General Information: README
***************************
($Revision: 5.28 $, for ESS 5.1.19)
This is the README file for the distribution of ESS version 5.1.19,
the alpha/beta series we are using on the way to producing 5.2 (the next
stable distribution). ESS is an Emacs-Lisp interface for interactive
statistical programming and data analysis. Languages supported include:
S dialects (S 3/4, S-PLUS 3.x, and R), LispStat dialects (XLispStat,
ViSta), and SAS. Stata and SPSS dialect (SPSS, PSPP) support is being
examined for possible future implementation (a preliminary Stata mode is
distributed).
Installation help can be found in sections for Unix Installation or
Windows Installion
For INSTALLATION, see way below.
ESS grew out of the desire for bug fixes and extensions to
S-mode-4.8. In particular, XEmacs support as well as extensions to
incorporate R were desired. In addition, with new modes being
developed for R, Stata, and SAS, it was felt that providing for a
unifying framework would eliminate differences in the user interface,
as well as to provide for faster development of production tools and
statistical analysis. 5.1.y has, for its guts, the basic framework
from S-mode. However, it has been cleaned, streamlined, brought closer
to conformance as a standard GNU Emacs package, and redesigned for
modularity and reuse.
The current development team is led by A.J. (Tony) Rossini
(<rossini@biostat.washington.edu>), who did the initial port to XEmacs
and has been the primary coder. Martin Maechler
(<maechler@stat.math.ethz.ch>) and Kurt Hornik
(<hornik@ci.tuwien.ac.at>) have assisted with S-PLUS, S4, R, and
XLispStat sub-modes, and Richard M. Heiberger
(<rmh@fisher.stat.temple.edu>) has done much of the work for
implementing the SAS sub-mode, as well as assisted with S-PLUS (under MS
Windows and remote access) and S4 development. Douglas Bates
(<bates@stat.wisc.edu>) contributed the initial S4 mode, as well as
provided disk space, ftp and http access to the source for development
purposes.
We are grateful to David M. Smith, the previous developer (for S-mode
3.x and 4.x), as well as to the initial developers of S-mode, Doug
Bates, Ed Kademan and Frank Ritter.
In addition, some of the code has been and will be borrowed from Tom
Cook (from his excellent SAS mode) and Thomas Lumley (preliminary Stata
mode), gratefully (from us) and with permission (from them).
The name is ESS. Not ESS-mode.
License
=======
ESS is free software; you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free
Software Foundation; either version 2, or (at your option) any later
version.
ESS is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
in the file COPYING in the same directory as this file for more details.
New Features
============
Changes/New Features in 5.1.19:
* S+6 now supported (Tony Rossini)
* New BUGS support through ESS[BUGS] mode (Rodney Sparapani)
Templates assist you in writing .bug and .cmd code (.cmd and .log
are replaced by .bmd and .bog to avoid emacs extension
collisions). "Substitution" parameters facilitate
"automagic" generation of "data...in" and "init...in"
filenames, "const N=" from your data file and
"monitor()/stats()" commands. Activated by pressing F12.
* Fixes for `ess-smart-underscore' SAS breakage (Rich Heiberger)
* You can change between PC and Unix, local and global SAS
function-key definitions interactively (Rich Heiberger)
* C-Submit a highlighted region to SAS batch (Rodney Sparapani)
* New and improved SAS syntax highlighting (Rodney Sparapani)
To get the new functionality, set ess-sas-run-make-regexp to nil.
Also available in .log files via F10.
* Open a permanent SAS dataset for viewing via F9 (Rodney Sparapani)
You must have the library defined in autoexec.sas for it to
work.
* User-friendly defaults for `sas-program',
`ess-sas-batch-pre-command' and `ess-sas-batch-post-command'
as well Customize support for these and other ESS[SAS]
variables (Rodney Sparapani)
* `ess-sas-suffix-2' now defaults to .dat via F11 (Rodney Sparapani)
* Emacs/XEmacs, Unix/Windows issues collectively handled in
ess-emcs.el
* defadvice solves problem of missing *ESS* (thanks to Jeff Mincy)
* Improved manual a bit by including things that were only in
`README'.
