ESS – Emacs Speaks Statistics

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ESS — Emacs Speaks Statistics

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ESS: Emacs Speaks Statistics

ESS version 16.10 

by  A.J. Rossini,
    R.M. Heiberger,
    K. Hornik,
    M. Maechler,
    R.A. Sparapani,
    S.J. Eglen,
    S.P. Luque,
    H. Redestig,
    V. Spinu,
and L. Henry.

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.

• 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



• Evaluating code:  Sending code to the ESS process



• Transcript Mode:  Manipulating saved transcript files



• Editing objects:  How to create/edit objects and functions



• Help:  Reading help files



• Completion:  Various completion mechanisms



• Developing with ESS:  Tools for package development and debugging



• Extras:  Other ESS features for the S family



• ESS for S:  Overview of ESS features for the S family



• ESS for SAS:  



• ESS for BUGS:  



• ESS for JAGS:  



• Mailing lists/bug reports:  How to get assistance with ESS



• Customization:  Customizing ESS



• Indices:  












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1 Introduction to ESS




The S family (S, Splus and R) and SAS statistical analysis packages
provide sophisticated statistical and graphical routines for manipulating
data.   Emacs Speaks Statistics (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,
and Stata with the level of support roughly in that order.



A bit of notation before we begin.  emacs refers to both
GNU Emacs by the Free Software Foundation, as well as
XEmacs by the XEmacs Project.  The emacs major
mode ESS[language], where language can take values such as
S, SAS, or XLS.  The inferior process interface
(the connection between emacs and the running process) referred to as inferior ESS
(iESS), is denoted in the modeline by ESS[dialect], where
dialect can take values such as S3, S4, S+3,
S+4, S+5, S+6, S+7, R, XLS, VST, SAS.



Currently, the documentation contains many references to ‘S’
where actually any supported (statistics) language is meant, i.e., ‘S’
could also mean ‘R’ or ‘SAS’.






For exclusively interactive users of S, ESS provides a number of
features to make life easier.  There is an easy to use command history
mechanism, including a quick prefix-search history.  To reduce typing,
command-line completion is provided for all S objects and “hot
keys” are provided for common S function calls.  Help files are
easily accessible, and a paging mechanism is provided to view them.
Finally, an incidental (but very useful) side-effect of ESS is that a
transcript of your session is kept for later saving or editing.




No special knowledge of Emacs is necessary when using S
interactively under ESS.




For those that use S in the typical edit–test–revise cycle when
programming S functions, ESS provides for editing of S functions
in Emacs edit buffers.  Unlike the typical use of S where the editor
is restarted every time an object is edited, ESS uses the current Emacs
session for editing.  In practical terms, this means that you can edit
more than one function at once, and that the ESS process is still
available for use while editing.  Error checking is performed on
functions loaded back into S, and a mechanism to jump directly to the
error is provided.  ESS also provides for maintaining text versions of
your S functions in specified source directories.





• 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












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1.1 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.






• Current Features:  












Up: Features   [Contents][Index]





1.1.1 Features Overview





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:





If you commonly create or modify S functions, you will have found
the standard facilities for this (the ‘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 S while
editing.  ESS corrects these problems by introducing the following
features:





Finally, ESS provides features for re-submitting commands from saved
transcript files, including:











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1.2 New features in ESS




Changes and New Features in 16.10:




Bug fixes in 16.10:




Changes and New Features in 16.04:




Bug fixes in 16.04:





Changes and New Features in 15.09:





Changes and New Features in 15.03-1:




Changes and New Features in 15.03:




Bug Fixes in 15.03:




Changes / Selected Bug Fixes in 14.09:




Changes / Selected Bug Fixes in 13.09-1:




Changes/New Features in 13.09:




Changes/New Features in 13.05:





Changes/Bug Fixes in 12.09-2:





Changes/New Features in 12.09-1:




Bug Fixes in 12.09-1:




Changes/New Features in 12.09:





Changes/Bug Fixes in 12.04-3:




Changes/New Features in 12.04-1:




Bug Fixes in 12.04-1:




Changes/New Features in 12.04:




Changes/New Features in 12.03:











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1.3 Authors of and contributors to ESS







The ESS environment is built on the open-source projects of many
contributors, dating back to 1989 where Doug Bates and Ed Kademan wrote
S-mode to edit S and Splus files in GNU Emacs.  Frank Ritter and Mike
Meyer added features, creating version 2.  Meyer and David Smith made
further contributions, creating version 3.  For version 4, David Smith
provided significant enhancements to allow for powerful process
interaction.



John Sall wrote GNU Emacs macros for SAS source code around 1990.  Tom
Cook added functions to submit jobs, review listing and log files, and
produce basic views of a dataset, thus creating a SAS-mode which was
distributed in 1994.



In 1994, A.J. Rossini extended S-mode to support XEmacs.  Together
with extensions written by Martin Maechler, this became version 4.7
and supported S, Splus, and R.  In 1995, Rossini extended SAS-mode to
work with XEmacs.



In 1997, Rossini merged S-mode and SAS-mode into a single Emacs
package for statistical programming; the product of this marriage was
called ESS version 5.  Richard M. Heiberger designed the inferior mode
for interactive SAS and SAS-mode was further integrated into ESS.
Thomas Lumley’s Stata mode, written around 1996, was also folded into
ESS.  More changes were made to support additional statistical
languages, particularly XLispStat.



ESS initially worked only with Unix statistics packages that used
standard-input and standard-output for both the command-line interface
and batch processing.  ESS could not communicate with statistical
packages that did not use this protocol.  This changed in 1998 when
Brian Ripley demonstrated use of the Windows Dynamic Data Exchange
(DDE) protocol with ESS.  Heiberger then used DDE to provide
interactive interfaces for Windows versions of Splus.  In 1999, Rodney
A. Sparapani and Heiberger implemented SAS batch for ESS relying
on files, rather than standard-input/standard-output, for Unix,
Windows and Mac.  In 2001, Sparapani added BUGS batch file processing
to ESS for Unix and Windows.





ESS is being developed and currently maintained by











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1.4 Getting the latest version of ESS



The latest released version of ESS is always available on the web at:
ESS web page or
StatLib





1.4.1 Git for ESS development


For development and experimentation on new ESS features, there is now a
GitHub branch for ESS, available at https://github.com/emacs-ess/ESS.












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1.5 How to read this manual



If you need to install ESS, read 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.  C-<chr> means hold
the CONTROL key while typing the character <chr>. 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 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 M-x R can accept an optional ‘prefix’
argument.  To specify the prefix argument, you would type C-u
before giving the command.  e.g. If you type 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 C-h f.  For example, if you type
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 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
M-x customize-group RET ess RET to get started.)
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.









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2 Installing ESS on your system




The following section details those steps necessary to get ESS running
on your system.





• Step by step instructions:  



• License:  



• Stability:  



• Requirements:  













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2.1 Step by step instructions



    

  1.  Download the latest zip or tgz archive from ESS 
downloads
area and unpack it into a directory where you would like ESS to
reside. We will denote this directory as /path/to/ESS/ hereafter.


    Alternatively you can use git to fetch the most
recent development version to your local machine with:

    

    

    git clone https://github.com/emacs-ess/ESS.git /path/to/ESS

    


  2.  Optionally, compile elisp files and build the documentation with:

    

    cd /path/to/ESS/
make

    

    Without this step, info, pdf and html documentation and reference card
will not be available.

    

  3.  Optionally, install into your local machine with
make install. You might need administrative privileges:


    

    make install

    


    The files are installed into /usr/share/emacs directory. For this step to
run correctly on Mac OS X, you will need to adjust the PREFIX
path in Makeconf. The necessary code and instructions are
commented in that file.

    

  4.  If you have performed the make install step from above, just add


    

    (require 'ess-site)

    


    to your ~/.emacs file. Otherwise, you should add
/path/to/ESS/lisp/ to your emacs load path and then load ESS with
the following lines in your ~/.emacs:

    

    

    (add-to-list 'load-path "/path/to/ESS/lisp/")
(load "ess-site")

    


  5.  Restart your Emacs and check that ESS was loaded from a correct
location with M-x ess-version.





Note for Windows and Mac OS X users: The most straightforward
way to install Emacs on your machine is by downloading
all-in-one Emacs binary
by Vincent Goulet.




Note for XEmacs users: Due to XEmacs lacking some features
that ESS requires, ESS support of XEmacs ends with ESS 12.04-4.  This
decision will be re-visited in the future as XEmacs continues to sync
with GNU Emacs.










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2.2 License


The source and documentation of ESS is free software.
You can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free
Software Foundation; either version 2, or (at your option) any later
version.



ESS is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
in the file COPYING in the same directory as this file for more
details.









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2.3 Stability


All recent released versions are meant to be release-quality versions.
While some new features are being introduced, we are cleaning up and
improving the interface.  We know that there are many remaining
opportunities for documentation improvements, but all contributors are
volunteers and time is precious. Patches or suggested fixes with bug
reports are much appreciated!










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2.4 Requirements


ESS is most likely to work with current/recent versions of the following
statistical packages: R/S-PLUS, SAS, Stata, OpenBUGS and JAGS.



ESS supports current, and recent, stable versions of GNU Emacs
(currently, the 24.x and 25.x series; alpha/beta/pre-release
versions are NOT SUPPORTED).  Non-Windows users beware: GNU Emacs 24.3 is 
preferable to 24.1 or 24.2: these broken builds suffer from bug 12463 
http://debbugs.gnu.org/cgi/bugreport.cgi?bug=12463 which 
will cause Emacs to get progressively slower over time.



Due to XEmacs lacking some features that ESS requires, ESS
support of XEmacs ended with ESS 12.04-4.  



To build the PDF documentation, you will need a version of TeX Live or
texinfo that includes texi2dvi (BEWARE: recent TeX Live, and some
texinfo RPMs, do NOT include texi2dvi).
















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3 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.






• Starting up:  



• Multiple ESS processes:  



• ESS processes on Remote Computers:  



• S+elsewhere and ESS-elsewhere:  



• Customizing startup:  












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3.1 Starting an ESS process





To start an S session on Unix or on Windows when you
use the Cygwin bash shell, simply type M-x S RET.



To start an S session on Windows when you
use the MSDOS prompt shell, simply type M-x S+6-msdos RET.










S will then (by default) ask the question



S starting data directory?



Enter the name of the directory you wish to start S from (that is,
the directory you would have cd’d to before starting S from
the shell).  This directory should have a .Data subdirectory.



You will then be popped into a buffer


with name ‘*S*’ which will be used
for interacting with the ESS process, and you can start entering commands.










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3.2 Running more than one ESS process




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

(process 1) is simply named (using S-PLUS as an example) ‘S+3:1’.
The name of the process is shown in the mode line in square brackets
(for example, ‘[S+3:2]’); this is useful if the process buffer is
renamed.  Without a prefix argument, M-x S starts a new ESS
process, using the first available process number.  With a prefix
argument (for R), C-u M-x R allows for the specification of
command line options.




You can switch to any active ESS process with the command
‘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.











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3.3 ESS processes on Remote Computers







ESS works with processes on remote computers as easily as with processes
on the local machine.  The recommended way to access a statistical
program on remote computer is to start it with tramp. Require tramp in your .emacs file:



(require 'tramp)



Now start an ssh session with ‘C-x C-f /ssh:user@host: RET’. Tramp
should open a dired buffer in your remote home directory. Now call your
favorite ESS process (R, Julia, stata etc) as you
would usually do on local machine: M-x R.



Alternatively you can start your process normally (M-x R). After
you are asked for starting directory, simply type ‘/ssh:user@host:
RET’. R process will be started on the remote machine.



To simplify the process even further create a "config" file in your
.ssh/ folder and add an account. For example if you use amazon
EC2, it might look like following:



   Host amazon
      Hostname ec2-54-215-203-181.us-west-1.compute.amazonaws.com
      User ubuntu
      IdentityFile ~/.ssh/my_amazon_key.pem
      ForwardX11 yes



With this configuration /ssh:amazon: is enough to start a
connection. The ForwardX11 is needed if you want to see R graphic device
showing on the current machine



Other ways to setup a remote ESS connection are through ess-remote.



    

  1.  Start a new shell, telnet or ssh buffer and connect to the remote computer
(e.g. use, ‘M-x shell’, ‘M-x telnet’ or ‘M-x ssh’; ssh.el is available at
http://www.splode.com/~friedman/software/emacs-lisp/src/ssh.el).


  2.  Start the ESS process on the remote machine, for example with one of
the commands ‘Splus’, or ‘R’, or ‘sas -stdio’.


  3.  Start ‘M-x ess-remote’.
You will be prompted for a program name with completion.  Choose
one. Your process is now known to ESS.  All the usual ESS commands
(‘C-c C-n’ and its relatives) now work with the S language
processes.  For SAS you need to use a different command ‘C-c i’
(that is a regular ‘i’, not a ‘C-i’) to send lines from your
myfile.sas to the remote SAS process. ‘C-c i’ sends lines
over invisibly.
With ess-remote you get teletype behavior—the data input, the
log, and the listing all appear in the same buffer.  To make this work,
you need to end every PROC and DATA step with a "RUN;" statement.  The
"RUN;" statement is what tells SAS that it should process the preceding
input statements.


  4.  Graphics (interactive) on the remote machine.  If you run X11
(See X11, X Windows)
on both the local and remote machines then you should be able to
display the graphs locally by setting the ‘DISPLAY’ environment
variable appropriately.  Windows users can download ‘xfree86’
from cygwin.


  5.  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 ‘.gif’ and ‘.jpg’
files.  Otherwise, a graphics file viewer will be needed.
Ghostscript/ghostview may be downloaded to display ‘.ps’ and
‘.eps’ files.  Viewers for GIF and JPEG are usually included with
operating systems.  See ESS(SAS)--Function keys for batch processing,
for more information on using the F12 key for displaying graphics files
with SAS.




Should you or a colleague inadvertently start a statistical process in
an ordinary ‘*shell*’ buffer, the ‘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.
See S+elsewhere and ESS-elsewhere.










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3.4 S+elsewhere and ESS-elsewhere



These commands are now deprecated.  We recommend ‘ess-remote’.  We
have two versions of the elsewhere function.  ‘S+elsewhere’ is
specific for the S-Plus program.  The more general function
‘ESS-elsewhere’ is not as stable.



    

  1.  Enter ‘M-x S+elsewhere’.
You will be prompted for a starting directory.  I usually give it my
project directory on the local machine, say  ‘~myname/myproject/’


    Or enter ‘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 ‘~myname/myproject/’

    

  2.  The ‘*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
‘C-g’ then move the cursor to the end with ‘M->’.
With ‘S+elsewhere’ the buffer name is based on the name of the ESS program.

  3.  Enter
‘telnet myname@other.machine’ (or ‘ssh myname@other.machine’).
You will be prompted for your password on the remote machine.
Use
‘M-x send-invisible’
before typing the password itself.


  4.  Before starting the ESS process, type ‘stty -echo nl’
at the unix prompt.  The ‘-echo’ turns off the echo, the
‘nl’ turns off the newline that you see as ‘^M’.


