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ESS --- Emacs Speaks Statistics
*******************************

ESS: Emacs Speaks Statistics
****************************

ESS version
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     by  A.J. Rossini,
         R.M. Heiberger,
         K. Hornik,
         M. Maechler,
         R.A. Sparapani
     and S.J. Eglen.

     Emacs Speaks Statistics (ESS) provides an intelligent, consistent interface between the user and the software.  ESS interfaces with SAS, S-PLUS, R, BUGS and other statistical analysis packages under the Unix, Microsoft Windows, and Apple Mac operating systems.  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 to ESS
*******************

The S family (Sl, 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, Stata and XLisp-Stat 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 `XLisp-Stat' 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 Sl objects and ``hot keys'' are provided for common Sl function calls.  Help files are easily accessible, and a paging mechanism is provided to view them. Finally, an incidental (but very useful) side-effect of ESS is that a transcript of your session is kept for later saving or editing.

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

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

Why should I use ESS?
=====================

Statistical packages are powerful software systems for manipulating and analyzing data, but their user interfaces often leave something something to be desired:  they offer weak editor functionality and they differ among themselves so markedly that you have to re-learn how to do those things for each package.  ESS is a package which is designed to make editing and interacting with statistical packages more uniform, user-friendly and give you the power of emacs as well.

ESS provides several features which make it easier to interact with the ESS process (a connection between your buffer and the statistical package which is waiting for you to input commands).  These include:

  * Command-line editing for fixing mistakes in commands before they are entered.  The -e flag for S-plus provides something similar to this, but here you have the full range of Emacs commands rather than a limited subset.  However, other packages such as XLisp-Stat and S3 do not necessarily have features like this built-in. See Command-line editing.

  * Searchable command history for recalling previously-submitted commands.  This provides all the features of the Splus -e history mechanism, plus added features such as history searching. See Command History.

  * Command-line completion of both object and file names for quick entry.  This is similar to tcsh's facility for filenames; here it also applies to object names and list components. See Completion.

  * Hot-keys for quick entry of commonly-used commands in `S' such as objects() and search(). See Hot keys.

  * Transcript recording for a complete record of all the actions in an S session. See Transcript.

  * Interface to the help system, with a specialized mode for viewing S help files. See Help.

If you commonly create or modify Sl 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 Sl while editing.  ESS corrects these problems by introducing the following features:

  * Object editing.  ESS allows you to edit more than one function simultaneously in dedicated Emacs buffers.  The ESS process may continue to be used while functions are being edited. See Edit buffer.

  * A specialized editing mode for Sl code, which provides syntactic indentation and highlighting. See Indenting.

  * Facilities for loading and error-checking source files, including a keystroke to jump straight to the position of an error in a source file. See Error Checking.

  * Source code revision maintenance, which allows you to keep historic versions of Sl source files. See Source Files.

  * Facilities for evaluating Sl code such as portions of source files, or line-by-line evaluation of files (useful for debugging). See Evaluating code.

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

  * Evaluation of previously entered commands, stripping away unnecessary prompts. See Transcript resubmit.

New features in ESS
===================

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Authors of and contributors to ESS
==================================

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Getting the latest version of ESS
=================================

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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.

Installing ESS on your system
*****************************

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

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Requirements
============

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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 an ESS process
=======================

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

To start an Sl 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 Sl from (that is, the directory you would have cd'd to before starting Sl 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.

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.

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 from a telnet or ssh buffer and then connect ESS to that buffer.

 1. Start a new telnet or ssh buffer and connect to the remote computer (e.g. use M-x telnet or M-x ssh; ssh.el is available at ftp://ftp.splode.com/pub/users/friedman/emacs-lisp/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. Enter the ESS command M-x ess-remote.  You will be prompted for a program name.  Enter sp6 or r or sas or another valid name.  Your telnet 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.

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 noone 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 X11, then you can write graphics to the postscript device and copy it to your PC with dired and display it with ghostscript.

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 Sl 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 Sl 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.

Interacting with the ESS process
********************************

The primary function of the ESS package is to provide an easy-to-use front end to the Sl interpreter.  This is achieved by running the S process from within an Emacs buffer, so that the Emacs editing commands are available to correct mistakes in commands, etc.  The features of Inferior Sl mode are similar to those provided by the standard Emacs shell mode (see Shell Mode (The Gnu Emacs Reference Manual)).  Command-line completion of Sl objects and a number of `hot keys' for commonly-used Sl commands are also provided for ease of typing.

