[rkward-cvs] SF.net SVN: rkward:[3401] branches/jss_dec_10/FINAL_JSS_TEX
tfry at users.sourceforge.net
tfry at users.sourceforge.net
Fri Jan 28 13:46:53 UTC 2011
Revision: 3401
http://rkward.svn.sourceforge.net/rkward/?rev=3401&view=rev
Author: tfry
Date: 2011-01-28 13:46:53 +0000 (Fri, 28 Jan 2011)
Log Message:
-----------
Assorted small changes. Mail follows.
Modified Paths:
--------------
branches/jss_dec_10/FINAL_JSS_TEX/GUI_elements.tex
branches/jss_dec_10/FINAL_JSS_TEX/RKWard_paper.tex
branches/jss_dec_10/FINAL_JSS_TEX/background.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/example_session.tex
branches/jss_dec_10/FINAL_JSS_TEX/revision_notes.txt
branches/jss_dec_10/FINAL_JSS_TEX/sources.bib
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 2011-01-28 12:32:29 UTC (rev 3400)
+++ branches/jss_dec_10/FINAL_JSS_TEX/GUI_elements.tex 2011-01-28 13:46:53 UTC (rev 3401)
@@ -299,8 +299,8 @@
basic recipe for most of the functionality provided by RKWard
(see Section~\ref{sec:technical_plugins} for details). For
the purpose of this article we will look at the standard
-elements of data handling functions by an example of importing CSV
-(comma separated values) data\footnote {
+elements of data handling functions by an example of importing comma-separated values (CSV)
+data\footnote {
Note that on purpose, RKWard does not have its
own file format for data import and export, but rather uses
\proglang{R} workspaces as default data format. Additionally, it is possible
@@ -451,8 +451,8 @@
pretty output. Rather, the focus is on making the results easily
accessible for further processing, typically in a dedicated word
processor. Output is based on
-\proglang{HTML} (hypertext markup language), and the raw
-\proglang{HTML} file and any images therein can be directly
+HTML, and the raw
+HTML file and any images therein can be directly
retrieved from a dedicated folder
($\sim\!$/.rkward, by default). It is also
possible to select and copy sections of the output directly from the
@@ -460,14 +460,13 @@
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 RKWard
with existing office suites. This
-will possibly also mean addition of different file formats such as ODF (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 \pkg{sweave} and \pkg{odfWeave}
\citep{Leisch2002, Kuhn2006}.
Images contained in the output are stored as
-PNG (portable network graphics)\footnote{\url{http://www.libpng.org/pub/png/}} by
-default, but JPEG\footnote{\url{http://www.jpeg.org/index.html}} and
-SVG (scalable vector graphics)\footnote{\url{http://www.w3.org/Graphics/SVG/}}
+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/}}
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
@@ -477,8 +476,8 @@
\subsection{Package management}
\label{sec:package_management}
-The number of \proglang{R} packages available from CRAN (the comprehensive \proglang{R} archive
-network), Omegahat\footnote{\url{http://www.omegahat.org/}} and Bioconductor \citep{Gentleman2004} has grown exponentially since \proglang{R}\, 1.3
+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
(2001) to \proglang{R}\, 2.7 (2008) \citep{Fox2008, Ligges2003, Visne2009}. RKWard
utilizes functionality from a growing number of these packages, but avoids
making the installation of all supported packages a pre-requirement to using
@@ -504,9 +503,9 @@
The file browser tool window can be
used to open supported file types (e.\,g., \proglang{R}
-scripts, \proglang{HTML} files) inside the main RKWard
-window. For unsupported file types (such as PDF; portable document format), the
-systems default external applications are used.
+scripts, HTML files) inside the main RKWard
+window. For unsupported file types (such as portable document format; PDF), the
+system's default external applications are used.
The command log window contains a log of the commands that have been
evaluated by the \proglang{R} engine, and any output
@@ -554,7 +553,7 @@
all loaded, or specific \proglang{R} packages for a specified topic.
