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

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

ESS version

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

     Emacs Speaks Statistics (ESS) provides an intelligent, consistent interface between the user and the software.  ESS interfaces with R, SAS, S-PLUS, BUGS/JAGS and other statistical analysis packages on GNU/Linux, other Unix-like systems such as macOS, 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.

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Introduction to ESS
*******************

ESS provides a generic interface, through Emacs, to statistical packages.  It currently supports R (and the rest of the S family), SAS, BUGS/JAGS, Stata, and Julia with the level of support roughly in that order.

Throughout this manual, Emacs refers to GNU Emacs by the Free Software Foundation.  Although previous versions of ESS supported other Emacsen, current versions only support GNU Emacs.

There are two main ways of interacting with ESS: through ``regular'' modes or ``inferior'' modes.  Regular modes act like normal Emacs major modes.  ESS major modes are displayed in the mode-line in the format ESS[dialect], where dialect can take values such as R, SAS, or S.

ESS also provides easy access to an ``inferior process,'' which is an Emacs buffer associated with a running process.  This can be an R session, for example.  These inferior processes are referred to as inferior ESS (iESS), and are shown in the modeline by iESS [dialect].

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

For exclusively interactive users of R, 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 R objects and ``hot keys'' are provided for common R 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 R interactively under ESS.

For those that use R in the typical edit--test--revise cycle when writing R functions, ESS provides for editing of R functions in Emacs buffers.  Unlike the typical use of R 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 R, and a mechanism to jump directly to the error is provided.  ESS also provides for maintaining text versions of your R 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 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.

Additionally, both Emacs and ESS (and R) are free software designed to give users full control over their computer.  For more on what this means, visit https://www.gnu.org/philosophy/free-sw.html.

Features Overview
-----------------

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For source code buffers, ESS offers several features:

  * Support for multiple indentation styles R code 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 R source files. See Source Files.

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

ESS also provides features that make it easier to interact with inferior ESS (iESS) 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.  See Command-line editing.

  * Searchable command history for recalling previously-submitted commands.  See Command History.

  * Command-line completion of both object and file names for quick entry.  See Completion.

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

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

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

  * 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.

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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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.  This section describes some of the basics of using Emacs.  If you are already familiar with basic Emacs functionality, skip this section.  You may also want to use the Emacs tutorial, accessible via C-h t.

In this manual we use the standard notation used by Emacs 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 key (usually ALT) 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 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.  For example, 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 a `self-documenting' text editor.  This applies to ESS in two ways.  First, some 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, C-h m pops up a complete list of keybindings available in each ESS mode and brief description of that mode.

Emacs is a versatile editor written in both C and a dialect of Lisp known as Elisp. ESS is written in Elisp and 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
*****************************

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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 R from within Emacs.  The Emacs convention is to name such processes running under its control as `inferior processes'.  Some users find this terminology confusing; you may prefer to think of these as `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 inferior R session on GNU/Linux, macOS, or Windows using the Cygwin bash shell, simply type M-x R RET. To start an R session on Windows when you use the MSDOS/powershell shell, simply type M-x S+6-msdos RET. R will then (by default) ask the question

     R starting data directory?

Enter the name of the directory you wish to have as the working directory (that is, the directory you wish to have getwd() return if using R).

You will then be popped into a buffer named *R* 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 iESS process simultaneously in the same session.  Each process has a name and a number; the initial process (process 1) is simply named R.  If you call M-x R again without killing the first R process, ESS will start a second R process with the name R:2.  To have the first buffer named R:1, customize the option ess-plain-first-buffername.  With a prefix argument, C-u M-x R allows for the specification of command line options.

 -- User Option: ess-plain-first-buffername
     If non-nil, name the first iESS process [R]. Otherwise, name it [R:1].

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 processes.  This is a good command to consider binding to a global key.

ESS processes on Remote Computers
=================================

ESS and TRAMP
-------------

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 see TRAMP User Manual.

