~ubuntu-branches/ubuntu/oneiric/ess/oneiric

\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
@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-localpkgs}) @*
@pindex ess-rutils-localpkgs
List all packages in all available libraries.

@item
@kbd{C-c C-. r} (@command{ess-rutils-repospkgs}) @*
@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-updatepkgs}) @*
@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-rmall}) @*
@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-loadwkspc}) @*
@pindex ess-rutils-loadwkspc
Load a workspace file into R.

@item
@kbd{C-c C-. s} (@command{ess-rutils-savewkspc}) @*
@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-htmldocs}) @*
@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-localpkgs}, @command{ess-rutils-repospkgs}, 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,  , 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@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: