/usr/share/doc/ess/html/ess.html is in ess 15.09.2-3.
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<body lang="en">
<h1 class="settitle" align="center">ESS – Emacs Speaks Statistics</h1>
<a name="SEC_Contents"></a>
<h2 class="contents-heading">Table of Contents</h2>
<div class="contents">
<ul class="no-bullet">
<li><a name="toc-Introduction-to-ESS" href="#Introduction">1 Introduction to ESS</a>
<ul class="no-bullet">
<li><a name="toc-Why-should-I-use-ESS_003f" href="#Features">1.1 Why should I use ESS?</a>
<ul class="no-bullet">
<li><a name="toc-Features-Overview" href="#Current-Features">1.1.1 Features Overview</a></li>
</ul></li>
<li><a name="toc-New-features-in-ESS" href="#New-features">1.2 New features in ESS</a></li>
<li><a name="toc-Authors-of-and-contributors-to-ESS" href="#Credits">1.3 Authors of and contributors to ESS</a></li>
<li><a name="toc-Getting-the-latest-version-of-ESS" href="#Latest-version">1.4 Getting the latest version of ESS</a>
<ul class="no-bullet">
<li><a name="toc-Git-for-ESS-development" href="#Git-for-ESS-development">1.4.1 Git for ESS development</a></li>
</ul></li>
<li><a name="toc-How-to-read-this-manual" href="#Manual">1.5 How to read this manual</a></li>
</ul></li>
<li><a name="toc-Installing-ESS-on-your-system" href="#Installation">2 Installing ESS on your system</a>
<ul class="no-bullet">
<li><a name="toc-Step-by-step-instructions-1" href="#Step-by-step-instructions">2.1 Step by step instructions</a></li>
<li><a name="toc-License-1" href="#License">2.2 License</a></li>
<li><a name="toc-Stability-1" href="#Stability">2.3 Stability</a></li>
<li><a name="toc-Requirements-1" href="#Requirements">2.4 Requirements</a></li>
</ul></li>
<li><a name="toc-Interacting-with-statistical-programs" href="#Interactive-ESS">3 Interacting with statistical programs</a>
<ul class="no-bullet">
<li><a name="toc-Starting-an-ESS-process" href="#Starting-up">3.1 Starting an ESS process</a></li>
<li><a name="toc-Running-more-than-one-ESS-process" href="#Multiple-ESS-processes">3.2 Running more than one ESS process</a></li>
<li><a name="toc-ESS-processes-on-Remote-Computers-1" href="#ESS-processes-on-Remote-Computers">3.3 ESS processes on Remote Computers</a></li>
<li><a name="toc-S_002belsewhere-and-ESS_002delsewhere-1" href="#S_002belsewhere-and-ESS_002delsewhere">3.4 S+elsewhere and ESS-elsewhere</a></li>
<li><a name="toc-Changing-the-startup-actions" href="#Customizing-startup">3.5 Changing the startup actions</a></li>
</ul></li>
<li><a name="toc-Interacting-with-the-ESS-process" href="#Entering-commands">4 Interacting with the ESS process</a>
<ul class="no-bullet">
<li><a name="toc-Entering-commands-and-fixing-mistakes" href="#Command_002dline-editing">4.1 Entering commands and fixing mistakes</a></li>
<li><a name="toc-Manipulating-the-transcript" href="#Transcript">4.2 Manipulating the transcript</a>
<ul class="no-bullet">
<li><a name="toc-Manipulating-the-output-from-the-last-command" href="#Last-command">4.2.1 Manipulating the output from the last command</a></li>
<li><a name="toc-Viewing-older-commands" href="#Process-buffer-motion">4.2.2 Viewing older commands</a></li>
<li><a name="toc-Re_002dsubmitting-commands-from-the-transcript" href="#Transcript-resubmit">4.2.3 Re-submitting commands from the transcript</a></li>
<li><a name="toc-Keeping-a-record-of-your-S-session" href="#Saving-transcripts">4.2.4 Keeping a record of your S session</a></li>
</ul></li>
<li><a name="toc-Command-History-1" href="#Command-History">4.3 Command History</a>
<ul class="no-bullet">
<li><a name="toc-Saving-the-command-history" href="#Saving-History">4.3.1 Saving the command history</a></li>
</ul></li>
<li><a name="toc-References-to-historical-commands" href="#History-expansion">4.4 References to historical commands</a></li>
<li><a name="toc-Hot-keys-for-common-commands" href="#Hot-keys">4.5 Hot keys for common commands</a></li>
<li><a name="toc-Is-the-Statistical-Process-running-under-ESS_003f" href="#Statistical-Process-running-in-ESS_003f">4.6 Is the Statistical Process running under ESS?</a></li>
<li><a name="toc-Using-emacsclient" href="#Emacsclient">4.7 Using emacsclient</a></li>
<li><a name="toc-Other-commands-provided-by-inferior_002dESS" href="#Other">4.8 Other commands provided by inferior-ESS</a></li>
</ul></li>
<li><a name="toc-Sending-code-to-the-ESS-process" href="#Evaluating-code">5 Sending code to the ESS process</a></li>
<li><a name="toc-Manipulating-saved-transcript-files" href="#Transcript-Mode">6 Manipulating saved transcript files</a>
<ul class="no-bullet">
<li><a name="toc-Resubmitting-commands-from-the-transcript-file" href="#Resubmit">6.1 Resubmitting commands from the transcript file</a></li>
<li><a name="toc-Cleaning-transcript-files" href="#Clean">6.2 Cleaning transcript files</a></li>
</ul></li>
<li><a name="toc-Editing-objects-and-functions" href="#Editing-objects">7 Editing objects and functions</a>
<ul class="no-bullet">
<li><a name="toc-Creating-or-modifying-S-objects" href="#Edit-buffer">7.1 Creating or modifying S objects</a></li>
<li><a name="toc-Loading-source-files-into-the-ESS-process" href="#Loading">7.2 Loading source files into the ESS process</a></li>
<li><a name="toc-Detecting-errors-in-source-files" href="#Error-Checking">7.3 Detecting errors in source files</a></li>
<li><a name="toc-Indenting-and-formatting-S-code" href="#Indenting">7.4 Indenting and formatting S code</a>
<ul class="no-bullet">
<li><a name="toc-Changing-indentation-styles" href="#Styles">7.4.1 Changing indentation styles</a></li>
</ul></li>
<li><a name="toc-Commands-for-motion_002c-completion-and-more" href="#Other-edit-buffer-commands">7.5 Commands for motion, completion and more</a></li>
<li><a name="toc-Maintaining-S-source-files" href="#Source-Files">7.6 Maintaining S source files</a></li>
<li><a name="toc-Names-and-locations-of-dump-files" href="#Source-Directories">7.7 Names and locations of dump files</a></li>
</ul></li>
<li><a name="toc-Reading-help-files" href="#Help">8 Reading help files</a></li>
<li><a name="toc-Completion-1" href="#Completion">9 Completion</a>
<ul class="no-bullet">
<li><a name="toc-Completion-of-object-names" href="#Object-names">9.1 Completion of object names</a></li>
<li><a name="toc-Completion-of-function-arguments" href="#Function-arguments">9.2 Completion of function arguments</a></li>
<li><a name="toc-Minibuffer-completion-1" href="#Minibuffer-completion">9.3 Minibuffer completion</a></li>
<li><a name="toc-Integration-with-auto_002dcomplete-package" href="#Auto_002dcomplete">9.4 Integration with auto-complete package</a></li>
<li><a name="toc-Icicles-1" href="#Icicles">9.5 Icicles</a></li>
</ul></li>
<li><a name="toc-Developing-with-ESS-1" href="#Developing-with-ESS">10 Developing with ESS</a>
<ul class="no-bullet">
<li><a name="toc-ESS-tracebug-1" href="#ESS-tracebug">10.1 ESS tracebug</a></li>
<li><a name="toc-Editing-documentation-1" href="#Editing-documentation">10.2 Editing documentation</a>
<ul class="no-bullet">
<li><a name="toc-Editing-R-documentation-_0028Rd_0029-files" href="#R-documentation-files">10.2.1 Editing R documentation (Rd) files</a></li>
<li><a name="toc-Editing-Roxygen-documentation" href="#Roxygen">10.2.2 Editing Roxygen documentation</a></li>
</ul></li>
<li><a name="toc-ESS-developer-1" href="#ESS-developer">10.3 ESS developer</a></li>
</ul></li>
<li><a name="toc-Other-ESS-features-and-tools" href="#Extras">11 Other ESS features and tools</a>
<ul class="no-bullet">
<li><a name="toc-ElDoc" href="#ESS-ElDoc">11.1 ElDoc</a></li>
<li><a name="toc-Handy-commands-1" href="#Handy-commands">11.2 Handy commands</a></li>
<li><a name="toc-Syntactic-highlighting-of-buffers" href="#Highlighting">11.3 Syntactic highlighting of buffers</a></li>
<li><a name="toc-Parenthesis-matching" href="#Parens">11.4 Parenthesis matching</a></li>
<li><a name="toc-Using-graphics-with-ESS" href="#Graphics">11.5 Using graphics with ESS</a>
<ul class="no-bullet">
<li><a name="toc-Using-ESS-with-the-printer_0028_0029-driver" href="#printer">11.5.1 Using ESS with the <code>printer()</code> driver</a></li>
<li><a name="toc-Using-ESS-with-windowing-devices" href="#X11">11.5.2 Using ESS with windowing devices</a></li>
<li><a name="toc-Java-Graphics-Device" href="#winjava">11.5.3 Java Graphics Device</a></li>
</ul></li>
<li><a name="toc-Imenu-1" href="#Imenu">11.6 Imenu</a></li>
<li><a name="toc-Toolbar-1" href="#Toolbar">11.7 Toolbar</a></li>
<li><a name="toc-TAGS-1" href="#TAGS">11.8 TAGS</a></li>
<li><a name="toc-Rdired-1" href="#Rdired">11.9 Rdired</a></li>
<li><a name="toc-Rutils-1" href="#Rutils">11.10 Rutils</a></li>
<li><a name="toc-Interaction-with-Org-mode" href="#Org">11.11 Interaction with Org mode</a></li>
<li><a name="toc-Support-for-Sweave-in-ESS-and-AUCTeX" href="#Sweave-and-AUCTeX">11.12 Support for Sweave in ESS and AUCTeX</a></li>
</ul></li>
<li><a name="toc-Overview-of-ESS-features-for-the-S-family" href="#ESS-for-S">12 Overview of ESS features for the S family</a>
<ul class="no-bullet">
<li><a name="toc-ESS_005bS_005d_002d_002dEditing-files" href="#ESS_0028S_0029_002d_002dEditing-files">12.1 ESS[S]–Editing files</a></li>
<li><a name="toc-iESS_005bS_005d_002d_002dInferior-ESS-processes" href="#iESS_0028S_0029_002d_002dInferior-ESS-processes">12.2 iESS[S]–Inferior ESS processes</a></li>
<li><a name="toc-ESS_002dhelp_002d_002dassistance-with-viewing-help-1" href="#ESS_002dhelp_002d_002dassistance-with-viewing-help">12.3 ESS-help–assistance with viewing help</a></li>
<li><a name="toc-Philosophies-for-using-ESS_005bS_005d" href="#Philosophies-for-using-ESS_0028S_0029">12.4 Philosophies for using ESS[S]</a></li>
<li><a name="toc-Scenarios-for-use-_0028possibilities_002d_002dbased-on-actual-usage_0029-1" href="#Scenarios-for-use-_0028possibilities_002d_002dbased-on-actual-usage_0029">12.5 Scenarios for use (possibilities–based on actual usage)</a></li>
<li><a name="toc-Customization-Examples-and-Solutions-to-Problems-1" href="#Customization-Examples-and-Solutions-to-Problems">12.6 Customization Examples and Solutions to Problems</a></li>
</ul></li>
<li><a name="toc-ESS-for-SAS-1" href="#ESS-for-SAS">13 ESS for SAS</a>
<ul class="no-bullet">
<li><a name="toc-ESS_005bSAS_005d_002d_002dDesign-philosophy" href="#ESS_0028SAS_0029_002d_002dDesign-philosophy">13.1 ESS[SAS]–Design philosophy</a></li>
<li><a name="toc-ESS_005bSAS_005d_002d_002dEditing-files" href="#ESS_0028SAS_0029_002d_002dEditing-files">13.2 ESS[SAS]–Editing files</a></li>
<li><a name="toc-ESS_005bSAS_005d_002d_002dTAB-key" href="#ESS_0028SAS_0029_002d_002dTAB-key">13.3 ESS[SAS]–<tt class="key">TAB</tt> key</a></li>
<li><a name="toc-ESS_005bSAS_005d_002d_002dBatch-SAS-processes" href="#ESS_0028SAS_0029_002d_002dBatch-SAS-processes">13.4 ESS[SAS]–Batch SAS processes</a></li>
<li><a name="toc-ESS_005bSAS_005d_002d_002dFunction-keys-for-batch-processing" href="#ESS_0028SAS_0029_002d_002dFunction-keys-for-batch-processing">13.5 ESS[SAS]–Function keys for batch processing</a></li>
<li><a name="toc-iESS_005bSAS_005d_002d_002dInteractive-SAS-processes" href="#iESS_0028SAS_0029_002d_002dInteractive-SAS-processes">13.6 iESS[SAS]–Interactive SAS processes</a></li>
<li><a name="toc-iESS_005bSAS_005d_002d_002dCommon-problems" href="#iESS_0028SAS_0029_002d_002dCommon-problems">13.7 iESS[SAS]–Common problems</a></li>
<li><a name="toc-ESS_005bSAS_005d_002d_002dGraphics" href="#ESS_0028SAS_0029_002d_002dGraphics">13.8 ESS[SAS]–Graphics</a></li>
<li><a name="toc-ESS_005bSAS_005d_002d_002dWindows" href="#ESS_0028SAS_0029_002d_002dWindows">13.9 ESS[SAS]–Windows</a></li>
</ul></li>
<li><a name="toc-ESS-for-BUGS-1" href="#ESS-for-BUGS">14 ESS for BUGS</a>
<ul class="no-bullet">
<li><a name="toc-ESS_005bBUGS_005d_002d_002dModel-files" href="#ESS_0028BUGS_0029_002d_002dModel-files">14.1 ESS[BUGS]–Model files</a></li>
<li><a name="toc-ESS_005bBUGS_005d_002d_002dCommand-files" href="#ESS_0028BUGS_0029_002d_002dCommand-files">14.2 ESS[BUGS]–Command files</a></li>
<li><a name="toc-ESS_005bBUGS_005d_002d_002dLog-files" href="#ESS_0028BUGS_0029_002d_002dLog-files">14.3 ESS[BUGS]–Log files</a></li>
</ul></li>
<li><a name="toc-ESS-for-JAGS-1" href="#ESS-for-JAGS">15 ESS for JAGS</a>
<ul class="no-bullet">
<li><a name="toc-ESS_005bJAGS_005d_002d_002dModel-files" href="#ESS_0028JAGS_0029_002d_002dModel-files">15.1 ESS[JAGS]–Model files</a></li>
<li><a name="toc-ESS_005bJAGS_005d_002d_002dCommand-files" href="#ESS_0028JAGS_0029_002d_002dCommand-files">15.2 ESS[JAGS]–Command files</a></li>
<li><a name="toc-ESS_005bJAGS_005d_002d_002dLog-files" href="#ESS_0028JAGS_0029_002d_002dLog-files">15.3 ESS[JAGS]–Log files</a></li>
</ul></li>
<li><a name="toc-Bugs-and-Bug-Reporting_002c-Mailing-Lists" href="#Mailing-lists_002fbug-reports">16 Bugs and Bug Reporting, Mailing Lists</a>
<ul class="no-bullet">
<li><a name="toc-Bugs-1" href="#Bugs">16.1 Bugs</a></li>
<li><a name="toc-Reporting-Bugs-1" href="#Reporting-Bugs">16.2 Reporting Bugs</a></li>
<li><a name="toc-Mailing-Lists-1" href="#Mailing-Lists">16.3 Mailing Lists</a></li>
<li><a name="toc-Help-with-emacs-1" href="#Help-with-emacs">16.4 Help with emacs</a></li>
</ul></li>
<li><a name="toc-Customizing-ESS" href="#Customization">Appendix A Customizing ESS</a></li>
<li><a name="toc-Indices-1" href="#Indices">Indices</a>
<ul class="no-bullet">
<li><a name="toc-Key-index-1" href="#Key-index">Key index</a></li>
<li><a name="toc-Function-and-program-index-1" href="#Function-and-program-index">Function and program index</a></li>
<li><a name="toc-Variable-index-1" href="#Variable-index">Variable index</a></li>
<li><a name="toc-Concept-Index" href="#Concept-index">Concept Index</a></li>
</ul></li>
</ul>
</div>
<a name="ESS-_002d_002d_002d-Emacs-Speaks-Statistics"></a>
<h2 class="majorheading">ESS — Emacs Speaks Statistics</h2>
<a name="Top"></a>
<div class="header">
<p>
Next: <a href="#Introduction" accesskey="n" rel="next">Introduction</a>, Up: <a href="dir.html#Top" accesskey="u" rel="up">(dir)</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS_003a-Emacs-Speaks-Statistics"></a>
<h1 class="top">ESS: Emacs Speaks Statistics</h1>
<p>ESS version
15.09-2
</p>
<div class="display">
<pre class="display">by A.J. Rossini,
R.M. Heiberger,
K. Hornik,
M. Maechler,
R.A. Sparapani,
S.J. Eglen,
S.P. Luque,
V. Spinu
and H. Redestig.
</pre></div>
<blockquote>
<p>Emacs Speaks Statistics (ESS) provides an intelligent, consistent
interface between the user and the software. ESS interfaces with SAS,
S-PLUS, R, BUGS/JAGS and other statistical analysis packages on Unix,
Linux and Microsoft Windows. ESS is itself a package within the emacs
text editor and uses emacs features to streamline the creation and use
of statistical software. ESS knows the syntax and grammar of
statistical analysis packages and provides consistent display and
editing features based on that knowledge. ESS assists in interactive
and batch execution of statements written in these statistical
analysis languages.
</p></blockquote>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Introduction" accesskey="1">Introduction</a>:</td><td> </td><td align="left" valign="top">Overview of features provided by this package
</td></tr>
<tr><td align="left" valign="top">• <a href="#Installation" accesskey="2">Installation</a>:</td><td> </td><td align="left" valign="top">Installing ESS on your system
</td></tr>
<tr><th colspan="3" align="left" valign="top"><pre class="menu-comment">
</pre></th></tr><tr><td align="left" valign="top">• <a href="#Interactive-ESS" accesskey="3">Interactive ESS</a>:</td><td> </td><td align="left" valign="top">Interacting with statistical programs
</td></tr>
<tr><td align="left" valign="top">• <a href="#Entering-commands" accesskey="4">Entering commands</a>:</td><td> </td><td align="left" valign="top">Interacting with the ESS process
</td></tr>
<tr><td align="left" valign="top">• <a href="#Evaluating-code" accesskey="5">Evaluating code</a>:</td><td> </td><td align="left" valign="top">Sending code to the ESS process
</td></tr>
<tr><td align="left" valign="top">• <a href="#Transcript-Mode" accesskey="6">Transcript Mode</a>:</td><td> </td><td align="left" valign="top">Manipulating saved transcript files
</td></tr>
<tr><td align="left" valign="top">• <a href="#Editing-objects" accesskey="7">Editing objects</a>:</td><td> </td><td align="left" valign="top">How to create/edit objects and functions
</td></tr>
<tr><td align="left" valign="top">• <a href="#Help" accesskey="8">Help</a>:</td><td> </td><td align="left" valign="top">Reading help files
</td></tr>
<tr><td align="left" valign="top">• <a href="#Completion" accesskey="9">Completion</a>:</td><td> </td><td align="left" valign="top">Various completion mechanisms
</td></tr>
<tr><td align="left" valign="top">• <a href="#Developing-with-ESS">Developing with ESS</a>:</td><td> </td><td align="left" valign="top">Tools for package development and debugging
</td></tr>
<tr><td align="left" valign="top">• <a href="#Extras">Extras</a>:</td><td> </td><td align="left" valign="top">Other ESS features for the S family
</td></tr>
<tr><th colspan="3" align="left" valign="top"><pre class="menu-comment">
</pre></th></tr><tr><td align="left" valign="top">• <a href="#ESS-for-S">ESS for S</a>:</td><td> </td><td align="left" valign="top">Overview of ESS features for the S family
</td></tr>
<tr><td align="left" valign="top">• <a href="#ESS-for-SAS">ESS for SAS</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#ESS-for-BUGS">ESS for BUGS</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#ESS-for-JAGS">ESS for JAGS</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Mailing-lists_002fbug-reports">Mailing lists/bug reports</a>:</td><td> </td><td align="left" valign="top">How to get assistance with ESS
</td></tr>
<tr><td align="left" valign="top">• <a href="#Customization">Customization</a>:</td><td> </td><td align="left" valign="top">Customizing ESS
</td></tr>
<tr><td align="left" valign="top">• <a href="#Indices">Indices</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Introduction"></a>
<div class="header">
<p>
Next: <a href="#Installation" accesskey="n" rel="next">Installation</a>, Previous: <a href="#Top" accesskey="p" rel="prev">Top</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Introduction-to-ESS"></a>
<h2 class="chapter">1 Introduction to ESS</h2>
<a name="index-introduction"></a>
<p>The S family (S, Splus and R) and SAS statistical analysis packages
provide sophisticated statistical and graphical routines for manipulating
data. <b>E</b>macs <b>S</b>peaks <b>S</b>tatistics (ESS) is based on the merger
of two pre-cursors, S-mode and SAS-mode, which provided support for the
S family and SAS respectively. Later on, Stata-mode was also incorporated.
</p>
<p>ESS provides a common, generic, and useful interface, through emacs, to
many statistical packages. It currently supports the S family, SAS, BUGS/JAGS,
and Stata with the level of support roughly in that order.
</p>
<p>A bit of notation before we begin. <em>emacs</em> refers to both
<em>GNU Emacs</em> by the Free Software Foundation, as well as
<em>XEmacs</em> by the XEmacs Project. The emacs major
mode <code>ESS[language]</code>, where <code>language</code> can take values such as
<code>S</code>, <code>SAS</code>, or <code>XLS</code>. The inferior process interface
(the connection between emacs and the running process) referred to as inferior ESS
(<code>iESS</code>), is denoted in the modeline by <code>ESS[dialect]</code>, where
<code>dialect</code> can take values such as <code>S3</code>, <code>S4</code>, <code>S+3</code>,
<code>S+4</code>, <code>S+5</code>, <code>S+6</code>, <code>S+7</code>, <code>R</code>, <code>XLS</code>, <code>VST</code>, <code>SAS</code>.
</p>
<p>Currently, the documentation contains many references to <cite>‘S’</cite>
where actually any supported (statistics) language is meant, i.e., ‘S’
could also mean ‘R’ or ‘SAS’.
</p>
<a name="index-interactive-use-of-S"></a>
<a name="index-using-S-interactively"></a>
<p>For exclusively interactive users of S, ESS provides a number of
features to make life easier. There is an easy to use command history
mechanism, including a quick prefix-search history. To reduce typing,
command-line completion is provided for all S objects and “hot
keys” are provided for common S function calls. Help files are
easily accessible, and a paging mechanism is provided to view them.
Finally, an incidental (but very useful) side-effect of ESS is that a
transcript of your session is kept for later saving or editing.
</p>
<a name="index-transcripts-of-S-sessions"></a>
<p>No special knowledge of Emacs is necessary when using S
interactively under ESS.
</p>
<a name="index-programming-in-S"></a>
<p>For those that use S in the typical edit–test–revise cycle when
programming S functions, ESS provides for editing of S functions
in Emacs edit buffers. Unlike the typical use of S where the editor
is restarted every time an object is edited, ESS uses the current Emacs
session for editing. In practical terms, this means that you can edit
more than one function at once, and that the ESS process is still
available for use while editing. Error checking is performed on
functions loaded back into S, and a mechanism to jump directly to the
error is provided. ESS also provides for maintaining text versions of
your S functions in specified source directories.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Features" accesskey="1">Features</a>:</td><td> </td><td align="left" valign="top">Why should I use ESS?
</td></tr>
<tr><td align="left" valign="top">• <a href="#New-features" accesskey="2">New features</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Credits" accesskey="3">Credits</a>:</td><td> </td><td align="left" valign="top">Authors of and contributors to ESS
</td></tr>
<tr><td align="left" valign="top">• <a href="#Latest-version" accesskey="4">Latest version</a>:</td><td> </td><td align="left" valign="top">Getting the latest version of ESS
</td></tr>
<tr><td align="left" valign="top">• <a href="#Manual" accesskey="5">Manual</a>:</td><td> </td><td align="left" valign="top">How to read this manual
</td></tr>
</table>
<hr>
<a name="Features"></a>
<div class="header">
<p>
Next: <a href="#New-features" accesskey="n" rel="next">New features</a>, Up: <a href="#Introduction" accesskey="u" rel="up">Introduction</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Why-should-I-use-ESS_003f"></a>
<h3 class="section">1.1 Why should I use ESS?</h3>
<p>Statistical packages are powerful software systems for manipulating and
analyzing data, but their user interfaces often leave something something
to be desired: they offer weak editor functionality and they differ
among themselves so markedly that you have to re-learn how to do those
things for each package. ESS is a package which is designed to make
editing and interacting with statistical packages more uniform,
user-friendly and give you the power of emacs as well.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Current-Features" accesskey="1">Current Features</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Current-Features"></a>
<div class="header">
<p>
Up: <a href="#Features" accesskey="u" rel="up">Features</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Features-Overview"></a>
<h4 class="subsection">1.1.1 Features Overview</h4>
<ul>
<li> Languages Supported:
<ul>
<li> S family (R and S+ AKA S-PLUS)
</li><li> SAS
</li><li> OpenBUGS/JAGS
</li><li> Stata
</li><li> Julia
</li></ul>
</li><li> Editing source code (S family, SAS, OpenBUGS/JAGS, Stata, Julia)
<ul>
<li> Syntactic indentation and highlighting of source code
</li><li> Partial evaluation of code
</li><li> Loading and error-checking of code
</li><li> Source code revision maintenance
</li><li> Batch execution (SAS, OpenBUGS/JAGS)
</li><li> Use of imenu to provide links to appropriate functions
</li></ul>
</li><li> Interacting with the process (S family, SAS, Stata, Julia)
<ul>
<li> Command-line editing
</li><li> Searchable Command history
</li><li> Command-line completion of S family object names and file names
</li><li> Quick access to object lists and search lists
</li><li> Transcript recording
</li><li> Interface to the help system
</li></ul>
</li><li> Transcript manipulation (S family, Stata)
<ul>
<li> Recording and saving transcript files
</li><li> Manipulating and editing saved transcripts
</li><li> Re-evaluating commands from transcript files
</li></ul>
</li><li> Interaction with Help Pages and other Documentation (R)
<ul>
<li> Fast Navigation
</li><li> Sending Examples to running ESS process.
</li><li> Fast Transfer to Further Help Pages
</li></ul>
</li><li> Help File Editing (R)
<ul>
<li> Syntactic indentation and highlighting of source code.
</li><li> Sending Examples to running ESS process.
</li><li> Previewing
</li></ul>
</li></ul>
<p>ESS provides several features which make it easier to interact with the
ESS process (a connection between your buffer and the statistical
package which is waiting for you to input commands). These include:
</p>
<ul>
<li> <b>Command-line editing</b> for fixing mistakes in commands before they are
entered. The ‘<samp>-e</samp>’ flag for S-plus provides something similar to
this, but here you have the full range of Emacs commands rather than a
limited subset. However, other packages do not
necessarily have features like this built-in.
See <a href="#Command_002dline-editing">Command-line editing</a>.
</li><li> <b>Searchable command history</b> for recalling previously-submitted
commands. This provides all the features of the ‘<samp>Splus -e</samp>’ history
mechanism, plus added features such as history searching.
See <a href="#Command-History">Command History</a>.
</li><li> <b>Command-line completion</b> of both object and file names for quick
entry. This is similar to <code>tcsh</code>’s facility for filenames; here it
also applies to object names and list components.
See <a href="#Completion">Completion</a>.
</li><li> <b>Hot-keys</b> for quick entry of commonly-used commands in ‘S’ such as
<code>objects()</code> and <code>search()</code>.
See <a href="#Hot-keys">Hot keys</a>.
</li><li> <b>Transcript recording</b> for a complete record of all the actions in an
S session.
See <a href="#Transcript">Transcript</a>.
</li><li> <b>Interface to the help system</b>, with a specialized mode for viewing S
help files.
See <a href="#Help">Help</a>.
</li></ul>
<p>If you commonly create or modify S functions, you will have found
the standard facilities for this (the ‘<samp>fix()</samp>’ function, for
example) severely limiting. Using S’s standard features, one can only
edit one function at a time, and you can’t continue to use S while
editing. ESS corrects these problems by introducing the following
features:
</p>
<ul>
<li> <b>Object editing</b>. ESS allows you to edit more than one function
simultaneously in dedicated Emacs buffers. The ESS process may
continue to be used while functions are being edited.
See <a href="#Edit-buffer">Edit buffer</a>.
</li><li> <b>A specialized editing mode</b> for S code, which provides syntactic
indentation and highlighting.
See <a href="#Indenting">Indenting</a>.
</li><li> <b>Facilities for loading and error-checking source files</b>, including a
keystroke to jump straight to the position of an error in a source file.
See <a href="#Error-Checking">Error Checking</a>.
</li><li> <b>Source code revision maintenance</b>, which allows you to keep historic
versions of S source files.
See <a href="#Source-Files">Source Files</a>.
</li><li> <b>Facilities for evaluating S code</b> such as portions of source
files, or line-by-line evaluation of files (useful for debugging).
See <a href="#Evaluating-code">Evaluating code</a>.
</li></ul>
<p>Finally, ESS provides features for re-submitting commands from saved
transcript files, including:
</p>
<ul>
<li> <b>Evaluation of previously entered commands</b>, stripping away
unnecessary prompts.
See <a href="#Transcript-resubmit">Transcript resubmit</a>.
</li></ul>
<hr>
<a name="New-features"></a>
<div class="header">
<p>
Next: <a href="#Credits" accesskey="n" rel="next">Credits</a>, Previous: <a href="#Features" accesskey="p" rel="prev">Features</a>, Up: <a href="#Introduction" accesskey="u" rel="up">Introduction</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="New-features-in-ESS"></a>
<h3 class="section">1.2 New features in ESS</h3>
<p>Changes and New Features in 15.09:
</p><ul>
<li> <acronym>ESS[R]</acronym>: The indentation logic has been refactored.
It should be faster, more consistent and more flexible. There are three
types of indentation settings, those starting with <code>ess-offset-</code>
give the actual offsets, those starting with <code>ess-indent-</code> are
control (commonly Boolean) variables, and those starting with
<code>ess-align-</code> are vertical alignment overrides which inhibit default
offsets in specific situations. See <code>ess-style-alist</code> for detailed
description of the new indentation system and provided default
indentation styles.
</li><li> <acronym>ESS[R]</acronym>: Deprecation of old indentation settings.
As a consequence of the indentation re-factoring
<code>ess-brace-imaginary-offset</code>, <code>ess-expression-offset</code> and all
delimiter-specific offsets are deprecated. The settings for indentation
of continued statements have been replaced by
<code>ess-offset-continuations</code>. It can be set to either <code>cascade</code>
or <code>straight</code> (the default). <code>ess-arg-function-offset</code> has
been replaced by <code>ess-indent-from-lhs</code> and has been generalised to
assignements. This setting now works with both statement blocks and
expressions and only takes effect for offsets set to <code>prev-call</code>
and <code>open-delim</code> in order to produce a consistent indentation.
</li><li> <acronym>ESS</acronym>: A test framework has been set up.
</li><li> <acronym>ESS[R]</acronym>: A new RStudio style is provided to mimic as closely
as possible R files indented via RStudio. To reproduce the setup of some
of the RStudio users, the RStudio- style with
<code>ess-offset-arguments</code> set to <code>prev-line</code> is also provided. In
addition, the new RRR+ style is equivalent to RRR except it indents
blocks in function calls relatively to the opening delimiter. This style
does not try to save horizontal space and produces more indentation.
</li><li> <acronym>ESS[R]</acronym>: Roxygen fields will now be indented on paragraph
refilling in order to make the documentation more readable. You can also
refill commented lines in the <code>examples</code> field without squashing
the surrounding code in the comments.
</li><li> <acronym>ESS[R]</acronym>: ESS can now format your code! This is controlled
through the settings <code>ess-fill-calls</code> and
<code>ess-fill-continuations</code>. When activated, <code>(fill-paragraph)</code>
formats your calls and your formulas/continuations while making sure
they don’t go past <code>fill-column</code>. Repeated refills cycle through
different styles (see the docstrings for more details). By default, the
refilled region blinks. Set <code>ess-blink-filling</code> to nil to prevent
this.
</li><li> <acronym>ESS[R]</acronym>: Fix occasional missing error location fontification
in inferior buffers.
</li><li> <acronym>ESS[R]</acronym>: ess-developer now correctly assigned the environment
of new functions to the package namespace.
</li><li> <acronym>ESS[Julia]</acronym>: ?[topic] now works in the *julia* buffer.
Note that support for editing Julia code now depends on
<samp>julia-mode.el</samp> from the Julia project. If you install ESS from
the official tarball/zip file, <samp>julia-mode.el</samp> is already included.
Otherwise, if you install ESS by
running <code>make</code>, then the latest version of <samp>julia-mode.el</samp> is
downloaded (and so you need an active internet connection to install)
during the installation process. Alternatively, if you run ESS without
running <code>make</code>, then ensure that you have the <code>julia-mode.el</code>,
which you can get easily from MELPA for example.
</li><li> i<acronym>ESS</acronym><!-- /@w -->: For naming inferior processes, ESS can use <code>projectile</code>’s
project root and it does so when <code>ess-gen-proc-buffer-name-function</code> is
set to <code>ess-gen-proc-buffer-name:projectile-or-simple</code> as by default,
or to another value beginning with <code>ess-gen-proc-buffer-name:projectile-*</code>.
</li></ul>
<p>Changes and New Features in 15.03-1:
</p><ul>
<li> <acronym>ESS[R]</acronym>: An indentation bug has been fixed (github issue 163)
</li><li> <acronym>ESS[R]</acronym>: On windows, if ‘ess-prefer-higher-bit’ is non-nil (the
default), then R-newest will try to run a 64 bit (rather than 32 bit)
version of R.
</li></ul>
<p>Changes and New Features in 15.03:
</p><ul>
<li> <acronym>ESS[R]</acronym>: Full native support for ‘company-mode‘.
</li><li> <acronym>ESS[R]</acronym>: More efficient caching algorithm for R completion.
</li><li> <acronym>ESS</acronym>: New offset variable ‘ess-close-paren-offset‘ to control
the indentation of the closing parentheses.
</li><li> <acronym>ESS[R]</acronym>: Ask for CRAN mirror only once per emacs session.
</li><li> <acronym>ESS[R]</acronym>: Detect <code>library</code> and <code>require</code> calls
for better completion caching.
</li><li> Buffer display is now customizable (<code>ess-show-buffer-action</code>).
</li><li> Use <code>y-or-n-p</code> instead of <code>yes-or-no-p</code> throughout.
</li><li> More support for ODS in ess-sas-graph-view.
</li><li> Makefiles are now both UNIX and GNU friendly.
</li><li> <acronym>ESS[R]</acronym>: Simplify directory lookup in <code>ess-developer</code> (#137).
</li><li> Make closed paren indentation consistent
</li></ul>
<p>Bug Fixes in 15.03:
</p><ul>
<li> Fix open brace indentation bug (#27 in ess/R-ESS-bugs.R).
</li><li> Fix git version lookup
</li><li> Don’t check directory modtime in R dialect.
</li><li> Declare all ess macros for edebug.
</li><li> Add <code>ess-smart-comma</code> to eldoc message functions.
</li><li> Inform users when retrieving RDA aliases.
</li><li> Line ending in ’~’ is also a continuation line.
</li><li> Filing roxy paragraphs works as expected now.
</li><li> In <code>ess-developer-add-package</code>, remove incorrect ‘wait‘
argument from <code>ess-get-words-from-vector</code> call.
</li><li> Fix #96, #117, #120, #125, #134, #137.
</li><li> Fix ess-quit-r. Call base::q() even if it is masked.
</li><li> Fix ‘ess-show-buffer‘ to always display the buffer in another window.
</li><li> Makefile: Fix cd bug for directories with spaces in them
</li><li> <code>ess-kill-buffer-and-go</code> modified to not restart R
</li></ul>
<p>Changes / Selected Bug Fixes in 14.09:
</p><ul>
<li> <acronym>ESS[Julia]</acronym>: Executable is changed to <code>julia</code>.
</li><li> <acronym>ESS[Julia]</acronym>: Completion and help system was adjusted to Julia
v.0.3.0. Julia v.0.2.x is no more supported.
</li><li> <acronym>ESS[R]</acronym>: Running R with <code>gdb</code> debugger now works as expected
</li><li> i<acronym>ESS</acronym><!-- /@w -->: Inferior ESS buffers are now derived from <code>comint-mode</code>
</li><li> <acronym>ESS[R]</acronym>: <code>ess-execute-screen-options</code> uses correct screen
width in terminal sessions
</li><li> <acronym>ESS</acronym>: <code>ess-build-tags-for-directory</code> works when no TAGS file
name was provided
</li><li> <acronym>ESS</acronym>: <code>ess-offset-statement-continued</code> is now respected everywhere
except inside of the <code>if</code> test condition.
</li><li> <acronym>ESS</acronym>: New variable <code>ess-offset-statement-first-continued</code> for
indentation of the first line in multiline statements.
</li><li> <acronym>ESSR</acronym>: Starting <kbd>,</kbd> in multiline statements indentation is now
ignored to achieve a more pleasant alignment.
</li><li> <acronym>ESSR</acronym>: Improved behavior of <kbd>RET</kbd> in roxygen blocks.
</li><li> <acronym>ESS[R]</acronym>: command cleaning with <kbd>C-u C-u C-y</kbd> was broken with
lines containing " + "
</li><li> <acronym>ESS[R]</acronym>: fixed "empty watch window bug"
</li><li> <acronym>ESS[R]</acronym>: don’t ask for help location on ac-quick-help (request of github #81)
</li><li> <acronym>ESS[R]</acronym>: "importClassesFrom" and "importMethodsFrom" were added to
the list of two-parameter roxygen commands
</li><li> <acronym>ESS[R]</acronym>: fix vignetes display and hyperlinks (were broken in 13.09-1)
</li><li> <acronym>ESS[Julia]</acronym>: recognize function names ending with !
</li><li> <acronym>ESS[Julia]</acronym>: fix indentation of "for" comprehension syntax within brackets.
</li></ul>
<p>Changes / Selected Bug Fixes in 13.09-1:
</p><ul>
<li> ess-remote and TRAMP: R support code is now downloaded in binary form instead
of being injected from local machine. The R code is stored in
<code>~/.config/ESSR/</code> directory on the remote machine
</li><li> TRAMP: PAGER environment variable is now correctly set to <code>inferior-ess-pager</code>
</li><li> retrieval of help topics on remote machines is fixed
</li><li> org-babel: source references of R code executed from org files correctly point
to source references in original org files (version 8.2.1 or higher of
org-mode is required for this feature)
</li><li> <code>ess-execute</code> is now bound to <kbd>C-c C-e C-e</kbd> in <code>ess-extra-map</code>.
</li><li> completion works again in <code>ess-execute</code>
</li><li> <acronym>ESS[R]</acronym>: <code>head</code> and <code>tail</code> methods were replaced by <code>htsummary</code> in
<code>ess-R-describe-object-at-point-commands</code>
</li><li> <acronym>ESS[roxygen]</acronym>: evaluation commands now work in roxygen blocks.
Leading comments are automatically removed before the evaluation
</li><li> <acronym>ESS[transcript]</acronym>: ’Clean Region’ now works with multiline statements;
<code>ess-transcript-clean-region</code> etc. correctly treat
multiline statements, i.e., no longer forgets the lines typically
preceded by ’+’
</li><li> <acronym>ESS[SAS]</acronym>: Three features/fixes with special thanks to Matthew Fidler
<a href="https://github.com/emacs-ess/ESS/pulls/mlf176f2">https://github.com/emacs-ess/ESS/pulls/mlf176f2</a>. Turn on SAS log mode
when appropriate. Indent comments and CARDS statement more appropriately.
</li><li> <acronym>ESS[SAS]</acronym>: <code>ess-sas-edit-keys-toggle</code> default returns to <code>nil</code>
</li><li> <acronym>ESS[R]</acronym>: support for <code>prettify-symbols-mode</code>:
contribution from Rudiger Sonderfeld <a href="https://github.com/emacs-ess/ESS/pull/65">https://github.com/emacs-ess/ESS/pull/65</a>
</li><li> <acronym>ESS[SWV]</acronym>: knitr now evaluates in the current frame
</li><li> <acronym>ESS[developer]</acronym>: ess-developer doesn’t kill open DESCRIPTION files anymore
</li><li> <acronym>ESS[roxygen]</acronym>: <code>ess-roxy-preview-HTML</code> is now on <kbd>C-c C-o C-w</kbd> and
<code>ess-roxy-preview-text</code> is now on <code>C-c C-o C-t</code>
</li><li> <acronym>ESS</acronym>: installation with <code>make install</code> was simplified and should work
out of the box on most *nix systems
</li><li> <acronym>ESS</acronym> installation instructions simplified
</li><li> fixed font-lock bug introduced in 13.09 that was causing very slow process output
</li></ul>
<p>Changes/New Features in 13.09:
</p><ul>
<li> font-lock in process buffers doesn’t "spill" over prompts.
Missing closing string delimiters should not cause wrong fontification
of the following command input.
</li><li> <acronym>ESS[julia]</acronym>: full features M-TAB completion and auto-complete support,
which now works for modules, structures and data types.
</li><li> <acronym>ESS[julia]</acronym>: a much better eldoc showing arguments of
methods and data type constructors
</li><li> ESS-developer:
<ul class="no-bullet">
<li>- ESS-developer work-flow pattern has been streamlined:
ESS-developer is now automatically activated on per-file basis if the
file is part of a developed package <code>ess-developer-packages</code>. The
old behavior (activation on per-process basis) is still available on
<code>M-x ess-developer</code> in a process buffer.
</li><li>- integration with <code>devtools</code> package. New command
<code>ess-developer-load-package</code> calls <code>load_all</code> on the package
containing current file. <code>ess-developer-add-package</code> now offers IDO
menu completions with available loading methods, currently
<code>library</code>, and <code>load_all</code>. Loading command can be customized
with <code>ess-developer-load-on-add-commands</code>.
</li></ul>
</li><li> <kbd>TAB</kbd> now indents region if region is active
(a contribution of Matthew Fidler in pull #41)
</li><li> <code>M-x ess-version</code> now reports full loading path
and recognizes git and ELPA versions.
</li><li> warning and error keyword are now highlighted with
<code>font-lock-warning-face</code> as they should be, (for quite some time
these keywords have been hijacked by compilation mode fontification).
</li><li> eldoc: Eldoc now recognizes multiple processes.
If current process is busy, or current buffer is not associated with a
process, eldoc picks its completions from the first available free
process.
</li><li> org-babel: evaluation is now org-friendly
</li><li> help: new help buffers now try to reuse ess-help buffers.
This behavior is controlled by <code>ess-help-reuse-window</code> custom
variable.
</li><li> help: ?foo pops IDO menu on multiple help files
(so far it worked only for <kbd>C-c C-v</kbd>)
</li><li> remote evaluation is considerably faster now on slow connections
</li><li> <acronym>ESS[R]</acronym> tracebug R source references regular expressions
are (mostly) language agnostic.
</li><li> <code>ess-function-call-face</code> inherits from
<code>font-lock-function-name-face</code> rather than <code>font-lock-builtin-face</code>.
</li><li> <code>ess-inject-source</code> now accepts <code>function-and-buffer</code> option.
</li><li> Documentation: The “New Features”
section (and <samp>NEWS</samp>) now represent recent changes: within the last
year or so. All changes can be found in the new <a href="news.html">news.html</a> (or <samp>NEWS</samp> and <samp>ONEWS</samp>).
</li><li> <acronym>ESS[R]</acronym> <code>ess-rep-regexp</code> should no longer inf.loop (rarely!),
and hence <code>M-x ess-fix-miscellaneous</code> should neither.
</li></ul>
<p>Changes/New Features in 13.05:
</p><ul>
<li> <acronym>ESS[gretl]</acronym>: Support for <code>gretl</code> (both editing and
sub-process interaction). A contribution of Ahmadou Dicko.
</li><li> <acronym>ESS</acronym>: process output display is 4-10 times faster due to new caching
and only occasional emacs re-display (for the moment this functionality
is available only when <code>ess-tracebug</code> is active).
</li><li> <acronym>ESS</acronym>: <kbd>C-c `</kbd> is now bound to <code>ess-show-traceback</code> and
<kbd>C-c ~</kbd> is bound to <code>ess-show-call-stack</code>.
</li><li> <acronym>ESS[R]</acronym>: ESS stores function in ’ESSR’ environment to
avoid kludging users’ global environment and accidental deletion.
</li><li> <acronym>ESS[R]</acronym>: new variable <code>ess-swv-processing-command</code> to control
weaving and tangling.
</li><li> <acronym>ESS[R]</acronym>: <code>ess-default-style</code> has been changed
(from <code>DEFAULT</code>) to <code>RRR</code>. Use something like
<code>(setq ess-default-style 'DEFAULT)</code> or
<code>(setq ess-indent-level 2)</code> in your <samp>~/.emacs</samp> equivalent
<em>before</em> loading ESS, if you do not like this new “incompatible”
default style.
</li><li> <acronym>ESS[julia]</acronym>: ESS stores its functions in ’ESS’ module.
</li><li> <acronym>ESS[julia]</acronym>: Eldoc is now supported in julia modes
</li><li> <acronym>ESS[julia]</acronym>: Adjusted error reference detection and interactive help
to julia internal changes
</li><li> <acronym>ESS[R]</acronym>: <code>ess-use-tracebug</code>’s default has been changed to
<code>t</code>. Set it to nil if you want to keep the previous behavior.
</li><li> <acronym>ESS[tracebug]</acronym>: Electric debug keys have been removed [breaking change]
The functionality was replaced with <code>ess-debug-minor-mode</code> and
<code>ess-debug-minor-mode-map</code>.
</li><li> <acronym>ESS[tracebug]</acronym>: <code>ess-tracebug-map</code> is an alias to
<code>ess-dev-map</code> <kbd>C-c C-t</kbd>.
</li><li> <acronym>ESS[tracebug]</acronym>: <code>ess-bp-toggle-state</code> (<kbd>C-c C-t o</kbd>)
can now be used during the debug session to toggle breakpoints on the fly
(suggestion by Ross Boylan).
</li><li> <acronym>ESS[tracebug]</acronym>: <code>ess-debug-flag-for-debugging</code> and
<code>ess-debug-unflag-for-debugging</code> work correctly from the debugging
contexts. These commands also recognize non-exported functions for the
packages listed in <code>ess-developer-packages</code> (<kbd>C-c C-t C-a</kbd>).
</li><li> <acronym>ESS[R]</acronym>: Eldoc (activated by <code>ess-use-eldoc</code>) has
become more sophisticated, and hence also more intruding in the interface
between the Statistics softare, e.g., R, and the user.
<p>Note that you can turn off ElDoc, by placing <code>(setq ess-use-eldoc nil)</code>
in your <samp>~/.emacs</samp> file, prior to loading ESS,
</p>
</li><li> <acronym>ESS[SAS]</acronym>: long over-looked <code>SAS-mode-hook</code> appears!
</li><li> <acronym>ESS[SAS]</acronym>: <code>ess-sas-edit-keys-toggle</code> now defaults to <code>t</code>
since <code>sas-indent-line</code> is still broken, i.e. <kbd>TAB</kbd> is now
bound to <code>ess-sas-tab-to-tab-stop</code> by default
</li></ul>
<p>Changes/Bug Fixes in 12.09-2:
</p><ul>
<li> <acronym>ESS</acronym>: new <code>ess-switch-to-end-of-proc-buffer</code> variable that controls
whether <kbd>C-c C-z</kbd> switches to the end of process buffer. The
default is <code>t</code>. You can use prefix argument to <kbd>C-c C-z</kbd> to
toggle this variable.