The help browser window is based on the \proglang{KDE}
-\proglang{HTML} viewer component and supports many standard
+HTML viewer component and supports many standard
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
Modified: branches/jss_dec_10/FINAL_JSS_TEX/RKWard_paper.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/RKWard_paper.tex 2011-01-28 12:32:29 UTC (rev 3400)
+++ branches/jss_dec_10/FINAL_JSS_TEX/RKWard_paper.tex 2011-01-28 13:46:53 UTC (rev 3401)
@@ -31,7 +31,7 @@
comprehensive cross-platform GUI and an integrated development environment
for \proglang{R}. RKWard is based on the \proglang{KDE} software libraries. Statistical
procedures and plots are implemented using an extendable plugin
-architecture based on \proglang{ECMAScript} (\proglang{JavaScript}), \proglang{R}, and \proglang{XML}. RKWard
+architecture based on \proglang{ECMAScript} (\proglang{JavaScript}), \proglang{R}, and XML. RKWard
provides an excellent tool to manage different types of data objects;
even allowing for seamless editing of certain types. The objective of
RKWard is to provide a portable and extensible \proglang{R} interface for both
Modified: branches/jss_dec_10/FINAL_JSS_TEX/background.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/background.tex 2011-01-28 12:32:29 UTC (rev 3400)
+++ branches/jss_dec_10/FINAL_JSS_TEX/background.tex 2011-01-28 13:46:53 UTC (rev 3401)
@@ -61,10 +61,10 @@
time. RKWard is designed to allow users to create custom GUI dialogs
easily (see Sections~\ref{sec:technical_plugins} and \ref{sec:example_plugin}).
-RKWard is licensed under the terms of the GNU GPL (General Public License) Version 2
+RKWard is licensed under the terms of the GNU General Public License Version 2
or higher. However, due to its dependencies, RKWard binaries are effectively
-distributable only under the terms of the GPL Version 2. Parts of the documentation are
-GFDL (GNU Free Documentation License) licensed. While the project remains in constant development, a growing
+distributable only under the terms of Version 2 of the license. Parts of the documentation are available under the
+GNU Free Documentation License. While the project remains in constant development, a growing
number of users employs 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 RKWard are
Modified: branches/jss_dec_10/FINAL_JSS_TEX/conclusion_summary_acknowledgments.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/conclusion_summary_acknowledgments.tex 2011-01-28 12:32:29 UTC (rev 3400)
+++ branches/jss_dec_10/FINAL_JSS_TEX/conclusion_summary_acknowledgments.tex 2011-01-28 13:46:53 UTC (rev 3401)
@@ -11,7 +11,7 @@
\item Provides full transparency about the \proglang{R} code that is used to carry out tasks.
\item Avoids introducing RKWard-specific \proglang{R} functions for central functionality (but uses some for output formatting).
\item Avoids hard dependencies on third-party \proglang{R} packages.
- \item Uses standard \proglang{R} formats \citep[see][]{RDCT2010c} for data storage, and open standards (\proglang{HTML}, PNG, SVG) for storage of output.
+ \item Uses standard \proglang{R} formats \citep[see][]{RDCT2010c} for data storage, and open standards (HTML, PNG, SVG) for storage of output.
\end{itemize}
Future versions of RKWard will continue to add value for both groups of users. Planned features include
Modified: branches/jss_dec_10/FINAL_JSS_TEX/example_plugin.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/example_plugin.tex 2011-01-28 12:32:29 UTC (rev 3400)
+++ branches/jss_dec_10/FINAL_JSS_TEX/example_plugin.tex 2011-01-28 13:46:53 UTC (rev 3401)
@@ -49,14 +49,14 @@
\subsection {Defining the dialog GUI}
\label{sec:defining_dialog_ui}
-The main \proglang{XML} file of each plugin defines the layout and behavior of the GUI, and references the
+The main 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 GUI settings and the help file (not included in this paper).
