\input texinfo @c -*-texinfo-*- @comment %**start of header @setfilename ess.info @settitle ESS --- Emacs Speaks Statistics @comment %**end of header @synindex pg vr @include ess-defs.texi @titlepage @title ESS --- Emacs Speaks Statistics ESS @w{version @ESSVER} @author The ESS Developers (A.J. Rossini, R.M. Heiberger, K. Hornik, @author M. Maechler, R.A. Sparapani, S.J. Eglen, @author S.P. Luque and H. Redestig) @c @author (Formerly by: Doug Bates, Ed Kademan, Frank Ritter @c @author and David Smith) @c @ifhtml @c <P><HR></P> @c @end ifhtml @c @author Current Documentation by The ESS Developers @author Copyright @copyright{} 2002--2010 The ESS Developers @author Copyright @copyright{} 1996--2001 A.J. Rossini @c (@email{rossini@@biostat.washington.edu}) @c @author Department of Biostatistics @c @author University of Washington, USA. @author Original Documentation by David M. Smith @author Copyright @copyright{} 1992--1995 David M. Smith @c (@email{D.M.Smith@@lancaster.ac.uk}) @c @author Department of Mathematics and Statistics @c @author Lancaster University, UK @c @page @c @vskip 0pt plus 1filll @c @sp 2 @author Permission is granted to make and distribute verbatim copies of this @author manual provided the copyright notice and this permission notice are @author preserved on all copies. @author Permission is granted to copy and distribute modified versions of this @author manual under the conditions for verbatim copying, provided that the @author entire resulting derived work is distributed under the terms of a @author permission notice identical to this one. @end titlepage @ifnottex @majorheading ESS --- Emacs Speaks Statistics @dircategory Emacs @direntry * ESS: (ess). Emacs Speaks Statistics (S/S+/R, SAS, BUGS/JAGS, Stata, XLisp-Stat). @end direntry @c node-name, next, previous, up @node Top, Introduction, (dir), (dir) @top ESS: Emacs Speaks Statistics ESS version @include ../VERSION @display by A.J. Rossini, R.M. Heiberger, K. Hornik, M. Maechler, R.A. Sparapani, S.J. Eglen, S.P. Luque and H. Redestig. @end display @c (Formerly: Doug @c Bates, Ed Kademan, Frank Ritter and David Smith). @quotation 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. @end quotation @end ifnottex @menu * Introduction:: Overview of features provided by this package * Installation:: Installing ESS on your system * Interactive ESS:: Interacting with statistical programs * Entering commands:: Interacting with the ESS process * Transcript Mode:: Manipulating saved transcript files * ESS for the S family:: * Editing:: How to create/edit objects and functions * Editing R documentation:: * Help:: Reading help files * ESS for SAS:: * ESS for BUGS:: * ESS for JAGS:: * Miscellaneous:: Other features of ESS * Mailing lists/bug reports:: How to get assistance with ESS * Customization:: Customizing ESS * Key Index:: * Concept Index:: * Variable and command index:: @c @c @detailmenu @c --- The Detailed Node Listing --- @c @c Introduction to ESS @c @c * Features:: Why should I use ESS? @c * New features:: @c * Credits:: Authors of and contributors to ESS @c * Latest version:: Getting the latest version of ESS @c * Manual:: How to read this manual @c @c Installing ESS on your system @c * Unix installation:: Installing ESS on your Unix system @c * Microsoft Windows installation:: Installing ESS on your MS Windows system @c * Requirements:: emacs, Operating Systems and Statistical Packages @c * System dependent:: Other variables you may need to change @c @c Starting the ESS process @c @c * Multiple ESS processes:: @c * ESS processes on Remote Computers:: @c * Customizing startup:: Changing the startup actions @c @c Help for the S family @c @c * ESS(S)--Editing files:: @c * iESS(S)--Inferior ESS processes:: @c * Handling and Reusing Transcripts:: @c * ESS-help--assistance with viewing help:: @c * Philosophies for using ESS(S):: @c * Scenarios for use (possibilities--based on actual usage):: @c * Customization Examples and Solutions to Problems:: @c @c Help for SAS @c @c * ESS(SAS)--Design philosophy:: @c * ESS(SAS)--Editing files:: @c * iESS(SAS)--Interactive SAS processes:: @c * ESS(SAS)--Batch SAS processes:: @c * ESS(SAS)--Function keys for batch processing:: @c * ESS(SAS)--TAB key:: @c * ESS(SAS)--Usage scenarios:: @c * iESS(SAS)--Common problems:: @c * ESS(SAS)--MS Windows:: @c @c Interacting with the ESS process @c @c * Command-line editing:: Entering commands and fixing mistakes @c * Completion:: Completion of object names @c * Completion details:: Advanced completion concepts @c * Transcript:: Manipulating the transcript @c * Command History:: Command History @c * History expansion:: References to historical commands @c * Hot keys:: Hot keys for common commands @c * Statistical Process running in ESS?:: @c * Other:: Other commands provided by inferior-ESS @c @c Manipulating the transcript @c @c * Last command:: Manipulating the output from the last command @c * Process buffer motion:: Viewing older commands @c * Transcript resubmit:: Re-submitting commands from the transcript @c * Saving transcripts:: Keeping a record of your S session @c @c Editing S functions @c @c * Edit buffer:: Edit objects in a specialized buffer @c * Loading:: Loading source files into the ESS process @c * Error Checking:: Detecting errors in source files @c * Evaluating code:: Sending code to the ESS process @c * Indenting:: Indenting and formatting @Sl{} code @c * Other edit buffer commands:: Commands for motion, completion and more @c * Source Files:: Maintaining @Sl{} source files @c * Source Directories:: Names and locations of dump files @c @c Manipulating saved transcript files @c @c * Resubmit:: Resubmitting commands from the transcript file @c * Clean:: Cleaning transcript files @c @c Other features of ESS @c @c * Highlighting:: Syntactic highlighting of buffers @c * Graphics:: Using graphics with ESS @c * Object Completion:: @c @c Using graphics with ESS @c @c * printer:: The printer() graphics driver @c * X11:: The X11() (and other X-windows based) driver @c @c Bugs and Bug Reporting, Mailing Lists @c @c * Bugs:: @c * Reporting Bugs:: @c * Mailing Lists:: @c @c Customizing ESS @c @c * Variables:: Variables for customization @c * Hooks:: Customizing ESS with hooks @c * Keybindings:: Changing the default ESS keybindings @c @c Variables for customization @c @c * Variables for starting ESS:: Variables for starting ESS @c * Dump file variables:: Variables for dump files @c * Indentation variables:: Variables controlling indentation @c * Variables controlling interaction:: Variables controlling interaction @c with the ESS process @c @end detailmenu @end menu @comment node-name, next, previous, up @node Introduction, Installation, Top, Top @chapter Introduction to ESS @cindex introduction The S family (@Sl{}, Splus and R) and SAS statistical analysis packages provide sophisticated statistical and graphical routines for manipulating data. @b{E}macs @b{S}peaks @b{S}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. ESS provides a common, generic, and useful interface, through emacs, to many statistical packages. It currently supports the S family, SAS, BUGS/JAGS, Stata and XLisp-Stat with the level of support roughly in that order. A bit of notation before we begin. @emph{emacs} refers to both @emph{GNU Emacs} by the Free Software Foundation, as well as @emph{XEmacs} by the XEmacs Project. The emacs major mode @code{ESS[language]}, where @code{language} can take values such as @code{S}, @code{SAS}, or @code{XLS}. The inferior process interface (the connection between emacs and the running process) referred to as inferior ESS (@code{iESS}), is denoted in the modeline by @code{ESS[dialect]}, where @code{dialect} can take values such as @code{S3}, @code{S4}, @code{S+3}, @code{S+4}, @code{S+5}, @code{S+6}, @code{S+7}, @code{R}, @code{XLS}, @code{VST}, @code{SAS}. Currently, the documentation contains many references to @cite{`S'} where actually any supported (statistics) language is meant, i.e., `S' could also mean `XLisp-Stat' or `SAS'. @cindex interactive use of S @cindex using S interactively 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 @Sl{} objects and ``hot keys'' are provided for common @Sl{} 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. @cindex transcripts of S sessions No special knowledge of Emacs is necessary when using @Sl{} interactively under ESS. @cindex programming in S For those that use @Sl{} in the typical edit--test--revise cycle when programming @Sl{} functions, ESS provides for editing of @Sl{} functions in Emacs edit buffers. Unlike the typical use of @Sl{} 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 @Sl{} functions in specified source directories. @menu * Features:: Why should I use ESS? * New features:: * Credits:: Authors of and contributors to ESS * Latest version:: Getting the latest version of ESS * Manual:: How to read this manual @end menu @comment node-name, next, previous, up @node Features, New features, Introduction, Introduction @section Why should I use ESS? 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. 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: @itemize @bullet @item @b{Command-line editing} for fixing mistakes in commands before they are entered. The @samp{-e} 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 such as XLisp-Stat and S3 do not necessarily have features like this built-in. @xref{Command-line editing}. @item @b{Searchable command history} for recalling previously-submitted commands. This provides all the features of the @samp{Splus -e} history mechanism, plus added features such as history searching. @xref{Command History}. @item @b{Command-line completion} of both object and file names for quick entry. This is similar to @code{tcsh}'s facility for filenames; here it also applies to object names and list components. @xref{Completion}. @item @b{Hot-keys} for quick entry of commonly-used commands in `S' such as @code{objects()} and @code{search()}. @xref{Hot keys}. @item @b{Transcript recording} for a complete record of all the actions in an S session. @xref{Transcript}. @item @b{Interface to the help system}, with a specialized mode for viewing S help files. @xref{Help}. @end itemize If you commonly create or modify @Sl{} functions, you will have found the standard facilities for this (the @samp{fix()} 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 @Sl{} while editing. ESS corrects these problems by introducing the following features: @itemize @bullet @item @b{Object editing}. 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. @xref{Edit buffer}. @item @b{A specialized editing mode} for @Sl{} code, which provides syntactic indentation and highlighting. @xref{Indenting}. @item @b{Facilities for loading and error-checking source files}, including a keystroke to jump straight to the position of an error in a source file. @xref{Error Checking}. @item @b{Source code revision maintenance}, which allows you to keep historic versions of @Sl{} source files. @xref{Source Files}. @item @b{Facilities for evaluating @Sl{} code} such as portions of source files, or line-by-line evaluation of files (useful for debugging). @xref{Evaluating code}. @end itemize Finally, ESS provides features for re-submitting commands from saved transcript files, including: @itemize @bullet @item @b{Evaluation of previously entered commands}, stripping away unnecessary prompts. @xref{Transcript resubmit}. @end itemize @comment node-name, next, previous, up @node New features, Credits, Features, Introduction @section New features in ESS @include newfeat.texi @include onewfeat.texi @comment node-name, next, previous, up @node Credits, Latest version, New features, Introduction @section Authors of and contributors to ESS @include credits.texi @comment node-name, next, previous, up @node Latest version, Manual, Credits, Introduction @section Getting the latest version of ESS @include getting.texi @comment node-name, next, previous, up @node Manual, , Latest version, Introduction @section How to read this manual If you need to install ESS, read @ref{Installation} for details on what needs to be done before proceeding to the next chapter. In this manual we use the standard notation for describing the keystrokes used to invoke certain commands. @kbd{C-<chr>} means hold the CONTROL key while typing the character <chr>. @kbd{M-<chr>} 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>. All ESS commands can be invoked by typing @kbd{M-x command}. 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. Some commands, such as @kbd{M-x R} can accept an optional `prefix' argument. To specify the prefix argument, you would type @kbd{C-u} before giving the command. e.g. If you type @kbd{C-u M-x R}, you will be asked for command line options that you wish to invoke the R process with. 