</li><li> <acronym>ESS</acronym>: fix in <code>ess-eval-linewise</code> that was causing emacs
to hang during R debugging with <code>ess-eval-visibly</code> equal to
<code>t</code>.
</li><li> <acronym>ESS</acronym>: fix in <code>ess-eval-linewise</code> that was causing emacs to recenter
the prompt in visible window
</li><li> <acronym>ESS[tracebug]</acronym>: A better handling of “Selection” prompts
and debug related singlekey commands.
</li><li> <acronym>ESS</acronym>: fix a bug in <code>ess-switch-process</code> that was causing
<code>*new*</code> selection to fail.
</li><li> <acronym>ESS[R]</acronym>: Solve missing <code>ess-local-process-name</code> bug in R-dired.
</li><li> <acronym>ESS[SWV]</acronym>: <code>ess-swv-PDF</code> doesn’t ask for a command to run if
there is only one command in <code>ess-swv-pdflatex-commands</code>.
</li><li> <acronym>ESS[SWV]</acronym>: <code>ess-swv-weave</code> gained an universal argument to
allow for an interactive choice between available weavers (sweave,
knitr).
</li><li> <acronym>ESS</acronym>: <code>ess-eval-*-and-step</code> functions go to next empty
line at eob, instead of staying at the last line.
</li></ul>
<p>Changes/New Features in 12.09-1:
</p><ul>
<li> <acronym>ESS</acronym> <em>Breaking Changes in Keys</em>:
<ul class="no-bullet">
<li>- New keymaps:
<code>ess-doc-map</code> bound to <kbd>C-c C-d</kbd>; <code>ess-extra-map</code> bound
to <kbd>C-c C-e</kbd>; <code>ess-dump-object-into-edit-buffer</code> was moved on
<kbd>C-c C-e C-d</kbd>
</li><li>- roxygen map was moved on <kbd>C-c C-o</kbd> and
<kbd>ess-roxy-update-entry</kbd> now resides on <kbd>C-c C-o C-o</kbd>
</li><li>- ess-handy-commands is not bound anymore
</li><li>- <code>ess-dev-map</code> (including <code>ess-tracebug</code> and <code>ess-developer</code>)
moved on <kbd>C-c C-t</kbd>
</li><li>- <code>C-c C-y</code> is deprecated in favor of <code>C-c C-z C-z</code>
</li></ul>
</li><li> <acronym>ESS[R]</acronym> new command <code>ess-describe-object-at-point</code>
bound to <kbd>C-c C-d C-e</kbd> (repeat <kbd>C-e</kbd> or <kbd>e</kbd> to cycle). It
was inspired by Erik Iverson’s <code>ess-R-object-tooltip</code>. Customize
<code>ess-describe-at-point-method</code> to use tooltip instead of an
electric buffer.
</li><li> <acronym>ESS</acronym>: New command <code>ess-build-tags-for-directory</code>
bound to <kbd>C-c C-e C-t</kbd> for building dialect specific tag
tables. After building tags use <kbd>M-.</kbd> to navigate to
function and objects definitions. By default <kbd>C-c C-e C-t</kbd> builds
tags based on imenu regular expressions and also include other common
languages <code>.c, .o, .cpp</code> etc. But it relies on external <code>find</code>
and <code>etags</code> commands. If <code>ess-build-tags-command</code> is defined
(for <code>R</code>), the inferior process is asked to build tags instead.
</li><li> <acronym>ESS</acronym>: <code>ess-switch-process</code> offers <code>*new*</code> alternative
to start a new process instead of switching to one of the currently
running processes.
</li><li> <acronym>ESS</acronym>: Switching between processes (<kbd>C-c C-s</kbd>) uses buffer names instead
of the internal process names. Use <code>M-x rename-buffer</code> command to
conveniently rename your process buffers.
</li><li> <acronym>ESS</acronym>: Process buffers can be automatically named on process creation
according to user specified scheme. Default schemes are *proc*,
*proc:dir* and *proc:abbr-long-dir* where <code>proc</code> stands for the
internal process name and <code>dir</code> stands for the directory where the
process was started in. The default is *proc*. For customization see
<code>ess-gen-proc-buffer-name-function</code>.
</li><li> <acronym>ESS</acronym>: <code>ess-eval-visibly-p</code> is deprecated in favor of <code>ess-eval-visibly</code>.
</li><li> <acronym>ESS</acronym>: New evaluation pattern <code>nowait</code>.
In addition to old <code>nil</code> and <code>t</code> values,
<code>ess-eval-visibly</code> accepts <code>nowait</code> for a visible evaluation
with no waiting for the process. See <code>ess-eval-visibly</code> for details
on evaluation patterns.
</li><li> <acronym>ESS</acronym>: New “Process” menu entry with process related commands and configuration
</li><li> i<acronym>ESS</acronym><!-- /@w -->: Process buffer is now automatically shown on errors
</li><li> <acronym>ESS</acronym>: New <code>ess-switch-to-inferior-or-script-buffer</code> command bound to <kbd>C-c C-z</kbd>
in both script and process buffers. If invoked form process buffer it
switches to the most recent buffer of the same dialect. It is a single
key command.
</li><li> <acronym>ESSR-help</acronym>: On multiple help pages with the same name, <kbd>C-c C-v</kbd>
now asks for user resolution directly in emacs.
</li><li> <acronym>ESS[R]</acronym> ess-roxy: new variable <code>ess-roxy-re</code> for fontification
of cases where the number of leading <kbd>#</kbd> differs from
<code>ess-roxy-str</code>.
</li><li> <acronym>ESS[R]</acronym> Eldoc was considerably enhanced.
It now finds hidden default S3 methods and displays non-default methods’
arguments after trailing ||.
</li><li> <acronym>ESS[R]</acronym>: New <code>ess-display-demos</code> command bound to <kbd>C-c C-d o</kbd> and <kbd>C-c C-d C-o</kbd>
</li><li> <acronym>ESS</acronym>: New <code>ess-help-web-search</code> command bound to <kbd>C-c C-d w</kbd> and <kbd>C-c C-d C-w</kbd>
to facilitate interactive search of web resources. Implemented for <code>R</code>,
<code>Stata</code> and <code>Julia</code>. See also <code>ess-help-web-search-command</code>.
</li><li> <acronym>ESS</acronym>: ess-pdf-viewer-pref accepts now command line arguments
</li><li> <acronym>ESS[Rnw]</acronym>: Add knitr support.
Customize <code>ess-swv-processor</code> for the default processor.
</li><li> <acronym>ESS[Rnw]</acronym>: More thorough renaming of remaining
<code>noweb-*</code> to <code>ess-noweb-*</code>.
</li><li> <acronym>ESS[Rnw]</acronym> new commands <code>ess-eval-chunk-and-step</code> and <code>ess-eval-chunk</code>
bound to <kbd>M-n C-c</kbd> and <kbd>M-n C-M-x</kbd> to mirror standard ess
commands in C-c map.
</li><li> <acronym>ESS[R]</acronym> Auto-completion: new variable
<code>ess-ac-R-argument-suffix</code> to customize the insertion of trailing
"=". Defaults to “ = “.
</li><li> <acronym>ESS[Julia]</acronym>: Added index, apropos and web-search to julia.
</li><li> <acronym>ESS</acronym> help: More evaluation commands were added to ess-help mode (<kbd>C-c C-c</kbd>, <kbd>C-M-x</kbd> etc)
</li></ul>
<p>Bug Fixes in 12.09-1:
</p><ul>
<li> i<acronym>ESShelp</acronym><!-- /@w -->: Multiple help pages with the same name are properly handled on <kbd>C-c C-v</kbd>
</li><li> i<acronym>ESSremote</acronym><!-- /@w -->: Evaluation with ESS remote no longer freezes emacs.
</li><li> i<acronym>ESS</acronym><!-- /@w -->: <code>comint-previous-prompt</code> <kbd>C-c C-p</kbd> no longer stops on secondary prompt “+”.
</li><li> i<acronym>ESS[R]</acronym><!-- /@w -->, i<acronym>ESS(Sqpe) [S]</acronym><!-- /@w --> on Windows:
The <code>options("editor")</code> is now initialized to <code>emacsclient</code>
instead of the previous <code>gnuclient</code>. The user may need to add the
line <code>(server-start)</code> to the emacs initialization
file. <code>emacsclient</code> has been included with emacs since GNU Emacs
22.1.
</li><li> <acronym>ESS[Rnw]</acronym> Fixed “connection to R” bug (in 12.09 only).
</li><li> <acronym>ESS[Rnw]</acronym> Explicit <code>ess-swv-stangle</code> and <code>ess-swv-sweave</code>
functions.
</li><li> <acronym>ESS[Rnw]</acronym> Fixed completion and smart underscore problems cause by unmatched “\”’
</li><li> <acronym>ESS[R]</acronym> is more careful with the <code>R</code> code injection.
It now happens only once at the start of the session.
</li><li> <acronym>ESS[R]</acronym>: Fixed auto-scrolling the comint buffer on evaluation.
</li><li> <acronym>ESS[Julia]</acronym>: Solve several indentation and word navigation problems.
</li><li> <acronym>ESS[Julia]</acronym>: Help system works again.
</li></ul>
<p>Changes/New Features in 12.09:
</p>
<ul>
<li> <b>Due to XEmacs lacking some features that ESS requires, ESS support of XEmacs
ends with ESS 12.04-4. This decision will be re-visited in the future as
XEmacs continues to sync with GNU Emacs.</b>
</li><li> <acronym>ESS[R]</acronym>: On Windows, there is now a new customizable variable
(currently called <code>ess-directory-containing-R</code>) to tell ESS where
to look for the <samp>Rterm.exe</samp> executables. The name of the variable
and the values it can take are both in beta and subject to change. Prior
to this variable, ESS searched only in the default installation
directory. Setting this variable now tells ESS how to find
<samp>Rterm.exe</samp> executables when they are installed somewhere else.
</li><li> <acronym>ESS[julia]</acronym>: <em>new</em> mode
for editing julia code (<samp>*.jl</samp>). Start with <code>M-x julia</code>.
<p>Full interaction interface, imenu and basic error referencing are available.
</p>
</li><li> <acronym>ESS[R]</acronym> noweb: <code>noweb-mode</code> and <code>noweb-font-lock-mode</code> have
been renamed to <code>ess-noweb-mode</code> and
<code>ess-noweb-font-lock-mode</code> to avoid conflicts with the “real” <code>noweb-mode</code>.
</li><li> <acronym>ESS[R]</acronym> noweb: The long standing font-lock bug has been solved
in <code>ess-noweb</code> interface.
</li><li> <acronym>ESS</acronym>: Basic evaluation keys are now bound to <code>ess-eval-region-*-</code> functions:
<ul class="no-bullet">
<li>- <kbd>C-M-x</kbd> is bound to <code>ess-eval-region-or-function-or-paragraph</code>
</li><li>- <kbd>C-c C-c</kbd> is bound to <code>ess-eval-region-or-function-or-paragraph-and-step</code>
</li><li>- <kbd>C-RET</kbd> is bound to <code>ess-eval-region-or-line-and-step</code>
</li></ul>
<p>Each of these functions first evaluates the region whenever the region
is active.
</p>
</li><li> <acronym>ESS</acronym>: <kbd>C-M-a</kbd>/<kbd>C-M-e</kbd> now step to beginning/end of
paragraph if no function has been detected.
</li><li> <acronym>ESS</acronym>: <code>ess-eval-*-and-step</code> family of functions are now smarter,
and don’t step to end of buffer or end of chunk code (<code>@</code>) when at
the end of the code.
</li><li> <acronym>ESS</acronym>: <code>ess-handy-commands</code> function is bound to <kbd>C-c h</kbd>
</li><li> <acronym>ESS</acronym>: ESS is now <em>blinking</em> the evaluated region.
Set <code>ess-blink-region</code> to nil to deactivate; <code>ess-blink-delay</code>
gives the duration of the blink. Evaluated region is “blinked” in
<code>highlight</code> face.
</li><li> <acronym>ESS[R-help]</acronym> New key <kbd>a</kbd> for “apropos()” in help buffers. Also available
through <kbd>C-c h</kbd>.
</li><li> <acronym>ESS[R-help]</acronym> All R commands of type foo?bar and foo??bar are recognized
and redirected into appropriate *ESS-help* buffers.
</li><li> <acronym>ESS[R]</acronym>: New customization interface for <em>font-lock</em>.
<p>ESS font-lock operates with predefined keywords. Default keywords are
listed in <code>ess-R-font-lock-keywords</code> and
<code>inferior-R-font-lock-keywords</code>, which see. The user can easily
customize those by adding new keywords. These variables can also be
interactively accessed and saved through <kbd>ESS/Font-lock</kbd> submenu.
</p>
<p>Several new fontification keywords have been added. Most notably the
keywords for highlighting of function calls, numbers and operators.
</p>
</li><li> <acronym>ESS[R]</acronym>: auto-complete is now activated by default whenever
auto-complete package is detected. Set <code>ess-use-auto-complete</code> to
nil to deactivate.
</li><li> <acronym>ESS[R]</acronym>: R AC sources are no longer auto-starting at 0 characters
but at the default <code>ac-auto-start</code> characters.
</li><li> <acronym>ESS</acronym> no longer redefines default ac-sources,
but only appends <code>ac-source-filename</code> to it.
</li><li> <acronym>ESS</acronym>: <code>ac-source-R</code> now concatenates “ = “ to function arguments.
</li><li> <acronym>ESS</acronym>: Menus for ESS and iESS have been reorganized and enriched with
<em>Tracebug</em> and <em>Developer</em> submenus.
</li><li> <acronym>ESS[R]</acronym>: <code>ess-developer</code> and <code>ess-tracebug</code> commands are available by default
in <code>ess-dev-map</code> which is bound to <kbd>C-c d</kbd> in ESS and iESS maps.
</li><li> <acronym>ESS[R]</acronym>: <code>eldoc</code> truncates long lines whenever <code>eldoc-echo-area-use-multiline-p</code>
is non-nil (the default). Set this variable to t if you insist on multiline eldoc.
See also <code>ess-eldoc-abbreviation-style</code>.
</li><li> <acronym>ESS[R]</acronym>: completion code pre-caches arguments
of heavy generics such as <code>plot</code> and <code>print</code> to eliminated the
undesirable delay on first request.
</li><li> i<acronym>ESS</acronym><!-- /@w -->: Prompts in inferior buffers are now highlighted uniformly with
<code>comint-highlight-prompt</code> face.
</li><li> <acronym>ESS[R]</acronym>: R process no longer wait for the completion of input in inferior buffer.
Thus, long running commands like <code>Sys.sleep(5)</code> no longer stall emacs.
</li><li> <acronym>ESS</acronym>: [R, S, Stata, Julia] have specialized <code>ess-X-post-run-hook</code>s, which
are run at the end of subprocess initialization.
</li><li> <acronym>ESS[Stata]</acronym>: All interactive evaluation commands work as expected.
On-line comments are removed before the evaluation and multiline
comments are skipped on <kbd>C-c C-c</kbd> and other interactive commands.
</li><li> <acronym>ESS</acronym> no longer auto-connects to a subprocess with a different dialect than
the current buffer’s one.
</li><li> <acronym>ESS</acronym>: <code>ess-arg-function-offset-new-line</code> is now a list for all
the ESS indentation styles, which results in the following indentation
after an open “(”:
<pre class="verbatim"> a <- some.function(other.function(
arg1,
arg2)
</pre>
</li><li> <acronym>ESS[SAS]</acronym>: Improved MS RTF support for GNU Emacs; try
<code>ess-sas-rtf-portrait</code> and <code>ess-sas-rtf-landscape</code>.
</li></ul>
<p>Changes/Bug Fixes in 12.04-3:
</p><ul>
<li> <acronym>ESS</acronym>: basic support for package.el compatibility
</li><li> <acronym>ESS[R]</acronym>: correct indentation of & and | continuation lines
</li><li> <code>M-x ess-version</code> shows the svn revision even after <code>make install</code>
</li><li> <acronym>ESS[SAS]</acronym>: improved XEmacs support
</li><li> i<acronym>ESS[R]</acronym><!-- /@w -->: better finding of previous prompt
</li><li> <acronym>ESS[Stata]</acronym>: adjusted prompt for mata mode
</li><li> <acronym>ESS[R]</acronym>: resolved name clashes with cl.el
</li><li> <acronym>ESS[R]</acronym>: removed dependence on obsolete package assoc
</li><li> New <code>make</code> target <code>lisp</code>, to build the lisp-only part, i.e., not building the docs.
</li></ul>
<p>Changes/New Features in 12.04-1:
</p><ul>
<li> i<acronym>ESS[Stata]</acronym><!-- /@w -->: New interactive help invocation.
</li><li> i<acronym>ESS[Stata]</acronym><!-- /@w -->: New custom variable <code>inferior-STA-start-file</code>.
</li><li> i<acronym>ESS[Stata]</acronym><!-- /@w -->: <code>inferior-STA-program-name</code> is now “stata”
and can be customized.
</li><li> <acronym>ESS[Stata]</acronym> New sections in stata help files
Syntax(<kbd>s-S</kbd>), Remarks(<kbd>r</kbd>), Title(<kbd>t</kbd>).
</li></ul>
<p>Bug Fixes in 12.04-1:
</p><ul>
<li> <acronym>ESS[R]</acronym>: Better <code>ess-tracebug</code> error handling.
</li><li> <acronym>ESS[R]</acronym>: Corrected <code>ess-eldoc</code> help string filtering
and improved argument caching.
</li><li> <acronym>ESS[R]</acronym>: Indentation of non-block if/else/for/while lines fixed.
</li><li> <code>M-x ess-version</code> should work better.
</li><li> <acronym>ESS</acronym>: Filename completion now again works inside strings.
</li><li> i<acronym>ESS[Stata]</acronym><!-- /@w -->: Fixed prompt detection issue.
</li><li> <acronym>ESS[Rd]</acronym>: R is autostarted also from here, when needed.
</li></ul>
<p>Changes/New Features in 12.04:
</p><ul>
<li> <acronym>ESS</acronym>: Reverting new behavior of 12.03, <kbd>TAB</kbd> in <code>ess-mode</code>
no longer completes by default. If you want smart <kbd>TAB</kbd> completion
in R and S scripts, similarly to i<acronym>ESS</acronym><!-- /@w --> behavior, set the variable
<code>ess-tab-complete-in-script</code> to <code>t</code>. Also see
<code>ess-first-tab-never-complete</code> for how to customize where first
<kbd>TAB</kbd> is allowed to complete.
</li><li> <acronym>ESS</acronym>: completion is consistently bound to <kbd>M-TAB</kbd> (aka <kbd>M-C-i</kbd>)
in both Emacs23 and Emacs24.
</li><li> <acronym>ESS</acronym>: The variable <code>ess-arg-function-offset-new-line</code>
introduced in <acronym>ESS(12.03)</acronym> now accepts a list with the first element a
number to indicate that the offset should be computed from the indent of
the previous line. For example setting it to ’(2) results in:
<pre class="verbatim"> a <- some.function(
arg1,
arg2)
</pre>
</li></ul>
<p>Changes/New Features in 12.03:
</p><ul>
<li> <acronym>ESS</acronym> indentation: new offset variable <code>ess-arg-function-offset-new-line</code>
controlling for the indentation of lines immediately following open
’(’. This is useful to shift backwards function arguments after a long
function call expression:
<pre class="verbatim"> a <- some.function(
arg1,
arg2)
</pre>
<p>instead of the old
</p>
<pre class="verbatim"> a <- some.function(
arg1,
arg2)
</pre>
<p>If ’(’ is not followed by new line the behavior is unchanged:
</p>
<pre class="verbatim"> a <- some.function(arg1,
arg2)
</pre>
<p>This variable should be set as part of indentation style lists, or in
ess-mode hook.
</p></li><li> <acronym>ESS[R]</acronym>: <kbd>C-c .</kbd> sets (indentation) style.
</li><li> <acronym>ESS</acronym>: In ESS buffers <code>yank</code>(<kbd>C-y</kbd>) command accepts
double argument <kbd>C-u C-u</kbd> to paste commands only. It deletes any
lines not beginning with a prompt, and then removes the prompt from
those lines that remain. Useful to paste code from emails,
documentation, inferior ESS buffers or transcript files.
</li><li> Documentation: ESS user manual has been rearranged and
completed with several new chapters and sections to reflect newly added
features (“Completion”, “Developing with ESS”, “ESS tracebug”,
“ESS developer”, “ESS ElDoc”, “IDO Completion” and “Evaluating
Code”)
</li><li> RefCard: Reference card was updated to include new features.
</li><li> Eldoc: Eldoc was rewritten and is activated by default.
See <code>ess-use-eldoc</code>, <code>ess-eldoc-show-on-symbol</code>,
<code>ess-eldoc-abbreviation-style</code> variables for how to change the default
behavior. <em>Note:</em> <code>skeleton-pair-insert-maybe</code> prohibits eldoc
display, on <kbd>(</kbd> insertion.
</li><li> <acronym>ESS[R]</acronym>: Eldoc shows arguments of a generic function whenever found.
</li><li> <acronym>ESS</acronym>: <kbd>TAB</kbd> in <code>ess-mode</code> now indents and completes,
if there is nothing to indent. Set
<code>ess-first-tab-never-completes-p</code> to <code>t</code> to make <kbd>TAB</kbd>
never complete on first invocation. Completion mechanism is similar to
the completion in the <code>inferior-ess-mode</code> – a filename expansion
is tried, if not found ESS completes the symbol by querying the
process.
</li><li> <acronym>ESS</acronym> for emacs version 24 or higher: ESS is fully compatible with
the emacs 24 completion scheme, i.e. all the completion is done by
<code>completion-at-point</code>. Also in accordance with emacs conventions,
ESS doesn’t bind <kbd>M-TAB</kbd> for emacs 24 or higher. <kbd>M-TAB</kbd> calls the
default <code>complete-symbol</code>.
</li><li> <acronym>ESS[R]</acronym>: Out of the box integration with <code>Auto
Completion</code> mode <a href="http://cx4a.org/software/auto-complete">http://cx4a.org/software/auto-complete</a> . Three AC
sources <code>ac-source-R-args</code>, <code>ac-source-R-objects</code> and
<code>ac-source-R</code> are provided. The last one combines the previous two
and makes them play nicely together. Set <code>ess-use-auto-complete</code> to
<code>t</code> to start using it. Refer to documentation string of
<code>ac-use-auto-complete</code> for further information.
</li><li> <acronym>ESS[R]</acronym>: New unified and fast argument completion system,
comprised of <code>ess-funname.start</code>, <code>ess-function-arguments</code>,
<code>ess-get-object-at-point</code>. Eldoc and auto-completion integration
are using this system.
</li><li> <acronym>ESS</acronym>: <code>ess-switch-to-end-of-ESS</code>(<kbd>C-c C-z</kbd>),
and <code>ess-switch-to-ESS</code>(<kbd>C-c C-y</kbd>): Automatically start the
process whenever needed.
</li><li> <acronym>ESS[R]</acronym>: <code>roxy</code> knows about previewing text version of the
documentation. Bound to <kbd>C-c C-e t</kbd>.
</li><li> <acronym>ESS[R]</acronym>: Solved the “nil filename” bug in roxygen support.
</li><li> <acronym>ESS[R]</acronym>: <code>ess-tracebug</code> is now part of <acronym>ESS</acronym>:
<p>New Features:
</p>
<ul class="no-bullet">
<li>- Source injection: Tracebug now can inject source references on the
fly during code evaluation, i.e. you don’t have to source your file, but
just evaluate your code in normal fashion. Variable
<code>ess-tracebug-inject-source-p</code> controls this behavior - if t,
always inject source reference, if <code>'function</code>, inject only for
functions (this is the default), if <code>nil</code>, never inject.
<p>During the source injection the value of <code>ess-eval-visibly</code> is
ignored.
</p></li><li>- Org-mode support: Visual debugger is now aware of the
temporary org source editing buffer (<kbd>C-c '</kbd>) and jumps through this
buffers if still alive, or in original org buffer otherwise.
</li><li>- New keys in watch mode: <kbd>?</kbd> and <kbd>d</kbd>
</li><li>- Two new hooks: ess-tracebug-enter-hook and ess-tracebug-exit-hook
</li></ul>
</li><li> <acronym>ESS[R]</acronym>: New package <code>ess-developer</code> to evaluate <code>R</code>
code directly in the package environment and namespace. It can be
toggled on and off with <kbd>C-c d t</kbd>. When <code>ess-developer</code> is on
all ESS evaluation commands are redefined to evaluate code in
appropriate environments. Add package names to the list of your
development packages with <kbd>C-d a</kbd>, and remove with <kbd>C-d
r</kbd>. Source the current file with <kbd>C-d s</kbd>.Evaluation function which
depend on <code>`ess-eval-region'</code> ask for the package to source the
code into, <code>ess-eval-function</code> and alternatives search for the
function name in the development packages’ environment and namespace and
insert the definition accordingly. See the documentation section
“Developing with ESS/ESS developer” for more details.
</li><li> <acronym>ESS[R]</acronym> help system:
<p>New Features:
</p>
<ul class="no-bullet">
<li>- <kbd>q</kbd> quits window instead of calling <code>ess-switch-to-end-of-ESS</code>.
This is consistent with emacs behavior help and other special buffers (<em>breaking change</em>).
</li><li>- <kbd>k</kbd> kills window without asking for the name (pointed by Sam Steingold)
</li><li>- Help map inherits from <code>special-mode-map</code> as sugested by Sam Steingold.
</li><li>- Package index: new function <code>ess-display-index</code> bound to
<kbd>i</kbd> in help mode map.
</li><li>- Package vignettes: new function <code>ess-display-vignettes</code> bound to
<kbd>v</kbd> in help mode map.
</li><li>- Display help in HTML browser: new function <code>ess-display-help-in-browser</code> bound to
<kbd>w</kbd> in help mode map. It depends on <code>R</code>’s <code>browser</code>
option.
</li><li>- New custom variable <code>ess-help-pop-to-buffer</code>: if non-nil
<acronym>ESS</acronym> help buffers are given focus on display. The default is
<code>t</code> (<em>breaking change</em>).
</li><li>- New menu entries for the above functions.
</li><li>- Bogus help buffers are no longer generated by default, i.e.
buffers of the form “No documentation for ’foo’ in specified packages and libraries:
you could try ’??foo’ ”. <code>ess-help-kill-bogus-buffers</code> now defaults to
<code>t</code>. Beware, there may be instances where the default is unsatisfactory
such as debugging and/or during R development. Thanks to Ross Boylan for
making the suggestion, Sam Steingold for reminding us of this variable and
Martin Maechler for the warning.
</li></ul>
</li><li> <acronym>ESS</acronym> now uses <code>IDO</code> completing read functionality
for all the interactive requests. It uses ido completion
mechanism whenever available, and falls back on classical
completing-read otherwise. You can set <code>ess-use-ido</code> to nil if you
don’t want the IDO completion. See the documentation string of
<code>ess-use-ido</code> for more information about <code>IDO</code> and <acronym>ESS</acronym>
configuration.
</li><li> <acronym>ESS[S]</acronym>: “<kbd>,</kbd>“ is bound to ess-smart-comma:
If comma is invoked at the process marker of an ESS inferior
buffer, request and execute a command from <code>`ess-handy-commands'</code>
list. If <code>ess-R-smart-operators</code> is t <code>`ess-smart-comma</code>
also inserts “ “ after comma.
</li><li> <acronym>ESS[S]</acronym>, notably <code>R</code>: Variable <code>`ess-handy-commands'</code>
stores an alist of useful commands which are called by <code>ess-smart-comma</code> in
the inferior buffer.
<p>Currently containing:
</p>
<dl compact="compact">
<dt>change-directory</dt>
<dd><p><code>ess-change-directory</code>
</p></dd>
<dt>help-index</dt>
<dd><p><code>ess-display-index</code>
</p></dd>
<dt>help-object</dt>
<dd><p><code>ess-display-help-on-object</code>
</p></dd>
<dt>vignettes</dt>
<dd><p><code>ess-display-vignettes</code>
</p></dd>
<dt>objects[ls]</dt>
<dd><p><code>ess-execute-objects</code>
</p></dd>
<dt>search</dt>
<dd><p><code>ess-execute-search</code>
</p></dd>
<dt>set-width</dt>
<dd><p><code>ess-execute-screen-options</code>
</p></dd>
<dt>install.packages</dt>
<dd><p><code>ess-install.packages</code>
</p></dd>
<dt>library</dt>
<dd><p><code>ess-library</code>
</p></dd>
<dt>setRepos</dt>
<dd><p><code>ess-setRepositories</code>
</p></dd>
<dt>sos</dt>
<dd><p><code>ess-sos</code>
</p></dd>
</dl>
<p>Handy commands: <code>ess-library</code>, <code>ess-install.packages</code>, etc -
ask for item with completion and execute the correspond
command. <code>ess-sos</code> is a interface to <code>findFn</code> function in
package <code>sos</code>. If package <code>sos</code> is not found, ask user for
interactive install.
</p>
</li><li> <acronym>ESS</acronym>: New dynamic mode line indicator: Process status is automatically
reflected in all mode-lines of associated with the process
buffers. Particularly useful for displaying debug status of
<code>ess-tracebug</code> and developer status of <code>ess-developer</code> in all
associated buffers.
</li><li> <acronym>ESS</acronym>: New <code>ess-completing-read</code> mechanism: <acronym>ESS</acronym> uses
<code>ido</code> completions whenever possible. Variable <code>ess-use-ido</code>
controls whether to use ido completion or not. Active by default.
</li><li> <acronym>ESS</acronym> now supports comint fields for output and input
detection. This feature is not used by default, but might be useful in
the future.
</li><li> <acronym>ESS[S]</acronym>: New custom variable <code>inferior-ess-S-prompt</code> to
customize prompt detection regular expression in the inferior ESS
buffers. You can customize this variable to enhance comint navigation
(<code>comint-previous-prompt</code> and <code>comint-next-prompt</code>) the
inferior buffers.
</li><li> <acronym>ESS[R]</acronym>: Internal <code>R</code> completion retrieval
(<code>ess-R-complete-object-name</code>) was rewritten and is faster now.
</li><li> <acronym>ESS</acronym> is using process plist to store process specific variables,
as opposed to buffer local variables as it was using before. The use of
buffer local variables to store process variables is discouraged.
</li><li> <acronym>ESS</acronym>: new functions to manipulate process plists:
<code>ess-process-get</code> and <code>ess-process-set</code>.
</li><li> <acronym>ESS</acronym>: Internal process waiting mechanism was completely rewritten. ESS
no more relies on prompt regular expressions for the prompt
detection. The only requirement on the primary process prompt is to end
in <code>> </code>. This could be overwritten by setting
<code>inferor-ess-primary-prompt</code>.
</li><li> <acronym>ESS[S]</acronym>, notably <code>R</code>: Saved command history:
<var>ess-history-file</var> now accepts <code>t</code> (default), <code>nil</code>, or a
file name. By setting it to <code>nil</code> no command line history is saved
anymore. <var>ess-history-directory</var> now allows to have the history
all saved in one “central” file.
</li><li> <acronym>ESS[R]</acronym>: more Roxygen improvements.
</li><li> <acronym>ESS[R]</acronym>: <kbd>C-c .</kbd> to set (indentation) style.
</li><li> <acronym>ESS[R]</acronym>: Functions with non-standard names (for example ’aaa-bbb:cc’) are
properly handled by font-lock and evaluation routines.
</li><li> <acronym>ESS[R]</acronym>:Several regexp bugs (described in etc/R-ESS-bugs.el) were
fixed in <code>ess-get-words-from-vector</code> and <code>ess-command</code>.
</li></ul>
<hr>
<a name="Credits"></a>
<div class="header">
<p>
Next: <a href="#Latest-version" accesskey="n" rel="next">Latest version</a>, Previous: <a href="#New-features" accesskey="p" rel="prev">New features</a>, Up: <a href="#Introduction" accesskey="u" rel="up">Introduction</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Authors-of-and-contributors-to-ESS"></a>
<h3 class="section">1.3 Authors of and contributors to ESS</h3>
<a name="index-comint"></a>
<a name="index-authors"></a>
<a name="index-credits"></a>
<p>The ESS environment is built on the open-source projects of many
contributors, dating back to 1989 where Doug Bates and Ed Kademan wrote
S-mode to edit S and Splus files in GNU Emacs. Frank Ritter and Mike
Meyer added features, creating version 2. Meyer and David Smith made
further contributions, creating version 3. For version 4, David Smith
provided significant enhancements to allow for powerful process
interaction.
</p>
<p>John Sall wrote GNU Emacs macros for SAS source code around 1990. Tom
Cook added functions to submit jobs, review listing and log files, and
produce basic views of a dataset, thus creating a SAS-mode which was
distributed in 1994.
</p>
<p>In 1994, A.J. Rossini extended S-mode to support XEmacs. Together
with extensions written by Martin Maechler, this became version 4.7
and supported S, Splus, and R. In 1995, Rossini extended SAS-mode to
work with XEmacs.
</p>
<p>In 1997, Rossini merged S-mode and SAS-mode into a single Emacs
package for statistical programming; the product of this marriage was
called ESS version 5. Richard M. Heiberger designed the inferior mode
for interactive SAS and SAS-mode was further integrated into ESS.
Thomas Lumley’s Stata mode, written around 1996, was also folded into
ESS. More changes were made to support additional statistical
languages, particularly XLispStat.
</p>
<p>ESS initially worked only with Unix statistics packages that used
standard-input and standard-output for both the command-line interface
and batch processing. ESS could not communicate with statistical
packages that did not use this protocol. This changed in 1998 when
Brian Ripley demonstrated use of the Windows Dynamic Data Exchange
(DDE) protocol with ESS. Heiberger then used DDE to provide
interactive interfaces for Windows versions of Splus. In 1999, Rodney
A. Sparapani and Heiberger implemented SAS batch for ESS relying
on files, rather than standard-input/standard-output, for Unix,
Windows and Mac. In 2001, Sparapani added BUGS batch file processing
to ESS for Unix and Windows.
</p>
<ul>
<li> The multiple process code, and the idea for
<code>ess-eval-line-and-next-line</code> are by Rod Ball.
</li><li> Thanks to Doug Bates for many useful suggestions.
</li><li> Thanks to Martin Maechler for reporting and fixing bugs, providing many
useful comments and suggestions, and for maintaining the ESS mailing
lists.
</li><li> Thanks to Frank Ritter for updates, particularly the menu code, and
invaluable comments on the manual.
</li><li> Thanks to Ken’ichi Shibayama for his excellent indenting code, and many
comments and suggestions.
</li><li> Thanks to Aki Vehtari for adding interactive BUGS support.
</li><li> Thanks to Brendan Halpin for bug-fixes and updates to Stata-mode.
</li><li> Last, but definitely not least, thanks to the many ESS users and
contributors to the ESS mailing lists.
</li></ul>
<p><em>ESS</em> is being developed and currently maintained by
</p>
<ul>
<li> <a href="mailto:blindglobe@gmail.com">A.J. Rossini</a>
</li><li> <a href="mailto:rmh@temple.edu">Richard M. Heiberger</a>
</li><li> <a href="mailto:Kurt.Hornik@R-project.org">Kurt Hornik</a>
</li><li> <a href="mailto:maechler@stat.math.ethz.ch">Martin Maechler</a>
</li><li> <a href="mailto:rsparapa@mcw.edu">Rodney A. Sparapani</a>
</li><li> <a href="mailto:stephen@gnu.org">Stephen Eglen</a>
</li><li> <a href="mailto:spluque@gmail.com">Sebastian P. Luque</a>
</li><li> <a href="mailto:henning.red@googlemail.com">Henning Redestig</a>
</li><li> <a href="mailto:spinuvit@gmail.com">Vitalie Spinu</a>
</li></ul>
<hr>
<a name="Latest-version"></a>
<div class="header">
<p>
Next: <a href="#Manual" accesskey="n" rel="next">Manual</a>, Previous: <a href="#Credits" accesskey="p" rel="prev">Credits</a>, Up: <a href="#Introduction" accesskey="u" rel="up">Introduction</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Getting-the-latest-version-of-ESS"></a>
<h3 class="section">1.4 Getting the latest version of ESS</h3>
<p>The latest released version of ESS is always available on the web at:
<a href="http://ess.r-project.org">ESS web page</a> or
<a href="http://lib.stat.cmu.edu/general/ESS/">StatLib</a>
</p>
<a name="Git-for-ESS-development"></a>
<h4 class="subsection">1.4.1 Git for ESS development</h4>
<p>For development and experimentation on new ESS features, there is now a
GitHub branch for <acronym>ESS</acronym>, available at <a href="https://github.com/emacs-ess/ESS">https://github.com/emacs-ess/ESS</a>.
</p>
<hr>
<a name="Manual"></a>
<div class="header">
<p>
Previous: <a href="#Latest-version" accesskey="p" rel="prev">Latest version</a>, Up: <a href="#Introduction" accesskey="u" rel="up">Introduction</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="How-to-read-this-manual"></a>
<h3 class="section">1.5 How to read this manual</h3>
<p>If you need to install ESS, read <a href="#Installation">Installation</a> for details on what
needs to be done before proceeding to the next chapter.
</p>
<p>In this manual we use the standard notation for describing the
keystrokes used to invoke certain commands. <kbd>C-<chr></kbd> means hold
the CONTROL key while typing the character <chr>. <kbd>M-<chr></kbd> means
hold the META or EDIT or ALT key down while typing <chr>. If there is no
META, EDIT or ALT key, instead press and release the ESC key and then
type <chr>.
</p>
<p>All ESS commands can be invoked by typing <kbd>M-x command</kbd>. Most of
the useful commands are bound to keystrokes for ease of use. Also, the
most popular commands are also available through the emacs menubar, and
finally, if available, a small subset are provided on the toolbar.
Where possible, keybindings are similar to other modes in emacs to
strive for a consistent user interface within emacs, regardless of the
details of which programming language is being edited, or process being
run.
</p>
<p>Some commands, such as <kbd>M-x R</kbd> can accept an optional ‘prefix’
argument. To specify the prefix argument, you would type <kbd>C-u</kbd>
before giving the command. e.g. If you type <kbd>C-u M-x R</kbd>, you will
be asked for command line options that you wish to invoke the R process
with.
</p>
<p>Emacs is often referred to as a ‘self-documenting’ text editor. This
applies to ESS in two ways. First, limited documentation about each ESS
command can be obtained by typing <kbd>C-h f</kbd>. For example, if you type
<kbd>C-h f ess-eval-region</kbd>, documentation for that command will appear
in a separate *Help* buffer. Second, a complete list of keybindings
that are available in each ESS mode and brief description of that mode
is available by typing <kbd>C-h m</kbd> within an ESS buffer.
</p>
<p>Emacs is a versatile editor written in both C and lisp; ESS is written
in the Emacs lisp dialect (termed ‘elisp’) and thus benefits from the
flexible nature of lisp. In particular, many aspects of ESS behaviour
can be changed by suitable customization of lisp variables. This manual
mentions some of the most frequent variables. A full list of them
however is available by using the Custom facility within emacs. (Type
<kbd>M-x customize-group RET ess RET</kbd> to get started.)
<a href="#Customization">Customization</a> provides details of common user variables you can
change to customize ESS to your taste, but it is recommended that you
defer this section until you are more familiar with ESS.
</p>
<hr>
<a name="Installation"></a>
<div class="header">
<p>
Next: <a href="#Interactive-ESS" accesskey="n" rel="next">Interactive ESS</a>, Previous: <a href="#Introduction" accesskey="p" rel="prev">Introduction</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Installing-ESS-on-your-system"></a>
<h2 class="chapter">2 Installing ESS on your system</h2>
<a name="index-installation"></a>
<p>The following section details those steps necessary to get ESS running
on your system.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Step-by-step-instructions" accesskey="1">Step by step instructions</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#License" accesskey="2">License</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Stability" accesskey="3">Stability</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Requirements" accesskey="4">Requirements</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Step-by-step-instructions"></a>
<div class="header">
<p>
Next: <a href="#License" accesskey="n" rel="next">License</a>, Up: <a href="#Installation" accesskey="u" rel="up">Installation</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Step-by-step-instructions-1"></a>
<h3 class="section">2.1 Step by step instructions</h3>
<ol>
<li> Download the latest zip or tgz archive from ESS
<a href="http://ess.r-project.org/index.php?Section=download">downloads
area</a> and unpack it into a directory where you would like ESS to
reside. We will denote this directory as <samp>/path/to/ESS/</samp> hereafter.
<p>Alternatively you can use <code>git</code> to fetch the most
recent development version to your local machine with:
</p>
<div class="example">
<pre class="example">git clone https://github.com/emacs-ess/ESS.git /path/to/ESS
</pre></div>
</li><li> <b>Optionally</b>, compile elisp files and build the documentation with:
<div class="example">
<pre class="example">cd /path/to/ESS/
make
</pre></div>
<p>Without this step, info, pdf and html documentation and reference card
will not be available.
</p>
</li><li> <b>Optionally</b>, install into your local machine with
<code>make install</code>. You might need administrative privileges:
<div class="example">
<pre class="example">make install
</pre></div>
<p>The files are installed into <code>/usr/share/emacs</code> directory. For this step to
run correctly on Mac OS X, you will need to adjust the <samp>PREFIX</samp>
path in <samp>Makeconf</samp>. The necessary code and instructions are
commented in that file.
</p>
</li><li> If you have performed the <code>make install</code> step from above, just add
<div class="example">
<pre class="example">(require 'ess-site)
</pre></div>
<p>to your <samp>~/.emacs</samp> file. Otherwise, you should add
<samp>/path/to/ESS/lisp/</samp> to your emacs load path and then load ESS with
the following lines in your <samp>~/.emacs</samp>:
</p>
<div class="example">
<pre class="example">(add-to-list 'load-path "/path/to/ESS/lisp/")
(load "ess-site")
</pre></div>
</li><li> Restart your Emacs and check that ESS was loaded from a correct
location with <code>M-x ess-version</code>.
</li></ol>
<p><em>Note for Windows and Mac OS X users:</em> The most straightforward
way to install Emacs on your machine is by downloading
<a href="http://vgoulet.act.ulaval.ca/en/emacs/">all-in-one</a> Emacs binary
by Vincent Goulet.
</p>
<p><em>Note for XEmacs users:</em> Due to XEmacs lacking some features
that ESS requires, ESS support of XEmacs ends with ESS 12.04-4. This
decision will be re-visited in the future as XEmacs continues to sync
with GNU Emacs.
</p>
<hr>
<a name="License"></a>
<div class="header">
<p>
Next: <a href="#Stability" accesskey="n" rel="next">Stability</a>, Previous: <a href="#Step-by-step-instructions" accesskey="p" rel="prev">Step by step instructions</a>, Up: <a href="#Installation" accesskey="u" rel="up">Installation</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="License-1"></a>
<h3 class="section">2.2 License</h3>
<p>The source and documentation of ESS is free software.
You can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free
Software Foundation; either version 2, or (at your option) any later
version.
</p>
<p>ESS is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
in the file COPYING in the same directory as this file for more
details.
</p>
<hr>
<a name="Stability"></a>
<div class="header">
<p>
Next: <a href="#Requirements" accesskey="n" rel="next">Requirements</a>, Previous: <a href="#License" accesskey="p" rel="prev">License</a>, Up: <a href="#Installation" accesskey="u" rel="up">Installation</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Stability-1"></a>
<h3 class="section">2.3 Stability</h3>
<p>All recent released versions are meant to be release-quality versions.
While some new features are being introduced, we are cleaning up and
improving the interface. We know that there are many remaining
opportunities for documentation improvements, but all contributors are
volunteers and time is precious. Patches or suggested fixes with bug
reports are much appreciated!
</p>
<hr>
<a name="Requirements"></a>
<div class="header">
<p>
Previous: <a href="#Stability" accesskey="p" rel="prev">Stability</a>, Up: <a href="#Installation" accesskey="u" rel="up">Installation</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Requirements-1"></a>
<h3 class="section">2.4 Requirements</h3>
<p>ESS is most likely to work with current/recent versions of the following
statistical packages: R/S-PLUS, SAS, Stata, OpenBUGS and JAGS.
</p>
<p>ESS supports current, and recent, stable versions of GNU Emacs
(currently, specifically, the 23.x and 24.x series; alpha/beta/pre-release
versions are NOT SUPPORTED). Non-Windows users beware: GNU Emacs 24.3 is
preferable to 24.1 or 24.2: these broken builds suffer from bug 12463
<a href="http://debbugs.gnu.org/cgi/bugreport.cgi?bug=12463">http://debbugs.gnu.org/cgi/bugreport.cgi?bug=12463</a> which
will cause emacs and ESS to get progressively slower over time.
</p>
<p>Due to XEmacs lacking some features that ESS requires, ESS
support of XEmacs ends with ESS 12.04-4. This decision will
be re-visited in the future as XEmacs continues to sync with
GNU Emacs.
</p>
<p>To build the PDF documentation, you will need a version of TeX Live or
texinfo that includes texi2dvi (BEWARE: recent TeX Live, and some
texinfo RPMs, do NOT include texi2dvi).
</p>
<hr>
<a name="Interactive-ESS"></a>
<div class="header">
<p>
Next: <a href="#Entering-commands" accesskey="n" rel="next">Entering commands</a>, Previous: <a href="#Installation" accesskey="p" rel="prev">Installation</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Interacting-with-statistical-programs"></a>
<h2 class="chapter">3 Interacting with statistical programs</h2>
<p>As well as using ESS to edit your source files for statistical programs,
you can use ESS to run these statistical programs. In this chapter, we
mostly will refer by example to running S from within emacs. The emacs
convention is to name such processes running under its control as
‘inferior processes’. This term can be slightly misleading, in which
case these processes can be thought of ‘interactive processes’. Either
way, we use the term ‘iESS’ to refer to the Emacs mode used to interact
with statistical programs.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Starting-up" accesskey="1">Starting up</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Multiple-ESS-processes" accesskey="2">Multiple ESS processes</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#ESS-processes-on-Remote-Computers" accesskey="3">ESS processes on Remote Computers</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#S_002belsewhere-and-ESS_002delsewhere" accesskey="4">S+elsewhere and ESS-elsewhere</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Customizing-startup" accesskey="5">Customizing startup</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Starting-up"></a>
<div class="header">
<p>
Next: <a href="#Multiple-ESS-processes" accesskey="n" rel="next">Multiple ESS processes</a>, Up: <a href="#Interactive-ESS" accesskey="u" rel="up">Interactive ESS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Starting-an-ESS-process"></a>
<h3 class="section">3.1 Starting an ESS process</h3>
<a name="index-starting-ESS"></a>
<a name="index-running-S"></a>
<p>To start an S session on Unix or on Windows when you
use the Cygwin bash shell, simply type <kbd>M-x S RET</kbd>.
</p>
<p>To start an S session on Windows when you
use the MSDOS prompt shell, simply type <kbd>M-x S+6-msdos RET</kbd>.
</p>
<a name="index-S"></a>
<a name="index-ESS-process-directory"></a>
<a name="index-starting-directory"></a>
<a name="index-working-directory"></a>
<a name="index-directories"></a>
<p>S will then (by default) ask the question
</p><div class="example">
<pre class="example">S starting data directory?
</pre></div>
<p>Enter the name of the directory you wish to start S from (that is,
the directory you would have <code>cd</code>’d to before starting S from
the shell). This directory should have a <samp>.Data</samp> subdirectory.
</p>
<p>You will then be popped into a buffer
<a name="index-ESS-process-buffer"></a>
<a name="index-process-buffer"></a>
with name ‘<samp>*S*</samp>’ which will be used
for interacting with the ESS process, and you can start entering commands.