-GUI logic can be defined directly in the \proglang{XML} file (the \code{<logic>} element).
+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.
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).
+The 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).
Modified: branches/jss_dec_10/FINAL_JSS_TEX/example_session.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/example_session.tex 2011-01-28 12:32:29 UTC (rev 3400)
+++ branches/jss_dec_10/FINAL_JSS_TEX/example_session.tex 2011-01-28 13:46:53 UTC (rev 3401)
@@ -55,7 +55,7 @@
\centering
\includegraphics[width=12.5cm]{../figures/t-test2.png}
\caption{A) Student's t-test dialog for two variables. The bottom area shows the \proglang{R} code corresponding to the settings.
- B) Test results in tabular \proglang{HTML} format.
+ B) Test results in tabular 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}
Modified: branches/jss_dec_10/FINAL_JSS_TEX/revision_notes.txt
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/revision_notes.txt 2011-01-28 12:32:29 UTC (rev 3400)
+++ branches/jss_dec_10/FINAL_JSS_TEX/revision_notes.txt 2011-01-28 13:46:53 UTC (rev 3401)
@@ -111,13 +111,13 @@
(using D-Bus, shell scripting, and many programming languages). Also, in the
context of this article, it is primarily used to name the KDE programming
libraries.
-* HTML, XML: We are not entirely sure, whether these markup languages are to be considered
- "programmable", but have decided to use the \proglang macro for these.
----- We have not used the \proglang macro on these items -----
* PNG, JPEG: Binary file formats.
* TSV, CSV: Text based file formats. We did not consider these as "programmable".
-* SVG, ODF: These are XML-based, and arguably "programmable". However, we decided not
+* HTML, XML: We are not entirely sure, whether these markup languages are to be considered
+ "programmable", but have decided not to use the \proglang macro for these.
+* SVG, ODF: These are XML-based, and, thus, arguably "programmable". However, we decided not
to use the \proglang macro, here, for consistency with the other file
storage formats.
* PDF: Although based on the PostScript programming language, we decided not to use
@@ -156,6 +156,8 @@
* Kate
* JPEG
* UNIX
+* HTML
+* XML
Further, we refrained from expanding the names of R packages such as "JGR", and any terms
marked up as \code.
@@ -168,11 +170,9 @@
* TDI (6)
* CSV (10)
* HTML (13)
-* ODF (13)
* PNG (13)
* SVG (13)
* CRAN (14)
* PDF (14-15)
* API (20)
-* XML (22)
* ECDF (25)
Modified: branches/jss_dec_10/FINAL_JSS_TEX/sources.bib
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/sources.bib 2011-01-28 12:32:29 UTC (rev 3400)
+++ branches/jss_dec_10/FINAL_JSS_TEX/sources.bib 2011-01-28 13:46:53 UTC (rev 3401)
@@ -292,7 +292,7 @@
@ARTICLE{Lecoutre2003,
author = {E Lecoutre},
- title = {The \pkg{R2HTML} Package - Formatting \proglang{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},
Modified: branches/jss_dec_10/FINAL_JSS_TEX/technical.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/technical.tex 2011-01-28 12:32:29 UTC (rev 3400)
+++ branches/jss_dec_10/FINAL_JSS_TEX/technical.tex 2011-01-28 13:46:53 UTC (rev 3401)
@@ -130,7 +130,7 @@
progress despite limited resources. Most importantly, the \proglang{KDE} libraries provide a
full featured text editor \citep{CullmannND} as a component which can be
seamlessly integrated into a host application using the KParts technology
-\citep{Faure2000}. Additionally, another KPart provides \proglang{HTML} browsing capabilities in a
+\citep{Faure2000}. Additionally, another KPart provides HTML browsing capabilities in a
similarly integrated way. The availability of KWord \citep{KWord} as an
embeddable KPart might prove useful in future versions of RKWard, when better
integration with office suites will be sought.