Changes/New Features in 5.1.18:
* New `ess-smart-underscore' function, now assigned to "_" by
default. Inserts `ess-S-assign' (customizable " <- "),
unless inside string and comments where plain "_" is used
instead. (MM)
* Fixes for longstanding interactive SAS breakage (RMH)
Changes/New Features in 5.1.17:
* Documentation for Windows Installation (Rich Heiberger
(<rmh@surfer.stat.temple.edu>))
* removal of ess-vars, finalization of customize support (in the
sense that there is no more use of ess-vars, but that we need to
fix ess-cust) (AJ Rossini (<rossini@u.washington.edu>))
* Many small (and large) fixes/contributions (MMaechler,
(<maechler@stat.math.ethz.ch>)).
* addition of the "S-equal" variable and provide M-x ess-add-MM-keys
a way to remap "_" to `ess-S-assign', typically " <- ", but
customizable. (MMaechler, (<maechler@stat.math.ethz.ch>)).
Changes/New Features in 5.1.16:
* BUG FIXES
* Better SAS support
Changes/New Features in 5.1.15:
* BUG FIXES
Changes/New Features in 5.1.14:
* Yet more fixes to SAS mode, (Rich Heiberger
(<rmh@surfer.stat.temple.edu>) and Rodney Sparapani
<rsparapa@mcw.edu>)).
* Customize support (for most Emacsen which support it) (AJRossini,
(<rossini@biostat.washington.edu>)
* ARC and ViSta support out of the box, and fixes for XLispStat
(AJRossini, <rossini@biostat.washington.edu>)
Changes/New Features in 5.1.13:
* Version numbering finally all depending on the ./VERSION file,
thanks to Martin Maechler.
* Yet more fixes to SAS mode, thanks to Rich Heiberger
(<rmh@surfer.stat.temple.edu>).
Changes/New Features in 5.1.12:
* Splus 5.1 stabilized, thanks to Martin Maechler, Bill Venables,
Chuck Taylor, and others.
* More fixes to SAS mode, thanks to Rodney Sparapani
(<rsparapa@mcw.edu>) and Rich Heiberger
(<rmh@surfer.stat.temple.edu>).
Changes/New Features in 5.1.11:
* More fixes to Stata mode, thanks to Brendan Halpin
(<brendan@essex.ac.uk>)
* fixed bugs in ESS-elsewhere, thanks to many testers
* README.SPLUS4WIN has DETAILED instructions for S-PLUS 2000, thanks
to David Brahm (<brahm@alum.mit.edu>).
* Fixes to SAS mode, thanks to Rodney Sparapani
(<rsparapa@mcw.edu>)
Changes/New Features in 5.1.10:
* More fixes to Stata mode
* primitive generic version of ESS-elsewhere
* Small fixes to SAS/Stata.
Changes/New Features in 5.1.9:
* Stata mode works
* Literate Data Analysis using Noweb works
Changes/New Features in 5.1.8:
* Bug fixes
* R documentation mode defaults changed
Changes/New Features in 5.1.2:
* able to use inferior iESS mode to communicate directly with a
running S-Plus 4.x process using the Microsoft DDE protocol. We
use the familiar (from Unix ESS) C-c C-n and related key sequences
to send lines from the S-mode file to the inferior S process. We
continue to edit S input files in ESS[S] mode and transcripts of
previous S sessions in ESS Transcript mode. All three modes know
the S language, syntax, and indentation patterns and provide the
syntactic highlighting that eases the programming tasks.
Current Features
================
* Languages Supported:
* S dialects (S 3/4, S-PLUS 3.x/4.x/5.x/6.x, and R)
* LispStat dialects (XLispStat, ViSta under development)
* SAS
* BUGS
* Stata
* SPSS dialects (SPSS, Fiasco (GNU project)) (under development)
* SCA (under development)
* Editing source code (S, LispStat, SAS, BUGS)
* Syntactic indentation and highlighting of source code
* Partial evaluations of code
* Loading and error-checking of code
* Source code revision maintenance
* Interacting with the process (S, LispStat, SAS)
* Command-line editing
* Searchable Command history
* Command-line completion of S object names and file names
* Quick access to object lists and search lists
* Transcript recording
* Interface to the help system
* Transcript manipulation (S3, S+3, S4, R, XLispStat)
* Recording and saving transcript files
* Manipulating and editing saved transcripts
* Re-evaluating commands from transcript files
* Help File Editing (R)
* Syntactic indentation and highlighting of source code.
* Sending Examples to running ESS process.
* Previewing
Stability
=========
Versions 5.1.x are meant as a beta-level releases. While some bugs
are fixed from 5.0, others have been introduced, especially with
regards to new features. See the file doc/TODO for details. Bug
reports are solicited; see the BUGS section below. Patches or
suggested coding fixes with bug reports are much appreciated!
