[rkward-cvs] SF.net SVN: rkward:[3275] branches/jss_dec_10/FINAL_JSS_TEX
sjar at users.sourceforge.net
sjar at users.sourceforge.net
Mon Dec 20 10:52:49 UTC 2010
Revision: 3275
http://rkward.svn.sourceforge.net/rkward/?rev=3275&view=rev
Author: sjar
Date: 2010-12-20 10:52:49 +0000 (Mon, 20 Dec 2010)
Log Message:
-----------
* sources.bib needed a cleanup
* another source added to paper
* some minor tweaks
Modified Paths:
--------------
branches/jss_dec_10/FINAL_JSS_TEX/GUI_elements.tex
branches/jss_dec_10/FINAL_JSS_TEX/background.tex
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 2010-12-20 08:49:15 UTC (rev 3274)
+++ branches/jss_dec_10/FINAL_JSS_TEX/GUI_elements.tex 2010-12-20 10:52:49 UTC (rev 3275)
@@ -356,7 +356,7 @@
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
-applied, since some of the \proglang{R} objects in
+applied, since some of the \proglang{R} objectsf in
question are no longer available, the user will be notified.} (see
figure \ref{seq:refFigure6}). Thus, the Run
Again feature combines the documentation of the result
@@ -398,8 +398,8 @@
\subsection{Package management}
\label{sec:package_management}
The number of \proglang{R} packages available from CRAN (the comprehensive \proglang{R} archive
-network), Omegahat and Bioconductor has grown exponentially since \proglang{R} v. 1.3
-(2001) to \proglang{R} v. 2.7 (2008) \citep{Fox2008, Ligges2003, Visne2009}. RKWard
+network), Omegahat\footnote{\url{http://www.omegahat.org/}} and Bioconductor \citep{Gentleman2004} has grown exponentially since \proglang{R} v. 1.3
+(2001) to \proglang{R} v. 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
RKWard at all. Once a non-installed package is required to conduct a certain
Modified: branches/jss_dec_10/FINAL_JSS_TEX/background.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/background.tex 2010-12-20 08:49:15 UTC (rev 3274)
+++ branches/jss_dec_10/FINAL_JSS_TEX/background.tex 2010-12-20 10:52:49 UTC (rev 3275)
@@ -41,7 +41,13 @@
complete code for all GUI actions. In doing so RKWard accepts relatively verbose
generated code, deliberately. In particular, RKWard limits itself to generate R
code from GUI settings. It avoids wrapping complex sequences of data
-manipulation or analysis into custom high-level \proglang{R} functions. The task of
+manipulation or analysis into custom high-level \proglang{R} functions. This distinguishes RKWard from
+other \proglang{R} GUIs like Red-R\footnote{\url{http://www.red-r.org/}.
+Red-R is a GUI for \proglang{R} which uses the concept of data-flow
+programming \citep{Sutherland1966} to allow the
+user a visual programming without deep knowledge of
+\proglang{R}.} which specifically aims to hide the
+programming complexety. The task of
providing high-level functions is logically independent of the development the
GUI frontend, and should best be solved in dedicated \proglang{R} packages, where needed.
This approach allows to make better use of the modular design of \proglang{R}, avoids
Modified: branches/jss_dec_10/FINAL_JSS_TEX/sources.bib
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/sources.bib 2010-12-20 08:49:15 UTC (rev 3274)
+++ branches/jss_dec_10/FINAL_JSS_TEX/sources.bib 2010-12-20 10:52:49 UTC (rev 3275)
@@ -23,8 +23,7 @@
}
@BOOK{RossiB2010,
- title = {Download Patterns and Releases in Open Source Software Projects:
- A Perfect Symbiosis?},
+ title = {Download Patterns and Releases in Open Source Software Projects: A Perfect Symbiosis?},
publisher = {Springer Boston},
year = {2010},
editor = {Springer Boston},
@@ -34,27 +33,12 @@
comment = {ISSN 1868-4238, ISBN 978-3-642-13243-8},
doi = {10.1007/978-3-642-13244-5_20},
owner = {tux},
- review = {Software usage by end-users is one of the factors used to evaluate
- the success of software projects. In the context of open source software,
- there is no single and non-controversial measure of usage, though.
