[rkward-cvs] SF.net SVN: rkward:[3626] branches/jss_dec_10

tfry at users.sourceforge.net tfry at users.sourceforge.net
Thu May 26 10:41:41 UTC 2011

Revision: 3626
Author:   tfry
Date:     2011-05-26 10:41:40 +0000 (Thu, 26 May 2011)

Log Message:
Redo Figure 8. Crop Figure 3. Updates for RKWard 0.5.6. Remove extra-figure section (see comment in the .tex)

Modified Paths:

Modified: branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/GUI_elements.tex
--- branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/GUI_elements.tex	2011-05-26 07:51:56 UTC (rev 3625)
+++ branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/GUI_elements.tex	2011-05-26 10:41:40 UTC (rev 3626)
@@ -144,10 +144,10 @@
 \proglang{R} and many other script types), code
 folding, block-wise indentation adjustments or commenting, automatic
 brackets, search and replace with plain text or regular expressions,
-and many more. The editor automatically saves snapshots of the
+and many more. Further, \pkg{Kate} can be extended by 
+customized actions implemented in \proglang{ECMAScript}\footnote{\url{http://kate-editor.org/2010/07/09/kate-scripted-actions}}.
+The editor automatically saves snapshots of the
 currently edited files at configurable intervals. 
-It is noteworthy that \pkg{Kate} is extendable by 
-customized \proglang{ECMAScript} (\proglang{JavaScript}) actions\footnote{\url{http://kate-editor.org/2010/07/09/kate-scripted-actions}}.
 For interaction with \proglang{R}, the editor has
 predefined shortcuts (and toolbar icons) for submitting the current line, the current 
@@ -441,10 +441,13 @@
- \caption{Sample contents of the output window (red square). \code{DNase} and \code{ChickWeight} data of the \pkg{datasets} packages were used. 
-  Standard elements of plugin output include a standardized header, and a 
+ \caption{Sample contents of the output window. Upper portion: Result of analyzing sample data (from the \code{DNase} and \code{ChickWeight}
+  datasets of the \pkg{datasets} package) in the ``Descriptive Statistics'' plugin. Standard elements of plugin output include a standardized header, and a 
   ``Run again''-link, which allows to repeat the analysis with identical or 
-  similar parameters (Details of the previous analysis are shown in the status bar when the mouse pointer hovers over the ``Run again''-link). See also Figure 4 in the supplementary section accompining this paper.}
+  similar parameters. Lower portion: A custom heading added using the \code{rk.header()} function, and a short transcript of R code and the 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)
@@ -456,7 +459,7 @@
 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
+(by default, this is a folder named ``.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, 
@@ -475,7 +478,11 @@
 files produced by \proglang{R} are not properly
 rendered by older supported versions of the
 \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, and the corresponding 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}
 The number of \proglang{R} packages available from the comprehensive \proglang{R} archive
@@ -521,7 +528,8 @@
 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 lists current \proglang{R} commands waiting for
+available. The ``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
 purposes, it can also be used to interrupt selected commands.

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	2011-05-26 07:51:56 UTC (rev 3625)
+++ branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/RKWard_annex.tex	2011-05-26 10:41:40 UTC (rev 3626)
@@ -88,6 +88,8 @@
+% TF: I'm worried that this will look like bike-shedding to the editors. So we have been given permission to keep our technical section,
+% but I don't think that counts as permission to add too much new content (with the expection to stuff that is new in 0.5.6).

Modified: branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/TODO
--- branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/TODO	2011-05-26 07:51:56 UTC (rev 3625)
+++ branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/TODO	2011-05-26 10:41:40 UTC (rev 3626)
@@ -3,7 +3,7 @@
 - Update screenshots:
 Figure number   |   Importance   |   Comments
 2                   high             no more Pending Jobs tool view, toolbar changed, status bar changed, could show an S4 object in workspace browser (please choose)
-3                   very low         could hide ".GlobalEnv", here (Done)
+3                   very low         reduced size (no purpose in showing workspace browser, etc., here. (Done)
 5                   high             see Figure 2. Should probably uncheck "Show all Environments" (Done)
 8                   medium           minimally improved default CSS. Should include short snippet of syntax highlighted commands / console transcript (Done?)
 10                  high             no longer shows ".GlobalEnv" (addresses reviewer comment) (Done)

Modified: branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/figures/code_hinting.png
(Binary files differ)

Modified: branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/figures/results_output_cropped.png
(Binary files differ)

Modified: branches/jss_dec_10/examples/demo.R
--- branches/jss_dec_10/examples/demo.R	2011-05-26 07:51:56 UTC (rev 3625)
+++ branches/jss_dec_10/examples/demo.R	2011-05-26 10:41:40 UTC (rev 3626)
@@ -71,8 +71,17 @@
 ## Figure 8
 rk.call.plugin ("rkward::descriptive", constMad.real="1.4628", length.state="1", mad.state="0", mad_type.string="average", mean.state="1", median.state="1", prod.state="0", range.state="1", sd.state="1", sum.state="0", trim.real="0.00", x.available="DNase[[\"density\"]]\nDNase[[\"conc\"]]\nChickWeight[[\"weight\"]]\nChickWeight[[\"Time\"]]", submit.mode="submit")
-ok.to.proceed ("<b>Replication of Figure 8</b>:<br>The result of running the 'Descriptive Statistics' plugin should now be visible in the output window. If it is not visible, use Windows->Show Output from the menu.")
+rk.header ("A custom heading")
+ok.to.proceed ("<b>Replication of Figure 8, upper portion</b>:<br>The result of running the 'Descriptive Statistics' plugin, and the
+text 'A custom heading' should now be visible in the output window. If it is not visible, use Windows->Show Output from the menu.")
+f <- function () {
+    # The only purpose of this function is to illustrate the documentation of
+    # custom R code and the corresponding R output in the RKWard output window
+    print ("A piece of output")
+f ()
+ok.to.proceed ("<b>Replication of Figure 8, lower portion</b>:<br>This part of the figure can only be reproduced by interacting with the GUI, manually:<br>Run->CC commands to ouptut... from the menu, and enable copying of commands entered in the console. Then, paste the code snippet to the console.")
 ## Figure 9
 rk.call.plugin ("rkward::import_csv", quick.string="csv", name.objectname="experiment.data", file.selection=paste (getwd (), "experiment.txt", sep="/"))

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