Start an ssh session using TRAMP 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).  When asked for starting directory, simply type /ssh:user@host: RET. The 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 the R graphic device showing on the current machine

ESS-remote
----------

TRAMP is the recommended way of starting a remote session.  The other way to start a remote ESS connection is 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 https://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 R, Splus, 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 R 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.

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.

You may also customize ess-post-run-hook and the dialect-specific ess-*-post-run-hook variables. For example, you may want to use ess-load-file to load a file when ESS starts R:

     (add-hook 'ess-r-post-run-hook (lambda () (ess-load-file "foo.R")))

If you like to keep a record of your R actions, 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, ask 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 (for R, you likely want it to end in .Rout). 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 inferior process itself is started. If you need to pass any arguments to this program, they may be specified in the variable inferior-S_PROGRAM_NAME-args.  For example, if inferior-ess-program is "R" then the variable to set is inferior-R-args. It is not normally necessary to pass arguments to the iESS program; in particular do not pass the -e option to Splus, since ESS provides its own command history mechanism.

ESS can set the width option of inferior processes automatically when the window configuration changes. To do so, set ess-auto-width to a non-nil value. By default, the change will not be shown in the inferior buffer. If you want it to be shown, set ess-auto-width-visible to a non-nil value.

Controlling buffer display
==========================

Users can control how buffers are displayed by customizing display-buffer-alist, see Window Choice (emacs). This section provides examples of how to achieve certain setups.

Users coming from RStudio may want the R process to appear at the bottom left of the frame, help buffers to appear at the bottom right, and ess-rdired buffers at the top right. To achieve that, you could this. Note that the order matters; *R Dired* would match *R if it came before in the alist.

     (setq display-buffer-alist
           `(("^\\*R Dired"
              (display-buffer-reuse-window display-buffer-in-side-window)
              (side . right)
              (slot . -1)
              (window-width . 0.33)
              (reusable-frames . nil))
             ("^\\*R"
              (display-buffer-reuse-window display-buffer-at-bottom)
              (window-width . 0.5)
              (reusable-frames . nil))
             ("^\\*Help"
              (display-buffer-reuse-window display-buffer-in-side-window)
              (side . right)
              (slot . 1)
              (window-width . 0.33)
              (reusable-frames . nil))))

Some users prefer working with multiple frames where one frame has the source code and the other frame has the inferior process. To achieve this, use this example.  For a detailed description of reusable-frames, see Buffer Display Action Alists (elisp).

     (setq display-buffer-alist
           '(("^\\*R"
              (display-buffer-reuse-window display-buffer-pop-up-frame)
              (reusable-frames . 0))))

Some users may want the process window to be dedicated to the process so that other buffers are not shown on top of that window. See Dedicated Windows (elisp). For example, this prevents help buffers from being displayed in the window showing the inferior R process.

     (setq display-buffer-alist
           '(("^\\*R"
              nil
              (dedicated . t))))

By default, ESS usually prefers splitting the frame into multiple windows so that you can work with both the R script and the R REPL visible at once. If you want to override this behavior so that the script buffer and the process buffer share the same window, you can do so like this:

     (setq display-buffer-alist
           '(("^\\*R" . ((display-buffer-same-window) (inhibit-same-window . nil)))
             ("\\.R$" . ((display-buffer-same-window) (inhibit-same-window . nil)))))

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

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

 -- 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 (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-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.

Manipulating the transcript
===========================

Most of the time, the cursor spends 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 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.

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-prompt Moves point to the preceding prompt in the process buffer.

C-c C-n
     comint-next-prompt Moves point to the next prompt 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 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 signaled).  Note all 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 (re)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.

Keeping a record of your R session
----------------------------------

To keep a record of your R 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 R 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 R by setting the variable ess-ask-about-transfile to t; see Customizing startup. For R files, naming transcript files *.Rout puts them in a special mode (ESS transcript mode --- see Transcript Mode) for editing transcript files which is automatically selected for files with this suffix.

