[rkward-cvs] SF.net SVN: rkward:[3273] branches/jss_dec_10/FINAL_JSS_TEX

tfry at users.sourceforge.net tfry at users.sourceforge.net
Mon Dec 20 08:24:43 UTC 2010

Revision: 3273
Author:   tfry
Date:     2010-12-20 08:24:42 +0000 (Mon, 20 Dec 2010)

Log Message:
Add section on package management, some formatting.

Modified Paths:

Modified: branches/jss_dec_10/FINAL_JSS_TEX/GUI_elements.tex
--- branches/jss_dec_10/FINAL_JSS_TEX/GUI_elements.tex	2010-12-20 07:41:08 UTC (rev 3272)
+++ branches/jss_dec_10/FINAL_JSS_TEX/GUI_elements.tex	2010-12-20 08:24:42 UTC (rev 3273)
@@ -15,7 +15,7 @@
 access point to most data import, manipulation, analysis and
 visualization features (see Section~\ref{sec:analyzing_data}) for which RKWard provides a GUI
 A status bar is shown at the bottom of the window. This contains (from
 right to left) an indication of the status of the
 \proglang{R} engine (busy or idle), a display of the
@@ -95,7 +95,7 @@
 however, it can also be configured to the submitted in the background,
-\subsection{Workspace browser and Object Viewer}
+\subsection{Workspace browser and object viewer}
 The workspace browser allows to view
@@ -123,15 +123,11 @@
 starting with a "."), or showing only the contents of .GlobalEnv as
 opposed to all environments on the search path.
-\subsection{Workspace browser and Object Viewer actions}
 Several actions are available from the context menu (by right-clicking
 on one of the objects), however some of these actions are only
 available for some types of objects. These allow to search the
 \proglang{R} help for information on that object, to
-open a window with detailed information about the object (see section
-XXX), to delete, rename or copy the object to a new symbol name, or to
+open a window with detailed information about the object, to delete, rename or copy the object to a new symbol name, or to
 copy it to the .GlobalEnv. Further the context menu allows to open
 supported types of objects for editing (see section ; currently, only
 data.frames can be edited, and only when inside the .GlobalEnv). 
@@ -141,16 +137,13 @@
 selection of objects to work with, e.g. in an analysis (see Section~\ref{sec:analyzing_data})
-\subsection{Object Viewer Window}
 Selecting View from the workspace
 browsers context menu opens a new window in the
 document area, which contains the basic information on the object. In
-addition this window has tabs which shows the output of
+addition this window has tabs which show the output of
 \code{print()}, and \code{summary()}.
-\subsection{Code Editor}
+\subsection{Code editor}
 RKWard comes with an advanced
@@ -245,7 +238,7 @@
 DeduceR. Correspondingly more than one data editor window can be opened
 at the same time (figure \ref{seq:refFigure4}).
-\subsection{Handling, Manipulating and Analyzing Data}
+\subsection{Handling, manipulating and analyzing data}
 Dealing with data, i.e. importing, transforming, filtering, analyzing, and visualizing data is the core
@@ -305,7 +298,7 @@
 action by clicking on the Run Again link
 (see section ).
-\subsection{Graphics Window and Plot Previews}
+\subsection{Graphics window and plot previews}
 For plotting, RKWard relies on the graphics capabilities provided by
@@ -400,8 +393,31 @@
 rendered by older supported versions of the
 \proglang{KDE} libraries.
+\subsection{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
+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
+action, the 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/Configure Packages``) for installing new or updating existing \proglang{R}
+packages. The underlying package management technology is that of \proglang{R}
+\citep{Ligges2003, Ripley2005}.
-\subsection{Further Tool Windows}
+RKWard supports installing packages to any user writable location. If no current
+library location is user writable, RKWard offers to create a new library
+location. On UNIX-systems, interactively acquiring administrator privileges for
+installation to the system-wide library is also supported. The dialog can be
+used for updating already installed packages. The user can choose whether to
+update all packages at once, or only selected packages. The installation process
+itself can be monitored from the interface for error tracking. At the time of this writing, RKWard has no
+built-in tools for the interactive exploration of \proglang{R} packages. However, it is
+possible to invoke external helpers \citep{Zhang2004}.
+\subsection{Further tool windows}
 The file browser tool window can be

Modified: branches/jss_dec_10/FINAL_JSS_TEX/example_session.tex
--- branches/jss_dec_10/FINAL_JSS_TEX/example_session.tex	2010-12-20 07:41:08 UTC (rev 3272)
+++ branches/jss_dec_10/FINAL_JSS_TEX/example_session.tex	2010-12-20 08:24:42 UTC (rev 3273)
@@ -1,4 +1,4 @@
-\section{Using RKWard- An example RKWard session}
+\section{Using RKWard - an example RKWard session}
 To see how RKWard works in practice an example session is described.
 This might be a routinely used procedure on changing data stets or
@@ -7,15 +7,15 @@
 treatment was given to 20 test subjects and the values of the dependent
 variable before and after the treatment should be compared. 
-\subsection{Importing Data}
+\subsection{Importing data}
 The data was saved as or exported to CSV format for example from a
 spread sheet application. RKWards import plugin can
 comfortably read it into a new \proglang{R} object.
-The import dialog ("File->Import->Import
-format->Import Text / CSV data") assists during the
+The import dialog (``File->Import->Import
+format->Import Text / CSV data'') assists during the
 selection of the data by a common point and click interface (Figure~\ref{fig:import_data}A). Within our
-example "comma" and "period" were chosen via "Quick mode" as field
+example ``comma'' and ``period'' were chosen via ``Quick mode'' as field
 separator character and decimal point character respectively. RKWard
 also takes care of name conflicts in the .GlobalEnv or suggests to
 overwrite or use another name.
@@ -24,7 +24,7 @@
 na.strings = NA, nrows = -1, skip = 0,
 check.names = TRUE, strip.white = FALSE, blank.lines.skip = TRUE)}
-Checking the "Edit Object" box will automatically open a data editor tab
+Checking the ``Edit Object'' box will automatically open a data editor tab
 showing the imported data (Figure~\ref{fig:import_data}B).
@@ -37,7 +37,7 @@
-\subsection{Conducting a Students t-test}
+\subsection{Conducting a Student's t-test}
 To test the hypothesis that the given treatment significantly increased
 the values of the dependent variable, a Students
@@ -52,16 +52,16 @@
-After the "Submit" button was pressed, RKWard opens the output document
+After the ``Submit'' button was pressed, RKWard opens the output document
 to show the results (Figure~\ref{fig:t_test}B).
-\subsection{Creating a Plot}
+\subsection{Creating a plot}
-To visualize the test data, "Boxplot" is chosen from the "Plots" menu
+To visualize the test data, ``Boxplot'' is chosen from the ``Plots'' menu
 and variables selected like for the Students t-test.
 The dialog allows to define custom variable labels (Figure~\ref{fig:boxplot1}).
-Checking the "Preview" box will open a graphics window, show the plot as
+Checking the ``Preview'' box will open a graphics window, show the plot as
 it is configured and update the window on changes in real time. From
 that window it can be exported directly to several data formats as
 well (Figure~\ref{fig:boxplot2}).

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