@@ -140,8 +140,8 @@
\citep{Faure2000}. This is especially helpful in providing an integrated GUI across
the many different kinds of document windows and tool views supported in RKWard.
-Plugins in RKWard rely on \proglang{XML} (extensible markup language)\footnote{\url{http://www.w3.org/XML/}}
-and \proglang{ECMAScript}\footnote{\url{http://www.ecmascript.org/}} (see Section~\ref{sec:technical_plugins}). \proglang{XML} is not
+Plugins in 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
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
@@ -222,13 +222,13 @@
\centering
\includegraphics[width=8cm]{../figures/plugin_structure.pdf}
\caption{Plugin structure of RKWard. One or more plugins are declared in a ``plugin map''. Each plugin is defined by
- two \proglang{XML} files, and one \proglang{ECMAScript} file.}
+ two XML files, and one \proglang{ECMAScript} file.}
\label{fig:plugin_structure}
\end{figure}
\begin{itemize}
\item
- An \proglang{XML} file (Section~\ref{sec:defining_menu_hierarchy}),
+ An XML file (Section~\ref{sec:defining_menu_hierarchy}),
called a ``plugin map'', is used to declare one or more plugins, each
with a unique identifier. For most plugins, the plugin map also defines the
placement in the menu hierarchy. Plugin maps are meant to represent groups of
@@ -236,10 +236,10 @@
complexity of the menu hierarchy.
\item
- A second \proglang{XML} file describes the plugin GUI layout itself (Section~\ref{sec:defining_dialog_ui}).
+ A second XML file describes the plugin GUI layout itself (Section~\ref{sec:defining_dialog_ui}).
Most importantly this includes
the definition of the GUI layout and GUI behavior. High level GUI elements can
- be defined with simple \proglang{XML}-tags. Layout is based on ``rows'' and ``columns'',
+ be defined with simple XML-tags. Layout is based on ``rows'' and ``columns'',
instead of pixel counts. In most cases this allows for a very sensible resizing
behavior. RKWard supports single-page dialogs and multi-page wizards, however,
most plugins define only a single-page GUI. GUI behavior can be programmed by
@@ -262,7 +262,7 @@
without the danger of overwriting user data.
\item
- A third \proglang{XML} file defines a help page. This help page usually links to the \proglang{R} help
+ A third XML file defines a help page. This help page usually links to the \proglang{R} help
pages of the main functions/concepts used by the plugin, as well as to other
related RKWard help pages. Compared to \proglang{R} help
pages, the plugin help pages try to give more hands-on advice on using the
@@ -277,14 +277,14 @@
RKWard supports several mechanisms for modularization and re-use of
functionality in plugins. File inclusion is one very simple but effective
mechanism, which can be used in the \proglang{ECMAScript} files, but is also supported in
-the \proglang{XML} files. In script files, this is most useful by defining common functions
-in an included file. For the \proglang{XML} files, the equivalent is to define ``snippets''
+the XML files. In script files, this is most useful by defining common functions
+in an included file. For the XML files, the equivalent is to define ``snippets''
in the included file, which can then be inserted.
A third mechanism allows to completely embed one plugin into another. For
instance the \code{plot\_options} plugin is used by many plugins in RKWard, to provide
common plot options such as labels, axis options, and grids. Other plugins
-can embed it using the \code{embed}-tag in their \proglang{XML} file (the plugin supports
+can embed it using the \code{embed}-tag in their XML file (the plugin supports
hiding irrelevant options). The generated code portions can be fetched from the
\proglang{ECMAScript} file just like any other GUI settings, and inserted into the complete
code. Other examples of embedded plugins are options for histograms, barplots,
@@ -306,7 +306,7 @@
tabular form is facilitated by \code{rk.results()}. A wide range of objects can be
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 \proglang{HTML} is possible, but
+implementation. The use of custom formatting with HTML is possible, but
discouraged. Standard elements such as a horizontal separator, and the ``Run again''
link (see Section~\ref{sec:results_output}) are inserted automatically, without the need to define
them for each plugin.
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