  5.  You are now talking to the unix prompt on the other machine in the
‘*S+3*’ buffer.  cd into the directory for the current project and start
the ESS process by entering
‘Splus’ or ‘R’ or ‘sas -stdio’
as appropriate.  If you can login remotely to your Windows 2000, then
you should be able to run ‘Sqpe’ on the Windows machine.  I haven’t
tested this and no-one has reported their tests to me.  You will not be
able to run the GUI through this text-only connection.


  6.  Once you get the S or R or SAS prompt, then you are completely connected.
All the ‘C-c C-n’ and related commands work correctly in sending
commands from ‘myfile.s’ or ‘myfile.r’ on the PC to the
‘*S+3*’ buffer running the S or R or SAS program on the remote machine.


  7.  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
‘xfree86’ on your PC.  If you don’t run X Windows, or X11, then you can write
graphics to the postscript device and copy it to your PC with dired and
display it with ghostscript.











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3.5 Changing the startup actions



If you do not wish ESS to prompt for a starting directory when starting
a new process, set the variable ess-ask-for-ess-directory to

nil.  In this case, the starting directory will be set using
one of the following methods:



    

  1.  If the variable ess-directory-function stores the name of a
function, the value returned by this function is used.  The default for
this variable is nil.


  2.  Otherwise, if the variable ess-directory stores the name of a
directory (ending in a slash), this value is used.  The default for this
variable is nil.


  3.  Otherwise, the working directory of the current buffer is used.





If ess-ask-for-ess-directory has a non-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,
ess-directory is an ideal variable to set in
ess-pre-run-hook.



If you like to keep a record of your S sessions, set the variable
ess-ask-about-transfile to t, and you will be asked for a
filename for the transcript before the ESS process starts.





User Option: ess-ask-about-transfile


If non-nil, as for a file name in which to save the session
transcript.





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 ‘.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 — see 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 inferior-ess-program.

If you need to pass any arguments to this program, they may be specified
in the variable inferior-S_program_name-args (e.g. if
inferior-ess-program is "S+" then the variable to set is
inferior-S+-args.

It is not normally necessary to pass arguments to the S program; in
particular do not pass the ‘-e’ option to 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 inferior-ess-own-frame.
Alternatively, change inferior-ess-same-window if you wish the
process to appear within another window of the current frame.









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4 Interacting with the ESS process






The primary function of the ESS package is to provide an easy-to-use
front end to the S interpreter.  This is achieved by running the S
process from within an Emacs buffer, called hereafter inferior
buffer, which has an active inferior-ess-mode. The features of
Inferior S mode are similar to those provided by the standard Emacs
shell mode (see Shell Mode in The Gnu Emacs Reference Manual).
Command-line completion of S objects and a number of ‘hot keys’ for
commonly-used S commands are also provided for ease of typing.





• Command-line editing:  Entering commands and fixing mistakes



• 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












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4.1 Entering commands and fixing mistakes




Sending a command to the ESS process is as simple as typing it in
and pressing the RETURN key:





Command: inferior-ess-send-input




RET Send the command on the current line to the ESS process.




If you make a typing error before pressing RET all the usual Emacs
editing commands are available to correct it (see Basic
editing commands in The GNU Emacs Reference Manual).  Once the
command has been corrected you can press RETURN (even if the
cursor is not at the end of the line) to send the corrected command to
the ESS process.



Emacs provides some other commands which are useful for fixing mistakes:





C-c C-w




backward-kill-word Deletes the previous word (such as an object
name) on the command line.





C-c C-u




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.





C-c C-a




comint-bol Move to the beginning of the line, and then skip
forwards past the prompt, if any.






See Shell Mode in The Gnu Emacs Reference Manual, for other
commands relevant to entering input.










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4.2 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

move back up through the buffer, to look at the output from previous
commands for example.



Within the process buffer, a paragraph

is defined as the prompt, the command after the prompt, and the output
from the command.  Thus M-{ and M-} move you backwards and
forwards, respectively, through commands in the transcript.  A
particularly useful command is M-h (mark-paragraph) which
will allow you to mark a command and its entire output (for deletion,
perhaps).  For more information about paragraph commands,
see Paragraphs in 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 (‘^L’)
character.  Thus pages in the ESS

process buffer correspond to ESS sessions.  Thus, for example, you may
use C-x [ and C-x ] to move backward and forwards through
ESS sessions in a single ESS process buffer.  For more information about
page commands, see Pages in The GNU Emacs
Reference Manual.





• 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












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4.2.1 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.
Whenever a command produces a longish output, it is possible that the
window will scroll, leaving the next prompt near the middle of the
window.  The first part of the command output may have scrolled off the
top of the window, even though the entire output would fit in the window
if the prompt were near the bottom of the window.  If this happens, you
can use the following comint commands:



comint-show-maximum-output to move to the end
of the buffer, and place cursor on bottom line of window to make more of
the last output visible.  To make this happen automatically for all
inputs, set the variable comint-scroll-to-bottom-on-input to
t or 'this.  If the first part of the output is still not
visible, use

C-c C-r (comint-show-output),

which moves cursor to the previous command line and places it at the
top of the window.



Finally, if you want to discard the last command output altogether, use

C-c C-o (comint-delete-output),

which deletes everything from the last command to the current prompt.
Use this command judiciously to keep your transcript to a more
manageable size.









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4.2.2 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:





C-c C-p




comint-previous-input Moves point to the preceding command in the
process buffer.





C-c C-n




comint-next-input Moves point to the next command in the process
buffer.






Note that these two commands are analogous to C-p and C-n
but apply to command lines rather than text lines.  And just like
C-p and C-n, passing a prefix argument to these commands
means to move to the ARG’th next (or previous) command.  (These
commands are also discussed in Shell History
Copying in 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 (see Syntax of Regular
Expression in The GNU Emacs Reference Manual), and then moves to
the next (previous) command matching the pattern.





comint-backward-matching-input regexp arg






comint-forward-matching-input regexp arg




Search backward (forward) through the transcript buffer for the
arg’th previous (next) command matching regexp.  arg
is the prefix argument; regexp is prompted for in the minibuffer.












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4.2.3 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 output,
an error is signalled).  Note all three commands involve the RETURN
key.





RET


inferior-ess-send-input See Command-line editing.





C-c RET




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.






When the cursor is not after the current prompt, the RETURN key
has a slightly different behavior than usual.  Pressing 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 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 commands work even if the current line is a continuation line
(i.e. the prompt is ‘+’ instead of ‘>’) — 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

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 Command History.









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4.2.4 Keeping a record of your S session



To keep a record of your S session in a disk file, use the Emacs
command C-x C-w (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
S as usual; just remember to save the file before you quit Emacs
with C-x C-s.  You can make ESS prompt you for a filename in which
to save the transcript every time you start S by setting the
variable

ess-ask-about-transfile to t; See Customizing startup.

We recommend you save your transcripts with filenames that end in
‘.St’.  There is a special mode (ESS transcript mode —
see Transcript Mode) for editing transcript files which is
automatically selected for files with this suffix.




S transcripts can get very large, so some judicious editing is
appropriate if you are saving it in a file.  Use 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
M-h C-w.  Also, remember that C-c C-x (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 S source code (suitable for using
with source() or inclusion in an S function) from a
transcript, then the command ess-transcript-clean-region may be
of use.  see Transcript Mode










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4.3 Command History






ESS provides easy-to-use facilities for re-executing or editing previous
commands.  An input history of the last few commands is maintained (by
default the last 500 commands are stored, although this can be changed by
setting the variable comint-input-ring-size in

inferior-ess-mode-hook.) The simplest history commands simply
select the next and previous commands in the input history:





M-p




comint-previous-input Select the previous command in the input
history.





M-n




comint-next-input Select the next command in the input history.






For example, pressing 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
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 (see Syntax of Regular
Expression in The GNU Emacs Reference Manual), to search for a
particular variable name for example, these commands are also available:





M-r




comint-history-isearch-backward-regexp Prompt for a regular
expression, and search backwards through the input history for a command
matching the expression.








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:





C-c M-r




comint-previous-matching-input-from-input Select the previous
command in the history which matches the string typed so far.





C-c M-s




comint-next-matching-input-from-input Select the next command in
the history which matches the string typed so far.






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 attach()
command, you may only need to type att and then C-c M-r and
RET.



See Shell History Ring in The GNU Emacs Reference
Manual, for a more detailed discussion of the history mechanism,
and do experiment with the In/Out menu to explore the possibilities.



Many ESS users like to have even easier access to these, and recommend
to add something like



  (eval-after-load "comint"
   '(progn
      (define-key comint-mode-map [up]
        'comint-previous-matching-input-from-input)
      (define-key comint-mode-map [down]
        'comint-next-matching-input-from-input)

      ;; also recommended for ESS use --
      (setq comint-scroll-to-bottom-on-output 'others)
      (setq comint-scroll-show-maximum-output t)
      ;; somewhat extreme, almost disabling writing in *R*, *shell* buffers above prompt:
      (setq comint-scroll-to-bottom-on-input 'this)
      ))



to your .emacs file,
where the last two settings are typically desirable for the situation where
you work with a script (e.g., code.R) and send code chunks to the
process buffer (e.g. *R*).
Note however that these settings influence all comint-using emacs
modes, not just the ESS ones, and for that reason, these customization
cannot be part of ESS itself.





• Saving History:  












Up: Command History   [Contents][Index]





4.3.1 Saving the command history



The ess-history-file variable, which is t by default,
together with  ess-history-directory, governs if and where the
command history is saved and restored between sessions.
By default, ess-history-directory is nil, and the command
history will be stored (as text file) in the ess-directory, e.g., as
.Rhistory.



Experienced ESS users often work exclusively with script files rather than
in a (e.g., *R) console session, and may not want to save any
history files, and hence have:





  (setq ess-history-file nil)




or will only want one global command history file and have:





  (setq ess-history-directory "~/.R/")




in your .emacs file.









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4.4 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 csh.  History references are introduced by a ‘!’ or
‘^’ character and have meanings as follows:





‘!!’


The immediately previous command





‘!-N’


The Nth previous command





‘!text’


The last command beginning with the string ‘text’





‘!?text’


The last command containing the string ‘text’






In addition, you may follow the reference with a word designator
to select particular 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 comint-delimiter-argument-list
to a list of characters that are allowed to separate words and

themselves form words.)  Words are numbered beginning with zero.  The
word designator usually begins with a ‘:’ (colon) character;
however it may be omitted if the word reference begins with a ‘^’,
‘$’, ‘*’ or ‘-’.  If the word is to be selected from the
previous command, the second ‘!’  character can be omitted from the
event specification.  For instance, ‘!!:1’ and ‘!:1’ both
refer to the first word of the previous command, while ‘!!$’ and
‘!$’ both refer to the last word in the previous command.  The
format of word designators is as follows:





‘0’


The zeroth word (i.e. the first one on the command line)





‘n’


The nth word, where n is a number





‘^’


The first word (i.e. the second one on the command line)





‘$’


The last word





‘x-y’


A range of words; ‘-y’ abbreviates ‘0-y’





‘*’


All the words except the zeroth word, or nothing if the command had just
one word (the zeroth)





‘x*’


Abbreviates x-$





‘x-’


Like ‘x*’, but omitting the last word






In addition, you may surround the entire reference except for the first
‘!’ 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
‘^old^new^’ means “the last command, but with the first occurrence
of the string ‘old’ replaced with the string ‘new’” (the last
‘^’ is optional).  Similarly, ‘^old^’ means “the last
command, with the first occurrence of the string ‘old’ deleted”
(again, the last ‘^’ is optional).



To convert a history reference as described above to an input suitable
for S, you need to expand the history reference, using the
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 SPC TAB.  This will convert the
history reference into an S command from the history, which you can
then edit or press RET to execute.



For example, to execute the last command that referenced the variable
data, type !?data SPC TAB RET.









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4.5 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 objects() or 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 following option:





User Option: ess-execute-in-process-buffer


If non-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 C-u)
will reverse the meaning of 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:





Command: ess-execute-objects posn






C-c C-x Sends the objects() command to the ESS process.  A
prefix argument specifies the position on the search list (use a
negative argument to toggle ess-execute-in-process-buffer as
well).  A quick way to see what objects are in your working directory.
A prefix argument of 2 or more means get objects for that position.  A
negative prefix argument posn gets the objects for that position,
as well as toggling ess-execute-in-process-buffer.






Command: ess-execute-search invert






C-c C-s Sends the inferior-ess-search-list-command command
to the ess-language process; search() in S.  Prefix
invert toggles ess-execute-in-process-buffer.




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;
see Keyboard Macros in The GNU
Emacs Reference Manual.





The following hot keys do not use 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:






Command: ess-load-file filename




C-c C-l Prompts for a file (filename) to load into the ESS
process using source().  If there is an error during loading, you
can jump to the error in the file with the following function.






Command: ess-parse-errors arg reset





C-c ` or C-x ` Visits next next-error message and
corresponding source code.  If all the error messages parsed so far have
been processed already, the message buffer is checked for new ones.  A
prefix arg specifies how many error messages to move; negative
means move back to previous error messages.  Just C-u as a prefix
means reparse the error message buffer and start at the first error.
The reset argument specifies restarting from the beginning.



See Error Checking, for more details.






Command: ess-display-help-on-object object command




C-c C-v Pops up a help buffer for an S object or
function.  If command is supplied, it is used instead of
inferior-ess-help-command.  See Help for more details.






Command: ess-quit











C-c C-q Issue an exiting command to the inferior process,
additionally also running ess-cleanup for disposing of any
temporary buffers (such as help buffers and edit buffers) that may have
been created.  Use this command when you have finished your S
session instead of simply quitting at the inferior process prompt,
otherwise you will need to issue the command ess-cleanup
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.











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4.6 Is the Statistical Process running under ESS?





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 options(STERM="iESS") for S language processes running
in an inferior iESS[S] or iESS[R] buffer.



ESS sets 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
ddeESS[S] buffer.



Other values of options()$STERM that we recommend are:





Additional values may be recommended in the future as new interaction
protocols are created.  Unlike the values iESS and ddeESS,
ESS can’t set these other values since the S language program is not
under the control of ESS.









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4.7 Using emacsclient




When starting R or S under Unix, ESS sets
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 iterator, typing 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 edit() rather than fix() means that the
function is not updated.  Finally, the S function page(x) will
also show a text representation of the object x in a temporary
Emacs buffer.










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4.8 Other commands provided by inferior-ESS



The following commands are also available in the process buffer:





Command: comint-interrupt-subjob






C-c C-c Sends a Control-C signal to the ESS process.  This has the
effect of aborting the current command.






Command: ess-switch-to-inferior-or-script-buffer toggle-eob




C-c C-z When in process buffer, return to the most recent script
buffer.  When in a script buffer pop to the associated process buffer.
This is a single key command, that is C-c C-z C-z from a script
buffer returns to the original buffer.



If toggle-eob is given, the value of
ess-switch-to-end-of-proc-buffer is toggled.






User Option: ess-switch-to-end-of-proc-buffer


If non-nil, ess-switch-to-inferior-or-script-buffer goes
to end of process buffer.




Other commands available in Inferior S mode are discussed in
Shell Mode in The Gnu Emacs Reference Manual.










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5 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 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:





User Option: ess-eval-visibly


Non-nil means ess-eval-* commands display commands and
output in the process buffer.  Default is t.