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}. For example, if you type @kbd{C-h f ess-eval-region}, 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} within an ESS buffer. 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} to get started.) @ref{Customization} 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. @comment node-name, next, previous, up @node Installation, Interactive ESS, Introduction, Top @chapter Installing ESS on your system @cindex installation The following section details those steps necessary to get ESS running on your system. @menu * Unix installation:: Installing ESS on your Unix system * Microsoft Windows installation:: Installing ESS on your MS Windows system * Requirements:: emacs, Operating Systems and Statistical Packages @end menu @c FIXME: the following contains @node s *and* is also included by readme.texi @c ----- which does *not* include 'requires.texi' @c ==> *must* give node pointer problems! @c @include inst_tar.texi @include unixlike.texi @include windows.texi @node Requirements, , Microsoft Windows installation, Installation @comment node-name, next, previous, up @section Requirements @include requires.texi @comment node-name, next, previous, up @node Interactive ESS, Entering commands, Installation, Top @chapter Interacting with statistical programs 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. @comment node-name, next, previous, up @menu * Starting up:: * Multiple ESS processes:: * ESS processes on Remote Computers:: * S+elsewhere and ESS-elsewhere:: * Customizing startup:: @end menu @node Starting up, Multiple ESS processes, Interactive ESS, Interactive ESS @section Starting an ESS process @cindex starting ESS @cindex running S To start an @Sl{} session on Unix or on Windows when you use the Cygwin bash shell, simply type @kbd{M-x S RET}. To start an @Sl{} session on Windows when you use the MSDOS prompt shell, simply type @kbd{M-x S+6-msdos RET}. @pindex S @cindex ESS process directory @cindex starting directory @cindex working directory @cindex directories S will then (by default) ask the question @example S starting data directory? @end example @noindent Enter the name of the directory you wish to start @Sl{} from (that is, the directory you would have @code{cd}'d to before starting @Sl{} from the shell). This directory should have a @file{.Data} subdirectory. You will then be popped into a buffer @cindex ESS process buffer @cindex process buffer with name @samp{*S*} which will be used for interacting with the ESS process, and you can start entering commands. @comment node-name, next, previous, up @node Multiple ESS processes, ESS processes on Remote Computers, Starting up, Interactive ESS @section Running more than one ESS process @cindex Multiple ESS processes 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 @cindex process names (process 1) is simply named (using S-PLUS as an example) @samp{S+3:1}. @comment You may start a new process by passing a numeric argument to @comment @kbd{M-x S}. For example, typing @kbd{ESC 2 M-x S} starts up @comment an ESS process with name @samp{S2}, in a buffer whose name @comment is initially @samp{*S2*}. The name of the process is shown in the mode line in square brackets (for example, @samp{[S+3:2]}); this is useful if the process buffer is renamed. Without a prefix argument, @kbd{M-x S} starts a new ESS process, using the first available process number. With a prefix argument (for R), @kbd{C-u M-x R} allows for the specification of command line options. @pindex ess-request-a-process You can switch to any active ESS process with the command @samp{M-x ess-request-a-process}. 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. @c SJE - commented outl the default behaviour now is to label *S* rather @c than *S:1*. @c @vindex ess-plain-first-buffername @c For the predecessor to ESS (S-mode 4.8), the initial process was not @c visibly numbered, i.e. S instead of S1 was used in the mode-line. To @c obtain this behavior, set the variable @code{ess-plain-first-buffername} @c to @code{t}. See @file{ess-site} for how to set this for all users. @comment node-name, next, previous, up @node ESS processes on Remote Computers, S+elsewhere and ESS-elsewhere, Multiple ESS processes, Interactive ESS @section ESS processes on Remote Computers @cindex Remote Computers @pindex ess-remote @pindex ESS-elsewhere @pindex S+elsewhere 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 from a telnet or ssh buffer and then connect ESS to that buffer. @enumerate @item Start a new telnet or ssh buffer and connect to the remote computer (e.g. use @samp{M-x telnet} or @samp{M-x ssh}; ssh.el is available at @uref{ftp://ftp.splode.com/pub/users/friedman/emacs-lisp/ssh.el}). @item Start the ESS process on the remote machine, for example with one of the commands @samp{Splus}, or @samp{R}, or @samp{sas -stdio}. @item Enter the ESS command @samp{M-x ess-remote}. You will be prompted for a program name. Enter @samp{sp6} or @samp{r} or @samp{sas} or another valid name. Your telnet process is now known to ESS. All the usual ESS commands (@samp{C-c C-n} and its relatives) now work with the S language processes. For SAS you need to use a different command @samp{C-c i} (that is a regular @samp{i}, not a @samp{C-i}) to send lines from your @file{myfile.sas} to the remote SAS process. @samp{C-c i} sends lines over invisibly. @c and lets SAS display them formatted correctly as in a SAS log file. 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. @item Graphics (interactive) on the remote machine. If you run X11 (@xref{X11}, X-windows) on both the local and remote machines then you should be able to display the graphs locally by setting the @samp{DISPLAY} environment variable appropriately. Windows users can download @samp{xfree86} from cygwin. @item 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} and @samp{.jpg} files. Otherwise, a graphics file viewer will be needed. Ghostscript/ghostview may be downloaded to display @samp{.ps} and @samp{.eps} files. Viewers for GIF and JPEG are usually included with operating systems. @xref{ESS(SAS)--Function keys for batch processing}, for more information on using the F12 key for displaying graphics files with SAS. @end enumerate Should you or a colleague inadvertently start a statistical process in an ordinary @samp{*shell*} buffer, the @samp{ess-remote} command can be used to convert it to an ESS buffer and allow you to use the ESS commands with it. We have two older commands, now deprecated, for accessing ESS processes on remote computers. @xref{S+elsewhere and ESS-elsewhere}. @comment node-name, next, previous, up @node S+elsewhere and ESS-elsewhere, Customizing startup, ESS processes on Remote Computers, Interactive ESS @section S+elsewhere and ESS-elsewhere These commands are now deprecated. We recommend @samp{ess-remote}. We have two versions of the elsewhere function. @samp{S+elsewhere} is specific for the S-Plus program. The more general function @samp{ESS-elsewhere} is not as stable. @enumerate @item Enter @samp{M-x S+elsewhere}. You will be prompted for a starting directory. I usually give it my project directory on the local machine, say @samp{~myname/myproject/} Or enter @samp{M-x ESS-elsewhere}. 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/} @item The @samp{*S+3*} 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} then move the cursor to the end with @samp{M->}. With @samp{S+elsewhere} the buffer name is based on the name of the ESS program. @item Enter @samp{telnet myname@@other.machine} (or @samp{ssh myname@@other.machine}). You will be prompted for your password on the remote machine. Use @samp{M-x send-invisible} before typing the password itself. @item Before starting the ESS process, type @samp{stty -echo nl} at the unix prompt. The @samp{-echo} turns off the echo, the @samp{nl} turns off the newline that you see as @samp{^M}. @item You are now talking to the unix prompt on the other machine in the @samp{*S+3*} buffer. cd into the directory for the current project and start the ESS process by entering @samp{Splus} or @samp{R} or @samp{sas -stdio} as appropriate. If you can login remotely to your Windows 2000, then you should be able to run @samp{Sqpe} on the Windows machine. I haven't tested this and noone has reported their tests to me. You will not be able to run the GUI through this text-only connection. @item Once you get the S or R or SAS prompt, then you are completely connected. All the @samp{C-c C-n} and related commands work correctly in sending commands from @samp{myfile.s} or @samp{myfile.r} on the PC to the @samp{*S+3*} buffer running the S or R or SAS program on the remote machine. @item 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} on your PC. If you don't run X11, then you can write graphics to the postscript device and copy it to your PC with dired and display it with ghostscript. @end enumerate @comment node-name, next, previous, up @node Customizing startup, , S+elsewhere and ESS-elsewhere, Interactive ESS @section Changing the startup actions 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} to @vindex ess-ask-for-ess-directory @code{nil}. In this case, the starting directory will be set using one of the following methods: @enumerate @item If the variable @code{ess-directory-function} stores the name of a function, the value returned by this function is used. The default for this variable is nil. @item Otherwise, if the variable @code{ess-directory} stores the name of a directory (ending in a slash), this value is used. The default for this variable is nil. @item Otherwise, the working directory of the current buffer is used. @end enumerate If @code{ess-ask-for-ess-directory} has a non-@code{nil} 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} is an ideal variable to set in @code{ess-pre-run-hook}. If you like to keep a record of your @Sl{} sessions, set the variable @code{ess-ask-about-transfile} to @code{t}, and you will be asked for a filename for the transcript before the ESS process starts. @defvr {User Option} ess-ask-about-transfile If non-@code{nil}, as for a file name in which to save the session transcript. @end defvr @cindex transcript file 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}); 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 --- @pxref{Saving transcripts}.) 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}. @vindex inferior-ess-program If you need to pass any arguments to this program, they may be specified in the variable @code{inferior-@var{S_program_name}-args} (e.g. if @code{inferior-ess-program} is @code{"S+"} then the variable to set is @code{inferior-S+-args}. @cindex arguments to S program It is not normally necessary to pass arguments to the @Sl{} program; in particular do not pass the @samp{-e} option to @code{Splus}, since ESS provides its own command history mechanism. 