang{R}
+(\texttt{Settings$\rightarrow$Configure Packages}) for installing new or updating existing \proglang{R}
packages. The underlying package management technology is that of \proglang{R}
\citep{Ligges2003, Ripley2005}.
\pkg{RKWard} supports installing packages to any user writable location. If no current
library location is user writable, \pkg{RKWard} offers to create a new one.
-On UNIX systems, interactively acquiring root privileges for
+On Unix systems, interactively acquiring root privileges for
installation to the system-wide libraries is also supported.
The installation process
itself can be monitored at the interface for error tracking. At the time of this writing, \pkg{RKWard} has no
@@ -536,7 +533,7 @@
has not yet started, or while another lengthy calculation is still
in progress. In these cases, commands are placed into a queue first, and
executed as soon as the \proglang{R} engine becomes
-available. The ``pending jobs'' window (not shown in the tool area by default)
+available. The \texttt{pending jobs} window (not shown in the tool area by default)
lists current \proglang{R} commands waiting for
evaluation by the \proglang{R} engine. While this
window is mostly of interest to application developers for diagnostic
@@ -558,9 +555,9 @@
An arbitrary number of help windows can be browsed simultaneously, in the
TDI view area (see Figure~\ref{fig:main_window}C) or in detached windows.
-A central access point to the help system is the ``Help'' menu. Further, help pages on
+A central access point to the help system is the \texttt{Help} menu. Further, help pages on
\nobreak{\pkg{RKWard}} GUI dialogs can be accessed from the dialog itself using the
-``Help'' button. A useful (``reverse'') feature here is that these pages include
+\texttt{Help} button. A useful (``reverse'') feature here is that these pages include
a link near the top of the page to start the corresponding GUI dialog directly.
Help on \proglang{R} specific functions can be invoked from multiple places,
such as, the context menu of the workspace browser, by pressing F2 (function
@@ -575,5 +572,5 @@
features like increasing or decreasing the font size and searching text
within a page. Additionally, \proglang{R} code inside a help
page can be sent to the \proglang{R} engine for
-evaluation by selecting it and pressing F8 (or via ``Run$\rightarrow$Run
-Selection'').
+evaluation by selecting it and pressing F8 (or via \texttt{Run$\rightarrow$Run
+Selection}).
Modified: branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/RKWard_annex.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/RKWard_annex.tex 2012-04-26 12:58:17 UTC (rev 4213)
+++ branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/RKWard_annex.tex 2012-04-27 17:07:17 UTC (rev 4214)
@@ -26,9 +26,7 @@
in detail technical aspects of \pkg{RKWard} including the usage of the \pkg{KDE}/\pkg{Qt} software libraries which are the base of \pkg{RKWard}.
Statistical procedures and plots are implemented as an extendable plugin architecture in \pkg{RKWard}.
This plugin architechture is based on \proglang{ECMAScript} (\proglang{JavaScript}), \proglang{R}, and XML. The general
-design is described and its application is exemplified on a t-test.
-\newline
-Disclaimer: This supplement was not part of the peer-review process of the Journal of Statistical Software.
+design is described and its application is exemplified on a Student's $t$~test.
\line(1,0){40}
\item$^{\ddag}$Equal contribution, $^{\S}$Corresponding authors
@@ -42,12 +40,12 @@
%% publication information
%% NOTE: Typically, this can be left commented and will be filled out by the technical editor
-%% \Volume{13}
-%% \Issue{9}
-%% \Month{September}
-%% \Year{2004}
-%% \Submitdate{2004-09-29}
-%% \Acceptdate{2004-09-29}
+\Volume{49}
+\Issue{9}
+\Month{June}
+\Year{2012}
+\Submitdate{2010-12-28}
+\Acceptdate{2011-05-06}
%% The address of (at least) one author should be given
%% in the following format:
@@ -56,8 +54,8 @@
Lausitz University of Applied Sciences\\
Department of Bio-, Chemistry and Process Engineering\\
AND\\
- Center for Cardiovascular Research (CCR)\\
- Charit\'e, Germany\\
+ Kardiologie-CCM, Charit\'e-Universit\"{a}tsmedizin Berlin\\
+ Germany\\
E-mail: \email{stefan\_roediger at gmx.de}\\
E-mail: \email{rkward-devel at lists.sourceforge.net}\\
}
Modified: branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/RKWard_paper.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/RKWard_paper.tex 2012-04-26 12:58:17 UTC (rev 4213)
+++ branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/RKWard_paper.tex 2012-04-27 17:07:17 UTC (rev 4214)
@@ -50,12 +50,12 @@
%% publication information
%% NOTE: Typically, this can be left commented and will be filled out by the technical editor
-%% \Volume{13}
-%% \Issue{9}
-%% \Month{September}
-%% \Year{2004}
-%% \Submitdate{2004-09-29}
-%% \Acceptdate{2004-09-29}
+\Volume{49}
+\Issue{9}
+\Month{June}
+\Year{2012}
+\Submitdate{2010-12-28}
+\Acceptdate{2011-05-06}
%% The address of (at least) one author should be given
%% in the following format:
@@ -64,8 +64,8 @@
Lausitz University of Applied Sciences\\
Department of Bio-, Chemistry and Process Engineering\\
AND\\
- Center for Cardiovascular Research (CCR)\\
- Charit\'e, Germany\\
+ Kardiologie-CCM, Charit\'e-Universit\"{a}tsmedizin Berlin\\
+ Germany\\
E-mail: \email{stefan\_roediger at gmx.de}\\
E-mail: \email{rkward-devel at lists.sourceforge.net}\\
}
Modified: branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/annex_figures_extended.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/annex_figures_extended.tex 2012-04-26 12:58:17 UTC (rev 4213)
+++ branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/annex_figures_extended.tex 2012-04-27 17:07:17 UTC (rev 4214)
@@ -14,6 +14,6 @@
\begin{figure}[!h]
\centering
\includegraphics[width=15.4cm]{./figures/settings.png}
- \caption{GUI dialog for settings of details shown in \pkg{RKWard} (``Settings$\rightarrow$Configure RKWard$\rightarrow$Workspace'').}
+ \caption{GUI dialog for settings of details shown in \pkg{RKWard} (\texttt{Settings$\rightarrow$Configure RKWard$\rightarrow$Workspace}).}
\label{fig:settings}
\end{figure}
\ No newline at end of file
Modified: branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/background.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/background.tex 2012-04-26 12:58:17 UTC (rev 4213)
+++ branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/background.tex 2012-04-27 17:07:17 UTC (rev 4214)
@@ -9,9 +9,8 @@
Development Core Team \citep{RDCT2001, RDCT2010, Ihaka_Gentlemen_1993}.