Requirements
============
ESS version 5.1.n (n >= 2) requires Emacs version 19.34(1) or later,
or version XEmacs 19.14 or later. It has been most thoroughly tested
with:
* S-PLUS versions 3.3, 3.4, 4.5, 5.0, 5.1, 6
* R versions >=0.49
* XLispStat versions >=3.50
* S4
* SAS
* Stata >=6.0
* BUGS 0.5 or 0.6
on the following platforms
* SunOS (all)
* Solaris (all)
* SGI (all)
* Linux (S-PLUS 5.0, 5.1, R, XLispStat, S4, Stata 6.0)
* Microsoft Windows 95/98/NT (SPLUS 4.5 and 2000)
with the following versions of emacs
* Emacs 19.34, 20.3, 20.4, 20.5, 20.6, 20.7
* XEmacs 19.16, 20.0, 20.4, 21.0, 21.1.13, 21.4.x
* Emacs 19.28, 19.29 with SAS (with additional modifications)
* NTEmacs 20.3.1 with S-PLUS 4.5.
---------- Footnotes ----------
(1) if you have Emacs 19.29, you _may_ get it to work after
unpacking `19.29.tar.gz', see the installation instructions
Getting the Latest Version
==========================
The latest versions of ESS are always available by WWW from:
`http://ess.stat.wisc.edu/' and
`ftp://ess.stat.wisc.edu/pub/ESS/'
The HTML version of the documentation can be found at:
`http://stat.ethz.ch/ESS/'
The latest (no more than 24 hours behind the developers) version of
ESS can also be retrieved using anonymous cvs:
You need a cvs client (that works with your firewall, if any)
the repository name is
`:pserver:anoncvs@ess.stat.wisc.edu:/home/anoncvs/src'
using a command-line cvs client (i.e. on Unix or DOS), first type:
`cvs -d :pserver:anoncvs@ess.stat.wisc.edu:/home/anoncvs/src login'
password is anoncvs
then type:
`cvs -d :pserver:anoncvs@ess.stat.wisc.edu:/home/anoncvs/src co ess'
Check the `README' file first to see which files you need. Look at
`ANNOUNCE' to learn about new user-visible features; also, many changes
are listed in the `ChangeLog' file.
Installation (from tar file)
============================
We now discuss installation, which might happen under Unix or
Microsoft Windows. First, we discuss Unix installation.
Please skip to the next
1. cd to a directory where you keep emacs lisp files, or create a
new directory to hold the distribution. This directory will be
referred to below as "the ESS distribution directory". It will
contain, at the end, the tar file `ESS-5.1.19.tar.gz', and a
directory for the ESS source, which will be termed "the
ESS-5.1.19 source directory".
Note that the .elc files may be installed elsewhere (as specified
in the Makefile) if desired.
2. Retrieve the compressed tar file from one of the FTP or WWW
archive sites via FTP (or HTTP).
3. Copy `ESS-5.1.19.tar.gz' to the location where you want the
ESS-5.1.19 directory, and cd there. Extract the files from the
distribution, which will unpack into a subdirectory, ESS-5.1.19.
gunzip ESS-5.1.19.tar.gz
tar vxf ESS-5.1.19.tar
(or: `gunzip < ESS-5.1.19.tar.gz | tar vxf -' ). (or using GNU
tar: `tar zvxf ESS-5.1.19.tar.gz').
The `tar' command will extract files into the current directory.
Do not create ESS-5.1.19 yourself, or you will get an extra level
of depth to your directory structure.
Note if you have a very ancient version of GNU emacs (_and_ really
can not upgrade to Emacs 20 or higher!) you can unpack the
`lisp/19.29.tar.gz' file, read the ensuing `lisp/19.29/README'
and you may succeed...
4. Edit the file `lisp/ess-site.el' as explained in the comments
section of that file. Installations that are using ESS only for
S-plus 3.x will probably not need to make any changes.
Installations that also have one or more of (S+5 S4 R SAS
XLispStat Stata) may need to uncomment corresponding lines in
`ess-site.el'.
5. READ THIS ITEM THOROUGHLY BEFORE STARTING:
In the ESS-5.1.19 directory, edit the file `Makeconf' (only if you
want to place the executables in other locations; see LISPDIR and
INFODIR) and then type:
make
If this works, then you might try:
make install
Note that the latter does the former as well, so if you are
feeling lucky, you might want to skip it.