Entering commands and fixing mistakes
=====================================

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

  * RET (inferior-ess-send-input)

     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 (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.

ESS 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 (The Gnu Emacs Reference Manual), for other commands relevant to entering input.

Completion of object names
==========================

In the process buffer, the TAB key is for completion, similar to that provided by Shell Mode for filenames.  In Inferior Sl mode, pressing the TAB key when the cursor is following the first few characters of an object name completes the object name; if the cursor is following a file name TAB completes the file name.

  * TAB (comint-dynamic-complete)

     Complete the Sl 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 Sl object names instead of file names.  ESS maintains a list of all objects known to S at any given time, which basically consists of all objects (functions and datasets) in every attached directory listed by the search() command along with the component objects of attached data frames (if your version of Sl 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 Sl 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-?.

  * M-? (ess-list-object-completions)

     List all possible completions of the object name at point.

ESS also provides completion over the components of named lists accessed using the $ notation, to any level of nested lists.  This feature is particularly useful for checking what components of a list object exist while partway through entering a command: simply type the object name and $ and press TAB to see the names of existing list components for that object.

Completion is also provided over file names, which is particularly useful when using Sl functions such as get() or scan() which require fully expanded file names.  Whenever the cursor is within an Sl string, pressing TAB completes the file name before point, and also expands any ~ or environment variable references.

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.

Completion details
==================

ESS automatically keeps track of any objects added or deleted to the system (such as new objects created, or directories added to the search list) to make completion as accurate as possible.  Whenever ESS notices that search list has changed (The variable ess-change-sp-regexp is a regular expression matching commands which change the search list.  You will need to modify this variable if you have defined custom commands (other than attach, detach, collection or library) which modify the search list.)  when you attach a directory or data frame, the objects associated with it immediately become available for a completion; when it is detached completion is no longer available on those objects.

To maintain a list of accessible objects for completion, ESS needs to determine which objects are contained in each directory or data frame on the search list.  This is done at the start of each Sl session, by running the objects() command on every element of the search list.

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.

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 (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 (The GNU Emacs Reference Manual).

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 command

  * C-c C-e (comint-show-maximum-output)

     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.)

If the first part of the output is still obscured, use

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

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

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

  * C-c C-o (comint-kill-output)

     Deletes everything from the last command to the current prompt.

to delete it.  Use this command judiciously to keep your transcript to a more manageable size.

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 (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 (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.

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)

     Copy the command under the cursor to the current command line, and execute it.

  * 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.

  * M-RET (ess-transcript-send-command-and-move)

     Copy the command under the cursor to the current command line, and execute it.  Moves the cursor to the following command.

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 two commands leave the cursor at the new command line, allowing you to continue with interactive use of S.  If you wish to resubmit a series of commands from the transcript, consider using M-RET instead, which leaves the cursor at the command line following the one you re-submitted.  Thus by using M-RET repeatedly, you can re-submit a whole series of commands.

These commands work even if if the current line is a continuation line (i.e. the prompt is + 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.

Keeping a record of your S session
----------------------------------

To keep a record of your Sl 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 Sl 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 Sl 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-e (and other hot keys) may be used for commands whose output you do not wish to appear in the transcript.  These suggestions are appropriate even if you are not saving your transcript to disk, since the larger the transcript, the more memory your Emacs process will use on the host machine.

Finally, if you intend to produce Sl source code (suitable for using with source() or inclusion in an Sl function) from a transcript, then the command M-x ess-transcript-clean-region may be of use. This command works in any Emacs buffer, and removes all prompts and command output from an ESS transcript within the current region, leaving only the commands.  Don't forget to remove any erroneous commands first!

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 50 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 (The GNU Emacs Reference Manual)), to search for a particular variable name for example, these commands are also available:

  * M-r (comint-previous-matching-input)

     Prompt for a regular expression, and search backwards through the input history for a command matching the expression.

  * M-s (comint-next-matching-input)

     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:

  * A-M-r (comint-previous-matching-input-from-input)

     Select the previous command in the history which matches the string typed so far.

  * A-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 A-M-r and RET.  (Note: you may not have an ALT key on your keyboard, in which case it may be a good idea to bind these commands to some other keys.)

See Shell History Ring (The GNU Emacs Reference Manual), for a more detailed discussion of the history mechanism.

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 Sl 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.

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 variable ess-execute-in-process-buffer which, 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:

  * C-c C-x (ess-execute-objects)

     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.