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}. Alternatively, change @code{inferior-ess-same-window} if you wish the process to appear within another window of the current frame. @comment node-name, next, previous, up @node Entering commands, Transcript Mode, Interactive ESS, Top @chapter Interacting with the ESS process @cindex entering commands @cindex commands @cindex sending input The primary function of the ESS package is to provide an easy-to-use front end to the @Sl{} interpreter. This is achieved by running the S process from within an Emacs buffer, so that the Emacs editing commands are available to correct mistakes in commands, etc. The features of Inferior @Sl{} mode are similar to those provided by the standard Emacs shell mode (@pxref{Shell Mode,,, emacs, The Gnu Emacs Reference Manual}). Command-line completion of @Sl{} objects and a number of `hot keys' for commonly-used @Sl{} commands are also provided for ease of typing. @menu * Command-line editing:: Entering commands and fixing mistakes * Completion:: Completion of object names * Completion details:: Advanced completion concepts * Transcript:: Manipulating the transcript * Command History:: Command History * History expansion:: References to historical commands * Hot keys:: Hot keys for common commands * Statistical Process running in ESS?:: * Emacsclient:: Using emacsclient * Other:: Other commands provided by inferior-ESS @end menu @comment node-name, next, previous, up @node Command-line editing, Completion, Entering commands, Entering commands @section Entering commands and fixing mistakes @cindex command-line editing Sending a command to the ESS process is as simple as typing it in and pressing the @key{RETURN} key: @itemize @bullet @item @kbd{RET} (@code{inferior-ess-send-input}) @* @pindex inferior-ess-send-input Send the command on the current line to the ESS process. @end itemize If you make a typing error before pressing @kbd{RET} all the usual Emacs editing commands are available to correct it (@pxref{Basic, Basic, Basic editing commands, emacs, The GNU Emacs Reference Manual}). Once the command has been corrected you can press @key{RETURN} (even if the cursor is not at the end of the line) to send the corrected command to the ESS process. ESS provides some other commands which are useful for fixing mistakes: @itemize @bullet @item @kbd{C-c C-w} (@code{backward-kill-word}) @* @pindex backward-kill-word Deletes the previous word (such as an object name) on the command line. @item @kbd{C-c C-u} (@code{comint-kill-input}) @* @pindex comint-kill-input Deletes everything from the prompt to point. Use this to abandon a command you have not yet sent to the ESS process. @item @kbd{C-c C-a} (@code{comint-bol}) @* @pindex comint-bol Move to the beginning of the line, and then skip forwards past the prompt, if any. @end itemize @xref{Shell Mode,,, emacs, The Gnu Emacs Reference Manual}, for other commands relevant to entering input. @comment node-name, next, previous, up @node Completion, Completion details, Command-line editing, Entering commands @section Completion of object names @cindex completion of object names @cindex command-line completion In the process buffer, the @key{TAB} key is for completion, similar to that provided by Shell Mode for filenames. In Inferior @Sl{} mode, pressing the @key{TAB} key when the cursor is following the first few characters of an object name @emph{completes} the object name; if the cursor is following a file name @kbd{TAB} completes the file name. @itemize @bullet @item @kbd{TAB} (@code{comint-dynamic-complete}) @* @pindex comint-dynamic-complete Complete the @Sl{} object name or filename before point. @end itemize When the cursor is just after a partially-completed object name, pressing @key{TAB} provides completion in a similar fashion to @code{tcsh} @cindex tcsh except that completion is performed over all known @Sl{} 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()} command @pindex search() along with the component objects of attached data frames @cindex data frames (if your version of @Sl{} supports them). For example, consider the three functions (available in Splus version 3.0) called @code{binomplot()}, @code{binom.test()} and @code{binomial()}. Typing @kbd{bin TAB} after the @Sl{} prompt will insert the characters @samp{om}, completing the longest prefix (@samp{binom}) which distinguishes these three commands. Pressing @kbd{TAB} once more provides a list of the three commands which have this prefix, allowing you to add more characters (say, @samp{.}) which specify the function you desire. After entering more characters pressing @kbd{TAB} 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-?}. @itemize @bullet @item @kbd{M-?} (@code{ess-list-object-completions}) @* @pindex ess-list-object-completions List all possible completions of the object name at point. @end itemize ESS also provides completion over the components of named lists accessed using the @samp{$} notation, to any level of nested lists. This feature is particularly useful for checking what components of a list object exist while partway through entering a command: simply type the object name and @samp{$} and press @kbd{TAB} to see the names of existing list components for that object. @cindex lists, completion on @cindex completion on lists @cindex completion on file names Completion is also provided over file names, which is particularly useful when using @Sl{} functions such as @code{get()} or @code{scan()} which require fully expanded file names. Whenever the cursor is within an @Sl{} string, pressing @kbd{TAB} completes the file name before point. Since ESS 5.11, it no longer also expands any @samp{~} or environment variable references. If the cursor is not in a string and does not follow a (partial) object name, the @key{TAB} key has a third use: it expands history references. @xref{History expansion}. @comment node-name, next, previous, up @node Completion details, Transcript, Completion, Entering commands @section Completion details ESS automatically keeps track of any objects added or deleted to the system (such as new objects created, or directories added to the search list) to make completion as accurate as possible. Whenever ESS notices that search list has changed @vindex ess-change-sp-regexp @footnote{The variable @code{ess-change-sp-regexp} is a regular expression matching commands which change the search list. You will need to modify this variable if you have defined custom commands (other than @code{attach}, @code{detach}, @code{collection} or @code{library}) which modify the search list.} when you attach a directory or data frame, the objects associated with it immediately become available for a completion; when it is detached completion is no longer available on those objects. To maintain a list of accessible objects for completion, ESS needs to determine which objects are contained in each directory or data frame on the search list. This is done at the start of each @Sl{} session, by running the @code{objects()} command on every element of the search list. @c On some systems, however, this can be rather slow; it's doubly @c frustrating when you consider that most of the directories on the search @c list are the standard @Sl{} libraries, which never change anyway! When @c ESS was installed, a database of the standard object names should have @c been created which should speed up this process at the start of an S @c session; if it has not been created you will get a warning like @c `S-namedb.el does not exist'. @xref{Installation}, for information on @c how to create this database. 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} is there), the command @kbd{M-x ess-resynch} @pindex ess-resynch forces the @emph{entire} cache to be refreshed, which should fix the problem. @comment node-name, next, previous, up @node Transcript, Command History, Completion details, Entering commands @section Manipulating the transcript 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 @cindex transcript move back up through the buffer, to look at the output from previous commands for example. Within the process buffer, a paragraph @cindex paragraphs in the process buffer is defined as the prompt, the command after the prompt, and the output from the command. Thus @kbd{M-@{} and @kbd{M-@}} move you backwards and forwards, respectively, through commands in the transcript. A particularly useful command is @kbd{M-h} (@code{mark-paragraph}) which will allow you to mark a command and its entire output (for deletion, perhaps). For more information about paragraph commands, @pxref{Paragraphs, Paragraphs, Paragraphs, emacs, The GNU Emacs Reference Manual}. 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}) character. Thus pages in the ESS @cindex pages in the process buffer process buffer correspond to ESS sessions. Thus, for example, you may use @kbd{C-x [} and @kbd{C-x ]} to move backward and forwards through ESS sessions in a single ESS process buffer. For more information about page commands, @pxref{Pages, Pages, Pages, emacs, The GNU Emacs Reference Manual}. @menu * Last command:: Manipulating the output from the last command * Process buffer motion:: Viewing older commands * Transcript resubmit:: Re-submitting commands from the transcript * Saving transcripts:: Keeping a record of your S session @end menu @comment node-name, next, previous, up @node Last command, Process buffer motion, Transcript, Transcript @subsection Manipulating the output from the last command Viewing the output of the command you have just entered is a common occurrence and ESS provides a number of facilities for doing this. @c Within the ESS process buffer, the variable @code{scroll-step} @c @vindex scroll-step @c is set to 4 (you can redefine this using @code{inferior-ess-mode-hook} @c @vindex inferior-ess-hook @c if you wish - @pxref{Hooks},) so that the cursor is usually near the @c bottom of the window. 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 command @itemize @bullet @item @kbd{C-c C-e} (@code{comint-show-maximum-output}) @* @pindex comint-show-maximum-output Move to the end of the buffer, and place cursor on bottom line of window. @end itemize @noindent 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} to @code{t}.) If the first part of the output is still obscured, use @cindex reading long command outputs @itemize @bullet @item @kbd{C-c C-r} (@code{comint-show-output}) @* @pindex comint-show-output Moves cursor to the previous command line and and places it at the top of the window. @end itemize @noindent to view it. Finally, if you want to discard the last command output altogether, use @itemize @bullet @item @kbd{C-c C-o} (@code{comint-kill-output}) @* @pindex comint-kill-output @cindex deleting output Deletes everything from the last command to the current prompt. @end itemize @noindent to delete it. Use this command judiciously to keep your transcript to a more manageable size. @comment node-name, next, previous, up @node Process buffer motion, Transcript resubmit, Last command, Transcript @subsection Viewing older commands 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: @itemize @bullet @item @kbd{C-c C-p} (@code{comint-previous-input}) @* @pindex comint-previous-input Moves point to the preceding command in the process buffer. @item @kbd{C-c C-n} (@code{comint-next-input}) @* @pindex comint-next-input Moves point to the next command in the process buffer. @end itemize @noindent Note that these two commands are analogous to @kbd{C-p} and @kbd{C-n} but apply to command lines rather than text lines. And just like @kbd{C-p} and @kbd{C-n}, passing a prefix argument to these commands means to move to the @var{ARG}'th next (or previous) command. (These commands are also discussed in @ref{Shell History Copying,,Shell History Copying,emacs, The GNU Emacs Reference Manual}.) 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 (@pxref{Regexps,,Syntax of Regular Expression,emacs, The GNU Emacs Reference Manual}), and then moves to the next (previous) command matching the pattern. @itemize @bullet @item @code{(comint-backward-matching-input regexp arg)} @* @pindex comint-backward-matching-input @code{(comint-forward-matching-input regexp arg)} @* @pindex comint-forward-matching-input Search backward (forward) through the transcript buffer for the @var{arg}'th previous (next) command matching @var{regexp}. @var{arg} is the prefix argument; @var{regexp} is prompted for in the minibuffer. @end itemize @comment node-name, next, previous, up @node Transcript resubmit, Saving transcripts, Process buffer motion, Transcript @subsection Re-submitting commands from the transcript 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 @emph{output}, an error is signalled). Note all three commands involve the @key{RETURN} key. @itemize @bullet @item @kbd{RET} (@code{inferior-ess-send-input}) @* @pindex inferior-ess-send-input Copy the command under the cursor to the current command line, and execute it. @item @kbd{C-c RET} (@code{comint-copy-old-input}) @* @pindex comint-copy-old-input 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. @item @kbd{M-RET} (@code{ess-transcript-send-command-and-move}) @* @pindex ess-transcript-send-command-and-move Copy the command under the cursor to the current command line, and execute it. Moves the cursor to the following command. @end itemize When the cursor is not after the current prompt, the @key{RETURN} key has a slightly different behavior than usual. Pressing @kbd{RET} 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} instead; it copies the command to the current prompt but does not execute it, allowing you to edit it before submitting it. These two commands leave the cursor at the new command line, allowing you to continue with interactive use of S. If you wish to resubmit a series of commands from the transcript, consider using @kbd{M-RET} instead, which leaves the cursor at the command line following the one you re-submitted. Thus by using @kbd{M-RET} repeatedly, you can re-submit a whole series of commands. These commands work even if if the current line is a continuation line (i.e. the prompt is @samp{+} instead of @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 @cindex multi-line commands, resubmitting 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 @ref{Command History}. @comment node-name, next, previous, up @node Saving transcripts, , Transcript resubmit, Transcript @subsection Keeping a record of your