</p>
<hr>
<a name="Multiple-ESS-processes"></a>
<div class="header">
<p>
Next: <a href="#ESS-processes-on-Remote-Computers" accesskey="n" rel="next">ESS processes on Remote Computers</a>, Previous: <a href="#Starting-up" accesskey="p" rel="prev">Starting up</a>, Up: <a href="#Interactive-ESS" accesskey="u" rel="up">Interactive ESS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Running-more-than-one-ESS-process"></a>
<h3 class="section">3.2 Running more than one ESS process</h3>
<a name="index-multiple-ESS-processes"></a>
<p>ESS allows you to run more than one ESS process simultaneously in the
same session. Each process has a name and a number; the initial process
<a name="index-process-names"></a>
(process 1) is simply named (using S-PLUS as an example) ‘<samp>S+3:1</samp>’.
The name of the process is shown in the mode line in square brackets
(for example, ‘<samp>[S+3:2]</samp>’); this is useful if the process buffer is
renamed. Without a prefix argument, <kbd>M-x S</kbd> starts a new ESS
process, using the first available process number. With a prefix
argument (for R), <kbd>C-u M-x R</kbd> allows for the specification of
command line options.
</p>
<a name="index-ess_002drequest_002da_002dprocess"></a>
<p>You can switch to any active ESS process with the command
‘<samp>M-x ess-request-a-process</samp>’. Just enter the name of the process
you require; completion is provided over the names of all running S
processes. This is a good command to consider binding to a global key.
</p>
<hr>
<a name="ESS-processes-on-Remote-Computers"></a>
<div class="header">
<p>
Next: <a href="#S_002belsewhere-and-ESS_002delsewhere" accesskey="n" rel="next">S+elsewhere and ESS-elsewhere</a>, Previous: <a href="#Multiple-ESS-processes" accesskey="p" rel="prev">Multiple ESS processes</a>, Up: <a href="#Interactive-ESS" accesskey="u" rel="up">Interactive ESS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS-processes-on-Remote-Computers-1"></a>
<h3 class="section">3.3 ESS processes on Remote Computers</h3>
<a name="index-ess_002dremote"></a>
<a name="index-remote-Computers"></a>
<a name="index-ESS_002delsewhere"></a>
<a name="index-S_002belsewhere"></a>
<p>ESS works with processes on remote computers as easily as with processes
on the local machine. The recommended way to access a statistical
program on remote computer is to start it with tramp. Require tramp in your .emacs file:
</p>
<p><code>(require 'tramp)</code>
</p>
<p>Now start an ssh session with ‘<samp>C-x f /ssh:user@host: RET</samp>’. Tramp
should open a dired buffer in your remote home directory. Now call your
favorite ESS process (<code>R</code>, <code>Julia</code>, <code>stata</code> etc) as you
would usually do on local machine: <code>M-x R</code>.
</p>
<p>Alternatively you can start your process normally (<code>M-x R</code>). After
you are asked for starting directory, simply type ‘<samp>/ssh:user@host:
RET</samp>’. R process will be started on the remote machine.
</p>
<p>To simplify the process even further create a "config" file in your
<code>.ssh/</code> folder and add an account. For example if you use amazon
EC2, it might look like following:
</p>
<pre class="verbatim"> Host amazon
Hostname ec2-54-215-203-181.us-west-1.compute.amazonaws.com
User ubuntu
IdentityFile ~/.ssh/my_amazon_key.pem
ForwardX11 yes
</pre>
<p>With this configuration <code>/ssh:amazon:</code> is enough to start a
connection. The ForwardX11 is needed if you want to see R graphic device
showing on the current machine
</p>
<p>Other ways to setup a remote ESS connection are through <code>ess-remote</code>.
</p>
<ol>
<li> Start a new shell, telnet or ssh buffer and connect to the remote computer
(e.g. use, ‘<samp>M-x shell</samp>’, ‘<samp>M-x telnet</samp>’ or ‘<samp>M-x ssh</samp>’; ssh.el is available at
<a href="http://www.splode.com/~friedman/software/emacs-lisp/src/ssh.el">http://www.splode.com/~friedman/software/emacs-lisp/src/ssh.el</a>).
</li><li> Start the ESS process on the remote machine, for example with one of
the commands ‘<samp>Splus</samp>’, or ‘<samp>R</samp>’, or ‘<samp>sas -stdio</samp>’.
</li><li> Start ‘<samp>M-x ess-remote</samp>’.
You will be prompted for a program name with completion. Choose
one. Your process is now known to ESS. All the usual ESS commands
(‘<samp>C-c C-n</samp>’ and its relatives) now work with the S language
processes. For SAS you need to use a different command ‘<samp>C-c i</samp>’
(that is a regular ‘<samp>i</samp>’, not a ‘<samp>C-i</samp>’) to send lines from your
<samp>myfile.sas</samp> to the remote SAS process. ‘<samp>C-c i</samp>’ sends lines
over invisibly.
With ess-remote you get teletype behavior—the data input, the
log, and the listing all appear in the same buffer. To make this work,
you need to end every PROC and DATA step with a "RUN;" statement. The
"RUN;" statement is what tells SAS that it should process the preceding
input statements.
</li><li> Graphics (interactive) on the remote machine. If you run X11
(See <a href="#X11">X11</a>, X Windows)
on both the local and remote machines then you should be able to
display the graphs locally by setting the ‘<samp>DISPLAY</samp>’ environment
variable appropriately. Windows users can download ‘<samp>xfree86</samp>’
from cygwin.
</li><li> Graphics (static) on the remote machine.
If you don’t run the X window system on the local machine, then you can write
graphics to a file on the remote machine, and display the file in
a graphics viewer on the local machine. Most statistical software can
write one or more of postscript, GIF, or JPEG files.
Depending on the versions of emacs and the operating system that you
are running, emacs itself may display ‘<samp>.gif</samp>’ and ‘<samp>.jpg</samp>’
files. Otherwise, a graphics file viewer will be needed.
Ghostscript/ghostview may be downloaded to display ‘<samp>.ps</samp>’ and
‘<samp>.eps</samp>’ files. Viewers for GIF and JPEG are usually included with
operating systems. See <a href="#ESS_0028SAS_0029_002d_002dFunction-keys-for-batch-processing">ESS(SAS)--Function keys for batch processing</a>,
for more information on using the F12 key for displaying graphics files
with SAS.
</li></ol>
<p>Should you or a colleague inadvertently start a statistical process in
an ordinary ‘<samp>*shell*</samp>’ buffer, the ‘<samp>ess-remote</samp>’ command can
be used to convert it to an ESS buffer and allow you to use the ESS
commands with it.
</p>
<p>We have two older commands, now deprecated, for accessing ESS processes
on remote computers.
See <a href="#S_002belsewhere-and-ESS_002delsewhere">S+elsewhere and ESS-elsewhere</a>.
</p>
<hr>
<a name="S_002belsewhere-and-ESS_002delsewhere"></a>
<div class="header">
<p>
Next: <a href="#Customizing-startup" accesskey="n" rel="next">Customizing startup</a>, Previous: <a href="#ESS-processes-on-Remote-Computers" accesskey="p" rel="prev">ESS processes on Remote Computers</a>, Up: <a href="#Interactive-ESS" accesskey="u" rel="up">Interactive ESS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="S_002belsewhere-and-ESS_002delsewhere-1"></a>
<h3 class="section">3.4 S+elsewhere and ESS-elsewhere</h3>
<p>These commands are now deprecated. We recommend ‘<samp>ess-remote</samp>’. We
have two versions of the elsewhere function. ‘<samp>S+elsewhere</samp>’ is
specific for the S-Plus program. The more general function
‘<samp>ESS-elsewhere</samp>’ is not as stable.
</p>
<ol>
<li> Enter ‘<samp>M-x S+elsewhere</samp>’.
You will be prompted for a starting directory. I usually give it my
project directory on the local machine, say ‘<samp>~myname/myproject/</samp>’
<p>Or enter ‘<samp>M-x ESS-elsewhere</samp>’. You will be prompted for an ESS
program and for a starting directory. I usually give it my project
directory on the local machine, say ‘<samp>~myname/myproject/</samp>’
</p>
</li><li> The ‘<samp>*S+3*</samp>’ buffer will appear with a prompt from the
local operating system (the unix prompt on a unix workstation or with
cygwin bash on a PC, or the msdos prompt on a PC without bash). emacs
may freeze because the cursor is at the wrong place. Unfreeze it with
‘<samp>C-g</samp>’ then move the cursor to the end with ‘<samp>M-></samp>’.
With ‘<samp>S+elsewhere</samp>’ the buffer name is based on the name of the ESS program.
</li><li> Enter
‘<samp>telnet myname@other.machine</samp>’ (or ‘<samp>ssh myname@other.machine</samp>’).
You will be prompted for your password on the remote machine.
Use
‘<samp>M-x send-invisible</samp>’
before typing the password itself.
</li><li> Before starting the ESS process, type ‘<samp>stty -echo nl</samp>’
at the unix prompt. The ‘<samp>-echo</samp>’ turns off the echo, the
‘<samp>nl</samp>’ turns off the newline that you see as ‘<samp>^M</samp>’.
</li><li> You are now talking to the unix prompt on the other machine in the
‘<samp>*S+3*</samp>’ buffer. cd into the directory for the current project and start
the ESS process by entering
‘<samp>Splus</samp>’ or ‘<samp>R</samp>’ or ‘<samp>sas -stdio</samp>’
as appropriate. If you can login remotely to your Windows 2000, then
you should be able to run ‘<samp>Sqpe</samp>’ on the Windows machine. I haven’t
tested this and no-one has reported their tests to me. You will not be
able to run the GUI through this text-only connection.
</li><li> Once you get the S or R or SAS prompt, then you are completely connected.
All the ‘<samp>C-c C-n</samp>’ and related commands work correctly in sending
commands from ‘<samp>myfile.s</samp>’ or ‘<samp>myfile.r</samp>’ on the PC to the
‘<samp>*S+3*</samp>’ buffer running the S or R or SAS program on the remote machine.
</li><li> Graphics on the remote machine works fine. If you run the X window
system on the remote unix machine you should be able to display them in
‘<samp>xfree86</samp>’ on your PC. If you don’t run X Windows, or X11, then you can write
graphics to the postscript device and copy it to your PC with dired and
display it with ghostscript.
</li></ol>
<hr>
<a name="Customizing-startup"></a>
<div class="header">
<p>
Previous: <a href="#S_002belsewhere-and-ESS_002delsewhere" accesskey="p" rel="prev">S+elsewhere and ESS-elsewhere</a>, Up: <a href="#Interactive-ESS" accesskey="u" rel="up">Interactive ESS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Changing-the-startup-actions"></a>
<h3 class="section">3.5 Changing the startup actions</h3>
<p>If you do not wish ESS to prompt for a starting directory when starting
a new process, set the variable <code>ess-ask-for-ess-directory</code> to
<a name="index-ess_002dask_002dfor_002dess_002ddirectory"></a>
<code>nil</code>. In this case, the starting directory will be set using
one of the following methods:
</p>
<ol>
<li> If the variable <code>ess-directory-function</code> stores the name of a
function, the value returned by this function is used. The default for
this variable is nil.
</li><li> Otherwise, if the variable <code>ess-directory</code> stores the name of a
directory (ending in a slash), this value is used. The default for this
variable is nil.
</li><li> Otherwise, the working directory of the current buffer is used.
</li></ol>
<p>If <code>ess-ask-for-ess-directory</code> has a non-<code>nil</code> value (as it
does by default) then the value determined by the above rules provides
the default when prompting for the starting directory. Incidentally,
<code>ess-directory</code> is an ideal variable to set in
<code>ess-pre-run-hook</code>.
</p>
<p>If you like to keep a record of your S sessions, set the variable
<code>ess-ask-about-transfile</code> to <code>t</code>, and you will be asked for a
filename for the transcript before the ESS process starts.
</p>
<dl>
<dt><a name="index-ess_002dask_002dabout_002dtransfile"></a>User Option: <strong>ess-ask-about-transfile</strong></dt>
<dd><p>If non-<code>nil</code>, as for a file name in which to save the session
transcript.
</p></dd></dl>
<a name="index-transcript-file"></a>
<p>Enter the name of a file in which to save the transcript at the prompt.
If the file doesn’t exist it will be created (and you should give it a
file name ending in ‘<samp>.St</samp>’); if the file already exists the
transcript will be appended to the file. (Note: if you don’t set this
variable but you still want to save the transcript, you can still do it
later — see <a href="#Saving-transcripts">Saving transcripts</a>.)
</p>
<p>Once these questions are answered (if they are asked at all) the S
process itself is started by calling the program name specified in the
variable <code>inferior-ess-program</code>.
<a name="index-inferior_002dess_002dprogram"></a>
If you need to pass any arguments to this program, they may be specified
in the variable <code>inferior-<var>S_program_name</var>-args</code> (e.g. if
<code>inferior-ess-program</code> is <code>"S+"</code> then the variable to set is
<code>inferior-S+-args</code>.
<a name="index-arguments-to-S-program"></a>
It is not normally necessary to pass arguments to the S program; in
particular do not pass the ‘<samp>-e</samp>’ option to <code>Splus</code>, since ESS
provides its own command history mechanism.
</p>
<p>By default, the new process will be displayed in the same window in the
current frame. If you wish your S process to appear in a separate
variable, customize the variable <code>inferior-ess-own-frame</code>.
Alternatively, change <code>inferior-ess-same-window</code> if you wish the
process to appear within another window of the current frame.
</p>
<hr>
<a name="Entering-commands"></a>
<div class="header">
<p>
Next: <a href="#Evaluating-code" accesskey="n" rel="next">Evaluating code</a>, Previous: <a href="#Interactive-ESS" accesskey="p" rel="prev">Interactive ESS</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Interacting-with-the-ESS-process"></a>
<h2 class="chapter">4 Interacting with the ESS process</h2>
<a name="index-entering-commands"></a>
<a name="index-commands"></a>
<a name="index-sending-input"></a>
<p>The primary function of the ESS package is to provide an easy-to-use
front end to the S interpreter. This is achieved by running the S
process from within an Emacs buffer, called hereafter <em>inferior</em>
buffer, which has an active <code>inferior-ess-mode</code>. The features of
Inferior S mode are similar to those provided by the standard Emacs
shell mode (see <a href="http://www.gnu.org/software/emacs/manual/html_mono/emacs.html#Shell-Mode">Shell Mode</a> in <cite>The Gnu Emacs Reference Manual</cite>).
Command-line completion of S objects and a number of ‘hot keys’ for
commonly-used S commands are also provided for ease of typing.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Command_002dline-editing" accesskey="1">Command-line editing</a>:</td><td> </td><td align="left" valign="top">Entering commands and fixing mistakes
</td></tr>
<tr><td align="left" valign="top">• <a href="#Transcript" accesskey="2">Transcript</a>:</td><td> </td><td align="left" valign="top">Manipulating the transcript
</td></tr>
<tr><td align="left" valign="top">• <a href="#Command-History" accesskey="3">Command History</a>:</td><td> </td><td align="left" valign="top">Command History
</td></tr>
<tr><td align="left" valign="top">• <a href="#History-expansion" accesskey="4">History expansion</a>:</td><td> </td><td align="left" valign="top">References to historical commands
</td></tr>
<tr><td align="left" valign="top">• <a href="#Hot-keys" accesskey="5">Hot keys</a>:</td><td> </td><td align="left" valign="top">Hot keys for common commands
</td></tr>
<tr><td align="left" valign="top">• <a href="#Statistical-Process-running-in-ESS_003f" accesskey="6">Statistical Process running in ESS?</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Emacsclient" accesskey="7">Emacsclient</a>:</td><td> </td><td align="left" valign="top">Using emacsclient
</td></tr>
<tr><td align="left" valign="top">• <a href="#Other" accesskey="8">Other</a>:</td><td> </td><td align="left" valign="top">Other commands provided by inferior-ESS
</td></tr>
</table>
<hr>
<a name="Command_002dline-editing"></a>
<div class="header">
<p>
Next: <a href="#Transcript" accesskey="n" rel="next">Transcript</a>, Up: <a href="#Entering-commands" accesskey="u" rel="up">Entering commands</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Entering-commands-and-fixing-mistakes"></a>
<h3 class="section">4.1 Entering commands and fixing mistakes</h3>
<a name="index-command_002dline-editing"></a>
<p>Sending a command to the ESS process is as simple as typing it in
and pressing the <tt class="key">RETURN</tt> key:
</p>
<dl>
<dt><a name="index-inferior_002dess_002dsend_002dinput"></a>Command: <strong>inferior-ess-send-input</strong></dt>
<dd><a name="index-RET"></a>
<p><kbd>RET</kbd> Send the command on the current line to the ESS process.
</p></dd></dl>
<p>If you make a typing error before pressing <kbd>RET</kbd> all the usual Emacs
editing commands are available to correct it (see <a href="http://www.gnu.org/software/emacs/manual/html_mono/emacs.html#Basic">Basic
editing commands</a> in <cite>The GNU Emacs Reference Manual</cite>). Once the
command has been corrected you can press <tt class="key">RETURN</tt> (even if the
cursor is not at the end of the line) to send the corrected command to
the ESS process.
</p>
<p>Emacs provides some other commands which are useful for fixing mistakes:
</p>
<dl compact="compact">
<dt><kbd>C-c C-w</kbd></dt>
<dd><a name="index-backward_002dkill_002dword"></a>
<p><code>backward-kill-word</code> Deletes the previous word (such as an object
name) on the command line.
</p>
</dd>
<dt><kbd>C-c C-u</kbd></dt>
<dd><a name="index-comint_002dkill_002dinput"></a>
<p><code>comint-kill-input</code> Deletes everything from the prompt to point.
Use this to abandon a command you have not yet sent to the ESS process.
</p>
</dd>
<dt><kbd>C-c C-a</kbd></dt>
<dd><a name="index-comint_002dbol"></a>
<p><code>comint-bol</code> Move to the beginning of the line, and then skip
forwards past the prompt, if any.
</p></dd>
</dl>
<p>See <a href="http://www.gnu.org/software/emacs/manual/html_mono/emacs.html#Shell-Mode">Shell Mode</a> in <cite>The Gnu Emacs Reference Manual</cite>, for other
commands relevant to entering input.
</p>
<hr>
<a name="Transcript"></a>
<div class="header">
<p>
Next: <a href="#Command-History" accesskey="n" rel="next">Command History</a>, Previous: <a href="#Command_002dline-editing" accesskey="p" rel="prev">Command-line editing</a>, Up: <a href="#Entering-commands" accesskey="u" rel="up">Entering commands</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Manipulating-the-transcript"></a>
<h3 class="section">4.2 Manipulating the transcript</h3>
<p>Most of the time, the cursor spends most of its time at the bottom of
the ESS process buffer, entering commands. However all the input
and output from the current (and previous) ESS sessions is stored in
the process buffer (we call this the transcript) and often we want to
<a name="index-transcript"></a>
move back up through the buffer, to look at the output from previous
commands for example.
</p>
<p>Within the process buffer, a paragraph
<a name="index-paragraphs-in-the-process-buffer"></a>
is defined as the prompt, the command after the prompt, and the output
from the command. Thus <kbd>M-{</kbd> and <kbd>M-}</kbd> move you backwards and
forwards, respectively, through commands in the transcript. A
particularly useful command is <kbd>M-h</kbd> (<code>mark-paragraph</code>) which
will allow you to mark a command and its entire output (for deletion,
perhaps). For more information about paragraph commands,
see <a href="http://www.gnu.org/software/emacs/manual/html_mono/emacs.html#Paragraphs">Paragraphs</a> in <cite>The GNU Emacs
Reference Manual</cite>.
</p>
<p>If an ESS process finishes and you restart it in the same process
buffer, the output from the new ESS process appears after the output
from the first ESS process separated by a form-feed (‘<samp>^L</samp>’)
character. Thus pages in the ESS
<a name="index-pages-in-the-process-buffer"></a>
process buffer correspond to ESS sessions. Thus, for example, you may
use <kbd>C-x [</kbd> and <kbd>C-x ]</kbd> to move backward and forwards through
ESS sessions in a single ESS process buffer. For more information about
page commands, see <a href="http://www.gnu.org/software/emacs/manual/html_mono/emacs.html#Pages">Pages</a> in <cite>The GNU Emacs
Reference Manual</cite>.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Last-command" accesskey="1">Last command</a>:</td><td> </td><td align="left" valign="top">Manipulating the output from the last command
</td></tr>
<tr><td align="left" valign="top">• <a href="#Process-buffer-motion" accesskey="2">Process buffer motion</a>:</td><td> </td><td align="left" valign="top">Viewing older commands
</td></tr>
<tr><td align="left" valign="top">• <a href="#Transcript-resubmit" accesskey="3">Transcript resubmit</a>:</td><td> </td><td align="left" valign="top">Re-submitting commands from the transcript
</td></tr>
<tr><td align="left" valign="top">• <a href="#Saving-transcripts" accesskey="4">Saving transcripts</a>:</td><td> </td><td align="left" valign="top">Keeping a record of your S session
</td></tr>
</table>
<hr>
<a name="Last-command"></a>
<div class="header">
<p>
Next: <a href="#Process-buffer-motion" accesskey="n" rel="next">Process buffer motion</a>, Up: <a href="#Transcript" accesskey="u" rel="up">Transcript</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Manipulating-the-output-from-the-last-command"></a>
<h4 class="subsection">4.2.1 Manipulating the output from the last command</h4>
<p>Viewing the output of the command you have just entered is a common
occurrence and ESS provides a number of facilities for doing this.
Whenever a command produces a longish output, it is possible that the
window will scroll, leaving the next prompt near the middle of the
window. The first part of the command output may have scrolled off the
top of the window, even though the entire output would fit in the window
if the prompt were near the bottom of the window. If this happens, you
can use the following comint commands:
</p>
<p><code>comint-show-maximum-output</code> to move to the end
of the buffer, and place cursor on bottom line of window to make more of
the last output visible. To make this happen automatically for all
inputs, set the variable <code>comint-scroll-to-bottom-on-input</code> to
<code>t</code> or <code>'this</code>. If the first part of the output is still not
visible, use
<a name="index-reading-long-command-outputs"></a>
<kbd>C-c C-r</kbd> (<code>comint-show-output</code>),
<a name="index-comint_002dshow_002doutput"></a>
which moves cursor to the previous command line and places it at the
top of the window.
</p>
<p>Finally, if you want to discard the last command output altogether, use
<a name="index-deleting-output"></a>
<kbd>C-c C-o</kbd> (<code>comint-kill-output</code>),
<a name="index-comint_002dkill_002doutput"></a>
which deletes everything from the last command to the current prompt.
Use this command judiciously to keep your transcript to a more
manageable size.
</p>
<hr>
<a name="Process-buffer-motion"></a>
<div class="header">
<p>
Next: <a href="#Transcript-resubmit" accesskey="n" rel="next">Transcript resubmit</a>, Previous: <a href="#Last-command" accesskey="p" rel="prev">Last command</a>, Up: <a href="#Transcript" accesskey="u" rel="up">Transcript</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Viewing-older-commands"></a>
<h4 class="subsection">4.2.2 Viewing older commands</h4>
<p>If you want to view the output from more historic commands than the
previous command, commands are also provided to move backwards and
forwards through previously entered commands in the process buffer:
</p>
<dl compact="compact">
<dt><kbd>C-c C-p</kbd></dt>
<dd><a name="index-comint_002dprevious_002dinput"></a>
<p><code>comint-previous-input</code> Moves point to the preceding command in the
process buffer.
</p>
</dd>
<dt><kbd>C-c C-n</kbd></dt>
<dd><a name="index-comint_002dnext_002dinput"></a>
<p><code>comint-next-input</code> Moves point to the next command in the process
buffer.
</p></dd>
</dl>
<p>Note that these two commands are analogous to <kbd>C-p</kbd> and <kbd>C-n</kbd>
but apply to command lines rather than text lines. And just like
<kbd>C-p</kbd> and <kbd>C-n</kbd>, passing a prefix argument to these commands
means to move to the <var>ARG</var>’th next (or previous) command. (These
commands are also discussed in <a href="http://www.gnu.org/software/emacs/manual/html_mono/emacs.html#Shell-History-Copying">Shell History
Copying</a> in <cite>The GNU Emacs Reference Manual</cite>.)
</p>
<p>There are also two similar commands (not bound to any keys by default)
which move to preceding or succeeding commands, but which first prompt
for a regular expression (see <a href="http://www.gnu.org/software/emacs/manual/html_mono/emacs.html#Regexps">Syntax of Regular
Expression</a> in <cite>The GNU Emacs Reference Manual</cite>), and then moves to
the next (previous) command matching the pattern.
</p>
<dl compact="compact">
<dt><code>comint-backward-matching-input regexp arg</code></dt>
<dd><a name="index-comint_002dbackward_002dmatching_002dinput"></a>
</dd>
<dt><code>comint-forward-matching-input regexp arg</code></dt>
<dd><a name="index-comint_002dforward_002dmatching_002dinput"></a>
<p>Search backward (forward) through the transcript buffer for the
<var>arg</var>’th previous (next) command matching <var>regexp</var>. <var>arg</var>
is the prefix argument; <var>regexp</var> is prompted for in the minibuffer.
</p></dd>
</dl>
<hr>
<a name="Transcript-resubmit"></a>
<div class="header">
<p>
Next: <a href="#Saving-transcripts" accesskey="n" rel="next">Saving transcripts</a>, Previous: <a href="#Process-buffer-motion" accesskey="p" rel="prev">Process buffer motion</a>, Up: <a href="#Transcript" accesskey="u" rel="up">Transcript</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Re_002dsubmitting-commands-from-the-transcript"></a>
<h4 class="subsection">4.2.3 Re-submitting commands from the transcript</h4>
<p>When moving through the transcript, you may wish to re-execute some of
the commands you find there. ESS provides three commands to do this;
these commands may be used whenever the cursor is within a command line
in the transcript (if the cursor is within some command <em>output</em>,
an error is signalled). Note all three commands involve the <tt class="key">RETURN</tt>
key.
</p>
<dl compact="compact">
<dt><kbd>RET</kbd></dt>
<dd><p><code>inferior-ess-send-input</code> See <a href="#Command_002dline-editing">Command-line editing</a>.
</p>
</dd>
<dt><kbd>C-c RET</kbd></dt>
<dd><a name="index-comint_002dcopy_002dold_002dinput"></a>
<p><code>comint-copy-old-input</code> Copy the command under the cursor to the
current command line, but don’t execute it. Leaves the cursor on the
command line so that the copied command may be edited.
</p></dd>
</dl>
<p>When the cursor is not after the current prompt, the <tt class="key">RETURN</tt> key
has a slightly different behavior than usual. Pressing <kbd>RET</kbd> on any
line containing a command that you entered (i.e. a line beginning with a
prompt) sends that command to the ESS process once again. If you
wish to edit the command before executing it, use <kbd>C-c RET</kbd> instead;
it copies the command to the current prompt but does not execute it,
allowing you to edit it before submitting it.
</p>
<p>These commands work even if the current line is a continuation line
(i.e. the prompt is ‘<samp>+</samp>’ instead of ‘<samp>></samp>’) — in this case all
the lines that form the multi-line command are concatenated together and
the resulting command is sent to the ESS process (currently this is
the only way to resubmit a multi-line command to the ESS process in
one go). If the current line does
<a name="index-multi_002dline-commands_002c-resubmitting"></a>
not begin with a prompt, an error is signalled. This feature, coupled
with the command-based motion commands described above, could be used as
a primitive history mechanism. ESS provides a more sophisticated
mechanism, however, which is described in <a href="#Command-History">Command History</a>.
</p>
<hr>
<a name="Saving-transcripts"></a>
<div class="header">
<p>
Previous: <a href="#Transcript-resubmit" accesskey="p" rel="prev">Transcript resubmit</a>, Up: <a href="#Transcript" accesskey="u" rel="up">Transcript</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Keeping-a-record-of-your-S-session"></a>
<h4 class="subsection">4.2.4 Keeping a record of your S session</h4>
<p>To keep a record of your S session in a disk file, use the Emacs
command <kbd>C-x C-w</kbd> (<code>write-file</code>) to attach a file to the ESS
process buffer. The name of the process buffer will (probably) change
to the name of the file, but this is not a problem. You can still use
S as usual; just remember to save the file before you quit Emacs
with <kbd>C-x C-s</kbd>. You can make ESS prompt you for a filename in which
to save the transcript every time you start S by setting the
variable
<a name="index-ess_002dask_002dabout_002dtransfile-1"></a>
<code>ess-ask-about-transfile</code> to <code>t</code>; See <a href="#Customizing-startup">Customizing startup</a>.
<a name="index-transcript-file-names"></a>
We recommend you save your transcripts with filenames that end in
‘<samp>.St</samp>’. There is a special mode (ESS transcript mode —
see <a href="#Transcript-Mode">Transcript Mode</a>) for editing transcript files which is
automatically selected for files with this suffix.
</p>
<a name="index-editing-transcripts"></a>
<p>S transcripts can get very large, so some judicious editing is
appropriate if you are saving it in a file. Use <kbd>C-c C-o</kbd> whenever
a command produces excessively long output (printing large arrays, for
example). Delete erroneous commands (and the resulting error messages
or other output) by moving to the command (or its output) and typing
<kbd>M-h C-w</kbd>. Also, remember that <kbd>C-c C-x</kbd> (and other hot keys)
may be used for commands whose output you do not wish to appear in the
transcript. These suggestions are appropriate even if you are not
saving your transcript to disk, since the larger the transcript, the
more memory your Emacs process will use on the host machine.
</p>
<p>Finally, if you intend to produce S source code (suitable for using
with <code>source()</code> or inclusion in an S function) from a
transcript, then the command <code>ess-transcript-clean-region</code> may be
of use. see <a href="#Clean">Transcript Mode</a>
</p>
<hr>
<a name="Command-History"></a>
<div class="header">
<p>
Next: <a href="#History-expansion" accesskey="n" rel="next">History expansion</a>, Previous: <a href="#Transcript" accesskey="p" rel="prev">Transcript</a>, Up: <a href="#Entering-commands" accesskey="u" rel="up">Entering commands</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Command-History-1"></a>
<h3 class="section">4.3 Command History</h3>
<a name="index-command-history"></a>
<a name="index-editing-commands"></a>
<a name="index-re_002dexecuting-commands"></a>
<p>ESS provides easy-to-use facilities for re-executing or editing previous
commands. An input history of the last few commands is maintained (by
default the last 500 commands are stored, although this can be changed by
setting the variable <code>comint-input-ring-size</code> in
<a name="index-comint_002dinput_002dring_002dsize"></a>
<code>inferior-ess-mode-hook</code>.) The simplest history commands simply
select the next and previous commands in the input history:
</p>
<dl compact="compact">
<dt><kbd>M-p</kbd></dt>
<dd><a name="index-comint_002dprevious_002dinput-1"></a>
<p><code>comint-previous-input</code> Select the previous command in the input
history.
</p>
</dd>
<dt><kbd>M-n</kbd></dt>
<dd><a name="index-comint_002dnext_002dinput-1"></a>
<p><code>comint-next-input</code> Select the next command in the input history.
</p></dd>
</dl>
<p>For example, pressing <kbd>M-p</kbd> once will re-enter the last command into
the process buffer after the prompt but does not send it to the ESS
process, thus allowing editing or correction of the command before the
ESS process sees it. Once corrections have been made, press
<kbd>RET</kbd> to send the edited command to the ESS process.
</p>
<p>If you want to select a particular command from the history by matching
it against a regular expression (see <a href="http://www.gnu.org/software/emacs/manual/html_mono/emacs.html#Regexps">Syntax of Regular
Expression</a> in <cite>The GNU Emacs Reference Manual</cite>), to search for a
particular variable name for example, these commands are also available:
</p>
<dl compact="compact">
<dt><kbd>M-r</kbd></dt>
<dd><a name="index-comint_002dhistory_002disearch_002dbackward_002dregexp"></a>
<p><code>comint-history-isearch-backward-regexp</code> Prompt for a regular
expression, and search backwards through the input history for a command
matching the expression.
</p>
</dd>
</dl>
<p>A common type of search is to find the last command that began with a
particular sequence of characters; the following two commands provide an
easy way to do this:
</p>
<dl compact="compact">
<dt><kbd>C-c M-r</kbd></dt>
<dd><a name="index-comint_002dprevious_002dmatching_002dinput_002dfrom_002dinput"></a>
<p><code>comint-previous-matching-input-from-input</code> Select the previous
command in the history which matches the string typed so far.
</p>
</dd>
<dt><kbd>C-c M-s</kbd></dt>
<dd><a name="index-comint_002dnext_002dmatching_002dinput_002dfrom_002dinput"></a>
<p><code>comint-next-matching-input-from-input</code> Select the next command in
the history which matches the string typed so far.
</p></dd>
</dl>
<p>Instead of prompting for a regular expression to match against, as they
instead select commands starting with those characters already entered.
For instance, if you wanted to re-execute the last <code>attach()</code>
command, you may only need to type <kbd>att</kbd> and then <kbd>C-c M-r</kbd> and
<kbd>RET</kbd>.
</p>
<p>See <a href="http://www.gnu.org/software/emacs/manual/html_mono/emacs.html#Shell-Ring">Shell History Ring</a> in <cite>The GNU Emacs Reference
Manual</cite>, for a more detailed discussion of the history mechanism,
and do experiment with the <code>In/Out</code> menu to explore the possibilities.
</p>
<p>Many ESS users like to have even easier access to these, and recommend
to add something like
</p><div class="example">
<pre class="example"> (eval-after-load "comint"
'(progn
(define-key comint-mode-map [up]
'comint-previous-matching-input-from-input)
(define-key comint-mode-map [down]
'comint-next-matching-input-from-input)
;; also recommended for ESS use --
(setq comint-scroll-to-bottom-on-output 'others)
(setq comint-scroll-show-maximum-output t)
;; somewhat extreme, almost disabling writing in *R*, *shell* buffers above prompt:
(setq comint-scroll-to-bottom-on-input 'this)
))
</pre></div>
<p>to your <samp>.emacs</samp> file,
where the last two settings are typically desirable for the situation where
you work with a script (e.g., <samp>code.R</samp>) and send code chunks to the
process buffer (e.g. <code>*R*</code>).
Note however that these settings influence all <code>comint</code>-using emacs
modes, not just the ESS ones, and for that reason, these customization
cannot be part of <code>ESS</code> itself.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Saving-History" accesskey="1">Saving History</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Saving-History"></a>
<div class="header">
<p>
Up: <a href="#Command-History" accesskey="u" rel="up">Command History</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Saving-the-command-history"></a>
<h4 class="subsection">4.3.1 Saving the command history</h4>
<p>The <code>ess-history-file</code> variable, which is <code>t</code> by default,
together with <code>ess-history-directory</code>, governs if and where the
command history is saved and restored between sessions.
By default, <code>ess-history-directory</code> is <code>nil</code>, and the command
history will be stored (as text file) in the <code>ess-directory</code>, e.g., as
<samp>.Rhistory</samp>.
</p>
<p>Experienced ESS users often work exclusively with script files rather than
in a (e.g., <code>*R</code>) console session, and may not want to save any
history files, and hence have:
</p>
<div class="smallexample">
<pre class="smallexample"> (setq ess-history-file nil)
</pre></div>
<p>or will only want one global command history file and have:
</p>
<div class="smallexample">
<pre class="smallexample"> (setq ess-history-directory "~/.R/")
</pre></div>
<p>in your <samp>.emacs</samp> file.
</p>
<hr>
<a name="History-expansion"></a>
<div class="header">
<p>
Next: <a href="#Hot-keys" accesskey="n" rel="next">Hot keys</a>, Previous: <a href="#Command-History" accesskey="p" rel="prev">Command History</a>, Up: <a href="#Entering-commands" accesskey="u" rel="up">Entering commands</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="References-to-historical-commands"></a>
<h3 class="section">4.4 References to historical commands</h3>
<p>Instead of searching through the command history using the command
described in the previous section, you can alternatively refer to a
historical command directly using a notation very similar to that used
in <code>csh</code>. History references are introduced by a ‘<samp>!</samp>’ or
‘<samp>^</samp>’ character and have meanings as follows:
</p>
<dl compact="compact">
<dt>‘<samp>!!</samp>’</dt>
<dd><p>The immediately previous command
</p>
</dd>
<dt>‘<samp>!-<var>N</var></samp>’</dt>
<dd><p>The <var>N</var>th previous command
</p>
</dd>
<dt>‘<samp>!text</samp>’</dt>
<dd><p>The last command beginning with the string ‘<samp>text</samp>’
</p>
</dd>
<dt>‘<samp>!?text</samp>’</dt>
<dd><p>The last command containing the string ‘<samp>text</samp>’
</p></dd>
</dl>
<p>In addition, you may follow the reference with a <em>word designator</em>
to select particular <em>words</em> of the input. A word is defined as a
sequence of characters separated by whitespace. (You can modify this
definition by setting the value of <code>comint-delimiter-argument-list</code>
to a list of characters that are allowed to separate words and
<a name="index-comint_002ddelimiter_002dargument_002dlist"></a>
themselves form words.) Words are numbered beginning with zero. The
word designator usually begins with a ‘<samp>:</samp>’ (colon) character;
however it may be omitted if the word reference begins with a ‘<samp>^</samp>’,
‘<samp>$</samp>’, ‘<samp>*</samp>’ or ‘<samp>-</samp>’. If the word is to be selected from the
previous command, the second ‘<samp>!</samp>’ character can be omitted from the
event specification. For instance, ‘<samp>!!:1</samp>’ and ‘<samp>!:1</samp>’ both
refer to the first word of the previous command, while ‘<samp>!!$</samp>’ and
‘<samp>!$</samp>’ both refer to the last word in the previous command. The
format of word designators is as follows:
</p>
<dl compact="compact">
<dt>‘<samp>0</samp>’</dt>
<dd><p>The zeroth word (i.e. the first one on the command line)
</p>
</dd>
<dt>‘<samp><var>n</var></samp>’</dt>
<dd><p>The <var>n</var>th word, where <var>n</var> is a number
</p>
</dd>
<dt>‘<samp>^</samp>’</dt>
<dd><p>The first word (i.e. the second one on the command line)
</p>
</dd>
<dt>‘<samp>$</samp>’</dt>
<dd><p>The last word
</p>
</dd>
<dt>‘<samp><var>x</var>-<var>y</var></samp>’</dt>
<dd><p>A range of words; ‘<samp>-<var>y</var></samp>’ abbreviates ‘<samp>0-<var>y</var></samp>’
</p>
</dd>
<dt>‘<samp>*</samp>’</dt>
<dd><p>All the words except the zeroth word, or nothing if the command had just
one word (the zeroth)
</p>
</dd>
<dt>‘<samp><var>x</var>*</samp>’</dt>
<dd><p>Abbreviates <var>x</var>-$
</p>
</dd>
<dt>‘<samp><var>x</var>-</samp>’</dt>
<dd><p>Like ‘<samp><var>x</var>*</samp>’, but omitting the last word
</p></dd>
</dl>
<p>In addition, you may surround the entire reference except for the first
‘<samp>!</samp>’ by braces to allow it to be followed by other (non-whitespace)
characters (which will be appended to the expanded reference).
</p>
<p>Finally, ESS also provides quick substitution; a reference like
‘<samp>^old^new^</samp>’ means “the last command, but with the first occurrence
of the string ‘<samp>old</samp>’ replaced with the string ‘<samp>new</samp>’” (the last
‘<samp>^</samp>’ is optional). Similarly, ‘<samp>^old^</samp>’ means “the last
command, with the first occurrence of the string ‘<samp>old</samp>’ deleted”
(again, the last ‘<samp>^</samp>’ is optional).
</p>
<p>To convert a history reference as described above to an input suitable
for S, you need to <em>expand</em> the history reference, using the
<tt class="key">TAB</tt> key. For this to work, the cursor must be preceded by a space
(otherwise it would try to complete an object name) and not be within a
string (otherwise it would try to complete a filename). So to expand
the history reference, type <kbd>SPC TAB</kbd>. This will convert the
history reference into an S command from the history, which you can
then edit or press <tt class="key">RET</tt> to execute.
</p>
<p>For example, to execute the last command that referenced the variable
<code>data</code>, type <kbd>!?data SPC TAB RET</kbd>.
</p>
<hr>
<a name="Hot-keys"></a>
<div class="header">
<p>
Next: <a href="#Statistical-Process-running-in-ESS_003f" accesskey="n" rel="next">Statistical Process running in ESS?</a>, Previous: <a href="#History-expansion" accesskey="p" rel="prev">History expansion</a>, Up: <a href="#Entering-commands" accesskey="u" rel="up">Entering commands</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Hot-keys-for-common-commands"></a>
<h3 class="section">4.5 Hot keys for common commands</h3>
<p>ESS provides a number of commands for executing the commonly used
functions. These commands below are basically information-gaining
commands (such as <code>objects()</code> or <code>search()</code>) which tend to
clutter up your transcript and for this reason some of the hot keys
display their output in a temporary buffer instead of the process buffer
by default. This behavior is controlled by the following option:
</p>
<dl>
<dt><a name="index-ess_002dexecute_002din_002dprocess_002dbuffer"></a>User Option: <strong>ess-execute-in-process-buffer</strong></dt>
<dd><p>If non-<code>nil</code>, means that these commands will produce their output
in the process buffer instead.
</p></dd></dl>
<p>In any case, passing a prefix argument to the commands (with <kbd>C-u</kbd>)
will reverse the meaning of <code>ess-execute-in-process-buffer</code> for
that command, i.e. the output will be displayed in the process buffer if
it usually goes to a temporary buffer, and vice-versa. These are the
hot keys that behave in this way:
</p>
<dl>
<dt><a name="index-ess_002dexecute_002dobjects"></a>Command: <strong>ess-execute-objects</strong> <em><var>posn</var></em></dt>
<dd><a name="index-C_002dc-C_002dx"></a>
<a name="index-objects_0028_0029"></a>
<a name="index-objects"></a>
<p><kbd>C-c C-x</kbd> Sends the <code>objects()</code> command to the ESS process. A
prefix argument specifies the position on the search list (use a
negative argument to toggle <code>ess-execute-in-process-buffer</code> as
well). A quick way to see what objects are in your working directory.
A prefix argument of 2 or more means get objects for that position. A
negative prefix argument <var>posn</var> gets the objects for that position,
as well as toggling <code>ess-execute-in-process-buffer</code>.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002dexecute_002dsearch"></a>Command: <strong>ess-execute-search</strong> <em><var>invert</var></em></dt>
<dd><a name="index-C_002dc-C_002ds"></a>
<a name="index-search_0028_0029"></a>
<a name="index-search-list"></a>
<p><kbd>C-c C-s</kbd> Sends the <code>inferior-ess-search-list-command</code> command
to the <code>ess-language</code> process; <code>search()</code> in S. Prefix
<var>invert</var> toggles <code>ess-execute-in-process-buffer</code>.
</p></dd></dl>
<p><code>ess-execute</code> may seem pointless when you could just type the
command in anyway, but it proves useful for ‘spot’ calculations which
would otherwise clutter your transcript, or for evaluating an expression
while partway through entering a command. You can also use this command
to generate new hot keys using the Emacs keyboard macro facilities;
see <a href="http://www.gnu.org/software/emacs/manual/html_mono/emacs.html#Keyboard-Macros">Keyboard Macros</a> in <cite>The GNU
Emacs Reference Manual</cite>.
<a name="index-hot-keys"></a>
<a name="index-keyboard-short-cuts"></a>
</p>
<p>The following hot keys do not use <code>ess-execute-in-process-buffer</code>
to decide where to display the output — they either always display in
the process buffer or in a separate buffer, as indicated:
</p>
<dl>
<dt><a name="index-ess_002dload_002dfile"></a>Command: <strong>ess-load-file</strong> <em><var>filename</var></em></dt>
<dd><a name="index-C_002dc-C_002dl"></a>
<p><kbd>C-c C-l</kbd> Prompts for a file (<var>filename</var>) to load into the ESS
process using <code>source()</code>. If there is an error during loading, you
can jump to the error in the file with the following function.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002dparse_002derrors"></a>Command: <strong>ess-parse-errors</strong> <em><var>arg</var> <var>reset</var></em></dt>
<dd><a name="index-C_002dx-_0060"></a>
<a name="index-C_002dc-_0060"></a>
<p><kbd>C-c `</kbd> or <kbd>C-x `</kbd> Visits next <code>next-error</code> message and
corresponding source code. If all the error messages parsed so far have
been processed already, the message buffer is checked for new ones. A
prefix <var>arg</var> specifies how many error messages to move; negative
means move back to previous error messages. Just <kbd>C-u</kbd> as a prefix
means reparse the error message buffer and start at the first error.
The <var>reset</var> argument specifies restarting from the beginning.
</p>
<p>See <a href="#Error-Checking">Error Checking</a>, for more details.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002ddisplay_002dhelp_002don_002dobject"></a>Command: <strong>ess-display-help-on-object</strong> <em><var>object</var> <var>command</var></em></dt>
<dd><a name="index-C_002dc-C_002dv"></a>
<p><kbd>C-c C-v</kbd> Pops up a help buffer for an S <var>object</var> or
function. If <var>command</var> is supplied, it is used instead of
<code>inferior-ess-help-command</code>. See <a href="#Help">Help</a> for more details.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002dquit"></a>Command: <strong>ess-quit</strong></dt>
<dd><a name="index-C_002dc-C_002dq"></a>
<a name="index-q_0028_0029"></a>
<a name="index-ess_002dcleanup"></a>
<a name="index-quitting-from-ESS"></a>
<a name="index-killing-the-ESS-process"></a>
<a name="index-cleaning-up"></a>
<a name="index-temporary-buffers_002c-killing"></a>
<a name="index-killing-temporary-buffers"></a>
<p><kbd>C-c C-q</kbd> Issue an exiting command to the inferior process,
additionally also running <code>ess-cleanup</code> for disposing of any
temporary buffers (such as help buffers and edit buffers) that may have
been created. Use this command when you have finished your S
session instead of simply quitting at the inferior process prompt,
otherwise you will need to issue the command <code>ess-cleanup</code>
explicitly to make sure that all the files that need to be saved have
been saved, and that all the temporary buffers have been killed.
</p></dd></dl>
<hr>
<a name="Statistical-Process-running-in-ESS_003f"></a>
<div class="header">
<p>
Next: <a href="#Emacsclient" accesskey="n" rel="next">Emacsclient</a>, Previous: <a href="#Hot-keys" accesskey="p" rel="prev">Hot keys</a>, Up: <a href="#Entering-commands" accesskey="u" rel="up">Entering commands</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Is-the-Statistical-Process-running-under-ESS_003f"></a>
<h3 class="section">4.6 Is the Statistical Process running under ESS?</h3>
<a name="index-STERM"></a>
<a name="index-STERM-1"></a>
<p>For the S languages (S, S-Plus, R) ESS sets an option in the current
process that programs in the language can check to determine the
environment in which they are currently running.
</p>
<p>ESS sets <code>options(STERM="iESS")</code> for S language processes running
in an inferior <code>i<acronym>ESS[S]</acronym><!-- /@w --></code> or <code>i<acronym>ESS[R]</acronym><!-- /@w --></code> buffer.
</p>
<p>ESS sets <code>options(STERM="ddeESS")</code> for independent S-Plus for
Windows processes running in the GUI and communicating with ESS via the
DDE (Microsoft Dynamic Data Exchange) protocol through a
<code>ddeESS[S]</code> buffer.
</p>
<p>Other values of <code>options()$STERM</code> that we recommend are:
</p>
<ul>
<li> <code>length</code>: Fixed length xterm or telnet window.
</li><li> <code>scrollable</code>: Unlimited length xterm or telnet window.
</li><li> <code>server</code>: S-Plus Stat Server.
</li><li> <code>BATCH</code>: BATCH.
</li><li> <code>Rgui</code>: R GUI.
</li><li> <code>Commands</code>: S-Plus GUI without DDE interface to ESS.
</li></ul>
<p>Additional values may be recommended in the future as new interaction
protocols are created. Unlike the values <code>iESS</code> and <code>ddeESS</code>,
ESS can’t set these other values since the S language program is not
under the control of ESS.