R 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.

You can use ess-transcript-clean-region to strip output from a transcript, leaving only source code suitable for inclusion in files source()-able from R.  see Transcript Mode

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 (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 (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 adding 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-move-point-for-output 'others)
           ;; somewhat extreme, almost disabling writing in *R*, *shell* buffers above prompt:
           (setq comint-scroll-to-bottom-on-input 'this)
           ))

to your Emacs configuration file, where the last two settings are typically desirable for the situation where you work with a script (for example, 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 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 a file) in the same directory as the iESS process.

ESS users may work exclusively with script files rather than in a iESS session, and may not want to save any history files.  To do so:

       (setq ess-history-file nil)

or if you prefer only one global command history file:

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

in your Emacs configuration file.

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 R, 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 R 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 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. In other words, 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).  This is 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 R.  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 (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 M-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
     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 R 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 R 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.

Is the Statistical Process running under ESS?
=============================================

For the R languages (R, S, S-Plus) 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 R 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 R 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 principal applies.  Within your R session, 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 R 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 available in the process buffer:

 -- Command: comint-interrupt-subjob
     C-c C-c Sends a Control-C signal to the iESS 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. Consecutive presses of C-z switch between the script and process buffers.

     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 iESS modes are discussed in Shell Mode (The Gnu Emacs Reference Manual).

Sending code to the ESS process
*******************************

Other commands are also available for evaluating portions of code in the R 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.  A value of t blocks Emacs while R is busy.  A value of nowait does not block Emacs but printing may be slightly off.

Passing a prefix (C-u) (in Elisp terms, the argument 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 evaluates the current line without showing the input in the iESS buffer.  The default value of ess-eval-visibly (t) means that ESS calls block Emacs until they finish. This may be undesirable, especially if commands take long to finish. Users who want input to be displayed and Emacs not to be blocked can set ess-eval-visibly to 'nowait. This sends the input to the iESS buffer but does not wait for the process to finish, ensuring Emacs is not blocked.

Primary commands for evaluating code are:

 -- Command: ess-eval-region-or-line-and-step VIS
     C-<RET> Sends 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 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 R 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-move-point-for-output to 'others or t.

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

Inferior R 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 .Rout.  The most obvious use for a transcript file is as a static record of the actions you have performed in a particular R 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 .Rout into Emacs, it is placed in R Transcript Mode.  Transcript Mode is similar to inferior R 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:

 -- 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 R 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 R 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 R mode, also available in R Transcript Mode.

Editing objects and functions
*****************************

ESS provides facilities for editing R objects within your Emacs session.  Most editing is performed on R 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 R functions.  Error-checking is performed when R code is loaded into the ESS process.

Creating or modifying R objects
===============================

To edit an object, type

 -- Command: ess-dump-object-into-edit-buffer OBJECT
     C-c C-e C-d Edit an object in its own edit buffer.

from within the iESS process buffer (*R*).  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 R source code.  Commands are provided to intelligently indent R code, evaluate portions of R code and to move around R 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 R 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 R'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.

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

The best way to get information --- particularly function definitions --- into R is to load them in as source file, using R'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 M-l). see Hot keys.

After typing C-c M-l you will prompt for the name of the file to load into R; 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.

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 R 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 `.

Indenting and formatting R code
===============================

ESS provides a sophisticated mechanism for indenting R source code.  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 roxygen2 entries which is R documentation maintained in the source code as comments see roxygen2.

The indentation commands provided by ESS are:

 -- Command: ess-indent-or-complete
     TAB Indents the current line as R code.

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

 -- 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 R (compound) expression which follows point.  Very useful for beautifying your R 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-dwim Call the comment command you want (Do What I Mean).

Changing styles for code indentation and alignment
--------------------------------------------------

The combined value of twelve variables (4 of three groups ess-indent-*, ess-offset-* and ess-align-*) 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, RRR+, Rstudio, Rstudio-, and CLB.  The variable ess-style-alist lists the value of each indentation variable per style (and its documentation contains more).