  * C-c C-s (ess-execute-search)

     Sends the search() command to the ESS process.

  * C-c C-e (ess-execute)

     Prompt for an ESS expression, and evaluate it.

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 (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:

  * C-c C-a (ess-execute-attach)

     Prompts for a directory to attach to the ESS process with the attach() command. If a numeric prefix argument is given it is used as the position on the search list to attach the directory; otherwise the Sl default of 2 is used.  The attach() command actually executed appears in the process buffer.

  * C-c C-l (ess-load-file)

     Prompts for a file 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 C-x ` (ess-parse-errors). See Error Checking, for more details.

  * C-c C-v (ess-display-help-on-object)
      Pops up a help buffer for an Sl object or function.  See Help for more details.

  * C-c C-q (ess-quit)

     Sends the q() command to the ESS process (or (exit) to the XLS process), and cleans up any temporary buffers (such as help buffers or edit buffers) you may have created along the way.  Use this command when you have finished your Sl session instead of simply typing q() yourself, otherwise you will need to issue the command M-x ess-cleanup command explicitly to make sure that all the files that need to be saved have been saved, and that all the temporary buffers have been killed.

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 [S] or [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:

  * length:     Fixed length xterm or telnet window.

  * scrollable: Unlimited length xterm or telnet window.

  * server:     S-Plus Stat Server.

  * BATCH:      BATCH.

  * Rgui:       R GUI.

  * Commands:   S-Plus GUI without DDE interface to ESS.

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.

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.

Other commands provided by inferior-ESS
=======================================

The following commands are also provided in the process buffer:

  * C-c C-c (comint-interrupt-subjob)

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

  * C-c C-z (ess-abort)

     Sends a STOP signal to the ESS process, killing it immediately. It's not a good idea to use this, in general: Neither q() nor .Last will be executed and device drivers will not finish cleanly.  This command is provided as a safety to comint-stop-subjob, which is usually bound to C-c C-z.  If you want to quit from S, use C-c C-q (ess-quit) instead.

  * C-c C-d (ess-dump-object-into-edit-buffer)

     Prompts for an object to be edited in an edit buffer.  See Editing.

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

Manipulating saved transcript files
***********************************

Inferior Sl mode records the transcript (the list of all commands executed, and their output) in the process buffer, which can be saved as a 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 Sl session. Sometimes, however, you may wish to re-execute commands recorded in the transcript file by submitting them to a running ESS process.  This is what Transcript Mode is for.

If you load file a with the suffix .St into Emacs, it is placed in S Transcript Mode.  Transcript Mode is similar to Inferior Sl 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.

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:

  * RET (ess-transcript-send-command)

     Send the current command line to the ESS process, and execute it.

  * C-c RET (ess-transcript-copy-command)

     Copy the current command to the ESS process, and switch to the ESS process buffer (ready to edit the copied command).

  * M-RET (ess-transcript-send-command-and-move)

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

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

Cleaning transcript files
=========================

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

  * C-c C-w (ess-transcript-clean-region)

     Deletes all prompts and command output in the region, leaving only the commands themselves.

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 Sl mode, also available in Sl Transcript Mode.

ESS for the S family
********************

     [file help-s.texi not included]

Editing S functions
*******************

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

Creating or modifying S objects
===============================

To edit an Sl object, type

  * C-c C-d (ess-dump-object-into-edit-buffer)

     Edit an Sl 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 Sl source code.  Commands are provided to intelligently indent Sl code, evaluate portions of Sl code and to move around Sl code constructs.

Note: when you dump a file with C-c C-d, ESS first checks to see whether there already exists an edit buffer containing that object and, if so, pops you directly to that buffer.  If not, ESS next checks whether there is a file in the appropriate place with the appropriate name (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 Sl 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-d.

Loading source files into the ESS process
=========================================

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

  * C-c C-l (ess-load-file)

     Loads a file into the ESS process using source().

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

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 Sl reported as containing the error.  You may then correct the error, and reload the file.  Note that none of the commands in an Sl source file will take effect if any part of the file contains errors.

Sometimes the error is not caused by a syntax error (loading a non-existent file for example). In this case typing 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 `.

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 ess-eval-visibly-p whose default is nil (display output only).  Passing a prefix argument (C-u) to any of the following commands, however, reverses the meaning of ess-eval-visibly-p for that command only --- for example C-u C-c C-j echoes the current line of S (or other) code in the ESS process buffer, followed by its output.  This method of evaluation is an alternative to S's 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.) The commands for evaluating code are:

  * C-c C-j (ess-eval-line)

     Send the line containing point to the ESS process.