</p>
<hr>
<a name="Emacsclient"></a>
<div class="header">
<p>
Next: <a href="#Other" accesskey="n" rel="next">Other</a>, Previous: <a href="#Statistical-Process-running-in-ESS_003f" accesskey="p" rel="prev">Statistical Process running in ESS?</a>, Up: <a href="#Entering-commands" accesskey="u" rel="up">Entering commands</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Using-emacsclient"></a>
<h3 class="section">4.7 Using emacsclient</h3>
<a name="index-emacsclient"></a>
<p>When starting R or S under Unix, ESS sets
<code>options(editor="emacsclient")</code>. (Under Microsoft Windows, it will
use gnuclient.exe rather than emacsclient, but the same principle
applies.) Within your R session, for example, if you have a function
called <code>iterator</code>, typing <code>fix(iterator)</code>, will show that
function in a temporary Emacs buffer. You can then correct the
function. When you kill the buffer, the definition of the function is
updated. Using <code>edit()</code> rather than <code>fix()</code> means that the
function is not updated. Finally, the S function <code>page(x)</code> will
also show a text representation of the object <code>x</code> in a temporary
Emacs buffer.
</p>
<hr>
<a name="Other"></a>
<div class="header">
<p>
Previous: <a href="#Emacsclient" accesskey="p" rel="prev">Emacsclient</a>, Up: <a href="#Entering-commands" accesskey="u" rel="up">Entering commands</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Other-commands-provided-by-inferior_002dESS"></a>
<h3 class="section">4.8 Other commands provided by inferior-ESS</h3>
<p>The following commands are also available in the process buffer:
</p>
<dl>
<dt><a name="index-comint_002dinterrupt_002dsubjob"></a>Command: <strong>comint-interrupt-subjob</strong></dt>
<dd><a name="index-C_002dc-C_002dc"></a>
<a name="index-aborting-S-commands"></a>
<a name="index-interrupting-S-commands"></a>
<p><kbd>C-c C-c</kbd> Sends a Control-C signal to the ESS process. This has the
effect of aborting the current command.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002dswitch_002dto_002dinferior_002dor_002dscript_002dbuffer"></a>Command: <strong>ess-switch-to-inferior-or-script-buffer</strong> <em><var>toggle-eob</var></em></dt>
<dd><a name="index-C_002dc-C_002dz"></a>
<p><kbd>C-c C-z</kbd> When in process buffer, return to the most recent script
buffer. When in a script buffer pop to the associated process buffer.
This is a single key command, that is <kbd>C-c C-z C-z</kbd> from a script
buffer returns to the original buffer.
</p>
<p>If <var>toggle-eob</var> is given, the value of
<code>ess-switch-to-end-of-proc-buffer</code> is toggled.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002dswitch_002dto_002dend_002dof_002dproc_002dbuffer"></a>User Option: <strong>ess-switch-to-end-of-proc-buffer</strong></dt>
<dd><p>If non-<code>nil</code>, <code>ess-switch-to-inferior-or-script-buffer</code> goes
to end of process buffer.
</p></dd></dl>
<p>Other commands available in Inferior S mode are discussed in
<a href="http://www.gnu.org/software/emacs/manual/html_mono/emacs.html#Shell-Mode">Shell Mode</a> in <cite>The Gnu Emacs Reference Manual</cite>.
</p>
<hr>
<a name="Evaluating-code"></a>
<div class="header">
<p>
Next: <a href="#Transcript-Mode" accesskey="n" rel="next">Transcript Mode</a>, Previous: <a href="#Entering-commands" accesskey="p" rel="prev">Entering commands</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Sending-code-to-the-ESS-process"></a>
<h2 class="chapter">5 Sending code to the ESS process</h2>
<p>Other commands are also available for evaluating portions of code in the
S process. These commands cause the selected code to be evaluated
directly by the ESS process as if you had typed them in at the
command line; the <code>source()</code> function is not used. You may choose
whether both the commands and their output appear in the process buffer
(as if you had typed in the commands yourself) or if the output alone is
echoed. The behavior is controlled by the variable:
</p>
<dl>
<dt><a name="index-ess_002deval_002dvisibly"></a>User Option: <strong>ess-eval-visibly</strong></dt>
<dd><p>Non-<code>nil</code> means <code>ess-eval-*</code> commands display commands and
output in the process buffer. Default is <code>t</code>.
</p></dd></dl>
<p>Passing a prefix (<kbd>C-u</kbd>) <var>vis</var> to any of the following commands,
however, reverses the meaning of <code>ess-eval-visibly</code> for that
command only — for example <kbd>C-u C-c C-j</kbd>
suppresses the current line of S (or other) code in the ESS process buffer.
This method of evaluation is an
alternative to S’s <code>source()</code> function
<a name="index-source_0028_0029"></a>
<a name="index-echoing-commands-when-evaluating"></a>
<a name="index-evaluating-code-with-echoed-commands"></a>
when you want the input as well as the output to be displayed. (You can
sort of do this with <code>source()</code> when the option <code>echo=T</code> is
set, except that prompts do not get displayed. ESS puts prompts in the
right places.)
</p>
<p>Primary commands for evaluating code are:
<a name="index-evaluating-S-expressions"></a>
</p>
<dl>
<dt><a name="index-ess_002deval_002dregion_002dor_002dline_002dand_002dstep"></a>Command: <strong>ess-eval-region-or-line-and-step</strong> <em><var>vis</var></em></dt>
<dd><p>Send the highlighted region or current line and step to next line of
code.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002deval_002dregion_002dor_002dfunction_002dor_002dparagraph"></a>Command: <strong>ess-eval-region-or-function-or-paragraph</strong> <em><var>vis</var></em></dt>
<dd><a name="index-C_002dM_002dx"></a>
<p><kbd>C-M-x</kbd> Sends the current selected region or function or paragraph.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002deval_002dregion_002dor_002dfunction_002dor_002dparagraph_002dand_002dstep"></a>Command: <strong>ess-eval-region-or-function-or-paragraph-and-step</strong> <em><var>vis</var></em></dt>
<dd><a name="index-C_002dC-C_002dc"></a>
<p><kbd>C-c C-c</kbd> Like <code>ess-eval-region-or-function-or-paragraph</code> but
steps to next line of code.
</p></dd></dl>
<p>Other, not so often used, evaluation commands are:
</p>
<dl>
<dt><a name="index-ess_002deval_002dline"></a>Command: <strong>ess-eval-line</strong> <em><var>vis</var></em></dt>
<dd><a name="index-C_002dC-C_002dj"></a>
<p><kbd>C-c C-j</kbd> Sends the current line to the ESS process.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002deval_002dline_002dand_002dgo"></a>Command: <strong>ess-eval-line-and-go</strong> <em><var>vis</var></em></dt>
<dd><a name="index-C_002dC-M_002dj"></a>
<p><kbd>C-c M-j</kbd> Like <code>ess-eval-line</code> but additionally switches point
to the ESS process.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002deval_002dfunction"></a>Command: <strong>ess-eval-function</strong> <em><var>vis</var> <var>no-error</var></em></dt>
<dd><a name="index-C_002dC-C_002df"></a>
<p><kbd>C-c C-f</kbd> Sends the S function containing point to the ESS
process.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002deval_002dfunction_002dand_002dgo"></a>Command: <strong>ess-eval-function-and-go</strong> <em><var>vis</var></em></dt>
<dd><a name="index-C_002dC-M_002df"></a>
<p><kbd>C-c M-f</kbd> Like <code>ess-eval-function</code> but additionally switches
point to the ESS process.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002deval_002dregion"></a>Command: <strong>ess-eval-region</strong> <em><var>start</var> <var>end</var> <var>toggle</var> <var>message</var></em></dt>
<dd><a name="index-C_002dC-C_002dr"></a>
<p><kbd>C-c C-r</kbd> Sends the current region to the ESS process.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002deval_002dregion_002dand_002dgo"></a>Command: <strong>ess-eval-region-and-go</strong> <em><var>start</var> <var>end</var> <var>vis</var></em></dt>
<dd><a name="index-C_002dC-M_002dr"></a>
<p><kbd>C-c M-r</kbd> Like <code>ess-eval-region</code> but additionally switches
point to the ESS process.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002deval_002dbuffer"></a>Command: <strong>ess-eval-buffer</strong> <em><var>vis</var></em></dt>
<dd><a name="index-C_002dC-C_002db"></a>
<p><kbd>C-c C-b</kbd> Sends the current buffer to the ESS process.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002deval_002dbuffer_002dand_002dgo"></a>Command: <strong>ess-eval-buffer-and-go</strong> <em><var>vis</var></em></dt>
<dd><a name="index-C_002dC-M_002db"></a>
<p><kbd>C-c M-b</kbd> Like <code>ess-eval-buffer</code> but additionally switches
point to the ESS process.
</p></dd></dl>
<p>All the above <code>ess-eval-*</code> commands are useful for evaluating small
amounts of code and observing the results in the process buffer for
debugging purposes, or for generating transcripts from source files.
When editing S functions, it is generally preferable to use <kbd>C-c
C-l</kbd> to update the function’s value. In particular,
<code>ess-eval-buffer</code> is now largely obsolete.
</p>
<p>A useful way to work is to divide the frame into two windows; one
containing the source code and the other containing the process buffer.
If you wish to make the process buffer scroll automatically when the
output reaches the bottom of the window, you will need to set the
variable <code>comint-scroll-to-bottom-on-output</code> to <code>'others</code> or
<code>t</code>.
</p>
<hr>
<a name="Transcript-Mode"></a>
<div class="header">
<p>
Next: <a href="#Editing-objects" accesskey="n" rel="next">Editing objects</a>, Previous: <a href="#Evaluating-code" accesskey="p" rel="prev">Evaluating code</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Manipulating-saved-transcript-files"></a>
<h2 class="chapter">6 Manipulating saved transcript files</h2>
<p>Inferior S mode records the transcript (the list of all commands
executed, and their output) in the process buffer, which can be saved as
a <em>transcript file</em>, which should normally have the suffix
<samp>.St</samp>. The most obvious use for a transcript file is as a static
record of the actions you have performed in a particular S session.
Sometimes, however, you may wish to re-execute commands recorded in the
transcript file by submitting them to a running ESS process. This
is what Transcript Mode is for.
</p>
<p>If you load file a with the suffix <samp>.St</samp> into Emacs, it is placed
in S Transcript Mode. Transcript Mode is similar to Inferior S mode
(see <a href="#Entering-commands">Entering commands</a>):
<a name="index-transcript-mode-motion"></a>
<a name="index-motion-in-transcript-mode"></a>
paragraphs are defined as a command and its output, and you can move
though commands either with the paragraph commands or with <kbd>C-c C-p</kbd>
and <kbd>C-c C-n</kbd>.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Resubmit" accesskey="1">Resubmit</a>:</td><td> </td><td align="left" valign="top">Resubmitting commands from the transcript file
</td></tr>
<tr><td align="left" valign="top">• <a href="#Clean" accesskey="2">Clean</a>:</td><td> </td><td align="left" valign="top">Cleaning transcript files
</td></tr>
</table>
<hr>
<a name="Resubmit"></a>
<div class="header">
<p>
Next: <a href="#Clean" accesskey="n" rel="next">Clean</a>, Up: <a href="#Transcript-Mode" accesskey="u" rel="up">Transcript Mode</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Resubmitting-commands-from-the-transcript-file"></a>
<h3 class="section">6.1 Resubmitting commands from the transcript file</h3>
<p>Three commands are provided to re-submit command lines from the
transcript file to a running ESS process. They are:
</p>
<dl>
<dt><a name="index-ess_002dtranscript_002dsend_002dcommand"></a>Command: <strong>ess-transcript-send-command</strong></dt>
<dd><a name="index-M_002dRET"></a>
<p><kbd>M-RET</kbd> Sends the current command line to the ESS process, and
execute it.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002dtranscript_002dcopy_002dcommand"></a>Command: <strong>ess-transcript-copy-command</strong></dt>
<dd><a name="index-C_002dc-RET"></a>
<p><kbd>C-c RET</kbd> Copy the current command to the ESS process, and switch to
it (ready to edit the copied command).
</p></dd></dl>
<dl>
<dt><a name="index-ess_002dtranscript_002dsend_002dcommand_002dand_002dmove"></a>Command: <strong>ess-transcript-send-command-and-move</strong></dt>
<dd><a name="index-RET-1"></a>
<p><kbd>RET</kbd> Sends the current command to the ESS process, and move to the
next command line. This command is useful for submitting a series of
commands.
</p></dd></dl>
<p>Note that the first two commands are similar to those on the same keys
in inferior S Mode. In all three cases, the commands should be
executed when the cursor is on a command line in the transcript; the
prompt is automatically removed before the command is submitted.
</p>
<hr>
<a name="Clean"></a>
<div class="header">
<p>
Previous: <a href="#Resubmit" accesskey="p" rel="prev">Resubmit</a>, Up: <a href="#Transcript-Mode" accesskey="u" rel="up">Transcript Mode</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Cleaning-transcript-files"></a>
<h3 class="section">6.2 Cleaning transcript files</h3>
<p>Yet another use for transcript files is to extract the command lines for
inclusion in an S source file or function. Transcript mode provides
one command which does just this:
</p>
<dl>
<dt><a name="index-ess_002dtranscript_002dclean_002dregion"></a>Command: <strong>ess-transcript-clean-region</strong> <em><var>beg</var> <var>end</var> <var>even-if-read-only</var></em></dt>
<dd><a name="index-C_002dc-C_002dw"></a>
<p><kbd>C-c C-w</kbd> Strip the transcript in the region (given by <var>beg</var> and
<var>end</var>), leaving only commands. Deletes any lines not beginning with
a prompt, and then removes the prompt from those lines that remain.
Prefix argument <var>even-if-read-only</var> means to clean even if the
buffer is read-only. Don’t forget to remove any erroneous commands
first!
</p></dd></dl>
<p>The remaining command lines may then be copied to a source file or edit
buffer for inclusion in a function definition, or may be evaluated
directly (see <a href="#Evaluating-code">Evaluating code</a>) using the code evaluation commands
from S mode, also available in S Transcript Mode.
</p>
<hr>
<a name="Editing-objects"></a>
<div class="header">
<p>
Next: <a href="#Help" accesskey="n" rel="next">Help</a>, Previous: <a href="#Transcript-Mode" accesskey="p" rel="prev">Transcript Mode</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Editing-objects-and-functions"></a>
<h2 class="chapter">7 Editing objects and functions</h2>
<a name="index-editing-functions"></a>
<p>ESS provides facilities for editing S objects within your Emacs
session. Most editing is performed on S functions, although in
theory you may edit datasets as well. Edit buffers are always
associated with files, although you may choose to make these files
temporary if you wish. Alternatively, you may make use of a simple yet
powerful mechanism for maintaining backups of text representations of
S functions. Error-checking is performed when S code is loaded
into the ESS process.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Edit-buffer" accesskey="1">Edit buffer</a>:</td><td> </td><td align="left" valign="top">Edit objects in a specialized buffer
</td></tr>
<tr><td align="left" valign="top">• <a href="#Loading" accesskey="2">Loading</a>:</td><td> </td><td align="left" valign="top">Loading source files into the ESS process
</td></tr>
<tr><td align="left" valign="top">• <a href="#Error-Checking" accesskey="3">Error Checking</a>:</td><td> </td><td align="left" valign="top">Detecting errors in source files
</td></tr>
<tr><td align="left" valign="top">• <a href="#Indenting" accesskey="4">Indenting</a>:</td><td> </td><td align="left" valign="top">Indenting and formatting S code
</td></tr>
<tr><td align="left" valign="top">• <a href="#Other-edit-buffer-commands" accesskey="5">Other edit buffer commands</a>:</td><td> </td><td align="left" valign="top">Commands for motion, completion and more
</td></tr>
<tr><td align="left" valign="top">• <a href="#Source-Files" accesskey="6">Source Files</a>:</td><td> </td><td align="left" valign="top">Maintaining S source files
</td></tr>
<tr><td align="left" valign="top">• <a href="#Source-Directories" accesskey="7">Source Directories</a>:</td><td> </td><td align="left" valign="top">Names and locations of dump files
</td></tr>
</table>
<hr>
<a name="Edit-buffer"></a>
<div class="header">
<p>
Next: <a href="#Loading" accesskey="n" rel="next">Loading</a>, Up: <a href="#Editing-objects" accesskey="u" rel="up">Editing objects</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Creating-or-modifying-S-objects"></a>
<h3 class="section">7.1 Creating or modifying S objects</h3>
<a name="index-edit-buffer"></a>
<p>To edit an S object, type
</p>
<dl>
<dt><a name="index-ess_002ddump_002dobject_002dinto_002dedit_002dbuffer"></a>Command: <strong>ess-dump-object-into-edit-buffer</strong> <em><var>object</var></em></dt>
<dd><a name="index-C_002dc-C_002de-C_002dd"></a>
<p><kbd>C-c C-e C-d</kbd> Edit an S <var>object</var> in its own edit buffer.
</p></dd></dl>
<p>from within the ESS process buffer (<code>*S*</code>). You will then be
prompted for an object to edit: you may either type in the name of an
existing object (for which completion is available using the <kbd>TAB</kbd>
key),
<a name="index-completion_002c-when-prompted-for-object-names"></a>
or you may enter the name of a new object.
<a name="index-creating-new-objects"></a>
<a name="index-new-objects_002c-creating"></a>
A buffer will be created containing the text representation of the
requested object or, if you entered the name of a non-existent object at
the prompt and the variable <code>ess-function-template</code>
<a name="index-ess_002dfunction_002dtemplate"></a>
is non-<code>nil</code>, you will be presented with a template defined by that
variable, which defaults to a skeleton function construct.
</p>
<p>You may then edit the function as required. The edit buffer generated
by <code>ess-dump-object-into-edit-buffer</code> is placed in the <code>ESS</code>
major mode which provides a number of commands to facilitate editing
S source code. Commands are provided to intelligently indent S
code, evaluate portions of S code and to move around S code
constructs.
</p>
<a name="index-dump-files"></a>
<a name="index-reverting-function-definitions"></a>
<p>Note: when you dump a file with <kbd>C-c C-e C-d</kbd>, ESS first checks
to see whether there already exists an edit buffer containing that
object and, if so, pops you directly to that buffer. If not, ESS next
checks whether there is a file in the appropriate place with the
appropriate name (see <a href="#Source-Files">Source Files</a>) and if so, reads in that file.
You can use this facility to return to an object you were editing in a
previous session (and which possibly was never loaded to the S
session). Finally, if both these tests fail, the ESS process is
consulted and a <code>dump()</code> command issued.
<a name="index-dump_0028_0029"></a>
If you want to force ESS to ask the ESS process for the object’s
definition (say, to reformat an unmodified buffer or to revert back to
S’s idea of the object’s definition) pass a prefix argument to
<code>ess-dump-object-into-edit-buffer</code> by typing <kbd>C-u C-c C-e C-d</kbd>.
</p>
<hr>
<a name="Loading"></a>
<div class="header">
<p>
Next: <a href="#Error-Checking" accesskey="n" rel="next">Error Checking</a>, Previous: <a href="#Edit-buffer" accesskey="p" rel="prev">Edit buffer</a>, Up: <a href="#Editing-objects" accesskey="u" rel="up">Editing objects</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Loading-source-files-into-the-ESS-process"></a>
<h3 class="section">7.2 Loading source files into the ESS process</h3>
<p>The best way to get information — particularly function definitions
— into S is to load them in as source file, using S’s
<code>source</code> function. You have already seen how to create source
files using <kbd>C-c C-e C-d</kbd>; ESS provides a complementary command for
loading source files (even files not created with ESS!) into the ESS
process, namely <code>ess-load-file</code> (<kbd>C-c C-l</kbd>).
<a name="index-ess_002dload_002dfile-1"></a>
<a name="index-source_0028_0029-1"></a>
see <a href="#Hot-keys">Hot keys</a>.
</p>
<p>After typing <kbd>C-c C-l</kbd> you will prompt for the name of the file to
load into S; usually this is the current buffer’s file which is the
default value (selected by simply pressing <kbd>RET</kbd> at the prompt).
You will be asked to save the buffer first if it has been modified (this
happens automatically if the buffer was generated with <kbd>C-c C-e
C-d</kbd>). The file will then be loaded, and if it loads successfully you
will be returned to the ESS process.
</p>
<hr>
<a name="Error-Checking"></a>
<div class="header">
<p>
Next: <a href="#Indenting" accesskey="n" rel="next">Indenting</a>, Previous: <a href="#Loading" accesskey="p" rel="prev">Loading</a>, Up: <a href="#Editing-objects" accesskey="u" rel="up">Editing objects</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Detecting-errors-in-source-files"></a>
<h3 class="section">7.3 Detecting errors in source files</h3>
<a name="index-errors"></a>
<a name="index-parsing-errors"></a>
<p>If any errors occur when loading a file with <code>C-c C-l</code>, ESS will
inform you of this fact. In this case, you can jump directly to the
line in the source file which caused the error by typing <kbd>C-c `</kbd>
(<code>ess-parse-errors</code>).
<a name="index-C_002dc-_0060-1"></a>
<a name="index-ess_002dparse_002derrors-1"></a>
You will be returned to the offending file (loading it into a buffer if
necessary) with point at the line S reported as containing the
error. You may then correct the error, and reload the file. Note that
none of the commands in an S source file will take effect if any
part of the file contains errors.
</p>
<p>Sometimes the error is not caused by a syntax error (loading a
non-existent file for example). In this case typing <kbd>C-c `</kbd> will
simply display a buffer containing S’s error message. You can force
this behavior (and avoid jumping to the file when there <em>is</em> a
syntax error) by passing a prefix argument to <code>ess-parse-errors</code>
with <kbd>C-u C-c `</kbd>.
</p>
<hr>
<a name="Indenting"></a>
<div class="header">
<p>
Next: <a href="#Other-edit-buffer-commands" accesskey="n" rel="next">Other edit buffer commands</a>, Previous: <a href="#Error-Checking" accesskey="p" rel="prev">Error Checking</a>, Up: <a href="#Editing-objects" accesskey="u" rel="up">Editing objects</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Indenting-and-formatting-S-code"></a>
<h3 class="section">7.4 Indenting and formatting S code</h3>
<p>ESS provides a sophisticated mechanism for indenting S source
code (thanks to Ken’ichi Shibayama). Compound statements (delimited by
‘<samp>{</samp>’ and ‘<samp>}</samp>’) are indented relative to their enclosing block.
In addition, the braces have been electrified to automatically indent to
the correct position when inserted, and optionally insert a newline at
the appropriate place as well. Lines which continue an incomplete
expression are indented relative to the first line of the expression.
Function definitions, <code>if</code> statements, calls to <code>expression()</code>
and loop constructs are all recognized and indented appropriately. User
variables are provided to control the amount of indentation in each
case, and there are also a number of predefined indentation styles to
choose from.
</p>
<a name="index-comments-in-S"></a>
<p>Comments are also handled specially by ESS, using an idea borrowed from
the Emacs-Lisp indentation style. By default,
comments beginning with ‘<samp>###</samp>’
are aligned to the beginning of the line. Comments beginning with
‘<samp>##</samp>’ are aligned to the current level of indentation for the block
containing the comment. Finally, comments beginning with ‘<samp>#</samp>’ are
aligned to a column on the right (the 40th column by default, but this
value is controlled by the variable <code>comment-column</code>,)
<a name="index-comment_002dcolumn"></a>
or just after the expression on the line containing the comment if it
extends beyond the indentation column. You turn off the default
behavior by adding the line
<code>(setq ess-indent-with-fancy-comments nil)</code> to your <samp>.emacs</samp> file.
<a name="index-ess_002dindent_002dwith_002dfancy_002dcomments"></a>
</p>
<p>ESS also supports Roxygen entries which is R documentation maintained in
the source code as comments See <a href="#Roxygen">Roxygen</a>.
</p>
<p>The indentation commands provided by ESS are:
<a name="index-indenting"></a>
<a name="index-formatting-source-code"></a>
</p>
<dl>
<dt><a name="index-ess_002dindent_002dor_002dcomplete"></a>Command: <strong>ess-indent-or-complete</strong></dt>
<dd><a name="index-TAB"></a>
<p><kbd>TAB</kbd> Indents the current line as S code.
</p>
<p>Try to indent first, and if code is already properly indented, complete
instead. In ess-mode, only tries completion if
<code>ess-tab-complete-in-script</code> is non-nil. See also
<code>ess-first-tab-never-complete</code>.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002dtab_002dcomplete_002din_002dscript"></a>User Option: <strong>ess-tab-complete-in-script</strong></dt>
<dd><p>If non-<code>nil</code>, <kbd>TAB</kbd> in script buffers tries to complete if
there is nothing to indent.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002dfirst_002dtab_002dnever_002dcomplete"></a>User Option: <strong>ess-first-tab-never-complete</strong></dt>
<dd><p>If non-<code>nil</code>, <kbd>TAB</kbd> never tries to complete in ess-mode. The
default <code>'symbol</code> does not try to complete if the next char is a valid
symbol constituent. There are more options, see the help (<kbd>C-h v</kbd>).
</p></dd></dl>
<dl>
<dt><a name="index-ess_002dindent_002dexp"></a>Command: <strong>ess-indent-exp</strong></dt>
<dd><a name="index-C_002dM_002dq"></a>
<a name="index-M_002dC_002dq"></a>
<a name="index-ESC-C_002dq"></a>
<p><kbd>TAB</kbd> Indents each line in the S (compound) expression which
follows point. Very useful for beautifying your S code.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002delectric_002dbrace"></a>Command: <strong>ess-electric-brace</strong></dt>
<dd><a name="index-_007b"></a>
<a name="index-_007d"></a>
<p><kbd>{</kbd> <kbd>}</kbd> The braces automatically indent to the correct
position when typed.
</p></dd></dl>
<p>The following Emacs command are also helpful:
</p>
<dl compact="compact">
<dt><kbd>RET</kbd></dt>
<dt><kbd>LFD</kbd></dt>
<dd><a name="index-C_002dj"></a>
<p><code>newline-and-indent</code> Insert a newline, and indent the next line.
(Note that most keyboards nowadays do not have a <tt class="key">LINEFEED</tt> key, but
<tt class="key">RET</tt> and <kbd>C-j</kbd> are equivalent.)
</p>
</dd>
<dt><kbd>M-;</kbd></dt>
<dd><a name="index-M_002d_003b"></a>
<p><code>indent-for-comment</code> Indents an existing comment line
appropriately, or inserts an appropriate comment marker.
</p></dd>
</dl>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Styles" accesskey="1">Styles</a>:</td><td> </td><td align="left" valign="top">Changing indentation styles
</td></tr>
</table>
<hr>
<a name="Styles"></a>
<div class="header">
<p>
Up: <a href="#Indenting" accesskey="u" rel="up">Indenting</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Changing-indentation-styles"></a>
<h4 class="subsection">7.4.1 Changing indentation styles</h4>
<p>The combined value of nine variables that control indentation are
collectively termed a <i>style</i>. ESS provides several styles covering the
common styles of indentation: <code>DEFAULT</code>, <code>OWN</code>, <code>GNU</code>,
<code>BSD</code>, <code>K&R</code>, <code>C++</code>, <code>RRR</code>, <code>CLB</code>. The
variable <code>ess-style-alist</code> lists the value of each indentation
variable per style.
</p>
<dl>
<dt><a name="index-ess_002dset_002dstyle"></a>Command: <strong>ess-set-style</strong></dt>
<dd><a name="index-C_002dc-_002e"></a>
<p><kbd>C-c .</kbd> Sets the formatting style in this buffer to be one of the
predefined styles, including <code>GNU</code>, <code>BSD</code>, <code>K&R</code>,
<code>CLB</code>, and <code>C++</code>. The <code>DEFAULT</code> style uses the default
values for the indenting variables; The <code>OWN</code> style allows you to
use your own private values of the indentation variable, see below.
</p><div class="example">
<pre class="example">(setq ess-default-style 'C++)
</pre></div>
</dd></dl>
<dl>
<dt><a name="index-ess_002ddefault_002dstyle"></a>User Option: <strong>ess-default-style</strong></dt>
<dd><p>The default value of <code>ess-style</code>. See the variable
<code>ess-style-alist</code> for how these groups (DEFAULT, OWN, GNU, BSD,
…) map onto different settings for variables.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002dstyle_002dalist"></a>User Option: <strong>ess-style-alist</strong></dt>
<dd><p>Predefined formatting styles for ESS code. Values for all groups,
except OWN, are fixed. To change the value of variables in the OWN
group, customize the variable <code>ess-own-style-list</code>. The default
style in use is controlled by <code>ess-default-style</code>.
</p></dd></dl>
<p>The styles <code>DEFAULT</code> and <code>OWN</code> are initially identical. If
you wish to edit some of the default values, set
<code>ess-default-style</code> to <code>'OWN</code> and change
<code>ess-own-style-list</code>.
See <a href="#Customization">Customization</a>, for convenient ways to set both these variables.
</p>
<p>If you prefer not to use the custom facility, you can change individual
indentation variables within a hook, for example:
</p>
<div class="example">
<pre class="example">(defun myindent-ess-hook ()
(setq ess-indent-level 4))
(add-hook 'ess-mode-hook 'myindent-ess-hook)
</pre></div>
<p>In the rare case that you’d like to add an entire new indentation style
of your own, copy the definition of <code>ess-own-style-list</code> to a new
variable and ensure that the last line of the <code>:set</code> declaration
calls <code>ess-add-style</code> with a unique name for your style
(e.g. <code>'MINE</code>). Finally, add <code>(setq ess-default-style 'MINE)</code>
to use your new style.
</p>
<hr>
<a name="Other-edit-buffer-commands"></a>
<div class="header">
<p>
Next: <a href="#Source-Files" accesskey="n" rel="next">Source Files</a>, Previous: <a href="#Indenting" accesskey="p" rel="prev">Indenting</a>, Up: <a href="#Editing-objects" accesskey="u" rel="up">Editing objects</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Commands-for-motion_002c-completion-and-more"></a>
<h3 class="section">7.5 Commands for motion, completion and more</h3>
<p>A number of commands are provided to move across function definitions
in the edit buffer:
</p>
<dl>
<dt><a name="index-ess_002dgoto_002dbeginning_002dof_002dfunction_002dor_002dpara"></a>Command: <strong>ess-goto-beginning-of-function-or-para</strong></dt>
<dd><a name="index-ESC-C_002da"></a>
<a name="index-C_002dM_002da"></a>
<p><kbd>ESC C-a</kbd> aka <kbd>C-M-a</kbd> If inside a function go to the beginning
of it, otherwise go to the beginning of paragraph.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002dgoto_002dend_002dof_002dfunction_002dor_002dpara"></a>Command: <strong>ess-goto-end-of-function-or-para</strong></dt>
<dd><a name="index-ESC-C_002de"></a>
<a name="index-C_002dM_002de"></a>
<p><kbd>ESC C-e</kbd> aka <kbd>C-M-e</kbd> Move point to the end of the function
containing point.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002dmark_002dfunction"></a>Command: <strong>ess-mark-function</strong></dt>
<dd><a name="index-ESC-C_002dh"></a>
<a name="index-C_002dM_002dh"></a>
<p><kbd>ESC C-h</kbd> aka <kbd>C-M-h</kbd> Place point at the beginning of the S
function containing point, and mark at the end.
</p></dd></dl>
<p>Don’t forget the usual Emacs commands for moving over balanced
expressions and parentheses: See <a href="Emacs.html#Lists">Lists and
Sexps</a> in <cite>The GNU Emacs Reference Manual</cite>.
</p>
<a name="index-completion-in-edit-buffer"></a>
<p>Completion is provided in the edit buffer in a similar fashion to the
process buffer: <tt class="key">TAB</tt> first indents, and if there is nothing to
indent, completes the object or file name; <kbd>M-?</kbd> lists file
completions. See See <a href="#Completion">Completion</a>, for more.
</p>
<p>Finally, <kbd>C-c C-z</kbd> (<code>ess-switch-to-inferior-or-script-buffer</code>)
returns you to the <code>iESS</code> process buffer, if done from a script
buffer, placing point at the end of the buffer. If this is done from
the <code>iESS</code> process buffer, point is taken to the script buffer.
</p>
<p>In addition some commands available in the process buffer are also
available in the script buffer. You can still read help files with
<kbd>C-c C-v</kbd>, edit another function with <kbd>C-c C-e C-d</kbd> and of
course <kbd>C-c C-l</kbd> can be used to load a source file into S.
</p>
<hr>
<a name="Source-Files"></a>
<div class="header">
<p>
Next: <a href="#Source-Directories" accesskey="n" rel="next">Source Directories</a>, Previous: <a href="#Other-edit-buffer-commands" accesskey="p" rel="prev">Other edit buffer commands</a>, Up: <a href="#Editing-objects" accesskey="u" rel="up">Editing objects</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Maintaining-S-source-files"></a>
<h3 class="section">7.6 Maintaining S source files</h3>
<p>Every edit buffer in ESS is associated with a <em>dump file</em> on disk.
Dump files are created whenever you type <kbd>C-c C-e C-d</kbd>
(<code>ess-dump-object-into-edit-buffer</code>), and may either be deleted
after use, or kept as a backup file or as a means of keeping several
versions of an S function.
<a name="index-dump-files-1"></a>
</p>
<dl>
<dt><a name="index-ess_002ddelete_002ddump_002dfiles"></a>User Option: <strong>ess-delete-dump-files</strong></dt>
<dd><p>If non-<code>nil</code>, dump files created with C-c C-e C-d are deleted
immediately after they are created by the ess-process.
</p></dd></dl>
<p>Since immediately after S dumps an object’s definition to a disk
file the source code on disk corresponds exactly to S’s idea of the
object’s definition, the disk file isn’t needed; deleting it now has the
advantage that if you <em>don’t</em> modify the file (say, because you
just wanted to look at the definition of one of the standard S
functions) the source dump file won’t be left around when you kill the
buffer. Note that this variable only applies to files generated with
S’s <code>dump</code> function; it doesn’t apply to source files which already
exist. The default value is <code>t</code>.
</p>
<dl>
<dt><a name="index-ess_002dkeep_002ddump_002dfiles"></a>User Option: <strong>ess-keep-dump-files</strong></dt>
<dd><p>Variable controlling whether to delete dump files after a successful
load. If ‘<samp>nil</samp>’: always delete. If ‘<samp>ask</samp>’, confirm to delete.
If ‘<samp>check</samp>’, confirm to delete, except for files created with
<code>ess-dump-object-into-edit-buffer</code>. Anything else, never delete.
This variable only affects the behaviour of <code>ess-load-file</code>. Dump
files are never deleted if an error occurs during the load.
</p></dd></dl>
<p>After an object has been successfully (i.e. without error) loaded
back into S with <kbd>C-c C-l</kbd>, the disk file again corresponds
exactly (well, almost — see below) to S’s record of the object’s
definition, and so some people prefer to delete the disk file rather
than unnecessarily use up space. This option allows you to do just
that.
</p>
<a name="index-comments"></a>
<a name="index-project-work-in-S"></a>
<a name="index-historic-backups"></a>
<p>If the value of <code>ess-keep-dump-files</code> is <code>t</code>, dump files are
never deleted after they are loaded. Thus you can maintain a complete
text record of the functions you have edited within ESS. Backup files
are kept as usual, and so by using the Emacs numbered backup facility —
see <a href="http://www.gnu.org/software/emacs/manual/html_mono/emacs.html#Backup-Names">Single or Numbered
Backups</a> in <cite>The Gnu Emacs Reference Manual</cite>, you can keep a historic
record of function definitions. Another possibility is to maintain the
files with a version-control system such as RCS See <a href="http://www.gnu.org/software/emacs/manual/html_mono/emacs.html#Version-Control">Version Control</a> in <cite>The Gnu Emacs Reference
Manual</cite>. As long as a dump file exists in the appropriate place for a
particular object, editing that object with <kbd>C-c C-e C-d</kbd> finds that
file for editing (unless a prefix argument is given) — the ESS
process is not consulted. Thus you can keep comments <em>outside</em> the
function definition as a means of documentation that does not clutter
the S object itself. Another useful feature is that you may format
the code in any fashion you please without S re-indenting the code
every time you edit it. These features are particularly useful for
project-based work.
</p>
<p>If the value of <code>ess-keep-dump-files</code> is nil, the dump file is always
silently deleted after a successful load with <kbd>C-c C-l</kbd>. While this
is useful for files that were created with <kbd>C-c C-e C-d</kbd> it also applies
to any other file you load (say, a source file of function
definitions), and so can be dangerous to use unless you are careful.
Note that since <code>ess-keep-dump-files</code> is buffer-local, you can make
sure particular files are not deleted by setting it to <code>t</code> in the
Local Variables section of the file See <a href="http://www.gnu.org/software/emacs/manual/html_mono/emacs.html#File-Variables">Local Variables in Files</a> in <cite>The Gnu Emacs
Reference Manual</cite>.
</p>
<p>A safer option is to set <code>ess-keep-dump-files</code> to <code>ask</code>; this
means that ESS will always ask for confirmation before deleting the
file. Since this can get annoying if you always want to delete dump
files created with <code>C-c C-e C-d</code>, but not any other files, setting
<code>ess-keep-dump-files</code> to <code>check</code> (the default value) will
silently delete dump files created with <kbd>C-c C-e C-d</kbd> in the current
Emacs session, but query for any other file. Note that in any case you
will only be asked for confirmation once per file, and your answer is
remembered for the rest of the Emacs session.
</p>
<p>Note that in all cases, if an error (such as a syntax error) is detected
while loading the file with <kbd>C-c C-l</kbd>, the dump file is <em>never</em>
deleted. This is so that you can edit the file in a new Emacs session
if you happen to quit Emacs before correcting the error.
</p>
<a name="index-autosaving"></a>
<p>Dump buffers are always autosaved, regardless of the value of
<code>ess-keep-dump-files</code>.
</p>
<hr>
<a name="Source-Directories"></a>
<div class="header">
<p>
Previous: <a href="#Source-Files" accesskey="p" rel="prev">Source Files</a>, Up: <a href="#Editing-objects" accesskey="u" rel="up">Editing objects</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Names-and-locations-of-dump-files"></a>
<h3 class="section">7.7 Names and locations of dump files</h3>
<a name="index-dump-file-names"></a>
<p>Every dump file should be given a unique file name, usually the dumped
object name with some additions.
</p>
<dl>
<dt><a name="index-ess_002ddump_002dfilename_002dtemplate"></a>User Option: <strong>ess-dump-filename-template</strong></dt>
<dd><p>Template for filenames of dumped objects. <code>%s</code> is replaced by the
object name.
</p></dd></dl>
<p>By default, dump file names are the user name, followed by ‘<samp>.</samp>’ and
the object and ending with ‘<samp>.S</samp>’. Thus if user <code>joe</code> dumps the
object <code>myfun</code> the dump file will have name <samp>joe.myfun.S</samp>.
The username part is included to avoid clashes when dumping into a
publicly-writable directory, such as <samp>/tmp</samp>; you may wish to remove
this part if you are dumping into a directory owned by you.
</p>
<a name="index-dump-file-directories"></a>
<p>You may also specify the directory in which dump files are written:
</p>
<dl>
<dt><a name="index-ess_002dsource_002ddirectory"></a>User Option: <strong>ess-source-directory</strong></dt>
<dd><p>Directory name (ending in a slash) where S dump files are to be written.
</p></dd></dl>
<p>By default, dump files are always written to <samp>/tmp</samp>, which is fine
when <code>ess-keep-dump-files</code> is <code>nil</code>. If you are keeping dump
files, then you will probably want to keep them somewhere in your home
directory, say <samp>~/S-source</samp>. This could be achieved by including
the following line in your <samp>.emacs</samp> file:
<a name="index-_002eemacs-file"></a>
</p><div class="example">
<pre class="example">(setq ess-source-directory (expand-file-name "~/S-source/"))
</pre></div>
<p>If you would prefer to keep your dump files in separate directories
depending on the value of some variable, ESS provides a facility for
this also. By setting <code>ess-source-directory</code> to a lambda
expression which evaluates to a directory name, you have a great deal of
flexibility in selecting the directory for a particular source file to
appear in. The lambda expression is evaluated with the process buffer
as the current buffer and so you can use the variables local to that
buffer to make your choice. For example, the following expression
causes source files to be saved in the subdirectory <samp>Src</samp> of the
directory the ESS process was run in.
</p>
<div class="example">
<pre class="example">(setq ess-source-directory
(lambda ()
(concat ess-directory "Src/")))
</pre></div>
<p><a name="index-ess_002ddirectory"></a>
(<code>ess-directory</code> is a buffer-local variable in process buffers
which records the directory the ESS process was run from.) This is
useful if you keep your dump files and you often edit objects with the
same name in different ESS processes. Alternatively, if you often
change your S working directory during an S session, you may
like to keep dump files in some subdirectory of the directory pointed to
by the first element of the current search list. This way you can edit
objects of the same name in different directories during the one S
session:
<a name="index-search-list-1"></a>
<a name="index-working-directory-1"></a>
</p><div class="example">
<pre class="example">(setq ess-source-directory
(lambda ()
(file-name-as-directory
(expand-file-name (concat
(car ess-search-list)
"/.Src")))))
</pre></div>
<a name="index-ess_002dsearch_002dlist"></a>
<p>If the directory generated by the lambda function does not exist but can
be created, you will be asked whether you wish to create the directory.
If you choose not to, or the directory cannot be created, you will not
be able to edit functions.
</p>
<hr>
<a name="Help"></a>
<div class="header">
<p>
Next: <a href="#Completion" accesskey="n" rel="next">Completion</a>, Previous: <a href="#Editing-objects" accesskey="p" rel="prev">Editing objects</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Reading-help-files"></a>
<h2 class="chapter">8 Reading help files</h2>
<a name="index-help-files"></a>
<p>ESS provides an easy-to-use facility for reading S help files from
within Emacs. From within the ESS process buffer or any ESS edit
buffer, typing <kbd>C-c C-v</kbd> (<code>ess-display-help-on-object</code>)
<a name="index-ess_002ddisplay_002dhelp_002don_002dobject-1"></a>
will prompt you for the name of an object for which you would like
documentation. Completion is provided over all objects which have help
files.
</p>
<p>If the requested object has documentation, you will be popped into a
buffer (named <code>*help(<var>obj-name</var>)*</code>) containing the help file.
This buffer is placed in a special ‘S Help’ mode which disables the
usual editing commands but which provides a number of keys for paging
through the help file.
</p>
<p>Help commands:
</p>
<dl compact="compact">
<dt><kbd>?</kbd></dt>
<dd><a name="index-ess_002ddescribe_002dhelp_002dmode"></a>
<p><code>ess-describe-help-mode</code> Pops up a help buffer with a list of the
commands available in S help mode.
</p>
</dd>
<dt><kbd>h</kbd></dt>
<dd><a name="index-ess_002ddisplay_002dhelp_002don_002dobject-2"></a>
<p><code>ess-display-help-on-object</code> Pop up a help buffer for a different
object.
</p></dd>
</dl>
<p>Paging commands:
<a name="index-paging-commands-in-help-buffers"></a>
</p>
<dl compact="compact">
<dt><kbd>b</kbd></dt>
<dt><kbd>DEL</kbd></dt>
<dd><p><code>scroll-down</code> Move one page backwards through the help file.
</p>
</dd>
<dt><kbd>SPC</kbd></dt>
<dd><p><code>scroll-up</code> Move one page forwards through the help file.
</p>
</dd>
<dt><kbd>></kbd></dt>
<dt><kbd><</kbd></dt>
<dd><p><code>end-of-buffer</code> Move to the beginning and end of the help file,
respectively.
</p></dd>
</dl>
<p>Section-based motion commands:
</p>
<dl compact="compact">
<dt><kbd>n</kbd></dt>
<dt><kbd>p</kbd></dt>
<dd><a name="index-ess_002dskip_002dto_002dnext_002dsection"></a>
<a name="index-ess_002dskip_002dto_002dprevious_002dsection"></a>
<p><code>ess-skip-to-previous-section</code> and <code>ess-skip-to-next-section</code>
Move to the next and previous section header in the help file,
respectively. A section header consists of a number of capitalized
words, followed by a colon.
</p></dd>
</dl>
<p>In addition, the <kbd>s</kbd> key followed by one of the following letters
will jump to a particular section in the help file.
Note that R uses capitalized instead of all-capital section headers,
e.g., ‘<samp>Description:</samp>’ instead of ‘<samp>DESCRIPTION:</samp>’ and also
only some versions of S(-plus) have
sections ‘<samp>BACKGROUND</samp>’, ‘<samp>BUGS</samp>’, ‘<samp>OPTIONAL ARGUMENTS</samp>’,
‘<samp>REQUIRED ARGUMENTS</samp>’, and ‘<samp>SIDE EFFECTS</samp>’.
</p>
<p>Do use <kbd>s ?</kbd> to get the current list of active key bindings.
<a name="index-ess_002dskip_002dto_002dhelp_002dsection"></a>
</p>
<dl compact="compact">
<dt>‘<samp>a</samp>’</dt>
<dd><p>ARGUMENTS:
</p>
</dd>
<dt>‘<samp>b</samp>’</dt>
<dd><p>BACKGROUND:
</p>
</dd>
<dt>‘<samp>B</samp>’</dt>
<dd><p>BUGS:
</p>
</dd>
<dt>‘<samp>d</samp>’</dt>
<dd><p>DESCRIPTION:
</p>
</dd>
<dt>‘<samp>D</samp>’</dt>
<dd><p>DETAILS:
</p>
</dd>
<dt>‘<samp>e</samp>’</dt>
<dd><p>EXAMPLES:
</p>
</dd>
<dt>‘<samp>n</samp>’</dt>
<dd><p>NOTE:
</p>
</dd>
<dt>‘<samp>O</samp>’</dt>
<dd><p>OPTIONAL ARGUMENTS:
</p>
</dd>
<dt>‘<samp>R</samp>’</dt>
<dd><p>REQUIRED ARGUMENTS:
</p>
</dd>
<dt>‘<samp>r</samp>’</dt>
<dd><p>REFERENCES:
</p>
</dd>
<dt>‘<samp>s</samp>’</dt>
<dd><p>SEE ALSO:
</p>
</dd>
<dt>‘<samp>S</samp>’</dt>
<dd><p>SIDE EFFECTS:
</p>
</dd>
<dt>‘<samp>u</samp>’</dt>
<dd><p>USAGE:
</p>
</dd>
<dt>‘<samp>v</samp>’</dt>
<dd><p>VALUE:
</p>
</dd>
<dt>‘<samp><</samp>’</dt>
<dd><p>Jumps to beginning of file
</p>
</dd>
<dt>‘<samp>></samp>’</dt>
<dd><p>Jumps to end of file
</p>
</dd>
<dt>‘<samp>?</samp>’</dt>
<dd><p>Pops up a help buffer with a list of the defined section motion keys.
</p></dd>
</dl>
<p>Evaluation:
</p>
<dl compact="compact">
<dt><kbd>l</kbd></dt>
<dd><a name="index-ess_002deval_002dline_002dand_002dstep"></a>
<p><code>ess-eval-line-and-step</code> Evaluates the current line in the ESS
process, and moves to the next line. Useful for running examples in
help files.
</p>
</dd>
<dt><kbd>r</kbd></dt>
<dd><a name="index-ess_002deval_002dregion-1"></a>
<p><code>ess-eval-region</code> Send the contents of the current region to the
ESS process. Useful for running examples in help files.
</p></dd>
</dl>
<p>Quit commands:
</p>
<dl compact="compact">
<dt><kbd>q</kbd></dt>
<dd><a name="index-ess_002dswitch_002dto_002dend_002dof_002dESS"></a>
<p><code>ess-help-quit</code> Return to previously selected buffer, and bury the
help buffer.
</p>
</dd>
<dt><kbd>k</kbd></dt>
<dd><p><code>kill-buffer</code> Return to previously selected buffer, and kills the
help buffer.
</p>
</dd>
<dt><kbd>x</kbd></dt>
<dd><p><code>ess-kill-buffer-and-go</code> Return to the ESS process, killing this
help buffer.
</p></dd>
</dl>
<p>Miscellaneous:
</p>
<dl compact="compact">
<dt><kbd>i</kbd></dt>
<dd><p><code>ess-display-index</code> Prompt for a package and display it’s help
index.
</p>
</dd>
<dt><kbd>v</kbd></dt>
<dd><p><code>ess-display-vignettes</code> Display all available vignettes.
</p>
</dd>
<dt><kbd>w</kbd></dt>
<dd><p><code>ess-display-help-in-browser</code> Display current help page with the
web browser.
</p>
</dd>
<dt><kbd>/</kbd></dt>
<dd><p><code>isearch-forward</code> Same as <kbd>C-s</kbd>.