 -- Command: ess-set-style
     C-c C-e C-s (or C-c C-e s) sets the formatting style in this buffer to be one of the predefined styles, see above.  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.

 -- User Option: ess-style
     The style to use. See the variable ess-style-alist for how these groups (DEFAULT, OWN, GNU, RRR, ...) map onto different settings for variables. You can set this in your Emacs configuration file:

          (setq ess-style 'C++)

 -- 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-style.

The styles DEFAULT and OWN are initially identical.  If you wish to edit some of the default values, set ess-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 customization 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-style 'MINE) to use your new style.

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 R 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: TAB first indents, and if there is nothing to indent, completes the object or file name; M-? lists file completions. 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 many 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 R.

Maintaining R 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 R 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 R dumps an object's definition to a disk file the source code on disk corresponds exactly to R'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 R 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 R'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 (without error) loaded back into R with C-c C-l, the disk file again corresponds exactly (well, almost --- see below) to R'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 git 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-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 R object itself.  Another useful feature is that you may format the code in any fashion you please without R 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 (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.

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 .R.  Thus if user joe dumps the object myfun the dump file will have name joe.myfun.R. 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 R 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 ~/R-source.  This could be achieved by including the following line in your Emacs configuration file:

     (setq ess-source-directory (expand-file-name "~/R-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 R working directory during an R 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 R 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.

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

ESS provides an easy-to-use facility for reading R 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 ESS 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 R help mode.

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

Paging commands:

DEL
     scroll-down-command Move one screen backwards through the help file.

SPC
     scroll-up-command Move one screen forwards through the help file.

>
<
     end/beginning-of-buffer Move to the end or beginning 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 the exact headings available and capitalization scheme may vary across languages.

You may 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:

?
     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 R 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.

Help buffers are displayed by calling the function ess-display-help. You can customize where these buffers are displayed by adding an entry in display-buffer-alist; for examples, see Controlling buffer display (ess). Or by customizing the options ess-help-own-frame, ess-help-frame-alist, and ess-display-buffer-reuse-frame.

Completion
**********

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 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 R 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 the rest of Emacs.  ESS maintains a list of all objects known to R 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

For example, consider three functions binomplot(), binom.test() and binomial().  Typing bin TAB 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-complete-object-name
     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 R functions such as get() or scan() which require fully expanded file names.

In the iESS 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 R; 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.

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.

In R versions newer than 2.14.1, ESS uses R's built-in completion engine and will honor its settings. You may read about them by issuing ?rc.options at the prompt. For example, to have the equals sign for function arguments contain spaces on both sides (e.g. lm(for) suggests formula =  rather than formula=), you can adjust funarg.suffix:

     utils::rc.options(funarg.suffix = " = ")

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

Minibuffer completion
=====================

ESS uses IDO mechanism (part of default Emacs) for minibuffer completion if the ido 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.

Company
=======

Another popular package for completion is company, short for complete anything.  ESS provides support for company out-of-the-box. To disable company support, set ess-use-company to nil. You can set it to 'script-only to only activate company in R scripts.

Icicles
=======

Another option for comprehensively handling completion in Emacs is via Icicles (https://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):

     (require 'icicles)
     (icy-mode 1)

Icicles can be toggled 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.

Developing with ESS
*******************

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

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.

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.

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")

Getting started with tracebug
-----------------------------

Consider a buffer with the following function:

test <- function(x){
  mean(x),
}

Evaluating the function (e.g. C-c C-c) results in an error about an unexpected comma. You can use next-error (bound by default to C-x `, M-g n, and M-g M-n) to jump to the place where the error occurred. Alternatively, use the mouse to click on the error to jump to where it occurred.

Correct the error by deleting the comma. Now put point on mean and set the breakpoint using C-c C-t b (ess-bp-set) and reevaluate the function. Jump to the inferior buffer (possibly using C-c C-z) and evaluate test(1:10). An interactive debug process starts, stopping at the breakpoint we just specified. Here you can debug your function (what is x at this point?). Use M-N to continue.