Passing a prefix (C-u) vis to any of the following commands,
however, reverses the meaning of ess-eval-visibly for that
command only — for example C-u C-c C-j
suppresses the current line of S (or other) code in the ESS process buffer.
This method of evaluation is an
alternative to S’s source() function



when you want the input as well as the output to be displayed.  (You can
sort of do this with source() when the option echo=T is
set, except that prompts do not get displayed.  ESS puts prompts in the
right places.)



Primary commands for evaluating code are:






Command: ess-eval-region-or-line-and-step vis


Send the highlighted region or current line and step to next line of
code.






Command: ess-eval-region-or-function-or-paragraph vis




C-M-x Sends the current selected region or function or paragraph.






Command: ess-eval-region-or-function-or-paragraph-and-step vis




C-c C-c Like ess-eval-region-or-function-or-paragraph but
steps to next line of code.




Other, not so often used, evaluation commands are:





Command: ess-eval-line vis




C-c C-j Sends the current line to the ESS process.






Command: ess-eval-line-and-go vis




C-c M-j Like ess-eval-line but additionally switches point
to the ESS process.






Command: ess-eval-function vis no-error




C-c C-f Sends the S function containing point to the ESS
process.






Command: ess-eval-function-and-go vis




C-c M-f Like ess-eval-function but additionally switches
point to the ESS process.






Command: ess-eval-region start end toggle message




C-c C-r Sends the current region to the ESS process.






Command: ess-eval-region-and-go start end vis




C-c M-r Like ess-eval-region but additionally switches
point to the ESS process.






Command: ess-eval-buffer vis




C-c C-b Sends the current buffer to the ESS process.






Command: ess-eval-buffer-and-go vis




C-c M-b Like ess-eval-buffer but additionally switches
point to the ESS process.




All the above ess-eval-* commands are useful for evaluating small
amounts of code and observing the results in the process buffer for
debugging purposes, or for generating transcripts from source files.
When editing S functions, it is generally preferable to use C-c
C-l to update the function’s value.  In particular,
ess-eval-buffer is now largely obsolete.



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 comint-scroll-to-bottom-on-output to 'others or
t.










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6 Manipulating saved transcript files



Inferior S mode records the transcript (the list of all commands
executed, and their output) in the process buffer, which can be saved as
a transcript file, which should normally have the suffix
.St.  The most obvious use for a transcript file is as a static
record of the actions you have performed in a particular S session.
Sometimes, however, you may wish to re-execute commands recorded in the
transcript file by submitting them to a running ESS process.  This
is what Transcript Mode is for.



If you load file a with the suffix .St into Emacs, it is placed
in S Transcript Mode.  Transcript Mode is similar to Inferior S mode
(see Entering commands):


paragraphs are defined as a command and its output, and you can move
though commands either with the paragraph commands or with C-c C-p
and C-c C-n.





• Resubmit:  Resubmitting commands from the transcript file



• Clean:  Cleaning transcript files












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6.1 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:





Command: ess-transcript-send-command




M-RET Sends the current command line to the ESS process, and
execute it.






Command: ess-transcript-copy-command




C-c RET Copy the current command to the ESS process, and switch to
it (ready to edit the copied command).






Command: ess-transcript-send-command-and-move




RET Sends the current command to the ESS process, and move to the
next command line.  This command is useful for submitting a series of
commands.




Note that the first two commands are similar to those on the same keys
in inferior S Mode.  In all three cases, the commands should be
executed when the cursor is on a command line in the transcript; the
prompt is automatically removed before the command is submitted.









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6.2 Cleaning transcript files



Yet another use for transcript files is to extract the command lines for
inclusion in an S source file or function.  Transcript mode provides
one command which does just this:





Command: ess-transcript-clean-region beg end even-if-read-only




C-c C-w Strip the transcript in the region (given by beg and
end), leaving only commands.  Deletes any lines not beginning with
a prompt, and then removes the prompt from those lines that remain.
Prefix argument even-if-read-only means to clean even if the
buffer is read-only.  Don’t forget to remove any erroneous commands
first!




The remaining command lines may then be copied to a source file or edit
buffer for inclusion in a function definition, or may be evaluated
directly (see Evaluating code) using the code evaluation commands
from S mode, also available in S Transcript Mode.










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7 Editing objects and functions




ESS provides facilities for editing S objects within your Emacs
session.  Most editing is performed on S functions, although in
theory you may edit datasets as well.  Edit buffers are always
associated with files, although you may choose to make these files
temporary if you wish.  Alternatively, you may make use of a simple yet
powerful mechanism for maintaining backups of text representations of
S functions.  Error-checking is performed when S code is loaded
into the ESS process.





• Edit buffer:  Edit objects in a specialized buffer



• Loading:  Loading source files into the ESS process



• Error Checking:  Detecting errors in source files



• Indenting:  Indenting and formatting S code



• Other edit buffer commands:  Commands for motion, completion and more



• Source Files:  Maintaining S source files



• Source Directories:  Names and locations of dump files












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7.1 Creating or modifying S objects




To edit an S object, type





Command: ess-dump-object-into-edit-buffer object




C-c C-e C-d Edit an S object in its own edit buffer.




from within the ESS process buffer (*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 TAB
key),

or you may enter the name of a new object.


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 ess-function-template

is non-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 ess-dump-object-into-edit-buffer is placed in the ESS
major mode which provides a number of commands to facilitate editing
S source code.  Commands are provided to intelligently indent S
code, evaluate portions of S code and to move around S code
constructs.





Note: when you dump a file with C-c C-e 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 (see 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 S
session).  Finally, if both these tests fail, the ESS process is
consulted and a dump() command issued.

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
ess-dump-object-into-edit-buffer by typing C-u C-c C-e C-d.









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7.2 Loading source files into the ESS process



The best way to get information — particularly function definitions
— into S is to load them in as source file, using S’s
source function.  You have already seen how to create source
files using C-c C-e C-d; ESS provides a complementary command for
loading source files (even files not created with ESS!) into the ESS
process, namely ess-load-file (C-c C-l).


see Hot keys.



After typing C-c C-l you will prompt for the name of the file to
load into S; usually this is the current buffer’s file which is the
default value (selected by simply pressing 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 C-c C-e
C-d).  The file will then be loaded, and if it loads successfully you
will be returned to the ESS process.









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7.3 Detecting errors in source files




If any errors occur when loading a file with 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 C-c `
(ess-parse-errors).


You will be returned to the offending file (loading it into a buffer if
necessary) with point at the line S reported as containing the
error.  You may then correct the error, and reload the file.  Note that
none of the commands in an S source file will take effect if any
part of the file contains errors.



Sometimes the error is not caused by a syntax error (loading a
non-existent file for example). In this case typing 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 is a
syntax error) by passing a prefix argument to ess-parse-errors
with C-u C-c `.









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7.4 Indenting and formatting S code



ESS provides a sophisticated mechanism for indenting S source
code (thanks to Ken’ichi Shibayama).  Compound statements (delimited by
‘{’ and ‘}’) 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, if statements, calls to expression()
and loop constructs are all recognized and indented appropriately.  User
variables are provided to control the amount of indentation in each
case, and there are also a number of predefined indentation styles to
choose from.




Comments are also handled specially by ESS, using an idea borrowed from
the Emacs-Lisp indentation style.  By default,
comments beginning with ‘###’
are aligned to the beginning of the line.  Comments beginning with
‘##’ are aligned to the current level of indentation for the block
containing the comment.  Finally, comments beginning with ‘#’ are
aligned to a column on the right (the 40th column by default, but this
value is controlled by the variable 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
(setq ess-indent-with-fancy-comments nil) to your .emacs file.




ESS also supports Roxygen entries which is R documentation maintained in
the source code as comments See Roxygen.



The indentation commands provided by ESS are:







Command: ess-indent-or-complete




TAB Indents the current line as S code.



Try to indent first, and if code is already properly indented, complete
instead.  In ess-mode, only tries completion if
ess-tab-complete-in-script is non-nil.  See also
ess-first-tab-never-complete.






User Option: ess-tab-complete-in-script


If non-nil, TAB in script buffers tries to complete if
there is nothing to indent.






User Option: ess-first-tab-never-complete


If non-nil, TAB never tries to complete in ess-mode.  The
default 'symbol does not try to complete if the next char is a valid
symbol constituent.  There are more options, see the help (C-h v).






Command: ess-indent-exp






TAB Indents each line in the S (compound) expression which
follows point.  Very useful for beautifying your S code.






Command: ess-electric-brace





{ } The braces automatically indent to the correct
position when typed.




The following Emacs command are also helpful:





RET


LFD




newline-and-indent Insert a newline, and indent the next line.
(Note that most keyboards nowadays do not have a LINEFEED key, but
RET and C-j are equivalent.)





M-;




indent-for-comment Indents an existing comment line
appropriately, or inserts an appropriate comment marker.








• Styles:  Changing indentation styles












Up: Indenting   [Contents][Index]





7.4.1 Changing indentation styles



The combined value of nine variables that control indentation are
collectively termed a style.  ESS provides several styles covering the
common styles of indentation: DEFAULT, OWN, GNU,
BSD, K&R, C++, RRR, CLB.  The
variable ess-style-alist lists the value of each indentation
variable per style.





Command: ess-set-style




C-c . Sets the formatting style in this buffer to be one of the
predefined styles, including GNU, BSD, K&R,
CLB, and C++. The DEFAULT style uses the default
values for the indenting variables; The OWN style allows you to
use your own private values of the indentation variable, see below.



(setq ess-default-style 'C++)








User Option: ess-default-style


The default value of ess-style.  See the variable
ess-style-alist for how these groups (DEFAULT, OWN, GNU, BSD,
…) map onto different settings for variables.






User Option: ess-style-alist


Predefined formatting styles for ESS code.  Values for all groups,
except OWN, are fixed.  To change the value of variables in the OWN
group, customize the variable ess-own-style-list.  The default
style in use is controlled by ess-default-style.




The styles DEFAULT and OWN are initially identical.  If
you wish to edit some of the default values, set
ess-default-style to 'OWN and change
ess-own-style-list.
See 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:





(defun myindent-ess-hook ()
  (setq ess-indent-level 4))
(add-hook 'ess-mode-hook 'myindent-ess-hook)




In the rare case that you’d like to add an entire new indentation style
of your own, copy the definition of ess-own-style-list to a new
variable and ensure that the last line of the :set declaration
calls ess-add-style with a unique name for your style
(e.g. 'MINE).  Finally, add (setq ess-default-style 'MINE)
to use your new style.









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7.5 Commands for motion, completion and more



A number of commands are provided to move across function definitions
in the edit buffer:





Command: ess-goto-beginning-of-function-or-para





ESC C-a aka C-M-a If inside a function go to the beginning
of it, otherwise go to the beginning of paragraph.






Command: ess-goto-end-of-function-or-para





ESC C-e aka C-M-e Move point to the end of the function
containing point.






Command: ess-mark-function





ESC C-h aka C-M-h Place point at the beginning of the S
function containing point, and mark at the end.




Don’t forget the usual Emacs commands for moving over balanced
expressions and parentheses: See Lists and
Sexps in The GNU Emacs Reference Manual.




Completion is provided in the edit buffer in a similar fashion to the
process buffer: TAB first indents, and if there is nothing to
indent, completes the object or file name; M-? lists file
completions. See See Completion, for more.



Finally, C-c C-z (ess-switch-to-inferior-or-script-buffer)
returns you to the iESS process buffer, if done from a script
buffer, placing point at the end of the buffer.  If this is done from
the iESS process buffer, point is taken to the script buffer.



In addition some commands available in the process buffer are also
available in the script buffer.  You can still read help files with
C-c C-v, edit another function with C-c C-e C-d and of
course C-c C-l can be used to load a source file into S.










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7.6 Maintaining S source files



Every edit buffer in ESS is associated with a dump file on disk.
Dump files are created whenever you type C-c C-e C-d
(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 S function.






User Option: ess-delete-dump-files


If non-nil, dump files created with C-c C-e C-d are deleted
immediately after they are created by the ess-process.




Since immediately after S dumps an object’s definition to a disk
file the source code on disk corresponds exactly to S’s idea of the
object’s definition, the disk file isn’t needed; deleting it now has the
advantage that if you 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 dump function; it doesn’t apply to source files which already
exist.  The default value is t.





User Option: ess-keep-dump-files


Variable controlling whether to delete dump files after a successful
load.  If ‘nil’: always delete.  If ‘ask’, confirm to delete.
If ‘check’, confirm to delete, except for files created with
ess-dump-object-into-edit-buffer.  Anything else, never delete.
This variable only affects the behaviour of ess-load-file.  Dump
files are never deleted if an error occurs during the load.




After an object has been successfully (i.e. without error) loaded
back into S with 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.






If the value of ess-keep-dump-files is 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 —
see Single or Numbered
Backups in 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 See Version Control in The Gnu Emacs Reference
Manual.  As long as a dump file exists in the appropriate place for a
particular object, editing that object with C-c C-e C-d finds that
file for editing (unless a prefix argument is given) — the ESS
process is not consulted.  Thus you can keep comments outside the
function definition as a means of documentation that does not clutter
the S object itself.  Another useful feature is that you may format
the code in any fashion you please without S re-indenting the code
every time you edit it.  These features are particularly useful for
project-based work.



If the value of ess-keep-dump-files is nil, the dump file is always
silently deleted after a successful load with C-c C-l.  While this
is useful for files that were created with C-c C-e 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 ess-keep-dump-files is buffer-local, you can make
sure particular files are not deleted by setting it to t in the
Local Variables section of the file See Local Variables in Files in The Gnu Emacs
Reference Manual.



A safer option is to set ess-keep-dump-files to 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 C-c C-e C-d, but not any other files, setting
ess-keep-dump-files to check (the default value) will
silently delete dump files created with C-c C-e 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 C-c C-l, the dump file is 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.




Dump buffers are always autosaved, regardless of the value of
ess-keep-dump-files.









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7.7 Names and locations of dump files




Every dump file should be given a unique file name, usually the dumped
object name with some additions.





User Option: ess-dump-filename-template


Template for filenames of dumped objects.  %s is replaced by the
object name.




By default, dump file names are the user name, followed by ‘.’ and
the object and ending with ‘.S’.  Thus if user joe dumps the
object myfun the dump file will have name joe.myfun.S.
The username part is included to avoid clashes when dumping into a
publicly-writable directory, such as /tmp; you may wish to remove
this part if you are dumping into a directory owned by you.




You may also specify the directory in which dump files are written:





User Option: ess-source-directory


Directory name (ending in a slash) where S dump files are to be written.




By default, dump files are always written to /tmp, which is fine
when ess-keep-dump-files is nil.  If you are keeping dump
files, then you will probably want to keep them somewhere in your home
directory, say ~/S-source.  This could be achieved by including
the following line in your .emacs file:




(setq ess-source-directory (expand-file-name "~/S-source/"))




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 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 Src of the
directory the ESS process was run in.





(setq ess-source-directory
      (lambda ()
         (concat ess-directory "Src/")))





(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 S working directory during an S session, you may
like to keep dump files in some subdirectory of the directory pointed to
by the first element of the current search list.  This way you can edit
objects of the same name in different directories during the one S
session:





(setq ess-source-directory
   (lambda ()
       (file-name-as-directory
        (expand-file-name (concat
                           (car ess-search-list)
                           "/.Src")))))





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.









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8 Reading help files




ESS provides an easy-to-use facility for reading S help files from
within Emacs.  From within the ESS process buffer or any ESS edit
buffer, typing C-c C-v (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 *help(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.