\proglang{R} does not include an advanced cross-platform graphical user interface (GUI) as known from other
statistical software packages. However, \proglang{R} includes tools for building GUIs
-mainly based on \proglang{Tlc/Tk} \citep{Dalgaard2001, Dalgaard2002}. Meanwhile a
-plethora of \proglang{R} GUIs have emerged (see \url{http://www.sciviews.org/_rgui/} for a
-comprehensive list). In 2005 John Fox released version 1.0 of \proglang{R} Commander (package \pkg{Rcmdr}), which
+mainly based on \proglang{Tcl/Tk} \citep{Dalgaard2001, Dalgaard2002}. Meanwhile a
+plethora of \proglang{R} GUIs have emerged \cite{RGUI}. In 2005 John Fox released version 1.0 of \proglang{R} Commander (package \pkg{Rcmdr} \cite{Fox2005}), which
can be considered a milestone in \proglang{R} GUI development; it was the first GUI
implementation that was able to make statistical tests,
plots and data manipulation easily accessible for \proglang{R} novices.
@@ -20,13 +19,13 @@
time beyond this \citep{Fox2005, Fox2007}. In November 2002 Thomas Friedrichsmeier
started the \pkg{RKWard} open-source software project with the goal to create a GUI for
\proglang{R} based on \pkg{KDE}\footnote{
- \pkg{KDE} is a desktop environment and software collection based on \pkg{Qt} (\url{http://www.kde.org/}).
+ \pkg{KDE} is a desktop environment and software collection based on \pkg{Qt} (http://www.kde.org/).
In the context of this paper, the term \pkg{KDE} is primarily used to refer to the programming library and
runtime environment of \pkg{KDE}, rather than the complete software collection. For an introduction to
\pkg{KDE} as a programming library, see \cite{Faure2000}.
} and \pkg{Qt}\footnote{
\pkg{Qt} is a \proglang{C++}-based cross-platform programming library with a focus on GUI development
- \citep{BlanchetteSummerfield2008}. Online documentation is available at \url{http://qt.nokia.com/}.
+ \citep{BlanchetteSummerfield2008}. Online documentation is available at http://qt.nokia.com/.
} technologies.
The scope of \pkg{RKWard} is deliberately broad, targeting both \proglang{R} novices and experts.
@@ -47,7 +46,7 @@
\pkg{RKWard} provides a high level of transparency about the steps that are needed to
perform any supported task in \proglang{R}, in order to make it easy for the user to see
complete codes for all GUI actions\footnote{
- This distinguishes \pkg{RKWard} from \proglang{R} GUIs such as \pkg{Red-R} (\url{http://www.red-r.org/}), which
+ This distinguishes \pkg{RKWard} from \proglang{R} GUIs such as \pkg{Red-R} (http://www.red-r.org/), which
specifically aims to hide the complexities of the \proglang{R} programming language, following the concept of visual data-flow
programming \citep{Sutherland1966}. In contrast, \pkg{RKWard} limits itself to generate \proglang{R} code from GUI settings.
}. In doing so, \pkg{RKWard} deliberately generates
@@ -60,7 +59,7 @@
customizing the generated code patterns.
While \pkg{RKWard} tries to address users wishing to learn \proglang{R}, it is specifically not
-designed as a teaching tool (such as \pkg{Rcmdr} or \pkg{TeachingDemos}), but as
+designed as a teaching tool (such as \pkg{Rcmdr} \cite{Fox2005} or \pkg{TeachingDemos} \cite{TeachingDemos2010}), but as
a productive tool. Since its incarnation \pkg{RKWard} has gained acceptance for usage in peer-reviewed
publications \citep{Zou2008, Zou2009, Rugg-Gunn2010, Yang2011, Roediger2011, Roediger_VS}.
Dialogs for statistical procedures in \pkg{RKWard} do not
@@ -79,10 +78,10 @@
which are not included in the official \pkg{RKWard} releases. Details on the definition of plugins,
and a commented example can be found in the technical supplement to this article.
-\pkg{RKWard} is licensed under the terms of the GNU General Public License\footnote{\url{http://www.gnu.org/licenses/gpl.html}} Version 2
+\pkg{RKWard} is licensed under the terms of the GNU General Public License\footnote{http://www.gnu.org/licenses/gpl.html} Version 2
or higher. However, due to its dependencies, \pkg{RKWard} binaries are effectively
distributable only under the terms of Version 2 of the license. Parts of the documentation are available under the
-GNU Free Documentation License\footnote{\url{http://www.gnu.org/licenses/fdl.html}}. While the project remains in constant development, a growing
+GNU Free Documentation License\footnote{http://www.gnu.org/licenses/fdl.html}. While the project remains in constant development, a growing
number of users employs \pkg{RKWard} in productive scenarios. The source code,
selected binaries and documentation is hosted at SourceForge
(\url{http://rkward.sourceforge.net/}). Selected key milestones of the development of \pkg{RKWard} are
Modified: branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/example_plugin.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/example_plugin.tex 2012-04-26 12:58:17 UTC (rev 4213)
+++ branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/example_plugin.tex 2012-04-27 17:07:17 UTC (rev 4214)
@@ -4,17 +4,17 @@
As discussed in Section~\ref{sec:technical_plugins}, plugins in \pkg{RKWard} are
defined by four separate files (Figure~\ref{fig:plugin_structure}). To give an impression of the technique,
this section shows (portions of) the relevant files for a plugin that provides
-a simple dialog for a t-test. For brevity, the help-file is omitted.