Let's replace our test function with one slightly more complicated:

test <- function(x){
  x <- x + 1
  y <- mean(x)
  x <- ifelse(x > 5, x, x - 100)
  list(x, y)
}

Try setting multiple breakpoints. You can unset a breakpoint by killing it with C-c C-t k. You can set conditional breakpoints too. Try setting one by placing point on the line x <- x + 1 and doing C-c C-t B. ESS will ask for the condition. Let's set it to !is.numeric(x). After re-evaluating test, try calling test(1:100) and test('foo').

You can remove all breakpoints with C-c C-t K.

You can flag a function for debugging (similar to calling debug(test) at R's prompt) by doing C-c C-t d. Try this yourself by putting point over test and doing C-c C-t d.

If an error occurs, you can get the complete call stack by doing C-c ` or C-c C-t ` (ess-show-traceback).

Tracebug also offers a watch window where you can watch values of objects. Open it with C-c C-t w (ess-watch). Initially you aren't watching anything. Add something with a (e.g. a test). The watch window displays what the object is at any given time and automatically updates. Quit the watch window with q.

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 roxygen2 package.

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).

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.  For example, 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)))

Editing roxygen2 documentation
------------------------------

The roxygen2 R package makes it possible to keep the intended contents for Rd files as structured comments in the R source files. roxygen2 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 roxygen2 documentation found via https://roxygen2.r-lib.org for more information on its usage. An example of an roxygen2 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 roxygen2 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.

roxygen2 is customized by the variables in the customization group ``Ess Roxy''. Customizations include the roxygen2 prefix, use of folding to toggle visibility of roxygen2 entries and the roxygen2 template.

All ESS roxygen2 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 roxygen2 template or update the parameter list in roxygen2 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 roxygen2 string on all lines in the marked region (between BEG and END. Convenient for transferring text to roxygen2 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 roxygen2 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 roxygen2 and tools packages to be installed.

 -- Command: ess-roxy-previous-entry
     C-c C-o p Go to start of the roxygen2 entry above point.

 -- Command: ess-roxy-next-entry
     C-c C-o n Go to end of the roxygen2 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 roxygen2 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 roxygen2 editing more intuitive:

TAB
     ess-R-complete-object-name Complete roxygen2 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 roxygen2 entry at point.

M-q
     fill-paragraph Fill the roxygen2 field at point.

C-a
     ess-roxy-move-beginning-of-line Move to the point directly to the right of the roxygen2 start string. If already there, move to the beginning of the line.

RET
     newline-and-indent Insert a new line and the roxygen2 prefix string.

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 https://cran.r-project.org/doc/manuals/R-ints.html#Namespaces.

Occasionally 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).

Other ESS features and tools
****************************

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

ElDoc
=====

In ElDoc mode, the echo area displays function's arguments at point. 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.

Flymake
=======

The minor mode flymake-mode provides on-the-fly syntax checking. ESS provides support for flymake in R-mode in Emacs versions 26 and newer. It is enabled by default, to disable it you may set ess-use-flymake to nil. In order to use it, you may need to install the lintr R package, available from CRAN.

 -- User Option: ess-use-flymake
     When non-nil, use flymake. If 'process, only use flymake when the buffer has an inferior process running.

 -- User Option: ess-r-flymake-linters
     This variable describes the linters to use. It can either be a string with an R expression to be used as-is or a list of strings where each element is passed to lintr::with_defaults. See the help page for lintr::default_linters for information on available linters and their defaults.

 -- User Option: ess-r-flymake-lintr-cache
     When t (the default), lintr uses a cache. Change to nil to disable lintr's caching mechanism.

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.

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

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

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.