Help commands:





?




ess-describe-help-mode Pops up a help buffer with a list of the
commands available in S help mode.





h




ess-display-help-on-object Pop up a help buffer for a different
object.






Paging commands:






b


DEL


scroll-down Move one page backwards through the help file.





SPC


scroll-up Move one page forwards through the help file.





>


<


end-of-buffer Move to the beginning and end of the help file,
respectively.






Section-based motion commands:





n


p





ess-skip-to-previous-section and ess-skip-to-next-section
Move to the next and previous section header in the help file,
respectively.  A section header consists of a number of capitalized
words, followed by a colon.






In addition, the 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., ‘Description:’ instead of  ‘DESCRIPTION:’ and also
only some versions of S(-plus) have
sections ‘BACKGROUND’, ‘BUGS’, ‘OPTIONAL ARGUMENTS’,
‘REQUIRED ARGUMENTS’, and ‘SIDE EFFECTS’.



Do use s ? to get the current list of active key bindings.






‘a’


ARGUMENTS:





‘b’


BACKGROUND:





‘B’


BUGS:





‘d’


DESCRIPTION:





‘D’


DETAILS:





‘e’


EXAMPLES:





‘n’


NOTE:





‘O’


OPTIONAL ARGUMENTS:





‘R’


REQUIRED ARGUMENTS:





‘r’


REFERENCES:





‘s’


SEE ALSO:





‘S’


SIDE EFFECTS:





‘u’


USAGE:





‘v’


VALUE:





‘<’


Jumps to beginning of file





‘>’


Jumps to end of file





‘?’


Pops up a help buffer with a list of the defined section motion keys.






Evaluation:





l




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.





r




ess-eval-region Send the contents of the current region to the
ESS process.  Useful for running examples in help files.






Quit commands:





q




ess-help-quit Return to previously selected buffer, and bury the
help buffer.





k


kill-buffer Return to previously selected buffer, and kills the
help buffer.





x


ess-kill-buffer-and-go Return to the ESS process, killing this
help buffer.






Miscellaneous:





i


ess-display-index Prompt for a package and display it’s help
index.





v


ess-display-vignettes Display all available vignettes.





w


ess-display-help-in-browser Display current help page with the
web browser.





/


isearch-forward Same as C-s.






In addition, all of the ESS commands available in the edit buffers are
also available in S help mode (see Edit buffer).  Of course, the
usual (non-editing) Emacs commands are available, and for convenience
the digits and - 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 C-u) to ess-display-help-on-object.



Help buffers are marked as temporary buffers in ESS, and are deleted
when ess-quit or 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 ess-help-own-frame.













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9 Completion




• Object names:  



• Function arguments:  



• Minibuffer completion:  



• Auto-complete:  



• Icicles:  












Next: , Up: Completion   [Contents][Index]





9.1 Completion of object names






The TAB key is for completion. The value of the variable
ess-first-tab-never-complete controls when completion is allowed
controls when completion is allowed to occur.  In ess-mode
TAB first tries to indent, and if there is nothing to indent,
complete the object name instead.





TAB




comint-dynamic-complete Complete the S object name or
filename before point.






When the cursor is just after a partially-completed object name,
pressing TAB provides completion in a similar fashion to
tcsh

except that completion is performed over all known S object names
instead of file names.  ESS maintains a list of all objects known to S
at any given time, which basically consists of all objects (functions
and datasets) in every attached directory listed by the search()
command

along with the component objects of attached data frames

(if your version of S supports them).



For example, consider the three functions (available in Splus version
3.0) called binomplot(), binom.test() and
binomial().  Typing bin TAB after the S prompt will
insert the characters ‘om’, completing the longest prefix
(‘binom’) which distinguishes these three commands.  Pressing
TAB once more provides a list of the three commands which have
this prefix, allowing you to add more characters (say, ‘.’) which
specify the function you desire.  After entering more characters
pressing 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 M-?.





Command: ess-list-object-completions




M-? List all possible completions of the object name at point.




ESS also provides completion over the components of named lists and
environments (after ‘$’), S4 classes slots (after @), package and
namespace objects (after :: and :::).  





Completion is also provided over file names, which is particularly
useful when using S functions such as get() or scan()
which require fully expanded file names.




In the Inferior ESS buffer, if the cursor is not in a string and does
not follow a (partial) object name, the TAB key has a third use:
it expands history references.  See History expansion.








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 know is there), the command M-x
ess-resynch

forces the entire cache to be refreshed, which should fix the
problem.









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9.2 Completion of function arguments



When inside a function call (i.e. following ‘(’), TAB
completion also provides function arguments. If function is a generic,
completion will provide all the arguments of S3 methods known to
R.



A related functionality is See ESS ElDoc, which displays function
arguments in the echo area whenever the point is inside a function call.









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9.3 Minibuffer completion





From version 12.03, ESS uses IDO mechanism (part of default
emacs) for minibuffer completion if ido.el package is available
and the value of ess-use-ido it t (the default). The
completion command ess-completing-read falls back on classic
completion-read interface if this feature is not available for
whatever reason.









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9.4 Integration with auto-complete package






ESS provides three sources for Auto Completion mode:
ac-source-R-args, ac-source-R-objects and
ac-source-R.  The last one combines the previous two and makes them
play nicely together.  See auto-complete package documentation
(http://cx4a.org/software/auto-complete/) for how to modify and
install your own completion sources.



For the default auto-complete ESS configuration, install the latest
version of auto-complete package. ESS automatically detect the
package and activates auto-complete in ESS buffers.




To deactivate AC, place the following into your init file:





(setq ess-use-auto-complete nil)




Or, to activate auto-completion only in the ess-mode buffers:





(setq ess-use-auto-complete 'script-only)




ESS provides AC help both for arguments and objects (default keys
C-?  or <f1>). You can bind M-h to display quick help
pop-ups:





(define-key ac-completing-map (kbd "M-h") 'ac-quick-help)




AC binds M-n, and M-p for the navigation in the
completion menu, which might be inconvenient if you want it to use in
the inferior R. Bind it to something else:





(define-key ac-completing-map "\M-n" nil) ;; was ac-next
(define-key ac-completing-map "\M-p" nil) ;; was ac-previous
(define-key ac-completing-map "\M-," 'ac-next)
(define-key ac-completing-map "\M-k" 'ac-previous)










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9.5 Icicles



Another option for comprehensively handling completion in Emacs is via
Icicles (http://www.emacswiki.org/emacs/Icicles).  It allows
users to have completions shown temporarily in the standard
‘*Completions*’ buffer, and interactively select completion
candidates using several methods.  As of version 2013.04.04, Icicles
provides support for completion in ESS.  Please consult Icicles
documentation, which is easily accessible via customize-group
Icicles, for more details on installation and customization options.



Once installed, Icicles can be activated by evaluating (maybe place in
~/.emacs):





(require 'icicles)
(icy-mode 1)




Icicles can be toggled at any moment by typing M-x icy.



When Icicles is on, TAB offers completion, provided the conditions
determined by ess-first-tab-never-complete allow it.  Typing
M-TAB will attempt completion regardless.  Typing M-?  in
ESS or iESS modes brings up the relevant completion
candidates from which to choose.  Minibuffer input filters the available
candidates.  Use TAB for prefix completion or S-TAB for
substring or regexp completion.  Use S-SPC to match an additional
pattern (repeatable).  You can cycle among the matching candidates,
choosing with RET or mouse-2.










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10 Developing with ESS



ESS provides several tools to help you with the development of your R
packages:





• ESS tracebug:  Visual debugging, breakpoints, tracing, watch etc.



• Editing documentation:  Tools to edit R documentation



• Namespaced Evaluation:  Develop your packages on the fly












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10.1 ESS tracebug





ESS tracebug offers visual debugging, interactive error
navigation, interactive backtrace, breakpoint manipulation, control over
R error actions, watch window and interactive flagging/unflagging of
functions for debugging.



From ESS13.05 ess-tracebug is on by default. You can toggle it on
and off with M-x ess-tracebug. To disable startup
activation of ess-tracebug set ess-use-tracebug to nil.



Tracebug functionality can be found on ess-dev-map, bound to
C-c C-t. Additionally, when subprocess is in a debugging state
ess-debug-minor-mode is active and the following additional
shortcuts are available:



* Interactive Debugging (`ess-debug-minor-mode-map'):

 M-C   . Continue                  . `ess-debug-command-continue'
 M-C-C . Continue multi            . `ess-debug-command-continue-multi'
 M-N   . Next step                 . `ess-debug-command-next'
 M-C-N . Next step multi           . `ess-debug-command-next-multi'
 M-U   . Up frame                  . `ess-debug-command-up'
 M-Q   . Quit debugging            . `ess-debug-command-quit'





These are all the tracebug commands defined in ess-dev-map
(C-c C-t ? to show this table):



* Breakpoints (`ess-dev-map'):

 b   . Set BP (repeat to cycle BP type) . `ess-bp-set'
 B   . Set conditional BP               . `ess-bp-set-conditional'
 k   . Kill BP                          . `ess-bp-kil'
 K   . Kill all BPs                     . `ess-bp-kill-all'
 o   . Toggle BP state                  . `ess-bp-toggle-state'
 l   . Set logger BP                    . `ess-bp-set-logger'
 n   . Goto next BP                     . `ess-bp-next'
 p   . Goto previous BP                 . `ess-bp-previous'

  (C- prefixed equivalents are also defined)

* Debugging (`ess-dev-map'):
 `   . Show traceback                       . `ess-show-traceback' (also on C-c `)
 ~   . Show callstack                       . `ess-show-call-stack' (also on C-c ~)
 e   . Toggle error action (repeat to cycle). `ess-debug-toggle-error-action'
 d   . Flag for debugging                   . `ess-debug-flag-for-debugging'
 u   . Unflag for debugging                 . `ess-debug-unflag-for-debugging'
 w   . Watch window                         . `ess-watch'

  (C- prefixed equivalents are also defined)

* Navigation to errors (general emacs functionality):

 C-x `, M-g n   . `next-error'
 M-g p          . `previous-error'

* Misc:

?   . Show this help		. `ess-tracebug-show-help'




To configure how electric watch window splits the display see
ess-watch-width-threshold and ess-watch-height-threshold
variables.



A more detailed ess-tracebug documentation with screenshots is available
at http://code.google.com/p/ess-tracebug/.



A short tutorial is at http://code.google.com/p/ess-tracebug/wiki/GettingStarted.




Note: Currently, ess-tracebug does not detect some of R’s debug
related messages in non-English locales. To set your R messages to
English add the following line to your .Rprofile init file:



   Sys.setlocale("LC_MESSAGES", "C")









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10.2 Editing 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.





• R documentation files:  Edit objects in a specialized buffer



• Roxygen:  Loading source files into the ESS process












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10.2.1 Editing R documentation (Rd) files



R objects are documented in files written in the R
documentation (“Rd”), a simple markup language closely resembling
(La)TeX, which can be processed into a variety of formats, including
LaTeX, 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 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 rd; to activate
ESS[Rd] support for this extension, you may need to add





(add-to-list 'auto-mode-alist '("\\.rd\\'" . Rd-mode))




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.





C-h m


Describe the features of Rd mode.





LFD


RET


Reindent the current line, insert a newline and indent the new line
(reindent-then-newline-and-indent).  An abbrev before point is
expanded if abbrev-mode is non-nil.





TAB


Indent current line based on its contents and on previous lines.
(indent-according-to-mode).





C-c C-e


Insert a “skeleton” with Rd markup for at least all mandatory entries
in Rd files (Rd-mode-insert-skeleton).  Note that many users
might prefer to use the R function 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).





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 (Rd-font).  C-c C-f is only a prefix; see
e.g. 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
C-c C-f.





C-c C-j


Insert a suitably indented  ‘\item{’ on the next line
(Rd-mode-insert-item).





C-c C-p


Preview a plain text version (“help file”, see Help) generated
from the Rd file (Rd-preview-help).






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.,
C-c C-v provides access to on-line help, and 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
C-h m for all available commands.



Rd mode also provides access to abbreviations for most of the Rd markup
commands.  Type 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.





User Option: Rd-mode-hook


Hook to be run when Rd mode is entered.






User Option: Rd-indent-level


The indentation of Rd code with respect to containing blocks.  Default
is 2.






User Option: Rd-to-help-command


The shell command used for converting Rd source to help text.  Default
is ‘R CMD Rd2txt’.




To automatically turn on the abbrev and font-lock features of Rd mode,
add the following lines to one of your Emacs startup files:





(add-hook 'Rd-mode-hook
          (lambda ()
           (abbrev-mode 1)
           (font-lock-mode 1)))










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10.2.2 Editing Roxygen documentation






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 NAMESPACE
files. See the Roxygen documentation found via http://roxygen.org
for more information on its usage. An example of an Roxygen entry for a
simple R function can look like this:





##' 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")



The entry is immediately preceding the object to document and all lines
start with the Roxygen prefix string, in this case ##'. 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 ess-roxy.el which is loaded
by default in ESS. The following special Emacs commands are provided.





Command: ess-roxy-update-entry




C-c C-o C-o 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
ess-roxy-fill-param-p is non-nil.






Command: ess-roxy-toggle-roxy-region beg end




C-c C-o C-c Toggle the presence of the leading Roxygen string on
all lines in the marked region (between beg and
end. Convenient for transferring text to Roxygen entries and to
evaluate example fields.






Command: ess-roxy-preview-Rd name-file




C-c C-o C-r 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 name-file,
i.e. 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.






Command: ess-roxy-preview-HTML visit-instead-of-open




C-c C-o C-t 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 visit-instead-of-open, i.e. C-u C-c C-e C-t,
visit the generated HTML file instead.  Requires the Roxygen and tools
packages to be installed.






Command: ess-roxy-previous-entry




C-c C-o p Go to start of the Roxygen entry above point.






Command: ess-roxy-next-entry




C-c C-o n Go to end of the Roxygen entry above point.






Command: ess-roxy-hide-all




C-c C-o C-h 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 advises the following standard editing functions in order to
make Roxygen editing more intuitive:





TAB




ess-R-complete-object-name Complete Roxygen tag at
point. E.g. doing TAB when the point is at the end of @par
completes to @param.





M-h




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.





TAB




ess-indent-command If hide-show support is enabled, fold away the
visibility of the Roxygen entry at point.





M-q




fill-paragraph Fill the Roxygen field at point.





C-a




move-beginning-of-line Move to the point directly to the right of
the Roxygen start string.





RET




newline-and-indent Insert a new line and the Roxygen prefix
string.












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10.3 Namespaced Evaluation




In non package files evaluation commands (See Evaluating code) send
portions of the current buffer environment (R_GlobalEnv. When
developing packages, ESS sends code to the corresponding package
namespace and (for visible objects) into package environment (visible on
search path). All objects that are assigned are displayed in the
minibuffer alongside the environment in which they are assigned.