+a simple dialog for a Student's $t$~test. For brevity, the help-file is omitted.
\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, a two variable t-test (see Figure~\ref{fig:ttest-gui-example}).
+A so called \code{.pluginmap} file declares each plugin, and, if appropriate, defines where it should
+be placed in the menu hierarchy. Usually each \code{.pluginmap} file declares many plugins. In this example
+we only show one, namely, a two variable Student's $t$~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 layout is defined in a hierarchical
structure by nesting \code{<menu>} elements to form toplevel menus and submenus. Menus with the same ``id''
-are merged across .pluginmap files. Moreover, the position within the menu can be explicitly defined (attribute ``index'').
+are merged across \code{.pluginmap} files. Moreover, the position within the menu can be explicitly defined (attribute ``index'').
This might be required if the menu entries are to be ordered non-alphabetically.
\begin{footnotesize}
@@ -53,14 +53,14 @@
\proglang{ECMAScript} file that is used for generating \proglang{R} code from GUI settings and the help file (not included in this paper).
GUI logic can be defined directly in the XML file (the \code{<logic>} element).
-In this example, the ``Assume equal variances'' checkbox is only enabled for paired sample tests.
+In this example, the \texttt{Assume equal variances} checkbox is only enabled for paired sample tests.
Optionally, GUI behavior can also be scripted in \proglang{ECMAScript}.
-The XML file defines the t-test plugin (\code{<!DOCTYPE rkplugin>}) to be organized in two tabs\footnote{
+The XML file defines the Student's $t$~test plugin (\code{<!DOCTYPE rkplugin>}) to be organized in two tabs\footnote{
A screenshot of the resulting dialog can be found the in the main article.
}.
-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
+On the first tab, two variables can be selected (\code{<varslot .../>}). These are set to be \texttt{required}, i.\,e.,
+the \texttt{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}
Modified: branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/example_session.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/example_session.tex 2012-04-26 12:58:17 UTC (rev 4213)
+++ branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/example_session.tex 2012-04-27 17:07:17 UTC (rev 4214)
@@ -13,22 +13,22 @@
\begin{figure}[b!]
\centering
\includegraphics[width=13.5cm]{./figures/import_data.png}
- \caption{A) CSV import dialog. Useful defaults for a variety of common text separated value formats can
- be set using the ``Quick Mode'' selector on the left. Beyond that, many options can be customized. B) Data editor. The imported CSV
- data from ``experiment.txt'' are presented (data visually trimmed).}
+ \caption{(A) CSV import dialog. Useful defaults for a variety of common text separated value formats can
+ be set using the \texttt{Quick Mode} selector on the left. Beyond that, many options can be customized. (B) Data editor. The imported CSV
+ data from \code{experiment.txt} are presented (data visually trimmed).}
\label{fig:import_data}
\end{figure}
Suppose that the data was saved as or exported to CSV format, for example, from a
spreadsheet application. \pkg{RKWard}'s import plugin can
comfortably read it into a new \proglang{R} object.
-The import dialog (``File$\rightarrow$Import$\rightarrow$Import
-format$\rightarrow$Import Text/CSV data''; Figure~\ref{fig:import_data}A) assists in reading the
+The import dialog (\texttt{File$\rightarrow$Import$\rightarrow$Import
+format$\rightarrow$Import Text/CSV data}; Figure~\ref{fig:import_data}A) assists in reading the
data by a common point \& click interface. In this
-example, ``comma'' and ``period'' were chosen via ``Quick mode'' as the field
+example, ``comma'' and ``period'' were chosen via \texttt{Quick mode} as the field
separator and decimal point characters respectively.
-The generated \proglang{R} code can be revealed by clicking on the ``Code'' button:
+The generated \proglang{R} code can be revealed by clicking on the \texttt{Code} button:
\begin{Code}
read.csv(file = '/media/software/experiment.txt',
@@ -36,55 +36,55 @@
check.names = TRUE, strip.white = FALSE, blank.lines.skip = TRUE)
\end{Code}
-Checking the ``Edit Object'' box automatically opens a data editor tab
+Checking the \texttt{Edit Object} box automatically opens a data editor tab
showing the imported data (Figure~\ref{fig:import_data}B).
-\subsection{Conducting a Student's t-Test}
+\subsection{Conducting a Student's $t$~test}
\label{sec:conducting_ttest}
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.
+$t$~test for a paired sample is conducted using the
+\texttt{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_dialog}).
-Pressing the ``Submit'' button conducts the test, and opens the output document tab
+Pressing the \texttt{Submit} button conducts the test, and opens the output document tab
showing the results, including the date of analysis and relevant test parameters (Figure~\ref{fig:t_test_results}).
\begin{figure}[b!]
\centering
\includegraphics[width=13.5cm]{./figures/t-test_dialog.png}
- \caption{Student's t-Test dialog for two variables. The bottom area shows the \proglang{R} code corresponding to the settings.}
+ \caption{Student's $t$~test dialog for two variables. The bottom area shows the \proglang{R} code corresponding to the settings.}
\label{fig:t_test_dialog}
\end{figure}
\begin{figure}[t!]
