ESS[S]--Editing files
=====================

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

  - proper indenting, generated by both [Tab] and [Return].

  - color and font choices based on syntax.

  - ability to send the contents of an entire buffer, a highlighted region, an S function, or a single line to an inferior S process, if one is currently running.

  - ability to switch between processes which would be the target of the buffer (for the above).

  - The ability to request help from an S process for variables and functions, and to have the results sent into a separate buffer.

  - completion of object names and file names.

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

iESS[S]--Inferior ESS processes
===============================

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

  - proper indenting, generated by both [Tab] and [Return].

  - color and font highlighting based on syntax.

  - ability to resubmit the contents of a multi-line command to the executing process with a single keystroke [RET].

  - The ability to request help from the current process for variables and functions, and to have the results sent into a separate buffer.

  - completion of object names and file names.

  - interactive history mechanism.

  - transcript recording and editing.

To start up iESS mode, use:

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

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

M-x S

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

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

C-u M-x R

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

--vanilla

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

If you have other versions of R or S-Plus available on the system, ESS is also able to start those versions.  How this works depend on which OS you are using:

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

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

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

ESS-help--assistance with viewing help
======================================

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

Philosophies for using ESS[S]
=============================

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

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

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

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

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

Scenarios for use (possibilities--based on actual usage)
========================================================

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Customization Examples and Solutions to Problems
================================================

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

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

     (setq ess-plain-first-buffername nil)

)

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

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