S session To keep a record of your @Sl{} session in a disk file, use the Emacs command @kbd{C-x C-w} (@code{write-file}) 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 @Sl{} as usual; just remember to save the file before you quit Emacs with @kbd{C-x C-s}. You can make ESS prompt you for a filename in which to save the transcript every time you start @Sl{} by setting the variable @vindex ess-ask-about-transfile @code{ess-ask-about-transfile} to @code{t}; see @ref{Customizing startup}. @cindex transcript file names We recommend you save your transcripts with filenames that end in @samp{.St}. There is a special mode (ESS transcript mode --- @pxref{Transcript Mode}) for editing transcript files which is automatically selected for files with this suffix. @cindex editing transcripts 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} 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}. Also, remember that @kbd{C-c C-e} (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. Finally, if you intend to produce @Sl{} source code (suitable for using with @code{source()} or inclusion in an @Sl{} function) from a transcript, then the command @kbd{M-x ess-transcript-clean-region} may be of use. @pindex ess-transcript-clean-region This command works in any Emacs buffer, and removes all prompts and command output from an ESS transcript within the current region, leaving only the commands. Don't forget to remove any erroneous commands first! @comment node-name, next, previous, up @node Command History, History expansion, Transcript, Entering commands @section Command History @cindex command history @cindex editing commands @cindex re-executing commands 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 50 commands are stored, although this can be changed by setting the variable @code{comint-input-ring-size} in @vindex comint-input-ring-size @code{inferior-ess-mode-hook}.) The simplest history commands simply select the next and previous commands in the input history: @itemize @bullet @item @kbd{M-p} (@code{comint-previous-input}) @* @pindex comint-previous-input Select the previous command in the input history. @item @kbd{M-n} (@code{comint-next-input}) @* @pindex comint-next-input Select the next command in the input history. @end itemize @noindent For example, pressing @kbd{M-p} 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} to send the edited command to the ESS process. If you want to select a particular command from the history by matching it against a regular expression (@pxref{Regexps,,Syntax of Regular Expression,emacs, The GNU Emacs Reference Manual}), to search for a particular variable name for example, these commands are also available: @itemize @bullet @item @kbd{M-r} (@code{comint-previous-matching-input}) @* @pindex comint-previous-matching-input Prompt for a regular expression, and search backwards through the input history for a command matching the expression. @item @kbd{M-s} (@code{comint-next-matching-input}) @* @pindex comint-next-matching-input Prompt for a regular expression, and search backwards through the input history for a command matching the expression. @end itemize @noindent 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: @itemize @bullet @item @kbd{A-M-r} (@code{comint-previous-matching-input-from-input}) @* @pindex comint-previous-matching-input-from-input Select the previous command in the history which matches the string typed so far. @item @kbd{A-M-s} (@code{comint-next-matching-input-from-input}) @* @pindex comint-next-matching-input-from-input Select the next command in the history which matches the string typed so far. @end itemize @noindent 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()} command, you may only need to type @kbd{att} and then @kbd{A-M-r} and @kbd{RET}. (Note: you may not have an @key{ALT} key on your keyboard, in which case it may be a good idea to bind these commands to some other keys.) @xref{Shell Ring,,Shell History Ring,emacs, The GNU Emacs Reference Manual}, for a more detailed discussion of the history mechanism. @comment node-name, next, previous, up @node History expansion, Hot keys, Command History, Entering commands @section References to historical commands 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}. History references are introduced by a @samp{!} or @samp{^} character and have meanings as follows: @table @samp @item !! The immediately previous command @item !-@var{N} The @var{N}th previous command @item !text The last command beginning with the string @samp{text} @item !?text The last command containing the string @samp{text} @end table In addition, you may follow the reference with a @dfn{word designator} to select particular @dfn{words} 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} to a list of characters that are allowed to separate words and @vindex comint-delimiter-argument-list themselves form words.) Words are numbered beginning with zero. The word designator usually begins with a @samp{:} (colon) character; however it may be omitted if the word reference begins with a @samp{^}, @samp{$}, @samp{*} or @samp{-}. If the word is to be selected from the previous command, the second @samp{!} character can be omitted from the event specification. For instance, @samp{!!:1} and @samp{!:1} both refer to the first word of the previous command, while @samp{!!$} and @samp{!$} both refer to the last word in the previous command. The format of word designators is as follows: @table @samp @item 0 The zeroth word (i.e. the first one on the command line) @item @var{n} The @var{n}th word, where @var{n} is a number @item ^ The first word (i.e. the second one on the command line) @item $ The last word @item @var{x}-@var{y} A range of words; @samp{-@var{y}} abbreviates @samp{0-@var{y}} @item * All the words except the zeroth word, or nothing if the command had just one word (the zeroth) @item @var{x}* Abbreviates @var{x}-$ @item @var{x}- Like @samp{@var{x}*}, but omitting the last word @end table In addition, you may surround the entire reference except for the first @samp{!} by braces to allow it to be followed by other (non-whitespace) characters (which will be appended to the expanded reference). Finally, ESS also provides quick substitution; a reference like @samp{^old^new^} means ``the last command, but with the first occurrence of the string @samp{old} replaced with the string @samp{new}'' (the last @samp{^} is optional). Similarly, @samp{^old^} means ``the last command, with the first occurrence of the string @samp{old} deleted'' (again, the last @samp{^} is optional). To convert a history reference as described above to an input suitable for S, you need to @dfn{expand} the history reference, using the @key{TAB} 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}. This will convert the history reference into an @Sl{} command from the history, which you can then edit or press @key{RET} to execute. For example, to execute the last command that referenced the variable @code{data}, type @kbd{!?data SPC TAB RET}. @comment node-name, next, previous, up @node Hot keys, Statistical Process running in ESS?, History expansion, Entering commands @section Hot keys for common commands ESS provides a number of commands for executing the commonly used functions. These commands below are basically information-gaining commands (such as @code{objects()} or @code{search()}) 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 variable @code{ess-execute-in-process-buffer} which, if @vindex ess-execute-in-process-buffer non-@code{nil}, means that these commands will produce their output in the process buffer instead. In any case, passing a prefix argument to the commands (with @kbd{C-u}) will reverse the meaning of @code{ess-execute-in-process-buffer} 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: @itemize @bullet @item @kbd{C-c C-x} (@code{ess-execute-objects}) @* @pindex ess-execute-objects Sends the @code{objects()} @pindex objects() 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} as well). A quick way to see what objects are in your working directory. @cindex objects @pindex objects() @item @kbd{C-c C-s} (@code{ess-execute-search}) @* @pindex ess-execute-search Sends the @code{search()} @pindex search() command to the ESS process. @cindex search list @pindex search() @item @kbd{C-c C-e} (@code{ess-execute}) @* @pindex ess-execute Prompt for an ESS expression, and evaluate it. @end itemize @code{ess-execute} 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; @pxref{Keyboard Macros, Keyboard Macros, Keyboard Macros, emacs, The GNU Emacs Reference Manual}. @cindex hot keys @cindex keyboard short cuts The following hot keys do not use @code{ess-execute-in-process-buffer} to decide where to display the output --- they either always display in the process buffer or in a separate buffer, as indicated: @itemize @bullet @item @kbd{C-c C-a} (@code{ess-execute-attach}) @* @pindex ess-execute-attach Prompts for a directory to attach to the ESS process with the @code{attach()} command. @pindex attach() If a numeric prefix argument is given it is used as the position on the search list to attach the directory; otherwise the @Sl{} default of 2 is used. The @code{attach()} command actually executed appears in the process buffer. @item @kbd{C-c C-l} (@code{ess-load-file}) @* @pindex ess-load-file Prompts for a file to load into the ESS process using @code{source()}. If there is an error during loading, you can jump to the error in the file with @kbd{C-x `} (@code{ess-parse-errors}). @pindex ess-parse-errors @xref{Error Checking}, for more details. @item @kbd{C-c C-v} (@code{ess-display-help-on-object}) @* Pops up a help buffer for an @Sl{} object or function. See @ref{Help} for more details. @item @kbd{C-c C-q} (@code{ess-quit}) @* @cindex quitting from ESS @cindex killing the ESS process Sends the @code{q()} @pindex q() command to the ESS process (or @code{(exit)} @pindex exit() to the @b{XLS} process), and cleans up any temporary buffers (such as help buffers or edit buffers) you may have created along the way. Use this command when you have finished your @Sl{} session instead of simply typing @code{q()} yourself, otherwise you will need to issue the command @kbd{M-x ess-cleanup} @pindex ess-cleanup @cindex cleaning up @cindex temporary buffers, killing @cindex killing temporary buffers command 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. @end itemize @comment node-name, next, previous, up @node Statistical Process running in ESS?, Emacsclient, Hot keys, Entering commands @section Is the Statistical Process running under ESS? @cindex STERM @pindex STERM 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. ESS sets @code{options(STERM="iESS")} for S language processes running in an inferior @code{@iESS{[S]}} or @code{@iESS{[R]}} buffer. ESS sets @code{options(STERM="ddeESS")} 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]} buffer. Other values of @code{options()$STERM} that we recommend are: @itemize @bullet @item @code{length}: Fixed length xterm or telnet window. @item @code{scrollable}: Unlimited length xterm or telnet window. @item @code{server}: S-Plus Stat Server. @item @code{BATCH}: BATCH. @item @code{Rgui}: R GUI. @item @code{Commands}: S-Plus GUI without DDE interface to ESS. @end itemize Additional values may be recommended in the future as new interaction protocols are created. Unlike the values @code{iESS} and @code{ddeESS}, ESS can't set these other values since the S language program is not under the control of ESS. @comment node-name, next, previous, up @node Emacsclient, Other, Statistical Process running in ESS?, Entering commands @section Using emacsclient @cindex emacsclient When starting R or S under Unix, ESS sets @code{options(editor="emacsclient")}. (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}, typing @code{fix(iterator)}, 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()} rather than @code{fix()} means that the function is not updated. Finally, the S function @code{page(x)} will also show a text representation of the object @code{x} in a temporary Emacs buffer. @comment node-name, next, previous, up @node Other, , Emacsclient, Entering commands @section Other commands provided by inferior-ESS The following commands are also provided in the process buffer: @itemize @bullet @item @kbd{C-c C-c} (@code{comint-interrupt-subjob}) @* @pindex comint-interrupt-subjob Sends a Control-C signal to the ESS process. This has the effect of @cindex aborting S commands @cindex interrupting S commands aborting the current command. @item @kbd{C-c C-z} (@code{ess-abort}) @* @pindex ess-abort @pindex comint-stop-subjob Sends a STOP signal to the ESS process, killing it immediately. It's not a