- Still, one of the most used and readily available measure is data
- about projects downloads. Nevertheless, download counts and averages
- do not convey as much information as the patterns in the original
- downloads time series. In this research, we propose a method to increase
- the expressiveness of mere download rates by considering download
- patterns against software releases. We apply experimentally our method
- to the most downloaded projects of SourceForge’s history crawled
- through the FLOSSMole repository. Findings show that projects with
- similar usage can have indeed different levels of sensitivity to
- releases, revealing different behaviors of users. Future research
- will develop further the pattern recognition approach to automatically
- categorize open source projects according to their download patterns.},
+ review = {Software usage by end-users is one of the factors used to evaluate the success of software projects. In the context of open source software, there is no single and non-controversial measure of usage, though. Still, one of the most used and readily available measure is data about projects downloads. Nevertheless, download counts and averages do not convey as much information as the patterns in the original downloads time series. In this research, we propose a method to increase the expressiveness of mere download rates by considering download patterns against software releases. We apply experimentally our method to the most downloaded projects of SourceForge’s history crawled through the FLOSSMole repository. Findings show that projects with similar usage can have indeed different levels of sensitivity to releases, revealing different behaviors of users. Future research will develop further the pattern recognition approach to automatically categorize open source projects according to their download patterns.},
timestamp = {2010.07.01}
}
@BOOK{BlanchetteSummerfield2008,
- title = {C++ GUI Programming with Qt 4 (2nd Edition) (Prentice Hall Open Source
- Software Development Series)},
+ title = {C++ GUI Programming with Qt 4 (2nd Edition) (Prentice Hall Open Source Software Development Series)},
publisher = {Prentice Hall},
year = {2008},
author = {Jasmin Blanchette and Mark Summerfield},
@@ -181,12 +165,7 @@
@MANUAL{Rcmdr2010,
title = {Rcmdr: R Commander},
- author = {John Fox and with contributions from Liviu Andronic and Michael Ash
- and Theophilius Boye and Stefano Calza and Andy Chang and Philippe
- Grosjean and Richard Heiberger and G. Jay Kerns and Renaud Lancelot
- and Matthieu Lesnoff and Uwe Ligges and Samir Messad and Martin Maechler
- and Robert Muenchen and Duncan Murdoch and Erich Neuwirth and Dan
- Putler and Brian Ripley and Miroslav Ristic and and Peter Wolf.},
+ author = {John Fox and with contributions from Liviu Andronic and Michael Ash and Theophilius Boye and Stefano Calza and Andy Chang and Philippe Grosjean and Richard Heiberger and G. Jay Kerns and Renaud Lancelot and Matthieu Lesnoff and Uwe Ligges and Samir Messad and Martin Maechler and Robert Muenchen and Duncan Murdoch and Erich Neuwirth and Dan Putler and Brian Ripley and Miroslav Ristic and and Peter Wolf.},
year = {2010},
note = {R package version 1.6-2},
owner = {tux},
@@ -203,6 +182,21 @@
url = {http://rkward.sourceforge.net/documents/devel/plugins/index.html}
}
+ at Article{Gentleman2004,
+AUTHOR = {Gentleman, Robert and Carey, Vincent and Bates, Douglas and Bolstad, Ben and Dettling, Marcel and Dudoit, Sandrine and Ellis, Byron and Gautier, Laurent and Ge, Yongchao and Gentry, Jeff and Hornik, Kurt and Hothorn, Torsten and Huber, Wolfgang and Iacus, Stefano and Irizarry, Rafael and Leisch, Friedrich and Li, Cheng and Maechler, Martin and Rossini, Anthony and Sawitzki, Gunther and Smith, Colin and Smyth, Gordon and Tierney, Luke and Yang, Jean and Zhang, Jianhua},
+TITLE = {Bioconductor: open software development for computational biology and bioinformatics},
+JOURNAL = {Genome Biology},
+VOLUME = {5},
+YEAR = {2004},
+NUMBER = {10},
+PAGES = {R80},
+URL = {http://genomebiology.com/2004/5/10/R80},
+DOI = {10.1186/gb-2004-5-10-r80},
+PubMedID = {15461798},
+ISSN = {1465-6906},
+ABSTRACT = {The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry 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.},
+}
+
@ARTICLE{HelbigTheus2005,
author = {Markus Helbig and Martin Theus},
title = {JGR: JAVA GUI FOR {R}},
@@ -245,18 +239,7 @@