</p></dd>
</dl>
<p>In addition, all of the ESS commands available in the edit buffers are
also available in S help mode (see <a href="#Edit-buffer">Edit buffer</a>). Of course, the
usual (non-editing) Emacs commands are available, and for convenience
the digits and <tt class="key">-</tt> act as prefix arguments.
</p>
<p>If a help buffer already exists for an object for which help is
requested, that buffer is popped to immediately; the ESS process is
not consulted at all. If the contents of the help file have changed,
you either need to kill the help buffer first, or pass a prefix argument
(with <kbd>C-u</kbd>) to <code>ess-display-help-on-object</code>.
</p>
<p>Help buffers are marked as temporary buffers in ESS, and are deleted
when <code>ess-quit</code> or <code>ess-cleanup</code> are called.
</p>
<p>Help buffers normally appear in another window within the current
frame. If you wish help buffers to appear in their own frame (either
one per help buffer, or one for all help buffers), you can customize the
variable <code>ess-help-own-frame</code>.
</p>
<a name="index-ess_002dquit-1"></a>
<a name="index-ess_002dcleanup-1"></a>
<a name="index-temporary-buffers"></a>
<hr>
<a name="Completion"></a>
<div class="header">
<p>
Next: <a href="#Developing-with-ESS" accesskey="n" rel="next">Developing with ESS</a>, Previous: <a href="#Help" accesskey="p" rel="prev">Help</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Completion-1"></a>
<h2 class="chapter">9 Completion</h2>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Object-names" accesskey="1">Object names</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Function-arguments" accesskey="2">Function arguments</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Minibuffer-completion" accesskey="3">Minibuffer completion</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Auto_002dcomplete" accesskey="4">Auto-complete</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Icicles" accesskey="5">Icicles</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Object-names"></a>
<div class="header">
<p>
Next: <a href="#Function-arguments" accesskey="n" rel="next">Function arguments</a>, Up: <a href="#Completion" accesskey="u" rel="up">Completion</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Completion-of-object-names"></a>
<h3 class="section">9.1 Completion of object names</h3>
<a name="index-completion-of-object-names"></a>
<a name="index-command_002dline-completion"></a>
<a name="index-ess_002dfirst_002dtab_002dnever_002dcomplete-1"></a>
<p>The <tt class="key">TAB</tt> key is for completion. The value of the variable
<code>ess-first-tab-never-complete</code> controls when completion is allowed
controls when completion is allowed to occur. In <code>ess-mode</code>
<tt class="key">TAB</tt> first tries to indent, and if there is nothing to indent,
complete the object name instead.
</p>
<dl compact="compact">
<dt><kbd>TAB</kbd></dt>
<dd><a name="index-comint_002ddynamic_002dcomplete"></a>
<p><code>comint-dynamic-complete</code> Complete the S object name or
filename before point.
</p></dd>
</dl>
<p>When the cursor is just after a partially-completed object name,
pressing <tt class="key">TAB</tt> provides completion in a similar fashion to
<code>tcsh</code>
<a name="index-tcsh"></a>
except that completion is performed over all known S object names
instead of file names. ESS maintains a list of all objects known to S
at any given time, which basically consists of all objects (functions
and datasets) in every attached directory listed by the <code>search()</code>
command
<a name="index-search_0028_0029-1"></a>
along with the component objects of attached data frames
<a name="index-data-frames"></a>
(if your version of S supports them).
</p>
<p>For example, consider the three functions (available in Splus version
3.0) called <code>binomplot()</code>, <code>binom.test()</code> and
<code>binomial()</code>. Typing <kbd>bin TAB</kbd> after the S prompt will
insert the characters ‘<samp>om</samp>’, completing the longest prefix
(‘<samp>binom</samp>’) which distinguishes these three commands. Pressing
<kbd>TAB</kbd> once more provides a list of the three commands which have
this prefix, allowing you to add more characters (say, ‘<samp>.</samp>’) which
specify the function you desire. After entering more characters
pressing <kbd>TAB</kbd> yet again will complete the object name up to
uniqueness, etc. If you just wish to see what completions exist without
adding any extra characters, type <kbd>M-?</kbd>.
</p>
<dl>
<dt><a name="index-ess_002dlist_002dobject_002dcompletions"></a>Command: <strong>ess-list-object-completions</strong></dt>
<dd><a name="index-M_002d_003f"></a>
<p><kbd>M-?</kbd> List all possible completions of the object name at point.
</p></dd></dl>
<p>ESS also provides completion over the components of named lists and
environments (after ‘<samp>$</samp>’), S4 classes slots (after @), package and
namespace objects (after :: and :::). <a name="index-lists_002c-completion-on"></a>
<a name="index-completion-on-lists"></a>
</p>
<a name="index-completion-on-file-names"></a>
<p>Completion is also provided over file names, which is particularly
useful when using S functions such as <code>get()</code> or <code>scan()</code>
which require fully expanded file names.
</p>
<p>In the Inferior ESS buffer, if the cursor is not in a string and does
not follow a (partial) object name, the <tt class="key">TAB</tt> key has a third use:
it expands history references. See <a href="#History-expansion">History expansion</a>.
</p>
<p>Efficiency in completion is gained by maintaining a cache of objects
currently known to S; when a new object becomes available or is deleted,
only one component of the cache corresponding to the associated
directory needs to be refreshed. If ESS ever becomes confused about
what objects are available for completion (such as when if refuses to
complete an object you <strong>know</strong> is there), the command <kbd>M-x
ess-resynch</kbd>
<a name="index-ess_002dresynch"></a>
forces the <em>entire</em> cache to be refreshed, which should fix the
problem.
</p>
<hr>
<a name="Function-arguments"></a>
<div class="header">
<p>
Next: <a href="#Minibuffer-completion" accesskey="n" rel="next">Minibuffer completion</a>, Previous: <a href="#Object-names" accesskey="p" rel="prev">Object names</a>, Up: <a href="#Completion" accesskey="u" rel="up">Completion</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Completion-of-function-arguments"></a>
<h3 class="section">9.2 Completion of function arguments</h3>
<p>When inside a function call (i.e. following ‘<code>(</code>’), <kbd>TAB</kbd>
completion also provides function arguments. If function is a generic,
completion will provide all the arguments of <code>S3</code> methods known to
<code>R</code>.
</p>
<p>A related functionality is See <a href="#ESS-ElDoc">ESS ElDoc</a>, which displays function
arguments in the echo area whenever the point is inside a function call.
</p>
<hr>
<a name="Minibuffer-completion"></a>
<div class="header">
<p>
Next: <a href="#Auto_002dcomplete" accesskey="n" rel="next">Auto-complete</a>, Previous: <a href="#Function-arguments" accesskey="p" rel="prev">Function arguments</a>, Up: <a href="#Completion" accesskey="u" rel="up">Completion</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Minibuffer-completion-1"></a>
<h3 class="section">9.3 Minibuffer completion</h3>
<a name="index-IDO-completions"></a>
<a name="index-ess_002duse_002dido_002c-ess_002dcompleting_002dread"></a>
<p>From version 12.03, ESS uses <code>IDO</code> mechanism (part of default
emacs) for minibuffer completion if <code>ido.el</code> package is available
and the value of <code>ess-use-ido</code> it <code>t</code> (the default). The
completion command <code>ess-completing-read</code> falls back on classic
<code>completion-read</code> interface if this feature is not available for
whatever reason.
</p>
<hr>
<a name="Auto_002dcomplete"></a>
<div class="header">
<p>
Next: <a href="#Icicles" accesskey="n" rel="next">Icicles</a>, Previous: <a href="#Minibuffer-completion" accesskey="p" rel="prev">Minibuffer completion</a>, Up: <a href="#Completion" accesskey="u" rel="up">Completion</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Integration-with-auto_002dcomplete-package"></a>
<h3 class="section">9.4 Integration with auto-complete package</h3>
<a name="index-auto_002dcomplete"></a>
<a name="index-ac_002dsource_002dR"></a>
<a name="index-ac_002dsource_002dR_002dargs"></a>
<a name="index-ac_002dsource_002dR_002dobjects"></a>
<p>ESS provides three sources for <code>Auto Completion</code> mode:
<code>ac-source-R-args</code>, <code>ac-source-R-objects</code> and
<code>ac-source-R</code>. The last one combines the previous two and makes them
play nicely together. See auto-complete package documentation
(<a href="http://cx4a.org/software/auto-complete/">http://cx4a.org/software/auto-complete/</a>) for how to modify and
install your own completion sources.
</p>
<p>For the default auto-complete ESS configuration, install the latest
version of <code>auto-complete</code> package. ESS automatically detect the
package and activates auto-complete in ESS buffers.
</p>
<p>To deactivate AC, place the following into your init file:
</p>
<div class="example">
<pre class="example">(setq ess-use-auto-complete nil)
</pre></div>
<p>Or, to activate auto-completion only in the <code>ess-mode</code> buffers:
</p>
<div class="example">
<pre class="example">(setq ess-use-auto-complete 'script-only)
</pre></div>
<p>ESS provides AC help both for arguments and objects (default keys
<kbd>C-?</kbd> or <kbd><f1></kbd>). You can bind <kbd>M-h</kbd> to display quick help
pop-ups:
</p>
<div class="example">
<pre class="example">(define-key ac-completing-map (kbd "M-h") 'ac-quick-help)
</pre></div>
<p><code>AC</code> binds <kbd>M-n</kbd>, and <kbd>M-p</kbd> for the navigation in the
completion menu, which might be inconvenient if you want it to use in
the inferior R. Bind it to something else:
</p>
<div class="example">
<pre class="example">(define-key ac-completing-map "\M-n" nil) ;; was ac-next
(define-key ac-completing-map "\M-p" nil) ;; was ac-previous
(define-key ac-completing-map "\M-," 'ac-next)
(define-key ac-completing-map "\M-k" 'ac-previous)
</pre></div>
<hr>
<a name="Icicles"></a>
<div class="header">
<p>
Previous: <a href="#Auto_002dcomplete" accesskey="p" rel="prev">Auto-complete</a>, Up: <a href="#Completion" accesskey="u" rel="up">Completion</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Icicles-1"></a>
<h3 class="section">9.5 Icicles</h3>
<a name="index-icicles"></a>
<p>Another option for comprehensively handling completion in Emacs is via
Icicles (<a href="http://www.emacswiki.org/emacs/Icicles">http://www.emacswiki.org/emacs/Icicles</a>). It allows
users to have completions shown temporarily in the standard
‘<samp>*Completions*</samp>’ buffer, and interactively select completion
candidates using several methods. As of version 2013.04.04, Icicles
provides support for completion in ESS. Please consult Icicles
documentation, which is easily accessible via <kbd>customize-group
Icicles</kbd>, for more details on installation and customization options.
</p>
<p>Once installed, Icicles can be activated by evaluating (maybe place in
<samp>~/.emacs</samp>):
</p>
<div class="example">
<pre class="example">(require 'icicles)
(icy-mode 1)
</pre></div>
<p>Icicles can be toggled at any moment by typing <kbd>M-x icy</kbd>.
</p>
<p>When Icicles is on, <kbd>TAB</kbd> offers completion, provided the conditions
determined by <code>ess-first-tab-never-complete</code> allow it. Typing
<kbd>M-TAB</kbd> will attempt completion regardless. Typing <kbd>M-?</kbd> in
<code>ESS</code> or <code>iESS</code> modes brings up the relevant completion
candidates from which to choose. Minibuffer input filters the available
candidates. Use <kbd>TAB</kbd> for prefix completion or <kbd>S-TAB</kbd> for
substring or regexp completion. Use <kbd>S-SPC</kbd> to match an additional
pattern (repeatable). You can cycle among the matching candidates,
choosing with <kbd>RET</kbd> or <kbd>mouse-2</kbd>.
</p>
<hr>
<a name="Developing-with-ESS"></a>
<div class="header">
<p>
Next: <a href="#Extras" accesskey="n" rel="next">Extras</a>, Previous: <a href="#Completion" accesskey="p" rel="prev">Completion</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Developing-with-ESS-1"></a>
<h2 class="chapter">10 Developing with ESS</h2>
<p>ESS provides several tools to help you with the development of your R
packages:
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#ESS-tracebug" accesskey="1">ESS tracebug</a>:</td><td> </td><td align="left" valign="top">Visual debugging, breakpoints, tracing, watch etc.
</td></tr>
<tr><td align="left" valign="top">• <a href="#Editing-documentation" accesskey="2">Editing documentation</a>:</td><td> </td><td align="left" valign="top">Tools to edit R documentation
</td></tr>
<tr><td align="left" valign="top">• <a href="#ESS-developer" accesskey="3">ESS developer</a>:</td><td> </td><td align="left" valign="top">Develop your packages on the fly
</td></tr>
</table>
<hr>
<a name="ESS-tracebug"></a>
<div class="header">
<p>
Next: <a href="#Editing-documentation" accesskey="n" rel="next">Editing documentation</a>, Up: <a href="#Developing-with-ESS" accesskey="u" rel="up">Developing with ESS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS-tracebug-1"></a>
<h3 class="section">10.1 ESS tracebug</h3>
<a name="index-ESS-tracebug"></a>
<a name="index-ess_002dtracebug"></a>
<p>ESS <code>tracebug</code> offers visual debugging, interactive error
navigation, interactive backtrace, breakpoint manipulation, control over
R error actions, watch window and interactive flagging/unflagging of
functions for debugging.
</p>
<p>From ESS13.05 <code>ess-tracebug</code> is on by default. You can toggle it on
and off with <kbd>M-x</kbd> <code>ess-tracebug</code>. To disable startup
activation of <code>ess-tracebug</code> set <code>ess-use-tracebug</code> to nil.
</p>
<p>Tracebug functionality can be found on <code>ess-dev-map</code>, bound to
<kbd>C-c C-t</kbd>. Additionally, when subprocess is in a debugging state
<code>ess-debug-minor-mode</code> is active and the following additional
shortcuts are available:
</p>
<pre class="verbatim">* Interactive Debugging (`ess-debug-minor-mode-map'):
M-C . Continue . `ess-debug-command-continue'
M-C-C . Continue multi . `ess-debug-command-continue-multi'
M-N . Next step . `ess-debug-command-next'
M-C-N . Next step multi . `ess-debug-command-next-multi'
M-U . Up frame . `ess-debug-command-up'
M-Q . Quit debugging . `ess-debug-command-quit'
</pre>
<p>These are all the tracebug commands defined in <code>ess-dev-map</code>
(<kbd>C-c C-t ?</kbd> to show this table):
</p>
<pre class="verbatim">
* Breakpoints (`ess-dev-map'):
b . Set BP (repeat to cycle BP type) . `ess-bp-set'
B . Set conditional BP . `ess-bp-set-conditional'
k . Kill BP . `ess-bp-kil'
K . Kill all BPs . `ess-bp-kill-all'
o . Toggle BP state . `ess-bp-toggle-state'
l . Set logger BP . `ess-bp-set-logger'
n . Goto next BP . `ess-bp-next'
p . Goto previous BP . `ess-bp-previous'
(C- prefixed equivalents are also defined)
* Debugging (`ess-dev-map'):
` . Show traceback . `ess-show-traceback' (also on C-c `)
~ . Show callstack . `ess-show-call-stack' (also on C-c ~)
e . Toggle error action (repeat to cycle). `ess-debug-toggle-error-action'
d . Flag for debugging . `ess-debug-flag-for-debugging'
u . Unflag for debugging . `ess-debug-unflag-for-debugging'
w . Watch window . `ess-watch'
(C- prefixed equivalents are also defined)
* Navigation to errors (general emacs functionality):
C-x `, M-g n . `next-error'
M-g p . `previous-error'
* Misc:
? . Show this help . `ess-tracebug-show-help'
</pre>
<p>To configure how electric watch window splits the display see
<code>ess-watch-width-threshold</code> and <code>ess-watch-height-threshold</code>
variables.
</p>
<p>A more detailed ess-tracebug documentation with screenshots is available
at <a href="http://code.google.com/p/ess-tracebug/">http://code.google.com/p/ess-tracebug/</a>.
</p>
<p>A short tutorial is at <a href="http://code.google.com/p/ess-tracebug/wiki/GettingStarted">http://code.google.com/p/ess-tracebug/wiki/GettingStarted</a>.
</p>
<p><em>Note:</em> Currently, ess-tracebug does not detect some of R’s debug
related messages in non-English locales. To set your R messages to
English add the following line to your .Rprofile init file:
</p>
<pre class="verbatim"> Sys.setlocale("LC_MESSAGES", "C")
</pre>
<hr>
<a name="Editing-documentation"></a>
<div class="header">
<p>
Next: <a href="#ESS-developer" accesskey="n" rel="next">ESS developer</a>, Previous: <a href="#ESS-tracebug" accesskey="p" rel="prev">ESS tracebug</a>, Up: <a href="#Developing-with-ESS" accesskey="u" rel="up">Developing with ESS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Editing-documentation-1"></a>
<h3 class="section">10.2 Editing documentation</h3>
<p>ESS provides two ways of writing documentation for R objects. Either
using the standard R documentation system or using in-source
documentation written as structured comment fields for use with the
Roxygen package.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#R-documentation-files" accesskey="1">R documentation files</a>:</td><td> </td><td align="left" valign="top">Edit objects in a specialized buffer
</td></tr>
<tr><td align="left" valign="top">• <a href="#Roxygen" accesskey="2">Roxygen</a>:</td><td> </td><td align="left" valign="top">Loading source files into the ESS process
</td></tr>
</table>
<hr>
<a name="R-documentation-files"></a>
<div class="header">
<p>
Next: <a href="#Roxygen" accesskey="n" rel="next">Roxygen</a>, Up: <a href="#Editing-documentation" accesskey="u" rel="up">Editing documentation</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Editing-R-documentation-_0028Rd_0029-files"></a>
<h4 class="subsection">10.2.1 Editing R documentation (Rd) files</h4>
<p>R objects are documented in files written in the <em>R
documentation</em> (“Rd”), a simple markup language closely resembling
(La)TeX, which can be processed into a variety of formats, including
LaTeX, <acronym>HTML</acronym>, and plain text. Rd format is described in
section “Rd format” of the “Writing R Extensions” manual in the R
distribution. ESS has several features that facilitate editing Rd files.
</p>
<p>Visiting an Rd file as characterized by its extension <samp>Rd</samp> will
activate Rd Mode, which provides several facilities for making editing R
documentation files more convenient, by helping with indentation,
insertions, even doing some of the typing for you (with Abbrev Mode),
and by showing Rd keywords, strings, etc. in different faces (with
Font Lock Mode).
</p>
<p>Note that R also accepts Rd files with extension <samp>rd</samp>; to activate
<acronym>ESS[Rd]</acronym> support for this extension, you may need to add
</p>
<div class="example">
<pre class="example">(add-to-list 'auto-mode-alist '("\\.rd\\'" . Rd-mode))
</pre></div>
<p>to one of your Emacs startup files.
</p>
<p>In Rd mode, the following special Emacs commands can be used in addition
to the standard Emacs commands.
</p>
<dl compact="compact">
<dt><kbd>C-h m</kbd></dt>
<dd><p>Describe the features of Rd mode.
</p>
</dd>
<dt><kbd>LFD</kbd></dt>
<dt><kbd>RET</kbd></dt>
<dd><p>Reindent the current line, insert a newline and indent the new line
(<code>reindent-then-newline-and-indent</code>). An abbrev before point is
expanded if <code>abbrev-mode</code> is non-<code>nil</code>.
</p>
</dd>
<dt><kbd>TAB</kbd></dt>
<dd><p>Indent current line based on its contents and on previous lines.
(<code>indent-according-to-mode</code>).
</p>
</dd>
<dt><kbd>C-c C-e</kbd></dt>
<dd><p>Insert a “skeleton” with Rd markup for at least all mandatory entries
in Rd files (<code>Rd-mode-insert-skeleton</code>). Note that many users
might prefer to use the R function <code>prompt</code> on an existing R object
to generate a non-empty Rd “shell” documenting the object (which
already has all information filled in which can be obtained from the
object).
</p>
</dd>
<dt><kbd>C-c C-f</kbd></dt>
<dd><p>Insert “font” specifiers for some of the Rd markup commands markup
available for emphasizing or quoting text, including markup for URLs and
email addresses (<code>Rd-font</code>). <kbd>C-c C-f</kbd> is only a prefix; see
e.g. <kbd>C-c C-f TAB</kbd> for the available bindings. Note that
currently, not all of the Rd text markup as described in section
“Marking text” of “Writing R Extensions” can be accessed via
<kbd>C-c C-f</kbd>.
</p>
</dd>
<dt><kbd>C-c C-j</kbd></dt>
<dd><p>Insert a suitably indented ‘<samp>\item{</samp>’ on the next line
(<code>Rd-mode-insert-item</code>).
</p>
</dd>
<dt><kbd>C-c C-p</kbd></dt>
<dd><p>Preview a plain text version (“help file”, see <a href="#Help">Help</a>) generated
from the Rd file (<code>Rd-preview-help</code>).
</p></dd>
</dl>
<p>In addition, when editing Rd files one can interact with a running R
process in a similar way as when editing R language files. E.g.,
<kbd>C-c C-v</kbd> provides access to on-line help, and <kbd>C-c C-n</kbd> sends
the current line to the R process for evaluation. This interaction is
particularly useful when editing the examples in the Rd file. See
<kbd>C-h m</kbd> for all available commands.
</p>
<p>Rd mode also provides access to abbreviations for most of the Rd markup
commands. Type <kbd>M-x list-abbrevs</kbd> with Abbrev mode turned on to
list all available abbrevs. Note that all Rd abbrevs start with a grave
accent.
</p>
<p>Rd mode can be customized via the following variables.
</p>
<dl>
<dt><a name="index-Rd_002dmode_002dhook"></a>User Option: <strong>Rd-mode-hook</strong></dt>
<dd><p>Hook to be run when Rd mode is entered.
</p></dd></dl>
<dl>
<dt><a name="index-Rd_002dindent_002dlevel"></a>User Option: <strong>Rd-indent-level</strong></dt>
<dd><p>The indentation of Rd code with respect to containing blocks. Default
is 2.
</p></dd></dl>
<dl>
<dt><a name="index-Rd_002dto_002dhelp_002dcommand"></a>User Option: <strong>Rd-to-help-command</strong></dt>
<dd><p>The shell command used for converting Rd source to help text. Default
is ‘<samp>R CMD Rd2txt</samp>’.
</p></dd></dl>
<p>To automatically turn on the abbrev and font-lock features of Rd mode,
add the following lines to one of your Emacs startup files:
</p>
<div class="example">
<pre class="example">(add-hook 'Rd-mode-hook
(lambda ()
(abbrev-mode 1)
(font-lock-mode 1)))
</pre></div>
<hr>
<a name="Roxygen"></a>
<div class="header">
<p>
Previous: <a href="#R-documentation-files" accesskey="p" rel="prev">R documentation files</a>, Up: <a href="#Editing-documentation" accesskey="u" rel="up">Editing documentation</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Editing-Roxygen-documentation"></a>
<h4 class="subsection">10.2.2 Editing Roxygen documentation</h4>
<a name="index-Roxygen"></a>
<a name="index-roxy"></a>
<a name="index-ess_002droxy"></a>
<p>The Roxygen R package makes it possible to keep the intended contents
for Rd files as structured comments in the R source files. Roxygen can
then parse R files and generate appropriate Rd files from these
comments, fill the usage fields as well as updating <samp>NAMESPACE</samp>
files. See the Roxygen documentation found via <a href="http://roxygen.org">http://roxygen.org</a>
for more information on its usage. An example of an Roxygen entry for a
simple R function can look like this:
</p>
<div class="example">
<pre class="verbatim">##' Description of the function
##'
##' Further details about this function
##' @title A title
##' @param me all parameters must be listed and documented
##' @return Description of the return value
##' @author The author
myfun <- function(me)
cat("Hello", me, "\n")
</pre></div>
<p>The entry is immediately preceding the object to document and all lines
start with the Roxygen prefix string, in this case <code>##'</code>. ESS
provides support to edit these documentation entries by providing line
filling, navigation, template generation etc. Syntax highlighting is
provided for Emacs but not for XEmacs.
</p>
<p>Roxygen is customized by the variables in the customization group “Ess
Roxy”. Customizables include the Roxygen prefix, use of folding
to toggle visibility of Roxygen entries and the Roxygen template.
</p>
<p>All ESS Roxygen support is defined in <samp>ess-roxy.el</samp> which is loaded
by default in ESS. The following special Emacs commands are provided.
</p>
<dl>
<dt><a name="index-ess_002droxy_002dupdate_002dentry"></a>Command: <strong>ess-roxy-update-entry</strong></dt>
<dd><a name="index-C_002dc-C_002do-C_002do"></a>
<p><kbd>C-c C-o C-o</kbd> Generate a Roxygen template or update the parameter
list in Roxygen entry at point (or above the function at the
point). Documented parameters that are not in the function are placed
last in the list, parameters that are not documented and not in the
definition are dropped. Parameter descriptions are filled if
<code>ess-roxy-fill-param-p</code> is non-nil.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002droxy_002dtoggle_002droxy_002dregion"></a>Command: <strong>ess-roxy-toggle-roxy-region</strong> <em><var>beg</var> <var>end</var></em></dt>
<dd><a name="index-C_002dc-C_002do-C_002dc"></a>
<p><kbd>C-c C-o C-c</kbd> Toggle the presence of the leading Roxygen string on
all lines in the marked region (between <var>beg</var> and
<var>end</var>. Convenient for transferring text to Roxygen entries and to
evaluate example fields.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002droxy_002dpreview_002dRd"></a>Command: <strong>ess-roxy-preview-Rd</strong> <em><var>name-file</var></em></dt>
<dd><a name="index-C_002dc-C_002do-C_002dr"></a>
<p><kbd>C-c C-o C-r</kbd> Use the attached R process to parse the entry at point
to obtain the Rd code. Convenient for previewing and checking
syntax. When used with the prefix argument <var>name-file</var>,
i.e. <kbd>C-u C-c C-e C-r</kbd>, place the content in a buffer associated
with a Rd file with the same name as the documentation. Requires the
Roxygen package to be installed.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002droxy_002dpreview_002dHTML"></a>Command: <strong>ess-roxy-preview-HTML</strong> <em><var>visit-instead-of-open</var></em></dt>
<dd><a name="index-C_002dc-C_002do-C_002dt"></a>
<p><kbd>C-c C-o C-t</kbd> Use the attached R process to parse the entry at to
generate HTML for the entry and open it in a browser. When used with the
prefix argument <var>visit-instead-of-open</var>, i.e. <kbd>C-u C-c C-e C-t</kbd>,
visit the generated HTML file instead. Requires the Roxygen and tools
packages to be installed.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002droxy_002dprevious_002dentry"></a>Command: <strong>ess-roxy-previous-entry</strong></dt>
<dd><a name="index-C_002dc-C_002do-p"></a>
<p><kbd>C-c C-o p</kbd> Go to start of the Roxygen entry above point.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002droxy_002dnext_002dentry"></a>Command: <strong>ess-roxy-next-entry</strong></dt>
<dd><a name="index-C_002dc-C_002do-n"></a>
<p><kbd>C-c C-o n</kbd> Go to end of the Roxygen entry above point.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002droxy_002dhide_002dall"></a>Command: <strong>ess-roxy-hide-all</strong></dt>
<dd><a name="index-C_002dc-C_002do-C_002dh"></a>
<p><kbd>C-c C-o C-h</kbd> Use the hideshow mode to fold away the visibility of
all Roxygen entries. Hide-show support must be enabled for this binding
to get defined.
</p></dd></dl>
<p>ESS also advises the following standard editing functions in order to
make Roxygen editing more intuitive:
</p>
<dl compact="compact">
<dt><kbd>TAB</kbd></dt>
<dd><a name="index-ess_002dR_002dcomplete_002dobject_002dname"></a>
<p><code>ess-R-complete-object-name</code> Complete Roxygen tag at
point. E.g. doing <kbd>TAB</kbd> when the point is at the end of <code>@par</code>
completes to <code>@param</code>.
</p>
</dd>
<dt><kbd>M-h</kbd></dt>
<dd><a name="index-mark_002dparagraph"></a>
<p><code>mark-paragraph</code> If the transient mark mode is active, place mark
and point at start end end of the field at point and activate the mark.
</p>
</dd>
<dt><kbd>TAB</kbd></dt>
<dd><a name="index-ess_002dindent_002dcommand"></a>
<p><code>ess-indent-command</code> If hide-show support is enabled, fold away the
visibility of the Roxygen entry at point.
</p>
</dd>
<dt><kbd>M-q</kbd></dt>
<dd><a name="index-fill_002dparagraph"></a>
<p><code>fill-paragraph</code> Fill the Roxygen field at point.
</p>
</dd>
<dt><kbd>C-a</kbd></dt>
<dd><a name="index-move_002dbeginning_002dof_002dline"></a>
<p><code>move-beginning-of-line</code> Move to the point directly to the right of
the Roxygen start string.
</p>
</dd>
<dt><kbd>RET</kbd></dt>
<dd><a name="index-newline_002dand_002dindent"></a>
<p><code>newline-and-indent</code> Insert a new line and the Roxygen prefix
string.
</p></dd>
</dl>
<hr>
<a name="ESS-developer"></a>
<div class="header">
<p>
Previous: <a href="#Editing-documentation" accesskey="p" rel="prev">Editing documentation</a>, Up: <a href="#Developing-with-ESS" accesskey="u" rel="up">Developing with ESS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS-developer-1"></a>
<h3 class="section">10.3 ESS developer</h3>
<a name="index-ess-developer"></a>
<p>Usual ESS evaluation commands, See <a href="#Evaluating-code">Evaluating code</a>, send portions of
the current buffer for the evaluation in the current environment
(usually <code>R_GlobalEnv</code>). Often, when developing packages with
namespaces, it is necessary to evaluate code directly in the package’s
environment or its namespace. The <code>ess-developer</code> utility provides
such a functionality with minimal disruption of the usual ESS work-flow.
</p>
<p>To understand how ess-developer works you must be familiar with
namespace system in R. In a nutshell, all objects defined in a package
’foo’ are stored in an environment called ’namespace:foo’. Parent
environment of ’namespace:foo’ is an environment ’imports:foo’ which
contains copies of all objects from other packages which ’foo’
imports. Parent environment of ’imports:foo’ is the
’namespace:base’. Parent environment of ’namespace:base’ is
.GlobalEnv. Thus functions and methods stored in ’namespace:foo’ see all
the objects in .GlobalEnv unless shadowed by objects in ’imports:foo’,
’namespace:base’, or ’namespace:foo’ itself. There is another
environment associated with ’foo’ - ’package:foo’. This environment
stores *copies* of exported objects from ’namespace:foo’ and is placed
on the search() path, i.e. if ’foo’ is loaded and if you start with
.GlobalEnv and iteratively call parent.env() you will get eventually to
’package:foo’. Thus all methods and functions defined in .GlobalEnv can
"see" objects in ’package:foo’ environment. See also
<a href="http://cran.r-project.org/doc/manuals/R-ints.html#Namespaces">http://cran.r-project.org/doc/manuals/R-ints.html#Namespaces</a>.
</p>
<p>In order to use ess-developer you must add names of the packages that
you are developing to <code>ess-developer-packages</code>. You can also do
that interactively with <kbd>C-c C-t C-a</kbd>. To remove packages from
<code>ess-developer-packages</code> use <kbd>C-c C-t C-r</kbd>. When developer mode
is on, the process mode line indicator displays a small or capital
letter "d".
</p>
<p>If variable <code>ess-developer-activate-in-package</code> is <code>t</code> (the
default) <code>R-mode</code> will check after visiting the file whether or not
the file is part of the package. If visited file is part of a package
listed in <code>ess-developer-packages</code>, developer mode is activated
automatically.
</p>
<p>Developer mode is usually activated on per-file basis and a small "d"
appears in the modeline. You can also activate ess-developer for all
buffers connected to current process. This is done by toggling
<code>ess-developer</code> in subprocess buffer. In this case a big "D" will
appear in the modeline.
</p>
<dl>
<dt><a name="index-ess_002ddeveloper"></a>Command: <strong>ess-developer</strong> <em><var>val</var></em></dt>
<dd><a name="index-C_002dc-C_002dt-C_002dt"></a>
<p><kbd>C-c C-t C-t</kbd> Toggle developer mode on and off. If called from
script buffer, toggle developer on file-by-file basis. When called from
process buffer, toggle developer on per-process basis.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002ddeveloper_002dadd_002dpackage"></a>Command: <strong>ess-developer-add-package</strong> <em><var>from-attached</var> <var>remove</var></em></dt>
<dd><a name="index-C_002dc-C_002dt-C_002da"></a>
<p><kbd>C-c C-t C-a</kbd> Add a package to your development list (<code>ess-developer-packages</code>).
</p></dd></dl>
<dl>
<dt><a name="index-ess_002ddeveloper_002dremove_002dpackage"></a>Command: <strong>ess-developer-remove-package</strong></dt>
<dd><a name="index-C_002dc-C_002dt-C_002dr"></a>
<p><kbd>C-c C-t C-r</kbd> Remove a package from your development list.
</p></dd></dl>
<p>When you add a package to <code>ess-developer-packages</code>, ESS will ask
for loading command. By default there are two options <code>library</code> and
<code>load_all</code> from <code>devtools</code> package. You can configure this
behavior in <code>ess-developer-load-on-add-commands</code>. To explicitly
load the package containing current file use <kbd>C-c C-t l</kbd>.
</p>
<dl>
<dt><a name="index-ess_002ddeveloper_002dload_002dpackage"></a>Command: <strong>ess-developer-load-package</strong></dt>
<dd><a name="index-C_002dc-C_002dt-l"></a>
<p><kbd>C-c C-t l</kbd> Load package with <code>load_all</code> utility from
<code>devtools</code> package.
</p></dd></dl>
<p>When developer mode is on, ESS evaluation commands behave differently:
</p>
<ul>
<li> <kbd>C-c C-l</kbd> (<code>ess-load-file</code>) asks for the package to source
into and inserts all redefined objects into the package:foo or
namespace:foo accordingly.
<ul class="no-bullet">
<li>- PLAIN OBJECTS and FUNCTIONS: <br>
If the object is found in an environment (package:foo or
namespace:foo), and differs from the old one it is assigned into the
corresponding environment. If the object is not found it is assigned
into .GlobalEnv. The environment of functions is set to namespace:foo.
</li><li>- CLASSES: <br>
Same as plain objects, with the difference that even if the class
definition is assigned into .GlobalEnv, it is still associated with the
package foo. Thus if you issue getClassDeff("foo") you will get a class
definition with the slot @package pointing to package "foo".
<p><em>Note:</em> Occasionally, after adding new classes you might get warnings
from "setClass". This is especially true if new class inherits or is
inherited by a class whose definition is not exported. You might get
something like:
<code>
Warning: Class "boo" is defined (with package slot ‘foo’) but no
metadata object found to revise subclass information---not exported?
</code>
</p>
<p>You can safely ignore this warnings.
</p>
</li><li>- S4 METHODS: <br>
Similarly to function definitions modified methods are assigned in the
local method table in the namespace:foo. New methods are assigned into
.GlobalEnv, but with the environment pointing to namespace:foo. There is
a subtle catch with method caching in R though. See the code in
etc/ESSR/developer.R for more details.
</li><li>- S3 METHODS: <br>
S3 methods are not automatically registered. You can register them
manually after you have inserted method_name.my_class into your package
environment using ess-developer, like follows:
<p>registerS3method("method_name", "my_class", my_package:::method_name.my_class)
</p>
<p>If you don’t register your S3 method, R will call the registered (aka
cached) S3 method instead of the new method that ess-developer inserted
in the package environment.
</p>
</li></ul>
</li><li> <kbd>C-c C-r</kbd>(<code>ess-eval-region</code>) and functions that depend on
it (<code>ess-eval-paragraph</code>, <code>ess-eval-buffer</code> etc.), behave as
<code>ess-load-file</code>, but restrict the evaluation to the corresponding region.
</li><li> <kbd>C-c C-f</kbd> (<code>ess-eval-function</code>) and friends check if the
current function’s name can be found in a namespace:foo or package:foo
for a ’foo’ from ‘ess-developer-packages’. If found, and new function
definition differs from the old one, the function is assigned into that
namespace. If not found, it is assigned into .GlobalEnv.
</li></ul>
<hr>
<a name="Extras"></a>
<div class="header">
<p>
Next: <a href="#ESS-for-S" accesskey="n" rel="next">ESS for S</a>, Previous: <a href="#Developing-with-ESS" accesskey="p" rel="prev">Developing with ESS</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Other-ESS-features-and-tools"></a>
<h2 class="chapter">11 Other ESS features and tools</h2>
<p>ESS has a few extra features, which didn’t fit anywhere else.
</p><table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#ESS-ElDoc" accesskey="1">ESS ElDoc</a>:</td><td> </td><td align="left" valign="top">Display function arguments in minibuffer
</td></tr>
<tr><td align="left" valign="top">• <a href="#Handy-commands" accesskey="2">Handy commands</a>:</td><td> </td><td align="left" valign="top">Usefully commands at your fingertips
</td></tr>
<tr><td align="left" valign="top">• <a href="#Highlighting" accesskey="3">Highlighting</a>:</td><td> </td><td align="left" valign="top">Syntactic highlighting of buffers
</td></tr>
<tr><td align="left" valign="top">• <a href="#Parens" accesskey="4">Parens</a>:</td><td> </td><td align="left" valign="top">Parenthesis matching
</td></tr>
<tr><td align="left" valign="top">• <a href="#Graphics" accesskey="5">Graphics</a>:</td><td> </td><td align="left" valign="top">Using graphics with ESS
</td></tr>
<tr><td align="left" valign="top">• <a href="#Imenu" accesskey="6">Imenu</a>:</td><td> </td><td align="left" valign="top">Support for Imenu in ESS
</td></tr>
<tr><td align="left" valign="top">• <a href="#Toolbar" accesskey="7">Toolbar</a>:</td><td> </td><td align="left" valign="top">Support for toolbar in ESS
</td></tr>
<tr><td align="left" valign="top">• <a href="#TAGS" accesskey="8">TAGS</a>:</td><td> </td><td align="left" valign="top">Using TAGS for S files
</td></tr>
<tr><td align="left" valign="top">• <a href="#Rdired" accesskey="9">Rdired</a>:</td><td> </td><td align="left" valign="top">Directory editor for R objects
</td></tr>
<tr><td align="left" valign="top">• <a href="#Rutils">Rutils</a>:</td><td> </td><td align="left" valign="top">R object/package management and help utilities
</td></tr>
<tr><td align="left" valign="top">• <a href="#Org">Org</a>:</td><td> </td><td align="left" valign="top">Interaction with Org mode
</td></tr>
<tr><td align="left" valign="top">• <a href="#Sweave-and-AUCTeX">Sweave and AUCTeX</a>:</td><td> </td><td align="left" valign="top">Support for Sweave in ESS and AUCTeX
</td></tr>
</table>
<hr>
<a name="ESS-ElDoc"></a>
<div class="header">
<p>
Next: <a href="#Handy-commands" accesskey="n" rel="next">Handy commands</a>, Up: <a href="#Extras" accesskey="u" rel="up">Extras</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ElDoc"></a>
<h3 class="section">11.1 ElDoc</h3>
<a name="index-ElDoc"></a>
<p>In <code>ElDoc</code> mode, the echo area displays function’s arguments at
point. From <acronym>ESS</acronym> version 12.03, ElDoc is active by default in
<code>ess-mode</code> and <code>inferior-ess-mode</code> buffers. To activate it
only in <code>ess-mode</code> buffers, place the following into your init
file:
</p>
<div class="example">
<pre class="example">(setq ess-use-eldoc 'script-only)
</pre></div>
<dl>
<dt><a name="index-ess_002duse_002deldoc"></a>User Option: <strong>ess-use-eldoc</strong></dt>
<dd><p>If ‘<samp>t</samp>’, activate eldoc in ess-mode and inferior-ess-mode buffers.
If ‘<samp>'script-only</samp>’ activate in ess-mode buffers only. Set
<code>ess-use-eldoc</code> to <code>nil</code> to stop using <code>ElDoc</code>
altogether.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002deldoc_002dshow_002don_002dsymbol"></a>User Option: <strong>ess-eldoc-show-on-symbol</strong></dt>
<dd><p>This variable controls whether the help is shown only inside function
calls. If set to ‘<samp>t</samp>’, <code>ElDoc</code> shows help string whenever the
point is on a symbol, otherwise (the default), shows only when the point
is in a function call, i.e. after ‘<samp>'('</samp>’.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002deldoc_002dabbreviation_002dstyle"></a>User Option: <strong>ess-eldoc-abbreviation-style</strong></dt>
<dd><p>The variable determines how the doc string should be abbreviated to fit
into minibuffer. Posible values are ‘<samp>nil</samp>’, ‘<samp>mild</samp>’,
‘<samp>normal</samp>’, ‘<samp>strong</samp>’ and ‘<samp>aggressive</samp>’. Please see the
documentation of the variable for more details. The default filter is
‘<samp>normal</samp>’.
</p></dd></dl>
<p>Ess-eldoc also honors the value of
<code>eldoc-echo-area-use-multiline-p</code>, which if set to ‘<samp>nil</samp>’, will
cause the truncation of doc string indifferent of the value of
<code>ess-eldoc-abbreviation-style</code>. This way you can combine different
filter levels with the truncation.
</p>
<hr>
<a name="Handy-commands"></a>
<div class="header">
<p>
Next: <a href="#Highlighting" accesskey="n" rel="next">Highlighting</a>, Previous: <a href="#ESS-ElDoc" accesskey="p" rel="prev">ESS ElDoc</a>, Up: <a href="#Extras" accesskey="u" rel="up">Extras</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Handy-commands-1"></a>
<h3 class="section">11.2 Handy commands</h3>
<a name="index-Handy-commands"></a>
<a name="index-ess_002dhandy_002dcommands"></a>
<a name="index-ess_002dhandy_002dcommands-2"></a>
<a name="index-ess_002dsmart_002dcomma"></a>
<a name="index-_002c"></a>
<dl>
<dt><a name="index-ess_002dhandy_002dcommands-1"></a>Command: <strong>ess-handy-commands</strong></dt>
<dd><p>Request and execute a command from <code>ess-handy-commands</code> list.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002dhandy_002dcommands-3"></a>User Option: <strong>ess-handy-commands</strong></dt>
<dd><p>An alist of custom ESS commands available for call by
<code>ess-handy-commands</code> and <code>ess-smart-comma</code> function.
</p>
<p>Currently contains:
</p>
<dl compact="compact">
<dt>change-directory</dt>
<dd><p><code>ess-change-directory</code>
</p></dd>
<dt>help-index</dt>
<dd><p><code>ess-display-index</code>
</p></dd>
<dt>help-object</dt>
<dd><p><code>ess-display-help-on-object</code>
</p></dd>
<dt>vignettes</dt>
<dd><p><code>ess-display-vignettes</code>
</p></dd>
<dt>objects[ls]</dt>
<dd><p><code>ess-execute-objects</code>
</p></dd>
<dt>search</dt>
<dd><p><code>ess-execute-search</code>
</p></dd>
<dt>set-width</dt>
<dd><p><code>ess-execute-screen-options</code>
</p></dd>
<dt>install.packages</dt>
<dd><p><code>ess-install.packages</code>
</p></dd>
<dt>library</dt>
<dd><p><code>ess-library</code>
</p></dd>
<dt>setRepos</dt>
<dd><p><code>ess-setRepositories</code>
</p></dd>
<dt>sos</dt>
<dd><p><code>ess-sos</code>
</p></dd>
</dl>
</dd></dl>
<p>Handy commands: <code>ess-library</code>, <code>ess-install.packages</code>, etc -
ask for item with completion and execute the correspond
command. <code>ess-sos</code> is a interface to <code>findFn</code> function in
package <code>sos</code>. If package <code>sos</code> is not found, ask user for
interactive install.
</p>
<hr>
<a name="Highlighting"></a>
<div class="header">
<p>
Next: <a href="#Parens" accesskey="n" rel="next">Parens</a>, Previous: <a href="#Handy-commands" accesskey="p" rel="prev">Handy commands</a>, Up: <a href="#Extras" accesskey="u" rel="up">Extras</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Syntactic-highlighting-of-buffers"></a>
<h3 class="section">11.3 Syntactic highlighting of buffers</h3>
<p>ESS provides Font-Lock (see <a href="http://www.gnu.org/software/emacs/manual/html_mono/emacs.html#Faces">Using Multiple Typefaces</a> in <cite>The Gnu Emacs Reference Manual</cite>) patterns for Inferior S Mode, S
Mode, and S Transcript Mode buffers.
<a name="index-font_002dlock-mode"></a>
<a name="index-highlighting"></a>
</p>
<p>Syntax highlighting within ESS buffers is controlled by:
</p>
<dl>
<dt><a name="index-ess_002dfont_002dlock_002dmode"></a>User Option: <strong>ess-font-lock-mode</strong></dt>
<dd><p>Non-‘<samp>nil</samp>’ means we use font lock support for ESS buffers. Default
is ‘<samp>t</samp>’, to use font lock support. If you change the value of this
variable, restart Emacs for it to take effect.
</p></dd></dl>
<p>The font-lock patterns are defined by the following variables, which you
may modify if desired:
</p>
<dl>
<dt><a name="index-inferior_002dR_002dfont_002dlock_002dkeywords"></a>User Option: <strong>inferior-R-font-lock-keywords</strong></dt>
<dd><p>Font-lock patterns for inferior *R* processes. (There is a
corresponding <code>inferior-S-font-lock-keywords</code> for *S* processes.)
The default value highlights prompts, inputs, assignments, output
messages, vector and matrix labels, and literals such as ‘<samp>NA</samp>’ and
<code>TRUE</code>.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002dR_002dfont_002dlock_002dkeywords"></a>User Option: <strong>ess-R-font-lock-keywords</strong></dt>
<dd><p>Font-lock patterns for ESS R programming mode. (There is a
corresponding <code>ess-S-font-lock-keywords</code> for S buffers.) The
default value highlights function names, literals, assignments, source
functions and reserved words.
</p></dd></dl>
<hr>
<a name="Parens"></a>
<div class="header">
<p>
Next: <a href="#Graphics" accesskey="n" rel="next">Graphics</a>, Previous: <a href="#Highlighting" accesskey="p" rel="prev">Highlighting</a>, Up: <a href="#Extras" accesskey="u" rel="up">Extras</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Parenthesis-matching"></a>
<h3 class="section">11.4 Parenthesis matching</h3>
<p>Emacs and XEmacs have facilities for highlighting the parenthesis
matching the parenthesis at point. This feature is very useful when
trying to examine which parentheses match each other. This highlighting
also indicates when parentheses are not matching. Depending on what
version of emacs you use, one of the following should work in your
initialisation file:
</p>
<div class="example">
<pre class="example">(paren-set-mode 'paren) ;for XEmacs
(show-paren-mode t) ;for Emacs
</pre></div>
<hr>
<a name="Graphics"></a>
<div class="header">
<p>
Next: <a href="#Imenu" accesskey="n" rel="next">Imenu</a>, Previous: <a href="#Parens" accesskey="p" rel="prev">Parens</a>, Up: <a href="#Extras" accesskey="u" rel="up">Extras</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Using-graphics-with-ESS"></a>
<h3 class="section">11.5 Using graphics with ESS</h3>
<a name="index-graphics"></a>
<p>One of the main features of the <code>S</code> package is its ability to
generate high-resolution graphics plots, and ESS provides a number of
features for dealing with such plots.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#printer" accesskey="1">printer</a>:</td><td> </td><td align="left" valign="top">The printer() graphics driver
</td></tr>
<tr><td align="left" valign="top">• <a href="#X11" accesskey="2">X11</a>:</td><td> </td><td align="left" valign="top">The X11() (and other X Windows based) driver
</td></tr>
<tr><td align="left" valign="top">• <a href="#winjava" accesskey="3">winjava</a>:</td><td> </td><td align="left" valign="top">Java Graphics Device
</td></tr>
</table>
<hr>
<a name="printer"></a>
<div class="header">
<p>
Next: <a href="#X11" accesskey="n" rel="next">X11</a>, Up: <a href="#Graphics" accesskey="u" rel="up">Graphics</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Using-ESS-with-the-printer_0028_0029-driver"></a>
<h4 class="subsection">11.5.1 Using ESS with the <code>printer()</code> driver</h4>
<p>This is the simplest (and least desirable) method of using graphics
within ESS. S’s <code>printer()</code> device driver produces crude character
based plots which can be contained within the ESS process buffer
itself. To start using character graphics, issue the S command
</p><div class="example">
<pre class="example">printer(width=79)
</pre></div>
<a name="index-printer_0028_0029"></a>
<p>(the <code>width=79</code> argument prevents Emacs line-wrapping at column
80 on an 80-column terminal. Use a different value for a terminal with
a different number of columns.) Plotting commands do not generate
graphics immediately, but are stored until the <code>show()</code> command
is issued, which displays the current figure.