\centering
\includegraphics[width=15.4cm]{./figures/t-test_results.png}
- \caption{Results of conducting a Student's t-Test in tabular HTML format.}
+ \caption{Results of conducting a Student's $t$~test in tabular HTML format.}
\label{fig:t_test_results}
\end{figure}
\subsection{Creating a plot}
\label{sec:create_plot}
-To visualize the data, ``Boxplot'' is chosen from the ``Plots'' menu
-and the two variables, corresponding to the t-Test above, are selected.
+To visualize the data, \texttt{Boxplot} is chosen from the \texttt{Plots} menu
+and the two variables, corresponding to the Student's $t$~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
+Checking the \texttt{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.
The plot can also be exported to several image formats, directly from the preview window (Figure~\ref{fig:boxplot2}).
\begin{figure}[b!]
\centering
\includegraphics[width=15.4cm]{./figures/boxplot1.png}
- \caption{Boxplot dialog. The first tab ``Variables'' is used to select the variables for analysis. It is possible to
- combine any data present in \code{.GlobalEnv}. The second tab ``Options'' allows further adjustments (e.\,g., the addition of mean and standard deviation) to the plot (not shown).}
+ \caption{Boxplot dialog. The first tab \texttt{Variables} is used to select the variables for analysis. It is possible to
+ combine any data present in \code{.GlobalEnv}. The second tab \texttt{Options} allows further adjustments (e.\,g., the addition of mean and standard deviation) to the plot (not shown).}
\label{fig:boxplot1}
\end{figure}
\begin{figure}[t!]
\centering
\includegraphics[width=14.5cm]{./figures/boxplot2.png}
- \caption{Plotted data and plot export dialog. The export dialog (``Device$\rightarrow$Export'') provides numerous
+ \caption{Plotted data and plot export dialog. The export dialog (\texttt{Device$\rightarrow$Export}) provides numerous
options like resolution and size for different vector formats (e.\,g., SVG, PDF) and
pixel formats (e.\,g., PNG, JPEG). (Note: For the shown figure, the optional
mean ($\blacksquare$) and standard deviation ($+$) parameters were selected in the boxplot plugin.)}
Modified: branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/installing_starting_RKWard.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/installing_starting_RKWard.tex 2012-04-26 12:58:17 UTC (rev 4213)
+++ branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/installing_starting_RKWard.tex 2012-04-27 17:07:17 UTC (rev 4214)
@@ -3,16 +3,16 @@
Contrary to some other \proglang{R} GUIs, such as \pkg{Rcmdr}, \pkg{RKWard} cannot be installed and started as a
regular \proglang{R} add-on package. Rather, it is started as a stand-alone application which embeds the
\proglang{R} engine, and needs to be installed in a platform dependent way, as detailed below\footnote{
- See \url{http://p.sf.net/rkward/download} for an overview and platform specific download links.
+ See http://p.sf.net/rkward/download for an overview and platform specific download links.
}. Besides the
-\pkg{KDE} runtime environment and \proglang{R}, \pkg{RKWard} utilizes a growing number of \pkg{R} add-on packages.
+\pkg{KDE} runtime environment and \proglang{R}, \pkg{RKWard} utilizes a growing number of \proglang{R} add-on packages.
However, these do not have to be installed before hand. Rather \pkg{RKWard} will prompt the user to install
missing packages interactively, on an as-needed basis (see Section~\ref{sec:package_management}).
\subsection{Installation on the GNU/Linux platform}
Historically, \pkg{RKWard} originated on the GNU/Linux platform, and binary packages are available for many
major GNU/Linux distributions, including Debian, Ubuntu, OpenSuse, Gentoo, Fedora, but also for other POSIX\footnote{
-\url{http://standards.ieee.org/develop/wg/POSIX.html}
+http://standards.ieee.org/develop/wg/POSIX.html
}
compliant systems such as FreeBSD. The exact size of the installation is system dependent. On Debian x86, the
package is currently around 1.5 MB (Megabyte) compressed, and 5.5 MB uncompressed. However, if the \pkg{KDE}
@@ -21,13 +21,13 @@
On systems which provide up-to-date packages of \proglang{R} and \pkg{KDE}, compilation from source is
generally unproblematic\footnote{
- See \url{http://p.sf.net/rkward/compilling} for details.
+ See http://p.sf.net/rkward/compilling for details.
}.
\subsection{Installation on Microsoft Windows}
\pkg{RKWard} will run on Windows XP, Windows Server 2003, Vista, and Windows 7. 32-bit binaries are
provided by the project\footnote{
- See \url{http://sourceforge.net/apps/mediawiki/rkward/?title=RKWard\_on\_Windows\#Installing}
+ See http://sourceforge.net/apps/mediawiki/rkward/?title=RKWard\_on\_Windows\#Installing
}. Users can
choose between a small installer (1.7 MB), which will add \pkg{RKWard} to pre-existing installations of
\proglang{R} and \pkg{KDE}, and an installation bundle, which provides \pkg{RKWard}, \proglang{R}, and
@@ -39,7 +39,7 @@
Source installation on the Microsoft Windows platform is comparatively difficult, since various tools need to
be installed\footnote{
- See \url{http://sourceforge.net/apps/mediawiki/rkward/?title=RKWard\_on\_Windows/Packaging} for details.
+ See http://sourceforge.net/apps/mediawiki/rkward/?title=RKWard\_on\_Windows/Packaging for details.
}.