author = {James Kim and Christof Lutteroth},
title = {Multi-Platform Document-Oriented GUIs},
year = {2010},
- abstract = {In recent years, increasing complexity of graphical user interfaces
- (GUIs) of applications has led to problems in GUI management, since
- there is no single layout to fulfill every user’s needs. GUI editors
- have been developed to enhance end-user options but they commonly
- fail to preserve personalized GUIs. This paper presents an extension
- to the GUI editor built into the Auckland Layout Model (ALM) that
- can permanently store user-defined GUI layouts and reproduce them
- on different platforms. A novel technique called the document-oriented
- approach has been exploited to empower end-user customization, which
- allows GUI layouts to be dynamically edited, saved using a standardized
- XML-based GUI description language, and loaded in a platform-independent
- manner.},
+ abstract = {In recent years, increasing complexity of graphical user interfaces (GUIs) of applications has led to problems in GUI management, since there is no single layout to fulfill every user’s needs. GUI editors have been developed to enhance end-user options but they commonly fail to preserve personalized GUIs. This paper presents an extension to the GUI editor built into the Auckland Layout Model (ALM) that can permanently store user-defined GUI layouts and reproduce them on different platforms. A novel technique called the document-oriented approach has been exploited to empower end-user customization, which allows GUI layouts to be dynamically edited, saved using a standardized XML-based GUI description language, and loaded in a platform-independent manner.},
institution = {CiteSeerX - Scientific Literature Digital Library and Search Engine
[http://citeseerx.ist.psu.edu/oai2] (United States)},
keywords = {GUI customization, platform-independent GUIs, ALM},
@@ -281,8 +264,7 @@
@ARTICLE{Lecoutre2003,
author = {E Lecoutre},
- title = {The R2HTML Package - Formatting HTML output on the fly or by using
- a template scheme},
+ title = {The R2HTML Package - Formatting HTML output on the fly or by using a template scheme},
journal = {R News},
year = {2003},
volume = {3},
@@ -301,10 +283,7 @@
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.},
+ 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}
}
@@ -355,8 +334,7 @@
@ARTICLE{Newton2007,
author = {Richard Newton and Lorenz Wernisch},
- title = {{Rwui}: A Web Application to Create User Friendly Web Interfaces
- for {R} Scripts},
+ title = {{Rwui}: A Web Application to Create User Friendly Web Interfaces for {R} Scripts},
journal = {R News},
year = {2007},
volume = {7},
@@ -493,37 +471,14 @@
}
@ARTICLE{Visne2009,
- author = {Visne, Ilhami and Dilaveroglu, Erkan and Vierlinger, Klemens and
- Lauss, Martin and Yildiz, Ahmet and Weinhaeusel, Andreas and Noehammer,
- Christa and Leisch, Friedrich and Kriegner, Albert},
+ author = {Visne, Ilhami and Dilaveroglu, Erkan and Vierlinger, Klemens and Lauss, Martin and Yildiz, Ahmet and Weinhaeusel, Andreas and Noehammer, Christa and Leisch, Friedrich and Kriegner, Albert},
title = {RGG: A general GUI Framework for R scripts},
journal = {BMC Bioinformatics},
year = {2009},
volume = {10},
pages = {74},
number = {1},
- abstract = {BACKGROUND:R is the leading open source statistics software with a
- vast number of biostatistical and bioinformatical analysis packages.
- To exploit the advantages of R, extensive scripting/programming skills
- are required.RESULTS:We have developed a software tool called R GUI
- Generator (RGG) which enables the easy generation of Graphical User
- Interfaces (GUIs) for the programming language R by adding a few
- Extensible Markup Language (XML) - tags. RGG consists of an XML-based
- GUI definition language and a Java-based GUI engine. GUIs are generated
- in runtime from defined GUI tags that are embedded into the R script.
- User-GUI input is returned to the R code and replaces the XML-tags.
- RGG files can be developed using any text editor. The current version
- of RGG is available as a stand-alone software (RGGRunner) and as
- a plug-in for JGR.CONCLUSION:RGG is a general GUI framework for R
- that has the potential to introduce R statistics (R packages, built-in
- functions and scripts) to users with limited programming skills and
- helps to bridge the gap between R developers and GUI-dependent users.