Parenthesis matching
====================

Emacs has 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. You may activate it putting this in your Emacs configuration file:

     (show-paren-mode)

Using graphics with ESS
=======================

One of the main features of R is its ability to generate high-resolution graphics plots. When using R in a windowing environment, no additional configuration is necessary; plots will be shown in a new (non-Emacs) window.

If not using a windowing environment or S, 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 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.

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.

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 R), support for Imenu is provided.  For example, in R mode buffers, the menubar should display an item called "Imenu-R".  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, for example 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.

Outline navigation
==================

R editing buffers integrate with outline-minor-mode.  When you toggle the minor mode (for example via M-x outline-minor-mode or by adding it to ess-r-mode-hook), ESS assigns ess-r-outline-level to outline-level and configures outline-regexp according to ess-r-outline-style so that comment headings drive folding.  By default, outline support is disabled (none), but you can enable it by setting ess-r-outline-style to RStudio or Org-like.  With the RStudio style, lines that begin with one or more #, followed by text and a trailing marker of ----, ====, or ####, are treated as outline headings.  This matches the section markers convention adopted by RStudio.

     # Setup ----
     ## Data ----
     ### Models ====
     #### Helpers ####

The number of leading # characters sets the outline depth.  When using the RStudio outline style, ess-indent-with-fancy-comments is automatically set to nil locally in the buffer to prevent single-hash comments from being treated as right-margin comments with comment-column 40.  When switching back to a different outline style, the original local binding is restored; if the variable was not buffer-local, the current global default applies.

Use standard Outline commands (such as C-c  C-t) to cycle visibility once the minor mode is active.  To enable Outlining automatically, add it to the R mode hook:

     (add-hook 'ess-r-mode-hook #'outline-minor-mode)

 -- User Option: ess-r-outline-style
     Select which outline convention ess-r-mode should use. The default none disables outline support to preserve backward compatibility.  Set to RStudio to recognise the comment rulers shown above, or choose Org-like to match the ### * Section pattern, inspired from org-mode:

          ### * Setup
          ### ** Data
          ### *** Models
          ### **** Helpers

     You can switch styles via M-x ess-r-set-outline-style or by customizing this option.

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.

Xref
====

Xref is an Emacs interface that supports finding ``identifiers,'' usually function definitions in ESS's view. ESS ships with support for Xref in Emacs versions 25.1 and higher. For how to use this feature, see Xref (The Gnu Emacs Reference Manual).

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).

Package listing
===============

ESS[R] provides several commands to list and manage packages and objects under the C-c C-. keymap:

 -- Command: ess-r-package-list-local-packages
     C-c C-. l List all packages in all available libraries.

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

 -- Command: ess-r-package-update-packages LIB REPOS
     C-c C-. u Update packages in a particular library LIB and repository REPOS.

 -- Command: ess-rutils-rm-all
     C-c C-. m Remove all R objects.

 -- Command: ess-rutils-load-workspace
     C-c C-. w Load a workspace file into R.

 -- Command: ess-rutils-save-workspace
     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.

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).

Interaction with Org mode
=========================

Org-mode (https://orgmode.org) now supports reproducible research and literate programming in many languages (including R) -- see chapter 15 of the Org manual (https://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.)

Support for Sweave in ESS and AUCTeX
====================================

Libraries for literate data analysis are obsolete and not loaded by default. This includes ess-noweb, ess-swv, and related functionality like Rnw-mode. Users are encouraged to switch to one of several other packages that deal with these modes. For example, polymode https://github.com/polymode/poly-R/, https://polymode.github.io/, or markdown-mode with edit-indirect https://jblevins.org/projects/markdown-mode.

ESS provides support for writing and processing Sweave (https://leisch.userweb.mwn.de/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 (https://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.

Overview of ESS features for the S family
*****************************************

     [file help-s.texi not included]

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

     [file help-sas.texi not included]

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

     [file help-bugs.texi not included]

ESS for JAGS
************

     [file help-jags.texi not included]

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 view-emacs-faq) and EmacsWiki (https://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 configuration 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.

Indices
*******