\subsection{Installation on Mac OS X}
Modified: branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/sources.bib
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/sources.bib 2012-04-26 12:58:17 UTC (rev 4213)
+++ branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/sources.bib 2012-04-27 17:07:17 UTC (rev 4214)
@@ -12,7 +12,7 @@
note = {ISSN 1609-3631},
owner = {tux},
timestamp = {2010.06.30},
- url = {http://cran.r-project.org/doc/Rnews/}
+ url = {http://CRAN.R-project.org/doc/Rnews/Rnews_2001-1.pdf}
}
@MANUAL{RDCT2010,
@@ -126,6 +126,14 @@
timestamp = {2010.12.16}
}
+ at BOOK{Eclipse,
+ title = {\pkg{Eclipse} IDE Pocket Guide},
+ publisher = {O'Reilly Media},
+ year = {2005},
+ author = {Ed Burnette},
+ note = {{ISBN} 0-596100-65-5}
+}
+
@MANUAL{CullmannND,
title = {\pkg{KatePart}},
author = {Christoph Cullmann},
@@ -144,8 +152,7 @@
pages = {25--27},
number = {3},
month = {December},
- pdf = {http://CRAN.R-project.org/doc/Rnews/Rnews_2002-3.pdf},
- url = {http://CRAN.R-project.org/doc/Rnews/}
+ url = {http://CRAN.R-project.org/doc/Rnews/Rnews_2002-3.pdf}
}
@ARTICLE{Dalgaard2001,
@@ -157,8 +164,7 @@
pages = {27--31},
number = {3},
month = {September},
- pdf = {http://CRAN.R-project.org/doc/Rnews/Rnews_2001-3.pdf},
- url = {http://CRAN.R-project.org/doc/Rnews/}
+ url = {http://CRAN.R-project.org/doc/Rnews/Rnews_2001-3.pdf}
}
@ARTICLE{Eddelbuettel2003,
@@ -228,29 +234,22 @@
pages = {46-52},
number = {3},
month = {December},
- pdf = {http://CRAN.R-project.org/doc/Rnews/Rnews_2007-3.pdf},
- url = {http://CRAN.R-project.org/doc/Rnews/}
+ url = {http://CRAN.R-project.org/doc/Rnews/Rnews_2007-3.pdf}
}
- at ARTICLE{Fox2005,
- author = {John Fox},
- title = {The \proglang{R} Commander: A Basic-Statistics Graphical User Interface
- to \proglang{R}},
- journal = {Journal of Statistical Software},
- year = {2005},
- volume = {14},
- pages = {1--42},
- number = {9},
- month = {8},
- accepted = {2005-08-19},
- bibdate = {2005-08-19},
- coden = {JSSOBK},
- day = {19},
- issn = {1548-7660},
- submitted = {2004-07-22},
- url = {http://www.jstatsoft.org/v14/i09}
+ at Article{Fox2005,
+ author = {John Fox},
+ title = {The \proglang{R} Commander: A Basic-Statistics
+ Graphical User Interface to \proglang{R}},
+ journal = {Journal of Statistical Software},
+ year = {2005},
+ volume = {14},
+ number = {9},
+ pages = {1--42},
+ url = {http://www.jstatsoft.org/v14/i09/}
}
+
@MANUAL{Rcmdr2010,
title = {\pkg{Rcmdr}: \proglang{R} Commander},
author = {John Fox and with contributions from Liviu Andronic and Michael Ash
@@ -297,11 +296,7 @@
into interdisciplinary scientific research, and promoting the achievement
of remote reproducibility of research results. We describe details
of our aims and methods, identify current challenges, compare Bioconductor
- to other open bioinformatics projects, and provide working examples.},
- doi = {10.1186/gb-2004-5-10-r80},
- issn = {1465-6906},
- pubmedid = {15461798},
- url = {http://genomebiology.com/2004/5/10/R80}
+ to other open bioinformatics projects, and provide working examples.}
}
@ARTICLE{Grothendieck2008,
@@ -322,6 +317,14 @@
url = {http://www.jstatsoft.org/v25/b02}
}
+ at MISC{KateScriptedActions,
+ author = {Dominik Haumann},
+ title = {\pkg{Kate}: Scripted Actions},
+ year = {2010},
+ timestamp = {2011.05.28},
+ url = {http://kate-editor.org/2010/07/09/kate-scripted-actions/}
+}
+
@ARTICLE{HelbigTheus2005,
author = {Markus Helbig and Martin Theus},
title = {\pkg{JGR}: \proglang{Java} GUI for \proglang{R}},
@@ -342,6 +345,13 @@
url = {http://CRAN.R-project.org/package=JGR}
}
+ at Misc{RGUI,
+ author = {Philippe Grosjean},
+ title = {\proglang{R} GUI Projects},
+ year = {2010},
+ url = {http://www.R-project.org/GUI}
+}
+
@MISC{Hopkins2005,
author = {Don Hopkins},
title = {HyperTIES Hypermedia Browser and Emacs Authoring Tool for NeWS},
@@ -381,11 +391,11 @@
author = {Jiang, Gonglue and Zhao, Chen and Scott, Matthew and Zou, Fang},
title = {Combinable Tabs: An Interactive Method of Information Comparison
Using a Combinable Tabbed Document Interface},
- booktitle = {Human-Computer Interaction \textendash INTERACT 2009},
+ booktitle = {Human-Computer Interaction \textendash INTERACT 2009},