  * C-c M-j (ess-eval-line-and-go)

     As above, but returns you to the ESS process buffer as well.

  * C-c C-f or ESC C-x (aka M-C-x) (ess-eval-function)

     Send the Sl function containing point to the ESS process.

  * C-c M-f (ess-eval-function-and-go)

     As above, but returns you to the ESS process buffer as well.

  * C-c C-r (ess-eval-region)

     Send the text between point and mark to the ESS process.

  * C-c M-r (ess-eval-region-and-go)

     As above, but returns you to the ESS process buffer as well.

  * C-c C-b (ess-eval-buffer)

     Send the contents of the edit buffer to the ESS process.

  * C-c M-b (ess-eval-buffer-and-go)

     As above, but returns you to the ESS process buffer as well.

  * C-c C-n (ess-eval-line-and-step)

     Sends the current line to the ESS process, echoing it in the process buffer, and moves point to the next line.  Useful when debugging for stepping through your code.

It should be stressed once again that these ess-eval- commands should only be used for evaluating small portions of code for debugging purposes, or for generating transcripts from source files.  When editing S functions, C-c C-l is the command to use to update the function's value.  In particular, ess-eval-buffer is now largely obsolete.

One final command is provided for spot-evaluations of Sl code:

     C-c C-t (ess-execute-in-tb)

     Prompt for an Sl expression and evaluate it.  Displays result in a temporary buffer.

This is useful for quick calculations, etc.

All the above commands are useful for evaluating small amounts of code and observing the results in the process buffer.  A useful way to work is to divide the frame into two windows; one containing the source code and the other containing the process buffer.  If you wish to make the process buffer scroll automatically when the output reaches the bottom of the window, you will need to set the variable comint-scroll-to-bottom-on-output to 'others or t.

Indenting and formatting S code
===============================

ESS now provides a sophisticated mechanism for indenting Sl 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 if 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-fancy-comments nil) to your .emacs file.

The indentation commands provided by ESS are:

  * TAB (ess-indent-command)

     Indents the current line as Sl code.  If a prefix argument is given, all following lines which are part of the same (compound) expression are indented by the same amount (but relative indents are preserved).

  * RET (newline-and-indent)

     LFD (newline-and-indent)

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

  * ESC C-q aka M-C-q aka C-M-q (ess-indent-exp)

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

  * { and } (ess-electric-brace)

     The braces automatically indent to the correct position when typed.

  * M-; (indent-for-comment)

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

  * M-x ess-set-style

     Set the formatting style in this buffer to be one of the predefined styles: GNU, BSD, K&R, CLB, and C++. The DEFAULT style uses the default values for the indenting variables (unless they have been modified in your .emacs file.) This command causes all of the formatting variables to be buffer-local.

Commands for motion, completion and more
========================================

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

  * ESC C-a aka C-M-a (ess-beginning-of-function)

     Moves point to the beginning of the function containing point.

  * ESC C-e aka C-M-e (ess-end-of-function)

     Moves point to the end of the function containing point.

  * ESC C-h aka C-M-h (ess-mark-function)

     Places point at the beginning of the Sl 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 (The GNU Emacs Reference Manual).

Completion is provided in the edit buffer in a similar fashion to the process buffer: M-TAB completes file names and M-? lists file completions.  Since TAB is used for indentation in the edit buffer, object completion is now performed with C-c TAB.  Note however that completion is only provided over globally known S objects (such as system functions) --- it will not work for arguments to functions or other variables local to the function you are editing.

Finally, two commands are provided for returning to the ESS process buffer:

  * C-c C-z (ess-switch-to-end-of-ESS)

     Returns you to the ESS process buffer, placing point at the end of the buffer.

  * C-c C-y (ess-switch-to-ESS)

     Also returns to to the ESS process buffer, but leaves point where it was.

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

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-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 Sl function.

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

Since immediately after Sl dumps an object's definition to a disk file the source code on disk corresponds exactly to S's idea of the object's definition, the disk file isn't needed; deleting it now has the advantage that if you 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
     Option controlling what to do with the dump file after an object has been successfully loaded into S.  Valid values are nil (always delete), ask (always ask whether to delete), check (delete files generated with C-c C-d in this Emacs session, otherwise ask --- this is the default) and t (never delete).  This variable is buffer-local.