good idea to use this, in general: Neither @code{q()} nor @code{.Last} will be executed and device drivers will not finish cleanly. This command is provided as a safety to @code{comint-stop-subjob}, which is usually bound to @kbd{C-c C-z}. If you want to quit from S, use @kbd{C-c C-q} (@code{ess-quit}) instead. @pindex ess-quit @cindex aborting the ESS process @item @kbd{C-c C-d} (@code{ess-dump-object-into-edit-buffer}) @* @pindex ess-dump-object-into-edit-buffer Prompts for an object to be edited in an edit buffer. @xref{Editing}. @end itemize Other commands available in Inferior @Sl{} mode are discussed in @ref{Shell Mode,,, emacs, The Gnu Emacs Reference Manual}. @comment node-name, next, previous, up @node Transcript Mode, ESS for the S family, Entering commands, Top @chapter Manipulating saved transcript files Inferior @Sl{} mode records the transcript (the list of all commands executed, and their output) in the process buffer, which can be saved as a @dfn{transcript file}, which should normally have the suffix @file{.St}. The most obvious use for a transcript file is as a static record of the actions you have performed in a particular @Sl{} 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. If you load file a with the suffix @file{.St} into Emacs, it is placed in S Transcript Mode. Transcript Mode is similar to Inferior @Sl{} mode (@pxref{Entering commands}): @cindex transcript mode motion @cindex motion in transcript mode 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} and @kbd{C-c C-n}. @menu * Resubmit:: Resubmitting commands from the transcript file * Clean:: Cleaning transcript files @end menu @comment node-name, next, previous, up @node Resubmit, Clean, Transcript Mode, Transcript Mode @section Resubmitting commands from the transcript file Three commands are provided to re-submit command lines from the transcript file to a running ESS process. They are: @itemize @bullet @item @kbd{RET} (@code{ess-transcript-send-command}) @* Send the current command line to the ESS process, and execute it. @pindex ess-transcript-send-command @item @kbd{C-c RET} (@code{ess-transcript-copy-command}) @* Copy the current command to the ESS process, and switch to the ESS process buffer (ready to edit the copied command). @pindex ess-transcript-copy-command @item @kbd{M-RET} (@code{ess-transcript-send-command-and-move}) @* Send the current command to the ESS process, and move to the next command line. This command is useful for submitting a series of commands. @end itemize @noindent Note that these commands are similar to those on the same keys in Inferior @Sl{} 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. @comment node-name, next, previous, up @node Clean, , Resubmit, Transcript Mode @section Cleaning transcript files Yet another use for transcript files is to extract the command lines for inclusion in an @Sl{} source file or function. Transcript mode provides one command which does just this: @itemize @bullet @item @kbd{C-c C-w} (@code{ess-transcript-clean-region}) @* Deletes all prompts and command output in the region, leaving only the commands themselves. @end itemize @noindent 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 (@pxref{Evaluating code}) using the code evaluation commands from @Sl{} mode, also available in @Sl{} Transcript Mode. @comment node-name, next, previous, up @node ESS for the S family, Editing, Transcript Mode, Top @chapter ESS for the S family @menu * ESS(S)--Editing files:: * iESS(S)--Inferior ESS processes:: * ESS-help--assistance with viewing help:: * Philosophies for using ESS(S):: * Scenarios for use (possibilities--based on actual usage):: * Customization Examples and Solutions to Problems:: @end menu @include help-s.texi @comment node-name, next, previous, up @node Editing, Editing R documentation, ESS for the S family, Top @chapter Editing S functions @cindex editing functions ESS provides facilities for editing @Sl{} objects within your Emacs session. Most editing is performed on @Sl{} 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 @Sl{} functions. Error-checking is performed when @Sl{} code is loaded into the ESS process. @menu * Edit buffer:: Edit objects in a specialized buffer * Loading:: Loading source files into the ESS process * Error Checking:: Detecting errors in source files * Evaluating code:: Sending code to the ESS process * Indenting:: Indenting and formatting S code * Other edit buffer commands:: Commands for motion, completion and more * Source Files:: Maintaining @Sl{} source files * Source Directories:: Names and locations of dump files @end menu @comment node-name, next, previous, up @node Edit buffer, Loading, Editing, Editing @section Creating or modifying S objects @cindex edit buffer To edit an @Sl{} object, type @itemize @bullet @item @kbd{C-c C-d} (@code{ess-dump-object-into-edit-buffer}) @* @pindex ess-dump-object-into-edit-buffer Edit an @Sl{} object in its own edit buffer. @end itemize from within the ESS process buffer (@code{*S*}). 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} key), @cindex completion, when prompted for object names or you may enter the name of a new object. @cindex creating new objects @cindex new objects, creating 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} @vindex ess-function-template is non-@code{nil}, you will be presented with a template defined by that variable, which defaults to a skeleton function construct. You may then edit the function as required. The edit buffer generated by @code{ess-dump-object-into-edit-buffer} is placed in the @code{ESS} major mode which provides a number of commands to facilitate editing @Sl{} source code. Commands are provided to intelligently indent @Sl{} code, evaluate portions of @Sl{} code and to move around @Sl{} code constructs. @cindex dump files @cindex reverting function definitions Note: when you dump a file with @kbd{C-c C-d}, 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 (@pxref{Source Files}) 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 @Sl{} session). Finally, if both these tests fail, the ESS process is consulted and a @code{dump()} command issued. @pindex dump() 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} by typing @kbd{C-u C-c C-d}. @comment node-name, next, previous, up @node Loading, Error Checking, Edit buffer, Editing @section Loading source files into the ESS process The best way to get information --- particularly function definitions --- into @Sl{} is to load them in as source file, using S's @code{source} function. You have already seen how to create source files using @kbd{C-c C-d}; ESS provides a complementary command for loading source files (even files not created with ESS!) into the ESS process: @itemize @bullet @item @kbd{C-c C-l} (@code{ess-load-file}) @* @pindex ess-load-file Loads a file into the ESS process using @code{source()}. @pindex source() @end itemize @noindent After typing @kbd{C-c C-l} you will prompted 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} 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-d}). The file will then be loaded, and if it loads successfully you will be returned to the ESS process. @comment node-name, next, previous, up @node Error Checking, Evaluating code, Loading, Editing @section Detecting errors in source files @cindex errors @cindex parsing errors If any errors occur when loading a file with @code{C-c C-l}, 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 `} (@code{ess-parse-errors}). @pindex ess-parse-errors You will be returned to the offending file (loading it into a buffer if necessary) with point at the line @Sl{} reported as containing the error. You may then correct the error, and reload the file. Note that none of the commands in an @Sl{} source file will take effect if any part of the file contains errors. Sometimes the error is not caused by a syntax error (loading a non-existent file for example). In this case typing @kbd{C-c `} will simply display a buffer containing S's error message. You can force this behavior (and avoid jumping to the file when there @emph{is} a syntax error) by passing a prefix argument to @code{ess-parse-errors} with @kbd{C-u C-c `}. @comment node-name, next, previous, up @node Evaluating code, Indenting, Error Checking, Editing @section Sending code to the ESS process 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()} 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 @code{ess-eval-visibly-p} whose default is @code{nil} @vindex ess-eval-visibly-p (display output only). Passing a prefix argument (@kbd{C-u}) to any of the following commands, however, reverses the meaning of @code{ess-eval-visibly-p} for that command only --- for example @kbd{C-u C-c C-j} echoes the current line of S (or other) code in the ESS process buffer, followed by its output. This method of evaluation is an alternative to S's @code{source()} function @pindex source() @cindex echoing commands when evaluating @cindex evaluating code with echoed commands when you want the input as well as the output to be displayed. (You can sort of do this with @code{source()} when the option @code{echo=T} is set, except that prompts do not get displayed. ESS puts prompts in the right places.) The commands for evaluating code are: @itemize @bullet @cindex evaluating S expressions @item @kbd{C-c C-j} (@code{ess-eval-line}) @* @pindex ess-eval-line Send the line containing point to the ESS process. @item @kbd{C-c M-j} (@code{ess-eval-line-and-go}) @* @pindex ess-eval-line-and-go As above, but returns you to the ESS process buffer as well. @item @kbd{C-c C-f} or @kbd{ESC C-x} (aka @kbd{M-C-x}) (@code{ess-eval-function}) @* @pindex ess-eval-function Send the @Sl{} function containing point to the ESS process. @item @kbd{C-c M-f} (@code{ess-eval-function-and-go}) @* @pindex ess-eval-function-and-go As above, but returns you to the ESS process buffer as well. @item @kbd{C-c C-r} (@code{ess-eval-region}) @* @pindex ess-eval-region Send the text between point and mark to the ESS process. @item @kbd{C-c M-r} (@code{ess-eval-region-and-go}) @* @pindex ess-eval-region-and-go As above, but returns you to the ESS process buffer as well. @item @kbd{C-c C-b} (@code{ess-eval-buffer}) @* @pindex ess-eval-buffer Send the contents of the edit buffer to the ESS process. @item @kbd{C-c M-b} (@code{ess-eval-buffer-and-go}) @* @pindex ess-eval-function-and-go As above, but returns you to the ESS process buffer as well. @item @kbd{C-c C-n} (@code{ess-eval-line-and-step}) @* @pindex ess-eval-line-and-step @cindex stepping through code @cindex debugging S functions Sends the current line to the ESS process, echoing it in the process buffer, and moves point to the next line. Useful when debugging for stepping through your code. @end itemize It should be stressed once again that these @code{ess-eval-} commands should only be used for evaluating small portions of code for debugging purposes, or for generating transcripts from source files. When editing S functions, @kbd{C-c C-l} is the command to use to update the function's value. In particular, @code{ess-eval-buffer} is now largely obsolete. One final command is provided for spot-evaluations of @Sl{} code: @itemize @bullet @kbd{C-c C-t} (@code{ess-execute-in-tb}) @* @pindex ess-execute-in-tb Prompt for an @Sl{} expression and evaluate it. Displays result in a temporary buffer. @end itemize @noindent This is useful for quick calculations, etc. All the above commands are useful for evaluating small amounts of code and observing the results in the process buffer. 