</p>
<hr>
<a name="X11"></a>
<div class="header">
<p>
Next: <a href="#winjava" accesskey="n" rel="next">winjava</a>, Previous: <a href="#printer" accesskey="p" rel="prev">printer</a>, Up: <a href="#Graphics" accesskey="u" rel="up">Graphics</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Using-ESS-with-windowing-devices"></a>
<h4 class="subsection">11.5.2 Using ESS with windowing devices</h4>
<a name="index-X-Windows"></a>
<p>Of course, the ideal way to use graphics with ESS is to use a windowing
system. Under X Windows, or X11, this requires that the DISPLAY environment
variable be appropriately set.
</p>
<hr>
<a name="winjava"></a>
<div class="header">
<p>
Previous: <a href="#X11" accesskey="p" rel="prev">X11</a>, Up: <a href="#Graphics" accesskey="u" rel="up">Graphics</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Java-Graphics-Device"></a>
<h4 class="subsection">11.5.3 Java Graphics Device</h4>
<a name="index-winjava"></a>
<p>S+6.1 and newer on Windows contains a java library that supports graphics. Send
the commands:
</p>
<div class="example">
<pre class="example">library(winjava)
java.graph()
</pre></div>
<p>to start the graphics driver. This allows you to use ESS for both
interaction and graphics within S-PLUS. (Thanks to Tim Hesterberg for
this information.)
</p>
<hr>
<a name="Imenu"></a>
<div class="header">
<p>
Next: <a href="#Toolbar" accesskey="n" rel="next">Toolbar</a>, Previous: <a href="#Graphics" accesskey="p" rel="prev">Graphics</a>, Up: <a href="#Extras" accesskey="u" rel="up">Extras</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Imenu-1"></a>
<h3 class="section">11.6 Imenu</h3>
<p>Imenu is an Emacs tool for providing mode-specific buffer indexes. In
some of the ESS editing modes (currently SAS and S), support for Imenu
is provided. For example, in S mode buffers, the menubar should display
an item called "Imenu-S". Within this menubar you will then be offered
bookmarks to particular parts of your source file (such as the starting
point of each function definition).
</p>
<p>Imenu works by searching your buffer for lines that match what ESS
thinks is the beginning of a suitable entry, e.g. the beginning of a
function definition. To examine the regular expression that ESS uses,
check the value of <code>imenu-generic-expression</code>. This value is set
by various ESS variables such as <code>ess-imenu-S-generic-expression</code>.
</p>
<hr>
<a name="Toolbar"></a>
<div class="header">
<p>
Next: <a href="#TAGS" accesskey="n" rel="next">TAGS</a>, Previous: <a href="#Imenu" accesskey="p" rel="prev">Imenu</a>, Up: <a href="#Extras" accesskey="u" rel="up">Extras</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Toolbar-1"></a>
<h3 class="section">11.7 Toolbar</h3>
<p>The R and S editing modes have support for a toolbar. This toolbar
provides icons to act as shortcuts for starting new S/R processes, or
for evaluating regions of your source buffers. The toolbar should be
present if your emacs can display images. See <a href="#Customization">Customization</a>, for ways
to change the toolbar.
</p>
<hr>
<a name="TAGS"></a>
<div class="header">
<p>
Next: <a href="#Rdired" accesskey="n" rel="next">Rdired</a>, Previous: <a href="#Toolbar" accesskey="p" rel="prev">Toolbar</a>, Up: <a href="#Extras" accesskey="u" rel="up">Extras</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="TAGS-1"></a>
<h3 class="section">11.8 TAGS</h3>
<p>The Emacs tags facility can be used to navigate around your files
containing definitions of S functions. This facility is independent of
ESS usage, but is written here since ESS users may wish to take
advantage of TAGS facility. Read more about emacs tags in an emacs
manual.
</p>
<p>Etags, the program that generates the TAGS file, does not yet know the
syntax to recognise function definitions in S files. Hence, you will
need to provide a regexp that matches your function definitions. Here
is an example call (broken over two lines; type as one line) that should
be appropriate.
</p>
<div class="example">
<pre class="example">etags --language=none
--regex='/\([^ \t]+\)[ \t]*<-[ \t]*function/\1/' *.R
</pre></div>
<p>This will find entries in your source file of the form:
</p>
<div class="example">
<pre class="example">some.name <- function
</pre></div>
<p>with the function name starting in column 0. Windows users may need to
change the single quotes to double quotes.
</p>
<p>R version 2.9.0 introduced a front-end script for finding R tags, which
calls the ‘<samp>rtags()</samp>’ function. By default, this script will
recursively search the directories for relevant tags in R/C/Rd files.
To use this script from the command line, try the following to get
started:
</p>
<div class="example">
<pre class="example">R CMD rtags --help
</pre></div>
<p>For further details, see <a href="http://developer.r-project.org/rtags.html">http://developer.r-project.org/rtags.html</a>
</p>
<hr>
<a name="Rdired"></a>
<div class="header">
<p>
Next: <a href="#Rutils" accesskey="n" rel="next">Rutils</a>, Previous: <a href="#TAGS" accesskey="p" rel="prev">TAGS</a>, Up: <a href="#Extras" accesskey="u" rel="up">Extras</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Rdired-1"></a>
<h3 class="section">11.9 Rdired</h3>
<p>Ess-rdired provides a dired-like buffer for viewing, editing and
plotting objects in your current R session. If you are used to using
the dired (directory editor) facility in Emacs, this mode gives you
similar functionality for R objects.
</p>
<p>Start an R session with <kbd>M-x R</kbd> and then store a few
variables, such as:
</p>
<div class="example">
<pre class="example">s <- sin(seq(from=0, to=8*pi, length=100))
x <- c(1, 4, 9)
y <- rnorm(20)
z <- TRUE
</pre></div>
<p>Then use <kbd>M-x ess-rdired</kbd> to create a buffer listing the
objects in your current environment and display it in a new window:
</p><div class="example">
<pre class="example"> mode length
s numeric 100
x numeric 3
y numeric 20
z logical 1
</pre></div>
<p>Type <kbd>C-h m</kbd> or <kbd>?</kbd> to get a list of the keybindings for this
mode. For example, with your point on the line of a variable, ‘p’ will
plot the object, ‘v’ will view it, and ‘d’ will mark the object for
deletion (‘x’ will actually perform the deletion).
</p>
<hr>
<a name="Rutils"></a>
<div class="header">
<p>
Next: <a href="#Org" accesskey="n" rel="next">Org</a>, Previous: <a href="#Rdired" accesskey="p" rel="prev">Rdired</a>, Up: <a href="#Extras" accesskey="u" rel="up">Extras</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Rutils-1"></a>
<h3 class="section">11.10 Rutils</h3>
<p>Ess-rutils builds up on ess-rdired, providing key bindings for
performing basic R functions in the inferior-ESS process buffer, such as
loading and managing packages, object manipulation (listing, viewing,
and deleting), and alternatives to <code>help.start()</code> and
<code>RSiteSearch()</code> that use the <code>browse-url</code> Emacs function.
The library can be loaded using <kbd>M-x load-file</kbd>, but the easiest is
to include:
</p>
<div class="lisp">
<pre class="lisp">(require 'ess-rutils)
</pre></div>
<p>in your .emacs. Once R is started with <kbd>M-x R</kbd>, and if the value of
the customizable variable <code>ess-rutils-keys</code> is true, several key
bindings become available in iESS process buffers:
</p>
<dl>
<dt><a name="index-ess_002drutils_002dlocal_002dpkgs"></a>Command: <strong>ess-rutils-local-pkgs</strong></dt>
<dd><a name="index-C_002dc-C_002d_002e-l"></a>
<p><kbd>C-c C-. l</kbd> List all packages in all available libraries.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002drutils_002drepos_002dpkgs"></a>Command: <strong>ess-rutils-repos-pkgs</strong></dt>
<dd><a name="index-C_002dc-C_002d_002e-r"></a>
<p><kbd>C-c C-. r</kbd> List available packages from repositories listed by
<code>getOptions(``repos'')</code> in the current R session.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002drutils_002dupdate_002dpkgs"></a>Command: <strong>ess-rutils-update-pkgs</strong> <em><var>lib</var> <var>repos</var></em></dt>
<dd><a name="index-C_002dc-C_002d_002e-u"></a>
<p><kbd>C-c C-. u</kbd> Update packages in a particular library <var>lib</var> and
repository <var>repos</var>.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002drutils_002dapropos"></a>Command: <strong>ess-rutils-apropos</strong></dt>
<dd><a name="index-C_002dc-C_002d_002e-a"></a>
<p><kbd>C-c C-. a</kbd> Search for a string using apropos.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002drutils_002drm_002dall"></a>Command: <strong>ess-rutils-rm-all</strong></dt>
<dd><a name="index-C_002dc-C_002d_002e-m"></a>
<p><kbd>C-c C-. m</kbd> Remove all R objects.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002drutils_002dobjs"></a>Command: <strong>ess-rutils-objs</strong></dt>
<dd><a name="index-C_002dc-C_002d_002e-o"></a>
<p><kbd>C-c C-. o</kbd> Manipulate R objects; wrapper for <code>ess-rdired</code>.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002drutils_002dload_002dwkspc"></a>Command: <strong>ess-rutils-load-wkspc</strong></dt>
<dd><a name="index-C_002dc-C_002d_002e-w"></a>
<p><kbd>C-c C-. w</kbd> Load a workspace file into R.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002drutils_002dsave_002dwkspc"></a>Command: <strong>ess-rutils-save-wkspc</strong></dt>
<dd><a name="index-C_002dc-C_002d_002e-s"></a>
<p><kbd>C-c C-. s</kbd> Save a workspace file.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002dchange_002ddirectory"></a>Command: <strong>ess-change-directory</strong></dt>
<dd><a name="index-C_002dc-C_002d_002e-d"></a>
<p><kbd>C-c C-. d</kbd> Change the working directory for the current R session.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002drutils_002dhtml_002ddocs"></a>Command: <strong>ess-rutils-html-docs</strong></dt>
<dd><a name="index-C_002dc-C_002d_002e-H"></a>
<p><kbd>C-c C-. H</kbd> Use <code>browse-url</code> to navigate R html
documentation.
</p></dd></dl>
<p>See the submenu ‘<samp>Rutils</samp>’ under the iESS menu for alternative access
to these functions. The function <code>ess-rutils-rsitesearch</code> is
provided without a particular key binding. This function is useful in
any Emacs buffer, so can be bound to a user-defined key:
</p>
<div class="lisp">
<pre class="lisp">(eval-after-load "ess-rutils"
'(global-set-key [(control c) (f6)] 'ess-rutils-rsitesearch))
</pre></div>
<a name="index-ess_002drutils_002drsitesearch"></a>
<p>Functions for listing objects and packages
(<code>ess-rutils-local-pkgs</code>, <code>ess-rutils-repos-pkgs</code>, and
<code>ess-rutils-objs</code>) show results in a separate buffer and window,
in <code>ess-rutils-mode</code>, providing useful key bindings in this mode
(type <kbd>?</kbd> in this buffer for a description).
</p>
<hr>
<a name="Org"></a>
<div class="header">
<p>
Next: <a href="#Sweave-and-AUCTeX" accesskey="n" rel="next">Sweave and AUCTeX</a>, Previous: <a href="#Rutils" accesskey="p" rel="prev">Rutils</a>, Up: <a href="#Extras" accesskey="u" rel="up">Extras</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Interaction-with-Org-mode"></a>
<h3 class="section">11.11 Interaction with Org mode</h3>
<p>Org-mode (<a href="http://orgmode.org">http://orgmode.org</a>) now supports reproducible research
and literate programming in many languages (including R) – see chapter
14 of the Org manual
(<a href="http://orgmode.org/org.html#Working-With-Source-Code">http://orgmode.org/org.html#Working-With-Source-Code</a>). For ESS
users, this offers a document-based work environment within which to
embed ESS usage. R code lives in code blocks of an Org document, from
which it can be edited in ess-mode, evaluated, extracted ("tangled") to
pure code files. The code can also be exported ("woven") with the
surrounding text to several formats including HTML and LaTeX. Results of
evaluation including figures can be captured in the Org document, and
data can be passed from the Org document (e.g. from a table) to the ESS
R process. (This section contributed by Dan Davison and Eric Schulte.)
</p>
<hr>
<a name="Sweave-and-AUCTeX"></a>
<div class="header">
<p>
Previous: <a href="#Org" accesskey="p" rel="prev">Org</a>, Up: <a href="#Extras" accesskey="u" rel="up">Extras</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Support-for-Sweave-in-ESS-and-AUCTeX"></a>
<h3 class="section">11.12 Support for Sweave in ESS and AUCTeX</h3>
<p>ESS provides support for writing and processing Sweave
(<a href="http://www.statistik.lmu.de/~leisch/Sweave">http://www.statistik.lmu.de/~leisch/Sweave</a>), building up on
Emacs’ ess-noweb-mode for literate programming. When working on an Sweave
document, the following key bindings are available:
</p>
<dl>
<dt><a name="index-ess_002dswv_002dweave"></a>Command: <strong>ess-swv-weave</strong> <em><var>choose</var></em></dt>
<dd><a name="index-M_002dn-s"></a>
<p><kbd>M-n s</kbd> Run Sweave on the current .Rnw file. If <var>choose</var> is
non-‘<samp>nil</samp>’, offer a menu of available weavers.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002dswv_002dlatex"></a>Command: <strong>ess-swv-latex</strong></dt>
<dd><a name="index-M_002dn-l"></a>
<p><kbd>M-n l</kbd> Run LaTeX after Sweave’ing.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002dswv_002dPS"></a>Command: <strong>ess-swv-PS</strong></dt>
<dd><p><kbd>M-n p</kbd> Generate and display a postscript file after LaTeX’ing.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002dswv_002dPDF"></a>Command: <strong>ess-swv-PDF</strong> <em><var>pdflatex-cmd</var></em></dt>
<dd><a name="index-M_002dn-P"></a>
<p><kbd>M-n P</kbd> Generate and display a PDF file after LaTeX’ing. Optional
argument <var>pdflatex-cmd</var> is the command to use, which by default, is
the command used to generate the PDF file is the first element of
<code>ess-swv-pdflatex-commands</code>.
</p></dd></dl>
<dl>
<dt><a name="index-ess_002dswv_002dpdflatex_002dcommands"></a>User Option: <strong>ess-swv-pdflatex-commands</strong></dt>
<dd><p>Commands used by <code>ess-swv-PDF</code> to run a version of pdflatex; the
first entry is the default command.
</p></dd></dl>
<p>Sweave’ing with <code>ess-swv-weave</code> starts an inferior-ESS process, if
one is not available. Other commands are available from the
‘<samp>Sweaving, Tangling, ...</samp>’ submenu of the Noweb menu.
</p>
<p>AUCTeX (<a href="http://www.gnu.org/software/auctex">http://www.gnu.org/software/auctex</a>) users may prefer to
set the variable <code>ess-swv-plug-into-AUCTeX-p</code> (available from the
“ESS Sweave” customization group) to t. Alternatively, the same can
be achieved by activating the entry “AUCTeX Interface” from the
‘<samp>Sweaving, Tangling, ...</samp>’ submenu, which toggles this variable on
or off. When the interface is activated, new entries for Sweave’ing and
LaTeX’ing thereafter are available from AUCTeX’s “Command” menu.
Sweave’ing can, thus, be done by <kbd>C-c C-c Sweave RET</kbd> without an
inferior-ESS process. Similarly, LaTeX’ing can be done by <kbd>C-c C-c
LaTeXSweave RET</kbd>. In both cases, the process can be monitored with
<kbd>C-c C-l</kbd> (<code>TeX-recenter-output-buffer</code>). Open the viewer with
<kbd>C-c C-v</kbd> (<code>TeX-view</code>), as usual in AUCTeX.
</p>
<hr>
<a name="ESS-for-S"></a>
<div class="header">
<p>
Next: <a href="#ESS-for-SAS" accesskey="n" rel="next">ESS for SAS</a>, Previous: <a href="#Extras" accesskey="p" rel="prev">Extras</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Overview-of-ESS-features-for-the-S-family"></a>
<h2 class="chapter">12 Overview of ESS features for the S family</h2>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#ESS_0028S_0029_002d_002dEditing-files" accesskey="1">ESS(S)--Editing files</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#iESS_0028S_0029_002d_002dInferior-ESS-processes" accesskey="2">iESS(S)--Inferior ESS processes</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#ESS_002dhelp_002d_002dassistance-with-viewing-help" accesskey="3">ESS-help--assistance with viewing help</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Philosophies-for-using-ESS_0028S_0029" accesskey="4">Philosophies for using ESS(S)</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Scenarios-for-use-_0028possibilities_002d_002dbased-on-actual-usage_0029" accesskey="5">Scenarios for use (possibilities--based on actual usage)</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Customization-Examples-and-Solutions-to-Problems" accesskey="6">Customization Examples and Solutions to Problems</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="ESS_0028S_0029_002d_002dEditing-files"></a>
<div class="header">
<p>
Next: <a href="#iESS_0028S_0029_002d_002dInferior-ESS-processes" accesskey="n" rel="next">iESS(S)--Inferior ESS processes</a>, Previous: <a href="#ESS-for-S" accesskey="p" rel="prev">ESS for S</a>, Up: <a href="#ESS-for-S" accesskey="u" rel="up">ESS for S</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS_005bS_005d_002d_002dEditing-files"></a>
<h3 class="section">12.1 ESS[S]–Editing files</h3>
<p><acronym>ESS[S]</acronym> is the mode for editing S language files. This mode handles:
</p>
<ul class="no-bullet">
<li>- proper indenting, generated by both [Tab] and [Return].
</li><li>- color and font choices based on syntax.
</li><li>- ability to send the contents of an entire buffer, a highlighted
region, an S function, or a single line to an inferior S process, if
one is currently running.
</li><li>- ability to switch between processes which would be the target of the
buffer (for the above).
</li><li>- The ability to request help from an S process for variables and
functions, and to have the results sent into a separate buffer.
</li><li>- completion of object names and file names.
</li></ul>
<p><acronym>ESS[S]</acronym> mode should be automatically turned on when loading a file with
the suffices found in ess-site (*.R, *.S, *.s, etc). Alternatively,
type <kbd>M-x R-mode</kbd> to put the current buffer into R mode. However, one
will have to start up an inferior process to take advantage of the
interactive features.
</p>
<hr>
<a name="iESS_0028S_0029_002d_002dInferior-ESS-processes"></a>
<div class="header">
<p>
Next: <a href="#ESS_002dhelp_002d_002dassistance-with-viewing-help" accesskey="n" rel="next">ESS-help--assistance with viewing help</a>, Previous: <a href="#ESS_0028S_0029_002d_002dEditing-files" accesskey="p" rel="prev">ESS(S)--Editing files</a>, Up: <a href="#ESS-for-S" accesskey="u" rel="up">ESS for S</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="iESS_005bS_005d_002d_002dInferior-ESS-processes"></a>
<h3 class="section">12.2 iESS[S]–Inferior ESS processes</h3>
<p>iESS (inferior ESS) is the mode for interfacing with active
statistical processes (programs). This mode handles:
</p>
<ul class="no-bullet">
<li>- proper indenting, generated by both [Tab] and [Return].
</li><li>- color and font highlighting based on syntax.
</li><li>- ability to resubmit the contents of a multi-line command
to the executing process with a single keystroke [RET].
</li><li>- The ability to request help from the current process for variables
and functions, and to have the results sent into a separate buffer.
</li><li>- completion of object names and file names.
</li><li>- interactive history mechanism.
</li><li>- transcript recording and editing.
</li></ul>
<p>To start up iESS mode, use:
</p><div class="example">
<pre class="example"> M-x S+3
M-x S4
M-x S+5
M-x S+6
M-x R
</pre></div>
<p>(for S-PLUS 3.x, S4, S+5, S+6 or S+7, and R, respectively. This assumes that
you have access to each). Usually the site will have defined one of
these programs (by default S+6) to the simpler name:
</p>
<p>M-x S
</p>
<a name="index-command-line-arguments"></a>
<p>In the (rare) case that you wish to pass command line arguments to the
starting S+6 process, set the variable <code>inferior-Splus-args</code>.
</p>
<p>Note that R has some extremely useful command line arguments. For
example, <code>--vanilla</code> will ensure R starts up without loading in any init
files. To enter a command line argument, call R using a "prefix
argument", by
</p>
<p>C-u M-x R
</p>
<p>and when ESS prompts for "Starting Args ? ", enter (for example):
</p>
<p><code>--vanilla</code>
</p>
<p>Then that R process will be started up using <code>R --vanilla</code>. If you
wish to always call R with certain arguments, set the variable
<code>inferior-R-args</code> accordingly.
</p>
<p>If you have other versions of R or S-Plus available on the system, ESS
is also able to start those versions. How this exactly works depend on
which OS you are using, as described in the following paragraphs. The
general principle, regardless of OS, is that ESS searches the paths
listed in the variable <code>exec-path</code> for R binaries. If ESS cannot
find your R binaries, on Unix you can change the unix environment
variable <code>PATH</code>, as this variable is used to set <code>exec-path</code>.
</p>
<p>R on Unix systems: If you have "R-1.8.1" on your <code>exec-path</code>, it
can be started using <kbd>M-x R-1.8.1</kbd>. By default, ESS will find
versions of R beginning "R-1" or "R-2". If your versions of R are
called other names, consider renaming them with a symbolic link or
change the variable <code>ess-r-versions</code>. To see which functions have
been created for starting different versions of R, type <kbd>M-x R-</kbd> and
then hit [Tab]. These other versions of R can also be started from the
"ESS->Start Process->Other" menu.
</p>
<p>R on Windows systems: If you have "rw1081" on your <code>exec-path</code>, it
can be started using <kbd>M-x rw1081</kbd>. By default, ESS will find
versions of R located in directories parallel to the version of R in
your <code>PATH</code>. If your versions of R are called other names, you
will need to change the variable <code>ess-rterm-versions</code>. To see
which functions have been created for starting different versions of R,
type <kbd>M-x rw</kbd> and then hit [Tab]. These other versions of
R can also be started from the "ESS->Start Process->Other" menu.
</p>
<p>Once ESS has found these extra versions of R, it will then create a new
function, called <kbd>M-x R-newest</kbd>, which will call the newest version
of R that it found. (ESS examines the date in the first line of
information from <code>R --version</code> to determine which is newest.)
</p>
<p>S on Unix systems: If you have "Splus7" on your <code>exec-path</code>, it can
be started using <kbd>M-x Splus7</kbd>. By default, ESS will find all
executables beginning "Splus" on your path. If your versions of S are
called other names, consider renaming them with a symbolic link or
change the variable <code>ess-s-versions</code>. To see which functions have
been created for starting different versions of Splus, type <kbd>M-x
Splus</kbd> and then hit [Tab]. These other versions of Splus can also be
started from the "ESS->Start Process->Other" menu.
</p>
<p>A second mechanism is also available for running other versions of Splus.
The variable <code>ess-s-versions-list</code> is a list of lists; each sublist
should be of the form: (DEFUN-NAME PATH ARGS). DEFUN-NAME is the name
of the new emacs function you wish to create to start the new S process;
PATH is the full path to the version of S you want to run; ARGS is an
optional string of command-line arguments to pass to the S process.
Here is an example setting:
</p><div class="example">
<pre class="example">(setq ess-s-versions-list
'( ("Splus64" "/usr/local/bin/Splus64")
("Splus64-j" "/usr/local/bin/Splus64" "-j")))
</pre></div>
<p>which will then allow you to do <kbd>M-x Splus64-j</kbd> to start Splus64
with the corresponding command line arguments.
</p>
<p>If you change the value of either <code>ess-s-versions</code> or
<code>ess-s-versions-list</code>, you should put them in your .emacs before
ess-site is loaded, since the new emacs functions are created when ESS
is loaded.
</p>
<p>Sqpe (S-Plus running inside an emacs buffer) on Windows systems: If you
have an older version of S-Plus (S-Plus 6.1 for example) on your system,
ir can be started inside an emacs buffer with <kbd>M-x splus61</kbd>. By
default, ESS will find versions of S-Plus located in the installation
directories that Insightful uses by default. If your versions of S-Plus
are anywhere else, you will need to change the variable
<code>ess-SHOME-versions</code>. To see which functions have been created for
starting different versions of S-Plus, type <kbd>M-x spl</kbd> and then hit
[Tab]. These other versions of S-Plus can also be started from the
"ESS->Start Process->Other" menu.
</p>
<hr>
<a name="ESS_002dhelp_002d_002dassistance-with-viewing-help"></a>
<div class="header">
<p>
Next: <a href="#Philosophies-for-using-ESS_0028S_0029" accesskey="n" rel="next">Philosophies for using ESS(S)</a>, Previous: <a href="#iESS_0028S_0029_002d_002dInferior-ESS-processes" accesskey="p" rel="prev">iESS(S)--Inferior ESS processes</a>, Up: <a href="#ESS-for-S" accesskey="u" rel="up">ESS for S</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS_002dhelp_002d_002dassistance-with-viewing-help-1"></a>
<h3 class="section">12.3 ESS-help–assistance with viewing help</h3>
<p>ESS has built-in facilities for viewing help files from S. See <a href="#Help">Help</a>.
</p>
<hr>
<a name="Philosophies-for-using-ESS_0028S_0029"></a>
<div class="header">
<p>
Next: <a href="#Scenarios-for-use-_0028possibilities_002d_002dbased-on-actual-usage_0029" accesskey="n" rel="next">Scenarios for use (possibilities--based on actual usage)</a>, Previous: <a href="#ESS_002dhelp_002d_002dassistance-with-viewing-help" accesskey="p" rel="prev">ESS-help--assistance with viewing help</a>, Up: <a href="#ESS-for-S" accesskey="u" rel="up">ESS for S</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Philosophies-for-using-ESS_005bS_005d"></a>
<h3 class="section">12.4 Philosophies for using ESS[S]</h3>
<p>The first is preferred, and configured for. The second one can be
retrieved again, by changing emacs variables.
</p>
<p>1: (preferred by the current group of developers): The source code is
real. The objects are realizations of the source code. Source
for EVERY user modified object is placed in a particular directory
or directories, for later editing and retrieval.
</p>
<p>2: (older version): S objects are real. Source code is a temporary
realization of the objects. Dumped buffers should not be saved.
_We_strongly_discourage_this_approach_. However, if you insist,
add the following lines to your .emacs file:
</p><div class="example">
<pre class="example">(setq ess-keep-dump-files 'nil)
(setq ess-delete-dump-files t)
(setq ess-mode-silently-save nil)
</pre></div>
<p>The second saves a small amount of disk space. The first allows for
better portability as well as external version control for code.
</p>
<hr>
<a name="Scenarios-for-use-_0028possibilities_002d_002dbased-on-actual-usage_0029"></a>
<div class="header">
<p>
Next: <a href="#Customization-Examples-and-Solutions-to-Problems" accesskey="n" rel="next">Customization Examples and Solutions to Problems</a>, Previous: <a href="#Philosophies-for-using-ESS_0028S_0029" accesskey="p" rel="prev">Philosophies for using ESS(S)</a>, Up: <a href="#ESS-for-S" accesskey="u" rel="up">ESS for S</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Scenarios-for-use-_0028possibilities_002d_002dbased-on-actual-usage_0029-1"></a>
<h3 class="section">12.5 Scenarios for use (possibilities–based on actual usage)</h3>
<p>We present some basic suggestions for using ESS to interact with S.
These are just a subset of approaches, many better approaches are
possible. Contributions of examples of how you work with ESS are
appreciated (especially since it helps us determine priorities on
future enhancements)! (comments as to what should be happening are
prefixed by "##").
</p><div class="display">
<pre class="display">1: ## Data Analysis Example (source code is real)
## Load the file you want to work with
C-x C-f myfile.s
## Edit as appropriate, and then start up S-PLUS 3.x
M-x S+3
## A new buffer *S+3:1* will appear. Splus will have been started
## in this buffer. The buffer is in iESS [S+3:1] mode.
## Split the screen and go back to the file editing buffer.
C-x 2 C-x b myfile.s
## Send regions, lines, or the entire file contents to S-PLUS. For regions,
## highlight a region with keystrokes or mouse and then send with:
C-c C-r
## Re-edit myfile.s as necessary to correct any difficulties. Add
## new commands here. Send them to S by region with C-c C-r, or
## one line at a time with C-c C-n.
## Save the revised myfile.s with C-x C-s.
## Save the entire *S+3:1* interaction buffer with C-c C-s. You
## will be prompted for a file name. The recommended name is
## myfile.St. With the *.St suffix, the file will come up in ESS
## Transcript mode the next time it is accessed from Emacs.
2: ## Program revision example (source code is real)
## Start up S-PLUS 3.x in a process buffer (this will be *S+3:1*)
M-x S+3
## Load the file you want to work with
C-x C-f myfile.s
## edit program, functions, and code in myfile.s, and send revised
## functions to S when ready with
C-c C-f
## or highlighted regions with
C-c C-r
## or individual lines with
C-c C-n
## or load the entire buffer with
C-c C-l
## save the revised myfile.s when you have finished
C-c C-s
3: ## Program revision example (S object is real)
## Start up S-PLUS 3.x in a process buffer (this will be *S+3:1*)
M-x S+3
## Dump an existing S object my.function into a buffer to work with
C-c C-d my.function
## a new buffer named yourloginname.my.function.S will be created with
## an editable copy of the object. The buffer is associated with the
## pathname /tmp/yourloginname.my.function.S and will amlost certainly not
## exist after you log off.
## enter program, functions, and code into work buffer, and send
## entire contents to S-PLUS when ready
C-c C-b
## Go to *S+3:1* buffer, which is the process buffer, and examine
## the results.
C-c C-y
## The sequence C-c C-y is a shortcut for: C-x b *S+3:1*
## Return to the work buffer (may/may not be prefixed)
C-x C-b yourloginname.my.function.S
## Fix the function that didn’t work, and resubmit by placing the
## cursor somewhere in the function and
C-c C-f
## Or you could’ve selected a region (using the mouse, or keyboard
## via setting point/mark) and
C-c C-r
## Or you could step through, line by line, using
C-c C-n
## Or just send a single line (without moving to the next) using
C-c C-j
## To fix that error in syntax for the "rchisq" command, get help
## by
C-c C-v rchisq
4: Data Analysis (S object is real)
## Start up S-PLUS 3.x, in a process buffer (this will be *S+3:1*)
M-x S+3
## Work in the process buffer. When you find an object that needs
## to be changed (this could be a data frame, or a variable, or a
## function), dump it to a buffer:
C-c C-d my.cool.function
## Edit the function as appropriate, and dump back in to the
## process buffer
C-c C-b
## Return to the S-PLUS process buffer
C-c C-y
## Continue working.
## When you need help, use
C-c C-v rchisq
## instead of entering: help("rchisq")
</pre></div>
<hr>
<a name="Customization-Examples-and-Solutions-to-Problems"></a>
<div class="header">
<p>
Previous: <a href="#Scenarios-for-use-_0028possibilities_002d_002dbased-on-actual-usage_0029" accesskey="p" rel="prev">Scenarios for use (possibilities--based on actual usage)</a>, Up: <a href="#ESS-for-S" accesskey="u" rel="up">ESS for S</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Customization-Examples-and-Solutions-to-Problems-1"></a>
<h3 class="section">12.6 Customization Examples and Solutions to Problems</h3>
<p>1. Suppose that you are primarily an SPLUS 3.4 user, occasionally
using S version 4, and sick and tired of the buffer-name *S+3*
we’ve stuck you with. Simply edit the "ess-dialect" alist entry in
the ess-sp3-d.el and ess-s4-d.el files to be "S" instead of "S4" and
"S+3". This will ensure that all the inferior process buffer names
are "*S*".
</p>
<p>2. Suppose that you WANT to have the first buffer name indexed by
":1", in the same manner as your S-PLUS processes 2,3,4, and 5 (for
you heavy simulation people). Then
add after your (require ’ess-site) or (load "ess-site") command
in your .emacs file, the line:
</p><div class="example">
<pre class="example">(setq ess-plain-first-buffername nil)
</pre></div>
<p>3. Fontlocking sometimes fails to behave nicely upon errors. When
Splus dumps, a mis-matched " (double-quote) can result in the
wrong font-lock face being used for the remainder of the buffer.
</p>
<p>Solution: add a " at the end of the "Dumped..." statement, to
revert the font-lock face back to normal.
</p>
<p>4. When you change directory within a *R* or *S* session using the
setwd() command, emacs does not recognise that you have changed the
current directory.
</p>
<p>Solution: Use <kbd>M-x ess-change-directory</kbd>. This will prompt you for
the directory to change to. It will then change directory within the
*S* buffer, and also update the emacs variable <code>default-directory</code>.
Alternatively, if you have already executed setwd(), press <kbd>M-RET</kbd>
within the *S* buffer so that Emacs can update <code>default-directory</code>.
</p>
<hr>
<a name="ESS-for-SAS"></a>
<div class="header">
<p>
Next: <a href="#ESS-for-BUGS" accesskey="n" rel="next">ESS for BUGS</a>, Previous: <a href="#ESS-for-S" accesskey="p" rel="prev">ESS for S</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS-for-SAS-1"></a>
<h2 class="chapter">13 ESS for SAS</h2>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#ESS_0028SAS_0029_002d_002dDesign-philosophy" accesskey="1">ESS(SAS)--Design philosophy</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#ESS_0028SAS_0029_002d_002dEditing-files" accesskey="2">ESS(SAS)--Editing files</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#ESS_0028SAS_0029_002d_002dTAB-key" accesskey="3">ESS(SAS)--TAB key</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#ESS_0028SAS_0029_002d_002dBatch-SAS-processes" accesskey="4">ESS(SAS)--Batch SAS processes</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#ESS_0028SAS_0029_002d_002dFunction-keys-for-batch-processing" accesskey="5">ESS(SAS)--Function keys for batch processing</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#iESS_0028SAS_0029_002d_002dInteractive-SAS-processes" accesskey="6">iESS(SAS)--Interactive SAS processes</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#iESS_0028SAS_0029_002d_002dCommon-problems" accesskey="7">iESS(SAS)--Common problems</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#ESS_0028SAS_0029_002d_002dGraphics" accesskey="8">ESS(SAS)--Graphics</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#ESS_0028SAS_0029_002d_002dWindows" accesskey="9">ESS(SAS)--Windows</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<p><acronym>ESS[SAS]</acronym> was designed for use with <acronym>SAS</acronym><!-- /@w -->. It is descended from emacs
macros developed by John Sall for editing <acronym>SAS</acronym><!-- /@w --> programs and <code>SAS-mode</code> by
Tom Cook. Those editing features and new advanced features are part of
<acronym>ESS[SAS]</acronym>. The user interface of <acronym>ESS[SAS]</acronym> has similarities with <acronym>ESS[S]</acronym>
and the <acronym>SAS</acronym><!-- /@w --> Display Manager.
</p>
<hr>
<a name="ESS_0028SAS_0029_002d_002dDesign-philosophy"></a>
<div class="header">
<p>
Next: <a href="#ESS_0028SAS_0029_002d_002dEditing-files" accesskey="n" rel="next">ESS(SAS)--Editing files</a>, Previous: <a href="#ESS-for-SAS" accesskey="p" rel="prev">ESS for SAS</a>, Up: <a href="#ESS-for-SAS" accesskey="u" rel="up">ESS for SAS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS_005bSAS_005d_002d_002dDesign-philosophy"></a>
<h3 class="section">13.1 ESS[SAS]–Design philosophy</h3>
<p><acronym>ESS[SAS]</acronym> was designed to aid the user in writing and maintaining <acronym>SAS</acronym><!-- /@w -->
programs, such as <samp><var>foo</var>.sas</samp>. Both interactive and batch
submission of <acronym>SAS</acronym><!-- /@w --> programs is supported.
</p>
<p><acronym>ESS[SAS]</acronym> was written with two primary goals.
</p><ol>
<li> The emacs text editor provides a powerful and flexible development
environment for programming languages. These features are a boon to all
programmers and, with the help of <acronym>ESS[SAS]</acronym>, to <acronym>SAS</acronym><!-- /@w --> users as well.
</li><li> Although a departure from <acronym>SAS</acronym><!-- /@w --> Display Manager, <acronym>ESS[SAS]</acronym> provides
similar key definitions to give novice <acronym>ESS[SAS]</acronym> users a head start.
Also, inconvenient <acronym>SAS</acronym><!-- /@w --> Display Manager features, like remote submission
and syntax highlighting, are provided transparently; appealing to
advanced <acronym>ESS[SAS]</acronym> users.
</li></ol>
<hr>
<a name="ESS_0028SAS_0029_002d_002dEditing-files"></a>
<div class="header">
<p>
Next: <a href="#ESS_0028SAS_0029_002d_002dTAB-key" accesskey="n" rel="next">ESS(SAS)--TAB key</a>, Previous: <a href="#ESS_0028SAS_0029_002d_002dDesign-philosophy" accesskey="p" rel="prev">ESS(SAS)--Design philosophy</a>, Up: <a href="#ESS-for-SAS" accesskey="u" rel="up">ESS for SAS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS_005bSAS_005d_002d_002dEditing-files"></a>
<h3 class="section">13.2 ESS[SAS]–Editing files</h3>
<p><acronym>ESS[SAS]</acronym> is the mode for editing <acronym>SAS</acronym><!-- /@w --> language files. This mode handles:
</p>
<ul>
<li> proper indenting, generated by both <tt class="key">TAB</tt> and <tt class="key">RET</tt>.
</li><li> color and font choices based on syntax.
</li><li> ability to save and submit the file you are working on as a batch
<acronym>SAS</acronym><!-- /@w --> process with a single keypress and to continue editing while it is runs
in the background.
</li><li> capability of killing the batch <acronym>SAS</acronym><!-- /@w --> process through the <samp>*shell*</samp> buffer or
allow the <acronym>SAS</acronym><!-- /@w --> process to keep on running after you exit emacs.
</li><li> single keypress navigation of <samp>.sas</samp>, <samp>.log</samp> and <samp>.lst</samp> files
(<samp>.log</samp> and <samp>.lst</samp> files are refreshed with each keypress).
</li><li> ability to send the contents of an entire buffer, a highlighted region,
or a single line to an interactive <acronym>SAS</acronym><!-- /@w --> process.
</li><li> ability to switch between processes which would be the target of the
buffer (for the above).
</li></ul>
<p><acronym>ESS[SAS]</acronym> is automatically turned on when editing a file with a <samp>.sas</samp>
suffix (or other extension, if specified via <code>auto-mode-alist</code>). The function
keys can be enabled to use the same function keys that
the <acronym>SAS</acronym><!-- /@w --> Display Manager does. The interactive capabilities of <acronym>ESS</acronym> require you
to start an inferior <acronym>SAS</acronym><!-- /@w --> process with <kbd><span class="nolinebreak">M-x</span> SAS</kbd><!-- /@w -->
(See <a href="#iESS_0028SAS_0029_002d_002dInteractive-SAS-processes">iESS(SAS)--Interactive SAS processes</a>.)
</p>
<p>At this writing, the indenting and syntax highlighting are generally
correct. Known issues: for multiple line <code>*</code> or <code>%*</code> comments, only the
first line is highlighted; for <samp>.log</samp> files, only the first line of a
<code>NOTE:</code>, <code>WARNING:</code> or <code>ERROR:</code> message is highlighted; unmatched
single/double quotes in <code>CARDS</code> data lines are <strong>NOT</strong> ignored; in an
iterative <code>DO</code> statement, <code>TO</code> and <code>BY</code> are not highlighted.
</p>
<hr>
<a name="ESS_0028SAS_0029_002d_002dTAB-key"></a>
<div class="header">
<p>
Next: <a href="#ESS_0028SAS_0029_002d_002dBatch-SAS-processes" accesskey="n" rel="next">ESS(SAS)--Batch SAS processes</a>, Previous: <a href="#ESS_0028SAS_0029_002d_002dEditing-files" accesskey="p" rel="prev">ESS(SAS)--Editing files</a>, Up: <a href="#ESS-for-SAS" accesskey="u" rel="up">ESS for SAS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS_005bSAS_005d_002d_002dTAB-key"></a>
<h3 class="section">13.3 ESS[SAS]–<tt class="key">TAB</tt> key</h3>
<p>Two options. The <tt class="key">TAB</tt> key is bound by default to
<code>sas-indent-line</code>. This function is used to syntactically indent
<acronym>SAS</acronym><!-- /@w --> code so <code>PROC</code> and <code>RUN</code> are in the left margin,
other statements are indented <code>sas-indent-width</code> spaces from the
margin, continuation lines are indented <code>sas-indent-width</code> spaces
in from the beginning column of that statement. This is the type of
functionality that emacs provides in most programming language modes.
This functionality is activated by placing the following line in your
initialization file prior to a <code>require</code>/<code>load</code>:
</p><div class="example">
<pre class="example">(setq ess-sas-edit-keys-toggle nil)
</pre></div>
<p><acronym>ESS</acronym> provides an alternate behavior for <tt class="key">TAB</tt> that makes it
behave as it does in <acronym>SAS</acronym><!-- /@w --> Display Manager, i.e. move the cursor to
the next stop. The alternate behavior also provides a "TAB"
backwards, <kbd><span class="nolinebreak">C-</span><span class="key">TAB</span></kbd><!-- /@w -->, that moves the cursor to the stop to
the left and deletes any characters between them. This functionality
is obtained by placing the following line in your initialization file
prior to a <code>require</code>/<code>load</code>:
</p><div class="example">
<pre class="example">(setq ess-sas-edit-keys-toggle t)
</pre></div>
<p>Under the alternate behavior, <tt class="key">TAB</tt> is bound to <kbd><span class="nolinebreak">M-x</span> <span class="nolinebreak">tab-to-tab-stop</span></kbd><!-- /@w -->
and the stops are defined by <code>ess-sas-tab-stop-list</code>.
</p>
<hr>
<a name="ESS_0028SAS_0029_002d_002dBatch-SAS-processes"></a>
<div class="header">
<p>
Next: <a href="#ESS_0028SAS_0029_002d_002dFunction-keys-for-batch-processing" accesskey="n" rel="next">ESS(SAS)--Function keys for batch processing</a>, Previous: <a href="#ESS_0028SAS_0029_002d_002dTAB-key" accesskey="p" rel="prev">ESS(SAS)--TAB key</a>, Up: <a href="#ESS-for-SAS" accesskey="u" rel="up">ESS for SAS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS_005bSAS_005d_002d_002dBatch-SAS-processes"></a>
<h3 class="section">13.4 ESS[SAS]–Batch SAS processes</h3>
<p>Submission of a <acronym>SAS</acronym><!-- /@w --> batch job is dependent on your environment.
<code>ess-sas-submit-method</code> is determined by your operating system and
your shell. It defaults to <code>'sh</code> unless you are running Windows or
Mac Classic. Under Windows, it will default to <code>'sh</code> if you are using
a <acronym>UNIX</acronym>-imitating shell; otherwise <code>'ms-dos</code> for an <acronym>MS-DOS</acronym>
shell. On Mac OS X, it will default to <code>'sh</code>, but under Mac Classic,
it defaults to <code>'apple-script</code>. You will also set this to <code>'sh</code>
if the <acronym>SAS</acronym><!-- /@w --> batch job needs to run on a remote machine rather than your
local machine. This works transparently if you are editing the remote file
via ange-ftp/EFS or tramp. Note that
<code>ess-sas-shell-buffer-remote-init</code> is a Local Variable that defaults
to <code>"ssh"</code> which will be used to open the buffer on the remote host
and it is assumed that no password is necessary, i.e. you are using
<code>ssh-agent</code>/<code>ssh-add</code> or the equivalent (see the discussion about
Local Variables below if you need to change the default).
</p>
<p>However, if you are editing the file locally and transferring it back and
forth with Kermit, you need some additional steps. First, start Kermit
locally before remotely logging in. Open a local copy of the file with the
<code>ess-kermit-prefix</code> character prepended (the default is <code>"#"</code>).
Execute the command <kbd><span class="nolinebreak">M-x</span> <span class="nolinebreak">ess-kermit-get</span></kbd><!-- /@w --> which automatically brings
the contents of the remote file into your local copy. If you transfer
files with Kermit manually in a <samp>*shell*</samp> buffer, then note that the
Kermit escape sequence is <kbd><span class="nolinebreak">C-q</span> <span class="nolinebreak">C-\</span> c</kbd><!-- /@w --> rather than <kbd><span class="nolinebreak">C-\</span> c</kbd><!-- /@w --> which
it would be in an ordinary terminal application, i.e. not in an emacs
buffer. Lastly, note that the remote Kermit command is specified by
<code>ess-kermit-command</code>.
</p>
<p>The command used by the <code>SUBMIT</code> function key (<tt class="key">F3</tt> or <tt class="key">F8</tt>)
to submit a batch <acronym>SAS</acronym><!-- /@w --> job, whether local or remote, is
<code>ess-sas-submit-command</code> which defaults to <code>sas-program</code>.
<code>sas-program</code> is <code>"invoke SAS using program file"</code> for Mac
Classic and <code>"sas"</code> otherwise. However, you may have to alter
<code>ess-sas-submit-command</code> for a particular program, so it is defined as
buffer-local. Conveniently, it can be set at the end of the program:
</p><div class="example">
<pre class="example">endsas;
Local variables:
ess-sas-submit-command: "sas8"
End:
</pre></div>
<p>The command line is also made of <code>ess-sas-submit-pre-command</code>,
<code>ess-sas-submit-post-command</code> and <code>ess-sas-submit-command-options</code>
(the last of which is also buffer-local).
Here are some examples for your <samp>~/.emacs</samp> or <samp>~/.xemacs/init.el</samp>
file (you may also use <kbd><span class="nolinebreak">M-x</span> <span class="nolinebreak">customize-variable</span></kbd><!-- /@w -->):
</p><div class="example">
<pre class="example">;'sh default
(setq ess-sas-submit-pre-command "nohup")
;'sh default
(setq ess-sas-submit-post-command "-rsasuser &")
;'sh example
(setq-default ess-sas-submit-command "/usr/local/sas/sas")
;'ms-dos default
(setq ess-sas-submit-pre-command "start")
;'ms-dos default
(setq ess-sas-submit-post-command "-rsasuser -icon")
;Windows example
(setq-default ess-sas-submit-command "c:/progra~1/sas/sas.exe")
;Windows example
(setq-default ess-sas-submit-command "c:\\progra~1\\sas\\sas.exe")
</pre></div>
<p>There is a built-in delay before a batch <acronym>SAS</acronym><!-- /@w --> job is submitted when using
a <acronym>UNIX</acronym>-imitating shell under Windows. This is necessary in many cases
since the shell might not be ready to receive a command. This delay is
currently set high enough so as not to be a problem. But, there may be
cases when it needs to be set higher, or could be set much lower to
speed things up. You can over-ride the default in your <samp>~/.emacs</samp> or <samp>~/.xemacs/init.el</samp> file by:
</p><div class="example">
<pre class="example">(setq ess-sleep-for 0.2)
</pre></div>
<p>For example, <code>(setq ess-sas-global-unix-keys t)</code> keys shown,
<code>(setq ess-sas-global-pc-keys t)</code> in parentheses;
<acronym>ESS[SAS]</acronym> function keys are presented in the next section.
Open the file you want to work with <kbd><span class="nolinebreak">C-x</span> <span class="nolinebreak">C-f</span> foo.sas</kbd><!-- /@w -->.
<samp><var>foo</var>.sas</samp> will be in <acronym>ESS[SAS]</acronym> mode. Edit as appropriate, then save and
submit the batch <acronym>SAS</acronym><!-- /@w --> job.