Here is a short overview of how namespace and package environments work
in R. All objects defined in a package ’foo’ are stored in an
environment called ’namespace:foo’. Parent environment of
’namespace:foo’ is an environment ’imports:foo’ which contains copies of
all objects from other packages which ’foo’ imports. Parent environment
of ’imports:foo’ is the ’namespace:base’. Parent environment of
’namespace:base’ is .GlobalEnv. Thus functions and methods stored in
’namespace:foo’ see all the objects in .GlobalEnv unless shadowed by
objects in ’imports:foo’, ’namespace:base’, or ’namespace:foo’
itself. There is another environment associated with ’foo’ -
’package:foo’. This environment stores *copies* of exported objects from
’namespace:foo’ and is placed on the search() path, i.e. if ’foo’ is
loaded and if you start with .GlobalEnv and iteratively call
parent.env() you will get eventually to ’package:foo’. Thus all methods
and functions defined in .GlobalEnv can "see" objects in ’package:foo’
environment. See also
http://cran.r-project.org/doc/manuals/R-ints.html#Namespaces.



Ocasionally you want to evaluate into a package from a non-package file,
or the other way around, evaluate into GlobalEnv from inside a
package. In such cases C-c C-t C-s is your friend.





Command: ess-r-set-evaluation-env arg




C-c C-t C-s Set or unset the current evaluation environment (a package). 










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11 Other ESS features and tools



ESS has a few extra features, which didn’t fit anywhere else.



• ESS ElDoc:  Display function arguments in minibuffer



• Handy commands:  Usefully commands at your fingertips



• Highlighting:  Syntactic highlighting of buffers



• Parens:  Parenthesis matching



• Graphics:  Using graphics with ESS



• Imenu:  Support for Imenu in ESS



• Toolbar:  Support for toolbar in ESS



• TAGS:  Using TAGS for S files



• Rdired:  Directory editor for R objects



• Rutils:  R object/package management and help utilities



• Org:  Interaction with Org mode



• Sweave and AUCTeX:  Support for Sweave in ESS and AUCTeX












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11.1 ElDoc



In ElDoc mode, the echo area displays function’s arguments at
point. From ESS version 12.03, ElDoc is active by default in
ess-mode and inferior-ess-mode buffers. To activate it
only in ess-mode buffers, place the following into your init
file:





(setq ess-use-eldoc 'script-only)






User Option: ess-use-eldoc


If ‘t’, activate eldoc in ess-mode and inferior-ess-mode buffers.
If ‘'script-only’ activate in ess-mode buffers only.  Set
ess-use-eldoc to nil to stop using ElDoc
altogether.






User Option: ess-eldoc-show-on-symbol


This variable controls whether the help is shown only inside function
calls. If set to ‘t’, ElDoc shows help string whenever the
point is on a symbol, otherwise (the default), shows only when the point
is in a function call, i.e. after ‘'('’.






User Option: ess-eldoc-abbreviation-style


The variable determines how the doc string should be abbreviated to fit
into minibuffer. Posible values are ‘nil’, ‘mild’,
‘normal’, ‘strong’ and ‘aggressive’. Please see the
documentation of the variable for more details. The default filter is
‘normal’.




Ess-eldoc also honors the value of
eldoc-echo-area-use-multiline-p, which if set to ‘nil’, will
cause the truncation of doc string indifferent of the value of
ess-eldoc-abbreviation-style. This way you can combine different
filter levels with the truncation.









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11.2 Handy commands










Command: ess-handy-commands


Request and execute a command from ess-handy-commands list.






User Option: ess-handy-commands


An alist of custom ESS commands available for call by
ess-handy-commands and ess-smart-comma function.



Currently contains:





change-directory


ess-change-directory



help-index


ess-display-index



help-object


ess-display-help-on-object



vignettes


ess-display-vignettes



objects[ls]


ess-execute-objects



search


ess-execute-search



set-width


ess-execute-screen-options



install.packages


ess-install.packages



library


ess-library



setRepos


ess-setRepositories



sos


ess-sos









Handy commands: ess-library, ess-install.packages, etc -
ask for item with completion and execute the correspond
command. ess-sos is a interface to findFn function in
package sos. If package sos is not found, ask user for
interactive install.










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11.3 Syntactic highlighting of buffers



ESS provides Font-Lock (see Using Multiple Typefaces in The Gnu Emacs Reference Manual) patterns for Inferior S Mode, S
Mode, and S Transcript Mode buffers.





Syntax highlighting within ESS buffers is controlled by:





User Option: ess-font-lock-mode


Non-‘nil’ means we use font lock support for ESS buffers.  Default
is ‘t’, to use font lock support.  If you change the value of this
variable, restart Emacs for it to take effect.





The font-lock patterns are defined by the following variables, which you
may modify if desired:





User Option: inferior-R-font-lock-keywords


Font-lock patterns for inferior *R* processes.  (There is a
corresponding inferior-S-font-lock-keywords for *S* processes.)
The default value highlights prompts, inputs, assignments, output
messages, vector and matrix labels, and literals such as ‘NA’ and
TRUE.






User Option: ess-R-font-lock-keywords


Font-lock patterns for ESS R programming mode.  (There is a
corresponding ess-S-font-lock-keywords for S buffers.) The
default value highlights function names, literals, assignments, source
functions and reserved words.












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11.4 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:





(paren-set-mode 'paren) ;for XEmacs
(show-paren-mode t) ;for Emacs











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11.5 Using graphics with ESS




One of the main features of the S package is its ability to
generate high-resolution graphics plots, and ESS provides a number of
features for dealing with such plots.





• printer:  The printer() graphics driver



• X11:  The X11() (and other X Windows based) driver



• winjava:  Java Graphics Device












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11.5.1 Using ESS with the printer() driver



This is the simplest (and least desirable) method of using graphics
within ESS.  S’s 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 S command



printer(width=79)




(the 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 show() command
is issued, which displays the current figure.









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11.5.2 Using ESS with windowing devices




Of course, the ideal way to use graphics with ESS is to use a windowing
system.  Under X Windows, or X11, this requires that the DISPLAY environment
variable be appropriately set.









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11.5.3 Java Graphics Device





S+6.1 and newer on Windows contains a java library that supports graphics.  Send
the commands:





library(winjava)
java.graph()




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.)









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11.6 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 imenu-generic-expression.  This value is set
by various ESS variables such as ess-imenu-S-generic-expression.









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11.7 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.  See Customization, for ways
to change the toolbar.









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11.8 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.





etags --language=none
--regex='/\([^ \t]+\)[ \t]*<-[ \t]*function/\1/' *.R




This will find entries in your source file of the form:





some.name <- function




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 ‘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:





R CMD rtags --help




For further details, see http://developer.r-project.org/rtags.html









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11.9 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.



Start an R session with M-x R and then store a few
variables, such as:





s <- sin(seq(from=0, to=8*pi, length=100))
x <- c(1, 4, 9)
y <- rnorm(20)
z <- TRUE




Then use M-x ess-rdired to create a buffer listing the
objects in your current environment and display it in a new window:



            mode length
  s      numeric    100
  x      numeric      3
  y      numeric     20
  z      logical      1




Type C-h m or ? 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).










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11.10 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 help.start() and
RSiteSearch() that use the browse-url Emacs function.
The library can be loaded using M-x load-file, but the easiest is
to include:





(require 'ess-rutils)




in your .emacs.  Once R is started with M-x R, and if the value of
the customizable variable ess-rutils-keys is true, several key
bindings become available in iESS process buffers:





Command: ess-rutils-local-pkgs




C-c C-. l List all packages in all available libraries.






Command: ess-rutils-repos-pkgs




C-c C-. r List available packages from repositories listed by
getOptions(``repos'') in the current R session.






Command: ess-rutils-update-pkgs lib repos




C-c C-. u Update packages in a particular library lib and
repository repos.






Command: ess-rutils-apropos




C-c C-. a Search for a string using apropos.






Command: ess-rutils-rm-all




C-c C-. m Remove all R objects.






Command: ess-rutils-objs




C-c C-. o Manipulate R objects; wrapper for ess-rdired.






Command: ess-rutils-load-wkspc




C-c C-. w Load a workspace file into R.






Command: ess-rutils-save-wkspc




C-c C-. s Save a workspace file.






Command: ess-change-directory




C-c C-. d Change the working directory for the current R session.






Command: ess-rutils-html-docs




C-c C-. H Use browse-url to navigate R html
documentation.




See the submenu ‘Rutils’ under the iESS menu for alternative access
to these functions.  The function 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:





(eval-after-load "ess-rutils"
  '(global-set-key [(control c) (f6)] 'ess-rutils-rsitesearch))





Functions for listing objects and packages
(ess-rutils-local-pkgs, ess-rutils-repos-pkgs, and
ess-rutils-objs) show results in a separate buffer and window,
in ess-rutils-mode, providing useful key bindings in this mode
(type ? in this buffer for a description).










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11.11 Interaction with Org mode



Org-mode (http://orgmode.org) now supports reproducible research
and literate programming in many languages (including R) – see chapter
14 of the Org manual
(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.)










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11.12 Support for Sweave in ESS and AUCTeX



ESS provides support for writing and processing Sweave
(http://www.statistik.lmu.de/~leisch/Sweave), building up on
Emacs’ ess-noweb-mode for literate programming.  When working on an Sweave
document, the following key bindings are available:





Command: ess-swv-weave choose




M-n s Run Sweave on the current .Rnw file.  If choose is
non-‘nil’, offer a menu of available weavers.






Command: ess-swv-latex




M-n l Run LaTeX after Sweave’ing.






Command: ess-swv-PS


M-n p Generate and display a postscript file after LaTeX’ing.






Command: ess-swv-PDF pdflatex-cmd




M-n P Generate and display a PDF file after LaTeX’ing.  Optional
argument pdflatex-cmd is the command to use, which by default, is
the command used to generate the PDF file is the first element of
ess-swv-pdflatex-commands.






User Option: ess-swv-pdflatex-commands


Commands used by ess-swv-PDF to run a version of pdflatex; the
first entry is the default command.




Sweave’ing with ess-swv-weave starts an inferior-ESS process, if
one is not available.  Other commands are available from the
‘Sweaving, Tangling, ...’ submenu of the Noweb menu.



AUCTeX (http://www.gnu.org/software/auctex) users may prefer to
set the variable ess-swv-plug-into-AUCTeX-p (available from the
“ESS Sweave” customization group) to t.  Alternatively, the same can
be achieved by activating the entry “AUCTeX Interface” from the
‘Sweaving, Tangling, ...’ submenu, which toggles this variable on
or off.  When the interface is activated, new entries for Sweave’ing and
LaTeX’ing thereafter are available from AUCTeX’s “Command” menu.
Sweave’ing can, thus, be done by C-c C-c Sweave RET without an
inferior-ESS process.  Similarly, LaTeX’ing can be done by C-c C-c
LaTeXSweave RET.  In both cases, the process can be monitored with
C-c C-l (TeX-recenter-output-buffer).  Open the viewer with
C-c C-v (TeX-view), as usual in AUCTeX.









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12 Overview of ESS features for the S family




• 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:  












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12.1 ESS[S]–Editing files



ESS[S] is the mode for editing S language files.  This mode handles:





ESS[S] mode should be automatically turned on when loading a file with
the suffices found in ess-site (*.R, *.S, *.s, etc).  Alternatively,
type M-x R-mode to put the current buffer into R mode.  However, one
will have to start up an inferior process to take advantage of the
interactive features.









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12.2 iESS[S]–Inferior ESS processes


iESS (inferior ESS) is the mode for interfacing with active
statistical processes (programs).  This mode handles:





To start up iESS mode, use:



   M-x S+3
   M-x S4
   M-x S+5
   M-x S+6
   M-x R




(for S-PLUS 3.x, S4, S+5, S+6 or S+7, and R, respectively.  This assumes that
you have access to each).  Usually the site will have defined one of
these programs (by default S+6) to the simpler name:



M-x S




In the (rare) case that you wish to pass command line arguments to the
starting S+6 process, set the variable inferior-Splus-args.



Note that R has some extremely useful command line arguments.  For
example, --vanilla will ensure R starts up without loading in any init
files.  To enter a command line argument, call R using a "prefix
argument", by



C-u M-x R



and when ESS prompts for "Starting Args ? ", enter (for example):



--vanilla



Then that R process will be started up using R --vanilla.  If you
wish to always call R with certain arguments, set the variable
inferior-R-args accordingly.




If you have other versions of R or S-Plus available on the system, ESS
is also able to start those versions.  How this exactly works depend on
which OS you are using, as described in the following paragraphs.  The
general principle, regardless of OS, is that ESS searches the paths
listed in the variable exec-path for R binaries.  If ESS cannot
find your R binaries, on Unix you can change the unix environment
variable PATH, as this variable is used to set exec-path.



R on Unix systems: If you have "R-1.8.1" on your exec-path, it
can be started using M-x R-1.8.1.  By default, ESS will find
versions of R beginning "R-1" or "R-2".  If your versions of R are
called other names, consider renaming them with a symbolic link or
change the variable ess-r-versions.  To see which functions have
been created for starting different versions of R, type M-x R- and
then hit [Tab].  These other versions of R can also be started from the
"ESS->Start Process->Other" menu.



R on Windows systems: If you have "rw1081" on your exec-path, it
can be started using M-x rw1081.  By default, ESS will find
versions of R located in directories parallel to the version of R in
your PATH.  If your versions of R are called other names, you
will need to change the variable ess-rterm-versions.  To see
which functions have been created for starting different versions of R,
type M-x rw and then hit [Tab].  These other versions of
R can also be started from the "ESS->Start Process->Other" menu.



Once ESS has found these extra versions of R, it will then create a new
function, called M-x R-newest, which will call the newest version
of R that it found.  (ESS examines the date in the first line of
information from R --version to determine which is newest.)



S on Unix systems: If you have "Splus7" on your exec-path, it can
be started using M-x Splus7.  By default, ESS will find all
executables beginning "Splus" on your path.  If your versions of S are
called other names, consider renaming them with a symbolic link or
change the variable ess-s-versions.  To see which functions have
been created for starting different versions of Splus, type M-x
Splus and then hit [Tab].  These other versions of Splus can also be
started from the "ESS->Start Process->Other" menu.



A second mechanism is also available for running other versions of Splus.
The variable ess-s-versions-list is a list of lists; each sublist
should be of the form: (DEFUN-NAME PATH ARGS).  DEFUN-NAME is the name
of the new emacs function you wish to create to start the new S process;
PATH is the full path to the version of S you want to run; ARGS is an
optional string of command-line arguments to pass to the S process.
Here is an example setting:



(setq ess-s-versions-list
      '( ("Splus64" "/usr/local/bin/Splus64")
         ("Splus64-j" "/usr/local/bin/Splus64" "-j")))



which will then allow you to do M-x Splus64-j to start  Splus64
with the corresponding command line arguments.




If you change the value of either ess-s-versions or
ess-s-versions-list, you should put them in your .emacs before
ess-site is loaded, since the new emacs functions are created when ESS
is loaded.






Sqpe (S-Plus running inside an emacs buffer) on Windows systems: If you
have an older version of S-Plus (S-Plus 6.1 for example) on your system,
ir can be started inside an emacs buffer with M-x splus61.  By
default, ESS will find versions of S-Plus located in the installation
directories that Insightful uses by default.  If your versions of S-Plus
are anywhere else, you will need to change the variable
ess-SHOME-versions.  To see which functions have been created for
starting different versions of S-Plus, type M-x spl and then hit
[Tab].  These other versions of S-Plus can also be started from the
"ESS->Start Process->Other" menu.