publisher = {Springer Berlin / Heidelberg},
year = {2009},
- editor = {Gross, Tom and Gulliksen, Jan and Kotz\'{e}, Paula and Oestreicher, Lars
- and Palanque, Philippe and Prates, Raquel and Winckler, Marco},
+ editor = {Gross, Tom and Gulliksen, Jan and Kotz\'{e}, Paula and Oestreicher,
+ Lars and Palanque, Philippe and Prates, Raquel and Winckler, Marco},
volume = {5726},
series = {Lecture Notes in Computer Science},
pages = {432--435},
@@ -411,6 +421,14 @@
url = {http://www.jstatsoft.org/v11/i09}
}
+ at MANUAL{KDevelop,
+ title = {\pkg{KDevelop}},
+ author = {{KDevelop{.}Org}},
+ year = {2011},
+ timestamp = {2011.05.28},
+ url = {http://www.kdevelop.org/}
+}
+
@ARTICLE{KimLutteroth2010,
author = {James Kim and Christof Lutteroth},
title = {Multi-Platform Document-Oriented GUIs},
@@ -433,33 +451,9 @@
location = {http://www.scientificcommons.org/55322653},
owner = {tux},
timestamp = {2010.12.16},
- url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.154.8895}
+ url = {http://www.scientificcommons.org/55322653}
}
- at MISC{KateScriptedActions,
- author = {Dominik Haumann},
- title = {\pkg{Kate}: Scripted Actions},
- year = {2010},
- timestamp = {2011.05.28},
- url = {http://kate-editor.org/2010/07/09/kate-scripted-actions/}
-}
-
- at BOOK{Eclipse,
- title = {\pkg{Eclipse} IDE Pocket Guide},
- author = {Ed Burnette},
- year = {2005},
- publisher = {O'Reilly Media},
- note = {{ISBN} 0-596100-65-5},
-}
-
- at MANUAL{KDevelop,
- title = {\pkg{KDevelop}},
- author = {{KDevelop{.}Org}},
- year = {2011},
- timestamp = {2011.05.28},
- url = {http://www.kdevelop.org/}
-}
-
@MANUAL{KWord,
title = {\pkg{KWord}},
author = {{KOffice{.}Org}},
@@ -477,14 +471,13 @@
pages = {2--8},
number = {4},
month = {October},
- pdf = {http://CRAN.R-project.org/doc/Rnews/Rnews_2006-4.pdf},
- url = {http://CRAN.R-project.org/doc/Rnews/}
+ url = {http://CRAN.R-project.org/doc/Rnews/Rnews_2006-4.pdf}
}
@ARTICLE{Lecoutre2003,
author = {E Lecoutre},
- title = {The \pkg{R2HTML} Package -- Formatting HTML Output on the Fly or by
- Using a Template Scheme},
+ title = {The \pkg{R2HTML} Package -- Formatting HTML Output on the Fly or
+ by Using a Template Scheme},
journal = {\proglang{R} News},
year = {2003},
volume = {3},
@@ -495,19 +488,16 @@
timestamp = {2010.07.02}
}
- at ARTICLE{Leisch2002,
- author = {F Leisch},
- title = {Sweave: Dynamic Generation of Statistical Reports Using Literate
- Data Analysis},
- journal = {Proceedings in Computational Statistics},
- year = {2002},
- pages = {575--580},
- eid = {Physica Verlag, Heidelberg},
- abstract = {. (2002) Sweave: dynamic generation of statistical reports using literate
- data analysis. In Hardle,W. and Ronz,B. (eds.) Proceedings in Computational
- Statistics. Physica Verlag, Heidelberg, pp. 575–580.},
- owner = {tux},
- timestamp = {2010.07.01}
+ at InProceedings{Leisch2002,
+ author = {Friedrich Leisch},
+ title = {Dynamic Generation of Statistical Reports Using
+ Literate Data Analysis},
+ booktitle = {COMPSTAT 2002 -- Proceedings in Computational Statistics},
+ pages = {575--580},
+ year = {2002},
+ editor = {W. H\"ardle and B. R\"onz},
+ address = {Heidelberg},
+ publisher = {Physica-Verlag}
}
@ARTICLE{Ligges2003,
@@ -519,8 +509,7 @@
pages = {37--39},
number = {3},
month = {December},
- pdf = {http://CRAN.R-project.org/doc/Rnews/Rnews_2003-3.pdf},
- url = {http://CRAN.R-project.org/doc/Rnews/}
+ url = {http://CRAN.R-project.org/doc/Rnews/Rnews_2003-3.pdf}
}
@MISC{MDN2010,
@@ -541,8 +530,7 @@
pages = {2--3},
number = {1},
month = {March},
- pdf = {http://CRAN.R-project.org/doc/Rnews/Rnews_2002-1.pdf},
- url = {http://CRAN.R-project.org/doc/Rnews/}
+ url = {http://CRAN.R-project.org/doc/Rnews/Rnews_2002-1.pdf}
}
@BOOK{Murrell_2005,
@@ -564,8 +552,7 @@
pages = {32--35},
number = {2},
month = {October},
- pdf = {http://CRAN.R-project.org/doc/Rnews/Rnews_2007-2.pdf},
- url = {http://CRAN.R-project.org/doc/Rnews/}
+ url = {http://CRAN.R-project.org/doc/Rnews/Rnews_2007-2.pdf}
}
@MISC{perens1999,
@@ -629,25 +616,22 @@
Also, the quality of microbeads can be evaluated. To our knowledge
this is the first report which applies a reversible noncovalent fluorescent
dye adsorption assay to quantify the degree of carboxylation on surfaces.