</p><div class="example">
<pre class="example"><span class="key">F3</span> (<span class="key">F8</span>)
</pre></div>
<p>The job runs in the <samp>*shell*</samp> buffer while you continue to edit
<samp><var>foo</var>.sas</samp>. If <code>ess-sas-submit-method</code> is <code>'sh</code>, then the
message buffer will display the shell notification when the
job is complete. The <code>'sh</code> setting also allows you to
terminate the <acronym>SAS</acronym><!-- /@w --> batch job before it is finished.
</p><div class="example">
<pre class="example"><span class="key">F8</span> (<span class="key">F3</span>)
</pre></div>
<p>Terminating a <acronym>SAS</acronym><!-- /@w --> batch in the <samp>*shell*</samp> buffer.
</p><div class="example">
<pre class="example">kill <var>PID</var>
</pre></div>
<p>You may want to visit the <samp>.log</samp> (whether the job is still running
or it is finished) and check for error messages. The <samp>.log</samp> will be
refreshed and you will be placed in it’s buffer. You will be
taken to the first error message, if any.
</p><div class="example">
<pre class="example"><span class="key">F5</span> (<span class="key">F6</span>)
</pre></div>
<p>Goto the next error message, if any.
</p><div class="example">
<pre class="example"><span class="key">F5</span> (<span class="key">F6</span>)
</pre></div>
<p>Now, ‘<samp>refresh</samp>’ the <samp>.lst</samp> and go to it’s buffer.
</p><div class="example">
<pre class="example"><span class="key">F6</span> (<span class="key">F7</span>)
</pre></div>
<p>If you wish to make changes, go to the <samp>.sas</samp> file with.
</p><div class="example">
<pre class="example"><span class="key">F4</span> (<span class="key">F5</span>)
</pre></div>
<p>Make your editing changes and submit again.
</p><div class="example">
<pre class="example"><span class="key">F3</span> (<span class="key">F8</span>)
</pre></div>
<hr>
<a name="ESS_0028SAS_0029_002d_002dFunction-keys-for-batch-processing"></a>
<div class="header">
<p>
Next: <a href="#iESS_0028SAS_0029_002d_002dInteractive-SAS-processes" accesskey="n" rel="next">iESS(SAS)--Interactive SAS processes</a>, Previous: <a href="#ESS_0028SAS_0029_002d_002dBatch-SAS-processes" accesskey="p" rel="prev">ESS(SAS)--Batch SAS processes</a>, Up: <a href="#ESS-for-SAS" accesskey="u" rel="up">ESS for SAS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS_005bSAS_005d_002d_002dFunction-keys-for-batch-processing"></a>
<h3 class="section">13.5 ESS[SAS]–Function keys for batch processing</h3>
<p>The setup of function keys for <acronym>SAS</acronym><!-- /@w --> batch processing
is unavoidably complex, but the usage of function keys is simple.
There are five distinct options:
</p>
<p>Option 1 (default). Function keys in <acronym>ESS[SAS]</acronym> are not bound to elisp
commands. This is in accordance with the GNU Elisp Coding Standards
(<acronym>GECS</acronym>) which do not allow function keys to be bound so that they are
available to the user.
</p>
<p>Options 2-5. Since <acronym>GECS</acronym> does not allow function keys to be bound by
modes, these keys are often unused. So, <acronym>ESS[SAS]</acronym> provides users with
the option of binding elisp commands to these keys. Users who are
familiar with <acronym>SAS</acronym><!-- /@w --> will, most likely, want to duplicate the function key
capabilities of the <acronym>SAS</acronym><!-- /@w --> Display Manager. There are four options (noted
in parentheses).
</p>
<ol>
<li> <acronym>SAS</acronym><!-- /@w --> Display Manager has different function key definitions for
<acronym>UNIX</acronym> (2, 4) and Windows (3, 5); <acronym>ESS[SAS]</acronym> can use either.
</li><li> The <acronym>ESS[SAS]</acronym> function key definitions can be active in all buffers
(global: 4, 5) or limited (local: 2, 3) only to buffers with files that
are associated with <acronym>ESS[SAS]</acronym> as specified in your <code>auto-mode-alist</code>.
</li></ol>
<p>The distinction between local and global is subtle. If you want the
<acronym>ESS[SAS]</acronym> definitions to work when you are in the <samp>*shell*</samp> buffer or when
editing files other than the file extensions that <acronym>ESS[SAS]</acronym> recognizes,
you will most likely want to use the global definitions. If you want
your function keys to understand <acronym>SAS</acronym><!-- /@w --> batch commands when you are editing
<acronym>SAS</acronym><!-- /@w --> files, and to behave normally when editing other files, then you
will choose the local definitions. The option can be chosen by the
person installing <acronym>ESS</acronym> for a site or by an individual.
</p>
<ol>
<li> For a site installation or an individual, place <strong>ONLY ONE</strong> of
the following lines in your initialization file prior to a
<code>require</code>/<code>load</code>. <acronym>ESS[SAS]</acronym> function keys are available
in <acronym>ESS[SAS]</acronym> if you choose either 2 or 3 and in all modes if you
choose 4 or 5:
<div class="example">
<pre class="example">;;2; (setq ess-sas-local-unix-keys t)
;;3; (setq ess-sas-local-pc-keys t)
;;4; (setq ess-sas-global-unix-keys t)
;;5; (setq ess-sas-global-pc-keys t)
</pre></div>
<p>The names <code>-unix-</code> and <code>-pc-</code> have nothing to do with the operating system
that you are running. Rather, they mimic the definitions that the <acronym>SAS</acronym><!-- /@w -->
Display Manager uses by default on those platforms.
</p>
</li><li> If your site installation has configured the keys contrary to your
liking, then you must call the appropriate function.
<div class="example">
<pre class="example"> (load "ess-site") ;; local-unix-keys
(ess-sas-global-pc-keys)
</pre></div>
</li></ol>
<p>Finally, we get to what the function keys actually do. You may recognize
some of the nicknames as <acronym>SAS</acronym><!-- /@w --> Display Manager commands (they are in all
capitals).
</p>
<table>
<tr><td><acronym>UNIX</acronym></td><td><acronym>PC</acronym></td><td>Nickname</td></tr>
<tr><td><tt class="key">F2</tt></td><td><tt class="key">F2</tt></td><td>‘<samp>refresh</samp>’</td></tr>
<tr><td></td><td></td><td>revert the current buffer with the file of the same
name if the file is newer than the buffer</td></tr>
<tr><td><tt class="key">F3</tt></td><td><tt class="key">F8</tt></td><td><code>SUBMIT</code></td></tr>
<tr><td></td><td></td><td>save the current <samp>.sas</samp> file (which is either the <samp>.sas</samp>
file in the current buffer or the <samp>.sas</samp> file associated
with the <samp>.lst</samp> or <samp>.log</samp> file in the current buffer)
and submit the file as a batch <acronym>SAS</acronym><!-- /@w --> job</td></tr>
<tr><td><tt class="key">F4</tt></td><td><tt class="key">F5</tt></td><td><code>PROGRAM</code></td></tr>
<tr><td></td><td></td><td>switch buffer to <samp>.sas</samp> file</td></tr>
<tr><td><tt class="key">F5</tt></td><td><tt class="key">F6</tt></td><td><code>LOG</code></td></tr>
<tr><td></td><td></td><td>switch buffer to <samp>.log</samp> file, ‘<samp>refresh</samp>’ and goto next
error message, if any</td></tr>
<tr><td><tt class="key">F6</tt></td><td><tt class="key">F7</tt></td><td><code>OUTPUT</code></td></tr>
<tr><td></td><td></td><td>switch buffer to <samp>.lst</samp> file and ‘<samp>refresh</samp>’</td></tr>
<tr><td><tt class="key">F7</tt></td><td><tt class="key">F4</tt></td><td>‘<samp>filetype-1</samp>’</td></tr>
<tr><td></td><td></td><td>switch buffer to ‘<samp>filetype-1</samp>’ (defaults to <samp>.txt</samp>) file
and ‘<samp>refresh</samp>’</td></tr>
<tr><td><tt class="key">F8</tt></td><td><tt class="key">F3</tt></td><td>‘<samp>shell</samp>’</td></tr>
<tr><td></td><td></td><td>switch buffer to <samp>*shell*</samp></td></tr>
<tr><td><tt class="key">F9</tt></td><td><tt class="key">F9</tt></td><td><code>VIEWTABLE</code></td></tr>
<tr><td></td><td></td><td>open an interactive <code>PROC FSEDIT</code> session on the <acronym>SAS</acronym><!-- /@w -->
dataset near point</td></tr>
<tr><td><tt class="key">F10</tt></td><td><tt class="key">F10</tt></td><td>toggle-log</td></tr>
<tr><td></td><td></td><td>toggle <acronym>ESS[SAS]</acronym> for <samp>.log</samp> files; useful for certain
debugging situations</td></tr>
<tr><td><tt class="key">F11</tt></td><td><tt class="key">F11</tt></td><td>‘<samp>filetype-2</samp>’</td></tr>
<tr><td></td><td></td><td>switch buffer to ‘<samp>filetype-2</samp>’ (defaults to <samp>.dat</samp>) file
and ‘<samp>refresh</samp>’</td></tr>
<tr><td><tt class="key">F12</tt></td><td><tt class="key">F12</tt></td><td>viewgraph</td></tr>
<tr><td></td><td></td><td>open a <code>GSASFILE</code> near point for viewing either in emacs
or with an external viewer</td></tr>
<tr><td><kbd>C-<span class="key">F1</span></kbd></td><td><kbd>C-<span class="key">F1</span></kbd></td><td>rtf-portrait</td></tr>
<tr><td></td><td></td><td>create an <small>MS RTF</small> portrait file from the current buffer
with a file extension of <samp>.rtf</samp></td></tr>
<tr><td><kbd>C-<span class="key">F2</span></kbd></td><td><kbd>C-<span class="key">F2</span></kbd></td><td>rtf-landscape</td></tr>
<tr><td></td><td></td><td>create an <small>MS RTF</small> landscape file from the current buffer
with a file extension of <samp>.rtf</samp></td></tr>
<tr><td><kbd>C-<span class="key">F3</span></kbd></td><td><kbd>C-<span class="key">F8</span></kbd></td><td>submit-region</td></tr>
<tr><td></td><td></td><td>write region to <samp>ess-temp.sas</samp> and submit</td></tr>
<tr><td><kbd>C-<span class="key">F5</span></kbd></td><td><kbd>C-<span class="key">F6</span></kbd></td><td>append-to-log</td></tr>
<tr><td></td><td></td><td>append <samp>ess-temp.log</samp> to the current <samp>.log</samp> file</td></tr>
<tr><td><kbd>C-<span class="key">F6</span></kbd></td><td><kbd>C-<span class="key">F7</span></kbd></td><td>append-to-output</td></tr>
<tr><td></td><td></td><td>append <samp>ess-temp.lst</samp> to the current <samp>.lst</samp> file</td></tr>
<tr><td><kbd>C-<span class="key">F9</span></kbd></td><td><kbd>C-<span class="key">F9</span></kbd></td><td><code>INSIGHT</code></td></tr>
<tr><td></td><td></td><td>open an interactive <code>PROC INSIGHT</code> session on the <acronym>SAS</acronym><!-- /@w -->
dataset near point</td></tr>
<tr><td><kbd>C-<span class="key">F10</span></kbd></td><td><kbd>C-<span class="key">F10</span></kbd></td><td>toggle-listing</td></tr>
<tr><td></td><td></td><td>toggle <acronym>ESS[SAS]</acronym> for <samp>.lst</samp> files; useful for toggling
read-only</td></tr>
</table>
<p><code>SUBMIT</code>, <code>PROGRAM</code>, <code>LOG</code> and <code>OUTPUT</code> need no further
explanation since they mimic the <acronym>SAS</acronym><!-- /@w --> Display Manager commands and
related function key definitions. However, six other keys have been
provided for convenience and are described below.
</p>
<p>‘<samp>shell</samp>’ switches you to the <samp>*shell*</samp> buffer where you can
interact with your operating system. This is especially helpful if you
would like to kill a <acronym>SAS</acronym><!-- /@w --> batch job. You can specify a different buffer
name to associate with a <acronym>SAS</acronym><!-- /@w --> batch job (besides <samp>*shell*</samp>) with the
buffer-local variable <code>ess-sas-shell-buffer</code>. This allows you to have
multiple buffers running <acronym>SAS</acronym><!-- /@w --> batch jobs on multiple local/remote
computers that may rely on different methods specified by the buffer-local
variable <code>ess-sas-submit-method</code>.
</p>
<p><tt class="key">F2</tt> performs the ‘<samp>refresh</samp>’ operation on the current buffer.
‘<samp>refresh</samp>’ compares the buffer’s last modified date/time with the
file’s last modified date/time and replaces the buffer with the file if the
file is newer. This is the same operation that is automatically performed
when <code>LOG</code>, <code>OUTPUT</code>, ‘<samp>filetype-1</samp>’ or <tt class="key">F11</tt> are pressed.
</p>
<p>‘<samp>filetype-1</samp>’ switches you to a file with the same file name as your <samp>.sas</samp>
file, but with a different extension (<samp>.txt</samp> by default) and performs
‘<samp>refresh</samp>’. You can over-ride the default extension; for example in your
<samp>~/.emacs</samp> or <samp>~/.xemacs/init.el</samp> file:
</p><div class="example">
<pre class="example">(setq ess-sas-suffix-1 "csv") ; for example
</pre></div>
<p><tt class="key">F9</tt> will prompt you for the name of a permanent <acronym>SAS</acronym><!-- /@w --> dataset near
point to be opened for viewing by <code>PROC FSEDIT</code>. You can control the
<acronym>SAS</acronym><!-- /@w --> batch command-line with <code>ess-sas-data-view-submit-options</code>.
For controlling the <acronym>SAS</acronym><!-- /@w --> batch commands, you have the global variables
<code>ess-sas-data-view-libname</code> and
<code>ess-sas-data-view-fsview-command</code> as well as the buffer-local
variable <code>ess-sas-data-view-fsview-statement</code>. If you have your
<acronym>SAS</acronym><!-- /@w --> <code>LIBNAME</code> defined in <samp>~/autoexec.sas</samp>, then the defaults
for these variables should be sufficient.
</p>
<p>Similarly, <kbd><span class="nolinebreak">C-</span><span class="key">F9</span></kbd><!-- /@w --> will prompt you for the name of a permanent
<acronym>SAS</acronym><!-- /@w --> dataset near point to be opened for viewing by <code>PROC INSIGHT</code>.
You can control the <acronym>SAS</acronym><!-- /@w --> batch command-line with
<code>ess-sas-data-view-submit-options</code>. For controlling the <acronym>SAS</acronym><!-- /@w --> batch
commands, you have the global variables <code>ess-sas-data-view-libname</code>
and <code>ess-sas-data-view-insight-command</code> as well as the buffer-local
variable <code>ess-sas-data-view-insight-statement</code>.
</p>
<p><tt class="key">F10</tt> toggles <acronym>ESS[SAS]</acronym> mode for <samp>.log</samp> files which is off by default
(technically, it is <code>SAS-log-mode</code>, but it looks the same). The syntax
highlighting can be helpful in certain debugging situations, but large
<samp>.log</samp> files may take a long time to highlight.
</p>
<p><tt class="key">F11</tt> is the same as ‘<samp>filetype-1</samp>’ except it is <samp>.dat</samp> by default.
</p>
<p><tt class="key">F12</tt> will prompt you for the name of a <code>GSASFILE</code> near the point in <samp>.log</samp> to
be opened for viewing either with emacs or with an external viewer.
Depending on your version of emacs and the operating system you are
using, emacs may support <samp>.gif</samp> and <samp>.jpg</samp> files internally. You may need
to change the following variables for your own situation.
<code>ess-sas-graph-view-suffix-regexp</code> is a regular expression of supported
file types defined via file name extensions.
<code>ess-sas-graph-view-viewer-default</code> is the default external viewer for
your platform. <code>ess-sas-graph-view-viewer-alist</code> is an alist of
exceptions to the default; i.e. file types and their associated
viewers which will be used rather than the default viewer.
</p><div class="example">
<pre class="example">(setq ess-sas-graph-view-suffix-regexp (concat "[.]\\([eE]?[pP][sS]\\|"
"[pP][dD][fF]\\|[gG][iI][fF]\\|[jJ][pP][eE]?[gG]\\|"
"[tT][iI][fF][fF]?\\)")) ;; default
(setq ess-sas-graph-view-viewer-default "kodakimg") ;; Windows default
(setq ess-sas-graph-view-viewer-default "sdtimage") ;; Solaris default
(setq ess-sas-graph-view-viewer-alist
'(("[eE]?[pP][sS]" . "gv") ("[pP][dD][fF]" . "gv")) ;; default w/ gv
</pre></div>
<p><kbd><span class="nolinebreak">C-</span><span class="key">F2</span></kbd><!-- /@w --> produces US landscape by default, however, it can produce A4
landscape (first line for "global" key mapping, second for "local"):
</p><div class="example">
<pre class="example">(global-set-key [(control f2)] 'ess-sas-rtf-a4-landscape)
(define-key sas-mode-local-map [(control f2)] 'ess-sas-rtf-a4-landscape)
</pre></div>
<hr>
<a name="iESS_0028SAS_0029_002d_002dInteractive-SAS-processes"></a>
<div class="header">
<p>
Next: <a href="#iESS_0028SAS_0029_002d_002dCommon-problems" accesskey="n" rel="next">iESS(SAS)--Common problems</a>, Previous: <a href="#ESS_0028SAS_0029_002d_002dFunction-keys-for-batch-processing" accesskey="p" rel="prev">ESS(SAS)--Function keys for batch processing</a>, Up: <a href="#ESS-for-SAS" accesskey="u" rel="up">ESS for SAS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="iESS_005bSAS_005d_002d_002dInteractive-SAS-processes"></a>
<h3 class="section">13.6 iESS[SAS]–Interactive SAS processes</h3>
<p>Inferior <acronym>ESS</acronym> (i<acronym>ESS</acronym><!-- /@w -->) is the method for interfacing with interactive
statistical processes (programs). i<acronym>ESS[SAS]</acronym><!-- /@w --> is what is needed for
interactive <acronym>SAS</acronym><!-- /@w --> programming. i<acronym>ESS[SAS]</acronym><!-- /@w --> works best
with the <acronym>SAS</acronym><!-- /@w --> command-line option settings
<code>"-stdio -linesize 80 -noovp -nosyntaxcheck"</code>
(the default of <code>inferior-SAS-args</code>).
</p>
<div class="display">
<pre class="display"><code>-stdio</code>
required to make the redirection of stdio work
<code>-linesize 80</code>
keeps output lines from folding on standard terminals
<code>-noovp</code>
prevents error messages from printing 3 times
<code>-nosyntaxcheck</code>
permits recovery after syntax errors
</pre></div>
<p>To start up i<acronym>ESS[SAS]</acronym><!-- /@w --> mode, use:
</p><div class="example">
<pre class="example"> <kbd>M-x SAS</kbd><!-- /@w -->
</pre></div>
<p>The <samp>*SAS:1.log*</samp> buffer in <code>ESStr</code> mode corresponds to the file
<samp><var>foo</var>.log</samp> in <acronym>SAS</acronym><!-- /@w --> batch usage and to the ‘<samp>SAS: LOG</samp>’ window in the
<acronym>SAS</acronym><!-- /@w --> Display Manager. All commands submitted to <acronym>SAS</acronym><!-- /@w -->, informative
messages, warnings, and errors appear here.
</p>
<p>The <samp>*SAS:1.lst*</samp> buffer in <code>ESSlst</code> mode corresponds to the file
<samp><var>foo</var>.lst</samp> in <acronym>SAS</acronym><!-- /@w --> batch usage and to the ‘<samp>SAS: OUTPUT</samp>’ window in the
<acronym>SAS</acronym><!-- /@w --> Display Manager. All printed output appears in this window.
</p>
<p>The <samp>*SAS:1*</samp> buffer exists solely as a communications buffer.
The user should never use this buffer directly.
Files are edited in the <samp><var>foo</var>.sas</samp> buffer. The <kbd><span class="nolinebreak">C-c</span> <span class="nolinebreak">C-r</span></kbd><!-- /@w --> key in
<acronym>ESS[SAS]</acronym> is the functional equivalent of bringing a file into the
‘<samp>SAS: PROGRAM EDITOR</samp>’ window followed by <code>SUBMIT</code>.
</p>
<p>For example, open the file you want to work with.
</p><div class="example">
<pre class="example"><kbd>C-x C-f foo.sas</kbd><!-- /@w -->
</pre></div>
<p><samp><var>foo</var>.sas</samp> will be in <acronym>ESS[SAS]</acronym> mode. Edit as appropriate, and then start
up <acronym>SAS</acronym><!-- /@w --> with the cursor in the <samp><var>foo</var>.sas</samp> buffer.
</p><div class="example">
<pre class="example"><kbd>M-x SAS</kbd><!-- /@w -->
</pre></div>
<p>Four buffers will appear on screen:
</p><table>
<tr><td>Buffer</td><td>Mode</td><td>Description</td></tr>
<tr><td><samp><var>foo</var>.sas</samp></td><td><code><acronym>ESS[SAS]</acronym></code></td><td>your source file</td></tr>
<tr><td><samp>*SAS:1*</samp></td><td><code>i<acronym>ESS[SAS:1]</acronym><!-- /@w --></code></td><td>i<acronym>ESS</acronym><!-- /@w --> communication buffer</td></tr>
<tr><td><samp>*SAS:1.log*</samp></td><td><code>Shell ESStr []</code></td><td><acronym>SAS</acronym><!-- /@w --> log information</td></tr>
<tr><td><samp>*SAS:1.lst*</samp></td><td><code>Shell ESSlst []</code></td><td><acronym>SAS</acronym><!-- /@w --> listing information</td></tr>
</table>
<p>If you would prefer each of the four buffers to appear in its
own individual frame, you can arrange for that. Place the
cursor in the buffer displaying <samp><var>foo</var>.sas</samp>. Enter the
sequence <kbd><span class="nolinebreak">C-c</span> <span class="nolinebreak">C-w</span></kbd><!-- /@w -->. The cursor will normally be in buffer
<samp><var>foo</var>.sas</samp>. If not, put it there and <kbd><span class="nolinebreak">C-x</span> b <var>foo</var>.sas</kbd><!-- /@w -->.
</p>
<p>Send regions, lines, or the entire file contents to <acronym>SAS</acronym><!-- /@w -->
(regions are most useful: a highlighted region will normally
begin with the keywords <code>DATA</code> or <code>PROC</code> and end with
<code>RUN;</code>), <kbd><span class="nolinebreak">C-c</span> <span class="nolinebreak">C-r</span></kbd><!-- /@w -->.
</p>
<p>Information appears in the log buffer, analysis results in the
listing buffer. In case of errors, make the corrections in the
<samp><var>foo</var>.sas</samp> buffer and resubmit with another <kbd><span class="nolinebreak">C-c</span> <span class="nolinebreak">C-r</span></kbd><!-- /@w -->.
</p>
<p>At the end of the session you may save the log and listing
buffers with the usual <kbd><span class="nolinebreak">C-x</span> <span class="nolinebreak">C-s</span></kbd><!-- /@w --> commands. You will be prompted
for a file name. Typically, the names <samp><var>foo</var>.log</samp> and <samp><var>foo</var>.lst</samp>
will be used. You will almost certainly want to edit the saved
files before including them in a report. The files are
read-only by default. You can make them writable by the emacs
command <kbd><span class="nolinebreak">C-x</span> <span class="nolinebreak">C-q</span></kbd><!-- /@w -->.
</p>
<p>At the end of the session, the input file <samp><var>foo</var>.sas</samp> will
typically have been revised. You can save it. It can be used
later as the beginning of another i<acronym>ESS[SAS]</acronym><!-- /@w --> session. It can
also be used as a batch input file to <acronym>SAS</acronym><!-- /@w -->.
</p>
<p>The <samp>*SAS:1*</samp> buffer is strictly for <acronym>ESS</acronym> use. The user should
never need to read it or write to it. Refer to the <samp>.lst</samp> and
<samp>.log</samp> buffers for monitoring output!
</p>
<p>Troubleshooting: See <a href="#iESS_0028SAS_0029_002d_002dCommon-problems">iESS(SAS)--Common problems</a>.
</p>
<hr>
<a name="iESS_0028SAS_0029_002d_002dCommon-problems"></a>
<div class="header">
<p>
Next: <a href="#ESS_0028SAS_0029_002d_002dGraphics" accesskey="n" rel="next">ESS(SAS)--Graphics</a>, Previous: <a href="#iESS_0028SAS_0029_002d_002dInteractive-SAS-processes" accesskey="p" rel="prev">iESS(SAS)--Interactive SAS processes</a>, Up: <a href="#ESS-for-SAS" accesskey="u" rel="up">ESS for SAS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="iESS_005bSAS_005d_002d_002dCommon-problems"></a>
<h3 class="section">13.7 iESS[SAS]–Common problems</h3>
<ol>
<li> i<acronym>ESS[SAS]</acronym><!-- /@w --> does not work on Windows. In order to run <acronym>SAS</acronym><!-- /@w --> inside
an emacs buffer, it is necessary to start <acronym>SAS</acronym><!-- /@w --> with the <code>-stdio</code> option.
<acronym>SAS</acronym><!-- /@w --> does not support the <code>-stdio</code> option on Windows.
</li><li> If <kbd><span class="nolinebreak">M-x</span> SAS</kbd><!-- /@w --> gives errors upon startup, check the following:
<ul>
<li> you are running Windows: see 1.
</li><li> <samp>ess-sas-sh-command</samp> (from the <acronym>ESS</acronym> <samp>etc</samp> directory) needs to be
executable; too check, type <kbd><span class="nolinebreak">M-x</span> dired</kbd><!-- /@w -->; if not, fix it as follows,
type <kbd>M-:</kbd>, then at the minibuffer prompt ‘<samp>Eval:</samp>’<!-- /@w -->,
type <code>(set-file-modes "ess-sas-sh-command" 493)</code>.
</li><li> <code>sas</code> isn’t in your executable path; to verify, type
<kbd>M-:</kbd> and at the minibuffer prompt ‘<samp>Eval:</samp>’, type
<code>(executable-find "sas")</code>
</li></ul>
</li><li> <kbd><span class="nolinebreak">M-x</span> SAS</kbd><!-- /@w --> starts <acronym>SAS</acronym><!-- /@w --> Display<!-- /@w --> Manager. Probably, the command <code>sas</code>
on your system calls a shell script. In that case you will need to locate
the real <code>sas</code> executable and link to it.
You can execute the <acronym>UNIX</acronym> command:
<div class="example">
<pre class="example">find / -name sas -print
</pre></div>
<p>Now place a soft link to the real <code>sas</code> executable in your <code>~/bin</code>
directory, with for example
</p><div class="example">
<pre class="example">cd ~/bin
ln -s /usr/local/sas9/sas sas
</pre></div>
</li></ol>
<p>Check your <code>PATH</code> environment variable to confirm that
<code>~/bin</code> appears before the directory in which the <code>sas</code>
shell script appears.
</p>
<hr>
<a name="ESS_0028SAS_0029_002d_002dGraphics"></a>
<div class="header">
<p>
Next: <a href="#ESS_0028SAS_0029_002d_002dWindows" accesskey="n" rel="next">ESS(SAS)--Windows</a>, Previous: <a href="#iESS_0028SAS_0029_002d_002dCommon-problems" accesskey="p" rel="prev">iESS(SAS)--Common problems</a>, Up: <a href="#ESS-for-SAS" accesskey="u" rel="up">ESS for SAS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS_005bSAS_005d_002d_002dGraphics"></a>
<h3 class="section">13.8 ESS[SAS]–Graphics</h3>
<p>Output from a <acronym>SAS/GRAPH</acronym><!-- /@w --> <code>PROC</code> can be displayed in a <acronym>SAS/GRAPH</acronym><!-- /@w -->
window for <acronym>SAS</acronym><!-- /@w --> batch on Windows or for both <acronym>SAS</acronym><!-- /@w --> batch and interactive
with XWindows on <acronym>UNIX</acronym>. If you need to create graphics files and view
them with <tt class="key">F12</tt>, then include the following (either in
<samp><var>foo</var>.sas</samp> or in <samp>~/autoexec.sas</samp>):
</p><div class="example">
<pre class="example">filename gsasfile 'graphics.ps';
goptions device=ps gsfname=gsasfile gsfmode=append;
</pre></div>
<p><code>PROC PLOT</code> graphs can be viewed in the listing buffer. You may
wish to control the vertical spacing to allow the entire plot
to be visible on screen, for example:
</p><div class="example">
<pre class="example">proc plot;
plot a*b / vpos=25;
run;
</pre></div>
<hr>
<a name="ESS_0028SAS_0029_002d_002dWindows"></a>
<div class="header">
<p>
Previous: <a href="#ESS_0028SAS_0029_002d_002dGraphics" accesskey="p" rel="prev">ESS(SAS)--Graphics</a>, Up: <a href="#ESS-for-SAS" accesskey="u" rel="up">ESS for SAS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS_005bSAS_005d_002d_002dWindows"></a>
<h3 class="section">13.9 ESS[SAS]–Windows</h3>
<ul>
<li> i<acronym>ESS[SAS]</acronym><!-- /@w --> does not work on Windows. See <a href="#iESS_0028SAS_0029_002d_002dCommon-problems">iESS(SAS)--Common problems</a>.
</li><li> <acronym>ESS[SAS]</acronym> mode for editing <acronym>SAS</acronym><!-- /@w --> language files works very well.
See <a href="#ESS_0028SAS_0029_002d_002dEditing-files">ESS(SAS)--Editing files</a>.
</li><li> There are two execution options for <acronym>SAS</acronym><!-- /@w --> on Windows.
You can use batch. See <a href="#ESS_0028SAS_0029_002d_002dBatch-SAS-processes">ESS(SAS)--Batch SAS processes</a>.
<p>Or you can mark regions with the mouse and submit the code with
‘submit-region’ or paste them into <acronym>SAS</acronym><!-- /@w --> Display Manager.
</p>
</li></ul>
<hr>
<a name="ESS-for-BUGS"></a>
<div class="header">
<p>
Next: <a href="#ESS-for-JAGS" accesskey="n" rel="next">ESS for JAGS</a>, Previous: <a href="#ESS-for-SAS" accesskey="p" rel="prev">ESS for SAS</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS-for-BUGS-1"></a>
<h2 class="chapter">14 ESS for BUGS</h2>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#ESS_0028BUGS_0029_002d_002dModel-files" accesskey="1">ESS(BUGS)--Model files</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#ESS_0028BUGS_0029_002d_002dCommand-files" accesskey="2">ESS(BUGS)--Command files</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#ESS_0028BUGS_0029_002d_002dLog-files" accesskey="3">ESS(BUGS)--Log files</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<p><acronym>ESS[BUGS]</acronym> was originally designed for use with BUGS software. Later,
it evolved to support JAGS as a dialect of the BUGS language via
<acronym>ESS[JAGS]</acronym>, however, <acronym>ESS[JAGS]</acronym> is documented in the section Help
for JAGS. <acronym>ESS[BUGS]</acronym> provides 5 features. First, BUGS syntax is
described to allow for proper fontification of statements,
distributions, functions, commands and comments in BUGS model files,
command files and log files. Second, <acronym>ESS</acronym> creates templates for the
command file from the model file so that a BUGS batch process can be
defined by a single file. Third, <acronym>ESS</acronym> provides a BUGS batch script
that allows <acronym>ESS</acronym> to set BUGS batch parameters. Fourth, key sequences
are defined to create a command file and submit a BUGS batch process.
Lastly, interactive submission of BUGS commands is also supported.
</p>
<hr>
<a name="ESS_0028BUGS_0029_002d_002dModel-files"></a>
<div class="header">
<p>
Next: <a href="#ESS_0028BUGS_0029_002d_002dCommand-files" accesskey="n" rel="next">ESS(BUGS)--Command files</a>, Previous: <a href="#ESS-for-BUGS" accesskey="p" rel="prev">ESS for BUGS</a>, Up: <a href="#ESS-for-BUGS" accesskey="u" rel="up">ESS for BUGS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS_005bBUGS_005d_002d_002dModel-files"></a>
<h3 class="section">14.1 ESS[BUGS]–Model files</h3>
<p>Model files with the <samp>.bug</samp> extension are edited in <acronym>ESS[BUGS]</acronym>
mode if <code>(require 'ess-bugs-d)</code> was performed. Model files with
the <samp>.jag</samp> extension are edited in <acronym>ESS[JAGS]</acronym> mode if
<code>(require 'ess-jags-d)</code> was performed. Three keys are bound for
your use in <acronym>ESS[BUGS]</acronym>, <kbd>F2</kbd>, <kbd>C-c C-c</kbd> and <kbd>=</kbd>. <kbd>F2</kbd>
performs the same action as it does in <acronym>ESS[SAS]</acronym>,
See <a href="#ESS_0028SAS_0029_002d_002dFunction-keys-for-batch-processing">ESS(SAS)--Function keys for batch processing</a>. <kbd>C-c C-c</kbd>
performs the function <code>ess-bugs-next-action</code> which you will use a
lot. Pressing it in an empty buffer for a model file will produce a
template for you. <kbd>=</kbd> inserts the set operator, <code><-</code>.
</p>
<hr>
<a name="ESS_0028BUGS_0029_002d_002dCommand-files"></a>
<div class="header">
<p>
Next: <a href="#ESS_0028BUGS_0029_002d_002dLog-files" accesskey="n" rel="next">ESS(BUGS)--Log files</a>, Previous: <a href="#ESS_0028BUGS_0029_002d_002dModel-files" accesskey="p" rel="prev">ESS(BUGS)--Model files</a>, Up: <a href="#ESS-for-BUGS" accesskey="u" rel="up">ESS for BUGS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS_005bBUGS_005d_002d_002dCommand-files"></a>
<h3 class="section">14.2 ESS[BUGS]–Command files</h3>
<p>To avoid extension name collision, <samp>.bmd</samp> is used for BUGS
command files and <samp>.jmd</samp> for JAGS command files. When you have
finished editing your model file and press <kbd>C-c C-c</kbd>, a command
file is created if one does not already exist.
When you are finished editing your command file, pressing <kbd>C-c C-c</kbd>
again will submit your command file as a batch job.
</p>
<hr>
<a name="ESS_0028BUGS_0029_002d_002dLog-files"></a>
<div class="header">
<p>
Previous: <a href="#ESS_0028BUGS_0029_002d_002dCommand-files" accesskey="p" rel="prev">ESS(BUGS)--Command files</a>, Up: <a href="#ESS-for-BUGS" accesskey="u" rel="up">ESS for BUGS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS_005bBUGS_005d_002d_002dLog-files"></a>
<h3 class="section">14.3 ESS[BUGS]–Log files</h3>
<p>To avoid extension name collision, <samp>.bog</samp> is used for BUGS log
files. The command line generated by <acronym>ESS</acronym> creates the
<samp>.bog</samp> transcript file.
Similarly, <samp>.jog</samp> is used for JAGS log files.
</p>
<hr>
<a name="ESS-for-JAGS"></a>
<div class="header">
<p>
Next: <a href="#Mailing-lists_002fbug-reports" accesskey="n" rel="next">Mailing lists/bug reports</a>, Previous: <a href="#ESS-for-BUGS" accesskey="p" rel="prev">ESS for BUGS</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS-for-JAGS-1"></a>
<h2 class="chapter">15 ESS for JAGS</h2>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#ESS_0028JAGS_0029_002d_002dModel-files" accesskey="1">ESS(JAGS)--Model files</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#ESS_0028JAGS_0029_002d_002dCommand-files" accesskey="2">ESS(JAGS)--Command files</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#ESS_0028JAGS_0029_002d_002dLog-files" accesskey="3">ESS(JAGS)--Log files</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<p><acronym>ESS[BUGS]</acronym> was originally designed for use with BUGS software.
Later, it evolved to support JAGS as a dialect of the
BUGS language via <acronym>ESS[JAGS]</acronym>. Since BUGS and JAGS are quite
similar, <acronym>ESS[BUGS]</acronym> and <acronym>ESS[JAGS]</acronym> are necessarily similar.
<acronym>ESS[JAGS]</acronym> provides 4 features. First, JAGS syntax is described to
allow for proper fontification of statements, distributions,
functions, commands and comments in JAGS model files, command files
and log files. Second, <acronym>ESS</acronym> creates templates for the command file
from the model file so that a JAGS batch process can be defined by a
single file. Third, <acronym>ESS</acronym> provides a JAGS batch script that allows <acronym>ESS</acronym>
to set JAGS batch parameters. Fourth, key sequences are defined to
create a command file and submit a JAGS batch process.
</p>
<hr>
<a name="ESS_0028JAGS_0029_002d_002dModel-files"></a>
<div class="header">
<p>
Next: <a href="#ESS_0028JAGS_0029_002d_002dCommand-files" accesskey="n" rel="next">ESS(JAGS)--Command files</a>, Previous: <a href="#ESS-for-JAGS" accesskey="p" rel="prev">ESS for JAGS</a>, Up: <a href="#ESS-for-JAGS" accesskey="u" rel="up">ESS for JAGS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS_005bJAGS_005d_002d_002dModel-files"></a>
<h3 class="section">15.1 ESS[JAGS]–Model files</h3>
<p>Model files with the <samp>.bug</samp> extension are edited in <acronym>ESS[BUGS]</acronym> mode
if <code>(require 'ess-bugs-d)</code> was performed or edited in <acronym>ESS[JAGS]</acronym> mode
if <code>(require 'ess-jags-d)</code>.
Three keys are bound for your use in <acronym>ESS[BUGS]</acronym>, <kbd>F2</kbd>, <kbd>C-c C-c</kbd> and <kbd>=</kbd>.
<kbd>F2</kbd> performs the same action as it does in <acronym>ESS[SAS]</acronym>,
See <a href="#ESS_0028SAS_0029_002d_002dFunction-keys-for-batch-processing">ESS(SAS)--Function keys for batch processing</a>. <kbd>C-c C-c</kbd> performs the
function <code>ess-bugs-next-action</code> which you will use a lot. Pressing it
in an empty buffer for a model file will produce a template for you. <kbd>=</kbd>
inserts the set operator, <code><-</code>.
</p>
<p><acronym>ESS[JAGS]</acronym> does not support "replacement" variables which were part of
<acronym>ESS[BUGS]</acronym>. Although, "replacement" variables are an extremely convenient
feature, creating the elisp code for their operation was challenging. So, a
more elisp-ish approach was adopted for <acronym>ESS[JAGS]</acronym>: elisp local variables.
These variables are
created as part of the template, i.e. with the first press of <kbd>C-c C-c</kbd>
in an empty buffer. For your <samp>.bug</samp> file, they are named
<code>ess-jags-chains</code>, <code>ess-jags-monitor</code>, <code>ess-jags-thin</code>,
<code>ess-jags-burnin</code> and <code>ess-jags-update</code>;
they appear in the <code>Local Variables</code> section. When you are
finished editing your model file, pressing <kbd>C-c C-c</kbd> will perform
the necessary actions to build your command file for you.
</p>
<p>The <code>ess-jags-chains</code> variable is the number of chains that
you want to initialize and sample from; defaults to 1.
The <code>ess-jags-monitor</code> variable is a list of variables
that you want monitored: encase each variable in double quotes.
When you press <kbd>C-c C-c</kbd>, the
appropriate statements are created in the command file to monitor the
list of variables. By default, no variables are explicitly monitored
which means JAGS will implicitly monitor all “default” variables.
The <code>ess-jags-thin</code> variable is the thinning parameter.
By default, the thinning parameter is set to 1, i.e. no thinning.
The <code>ess-jags-burnin</code> variable is the number of initial samples
to discard. By default, the burnin parameter is set to 10000.
The <code>ess-jags-update</code> variable is the number of post-burnin samples
to keep. By default, the update parameter is set to 10000. Both
<code>ess-jags-burnin</code> and <code>ess-jags-update</code> are multiplied by
<code>ess-jags-thin</code> since JAGS does not do it automatically.
</p>
<hr>
<a name="ESS_0028JAGS_0029_002d_002dCommand-files"></a>
<div class="header">
<p>
Next: <a href="#ESS_0028JAGS_0029_002d_002dLog-files" accesskey="n" rel="next">ESS(JAGS)--Log files</a>, Previous: <a href="#ESS_0028JAGS_0029_002d_002dModel-files" accesskey="p" rel="prev">ESS(JAGS)--Model files</a>, Up: <a href="#ESS-for-JAGS" accesskey="u" rel="up">ESS for JAGS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS_005bJAGS_005d_002d_002dCommand-files"></a>
<h3 class="section">15.2 ESS[JAGS]–Command files</h3>
<p>To avoid extension name collision, <samp>.bmd</samp> is used for BUGS
command files and <samp>.jmd</samp> for JAGS command files. For your
<samp>.jmd</samp> file, there is only one variable, <code>ess-jags-command</code>,
in the <code>Local Variables</code> section. When you have
finished editing your model file and press <kbd>C-c C-c</kbd>, a command
file is created if one does not already exist.
When you are finished editing your command file, pressing <kbd>C-c C-c</kbd>
again will submit your command file as a batch job.
The <code>ess-jags-command</code> variable allows you to specify a different
JAGS program to use to run your model; defaults to “jags”.
</p>
<hr>
<a name="ESS_0028JAGS_0029_002d_002dLog-files"></a>
<div class="header">
<p>
Previous: <a href="#ESS_0028JAGS_0029_002d_002dCommand-files" accesskey="p" rel="prev">ESS(JAGS)--Command files</a>, Up: <a href="#ESS-for-JAGS" accesskey="u" rel="up">ESS for JAGS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ESS_005bJAGS_005d_002d_002dLog-files"></a>
<h3 class="section">15.3 ESS[JAGS]–Log files</h3>
<p>The <samp>.jog</samp> extension is used for JAGS log
files. You may find <kbd>F2</kbd> useful to refresh the <samp>.jog</samp> if the batch
process over-writes or appends it.
</p>
<hr>
<a name="Mailing-lists_002fbug-reports"></a>
<div class="header">
<p>
Next: <a href="#Customization" accesskey="n" rel="next">Customization</a>, Previous: <a href="#ESS-for-JAGS" accesskey="p" rel="prev">ESS for JAGS</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Bugs-and-Bug-Reporting_002c-Mailing-Lists"></a>
<h2 class="chapter">16 Bugs and Bug Reporting, Mailing Lists</h2>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Bugs" accesskey="1">Bugs</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Reporting-Bugs" accesskey="2">Reporting Bugs</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Mailing-Lists" accesskey="3">Mailing Lists</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Help-with-emacs" accesskey="4">Help with emacs</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Bugs"></a>
<div class="header">
<p>
Next: <a href="#Reporting-Bugs" accesskey="n" rel="next">Reporting Bugs</a>, Up: <a href="#Mailing-lists_002fbug-reports" accesskey="u" rel="up">Mailing lists/bug reports</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Bugs-1"></a>
<h3 class="section">16.1 Bugs</h3>
<a name="index-bugs"></a>
<ul>
<li> Commands like <code>ess-display-help-on-object</code> and list completion
cannot be used while the user is entering a multi-line command. The
only real fix in this situation is to use another ESS process.
</li><li> The <code>ess-eval-</code> commands can leave point in the ESS process
buffer in the wrong place when point is at the same position as the last
process output. This proves difficult to fix, in general, as we need to
consider all <em>windows</em> with <code>window-point</code> at the right place.
</li><li> It’s possible to clear the modification flag (say, by saving the buffer)
with the edit buffer not having been loaded into S.
</li><li> Backup files can sometimes be left behind, even when
<code>ess-keep-dump-files</code> is <code>nil</code>.
</li><li> Passing an incomplete S expression to <code>ess-execute</code> causes ESS
to hang.
</li><li> The function-based commands don’t always work as expected on functions
whose body is not a parenthesized or compound expression, and don’t even
recognize anonymous functions (i.e. functions not assigned to any
variable).
</li><li> Multi-line commands could be handled better by the command history
mechanism.
</li><li> Changes to the continutation prompt in R (e.g.
<code>options(continue = " ")</code>) are not automatically detected by ESS.
Hence, for now, the best thing is not to change the continuation prompt.
If you do change the continuation prompt, you will need to change
accordingly the value of <code>inferior-ess-secondary-prompt</code> in
<code>R-customize-alist</code>.
</li></ul>
<hr>
<a name="Reporting-Bugs"></a>
<div class="header">
<p>
Next: <a href="#Mailing-Lists" accesskey="n" rel="next">Mailing Lists</a>, Previous: <a href="#Bugs" accesskey="p" rel="prev">Bugs</a>, Up: <a href="#Mailing-lists_002fbug-reports" accesskey="u" rel="up">Mailing lists/bug reports</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Reporting-Bugs-1"></a>
<h3 class="section">16.2 Reporting Bugs</h3>
<a name="index-bug-reports"></a>
<a name="index-ess_002dsubmit_002dbug_002dreport"></a>
<p>Please send bug reports, suggestions etc. to
<a href="mailto:ESS-bugs@stat.math.ethz.ch">ESS-bugs@stat.math.ethz.ch</a>
</p>
<p>The easiest way to do this is within Emacs by typing
</p>
<p><kbd>M-x ess-submit-bug-report</kbd>
</p>
<p>This also gives the maintainers valuable information about your
installation which may help us to identify or even fix the bug.
</p>
<p>If Emacs reports an error, backtraces can help us debug the problem.
Type "M-x set-variable RET debug-on-error RET t RET". Then run the
command that causes the error and you should see a *Backtrace* buffer
containing debug information; send us that buffer.
</p>
<p>Note that comments, suggestions, words of praise and large cash
donations are also more than welcome.
</p>
<hr>
<a name="Mailing-Lists"></a>
<div class="header">
<p>
Next: <a href="#Help-with-emacs" accesskey="n" rel="next">Help with emacs</a>, Previous: <a href="#Reporting-Bugs" accesskey="p" rel="prev">Reporting Bugs</a>, Up: <a href="#Mailing-lists_002fbug-reports" accesskey="u" rel="up">Mailing lists/bug reports</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Mailing-Lists-1"></a>
<h3 class="section">16.3 Mailing Lists</h3>
<p>There is a mailing list for discussions and announcements relating to
ESS. Join the list by sending an e-mail with "subscribe ess-help" (or
"help") in the body to <a href="mailto:ess-help-request@stat.math.ethz.ch">ess-help-request@stat.math.ethz.ch</a>;
contributions to the list may be mailed to
<a href="mailto:ess-help@stat.math.ethz.ch">ess-help@stat.math.ethz.ch</a>. Rest assured, this is a fairly
low-volume mailing list.
</p>
<p>The purposes of the mailing list include
</p>
<ul>
<li> helping users of ESS to get along with it.
</li><li> discussing aspects of using ESS on Emacs and XEmacs.
</li><li> suggestions for improvements.
</li><li> announcements of new releases of ESS.
</li><li> posting small patches to ESS.
</li></ul>
<hr>
<a name="Help-with-emacs"></a>
<div class="header">
<p>
Previous: <a href="#Mailing-Lists" accesskey="p" rel="prev">Mailing Lists</a>, Up: <a href="#Mailing-lists_002fbug-reports" accesskey="u" rel="up">Mailing lists/bug reports</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Help-with-emacs-1"></a>
<h3 class="section">16.4 Help with emacs</h3>
<p>Emacs is a complex editor with many abilities that we do not have space
to describe here. If you have problems with other features of emacs
(e.g. printing), there are several sources to consult, including the
emacs FAQs (try <kbd>M-x xemacs-www-faq</kbd> or <kbd>M-x view-emacs-FAQ</kbd>)
and EmacsWiki (<a href="http://www.emacswiki.org">http://www.emacswiki.org</a>). Please consult them
before asking on the mailing list about issues that are not specific to
ESS.
</p>
<hr>
<a name="Customization"></a>
<div class="header">
<p>
Next: <a href="#Indices" accesskey="n" rel="next">Indices</a>, Previous: <a href="#Mailing-lists_002fbug-reports" accesskey="p" rel="prev">Mailing lists/bug reports</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Customizing-ESS"></a>
<h2 class="appendix">Appendix A Customizing ESS</h2>
<a name="index-customization"></a>
<p>ESS can be easily customized to your taste simply by including the
appropriate lines in your <samp>.emacs</samp> file. There are numerous
variables which affect the behavior of ESS in certain situations which
can be modified to your liking. Keybindings may be set or changed to
your preferences, and for per-buffer customizations hooks are also
available.