This will install the info files (and the lisp files, if they are
to go in another directory). Don't forget to edit the file
`dir' in the info directory specified by `INFODIR' in
`doc/Makefile'. See the sample `dir' file for an example of the
line to add.
If you are using XEmacs, you might do:
make EMACS=xemacs
and then
make EMACS=xemacs install
instead of editing the Makefile.
_Note_ that you might need to use GNU make for everything to
work properly
An alternative, if you are running XEmacs and have access to the
XEmacs system directories, would be to place the directory in the
site-lisp directory, and simply type `make' (and copy the
documentation as appropriate).
For Emacs, you would still have to move the files into the top
level site-lisp directory.
6. Add the line
(load "/PATH/ess-site")
to your .emacs file (or default.el or site-init.el, for a
site-wide installation). Replace `/PATH' above with the value of
ess-lisp-directory as defined in ess-site.el.
Alternatively, if ess-site.el is in your current Lisp path, you can
do:
(require 'ess-site)
to configure Emacs for ESS.
7. (OPTIONAL) If you are running S-PLUS or R, you might consider
installing the database files. From within (X)Emacs, `C-x d' to
the directory containing ESS. Now:
M-x S+3
(or `M-x S+5': get running. once you have reached the SPLUS
prompt, do:)
M-x ess-create-object-name-db
(this will create the file `ess-s+3-namedb.el'; if it isn't in
the ESS directory, move it there).
Then, completions will be autoloaded and will not be regenerated
for every session.
For R, do the same, using
M-x R
and then `M-x ess-create-object-name-db' creating
`ess-r-namedb.el'; if it isn't in the ESS directory, move it
there).
8. For more information on using ESS in your daily work, see the
files README.S, README.SAS, and README.XLispStat.
For the impatient, the quick version of usage follows:
9. To edit statistical programs, load the files with the requiste
extensions (".sas" for SAS, ".S" for S-PLUS, ".R" for R, and
".lsp" for XLispStat).
10. To run statistical processes under (X)Emacs:
Run S-PLUS 3.x with:
M-x S+3
(or M-x S using backwards compatibility). You will then be
asked for a pathname ("S starting data directory?"), from which
to start the process. Similarly for S-PLUS 5.x.
If you wish to run R, you can start it with:
M-x R
XLispStat can be run with
M-x XLS
SAS can be run with:
M-x SAS
11. That's it!
For Microsoft Windows installation, please follow the next steps:
(see separate instructions above for UNIX)
1. cd to a directory where you keep emacs lisp files, or create a
new directory (for example, `c:\emacs\') to hold the
distribution. This directory will be referred to below as "the
ESS distribution directory". It will contain, at the end,
either the tar file `ESS-5.1.19.tar.gz' or the zip file
`ESS-5.1.19.zip', and a directory for the ESS source, which
will be termed "the ESS-5.1.19 source directory".
2. Retrieve the compressed tar file `ESS-5.1.19.tar.gz' or the
zipped file `ESS-5.1.19.zip' from one of the FTP or WWW
archive sites via FTP (or HTTP). Be aware that http browsers
on Windows frequently change the "." and "-" characters in
filenames to other punctuation. Please change the names back
to their original form.
3. Copy `ESS-5.1.19.tar.gz' to the location where you want the
ESS-5.1.19 directory, for example to
`c:\emacs\ESS-5.1.19.tar.gz', and cd there. For example,
cd c:\emacs
Extract the files from the distribution, which will unpack
into a subdirectory, `ess-5.1.19'.
gunzip ESS-5.1.19.tar.gz
tar vxf ESS-5.1.19.tar
(or: `gunzip < ESS-5.1.19.tar.gz | tar vxf -' ).
(or: from the zip file: `unzip ESS-5.1.19.zip')
The `tar' command will extract files into the current directory.
Do not create `ess-5.1.19' yourself, or you will get an extra level
of depth to your directory structure.
4. Windows users will usually be able to use the
`lisp/ess-site.el' as distributed. Only rarely will changes
be needed.
5. Windows users will need to make sure that the directories
for the software they will be using is in the PATH
environment variable. On Windows 9x, add lines similar to
the following to your `c:\autoexec.bat' file:
path=%PATH%;c:\progra~1\spls2000\cmd
On Windows NT/2000, add the directories to the PATH using the
MyComputer menu. Note that the directory containing the
program is added to the PATH, not the program itself. One
such line is needed for each software program. Be sure to
use the abbreviation `progra~1' and not the long version with
embedded blanks. Use backslashes "\".