- },
- doi = {10.1021/ac103277s},
- eprint = {http://pubs.acs.org/doi/pdf/10.1021/ac103277s},
- url = {http://pubs.acs.org/doi/abs/10.1021/ac103277s}
+ }
}
@ARTICLE{Roediger_VS,
- author = {Stefan R\"{o}diger and Peter Schierack and Alexander B\"{o}hm and J\"{o}rg Nitschke
- and Ingo Berger and Ulrike Fr\"{o}mmel and Carsten Schmidt and Mirko
- Ruhland and Ingolf Schimke and Dirk Roggenbuck and Werner Lehmann
- and Christian Schr\"{o}der},
+ author = {Stefan R\"{o}diger and Peter Schierack and Alexander B\"{o}hm and
+ J\"{o}rg Nitschke and Ingo Berger and Ulrike Fr\"{o}mmel and Carsten
+ Schmidt and Mirko Ruhland and Ingolf Schimke and Dirk Roggenbuck
+ and Werner Lehmann and Christian Schr\"{o}der},
title = {A Highly Versatile Microscope Imaging Technology Platform for the
Multiplex Real-Time Detection of Biomolecules and Autoimmune Antibodies},
journal = {Advances in Biochemical Bioengineering/Biotechnology},
- note = {In press},
- year = {2011},
+ year = {2012},
+ note = {ISSN 1616-8542},
owner = {tux},
timestamp = {2011.11.16},
- url = {http://www.springer.com/}
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/22437246}
}
@ARTICLE{Raaphorst2003,
@@ -683,10 +667,7 @@
of CGH data, and microarray quality control and normalization.Availability:
RReportGenerator, a user manual and a collection of analysis scenarios
are available under a GNU public license on http://www-bio3d-igbmc.u-strasbg.fr/~wraffContact:
- wolfgang.raffelsberger at igbmc.u-strasbg.fr},
- doi = {10.1093/bioinformatics/btm556},
- eprint = {http://bioinformatics.oxfordjournals.org/content/24/2/276.full.pdf+html},
- url = {http://bioinformatics.oxfordjournals.org/content/24/2/276.abstract}
+ wolfgang.raffelsberger at igbmc.u-strasbg.fr}
}
@ARTICLE{Ripley2005,
@@ -698,8 +679,7 @@
pages = {8--11},
number = {1},
month = {May},
- pdf = {http://CRAN.R-project.org/doc/Rnews/Rnews_2005-1.pdf},
- url = {http://CRAN.R-project.org/doc/Rnews/}
+ url = {http://CRAN.R-project.org/doc/Rnews/Rnews_2005-1.pdf}
}
@ARTICLE{Ripley2005a,
@@ -712,7 +692,7 @@
note = {ISSN 1609-3631},
owner = {tux},
timestamp = {2010.07.01},
- url = {http://CRAN.R-project.org/doc/Rnews/}
+ url = {http://CRAN.R-project.org/doc/Rnews/Rnews_2005-1.pdf}
}
@ARTICLE{Ripley2004,
@@ -724,8 +704,7 @@
pages = {2--4},
number = {2},
month = {September},
- pdf = {http://CRAN.R-project.org/doc/Rnews/Rnews_2004-2.pdf},
- url = {http://CRAN.R-project.org/doc/Rnews/}
+ url = {http://CRAN.R-project.org/doc/Rnews/Rnews_2004-2.pdf}
}
@ARTICLE{Rizopoulos2006,
@@ -770,10 +749,7 @@
reflect the extraembryonic stem cell lines. These studies indicate
that histone modification mechanisms may differ between early embryo
lineages and emphasize the importance of examining in vivo and in
- vitro progenitor cells.},
- doi = {10.1073/pnas.0914507107},
- eprint = {http://www.pnas.org/content/107/24/10783.full.pdf+html},
- url = {http://www.pnas.org/content/107/24/10783.abstract}
+ vitro progenitor cells.}
}
@BOOK{Sarkar2008,
@@ -786,14 +762,12 @@
url = {http://lmdvr.r-forge.r-project.org}
}
- at MANUAL{TeachingDemos2010,
- title = {\pkg{TeachingDemos}: Demonstrations for Teaching and Learning},
- author = {Greg Snow},
- year = {2010},
- note = {\proglang{R} Package Version 2.7},
- owner = {tux},
- timestamp = {2010.12.16},
- url = {http://CRAN.R-project.org/package=TeachingDemos}
+ at Manual{TeachingDemos2010,
+ title = {\pkg{TeachingDemos}: Demonstrations for Teaching and Learning},
+ author = {Greg Snow},
+ year = {2012},
+ note = {\proglang{R}~package version~2.8},
+ url = {http://CRAN.R-project.org/package=TeachingDemos},
}
@PHDTHESIS{Sutherland1966,
@@ -849,17 +823,16 @@
integrated in any software. The RGG project further includes the
development of a web-based repository for RGG-GUIs. RGG is an open
source project licensed under the Lesser General Public License (LGPL)
- and can be downloaded freely at http://rgg.r-forge.r-project.org},
- doi = {10.1186/1471-2105-10-74},
+ and can be downloaded freely at http://rgg.r-forge.r-project.org}
issn = {1471-2105},
owner = {tux},
pubmedid = {19254356},
- timestamp = {2010.12.16},
- url = {http://www.biomedcentral.com/1471-2105/10/74}
+ timestamp = {2010.12.16}
}
@ARTICLE{Yang2011,
- author = {Ling Yang and Jun Liu and Mu Liu and Meirui Qian and Minzhou Zhang and Huajun Hu},
+ author = {Ling Yang and Jun Liu and Mu Liu and Meirui Qian and Minzhou Zhang
+ and Huajun Hu},
title = {Identification of Fatty Acid Synthase from the Pacific White Shrimp,
Litopenaeus vannamei and its Specific Expression Profiles During
White Spot Syndrome Virus Infection},
@@ -868,10 +841,8 @@
volume = {30},
pages = {744--749},
number = {2},
- doi = {DOI: 10.1016/j.fsi.2010.12.026},
issn = {1050-4648},
- keywords = {Fatty acid synthase},
- url = {http://www.sciencedirect.com/science/article/B6WFN-51VB7WR-2/2/a0361cb4e49d4ec5ef9cf6755dfc468f}
+ keywords = {Fatty acid synthase}
}
@ARTICLE{Young_2004,
@@ -892,8 +863,7 @@
pages = {20--25},
number = {1},
month = {June},
- pdf = {http://CRAN.R-project.org/doc/Rnews/Rnews_2004-1.pdf},
- url = {http://CRAN.R-project.org/doc/Rnews/}
+ url = {http://CRAN.R-project.org/doc/Rnews/Rnews_2004-1.pdf}
}
@ARTICLE{Zhou2005,
@@ -916,10 +886,8 @@
year = {2009},
volume = {2},
pages = {638--666},
- number = {2},
- doi = {10.3390/a2020638},
- issn = {1999-4893},
- url = {http://www.mdpi.com/1999-4893/2/2/638/}
+ number = {2}
+ issn = {1999-4893}
}
@ARTICLE{Zou2008,
@@ -951,11 +919,9 @@
and advanced data mining techniques provides a powerful metabolomic
approach for biomarker discovery among small molecules. Utilizing
GA for feature selection allowed the generation of small subsets
- of potent classifiers. Copyright © 2008 John Wiley & Sons, Ltd.},
- doi = {10.1002/rcm.3507},
+ of potent classifiers. Copyright © 2008 John Wiley & Sons, Ltd.}
issn = {1097-0231},
- publisher = {John Wiley \& Sons, Ltd.},
- url = {http://dx.doi.org/10.1002/rcm.3507}
+ publisher = {John Wiley \& Sons, Ltd.}
}
@comment{jabref-meta: selector_publisher:}
Modified: branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/technical.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/technical.tex 2012-04-26 12:58:17 UTC (rev 4213)
+++ branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/technical.tex 2012-04-27 17:07:17 UTC (rev 4214)
@@ -151,8 +151,8 @@
\citep{Faure2000}. This is especially helpful in providing an integrated GUI across
the many different kinds of document windows and tool views supported in \pkg{RKWard}.