</p>
<p>Most of these variables can be viewed and set using the Custom facility
within Emacs. Type <kbd>M-x customize-group RET ess RET</kbd> to see all the
ESS variables that can be customized. Variables are grouped by subject
to make it easy to find related variables.
</p>
<hr>
<a name="Indices"></a>
<div class="header">
<p>
Previous: <a href="#Customization" accesskey="p" rel="prev">Customization</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Indices-1"></a>
<h2 class="unnumbered">Indices</h2>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Key-index" accesskey="1">Key index</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Function-and-program-index" accesskey="2">Function and program index</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Variable-index" accesskey="3">Variable index</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Concept-index" accesskey="4">Concept index</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Key-index"></a>
<div class="header">
<p>
Next: <a href="#Function-and-program-index" accesskey="n" rel="next">Function and program index</a>, Up: <a href="#Indices" accesskey="u" rel="up">Indices</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Key-index-1"></a>
<h3 class="unnumberedsec">Key index</h3>
<table><tr><th valign="top">Jump to: </th><td><a class="summary-letter" href="#Key-index_ky_symbol-1"><b>,</b></a>
<a class="summary-letter" href="#Key-index_ky_symbol-2"><b>{</b></a>
<a class="summary-letter" href="#Key-index_ky_symbol-3"><b>}</b></a>
<br>
<a class="summary-letter" href="#Key-index_ky_letter-C"><b>C</b></a>
<a class="summary-letter" href="#Key-index_ky_letter-E"><b>E</b></a>
<a class="summary-letter" href="#Key-index_ky_letter-M"><b>M</b></a>
<a class="summary-letter" href="#Key-index_ky_letter-R"><b>R</b></a>
<a class="summary-letter" href="#Key-index_ky_letter-T"><b>T</b></a>
</td></tr></table>
<table class="index-ky" border="0">
<tr><td></td><th align="left">Index Entry</th><td> </td><th align="left"> Section</th></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Key-index_ky_symbol-1">,</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-_002c"><code>,</code></a>:</td><td> </td><td valign="top"><a href="#Handy-commands">Handy commands</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Key-index_ky_symbol-2">{</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-_007b"><code>{</code></a>:</td><td> </td><td valign="top"><a href="#Indenting">Indenting</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Key-index_ky_symbol-3">}</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-_007d"><code>}</code></a>:</td><td> </td><td valign="top"><a href="#Indenting">Indenting</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Key-index_ky_letter-C">C</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-_002e"><code>C-c .</code></a>:</td><td> </td><td valign="top"><a href="#Styles">Styles</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002d_002e-a"><code>C-c C-. a</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002d_002e-d"><code>C-c C-. d</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002d_002e-H"><code>C-c C-. H</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002d_002e-l"><code>C-c C-. l</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002d_002e-m"><code>C-c C-. m</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002d_002e-o"><code>C-c C-. o</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002d_002e-r"><code>C-c C-. r</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002d_002e-s"><code>C-c C-. s</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002d_002e-u"><code>C-c C-. u</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002d_002e-w"><code>C-c C-. w</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dC-C_002db"><code>C-C C-b</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002dc"><code>C-c C-c</code></a>:</td><td> </td><td valign="top"><a href="#Other">Other</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dC-C_002dc"><code>C-C C-c</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002de-C_002dd"><code>C-c C-e C-d</code></a>:</td><td> </td><td valign="top"><a href="#Edit-buffer">Edit buffer</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dC-C_002df"><code>C-C C-f</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dC-C_002dj"><code>C-C C-j</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002dl"><code>C-c C-l</code></a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002do-C_002dc"><code>C-c C-o C-c</code></a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002do-C_002dh"><code>C-c C-o C-h</code></a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002do-C_002do"><code>C-c C-o C-o</code></a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002do-C_002dr"><code>C-c C-o C-r</code></a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002do-C_002dt"><code>C-c C-o C-t</code></a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002do-n"><code>C-c C-o n</code></a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002do-p"><code>C-c C-o p</code></a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002dq"><code>C-c C-q</code></a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dC-C_002dr"><code>C-C C-r</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002ds"><code>C-c C-s</code></a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002dt-C_002da"><code>C-c C-t C-a</code></a>:</td><td> </td><td valign="top"><a href="#ESS-developer">ESS developer</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002dt-C_002dr"><code>C-c C-t C-r</code></a>:</td><td> </td><td valign="top"><a href="#ESS-developer">ESS developer</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002dt-C_002dt"><code>C-c C-t C-t</code></a>:</td><td> </td><td valign="top"><a href="#ESS-developer">ESS developer</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002dt-l"><code>C-c C-t l</code></a>:</td><td> </td><td valign="top"><a href="#ESS-developer">ESS developer</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002dv"><code>C-c C-v</code></a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002dw"><code>C-c C-w</code></a>:</td><td> </td><td valign="top"><a href="#Clean">Clean</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002dx"><code>C-c C-x</code></a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-C_002dz"><code>C-c C-z</code></a>:</td><td> </td><td valign="top"><a href="#Other">Other</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dC-M_002db"><code>C-C M-b</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dC-M_002df"><code>C-C M-f</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dC-M_002dj"><code>C-C M-j</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dC-M_002dr"><code>C-C M-r</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-RET"><code>C-c RET</code></a>:</td><td> </td><td valign="top"><a href="#Resubmit">Resubmit</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-_0060"><code>C-c `</code></a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dc-_0060-1"><code>C-c `</code></a>:</td><td> </td><td valign="top"><a href="#Error-Checking">Error Checking</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dj"><code>C-j</code></a>:</td><td> </td><td valign="top"><a href="#Indenting">Indenting</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dM_002da"><code>C-M-a</code></a>:</td><td> </td><td valign="top"><a href="#Other-edit-buffer-commands">Other edit buffer commands</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dM_002de"><code>C-M-e</code></a>:</td><td> </td><td valign="top"><a href="#Other-edit-buffer-commands">Other edit buffer commands</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dM_002dh"><code>C-M-h</code></a>:</td><td> </td><td valign="top"><a href="#Other-edit-buffer-commands">Other edit buffer commands</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dM_002dq"><code>C-M-q</code></a>:</td><td> </td><td valign="top"><a href="#Indenting">Indenting</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dM_002dx"><code>C-M-x</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-C_002dx-_0060"><code>C-x `</code></a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Key-index_ky_letter-E">E</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-ESC-C_002da"><code>ESC C-a</code></a>:</td><td> </td><td valign="top"><a href="#Other-edit-buffer-commands">Other edit buffer commands</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ESC-C_002de"><code>ESC C-e</code></a>:</td><td> </td><td valign="top"><a href="#Other-edit-buffer-commands">Other edit buffer commands</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ESC-C_002dh"><code>ESC C-h</code></a>:</td><td> </td><td valign="top"><a href="#Other-edit-buffer-commands">Other edit buffer commands</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ESC-C_002dq"><code>ESC C-q</code></a>:</td><td> </td><td valign="top"><a href="#Indenting">Indenting</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Key-index_ky_letter-M">M</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-M_002d_003b"><code>M-;</code></a>:</td><td> </td><td valign="top"><a href="#Indenting">Indenting</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-M_002d_003f"><code>M-?</code></a>:</td><td> </td><td valign="top"><a href="#Object-names">Object names</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-M_002dC_002dq"><code>M-C-q</code></a>:</td><td> </td><td valign="top"><a href="#Indenting">Indenting</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-M_002dn-l"><code>M-n l</code></a>:</td><td> </td><td valign="top"><a href="#Sweave-and-AUCTeX">Sweave and AUCTeX</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-M_002dn-P"><code>M-n P</code></a>:</td><td> </td><td valign="top"><a href="#Sweave-and-AUCTeX">Sweave and AUCTeX</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-M_002dn-s"><code>M-n s</code></a>:</td><td> </td><td valign="top"><a href="#Sweave-and-AUCTeX">Sweave and AUCTeX</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-M_002dRET"><code>M-RET</code></a>:</td><td> </td><td valign="top"><a href="#Resubmit">Resubmit</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Key-index_ky_letter-R">R</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-RET"><code>RET</code></a>:</td><td> </td><td valign="top"><a href="#Command_002dline-editing">Command-line editing</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-RET-1"><code>RET</code></a>:</td><td> </td><td valign="top"><a href="#Resubmit">Resubmit</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Key-index_ky_letter-T">T</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-TAB"><code>TAB</code></a>:</td><td> </td><td valign="top"><a href="#Indenting">Indenting</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
</table>
<table><tr><th valign="top">Jump to: </th><td><a class="summary-letter" href="#Key-index_ky_symbol-1"><b>,</b></a>
<a class="summary-letter" href="#Key-index_ky_symbol-2"><b>{</b></a>
<a class="summary-letter" href="#Key-index_ky_symbol-3"><b>}</b></a>
<br>
<a class="summary-letter" href="#Key-index_ky_letter-C"><b>C</b></a>
<a class="summary-letter" href="#Key-index_ky_letter-E"><b>E</b></a>
<a class="summary-letter" href="#Key-index_ky_letter-M"><b>M</b></a>
<a class="summary-letter" href="#Key-index_ky_letter-R"><b>R</b></a>
<a class="summary-letter" href="#Key-index_ky_letter-T"><b>T</b></a>
</td></tr></table>
<hr>
<a name="Function-and-program-index"></a>
<div class="header">
<p>
Next: <a href="#Variable-index" accesskey="n" rel="next">Variable index</a>, Previous: <a href="#Key-index" accesskey="p" rel="prev">Key index</a>, Up: <a href="#Indices" accesskey="u" rel="up">Indices</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Function-and-program-index-1"></a>
<h3 class="unnumberedsec">Function and program index</h3>
<table><tr><th valign="top">Jump to: </th><td><a class="summary-letter" href="#Function-and-program-index_fn_letter-B"><b>B</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-C"><b>C</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-D"><b>D</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-E"><b>E</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-F"><b>F</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-I"><b>I</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-M"><b>M</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-N"><b>N</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-O"><b>O</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-P"><b>P</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-Q"><b>Q</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-S"><b>S</b></a>
</td></tr></table>
<table class="index-fn" border="0">
<tr><td></td><th align="left">Index Entry</th><td> </td><th align="left"> Section</th></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-program-index_fn_letter-B">B</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-backward_002dkill_002dword"><code>backward-kill-word</code></a>:</td><td> </td><td valign="top"><a href="#Command_002dline-editing">Command-line editing</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-program-index_fn_letter-C">C</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-comint_002dbackward_002dmatching_002dinput"><code>comint-backward-matching-input</code></a>:</td><td> </td><td valign="top"><a href="#Process-buffer-motion">Process buffer motion</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-comint_002dbol"><code>comint-bol</code></a>:</td><td> </td><td valign="top"><a href="#Command_002dline-editing">Command-line editing</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-comint_002dcopy_002dold_002dinput"><code>comint-copy-old-input</code></a>:</td><td> </td><td valign="top"><a href="#Transcript-resubmit">Transcript resubmit</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-comint_002ddynamic_002dcomplete"><code>comint-dynamic-complete</code></a>:</td><td> </td><td valign="top"><a href="#Object-names">Object names</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-comint_002dforward_002dmatching_002dinput"><code>comint-forward-matching-input</code></a>:</td><td> </td><td valign="top"><a href="#Process-buffer-motion">Process buffer motion</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-comint_002dhistory_002disearch_002dbackward_002dregexp"><code>comint-history-isearch-backward-regexp</code></a>:</td><td> </td><td valign="top"><a href="#Command-History">Command History</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-comint_002dinterrupt_002dsubjob"><code>comint-interrupt-subjob</code></a>:</td><td> </td><td valign="top"><a href="#Other">Other</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-comint_002dkill_002dinput"><code>comint-kill-input</code></a>:</td><td> </td><td valign="top"><a href="#Command_002dline-editing">Command-line editing</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-comint_002dkill_002doutput"><code>comint-kill-output</code></a>:</td><td> </td><td valign="top"><a href="#Last-command">Last command</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-comint_002dnext_002dinput"><code>comint-next-input</code></a>:</td><td> </td><td valign="top"><a href="#Process-buffer-motion">Process buffer motion</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-comint_002dnext_002dinput-1"><code>comint-next-input</code></a>:</td><td> </td><td valign="top"><a href="#Command-History">Command History</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-comint_002dnext_002dmatching_002dinput_002dfrom_002dinput"><code>comint-next-matching-input-from-input</code></a>:</td><td> </td><td valign="top"><a href="#Command-History">Command History</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-comint_002dprevious_002dinput"><code>comint-previous-input</code></a>:</td><td> </td><td valign="top"><a href="#Process-buffer-motion">Process buffer motion</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-comint_002dprevious_002dinput-1"><code>comint-previous-input</code></a>:</td><td> </td><td valign="top"><a href="#Command-History">Command History</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-comint_002dprevious_002dmatching_002dinput_002dfrom_002dinput"><code>comint-previous-matching-input-from-input</code></a>:</td><td> </td><td valign="top"><a href="#Command-History">Command History</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-comint_002dshow_002doutput"><code>comint-show-output</code></a>:</td><td> </td><td valign="top"><a href="#Last-command">Last command</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-program-index_fn_letter-D">D</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-dump_0028_0029">dump()</a>:</td><td> </td><td valign="top"><a href="#Edit-buffer">Edit buffer</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-program-index_fn_letter-E">E</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dchange_002ddirectory"><code>ess-change-directory</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dcleanup"><code>ess-cleanup</code></a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dcleanup-1"><code>ess-cleanup</code></a>:</td><td> </td><td valign="top"><a href="#Help">Help</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002ddescribe_002dhelp_002dmode"><code>ess-describe-help-mode</code></a>:</td><td> </td><td valign="top"><a href="#Help">Help</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002ddeveloper"><code>ess-developer</code></a>:</td><td> </td><td valign="top"><a href="#ESS-developer">ESS developer</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002ddeveloper_002dadd_002dpackage"><code>ess-developer-add-package</code></a>:</td><td> </td><td valign="top"><a href="#ESS-developer">ESS developer</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002ddeveloper_002dload_002dpackage"><code>ess-developer-load-package</code></a>:</td><td> </td><td valign="top"><a href="#ESS-developer">ESS developer</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002ddeveloper_002dremove_002dpackage"><code>ess-developer-remove-package</code></a>:</td><td> </td><td valign="top"><a href="#ESS-developer">ESS developer</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002ddisplay_002dhelp_002don_002dobject"><code>ess-display-help-on-object</code></a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002ddisplay_002dhelp_002don_002dobject-1"><code>ess-display-help-on-object</code></a>:</td><td> </td><td valign="top"><a href="#Help">Help</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002ddisplay_002dhelp_002don_002dobject-2"><code>ess-display-help-on-object</code></a>:</td><td> </td><td valign="top"><a href="#Help">Help</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002ddump_002dobject_002dinto_002dedit_002dbuffer"><code>ess-dump-object-into-edit-buffer</code></a>:</td><td> </td><td valign="top"><a href="#Edit-buffer">Edit buffer</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002delectric_002dbrace"><code>ess-electric-brace</code></a>:</td><td> </td><td valign="top"><a href="#Indenting">Indenting</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002deval_002dbuffer"><code>ess-eval-buffer</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002deval_002dbuffer_002dand_002dgo"><code>ess-eval-buffer-and-go</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002deval_002dfunction"><code>ess-eval-function</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002deval_002dfunction_002dand_002dgo"><code>ess-eval-function-and-go</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002deval_002dline"><code>ess-eval-line</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002deval_002dline_002dand_002dgo"><code>ess-eval-line-and-go</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002deval_002dline_002dand_002dstep"><code>ess-eval-line-and-step</code></a>:</td><td> </td><td valign="top"><a href="#Help">Help</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002deval_002dregion"><code>ess-eval-region</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002deval_002dregion-1"><code>ess-eval-region</code></a>:</td><td> </td><td valign="top"><a href="#Help">Help</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002deval_002dregion_002dand_002dgo"><code>ess-eval-region-and-go</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002deval_002dregion_002dor_002dfunction_002dor_002dparagraph"><code>ess-eval-region-or-function-or-paragraph</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002deval_002dregion_002dor_002dfunction_002dor_002dparagraph_002dand_002dstep"><code>ess-eval-region-or-function-or-paragraph-and-step</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002deval_002dregion_002dor_002dline_002dand_002dstep"><code>ess-eval-region-or-line-and-step</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dexecute_002dobjects"><code>ess-execute-objects</code></a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dexecute_002dsearch"><code>ess-execute-search</code></a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dgoto_002dbeginning_002dof_002dfunction_002dor_002dpara"><code>ess-goto-beginning-of-function-or-para</code></a>:</td><td> </td><td valign="top"><a href="#Other-edit-buffer-commands">Other edit buffer commands</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dgoto_002dend_002dof_002dfunction_002dor_002dpara"><code>ess-goto-end-of-function-or-para</code></a>:</td><td> </td><td valign="top"><a href="#Other-edit-buffer-commands">Other edit buffer commands</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dhandy_002dcommands"><code>ess-handy-commands</code></a>:</td><td> </td><td valign="top"><a href="#Handy-commands">Handy commands</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dhandy_002dcommands-1"><code>ess-handy-commands</code></a>:</td><td> </td><td valign="top"><a href="#Handy-commands">Handy commands</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dindent_002dcommand"><code>ess-indent-command</code></a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dindent_002dexp"><code>ess-indent-exp</code></a>:</td><td> </td><td valign="top"><a href="#Indenting">Indenting</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dindent_002dor_002dcomplete"><code>ess-indent-or-complete</code></a>:</td><td> </td><td valign="top"><a href="#Indenting">Indenting</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dlist_002dobject_002dcompletions"><code>ess-list-object-completions</code></a>:</td><td> </td><td valign="top"><a href="#Object-names">Object names</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dload_002dfile"><code>ess-load-file</code></a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dload_002dfile-1"><code>ess-load-file</code></a>:</td><td> </td><td valign="top"><a href="#Loading">Loading</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dmark_002dfunction"><code>ess-mark-function</code></a>:</td><td> </td><td valign="top"><a href="#Other-edit-buffer-commands">Other edit buffer commands</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dparse_002derrors"><code>ess-parse-errors</code></a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dparse_002derrors-1"><code>ess-parse-errors</code></a>:</td><td> </td><td valign="top"><a href="#Error-Checking">Error Checking</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dquit"><code>ess-quit</code></a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dquit-1"><code>ess-quit</code></a>:</td><td> </td><td valign="top"><a href="#Help">Help</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dR_002dcomplete_002dobject_002dname"><code>ess-R-complete-object-name</code></a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dremote"><code>ess-remote</code></a>:</td><td> </td><td valign="top"><a href="#ESS-processes-on-Remote-Computers">ESS processes on Remote Computers</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002drequest_002da_002dprocess"><code>ess-request-a-process</code></a>:</td><td> </td><td valign="top"><a href="#Multiple-ESS-processes">Multiple ESS processes</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dresynch"><code>ess-resynch</code></a>:</td><td> </td><td valign="top"><a href="#Object-names">Object names</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002droxy_002dhide_002dall"><code>ess-roxy-hide-all</code></a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002droxy_002dnext_002dentry"><code>ess-roxy-next-entry</code></a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002droxy_002dpreview_002dHTML"><code>ess-roxy-preview-HTML</code></a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002droxy_002dpreview_002dRd"><code>ess-roxy-preview-Rd</code></a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002droxy_002dprevious_002dentry"><code>ess-roxy-previous-entry</code></a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002droxy_002dtoggle_002droxy_002dregion"><code>ess-roxy-toggle-roxy-region</code></a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002droxy_002dupdate_002dentry"><code>ess-roxy-update-entry</code></a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002drutils_002dapropos"><code>ess-rutils-apropos</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002drutils_002dhtml_002ddocs"><code>ess-rutils-html-docs</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002drutils_002dload_002dwkspc"><code>ess-rutils-load-wkspc</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002drutils_002dlocal_002dpkgs"><code>ess-rutils-local-pkgs</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002drutils_002dobjs"><code>ess-rutils-objs</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002drutils_002drepos_002dpkgs"><code>ess-rutils-repos-pkgs</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002drutils_002drm_002dall"><code>ess-rutils-rm-all</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002drutils_002drsitesearch"><code>ess-rutils-rsitesearch</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002drutils_002dsave_002dwkspc"><code>ess-rutils-save-wkspc</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002drutils_002dupdate_002dpkgs"><code>ess-rutils-update-pkgs</code></a>:</td><td> </td><td valign="top"><a href="#Rutils">Rutils</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dset_002dstyle"><code>ess-set-style</code></a>:</td><td> </td><td valign="top"><a href="#Styles">Styles</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dskip_002dto_002dhelp_002dsection"><code>ess-skip-to-help-section</code></a>:</td><td> </td><td valign="top"><a href="#Help">Help</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dskip_002dto_002dnext_002dsection"><code>ess-skip-to-next-section</code></a>:</td><td> </td><td valign="top"><a href="#Help">Help</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dskip_002dto_002dprevious_002dsection"><code>ess-skip-to-previous-section</code></a>:</td><td> </td><td valign="top"><a href="#Help">Help</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dsmart_002dcomma"><code>ess-smart-comma</code></a>:</td><td> </td><td valign="top"><a href="#Handy-commands">Handy commands</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dsubmit_002dbug_002dreport"><code>ess-submit-bug-report</code></a>:</td><td> </td><td valign="top"><a href="#Reporting-Bugs">Reporting Bugs</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dswitch_002dto_002dend_002dof_002dESS"><code>ess-switch-to-end-of-ESS</code></a>:</td><td> </td><td valign="top"><a href="#Help">Help</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dswitch_002dto_002dinferior_002dor_002dscript_002dbuffer"><code>ess-switch-to-inferior-or-script-buffer</code></a>:</td><td> </td><td valign="top"><a href="#Other">Other</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dswv_002dlatex"><code>ess-swv-latex</code></a>:</td><td> </td><td valign="top"><a href="#Sweave-and-AUCTeX">Sweave and AUCTeX</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dswv_002dPDF"><code>ess-swv-PDF</code></a>:</td><td> </td><td valign="top"><a href="#Sweave-and-AUCTeX">Sweave and AUCTeX</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dswv_002dPS"><code>ess-swv-PS</code></a>:</td><td> </td><td valign="top"><a href="#Sweave-and-AUCTeX">Sweave and AUCTeX</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dswv_002dweave"><code>ess-swv-weave</code></a>:</td><td> </td><td valign="top"><a href="#Sweave-and-AUCTeX">Sweave and AUCTeX</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dtracebug"><code>ess-tracebug</code></a>:</td><td> </td><td valign="top"><a href="#ESS-tracebug">ESS tracebug</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dtranscript_002dclean_002dregion"><code>ess-transcript-clean-region</code></a>:</td><td> </td><td valign="top"><a href="#Clean">Clean</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dtranscript_002dcopy_002dcommand"><code>ess-transcript-copy-command</code></a>:</td><td> </td><td valign="top"><a href="#Resubmit">Resubmit</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dtranscript_002dsend_002dcommand"><code>ess-transcript-send-command</code></a>:</td><td> </td><td valign="top"><a href="#Resubmit">Resubmit</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dtranscript_002dsend_002dcommand_002dand_002dmove"><code>ess-transcript-send-command-and-move</code></a>:</td><td> </td><td valign="top"><a href="#Resubmit">Resubmit</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002duse_002dido_002c-ess_002dcompleting_002dread"><code>ess-use-ido, ess-completing-read</code></a>:</td><td> </td><td valign="top"><a href="#Minibuffer-completion">Minibuffer completion</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-program-index_fn_letter-F">F</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-fill_002dparagraph"><code>fill-paragraph</code></a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-program-index_fn_letter-I">I</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-inferior_002dess_002dsend_002dinput"><code>inferior-ess-send-input</code></a>:</td><td> </td><td valign="top"><a href="#Command_002dline-editing">Command-line editing</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-program-index_fn_letter-M">M</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-mark_002dparagraph"><code>mark-paragraph</code></a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-move_002dbeginning_002dof_002dline"><code>move-beginning-of-line</code></a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-program-index_fn_letter-N">N</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-newline_002dand_002dindent"><code>newline-and-indent</code></a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-program-index_fn_letter-O">O</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-objects_0028_0029">objects()</a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-program-index_fn_letter-P">P</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-printer_0028_0029">printer()</a>:</td><td> </td><td valign="top"><a href="#printer">printer</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-program-index_fn_letter-Q">Q</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-q_0028_0029">q()</a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-program-index_fn_letter-S">S</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-S">S</a>:</td><td> </td><td valign="top"><a href="#Starting-up">Starting up</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-search_0028_0029">search()</a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-search_0028_0029-1">search()</a>:</td><td> </td><td valign="top"><a href="#Object-names">Object names</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-source_0028_0029">source()</a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-source_0028_0029-1">source()</a>:</td><td> </td><td valign="top"><a href="#Loading">Loading</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-STERM-1">STERM</a>:</td><td> </td><td valign="top"><a href="#Statistical-Process-running-in-ESS_003f">Statistical Process running in ESS?</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
</table>
<table><tr><th valign="top">Jump to: </th><td><a class="summary-letter" href="#Function-and-program-index_fn_letter-B"><b>B</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-C"><b>C</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-D"><b>D</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-E"><b>E</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-F"><b>F</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-I"><b>I</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-M"><b>M</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-N"><b>N</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-O"><b>O</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-P"><b>P</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-Q"><b>Q</b></a>
<a class="summary-letter" href="#Function-and-program-index_fn_letter-S"><b>S</b></a>
</td></tr></table>
<hr>
<a name="Variable-index"></a>
<div class="header">
<p>
Next: <a href="#Concept-index" accesskey="n" rel="next">Concept index</a>, Previous: <a href="#Function-and-program-index" accesskey="p" rel="prev">Function and program index</a>, Up: <a href="#Indices" accesskey="u" rel="up">Indices</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Variable-index-1"></a>
<h3 class="unnumberedsec">Variable index</h3>
<table><tr><th valign="top">Jump to: </th><td><a class="summary-letter" href="#Variable-index_vr_letter-A"><b>A</b></a>
<a class="summary-letter" href="#Variable-index_vr_letter-C"><b>C</b></a>
<a class="summary-letter" href="#Variable-index_vr_letter-E"><b>E</b></a>
<a class="summary-letter" href="#Variable-index_vr_letter-I"><b>I</b></a>
<a class="summary-letter" href="#Variable-index_vr_letter-R"><b>R</b></a>
</td></tr></table>
<table class="index-vr" border="0">
<tr><td></td><th align="left">Index Entry</th><td> </td><th align="left"> Section</th></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Variable-index_vr_letter-A">A</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-ac_002dsource_002dR"><code>ac-source-R</code></a>:</td><td> </td><td valign="top"><a href="#Auto_002dcomplete">Auto-complete</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ac_002dsource_002dR_002dargs"><code>ac-source-R-args</code></a>:</td><td> </td><td valign="top"><a href="#Auto_002dcomplete">Auto-complete</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ac_002dsource_002dR_002dobjects"><code>ac-source-R-objects</code></a>:</td><td> </td><td valign="top"><a href="#Auto_002dcomplete">Auto-complete</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Variable-index_vr_letter-C">C</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-comint_002ddelimiter_002dargument_002dlist"><code>comint-delimiter-argument-list</code></a>:</td><td> </td><td valign="top"><a href="#History-expansion">History expansion</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-comint_002dinput_002dring_002dsize"><code>comint-input-ring-size</code></a>:</td><td> </td><td valign="top"><a href="#Command-History">Command History</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-comment_002dcolumn"><code>comment-column</code></a>:</td><td> </td><td valign="top"><a href="#Indenting">Indenting</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Variable-index_vr_letter-E">E</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dask_002dabout_002dtransfile"><code>ess-ask-about-transfile</code></a>:</td><td> </td><td valign="top"><a href="#Customizing-startup">Customizing startup</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dask_002dabout_002dtransfile-1"><code>ess-ask-about-transfile</code></a>:</td><td> </td><td valign="top"><a href="#Saving-transcripts">Saving transcripts</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dask_002dfor_002dess_002ddirectory"><code>ess-ask-for-ess-directory</code></a>:</td><td> </td><td valign="top"><a href="#Customizing-startup">Customizing startup</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002ddefault_002dstyle"><code>ess-default-style</code></a>:</td><td> </td><td valign="top"><a href="#Styles">Styles</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002ddelete_002ddump_002dfiles"><code>ess-delete-dump-files</code></a>:</td><td> </td><td valign="top"><a href="#Source-Files">Source Files</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002ddirectory"><code>ess-directory</code></a>:</td><td> </td><td valign="top"><a href="#Source-Directories">Source Directories</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002ddump_002dfilename_002dtemplate"><code>ess-dump-filename-template</code></a>:</td><td> </td><td valign="top"><a href="#Source-Directories">Source Directories</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002deldoc_002dabbreviation_002dstyle"><code>ess-eldoc-abbreviation-style</code></a>:</td><td> </td><td valign="top"><a href="#ESS-ElDoc">ESS ElDoc</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002deldoc_002dshow_002don_002dsymbol"><code>ess-eldoc-show-on-symbol</code></a>:</td><td> </td><td valign="top"><a href="#ESS-ElDoc">ESS ElDoc</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002deval_002dvisibly"><code>ess-eval-visibly</code></a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dexecute_002din_002dprocess_002dbuffer"><code>ess-execute-in-process-buffer</code></a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dfirst_002dtab_002dnever_002dcomplete"><code>ess-first-tab-never-complete</code></a>:</td><td> </td><td valign="top"><a href="#Indenting">Indenting</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dfirst_002dtab_002dnever_002dcomplete-1"><code>ess-first-tab-never-complete</code></a>:</td><td> </td><td valign="top"><a href="#Object-names">Object names</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dfont_002dlock_002dmode"><code>ess-font-lock-mode</code></a>:</td><td> </td><td valign="top"><a href="#Highlighting">Highlighting</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dfunction_002dtemplate"><code>ess-function-template</code></a>:</td><td> </td><td valign="top"><a href="#Edit-buffer">Edit buffer</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dhandy_002dcommands-2"><code>ess-handy-commands</code></a>:</td><td> </td><td valign="top"><a href="#Handy-commands">Handy commands</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dhandy_002dcommands-3"><code>ess-handy-commands</code></a>:</td><td> </td><td valign="top"><a href="#Handy-commands">Handy commands</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dindent_002dwith_002dfancy_002dcomments"><code>ess-indent-with-fancy-comments</code></a>:</td><td> </td><td valign="top"><a href="#Indenting">Indenting</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dkeep_002ddump_002dfiles"><code>ess-keep-dump-files</code></a>:</td><td> </td><td valign="top"><a href="#Source-Files">Source Files</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dR_002dfont_002dlock_002dkeywords"><code>ess-R-font-lock-keywords</code></a>:</td><td> </td><td valign="top"><a href="#Highlighting">Highlighting</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dsearch_002dlist"><code>ess-search-list</code></a>:</td><td> </td><td valign="top"><a href="#Source-Directories">Source Directories</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dsource_002ddirectory"><code>ess-source-directory</code></a>:</td><td> </td><td valign="top"><a href="#Source-Directories">Source Directories</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dstyle_002dalist"><code>ess-style-alist</code></a>:</td><td> </td><td valign="top"><a href="#Styles">Styles</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dswitch_002dto_002dend_002dof_002dproc_002dbuffer"><code>ess-switch-to-end-of-proc-buffer</code></a>:</td><td> </td><td valign="top"><a href="#Other">Other</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dswv_002dpdflatex_002dcommands"><code>ess-swv-pdflatex-commands</code></a>:</td><td> </td><td valign="top"><a href="#Sweave-and-AUCTeX">Sweave and AUCTeX</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002dtab_002dcomplete_002din_002dscript"><code>ess-tab-complete-in-script</code></a>:</td><td> </td><td valign="top"><a href="#Indenting">Indenting</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002duse_002deldoc"><code>ess-use-eldoc</code></a>:</td><td> </td><td valign="top"><a href="#ESS-ElDoc">ESS ElDoc</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Variable-index_vr_letter-I">I</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-inferior_002dess_002dprogram"><code>inferior-ess-program</code></a>:</td><td> </td><td valign="top"><a href="#Customizing-startup">Customizing startup</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-inferior_002dR_002dfont_002dlock_002dkeywords"><code>inferior-R-font-lock-keywords</code></a>:</td><td> </td><td valign="top"><a href="#Highlighting">Highlighting</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Variable-index_vr_letter-R">R</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-Rd_002dindent_002dlevel"><code>Rd-indent-level</code></a>:</td><td> </td><td valign="top"><a href="#R-documentation-files">R documentation files</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Rd_002dmode_002dhook"><code>Rd-mode-hook</code></a>:</td><td> </td><td valign="top"><a href="#R-documentation-files">R documentation files</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Rd_002dto_002dhelp_002dcommand"><code>Rd-to-help-command</code></a>:</td><td> </td><td valign="top"><a href="#R-documentation-files">R documentation files</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
</table>
<table><tr><th valign="top">Jump to: </th><td><a class="summary-letter" href="#Variable-index_vr_letter-A"><b>A</b></a>
<a class="summary-letter" href="#Variable-index_vr_letter-C"><b>C</b></a>
<a class="summary-letter" href="#Variable-index_vr_letter-E"><b>E</b></a>
<a class="summary-letter" href="#Variable-index_vr_letter-I"><b>I</b></a>
<a class="summary-letter" href="#Variable-index_vr_letter-R"><b>R</b></a>
</td></tr></table>
<hr>
<a name="Concept-index"></a>
<div class="header">
<p>
Previous: <a href="#Variable-index" accesskey="p" rel="prev">Variable index</a>, Up: <a href="#Indices" accesskey="u" rel="up">Indices</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Indices" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Concept-Index"></a>
<h3 class="unnumberedsec">Concept Index</h3>
<table><tr><th valign="top">Jump to: </th><td><a class="summary-letter" href="#Concept-index_cp_symbol-1"><b>.</b></a>
<br>
<a class="summary-letter" href="#Concept-index_cp_letter-A"><b>A</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-B"><b>B</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-C"><b>C</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-D"><b>D</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-E"><b>E</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-F"><b>F</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-G"><b>G</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-H"><b>H</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-I"><b>I</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-K"><b>K</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-L"><b>L</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-M"><b>M</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-N"><b>N</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-O"><b>O</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-P"><b>P</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-Q"><b>Q</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-R"><b>R</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-S"><b>S</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-T"><b>T</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-U"><b>U</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-W"><b>W</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-X"><b>X</b></a>
</td></tr></table>
<table class="index-cp" border="0">
<tr><td></td><th align="left">Index Entry</th><td> </td><th align="left"> Section</th></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_symbol-1">.</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-_002eemacs-file"><samp>.emacs</samp> file</a>:</td><td> </td><td valign="top"><a href="#Source-Directories">Source Directories</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-A">A</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-aborting-S-commands">aborting S commands</a>:</td><td> </td><td valign="top"><a href="#Other">Other</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-arguments-to-S-program">arguments to S program</a>:</td><td> </td><td valign="top"><a href="#Customizing-startup">Customizing startup</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-authors">authors</a>:</td><td> </td><td valign="top"><a href="#Credits">Credits</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-auto_002dcomplete">auto-complete</a>:</td><td> </td><td valign="top"><a href="#Auto_002dcomplete">Auto-complete</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-autosaving">autosaving</a>:</td><td> </td><td valign="top"><a href="#Source-Files">Source Files</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-B">B</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-bug-reports">bug reports</a>:</td><td> </td><td valign="top"><a href="#Reporting-Bugs">Reporting Bugs</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-bugs">bugs</a>:</td><td> </td><td valign="top"><a href="#Bugs">Bugs</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-C">C</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-cleaning-up">cleaning up</a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-comint">comint</a>:</td><td> </td><td valign="top"><a href="#Credits">Credits</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-command-history">command history</a>:</td><td> </td><td valign="top"><a href="#Command-History">Command History</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-command-line-arguments">command line arguments</a>:</td><td> </td><td valign="top"><a href="#iESS_0028S_0029_002d_002dInferior-ESS-processes">iESS(S)--Inferior ESS processes</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-command_002dline-completion">command-line completion</a>:</td><td> </td><td valign="top"><a href="#Object-names">Object names</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-command_002dline-editing">command-line editing</a>:</td><td> </td><td valign="top"><a href="#Command_002dline-editing">Command-line editing</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-commands">commands</a>:</td><td> </td><td valign="top"><a href="#Entering-commands">Entering commands</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-comments">comments</a>:</td><td> </td><td valign="top"><a href="#Source-Files">Source Files</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-comments-in-S">comments in S</a>:</td><td> </td><td valign="top"><a href="#Indenting">Indenting</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-completion-in-edit-buffer">completion in edit buffer</a>:</td><td> </td><td valign="top"><a href="#Other-edit-buffer-commands">Other edit buffer commands</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-completion-of-object-names">completion of object names</a>:</td><td> </td><td valign="top"><a href="#Object-names">Object names</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-completion-on-file-names">completion on file names</a>:</td><td> </td><td valign="top"><a href="#Object-names">Object names</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-completion-on-lists">completion on lists</a>:</td><td> </td><td valign="top"><a href="#Object-names">Object names</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-completion_002c-when-prompted-for-object-names">completion, when prompted for object names</a>:</td><td> </td><td valign="top"><a href="#Edit-buffer">Edit buffer</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-creating-new-objects">creating new objects</a>:</td><td> </td><td valign="top"><a href="#Edit-buffer">Edit buffer</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-credits">credits</a>:</td><td> </td><td valign="top"><a href="#Credits">Credits</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-customization">customization</a>:</td><td> </td><td valign="top"><a href="#Customization">Customization</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-D">D</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-data-frames">data frames</a>:</td><td> </td><td valign="top"><a href="#Object-names">Object names</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-deleting-output">deleting output</a>:</td><td> </td><td valign="top"><a href="#Last-command">Last command</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-directories">directories</a>:</td><td> </td><td valign="top"><a href="#Starting-up">Starting up</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-dump-file-directories">dump file directories</a>:</td><td> </td><td valign="top"><a href="#Source-Directories">Source Directories</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-dump-file-names">dump file names</a>:</td><td> </td><td valign="top"><a href="#Source-Directories">Source Directories</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-dump-files">dump files</a>:</td><td> </td><td valign="top"><a href="#Edit-buffer">Edit buffer</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-dump-files-1">dump files</a>:</td><td> </td><td valign="top"><a href="#Source-Files">Source Files</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-E">E</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-echoing-commands-when-evaluating">echoing commands when evaluating</a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-edit-buffer">edit buffer</a>:</td><td> </td><td valign="top"><a href="#Edit-buffer">Edit buffer</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-editing-commands">editing commands</a>:</td><td> </td><td valign="top"><a href="#Command-History">Command History</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-editing-functions">editing functions</a>:</td><td> </td><td valign="top"><a href="#Editing-objects">Editing objects</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-editing-transcripts">editing transcripts</a>:</td><td> </td><td valign="top"><a href="#Saving-transcripts">Saving transcripts</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ElDoc">ElDoc</a>:</td><td> </td><td valign="top"><a href="#ESS-ElDoc">ESS ElDoc</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-emacsclient">emacsclient</a>:</td><td> </td><td valign="top"><a href="#Emacsclient">Emacsclient</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-entering-commands">entering commands</a>:</td><td> </td><td valign="top"><a href="#Entering-commands">Entering commands</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-errors">errors</a>:</td><td> </td><td valign="top"><a href="#Error-Checking">Error Checking</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess-developer">ess developer</a>:</td><td> </td><td valign="top"><a href="#ESS-developer">ESS developer</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ESS-process-buffer">ESS process buffer</a>:</td><td> </td><td valign="top"><a href="#Starting-up">Starting up</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ESS-process-directory">ESS process directory</a>:</td><td> </td><td valign="top"><a href="#Starting-up">Starting up</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ESS-tracebug">ESS tracebug</a>:</td><td> </td><td valign="top"><a href="#ESS-tracebug">ESS tracebug</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ESS_002delsewhere">ESS-elsewhere</a>:</td><td> </td><td valign="top"><a href="#ESS-processes-on-Remote-Computers">ESS processes on Remote Computers</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ess_002droxy">ess-roxy</a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-evaluating-code-with-echoed-commands">evaluating code with echoed commands</a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-evaluating-S-expressions">evaluating S expressions</a>:</td><td> </td><td valign="top"><a href="#Evaluating-code">Evaluating code</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-F">F</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-font_002dlock-mode">font-lock mode</a>:</td><td> </td><td valign="top"><a href="#Highlighting">Highlighting</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-formatting-source-code">formatting source code</a>:</td><td> </td><td valign="top"><a href="#Indenting">Indenting</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-G">G</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-graphics">graphics</a>:</td><td> </td><td valign="top"><a href="#Graphics">Graphics</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-H">H</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-Handy-commands">Handy commands</a>:</td><td> </td><td valign="top"><a href="#Handy-commands">Handy commands</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-help-files">help files</a>:</td><td> </td><td valign="top"><a href="#Help">Help</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-highlighting">highlighting</a>:</td><td> </td><td valign="top"><a href="#Highlighting">Highlighting</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-historic-backups">historic backups</a>:</td><td> </td><td valign="top"><a href="#Source-Files">Source Files</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-hot-keys">hot keys</a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-I">I</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-icicles">icicles</a>:</td><td> </td><td valign="top"><a href="#Icicles">Icicles</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-IDO-completions">IDO completions</a>:</td><td> </td><td valign="top"><a href="#Minibuffer-completion">Minibuffer completion</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-indenting">indenting</a>:</td><td> </td><td valign="top"><a href="#Indenting">Indenting</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-installation">installation</a>:</td><td> </td><td valign="top"><a href="#Installation">Installation</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-interactive-use-of-S">interactive use of S</a>:</td><td> </td><td valign="top"><a href="#Introduction">Introduction</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-interrupting-S-commands">interrupting S commands</a>:</td><td> </td><td valign="top"><a href="#Other">Other</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-introduction">introduction</a>:</td><td> </td><td valign="top"><a href="#Introduction">Introduction</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-K">K</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-keyboard-short-cuts">keyboard short cuts</a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-killing-temporary-buffers">killing temporary buffers</a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-killing-the-ESS-process">killing the ESS process</a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-L">L</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-lists_002c-completion-on">lists, completion on</a>:</td><td> </td><td valign="top"><a href="#Object-names">Object names</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-M">M</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-motion-in-transcript-mode">motion in transcript mode</a>:</td><td> </td><td valign="top"><a href="#Transcript-Mode">Transcript Mode</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-multi_002dline-commands_002c-resubmitting">multi-line commands, resubmitting</a>:</td><td> </td><td valign="top"><a href="#Transcript-resubmit">Transcript resubmit</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-multiple-ESS-processes">multiple ESS processes</a>:</td><td> </td><td valign="top"><a href="#Multiple-ESS-processes">Multiple ESS processes</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-N">N</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-new-objects_002c-creating">new objects, creating</a>:</td><td> </td><td valign="top"><a href="#Edit-buffer">Edit buffer</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-O">O</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-objects">objects</a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-P">P</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-pages-in-the-process-buffer">pages in the process buffer</a>:</td><td> </td><td valign="top"><a href="#Transcript">Transcript</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-paging-commands-in-help-buffers">paging commands in help buffers</a>:</td><td> </td><td valign="top"><a href="#Help">Help</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-paragraphs-in-the-process-buffer">paragraphs in the process buffer</a>:</td><td> </td><td valign="top"><a href="#Transcript">Transcript</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-parsing-errors">parsing errors</a>:</td><td> </td><td valign="top"><a href="#Error-Checking">Error Checking</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-process-buffer">process buffer</a>:</td><td> </td><td valign="top"><a href="#Starting-up">Starting up</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-process-names">process names</a>:</td><td> </td><td valign="top"><a href="#Multiple-ESS-processes">Multiple ESS processes</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-programming-in-S">programming in S</a>:</td><td> </td><td valign="top"><a href="#Introduction">Introduction</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-project-work-in-S">project work in S</a>:</td><td> </td><td valign="top"><a href="#Source-Files">Source Files</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-Q">Q</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-quitting-from-ESS">quitting from ESS</a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-R">R</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-re_002dexecuting-commands">re-executing commands</a>:</td><td> </td><td valign="top"><a href="#Command-History">Command History</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-reading-long-command-outputs">reading long command outputs</a>:</td><td> </td><td valign="top"><a href="#Last-command">Last command</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-remote-Computers">remote Computers</a>:</td><td> </td><td valign="top"><a href="#ESS-processes-on-Remote-Computers">ESS processes on Remote Computers</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-reverting-function-definitions">reverting function definitions</a>:</td><td> </td><td valign="top"><a href="#Edit-buffer">Edit buffer</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-roxy">roxy</a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Roxygen">Roxygen</a>:</td><td> </td><td valign="top"><a href="#Roxygen">Roxygen</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-running-S">running S</a>:</td><td> </td><td valign="top"><a href="#Starting-up">Starting up</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-S">S</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-S_002belsewhere">S+elsewhere</a>:</td><td> </td><td valign="top"><a href="#ESS-processes-on-Remote-Computers">ESS processes on Remote Computers</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-search-list">search list</a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-search-list-1">search list</a>:</td><td> </td><td valign="top"><a href="#Source-Directories">Source Directories</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-sending-input">sending input</a>:</td><td> </td><td valign="top"><a href="#Entering-commands">Entering commands</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-starting-directory">starting directory</a>:</td><td> </td><td valign="top"><a href="#Starting-up">Starting up</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-starting-ESS">starting ESS</a>:</td><td> </td><td valign="top"><a href="#Starting-up">Starting up</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-STERM">STERM</a>:</td><td> </td><td valign="top"><a href="#Statistical-Process-running-in-ESS_003f">Statistical Process running in ESS?</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-T">T</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-tcsh">tcsh</a>:</td><td> </td><td valign="top"><a href="#Object-names">Object names</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-temporary-buffers">temporary buffers</a>:</td><td> </td><td valign="top"><a href="#Help">Help</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-temporary-buffers_002c-killing">temporary buffers, killing</a>:</td><td> </td><td valign="top"><a href="#Hot-keys">Hot keys</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-transcript">transcript</a>:</td><td> </td><td valign="top"><a href="#Transcript">Transcript</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-transcript-file">transcript file</a>:</td><td> </td><td valign="top"><a href="#Customizing-startup">Customizing startup</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-transcript-file-names">transcript file names</a>:</td><td> </td><td valign="top"><a href="#Saving-transcripts">Saving transcripts</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-transcript-mode-motion">transcript mode motion</a>:</td><td> </td><td valign="top"><a href="#Transcript-Mode">Transcript Mode</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-transcripts-of-S-sessions">transcripts of S sessions</a>:</td><td> </td><td valign="top"><a href="#Introduction">Introduction</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-U">U</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-using-S-interactively">using S interactively</a>:</td><td> </td><td valign="top"><a href="#Introduction">Introduction</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-W">W</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-winjava">winjava</a>:</td><td> </td><td valign="top"><a href="#winjava">winjava</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-working-directory">working directory</a>:</td><td> </td><td valign="top"><a href="#Starting-up">Starting up</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-working-directory-1">working directory</a>:</td><td> </td><td valign="top"><a href="#Source-Directories">Source Directories</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-X">X</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-X-Windows">X Windows</a>:</td><td> </td><td valign="top"><a href="#X11">X11</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
</table>
<table><tr><th valign="top">Jump to: </th><td><a class="summary-letter" href="#Concept-index_cp_symbol-1"><b>.</b></a>
<br>
<a class="summary-letter" href="#Concept-index_cp_letter-A"><b>A</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-B"><b>B</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-C"><b>C</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-D"><b>D</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-E"><b>E</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-F"><b>F</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-G"><b>G</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-H"><b>H</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-I"><b>I</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-K"><b>K</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-L"><b>L</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-M"><b>M</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-N"><b>N</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-O"><b>O</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-P"><b>P</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-Q"><b>Q</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-R"><b>R</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-S"><b>S</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-T"><b>T</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-U"><b>U</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-W"><b>W</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-X"><b>X</b></a>
</td></tr></table>
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