- RGG aims to abstract the GUI development from individual GUI toolkits
- by using an XML-based GUI definition language. Thus RGG can be easily
- 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},
+ abstract = {BACKGROUND:R is the leading open source statistics software with a vast number of biostatistical and bioinformatical analysis packages. To exploit the advantages of R, extensive scripting/programming skills are required.RESULTS:We have developed a software tool called R GUI Generator (RGG) which enables the easy generation of Graphical User Interfaces (GUIs) for the programming language R by adding a few Extensible Markup Language (XML) - tags. RGG consists of an XML-based GUI definition language and a Java-based GUI engine. GUIs are generated in runtime from defined GUI tags that are embedded into the R script. User-GUI input is returned to the R code and replaces the XML-tags. RGG files can be developed using any text editor. The current version of RGG is available as a stand-alone software (RGGRunner) and as a plug-in for JGR.CONCLUSION:RGG is a general GUI framework for R that has the potential to introduce R statistics (R packages, built-in functions and scripts) to users with limited programming skills and helps to bridge the gap between R developers and GUI-dependent users. RGG aims to abstract the GUI development from individual GUI toolkits by using an XML-based GUI definition language. Thus RGG can be easily 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},
issn = {1471-2105},
owner = {tux},
@@ -532,32 +487,18 @@
url = {http://www.biomedcentral.com/1471-2105/10/74}
}
- at ARTICLE{RaffelsbergerW2008,
- author = {W Raffelsberger,Y Krause,L Moulinier,D Kieffer,AL Morand, L Brino
- and O Poch},
- title = {RReportGenerator: automatic reports from routine statistical analysis
- using R},
- journal = {BIOINFORMATICS},
- year = {2008},
- volume = {24},
- pages = {276-278},
- number = {2},
- abstract = {Summary: With the establishment of high-throughput (HT) screening
- methods there is an increasing need for automatic analysis methods.
- Here we present RReportGenerator, a user-friendly portal for automatic
- routine analysis using the statistical platform R and Bioconductor.
- RReportGenerator is designed to analyze data using predefined analysis
- scenarios via a graphical user interface (GUI). A report in pdf format
- combining text, figures and tables is auto- matically generated and
- results may be exported. To demonstrate suitable analysis tasks we
- provide direct web access to a collection of analysis scenarios for
- summarizing data from transfected cell arrays (TCA), segmentation
- 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/~wraff},
- doi = {Vol. 24 no. 2 2008, pages 276–278 doi:10.1093/bioinformatics/btm556},
- owner = {tux},
- timestamp = {2010.07.01}
+ at article{RaffelsbergerW2008,
+author = {Raffelsberger, Wolfgang and Krause, Yannick and Moulinier, Luc and Kieffer, David and Morand, Anne-Laure and Brino, Laurent and Poch, Olivier},
+title = {{RReportGenerator: automatic reports from routine statistical analysis using R}},
+volume = {24},
+number = {2},
+pages = {276-278},
+year = {2008},
+doi = {10.1093/bioinformatics/btm556},
+abstract ={Summary: With the establishment of high-throughput (HT) screening methods there is an increasing need for automatic analysis methods. Here we present RReportGenerator, a user-friendly portal for automatic routine analysis using the statistical platform R and Bioconductor. RReportGenerator is designed to analyze data using predefined analysis scenarios via a graphical user interface (GUI). A report in pdf format combining text, figures and tables is automatically generated and results may be exported. To demonstrate suitable analysis tasks we provide direct web access to a collection of analysis scenarios for summarizing data from transfected cell arrays (TCA), segmentation 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},
+URL = {http://bioinformatics.oxfordjournals.org/content/24/2/276.abstract},
+eprint = {http://bioinformatics.oxfordjournals.org/content/24/2/276.full.pdf+html},
+journal = {Bioinformatics}
}
@ARTICLE{Young_2004,
@@ -588,8 +529,7 @@
journal = {ACM},
year = {2005},
pages = {67-72},
- comment = {Open Source Application Spaces: Fifth Workshop on Open Source Software
- Engineering (5-WOSSE)},
+ comment = {Open Source Application Spaces: Fifth Workshop on Open Source Software Engineering (5-WOSSE)},
owner = {tux},
timestamp = {2010.07.01}
}
Modified: branches/jss_dec_10/FINAL_JSS_TEX/technical.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/technical.tex 2010-12-20 08:49:15 UTC (rev 3274)
+++ branches/jss_dec_10/FINAL_JSS_TEX/technical.tex 2010-12-20 10:52:49 UTC (rev 3275)
@@ -150,7 +150,7 @@
Contrary to the approach used in \pkg{JGR} \citep{HelbigTheus2005}, RKWard does
not technically provide a custom on-screen graphics device. RKWard detects when
new graphics windows are created via calls to \code{X11()} or \code{windows()}. These windows
-are then “captured” in a platform dependent way (based on the XEmbed\footnote{\citep{Ettrich2002}} protocol
+are then "captured" in a platform dependent way (based on the XEmbed\footnote{\citep{Ettrich2002}} protocol
for X11, on reparenting for the Windows platform). An RKWard menu bar and a
toolbar is then added to these windows to provide added functionality. While
this approach requires some platform dependent code, any corrections or
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