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12.3 ESS-help–assistance with viewing help



ESS has built-in facilities for viewing help files from S.  See Help.










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12.4 Philosophies for using ESS[S]



The first is preferred, and configured for.  The second one can be
retrieved again, by changing emacs variables.



1: (preferred by the current group of developers):  The source code is
   real.  The objects are realizations of the source code.  Source
   for EVERY user modified object is placed in a particular directory
   or directories, for later editing and retrieval.



2: (older version): S objects are real.  Source code is a temporary
   realization of the objects.  Dumped buffers should not be saved.
   _We_strongly_discourage_this_approach_.  However, if you insist,
   add the following lines to your .emacs file:



(setq ess-keep-dump-files 'nil)
(setq ess-delete-dump-files t)
(setq ess-mode-silently-save nil)



The second saves a small amount of disk space.  The first allows for
better portability as well as external version control for code.









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12.5 Scenarios for use (possibilities–based on actual usage)



We present some basic suggestions for using ESS to interact with S.
These are just a subset of approaches, many better approaches are
possible.  Contributions of examples of how you work with ESS are
appreciated (especially since it helps us determine priorities on
future enhancements)! (comments as to what should be happening are
prefixed by "##").



1:  ##    Data Analysis Example (source code is real)
    ## Load the file you want to work with
    C-x C-f myfile.s

    ## Edit as appropriate, and then start up S-PLUS 3.x
    M-x S+3

    ## A new buffer *S+3:1* will appear.  Splus will have been started
    ## in this buffer.  The buffer is in iESS [S+3:1] mode.

    ## Split the screen and go back to the file editing buffer.
    C-x 2 C-x b myfile.s

    ## Send regions, lines, or the entire file contents to S-PLUS.  For regions,
    ## highlight a region with keystrokes or mouse and then send with:
    C-c C-r

    ## Re-edit myfile.s as necessary to correct any difficulties.  Add
    ## new commands here.  Send them to S by region with C-c C-r, or
    ## one line at a time with C-c C-n.

    ## Save the revised myfile.s with C-x C-s.

    ## Save the entire *S+3:1* interaction buffer with C-c C-s.  You
    ## will be prompted for a file name.  The recommended name is
    ## myfile.St.  With the *.St suffix, the file will come up in ESS
    ## Transcript mode the next time it is accessed from Emacs.



2:  ## Program revision example (source code is real)

    ## Start up S-PLUS 3.x in a process buffer (this will be *S+3:1*)
    M-x S+3

    ## Load the file you want to work with
    C-x C-f myfile.s

    ## edit program, functions, and code in myfile.s, and send revised
    ## functions to S when ready with
    C-c C-f
    ## or highlighted regions with
    C-c C-r
    ## or individual lines with
    C-c C-n
    ## or load the entire buffer with
    C-c C-l

    ## save the revised myfile.s when you have finished
    C-c C-s



3:  ## Program revision example (S object is real)

    ## Start up S-PLUS 3.x in a process buffer (this will be *S+3:1*)
    M-x S+3

    ## Dump an existing S object my.function into a buffer to work with
    C-c C-d my.function
    ## a new buffer named yourloginname.my.function.S will be created with
    ## an editable copy of the object.  The buffer is associated with the
    ## pathname /tmp/yourloginname.my.function.S and will amlost certainly not
    ## exist after you log off.

    ## enter program, functions, and code into work buffer, and send
    ## entire contents to S-PLUS when ready
    C-c C-b

    ## Go to *S+3:1* buffer, which is the process buffer, and examine
    ## the results.
    C-c C-y
    ## The sequence C-c C-y is a shortcut for:  C-x b *S+3:1*

    ## Return to the work buffer (may/may not be prefixed)
    C-x C-b yourloginname.my.function.S
    ## Fix the function that didn’t work, and resubmit by placing the
    ## cursor somewhere in the function and
    C-c C-f
    ## Or you could’ve selected a region (using the mouse, or keyboard
    ## via setting point/mark) and
    C-c C-r
    ## Or you could step through, line by line, using
    C-c C-n
    ## Or just send a single line (without moving to the next) using
    C-c C-j
    ## To fix that error in syntax for the "rchisq" command, get help
    ## by
    C-c C-v rchisq


4:    Data Analysis (S object is real)
    ## Start up S-PLUS 3.x, in a process buffer (this will be *S+3:1*)
    M-x S+3

    ## Work in the process buffer.  When you find an object that needs
    ## to be changed (this could be a data frame, or a variable, or a
    ## function), dump it to a buffer:
    C-c C-d my.cool.function

    ## Edit the function as appropriate, and dump back in to the
    ## process buffer
    C-c C-b

    ## Return to the S-PLUS process buffer
    C-c C-y
    ## Continue working.

    ## When you need help, use
    C-c C-v rchisq
    ## instead of entering:   help("rchisq")











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12.6 Customization Examples and Solutions to Problems



1. Suppose that you are primarily an SPLUS 3.4 user, occasionally
   using S version 4, and sick and tired of the buffer-name *S+3*
   we’ve stuck you with.  Simply edit the "ess-dialect" alist entry in
   the ess-sp3-d.el and ess-s4-d.el files to be "S" instead of "S4" and
   "S+3".  This will ensure that all the inferior process buffer names
   are "*S*".



2. Suppose that you WANT to have the first buffer name indexed by
   ":1", in the same manner as your S-PLUS processes 2,3,4, and 5 (for
   you heavy simulation people).  Then
   add after your (require ’ess-site) or (load "ess-site") command
    in your .emacs file, the line:



(setq ess-plain-first-buffername nil)




3. Fontlocking sometimes fails to behave nicely upon errors.  When
   Splus dumps, a mis-matched "  (double-quote) can result in the
   wrong font-lock face being used for the remainder of the buffer.



Solution: add a " at the end of the "Dumped..." statement, to
   revert the font-lock face back to normal.



4. When you change directory within a *R* or *S* session using the
setwd() command, emacs does not recognise that you have changed the
current directory.



Solution: Use M-x ess-change-directory.  This will prompt you for
the directory to change to.  It will then change directory within the
*S* buffer, and also update the emacs variable default-directory.
Alternatively, if you have already executed setwd(), press M-RET
within the *S* buffer so that Emacs can update default-directory.









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13 ESS for SAS





• 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:  





ESS[SAS] was designed for use with SAS.  It is descended from emacs
macros developed by John Sall for editing SAS programs and SAS-mode by
Tom Cook.  Those editing features and new advanced features are part of
ESS[SAS].  The user interface of ESS[SAS] has similarities with ESS[S]
and the SAS Display Manager.









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13.1 ESS[SAS]–Design philosophy



ESS[SAS] was designed to aid the user in writing and maintaining SAS
programs, such as foo.sas.  Both interactive and batch
submission of SAS programs is supported.



ESS[SAS] was written with two primary goals.

    

  1.  The emacs text editor provides a powerful and flexible development
environment for programming languages.  These features are a boon to all
programmers and, with the help of ESS[SAS], to SAS users as well.

  2.  Although a departure from SAS Display Manager, ESS[SAS] provides
similar key definitions to give novice ESS[SAS] users a head start.
Also, inconvenient SAS Display Manager features, like remote submission
and syntax highlighting, are provided transparently; appealing to
advanced ESS[SAS] users.










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13.2 ESS[SAS]–Editing files



ESS[SAS] is the mode for editing SAS language files.  This mode handles:





ESS[SAS] is automatically turned on when editing a file with a .sas
suffix (or other extension, if specified via auto-mode-alist).  The function
keys can be enabled to use the same function keys that
the SAS Display Manager does.  The interactive capabilities of ESS require you
to start an inferior SAS process with M-x SAS
(See iESS(SAS)--Interactive SAS processes.)



At this writing, the indenting and syntax highlighting are generally
correct.  Known issues: for multiple line * or %* comments, only the
first line is highlighted; for .log files, only the first line of a
NOTE:, WARNING: or ERROR: message is highlighted; unmatched
single/double quotes in CARDS data lines are NOT ignored; in an
iterative DO statement, TO and BY are not highlighted.









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13.3 ESS[SAS]–TAB key



Two options.  The TAB key is bound by default to
sas-indent-line.  This function is used to syntactically indent
SAS code so PROC and RUN are in the left margin,
other statements are indented sas-indent-width spaces from the
margin, continuation lines are indented sas-indent-width spaces
in from the beginning column of that statement.  This is the type of
functionality that emacs provides in most programming language modes.
This functionality is activated by placing the following line in your
initialization file prior to a require/load:



(setq ess-sas-edit-keys-toggle nil)




ESS provides an alternate behavior for TAB that makes it
behave as it does in SAS Display Manager, i.e. move the cursor to
the next stop.  The alternate behavior also provides a "TAB"
backwards, C-TAB, that moves the cursor to the stop to
the left and deletes any characters between them.  This functionality
is obtained by placing the following line in your initialization file
prior to a require/load:



(setq ess-sas-edit-keys-toggle t)



Under the alternate behavior, TAB is bound to M-x tab-to-tab-stop
and the stops are defined by ess-sas-tab-stop-list.









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13.4 ESS[SAS]–Batch SAS processes



Submission of a SAS batch job is dependent on your environment.
ess-sas-submit-method is determined by your operating system and
your shell.  It defaults to 'sh unless you are running Windows or
Mac Classic.  Under Windows, it will default to 'sh if you are using
a UNIX-imitating shell; otherwise 'ms-dos for an MS-DOS
shell.  On Mac OS X, it will default to 'sh, but under Mac Classic,
it defaults to 'apple-script.  You will also set this to 'sh
if the SAS batch job needs to run on a remote machine rather than your
local machine.  This works transparently if you are editing the remote file
via ange-ftp/EFS or tramp.  Note that
ess-sas-shell-buffer-remote-init is a Local Variable that defaults
to "ssh" which will be used to open the buffer on the remote host
and it is assumed that no password is necessary, i.e. you are using
ssh-agent/ssh-add or the equivalent (see the discussion about
Local Variables below if you need to change the default).



However, if you are editing the file locally and transferring it back and
forth with Kermit, you need some additional steps.  First, start Kermit
locally before remotely logging in.  Open a local copy of the file with the
ess-kermit-prefix character prepended (the default is "#").
Execute the command M-x ess-kermit-get which automatically brings
the contents of the remote file into your local copy.  If you transfer
files with Kermit manually in a *shell* buffer, then note that the
Kermit escape sequence is C-q C-\ c rather than C-\ c which
it would be in an ordinary terminal application, i.e. not in an emacs
buffer.  Lastly, note that the remote Kermit command is specified by
ess-kermit-command.



The command used by the SUBMIT function key (F3 or F8)
to submit a batch SAS job, whether local or remote, is
ess-sas-submit-command which defaults to sas-program.
sas-program is "invoke SAS using program file" for Mac
Classic and "sas" otherwise.  However, you may have to alter
ess-sas-submit-command for a particular program, so it is defined as
buffer-local.  Conveniently, it can be set at the end of the program:



endsas;
Local variables:
ess-sas-submit-command: "sas8"
End:




The command line is also made of ess-sas-submit-pre-command,
ess-sas-submit-post-command and ess-sas-submit-command-options
(the last of which is also buffer-local).
Here are some examples for your ~/.emacs or ~/.xemacs/init.el
file (you may also use M-x customize-variable):



;'sh default
(setq ess-sas-submit-pre-command "nohup")
;'sh default
(setq ess-sas-submit-post-command "-rsasuser &")
;'sh example
(setq-default ess-sas-submit-command "/usr/local/sas/sas")
;'ms-dos default
(setq ess-sas-submit-pre-command "start")
;'ms-dos default
(setq ess-sas-submit-post-command "-rsasuser -icon")
;Windows example
(setq-default ess-sas-submit-command "c:/progra~1/sas/sas.exe")
;Windows example
(setq-default ess-sas-submit-command "c:\\progra~1\\sas\\sas.exe")




There is a built-in delay before a batch SAS job is submitted when using
a UNIX-imitating shell under Windows.  This is necessary in many cases
since the shell might not be ready to receive a command.  This delay is
currently set high enough so as not to be a problem.  But, there may be
cases when it needs to be set higher, or could be set much lower to
speed things up.  You can over-ride the default in your ~/.emacs or ~/.xemacs/init.el file by:



(setq ess-sleep-for 0.2)




For example, (setq ess-sas-global-unix-keys t) keys shown,
(setq ess-sas-global-pc-keys t) in parentheses;
ESS[SAS] function keys are presented in the next section.
Open the file you want to work with C-x C-f foo.sas.
foo.sas will be in ESS[SAS] mode.  Edit as appropriate, then save and
submit the batch SAS job.



F3 (F8)



The job runs in the *shell* buffer while you continue to edit
foo.sas.  If ess-sas-submit-method is 'sh, then the
message buffer will display the shell notification when the
job is complete.  The 'sh setting also allows you to
terminate the SAS batch job before it is finished.



F8 (F3)



Terminating a SAS batch in the *shell* buffer.



kill PID



You may want to visit the .log (whether the job is still running
or it is finished) and check for error messages.  The .log will be
refreshed and you will be placed in it’s buffer.  You will be
taken to the first error message, if any.



F5 (F6)



Goto the next error message, if any.



F5 (F6)



Now, ‘refresh’ the .lst and go to it’s buffer.



F6 (F7)



If you wish to make changes, go to the .sas file with.



F4 (F5)



Make your editing changes and submit again.



F3 (F8)










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13.5 ESS[SAS]–Function keys for batch processing



The setup of function keys for SAS batch processing
is unavoidably complex, but the usage of function keys is simple.
There are five distinct options:



Option 1 (default).  Function keys in ESS[SAS] are not bound to elisp
commands.  This is in accordance with the GNU Elisp Coding Standards
(GECS) which do not allow function keys to be bound so that they are
available to the user.



Options 2-5.  Since GECS does not allow function keys to be bound by
modes, these keys are often unused.  So, ESS[SAS] provides users with
the option of binding elisp commands to these keys.  Users who are
familiar with SAS will, most likely, want to duplicate the function key
capabilities of the SAS Display Manager.  There are four options (noted
in parentheses).



    

  1.  SAS Display Manager has different function key definitions for
UNIX (2, 4) and Windows (3, 5); ESS[SAS] can use either.

  2.  The ESS[SAS] function key definitions can be active in all buffers
(global: 4, 5) or limited (local: 2, 3) only to buffers with files that
are associated with ESS[SAS] as specified in your auto-mode-alist.




The distinction between local and global is subtle.  If you want the
ESS[SAS] definitions to work when you are in the *shell* buffer or when
editing files other than the file extensions that ESS[SAS] recognizes,
you will most likely want to use the global definitions.  If you want
your function keys to understand SAS batch commands when you are editing
SAS files, and to behave normally when editing other files, then you
will choose the local definitions.  The option can be chosen by the
person installing ESS for a site or by an individual.



    

  1.  For a site installation or an individual, place ONLY ONE of
the following lines in your initialization file prior to a
require/load.  ESS[SAS] function keys are available
in ESS[SAS] if you choose either 2 or 3 and in all modes if you
choose 4 or 5:

    

    ;;2; (setq ess-sas-local-unix-keys t)
;;3; (setq ess-sas-local-pc-keys t)
;;4; (setq ess-sas-global-unix-keys t)
;;5; (setq ess-sas-global-pc-keys t)

    


    The names -unix- and -pc- have nothing to do with the operating system
that you are running.  Rather, they mimic the definitions that the SAS
Display Manager uses by default on those platforms.