6. Add the line
(load "/PATH/ess-site")
to your .emacs (or _emacs) file (or default.el or
site-init.el, for a site-wide installation). Replace `/PATH'
above with the value of ess-lisp-directory as defined in
`ess-site.el'. Use forwardslashes `/'.
7. (OPTIONAL) If you are running Sqpe or R, you might consider
installing the database files. From within (X)Emacs, `C-x d'
to the directory containing ESS. Now:
M-x Sqpe+4
(get running. once you have reached the SPLUS prompt, do:)
M-x ess-create-object-name-db
(this will create the file `ess-s+4-namedb.el'; if it isn't
in the ESS directory, move it there).
Then, completions will be autoloaded and will not be regenerated
for every session.
For R, do the same, using
M-x R
and then `M-x ess-create-object-name-db' creating
`ess-r-namedb.el'; if it isn't in the ESS directory, move it
there).
8. For more information on using ESS in your daily work, see the
files doc/README.SPLUS4WIN, doc/README.S, doc/README.SAS, and
doc/README.XLispStat.
For the impatient, the quick version of usage follows:
9. To edit statistical programs, load the files with the
requisite extensions (".sas" for SAS, ".S" or "s" or "q" or
"Q" for S-PLUS, ".r" or ".R" for R, and ".lsp" for
XLispStat).
10. To run statistical processes under (X)Emacs:
Run S-PLUS 4.x or 2000 with:
M-x S+4
(or `M-x S'). You will then be asked for a pathname
("S starting data directory?"), from which to start the
process. The prompt will propose your current directory as
the default. Similarly for S-PLUS 6.x. Send lines or regions
from the emacs buffer containing your S program (for example,
`myfile.s') to the S-Plus Commands Window with the `C-c C-n'
or `C-c C-r' keys.
Run S-PLUS 4.x or 2000 inside an emacs buffer
M-x Sqpe+4
You will then be asked for a pathname ("S starting data
directory?"), from which to start the process. The prompt will
propose your current directory as the default. Similarly for
S-PLUS 6.x. Send lines or regions from the emacs buffer
containing your S program (for example, `myfile.s') to the
*S+4* buffer with the `C-c C-n' or `C-c C-r' keys. You do
not have access to interactive graphics in this mode.
You get Unix-like behavior, in particular the entire
transcript is available for emacs-style search commands.
If you wish to run R, you can start it with:
M-x R
XLispStat can not currently be run with
M-x XLS
Hopefully, this will change. However, you can still edit with
Emacs, and cut and paste the results into the XLispStat
*Listener* Window under Microsoft Windows.
SAS for Windows uses the batch access with function keys that is
described in `doc/README.SAS'.
SAS for Windows cannot be run with:
M-x SAS
Reason: we use ddeclient to interface with programs and SAS
doesn't provide the corresponding ddeserver capability.
11. That's it!
Reporting Bugs
==============
Please send bug reports, suggestions etc. to
<ESS-bugs@stat.math.ethz.ch>
The easiest way to do this is within Emacs by typing
`M-x ess-submit-bug-report'
This also gives the maintainers valuable information about your
installation which may help us to identify or even fix the bug.
Note that comments, suggestions, words of praise and large cash
donations are also more than welcome.
Mailing Lists
=============
There is a mailing list for discussions and announcements relating to
ESS. Join the list by sending an e-mail with "subscribe ess-help" (or
"help") in the body to <ess-help-request@stat.math.ethz.ch>;
contributions to the list may be mailed to
<ess-help@stat.math.ethz.ch>. Rest assured, this is a fairly
low-volume mailing list.
The purposes of the mailing list include
* helping users of ESS to get along with it.
* discussing aspects of using ESS on Emacs and XEmacs.
* suggestions for improvements.
* announcements of new [beta] releases of ESS.
* posting small patches to ESS.
Authors
=======
* A.J. Rossini (http://www.biostat.washington.edu/~rossini/)
<rossini@u.washington.edu>
* Richard M. Heiberger
(http://www.sbm.temple.edu/departments/statistics/)
<rmh@fisher.stat.temple.edu>
* Kurt Hornik (http://www.ci.tuwien.ac.at/~hornik)
<hornik@ci.tuwien.ac.at>
* Martin Maechler (http://stat.ethz.ch/~maechler/)
<maechler@stat.math.ethz.ch>
* Rodney Sparapani (http://www.mcw.edu/pcor/rsparapa)
<rsparapa@mcw.edu>