After an object has been successfully (i.e. without error) loaded back into Sl 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 (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 (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-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 Sl object itself.  Another useful feature is that you may format the code in any fashion you please without Sl re-indenting the code every time you edit it.  These features are particularly useful for project-based work.

If the value of 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-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 (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-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-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.

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

     (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.

Editing R documentation files
*****************************

ESS also provides support for editing R documentation (``Rd'') files.  R objects are documented in files written in Rd format, 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.

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 [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.

Rd-mode-hook
     Hook to be run when Rd mode is entered.

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

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)))

Reading help files
******************

ESS provides an easy-to-use facility for reading Sl help files from within Emacs.  From within the ESS process buffer or any ESS edit buffer, typing 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 Sl help mode.

  * h (ess-display-help-on-object)

     Pop up a help buffer for a different object

     Paging commands:

  * b or DEL (scroll-down)

     Move one page backwards through the help file.

  * SPC (scroll-up)

     Move one page forwards through the help file.

  * > (beginning-of-buffer) and < (end-of-buffer) Move to the beginning and end of the help file, respectively.

     Section-based motion commands:

  * n (ess-skip-to-next-section) and p (ess-skip-to-previous-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:

     a
          ARGUMENTS:

     b
          BACKGROUND:

     B
          BUGS:

     d
          DETAILS:

     D
          DESCRIPTION:

     e
          EXAMPLES:

     n
          NOTE:

     o
          OPTIONAL ARGUMENTS:

     r
          REQUIRED ARGUMENTS:

     R
          REFERENCES:

     s
          SIDE EFFECTS:

     s
          SEE ALSO:

     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.

     Miscellaneous:

  * 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.

  * / (isearch-forward)

     Same as C-s.

     Quit commands:

  * q (ess-switch-to-end-of-ESS)

     Returns to the ESS process buffer in another window, leaving the help window visible.

  * k (kill-buffer)

     Kills the help buffer.

  * x (ess-kill-buffer-and-go)

     Return to the ESS process, killing this help buffer.

In addition, all of the ESS commands available in the edit buffers are also available in Sl 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.

ESS for SAS
***********

     [file help-sas.texi not included]

ESS for BUGS
************

     [file help-bugs.texi not included]

Other features of ESS
*********************

ESS has a few miscellaneous features, which didn't fit anywhere else.

Syntactic highlighting of buffers
=================================

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

To activate highlighting, you need to turn on Font Lock mode in the appropriate buffers.  This can be done on a per-buffer basis with M-x font-lock-mode, or may be done by adding turn-on-font-lock to inferior-ess-mode-hook, ess-mode-hook and ess-transcript-mode-hook.  Your systems administrator may have done this for you in ess-site.el (see Customization).

The font-lock patterns are defined in three variables, which you may modify if desired:

 -- Variable: inferior-ess-font-lock-keywords
     Font-lock patterns for Inferior ESS Mode.  The default value highlights prompts, inputs, assignments, output messages, vector and matrix labels, and literals such as NA and TRUE.

 -- Variable: ess-mode-font-lock-keywords
     Font-lock patterns for ESS programming mode.  The default value highlights function names, literals, assignments, source functions and reserved words.

 -- Variable: ess-trans-font-lock-keywords
     Font-lock patterns for ESS Transcript Mode.  The default value highlights the same patterns as in Inferior ESS Mode.

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

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.

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 Sl 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.

Using ESS with windowing devices
--------------------------------

Of course, the ideal way to use graphics with ESS is to use a windowing system.  Under X11, this requires that the DISPLAY environment variable be appropriately set, which may not always be the case within your Emacs process.  ESS provides a facility for setting the value of DISPLAY before the ESS process is started if the variable ess-ask-about-display is non-nil.

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.)

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.

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.

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.

Rdired
======

Ess-rdired provides a dired-like buffer for viewing, editing and plotting objects in your current R session.  If you are used to using the dired (directory editor) facility in Emacs, this mode gives you similar functionality for R objects.

To get started, first make sure you can load ess-rdired.  Add the following to your .emacs and then restart emacs.

     (autoload 'ess-rdired "ess-rdired"
       "View *R* objects in a dired-like buffer." t)

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).

Bugs and Bug Reporting, Mailing Lists
*************************************

Bugs
====

     [file bugs.texi not included]

Reporting Bugs
==============

     [file bugrept.texi not included]

Mailing Lists
=============

     [file mailing.texi not included]

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.

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.