-Plugins in \pkg{RKWard} rely on XML\footnote{\url{http://www.w3.org/XML/}}
-and \proglang{ECMAScript}\footnote{\url{http://www.ecmascript.org/}} (see Section~\ref{sec:technical_plugins}). XML is not
+Plugins in \pkg{RKWard} rely on XML\footnote{http://www.w3.org/XML/}
+and \proglang{ECMAScript}\footnote{http://www.ecmascript.org/} (see Section~\ref{sec:technical_plugins}). XML is not
only well suited to describe the layout of the GUI of plugins, but simple
functional logic can also be represented \citep[see also][]{Visne2009}. \proglang{ECMAScript} was
chosen for the generation of \proglang{R} commands within plugins, in particular due to its
@@ -306,8 +306,8 @@
\label{sec:technical_plugins_consistency}
\pkg{RKWard} tries to make it easy to create a consistent interface in all plugins.
GUI-wise this is supported by providing high-level GUI elements, and embeddable
-clients. Also, the standard elements of each dialog (``Submit'', and
-``Cancel'' buttons, on-the-fly code view, etc.) are hard coded. Up to version
+clients. Also, the standard elements of each dialog (\texttt{Submit}, and
+\texttt{Cancel} buttons, on-the-fly code view, etc.) are hard coded. Up to version
0.5.3 of \pkg{RKWard} it was not possible to use any GUI elements in plugins which
were not explicitly defined for this purpose. In the current development
version, theoretically, all GUI elements available from \pkg{Qt} can be inserted,
@@ -319,7 +319,7 @@
printed using \code{rk.print()}, which is just a thin wrapper around the
\code{HTML()} function of the \pkg{R2HTML} package \citep{Lecoutre2003} in the current
implementation. The use of custom formatting with HTML is possible, but
-discouraged. Standard elements such as a horizontal separator, and the ``Run again''
+discouraged. Standard elements such as a horizontal separator, and the \texttt{Run again}
link (see the section on the results output in the main article) are inserted automatically, without the need to define
them for each plugin.
@@ -346,7 +346,7 @@
\subsection[Handling of R package dependencies]{Handling of \proglang{R} package dependencies}
\label{sec:technical_plugins_dependencies}
A wide range of plugins for diverse functionality is present in \pkg{RKWard},
-including plots (e.\,g., boxplot) or standard tests (e.\,g., Student's t-test)\footnote{
+including plots (e.\,g., boxplot) or standard tests (e.\,g., Student's $t$~test)\footnote{
At the time of this writing, there are 164 user-accessible plugins in \pkg{RKWard}.
Listing all is beyond the scope of this article.
}. Some
@@ -376,17 +376,17 @@
appropriate plugin map.
With the release of version 0.5.5, \pkg{RKWard} gained support for downloading additional sets
-of plugins directly from the internet. By simply clicking an ``Install'' button in a graphical dialog
-(``Settings$\rightarrow$Configure RKWard$\rightarrow$Plugins''), an
+of plugins directly from the internet. By simply clicking an \texttt{Install} button in a graphical dialog
+(\texttt{Settings$\rightarrow$Configure RKWard$\rightarrow$Plugins}), an
external plugin set is downloaded, unpacked and its plugin map added to \pkg{RKWard}'s configuration, so
it becomes instantly available after the configuration dialog is closed. External plugin sets are
neither officially included nor supported by the \pkg{RKWard} developers. However, they allow plugin
developers to easily extend \pkg{RKWard} with state-of-the-art or highly specialized features. To
achieve this, \pkg{RKWard} draws on \pkg{KNewStuff2}\footnote{
- \url{http://websvn.kde.org/trunk/KDE/kdelibs/knewstuff/}
+ http://websvn.kde.org/trunk/KDE/kdelibs/knewstuff/
}, a \pkg{KDE} library providing support for \pkg{GHNS}\footnote{
\pkg{GHNS} (Get Hot New Stuff) is a technology platform (software and specifications) for desktop users to share their work. It is hosted
-under the umbrella of the freedesktop.org project (\url{http://ghns.freedesktop.org}).}.
+under the umbrella of the freedesktop.org project (http://ghns.freedesktop.org).}.
\subsubsection{Automated testing}
\label{sec:technical_processes_automatedtesting}
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