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} to @code{'others} or @code{t}. @comment node-name, next, previous, up @node Indenting, Other edit buffer commands, Evaluating code, Editing @section Indenting and formatting S code ESS provides a sophisticated mechanism for indenting @Sl{} source code (thanks to Ken'ichi Shibayama). Compound statements (delimited by @samp{@{} and @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} statements, calls to @code{expression()} and loop constructs are all recognized and indented appropriately. User variables are provided to control the amount if indentation in each case, and there are also a number of predefined indentation styles to choose from. @cindex comments in S Comments are also handled specially by ESS, using an idea borrowed from the Emacs-Lisp indentation style. By default, comments beginning with @samp{###} are aligned to the beginning of the line. Comments beginning with @samp{##} are aligned to the current level of indentation for the block containing the comment. Finally, comments beginning with @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},) @vindex comment-column 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-fancy-comments nil)} to your @file{.emacs} file. @vindex ess-fancy-comments ESS also supports Roxygen entries which is R documentation maintained in the source code as comments @xref{Roxygen}. The indentation commands provided by ESS are: @cindex indenting @cindex formatting source code @itemize @bullet @item @kbd{TAB} (@code{ess-indent-command}) @* Indents the current line as @Sl{} code. If a prefix argument is given, all following lines which are part of the same (compound) expression are indented by the same amount (but relative indents are preserved). @item @kbd{RET} (@code{newline-and-indent}) @* @kbd{LFD} (@emph{newline-and-indent}) @* Insert a newline, and indent the next line. (Note that most keyboards nowadays do not have a @key{LINEFEED} key, but @kbd{C-j} is equivalent.) @item @kbd{ESC C-q} aka @kbd{M-C-q} aka @kbd{C-M-q} (@code{ess-indent-exp}) @* Indents each line in the @Sl{} (compound) expression which follows point. Very useful for beautifying your @Sl{} code. @item @kbd{@{} and @kbd{@}} (@code{ess-electric-brace}) @* The braces automatically indent to the correct position when typed. @item @kbd{M-;} (@code{indent-for-comment}) @* Indents an existing comment line appropriately, or inserts an appropriate comment marker. @item @kbd{M-x ess-set-style} @* Set the formatting style in this buffer to be one of the predefined styles, including @code{GNU}, @code{BSD}, @code{K&R}, @code{CLB}, and @code{C++}. The @code{DEFAULT} style uses the default values for the indenting variables; The @code{OWN} style allows you to use your own private values of the indentation variable, see below. @end itemize @menu * Styles:: Changing indentation styles @end menu @comment node-name, next, previous, up @node Styles, , Indenting, Indenting @subsection Changing indentation styles The combined value of nine variables that control indentation are collectively termed a @i{style}. ESS provides several styles covering the common styles of indentation: @code{DEFAULT}, @code{OWN}, @code{GNU}, @code{BSD}, @code{K&R}, @code{C++}, @code{RRR}, @code{CLB}. The variable @code{ess-style-alist} lists the value of each indentation variable per style. If you wish to change from one predefined style to another, change the variable @code{ess-default-style}, for example: @example (setq ess-default-style 'C++) @end example The styles @code{DEFAULT} and @code{OWN} are initially identical. If you wish to edit some of the default values, set @code{ess-default-style} to @code{'OWN} and change @code{ess-own-style-list}. @xref{Customization}, for convenient ways to set both these variables. If you prefer not to use the custom facility, you can change individual indentation variables within a hook, for example: @example (defun myindent-ess-hook () (setq ess-indent-level 4)) (add-hook 'ess-mode-hook 'myindent-ess-hook) @end example 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} to a new variable and ensure that the last line of the @code{:set} declaration calls @code{ess-add-style} with a unique name for your style (e.g. @code{'MINE}). Finally, add @code{(setq ess-default-style 'MINE)} to use your new style. @comment node-name, next, previous, up @node Other edit buffer commands, Source Files, Indenting, Editing @section Commands for motion, completion and more A number of commands are provided to move across function definitions in the edit buffer: @itemize @bullet @item @kbd{ESC C-a} aka @kbd{C-M-a} (@code{ess-beginning-of-function}) @* @pindex ess-beginning-of-function Moves point to the beginning of the function containing point. @item @kbd{ESC C-e} aka @kbd{C-M-e} (@code{ess-end-of-function}) @* @pindex ess-end-of-function Moves point to the end of the function containing point. @item @kbd{ESC C-h} aka @kbd{C-M-h} (@code{ess-mark-function}) @* Places point at the beginning of the @Sl{} function containing point, and mark at the end. @end itemize @noindent Don't forget the usual Emacs commands for moving over balanced expressions and parentheses: @xref{Lists, Lists and Sexps, Lists and Sexps, Emacs, The GNU Emacs Reference Manual}. @cindex completion in edit buffer Completion is provided in the edit buffer in a similar fashion to the process buffer: @kbd{M-TAB} completes file names and @kbd{M-?} lists file completions. Since @key{TAB} is used for indentation in the edit buffer, object completion is now performed with @kbd{C-c TAB}. Note however that completion is only provided over globally known S objects (such as system functions) --- it will @emph{not} work for arguments to functions or other variables local to the function you are editing. Finally, two commands are provided for returning to the ESS process buffer: @itemize @bullet @item @kbd{C-c C-z} (@code{ess-switch-to-end-of-ESS}) @* @pindex ess-switch-to-end-of-ESS Returns you to the ESS process buffer, placing point at the end of the buffer. @item @kbd{C-c C-y} (@code{ess-switch-to-ESS}) @* @pindex ess-switch-to-ESS Also returns to to the ESS process buffer, but leaves point where it was. @end itemize In addition some commands available in the process buffer are also available in the edit buffer. You can still read help files with @kbd{C-c C-v}, edit another function with @kbd{C-c C-d} and of course @kbd{C-c C-l} can be used to load a source file into S. @xref{Other}, for more details on these commands. @comment node-name, next, previous, up @node Source Files, Source Directories, Other edit buffer commands, Editing @section Maintaining S source files Every edit buffer in ESS is associated with a @dfn{dump file} on disk. Dump files are created whenever you type @kbd{C-c C-d} (@code{ess-dump-object-into-edit-buffer}), and may either be deleted after use, or kept as a backup file or as a means of keeping several versions of an @Sl{} function. @cindex dump files @defvr {User Option} ess-delete-dump-files If non-@code{nil}, dump files created with C-c C-d are deleted immediately after they are created by the ess-process. @end defvr Since immediately after @Sl{} 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 @emph{don't} 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} function; it doesn't apply to source files which already exist. The default value is @code{t}. @defvr {User Option} ess-keep-dump-files Option controlling what to do with the dump file after an object has been successfully loaded into S. Valid values are @code{nil} (always delete), @code{ask} (always ask whether to delete), @code{check} (delete files generated with @kbd{C-c C-d} in this Emacs session, otherwise ask --- this is the default) and @code{t} (never delete). This variable is buffer-local. @end defvr After an object has been successfully (i.e. without error) loaded back into @Sl{} with @kbd{C-c C-l}, 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. @cindex comments @cindex project work in S @cindex historic backups If the value of @code{ess-keep-dump-files} is @code{t}, 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 --- @pxref{Backup Names, Single or Numbered Backups, Single or Numbered Backups, emacs, The Gnu Emacs Reference Manual}, you can keep a historic record of function definitions. Another possibility is to maintain the files with a version-control system such as RCS @xref{Version Control, Version Control, Version Control, emacs, The Gnu Emacs Reference Manual}. As long as a dump file exists in the appropriate place for a particular object, editing that object with @kbd{C-c C-d} finds that file for editing (unless a prefix argument is given) --- the ESS process is not consulted. Thus you can keep comments @emph{outside} the function definition as a means of documentation that does not clutter the @Sl{} object itself. Another useful feature is that you may format the code in any fashion you please without @Sl{} re-indenting the code every time you edit it. These features are particularly useful for project-based work. If the value of @code{ess-keep-dump-files} is nil, the dump file is always silently deleted after a successful load with @kbd{C-c C-l}. While this is useful for files that were created with @kbd{C-c C-d} 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} is buffer-local, you can make sure particular files are not deleted by setting it to @code{t} in the Local Variables section of the file @xref{File Variables, Local Variables in Files, Local Variables in Files, emacs, The Gnu Emacs Reference Manual}. A safer option is to set @code{ess-keep-dump-files} to @code{ask}; 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-d}, but not any other files, setting @code{ess-keep-dump-files} to @code{check} (the default value) will silently delete dump files created with @kbd{C-c C-d} 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. 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}, the dump file is @emph{never} 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. @cindex autosaving Dump buffers are always autosaved, regardless of the value of @code{ess-keep-dump-files}. @comment node-name, next, previous, up @node Source Directories, , Source Files, Editing @section Names and locations of dump files @cindex dump file names Every dump file should be given a unique file name, usually the dumped object name with some additions. @defvr {User Option} ess-dump-filename-template Template for filenames of dumped objects. @code{%s} is replaced by the object name. @end defvr @noindent By default, dump file names are the user name, followed by @samp{.} and the object and ending with @samp{.S}. Thus if user @code{joe} dumps the object @code{myfun} the dump file will have name @file{joe.myfun.S}. The username part is included to avoid clashes when dumping into a publicly-writable directory, such as @file{/tmp}; you may wish to remove this part if you are dumping into a directory owned by you. @cindex dump file directories You may also specify the directory in which dump files are written: @defvr {User Option} ess-source-directory Directory name (ending in a slash) where @Sl{} dump files are to be written. @end defvr By default, dump files are always written to @file{/tmp}, which is fine when @code{ess-keep-dump-files} is @code{nil}. If you are keeping dump files, then you will probably want to keep them somewhere in your home directory, say @file{~/S-source}. This could be achieved by including the following line in your @file{.emacs} file: @cindex @file{.emacs} file @example (setq ess-source-directory (expand-file-name "~/S-source/")) @end example 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} 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 @file{Src} of the directory the ESS process was run in. @example (setq ess-source-directory (lambda () (concat ess-directory "Src/"))) @end example @noindent @vindex ess-directory (@code{ess-directory} 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 @Sl{} working directory during an @Sl{} 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: @cindex search list @cindex working directory @example (setq ess-source-directory (lambda () (file-name-as-directory (expand-file-name (concat (car ess-search-list) "/.Src"))))) @end example @vindex ess-search-list 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. @node Editing R documentation, Help, Editing, Top @chapter Editing R documentation 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. @menu * R documentation files:: Edit objects in a specialized buffer * Roxygen:: Loading source files into the ESS process @end menu @node R documentation files, Roxygen, Editing R documentation, Editing R documentation @section Editing R documentation (Rd) files @R{} objects are documented in files written in the @dfn{R documentation} (``Rd''), a simple markup language closely resembling (La)@TeX{}, which can be processed into a variety of formats, including La@TeX{}, @acronym{HTML}, 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. Visiting an Rd file as characterized by its extension @file{Rd} 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). Note that R also accepts Rd files with extension @file{rd}; to activate @ESS{[Rd]} support for this extension, you may need to add @example (add-to-list 'auto-mode-alist '("\\.rd\\'" . Rd-mode)) @end example @noindent to one of your Emacs startup files. In Rd mode, the following special Emacs commands can be used in addition to the standard Emacs commands. @table @kbd @item C-h m Describe the features of Rd mode. @item LFD @itemx RET Reindent the current line, insert a newline and indent the new line (@code{reindent-then-newline-and-indent}). An abbrev before point is expanded if @code{abbrev-mode} is non-@code{nil}. @item TAB Indent current line based on its contents and on previous lines (@code{indent-according-to-mode}). @item C-c C-e Insert a ``skeleton'' with Rd markup for at least all mandatory entries in Rd files (@code{Rd-mode-insert-skeleton}). Note that many users might prefer to use the R function @code{prompt} 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). @item C-c C-f 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}). @kbd{C-c C-f} is only a prefix; see e.g.