    

  2.  If your site installation has configured the keys contrary to your
liking, then you must call the appropriate function.

    

     (load "ess-site") ;; local-unix-keys
 (ess-sas-global-pc-keys)

    




Finally, we get to what the function keys actually do.  You may recognize
some of the nicknames as SAS Display Manager commands (they are in all
capitals).





UNIXPCNickname


F2F2‘refresh’


revert the current buffer with the file of the same
                    name if the file is newer than the buffer


F3F8SUBMIT


save the current .sas file (which is either the .sas
                    file in the current buffer or the .sas file associated
                    with the .lst or .log file in the current buffer)
                    and submit the file as a batch SAS job


F4F5PROGRAM


switch buffer to .sas file


F5F6LOG


switch buffer to .log file, ‘refresh’ and goto next
                    error message, if any


F6F7OUTPUT


switch buffer to .lst file and ‘refresh’


F7F4‘filetype-1’


switch buffer to ‘filetype-1’ (defaults to .txt) file
                    and ‘refresh’


F8F3‘shell’


switch buffer to *shell*


F9F9VIEWTABLE


open an interactive PROC FSEDIT session on the SAS
                    dataset near point


F10F10toggle-log


toggle ESS[SAS] for .log files; useful for certain
                    debugging situations


F11F11‘filetype-2’


switch buffer to ‘filetype-2’ (defaults to .dat) file
                    and ‘refresh’


F12F12viewgraph


open a GSASFILE near point for viewing either in emacs
                    or with an external viewer


C-F1C-F1rtf-portrait


create an MS RTF portrait file from the current buffer
                    with a file extension of .rtf


C-F2C-F2rtf-landscape


create an MS RTF landscape file from the current buffer
                    with a file extension of .rtf


C-F3C-F8submit-region


write region to ess-temp.sas and submit


C-F5C-F6append-to-log


append ess-temp.log to the current .log file


C-F6C-F7append-to-output


append ess-temp.lst to the current .lst file


C-F9C-F9INSIGHT


open an interactive PROC INSIGHT session on the SAS
                    dataset near point


C-F10C-F10toggle-listing


toggle ESS[SAS] for .lst files; useful for toggling
                    read-only





SUBMIT, PROGRAM, LOG and OUTPUT need no further
explanation since they mimic the SAS Display Manager commands and
related function key definitions.  However, six other keys have been
provided for convenience and are described below.



‘shell’ switches you to the *shell* buffer where you can
interact with your operating system.  This is especially helpful if you
would like to kill a SAS batch job.  You can specify a different buffer
name to associate with a SAS batch job (besides *shell*) with the
buffer-local variable ess-sas-shell-buffer.  This allows you to have
multiple buffers running SAS batch jobs on multiple local/remote
computers that may rely on different methods specified by the buffer-local
variable ess-sas-submit-method.



F2 performs the ‘refresh’ operation on the current buffer.
‘refresh’ compares the buffer’s last modified date/time with the
file’s last modified date/time and replaces the buffer with the file if the
file is newer.  This is the same operation that is automatically performed
when LOG, OUTPUT, ‘filetype-1’ or F11 are pressed.



‘filetype-1’ switches you to a file with the same file name as your .sas
file, but with a different extension (.txt by default) and performs
‘refresh’.  You can over-ride the default extension; for example in your
~/.emacs or ~/.xemacs/init.el file:



(setq ess-sas-suffix-1 "csv") ; for example




F9 will prompt you for the name of a permanent SAS dataset near
point to be opened for viewing by PROC FSEDIT.  You can control the
SAS batch command-line with ess-sas-data-view-submit-options.
For controlling the SAS batch commands, you have the global variables
ess-sas-data-view-libname and
ess-sas-data-view-fsview-command as well as the buffer-local
variable ess-sas-data-view-fsview-statement.  If you have your
SAS LIBNAME defined in ~/autoexec.sas, then the defaults
for these variables should be sufficient.



Similarly, C-F9 will prompt you for the name of a permanent
SAS dataset near point to be opened for viewing by PROC INSIGHT.
You can control the SAS batch command-line with
ess-sas-data-view-submit-options.  For controlling the SAS batch
commands, you have the global variables ess-sas-data-view-libname
and ess-sas-data-view-insight-command as well as the buffer-local
variable ess-sas-data-view-insight-statement.



F10 toggles ESS[SAS] mode for .log files which is off by default
(technically, it is SAS-log-mode, but it looks the same).  The syntax
highlighting can be helpful in certain debugging situations, but large
.log files may take a long time to highlight.



F11 is the same as ‘filetype-1’ except it is .dat by default.



F12 will prompt you for the name of a GSASFILE near the point in .log to
be opened for viewing either with emacs or with an external viewer.
Depending on your version of emacs and the operating system you are
using, emacs may support .gif and .jpg files internally.  You may need
to change the following variables for your own situation.
ess-sas-graph-view-suffix-regexp is a regular expression of supported
file types defined via file name extensions.
ess-sas-graph-view-viewer-default is the default external viewer for
your platform.  ess-sas-graph-view-viewer-alist is an alist of
exceptions to the default; i.e. file types and their associated
viewers which will be used rather than the default viewer.



(setq ess-sas-graph-view-suffix-regexp (concat "[.]\\([eE]?[pP][sS]\\|"
"[pP][dD][fF]\\|[gG][iI][fF]\\|[jJ][pP][eE]?[gG]\\|"
"[tT][iI][fF][fF]?\\)")) ;; default
(setq ess-sas-graph-view-viewer-default "kodakimg") ;; Windows default
(setq ess-sas-graph-view-viewer-default "sdtimage") ;; Solaris default
(setq ess-sas-graph-view-viewer-alist
  '(("[eE]?[pP][sS]" . "gv") ("[pP][dD][fF]" . "gv")) ;; default w/ gv




C-F2 produces US landscape by default, however, it can produce A4
landscape (first line for "global" key mapping, second for "local"):



(global-set-key [(control f2)] 'ess-sas-rtf-a4-landscape)
(define-key sas-mode-local-map [(control f2)] 'ess-sas-rtf-a4-landscape)











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13.6 iESS[SAS]–Interactive SAS processes



Inferior ESS (iESS) is the method for interfacing with interactive
statistical processes (programs).  iESS[SAS] is what is needed for
interactive SAS programming.  iESS[SAS] works best
with the SAS command-line option settings
"-stdio -linesize 80 -noovp -nosyntaxcheck"
(the default of inferior-SAS-args).





-stdio
            required to make the redirection of stdio work
-linesize 80
            keeps output lines from folding on standard terminals
-noovp
            prevents error messages from printing 3 times
-nosyntaxcheck
            permits recovery after syntax errors




To start up iESS[SAS] mode, use:



   M-x SAS




The *SAS:1.log* buffer in ESStr mode corresponds to the file
foo.log in SAS batch usage and to the ‘SAS: LOG’ window in the
SAS Display Manager.  All commands submitted to SAS, informative
messages, warnings, and errors appear here.



The *SAS:1.lst* buffer in ESSlst mode corresponds to the file
foo.lst in SAS batch usage and to the ‘SAS: OUTPUT’ window in the
SAS Display Manager.  All printed output appears in this window.



The *SAS:1* buffer exists solely as a communications buffer.
The user should never use this buffer directly.
Files are edited in the foo.sas buffer.  The C-c C-r key in
ESS[SAS] is the functional equivalent of bringing a file into the
‘SAS: PROGRAM EDITOR’ window followed by SUBMIT.



For example, open the file you want to work with.



C-x C-f foo.sas



foo.sas will be in ESS[SAS] mode.  Edit as appropriate, and then start
up SAS with the cursor in the foo.sas buffer.



M-x SAS



Four buffers will appear on screen:



BufferModeDescription


foo.sasESS[SAS]your source file


*SAS:1*iESS[SAS:1]iESS communication buffer


*SAS:1.log*Shell ESStr []SAS log information


*SAS:1.lst*Shell ESSlst []SAS listing information




If you would prefer each of the four buffers to appear in its
own individual frame, you can arrange for that.  Place the
cursor in the buffer displaying foo.sas.  Enter the
sequence C-c C-w. The cursor will normally be in buffer
foo.sas.  If not, put it there and C-x b foo.sas.



Send regions, lines, or the entire file contents to SAS
(regions are most useful:  a highlighted region will normally
begin with the keywords DATA or PROC and end with
RUN;), C-c C-r.



Information appears in the log buffer, analysis results in the
listing buffer.  In case of errors, make the corrections in the
foo.sas buffer and resubmit with another C-c C-r.



At the end of the session you may save the log and listing
buffers with the usual C-x C-s commands.  You will be prompted
for a file name.  Typically, the names foo.log and foo.lst
will be used.  You will almost certainly want to edit the saved
files before including them in a report.  The files are
read-only by default.  You can make them writable by the emacs
command C-x C-q.



At the end of the session, the input file foo.sas will
typically have been revised.  You can save it.  It can be used
later as the beginning of another iESS[SAS] session.  It can
also be used as a batch input file to SAS.



The *SAS:1* buffer is strictly for ESS use.  The user should
never need to read it or write to it.  Refer to the .lst and
.log buffers for monitoring output!



Troubleshooting: See iESS(SAS)--Common problems.









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13.7 iESS[SAS]–Common problems



    

  1.  iESS[SAS] does not work on Windows.  In order to run SAS inside
an emacs buffer, it is necessary to start SAS with the -stdio option.
SAS does not support the -stdio option on Windows.

  2.  If M-x SAS gives errors upon startup, check the following:


  3.  M-x SAS starts SAS Display Manager.  Probably, the command sas
on your system calls a shell script.  In that case you will need to locate
the real  sas executable and link to it.
You can execute the UNIX command:

    

    find / -name sas -print

    

    Now place a soft link to the real sas executable in your ~/bin
directory, with for example

    

    cd ~/bin
ln -s /usr/local/sas9/sas sas

    



Check your PATH environment variable to confirm that
~/bin appears before the directory in which the sas
shell script appears.










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13.8 ESS[SAS]–Graphics



Output from a SAS/GRAPH PROC can be displayed in a SAS/GRAPH
window for SAS batch on Windows or for both SAS batch and interactive
with XWindows on UNIX.  If you need to create graphics files and view
them with F12, then include the following (either in
foo.sas or in ~/autoexec.sas):



filename gsasfile 'graphics.ps';
goptions device=ps gsfname=gsasfile gsfmode=append;



PROC PLOT graphs can be viewed in the listing buffer.  You may
wish to control the vertical spacing to allow the entire plot
to be visible on screen, for example:



proc plot;
    plot a*b / vpos=25;
run;










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13.9 ESS[SAS]–Windows












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14 ESS for BUGS





• ESS(BUGS)--Model files:  



• ESS(BUGS)--Command files:  



• ESS(BUGS)--Log files:  





ESS[BUGS] was originally designed for use with BUGS software.  Later,
it evolved to support JAGS as a dialect of the BUGS language via
ESS[JAGS], however, ESS[JAGS] is documented in the section Help
for JAGS.  ESS[BUGS] provides 5 features.  First, BUGS syntax is
described to allow for proper fontification of statements,
distributions, functions, commands and comments in BUGS model files,
command files and log files.  Second, ESS creates templates for the
command file from the model file so that a BUGS batch process can be
defined by a single file.  Third, ESS provides a BUGS batch script
that allows ESS to set BUGS batch parameters.  Fourth, key sequences
are defined to create a command file and submit a BUGS batch process.
Lastly, interactive submission of BUGS commands is also supported.









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14.1 ESS[BUGS]–Model files



Model files with the .bug extension are edited in ESS[BUGS]
mode if (require 'ess-bugs-d) was performed.  Model files with
the .jag extension are edited in ESS[JAGS] mode if
(require 'ess-jags-d) was performed.  Three keys are bound for
your use in ESS[BUGS], F2, C-c C-c and =.  F2
performs the same action as it does in ESS[SAS],
See ESS(SAS)--Function keys for batch processing.  C-c C-c
performs the function ess-bugs-next-action which you will use a
lot.  Pressing it in an empty buffer for a model file will produce a
template for you.  = inserts the set operator, <-.










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14.2 ESS[BUGS]–Command files



To avoid extension name collision, .bmd is used for BUGS
command files and .jmd for JAGS command files.  When you have
finished editing your model file and press C-c C-c, a command
file is created if one does not already exist.  
When you are finished editing your command file, pressing C-c C-c 
again will submit your command file as a batch job.  









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14.3 ESS[BUGS]–Log files



To avoid extension name collision, .bog is used for BUGS log
files.  The command line generated by ESS creates the
.bog transcript file.
Similarly, .jog is used for JAGS log files.










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15 ESS for JAGS





• ESS(JAGS)--Model files:  



• ESS(JAGS)--Command files:  



• ESS(JAGS)--Log files:  





ESS[BUGS] was originally designed for use with BUGS software.  
Later, it evolved to support JAGS as a dialect of the
BUGS language via ESS[JAGS].  Since BUGS and JAGS are quite
similar, ESS[BUGS] and ESS[JAGS] are necessarily similar.
ESS[JAGS] provides 4 features.  First, JAGS syntax is described to
allow for proper fontification of statements, distributions,
functions, commands and comments in JAGS model files, command files
and log files.  Second, ESS creates templates for the command file
from the model file so that a JAGS batch process can be defined by a
single file.  Third, ESS provides a JAGS batch script that allows ESS
to set JAGS batch parameters.  Fourth, key sequences are defined to
create a command file and submit a JAGS batch process. 









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15.1 ESS[JAGS]–Model files



Model files with the .bug extension are edited in ESS[BUGS] mode
if (require 'ess-bugs-d) was performed or edited in ESS[JAGS] mode
if (require 'ess-jags-d).
Three keys are bound for your use in ESS[BUGS], F2, C-c C-c and =.
F2 performs the same action as it does in ESS[SAS],
See ESS(SAS)--Function keys for batch processing.  C-c C-c performs the
function ess-bugs-next-action which you will use a lot.  Pressing it
in an empty buffer for a model file will produce a template for you.  =
inserts the set operator, <-.



ESS[JAGS] does not support "replacement" variables which were part of
ESS[BUGS].  Although, "replacement" variables are an extremely convenient
feature, creating the elisp code for their operation was challenging.  So, a
more elisp-ish approach was adopted for ESS[JAGS]:  elisp local variables.
These variables are
created as part of the template, i.e. with the first press of C-c C-c 
in an empty buffer.  For your .bug file, they are named 
ess-jags-chains, ess-jags-monitor, ess-jags-thin,  
ess-jags-burnin and ess-jags-update;
they appear in the Local Variables section.  When you are
finished editing your model file, pressing C-c C-c will perform
the necessary actions to build your command file for you. 



The ess-jags-chains variable is the number of chains that
you want to initialize and sample from; defaults to 1.
The ess-jags-monitor variable is a list of variables
that you want monitored: encase each variable in double quotes.  
When you press C-c C-c, the
appropriate statements are created in the command file to monitor the
list of variables.  By default, no variables are explicitly monitored 
which means JAGS will implicitly monitor all “default” variables. 
The ess-jags-thin variable is the thinning parameter.  
By default, the thinning parameter is set to 1, i.e. no thinning. 
The ess-jags-burnin variable is the number of initial samples
to discard.  By default, the burnin parameter is set to 10000.
The ess-jags-update variable is the number of post-burnin samples
to keep.  By default, the update parameter is set to 10000.  Both 
ess-jags-burnin and ess-jags-update are multiplied by
ess-jags-thin since JAGS does not do it automatically.









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15.2 ESS[JAGS]–Command files



To avoid extension name collision, .bmd is used for BUGS
command files and .jmd for JAGS command files.  For your 
.jmd file, there is only one variable, ess-jags-command, 
in the Local Variables section.  When you have
finished editing your model file and press C-c C-c, a command
file is created if one does not already exist.  
When you are finished editing your command file, pressing C-c C-c 
again will submit your command file as a batch job. 
The ess-jags-command variable allows you to specify a different
JAGS program to use to run your model; defaults to “jags”.









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15.3 ESS[JAGS]–Log files



The .jog extension is used for JAGS log
files.  You may find F2 useful to refresh the .jog if the batch
process over-writes or appends it.











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16 Bugs and Bug Reporting, Mailing Lists





• Bugs:  



• Reporting Bugs:  



• Mailing Lists:  



• Help with emacs:  












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16.1 Bugs











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16.2 Reporting Bugs




Please send bug reports, suggestions etc. to
ESS-bugs@r-project.org



The easiest way to do this is within Emacs by typing



M-x ess-submit-bug-report



This also gives the maintainers valuable information about your
installation which may help us to identify or even fix the bug.



If Emacs reports an error, backtraces can help us debug the problem.
Type "M-x set-variable RET debug-on-error RET t RET".  Then run the
command that causes the error and you should see a *Backtrace* buffer
containing debug information; send us that buffer.



Note that comments, suggestions, words of praise and large cash
donations are also more than welcome.









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16.3 Mailing Lists




There is a mailing list for discussions and announcements relating to
ESS.  Join the list by sending an e-mail with "subscribe ess-help" (or
"help") in the body to ess-help-request@r-project.org;
contributions to the list may be mailed to
ess-help@r-project.org.  Rest assured, this is a fairly
low-volume mailing list.



The purposes of the mailing list include











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16.4 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 M-x xemacs-www-faq or M-x view-emacs-FAQ)
and EmacsWiki (http://www.emacswiki.org).  Please consult them
before asking on the mailing list about issues that are not specific to
ESS.












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Appendix A Customizing ESS




ESS can be easily customized to your taste simply by including the
appropriate lines in your .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 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.











Previous: , Up: Top   [Contents][Index]





Indices





• Key index:  



• Function and program index:  



• Variable index:  



• Concept index:  












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Key index


Jump to:   ,
   
{
   
}
   


C
   
E
   
M
   
R
   
T
   





Index Entry  Section


 


,


,: Handy commands


 


{


{: Indenting


 


}


}: Indenting


 


C


C-c .: Styles


C-c C-. a: Rutils


C-c C-. d: Rutils


C-c C-. H: Rutils


C-c C-. l: Rutils


C-c C-. m: Rutils


C-c C-. o: Rutils


C-c C-. r: Rutils


C-c C-. s: Rutils


C-c C-. u: Rutils


C-c C-. w: Rutils


C-C C-b: Evaluating code


C-c C-c: Other


C-C C-c: Evaluating code


C-c C-e C-d: Edit buffer


C-C C-f: Evaluating code


C-C C-j: Evaluating code


C-c C-l: Hot keys


C-c C-o C-c: Roxygen


C-c C-o C-h: Roxygen


C-c C-o C-o: Roxygen


C-c C-o C-r: Roxygen


C-c C-o C-t: Roxygen


C-c C-o n: Roxygen


C-c C-o p: Roxygen


C-c C-q: Hot keys


C-C C-r: Evaluating code


C-c C-s: Hot keys


C-c C-t C-s: Namespaced Evaluation


C-c C-v: Hot keys


C-c C-w: Clean


C-c C-x: Hot keys


C-c C-z: Other


C-C M-b: Evaluating code


C-C M-f: Evaluating code


C-C M-j: Evaluating code


C-C M-r: Evaluating code


C-c RET: Resubmit


C-c `: Hot keys


C-c `: Error Checking


C-j: Indenting


C-M-a: Other edit buffer commands


C-M-e: Other edit buffer commands


C-M-h: Other edit buffer commands


C-M-q: Indenting


C-M-x: Evaluating code


C-x `: Hot keys


 


E


ESC C-a: Other edit buffer commands


ESC C-e: Other edit buffer commands


ESC C-h: Other edit buffer commands


ESC C-q: Indenting


 


M


M-;: Indenting


M-?: Object names


M-C-q: Indenting


M-n l: Sweave and AUCTeX


M-n P: Sweave and AUCTeX


M-n s: Sweave and AUCTeX


M-RET: Resubmit


 


R


RET: Command-line editing


RET: Resubmit


 


T


TAB: Indenting


 




Jump to:   ,
   
{
   
}
   


C
   
E
   
M
   
R
   
T
   










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Function and program index


Jump to:   B
   
C
   
D
   
E
   
F
   
I
   
M
   
N
   
O
   
P
   
Q
   
S
   





Index Entry  Section


 


B


backward-kill-word: Command-line editing


 


C


comint-backward-matching-input: Process buffer motion


comint-bol: Command-line editing


comint-copy-old-input: Transcript resubmit


comint-delete-output: Last command


comint-dynamic-complete: Object names


comint-forward-matching-input: Process buffer motion


comint-history-isearch-backward-regexp: Command History


comint-interrupt-subjob: Other


comint-kill-input: Command-line editing


comint-next-input: Process buffer motion


comint-next-input: Command History


comint-next-matching-input-from-input: Command History


comint-previous-input: Process buffer motion


comint-previous-input: Command History


comint-previous-matching-input-from-input: Command History


comint-show-output: Last command


 


D


dump(): Edit buffer


 


E


ess-change-directory: Rutils


ess-cleanup: Hot keys


ess-cleanup: Help


ess-describe-help-mode: Help


ess-display-help-on-object: Hot keys


ess-display-help-on-object: Help


ess-display-help-on-object: Help


ess-dump-object-into-edit-buffer: Edit buffer


ess-electric-brace: Indenting


ess-eval-buffer: Evaluating code


ess-eval-buffer-and-go: Evaluating code


ess-eval-function: Evaluating code


ess-eval-function-and-go: Evaluating code


ess-eval-line: Evaluating code


ess-eval-line-and-go: Evaluating code


ess-eval-line-and-step: Help


ess-eval-region: Evaluating code


ess-eval-region: Help


ess-eval-region-and-go: Evaluating code


ess-eval-region-or-function-or-paragraph: Evaluating code


ess-eval-region-or-function-or-paragraph-and-step: Evaluating code


ess-eval-region-or-line-and-step: Evaluating code


ess-execute-objects: Hot keys


ess-execute-search: Hot keys


ess-goto-beginning-of-function-or-para: Other edit buffer commands


ess-goto-end-of-function-or-para: Other edit buffer commands


ess-handy-commands: Handy commands


ess-handy-commands: Handy commands


ess-indent-command: Roxygen


ess-indent-exp: Indenting


ess-indent-or-complete: Indenting


ess-list-object-completions: Object names


ess-load-file: Hot keys


ess-load-file: Loading


ess-mark-function: Other edit buffer commands


ess-parse-errors: Hot keys


ess-parse-errors: Error Checking


ess-quit: Hot keys


ess-quit: Help


ess-R-complete-object-name: Roxygen


ess-r-set-evaluation-env: Namespaced Evaluation


ess-remote: ESS processes on Remote Computers


ess-request-a-process: Multiple ESS processes


ess-resynch: Object names


ess-roxy-hide-all: Roxygen


ess-roxy-next-entry: Roxygen


ess-roxy-preview-HTML: Roxygen


ess-roxy-preview-Rd: Roxygen


ess-roxy-previous-entry: Roxygen


ess-roxy-toggle-roxy-region: Roxygen


ess-roxy-update-entry: Roxygen


ess-rutils-apropos: Rutils


ess-rutils-html-docs: Rutils


ess-rutils-load-wkspc: Rutils


ess-rutils-local-pkgs: Rutils


ess-rutils-objs: Rutils


ess-rutils-repos-pkgs: Rutils


ess-rutils-rm-all: Rutils


ess-rutils-rsitesearch: Rutils


ess-rutils-save-wkspc: Rutils


ess-rutils-update-pkgs: Rutils


ess-set-style: Styles


ess-skip-to-help-section: Help


ess-skip-to-next-section: Help


ess-skip-to-previous-section: Help


ess-smart-comma: Handy commands


ess-submit-bug-report: Reporting Bugs


ess-switch-to-end-of-ESS: Help


ess-switch-to-inferior-or-script-buffer: Other


ess-swv-latex: Sweave and AUCTeX


ess-swv-PDF: Sweave and AUCTeX


ess-swv-PS: Sweave and AUCTeX


ess-swv-weave: Sweave and AUCTeX


ess-tracebug: ESS tracebug


ess-transcript-clean-region: Clean


ess-transcript-copy-command: Resubmit


ess-transcript-send-command: Resubmit


ess-transcript-send-command-and-move: Resubmit


ess-use-ido, ess-completing-read: Minibuffer completion


 


F


fill-paragraph: Roxygen


 


I


inferior-ess-send-input: Command-line editing


 


M


mark-paragraph: Roxygen


move-beginning-of-line: Roxygen


 


N


newline-and-indent: Roxygen


 


O


objects(): Hot keys


 


P


printer(): printer


 


Q


q(): Hot keys


 


S


S: Starting up


search(): Hot keys


search(): Object names


source(): Evaluating code


source(): Loading


STERM: Statistical Process running in ESS?


 




Jump to:   B
   
C
   
D
   
E
   
F
   
I
   
M
   
N
   
O
   
P
   
Q
   
S
   










Next: , Previous: , Up: Indices   [Contents][Index]





Variable index


Jump to:   A
   
C
   
E
   
I
   
R
   





Index Entry  Section


 


A


ac-source-R: Auto-complete


ac-source-R-args: Auto-complete


ac-source-R-objects: Auto-complete


 


C


comint-delimiter-argument-list: History expansion


comint-input-ring-size: Command History


comment-column: Indenting


 


E


ess-ask-about-transfile: Customizing startup


ess-ask-about-transfile: Saving transcripts


ess-ask-for-ess-directory: Customizing startup


ess-default-style: Styles


ess-delete-dump-files: Source Files


ess-directory: Source Directories


ess-dump-filename-template: Source Directories


ess-eldoc-abbreviation-style: ESS ElDoc


ess-eldoc-show-on-symbol: ESS ElDoc


ess-eval-visibly: Evaluating code


ess-execute-in-process-buffer: Hot keys


ess-first-tab-never-complete: Indenting


ess-first-tab-never-complete: Object names


ess-font-lock-mode: Highlighting


ess-function-template: Edit buffer


ess-handy-commands: Handy commands


ess-handy-commands: Handy commands


ess-indent-with-fancy-comments: Indenting


ess-keep-dump-files: Source Files


ess-R-font-lock-keywords: Highlighting


ess-search-list: Source Directories


ess-source-directory: Source Directories


ess-style-alist: Styles


ess-switch-to-end-of-proc-buffer: Other


ess-swv-pdflatex-commands: Sweave and AUCTeX


ess-tab-complete-in-script: Indenting


ess-use-eldoc: ESS ElDoc


 


I


inferior-ess-program: Customizing startup


inferior-R-font-lock-keywords: Highlighting


 


R


Rd-indent-level: R documentation files


Rd-mode-hook: R documentation files


Rd-to-help-command: R documentation files


 




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Concept Index


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Index Entry  Section


 


.


.emacs file: Source Directories


 


A


aborting S commands: Other


arguments to S program: Customizing startup


authors: Credits


auto-complete: Auto-complete


autosaving: Source Files


 


B


bug reports: Reporting Bugs


bugs: Bugs


 


C


cleaning up: Hot keys


comint: Credits


command history: Command History


command line arguments: iESS(S)--Inferior ESS processes


command-line completion: Object names


command-line editing: Command-line editing


commands: Entering commands


comments: Source Files


comments in S: Indenting


completion in edit buffer: Other edit buffer commands


completion of object names: Object names


completion on file names: Object names


completion on lists: Object names


completion, when prompted for object names: Edit buffer


creating new objects: Edit buffer


credits: Credits


customization: Customization


 


D


data frames: Object names


deleting output: Last command


directories: Starting up


dump file directories: Source Directories


dump file names: Source Directories


dump files: Edit buffer


dump files: Source Files


 


E


echoing commands when evaluating: Evaluating code


edit buffer: Edit buffer


editing commands: Command History


editing functions: Editing objects


editing transcripts: Saving transcripts


ElDoc: ESS ElDoc


emacsclient: Emacsclient


entering commands: Entering commands


errors: Error Checking


ess developer: Namespaced Evaluation


ESS process buffer: Starting up


ESS process directory: Starting up


ESS tracebug: ESS tracebug


ESS-elsewhere: ESS processes on Remote Computers


ess-roxy: Roxygen


evaluating code with echoed commands: Evaluating code


evaluating S expressions: Evaluating code


 


F


font-lock mode: Highlighting


formatting source code: Indenting


 


G


graphics: Graphics


 


H


Handy commands: Handy commands


help files: Help


highlighting: Highlighting


historic backups: Source Files


hot keys: Hot keys


 


I


icicles: Icicles


IDO completions: Minibuffer completion


indenting: Indenting


installation: Installation


interactive use of S: Introduction


interrupting S commands: Other


introduction: Introduction


 


K


keyboard short cuts: Hot keys


killing temporary buffers: Hot keys


killing the ESS process: Hot keys


 


L


lists, completion on: Object names


 


M


motion in transcript mode: Transcript Mode


multi-line commands, resubmitting: Transcript resubmit


multiple ESS processes: Multiple ESS processes


 


N


new objects, creating: Edit buffer


 


O


objects: Hot keys


 


P


pages in the process buffer: Transcript


paging commands in help buffers: Help


paragraphs in the process buffer: Transcript


parsing errors: Error Checking


process buffer: Starting up


process names: Multiple ESS processes


programming in S: Introduction


project work in S: Source Files


 


Q


quitting from ESS: Hot keys


 


R


re-executing commands: Command History


reading long command outputs: Last command


remote Computers: ESS processes on Remote Computers


reverting function definitions: Edit buffer


roxy: Roxygen


Roxygen: Roxygen


running S: Starting up


 


S


S+elsewhere: ESS processes on Remote Computers


search list: Hot keys


search list: Source Directories


sending input: Entering commands


starting directory: Starting up


starting ESS: Starting up


STERM: Statistical Process running in ESS?


 


T


tcsh: Object names


temporary buffers: Help


temporary buffers, killing: Hot keys


transcript: Transcript


transcript file: Customizing startup


transcript file names: Saving transcripts


transcript mode motion: Transcript Mode


transcripts of S sessions: Introduction


 


U


using S interactively: Introduction


 


W


winjava: winjava


working directory: Starting up


working directory: Source Directories


 


X


X Windows: X11


 




Jump to:   .
   


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G
   
H
   
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K
   
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N
   
O
   
P
   
Q
   
R
   
S
   
T
   
U
   
W
   
X