@: @kbd{C-c C-f TAB} 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}. @item C-c C-j Insert a suitably indented @samp{\item@{} on the next line (@code{Rd-mode-insert-item}). @item C-c C-p Preview a plain text version (``help file'', @pxref{Help}) generated from the Rd file (@code{Rd-preview-help}). @end table 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} provides access to on-line help, and @kbd{C-c C-n} 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} for all available commands. Rd mode also provides access to abbreviations for most of the Rd markup commands. Type @kbd{M-x list-abbrevs} with Abbrev mode turned on to list all available abbrevs. Note that all Rd abbrevs start with a grave accent. Rd mode can be customized via the following variables. @table @code @item Rd-mode-hook Hook to be run when Rd mode is entered. @item Rd-indent-level The indentation of Rd code with respect to containing blocks. Default is 2. @item Rd-to-help-command The shell command used for converting Rd source to help text. Default is @samp{R CMD Rd2txt}. @end table To automatically turn on the abbrev and font-lock features of Rd mode, add the following lines to one of your Emacs startup files: @example (add-hook 'Rd-mode-hook (lambda () (abbrev-mode 1) (font-lock-mode 1))) @end example @node Roxygen, , R documentation files, Editing R documentation @section Editing Roxygen documentation @cindex Roxygen @cindex roxy @cindex ess-roxy 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 @file{NAMESPACE} files. See the Roxygen documentation found via @uref{http://roxygen.org} for more information its usage. An example of an Roxygen entry for a simple R function can look like this: @example @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") @end verbatim @end example The entry is immediately preceding the object to document and all lines start with the Roxygen prefix string, in this case @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. 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. All ESS Roxygen support is defined in @file{ess-roxy.el} which is loaded by default in ESS. The following special Emacs commands are provided. @itemize @bullet @item @kbd{C-c C-o} (@code{ess-roxy-update-entry}) @* @pindex ess-roxy-update-entry 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} is non-nil. @item @kbd{C-c C-e C-c} (@code{ess-roxy-toggle-roxy-region}) @* @pindex ess-roxy-toggle-roxy-region Toggle the presence of the leading Roxygen string on all lines in the marked region. Convenient for transferring text to Roxygen entries and to evaluate example fields. @item @kbd{C-c C-e C-r} (@code{ess-roxy-preview-Rd}) @* @pindex ess-roxy-preview-Rd 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, i.e. @kbd{C-u C-c C-e C-r}, 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. @item @kbd{C-c C-e C-t} (@code{ess-roxy-preview-HTML}) @* @pindex ess-roxy-preview-Rd 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, i.e. @kbd{C-u C-c C-e C-t}, visit the generated HTML file instead. Requires the Roxygen and tools packages to be installed. @item @kbd{C-c C-e p} (@code{ess-roxy-previous-entry}) @* @pindex ess-roxy-previous-entry Go to start of the Roxygen entry above point. @item @kbd{C-c C-e n} (@code{ess-roxy-next-entry}) @* @pindex ess-roxy-next-entry Go to end of the Roxygen entry above point. @item @kbd{C-c C-e C-h} (@code{ess-roxy-hide-all}) @* @pindex ess-roxy-hide-all 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. ESS also advices the following standard editing functions in order to make Roxygen editing more intuitive: @item @kbd{C-c TAB} (@code{ess-R-complete-object-name}) @* @pindex ess-R-complete-object-name Complete Roxygen tag at point. E.g. doing @kbd{C-c TAB} when the point is at the end of @code{@@par} completes to @code{@@param}. @item @kbd{M-h} (@code{mark-paragraph}) @* @pindex mark-paragraph If the transient mark mode is active, place mark and point at start end end of the field at point and activate the mark. @item @kbd{TAB} (@code{ess-indent-command}) @* @pindex ess-indent-command If hide-show support is enabled, fold away the visibility of the Roxygen entry at point. @item @kbd{M-q} (@code{fill-paragraph}) @* @pindex fill-paragraph Fill the Roxygen field at point. @item @kbd{C-a} (@code{move-beginning-of-line}) @* @pindex move-beginning-of-line Move to the point directly to the right of the Roxygen start string. @item @kbd{ENTER} (@code{newline-and-indent}) @* @pindex newline-and-indent Insert a new line and the Roxygen prefix string. @end itemize @comment node-name, next, previous, up @node Help, ESS for SAS, Editing R documentation, Top @chapter Reading help files @cindex help files ESS provides an easy-to-use facility for reading @Sl{} help files from within Emacs. From within the ESS process buffer or any ESS edit buffer, typing @kbd{C-c C-v} (@code{ess-display-help-on-object}) @pindex ess-display-help-on-object 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. If the requested object has documentation, you will be popped into a buffer (named @code{*help(@var{obj-name})*}) 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: @itemize @bullet Help commands: @item @kbd{?} (@code{ess-describe-help-mode}) @* @pindex ess-describe-help-mode Pops up a help buffer with a list of the commands available in @Sl{} help mode. @item @kbd{h} (@code{ess-display-help-on-object}) @* @pindex ess-display-help-on-object Pop up a help buffer for a different object Paging commands: @cindex paging commands in help buffers @item @kbd{b} or @kbd{DEL} (@code{scroll-down}) @* Move one page backwards through the help file. @item @kbd{SPC} (@code{scroll-up}) @* Move one page forwards through the help file. @item @kbd{>} (@code{beginning-of-buffer}) and @kbd{<} (@code{end-of-buffer}) @* Move to the beginning and end of the help file, respectively. Section-based motion commands: @item @kbd{n} (@code{ess-skip-to-next-section}) and @kbd{p} (@code{ess-skip-to-previous-section}) @* Move to the next and previous @pindex ess-skip-to-next-section @pindex ess-skip-to-previous-section section header in the help file, respectively. A section header consists of a number of capitalized words, followed by a colon. In addition, the @kbd{s} 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:} instead of @samp{DESCRIPTION:} and also only some versions of S(-plus) have sections @samp{BACKGROUND}, @samp{BUGS}, @samp{OPTIONAL ARGUMENTS}, @samp{REQUIRED ARGUMENTS}, and @samp{SIDE EFFECTS}. @c The bindings are all in ../lisp/ess-s-l.el @c ess-help-*-sec-keys-alist @c @c S-plus only: @c @item b BACKGROUND: @c @item B BUGS: @c @item O OPTIONAL ARGUMENTS: @c @item R REQUIRED ARGUMENTS: @c S and S-plus only: @c @item S SIDE EFFECTS: Do use @kbd{s ?} to get the current list of active key bindings. @pindex ess-skip-to-help-section @table @samp @item a ARGUMENTS: @item b BACKGROUND: @item B BUGS: @item d DESCRIPTION: @item D DETAILS: @item e EXAMPLES: @item n NOTE: @item O OPTIONAL ARGUMENTS: @item R REQUIRED ARGUMENTS: @item r REFERENCES: @item s SEE ALSO: @item S SIDE EFFECTS: @item u USAGE: @item v VALUE: @item < Jumps to beginning of file @item > Jumps to end of file @item ? Pops up a help buffer with a list of the defined section motion keys. @end table Miscellaneous: @item @kbd{l} (@code{ess-eval-line-and-step}) @* @pindex ess-eval-line-and-step Evaluates the current line in the ESS process, and moves to the next line. Useful for running examples in help files. @item @kbd{r} (@code{ess-eval-region}) @* @pindex ess-eval-region Send the contents of the current region to the ESS process. Useful for running examples in help files. @item @kbd{/} (@code{isearch-forward}) @* Same as @kbd{C-s}. Quit commands: @item @kbd{q} (@code{ess-switch-to-end-of-ESS}) @* @pindex ess-switch-to-end-of-ESS Returns to the ESS process buffer in another window, leaving the help window visible. @item @kbd{k} (@code{kill-buffer}) @* Kills the help buffer. @item @kbd{x} (@code{ess-kill-buffer-and-go}) @* Return to the ESS process, killing this help buffer. @end itemize In addition, all of the ESS commands available in the edit buffers are also available in @Sl{} help mode (@pxref{Edit buffer}). Of course, the usual (non-editing) Emacs commands are available, and for convenience the digits and @key{-} act as prefix arguments. 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}) to @code{ess-display-help-on-object}. Help buffers are marked as temporary buffers in ESS, and are deleted when @code{ess-quit} or @code{ess-cleanup} are called. 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}. @pindex ess-quit @pindex ess-cleanup @cindex temporary buffers @comment node-name, next, previous, up @node ESS for SAS, ESS for BUGS, Help, Top @chapter ESS for SAS @menu * ESS(SAS)--Design philosophy:: * ESS(SAS)--Editing files:: * ESS(SAS)--TAB key:: * ESS(SAS)--Batch SAS processes:: * ESS(SAS)--Function keys for batch processing:: * iESS(SAS)--Interactive SAS processes:: * iESS(SAS)--Common problems:: * ESS(SAS)--Graphics:: * ESS(SAS)--Windows:: @end menu @include help-sas.texi @comment node-name, next, previous, up @node ESS for BUGS, ESS for JAGS, ESS for SAS, Top @chapter ESS for BUGS @menu * ESS(BUGS)--Model files:: * ESS(BUGS)--Command files:: * ESS(BUGS)--Log files:: @end menu @include help-bugs.texi @comment node-name, next, previous, up @node ESS for JAGS, Miscellaneous, ESS for BUGS, Top @chapter ESS for JAGS @menu * ESS(JAGS)--Model files:: * ESS(JAGS)--Command files:: * ESS(JAGS)--Log files:: @end menu @include help-jags.texi @comment node-name, next, previous, up @node Miscellaneous, Mailing lists/bug reports, ESS for JAGS, Top @chapter Other features of ESS ESS has a few miscellaneous features, which didn't fit anywhere else. @menu * Highlighting:: Syntactic highlighting of buffers * Parens:: Parenthesis matching * Graphics:: Using graphics with ESS * Imenu:: Support for Imenu in ESS * Toolbar:: Support for toolbar in ESS * TAGS:: Using TAGS for S files * Rdired:: Directory editor for R objects * Rutils:: R object/package management and help utilities * Org:: Interaction with Org mode * Sweave and AUCTeX:: Support for Sweave in ESS and AUCTeX * Debugging R:: Debugging R code in ESS @end menu @comment node-name, next, previous, up @node Highlighting, Parens, Miscellaneous, Miscellaneous @section Syntactic highlighting of buffers ESS provides Font-Lock (@pxref{Faces,,Using Multiple Typefaces, emacs, The Gnu Emacs Reference Manual}) patterns for Inferior @Sl{} Mode, S Mode, and @Sl{} Transcript Mode buffers. @cindex Font-lock mode @cindex highlighting Syntax highlighting within ESS buffers is controlled by the variable @code{ess-font-lock-mode}, which by default is true. Input to inferior ESS processes is also highlighted syntactically if @code{inferior-ess-font-lock-input} is non-nil (the default). If you change the value of either of these varibles, you need to restart emacs for your changes to take effect. @c To activate highlighting, you need to turn on Font Lock mode in the @c appropriate buffers. This can be done on a per-buffer basis with @c @kbd{M-x font-lock-mode}, or may be done by adding @c @code{turn-on-font-lock} to @code{inferior-ess-mode-hook}, @c @code{ess-mode-hook} and @code{ess-transcript-mode-hook}. Your systems @c administrator may have done this for you in @file{ess-site.el} @c (@pxref{Customization}). The font-lock patterns are defined in the following variables, which you may modify if desired: @defvar inferior-ess-R-font-lock-keywords Font-lock patterns for inferior *R* processes. (There is a corresponding @code{inferior-ess-S-font-lock-keywords} for *S* processes.) The default value highlights prompts, inputs, assignments, output messages, vector and matrix labels, and literals such as @samp{NA} and @code{TRUE}. @end defvar @defvar ess-R-mode-font-lock-keywords Font-lock patterns for ESS R programming mode. (There is a corresponding @code{ess-S-mode-font-lock-keywords} for S buffers.) The default value highlights function names, literals, assignments, source functions and reserved words. @end defvar @c 2007-11-08 - this var no longer exists. @c @defvar ess-trans-font-lock-keywords @c Font-lock patterns for ESS Transcript Mode. The default value @c highlights the same patterns as in Inferior ESS Mode. @c @end defvar @comment node-name, next, previous, up @node Parens, Graphics, Highlighting, Miscellaneous @section Parenthesis matching 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: @example (paren-set-mode 'paren) ;for XEmacs (show-paren-mode t) ;for Emacs @end example @comment node-name, next, previous, up @node Graphics, Imenu, Parens, Miscellaneous @section Using graphics with ESS @cindex graphics One of the main features of the @code{S} package is its ability to generate high-resolution graphics plots, and ESS provides a number of features for dealing with such plots. @menu * printer:: The printer() graphics driver * X11:: The X11() (and other X-windows based) driver * winjava:: Java Graphics Device @end menu @comment node-name, next, previous, up @node printer, X11, Graphics, Graphics @subsection Using ESS with the @code{printer()} driver This is the simplest (and least desirable) method of using graphics within ESS. S's @code{printer()} device driver produces crude character based plots which can be contained within the ESS process buffer itself. To start using character graphics, issue the @Sl{} command @example printer(width=79) @end example @pindex printer() (the @code{width=79} 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()} command is issued, which displays the current figure. @comment node-name, next, previous, up @node X11, winjava, printer, Graphics @subsection Using ESS with windowing devices @cindex X windows Of course, the ideal way to use graphics with ESS is to use a windowing system. Under X11, this requires that the DISPLAY environment variable be appropriately set, which may not always be the case within your Emacs process. ESS provides a facility for setting the value of DISPLAY before the ESS process is started if the variable @code{ess-ask-about-display} @pindex ess-ask-about-display is non-@code{nil}. @comment node-name, next, previous, up @node winjava, , X11, Graphics @subsection Java Graphics Device @cindex winjava S+6.1 and newer on Windows contains a java library that supports graphics. Send the commands: @example library(winjava) java.graph() @end example @noindent 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.) @comment node-name, next, previous, up @node Imenu, Toolbar, Graphics, Miscellaneous @section Imenu 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). 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}. This value is set by various ESS variables such as @code{ess-imenu-S-generic-expression}. @comment node-name, next, previous, up @node Toolbar, TAGS, Imenu, Miscellaneous @section Toolbar 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. @xref{Customization}, for ways to change the toolbar. @comment node-name, next, previous, up @node TAGS, Rdired, Toolbar, Miscellaneous @section TAGS 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. 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. @example etags --language=none --regex='/\([^ \t]+\)[ \t]*<-[ \t]*function/\1/' *.R @end example This will find entries in your source file of the form: @example some.name <- function @end example with the function name starting in column 0. Windows users may need to change the single quotes to double quotes. R version 2.9.0 introduced a front-end script for finding R tags, which calls the @samp{rtags()} 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: @example R CMD rtags --help @end example For further details, see @uref{http://developer.r-project.org/rtags.html} @comment node-name, next, previous, up @node Rdired, Rutils, TAGS, Miscellaneous @section Rdired 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. To get started, first make sure you can load ess-rdired. Add the following to your .emacs and then restart emacs. @example (autoload 'ess-rdired "ess-rdired" "View *R* objects in a dired-like buffer." t) @end example Start an R session with @kbd{M-x R} and then store a few variables, such as: @example s <- sin(seq(from=0, to=8*pi, length=100)) x <- c(1, 4, 9) y <- rnorm(20) z <- TRUE @end example Then use @kbd{M-x ess-rdired} to create a buffer listing the objects in your current environment and display it in a new window: @example mode length s numeric 100 x numeric 3 y numeric 20 z logical 1 @end example Type @kbd{C-h m} or @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). @comment node-name, next, previous, up @node Rutils, Org, Rdired, Miscellaneous @section Rutils 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()} and @code{RSiteSearch()} that use the @command{browse-url} Emacs function. The library can be loaded using @kbd{M-x load-file}, but the easiest is to include: @lisp (require 'ess-rutils) @end lisp in your .emacs. Once R is started with @kbd{M-x R}, and if the value of the customizable variable @code{ess-rutils-keys} is true, several key bindings become available in iESS process buffers: @itemize @bullet @item @kbd{C-c C-. l} (@command{ess-rutils-local-pkgs}) @* @pindex ess-rutils-localpkgs List all packages in all available libraries. @item @kbd{C-c C-. r} (@command{ess-rutils-repos-pkgs}) @* @pindex ess-rutils-repospkgs List available packages from repositories listed by @command{getOptions(``repos'')} in the current R session. @item @kbd{C-c C-. u} (@command{ess-rutils-update-pkgs}) @* @pindex ess-rutils-updatepkgs Update packages in a particular library and repository. @item @kbd{C-c C-. a} (@command{ess-rutils-apropos}) @* @pindex ess-rutils-apropos Search for a string using apropos. @item @kbd{C-c C-. m} (@command{ess-rutils-rm-all}) @* @pindex ess-rutils-rmall Remove all R objects. @item @kbd{C-c C-. o} (@command{ess-rutils-objs}) @* @pindex ess-rutils-objs Manipulate R objects; wrapper for @command{ess-rdired}. @item @kbd{C-c C-. w} (@command{ess-rutils-load-wkspc}) @* @pindex ess-rutils-loadwkspc Load a workspace file into R. @item @kbd{C-c C-. s} (@command{ess-rutils-save-wkspc}) @* @pindex ess-rutils-savewkspc Save a workspace file. @item @kbd{C-c C-. d} (@command{ess-change-directory}) @* @pindex ess-change-directory Change the working directory for the current R session. @item @kbd{C-c C-. H} (@command{ess-rutils-html-docs}) @* @pindex ess-rutils-htmldocs Use @command{browse-url} to navigate R html documentation. @end itemize See the submenu @samp{Rutils} under the iESS menu for alternative access to these functions. The function @command{ess-rutils-rsitesearch} is provided without a particular key binding. This function is useful in any Emacs buffer, so can be bound to a user-defined key: @lisp (eval-after-load "ess-rutils" '(global-set-key [(control c) (f6)] 'ess-rutils-rsitesearch)) @end lisp @pindex ess-rutils-rsitesearch Functions for listing objects and packages (@command{ess-rutils-local-pkgs}, @command{ess-rutils-repos-pkgs}, and @command{ess-rutils-objs}) show results in a separate buffer and window, in @code{ess-rutils-mode}, providing useful key bindings in this mode (type @kbd{?} in this buffer for a description). @comment node-name, next, previous, up @node Org, Sweave and AUCTeX, Rutils, Miscellaneous @section Interaction with Org mode Org-mode (@uref{http://orgmode.org}) now supports reproducible research and literate programming in many languages (including R) -- see chapter 14 of the Org manual (@uref{http://orgmode.org/org.html#Working-With-Source-Code}). 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.) @comment node-name, next, previous, up @node Sweave and AUCTeX, Debugging R, Org, Miscellaneous @section Support for Sweave in ESS and AUCTeX ESS provides support for writing and processing Sweave (@uref{http://www.statistik.lmu.de/~leisch/Sweave}), building up on Emacs' noweb-mode for literate programming. When working on an Sweave document, the following key bindings are available: @itemize @bullet @item @kbd{M-n s} (@command{ess-swv-weave}) @* @pindex ess-swv-weave Run Sweave on the current .Rnw file. @item @kbd{M-n l} (@command{ess-swv-latex}) @* @pindex ess-swv-latex Run LaTeX after Sweave'ing. @item @kbd{M-n p} (@command{ess-swv-PS}) @* @pindex ess-swv-PS Generate and display a postscript file after LaTeX'ing. @item @kbd{M-n P} (@command{ess-swv-PDF}) @* @pindex ess-swv-PDF Generate and display a PDF file after LaTeX'ing. The command used to generate the PDF file is the first element of @code{ess-swv-pdflatex-commands}. @end itemize Sweave'ing with @code{ess-swv-weave} starts an inferior-ESS process, if one is not available. Other commands are available from the @samp{Sweaving, Tangling, ...} submenu of the Noweb menu. AUCTeX (@uref{http://www.gnu.org/software/auctex}) users may prefer to set the variable @code{ess-swv-plug-into-AUCTeX-p} (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, ...} 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} without an inferior-ESS process. Similarly, LaTeX'ing can be done by @kbd{C-c C-c LaTeXSweave RET}. In both cases, the process can be monitored with @kbd{C-c C-l} (@code{TeX-recenter-output-buffer}). Open the viewer with @kbd{C-c C-v} (@code{TeX-view}), as usual in AUCTeX. @comment node-name, next, previous, up @node Debugging R, , Sweave and AUCTeX, Miscellaneous @section Debugging R code in ESS There are currently two extra facilities that have been developed for debugging R code within ESS. @itemize @bullet @item ``Ess-tracebug is a package for interactive visual debugging of R code from ESS. It provides visual debugging, browser, recover and conditional breakpoints; watch window and loggers; interactive debug/undebug of R functions and methods at point; highlighting and easy error navigation and interactive traceback.'' @uref{http://code.google.com/p/ess-tracebug/} @item The R package edtdbg ``integrates R's debugging facilities with your text editor, featuring code tracking, variable display, quick breakpoint setting, and easy toggling of function debug status.'' It provides support for both Emacs and VIM. Package available from CRAN mirrors. @end itemize @comment node-name, next, previous, up@chapter Using S4 @node Mailing lists/bug reports, Customization, Miscellaneous, Top @chapter Bugs and Bug Reporting, Mailing Lists @menu * Bugs:: * Reporting Bugs:: * Mailing Lists:: * Help with emacs:: @end menu @node Bugs, Reporting Bugs, Mailing lists/bug reports, Mailing lists/bug reports @section Bugs @cindex bugs @include bugs.texi @comment node-name, next, previous, up @node Reporting Bugs, Mailing Lists, Bugs, Mailing lists/bug reports @section Reporting Bugs @cindex Bug reports @pindex ess-submit-bug-report @include bugrept.texi @comment node-name, next, previous, up @node Mailing Lists, Help with emacs, Reporting Bugs, Mailing lists/bug reports @section Mailing Lists @include mailing.texi @comment node-name, next, previous, up @node Help with emacs, , Mailing Lists, Mailing lists/bug reports @section Help with emacs 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} or @kbd{M-x view-emacs-FAQ}) and EmacsWiki (@uref{http://www.emacswiki.org}). Please consult them before asking on the mailing list about issues that are not specific to ESS. @c _not_yet_ @node Help OS, Installation, Help for Statistical Packages, Top @c _not_yet_ @comment node-name, next, previous, up @c _not_yet_ @chapter Help, arranged by Operating System @c _not_yet_ @c _not_yet_ @menu @c _not_yet_ * Unix installation:: @c _not_yet_ * Microsoft Windows installation:: @c _not_yet_ * System dependent:: Other variables you may need to change @c _not_yet_ @end menu @comment node-name, next, previous, up @node Customization, Key Index, Mailing lists/bug reports, Top @appendix Customizing ESS @cindex customization ESS can be easily customized to your taste simply by including the appropriate lines in your @file{.emacs} 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. Most of these variables can be viewed and set using the Custom facility within Emacs. Type @kbd{M-x customize-group RET ess RET} to see all the ESS variables that can be customized. Variables are grouped by subject to make it easy to find related variables. @c Stephen deleted incomplete variable list Wed 25 Aug 2004. @node Key Index, Concept Index, Customization, Top @unnumbered Key (Character) Index @printindex ky @c @node Command Index, Concept Index, Key Index, Top @c @unnumbered Command and Function Index @c @printindex fn @comment node-name, next, previous, up @node Concept Index, Variable and command index, Key Index, Top @unnumbered Concept Index @printindex cp @node Variable and command index, , Concept Index, Top @unnumbered Variable and command index @printindex vr @contents @bye @c Remember to delete these lines before creating the info file. @c Why? I makeinfo all of the time without following this advice. @iftex @lucidbook @bindingoffset = 0.5in @parindent = 0pt @end iftex @comment Local Variables: @comment TeX-master: "ess.texi" @comment End: