This is ess.info, produced by makeinfo version 4.2 from ess.texi. ESS -- Emacs Speaks Statistics ****************************** START-INFO-DIR-ENTRY * ESS: (ess). Emacs Speaks Statistics (S/S+/R, SAS, BUGS, Stata, XLisp-Stat). END-INFO-DIR-ENTRY  File: ess.info, Node: Top, Next: Introduction, Prev: (dir), Up: (dir) ESS: Emacs Speaks Statistics **************************** ESS version 5.2.1 (Documentation $Revision: 1.6 $ $Date: 2004/07/04 17:20:36 $). by A.J. Rossini, R.M. Heiberger, K. Hornik, M. Maechler, R.A. Sparapani and S.J. Eglen. Emacs Speaks Statistics (ESS) provides an intelligent, consistent interface between the user and the software. ESS interfaces with SAS, S-PLUS, R, BUGS and other statistical analysis packages under the Unix, Microsoft Windows, and Apple Mac operating systems. ESS is itself a package within the emacs text editor and uses emacs features to streamline the creation and use of statistical software. ESS knows the syntax and grammar of statistical analysis packages and provides consistent display and editing features based on that knowledge. ESS assists in interactive and batch execution of statements written in these statistical analysis languages. * Menu: * Introduction:: Overview of features provided by this package * Installation:: Installing ESS on your system * Interactive ESS:: Interacting with statistical programs * Help for the S family:: * Help for SAS:: * Help for BUGS:: * Entering commands:: Interacting with the process buffer * Editing:: How to create or edit S objects or functions * Help:: Reading help files in ESS * Transcript Mode:: Manipulating saved transcript files * Miscellaneous:: Other features of ESS * Bugs Etc:: * Customization:: Customizing ESS * Key Index:: * Concept Index:: * Variable and command index::  File: ess.info, Node: Introduction, Next: Installation, Prev: Top, Up: Top Introduction to ESS ******************* The S family (S, Splus and R) and SAS statistical analysis packages provide sophisticated statistical and graphical routines for manipulating data. Emacs Speaks Statistics (ESS) is based on the merger of two pre-cursors, S-mode and SAS-mode, which provided support for the S family and SAS respectively. Later on, Stata-mode was also incorporated. ESS provides a common, generic, and useful interface, through emacs, to many statistical packages. It currently supports the S family, SAS, BUGS, Stata and XLisp-Stat with the level of support roughly in that order. A bit of notation before we begin. _emacs_ refers to both _GNU Emacs_ by the Free Software Foundation, as well as _XEmacs_ by the XEmacs Project. The emacs major mode `ESS[language]', where `language' can take values such as `S', `SAS', or `XLS'. The inferior process interface (the connection between emacs and the running process) referred to as inferior ESS (`iESS'), is denoted in the modeline by `ESS[dialect]', where `dialect' can take values such as `S3', `S4', `S+3', `S+4', `S+5', `S+6', `R', `XLS', `VST', `SAS'. Currently, the documentation contains many references to ``S'' where actually any supported (statistics) language is meant, i.e., `S' could also mean `XLisp-Stat' or `SAS'. For exclusively interactive users of S, ESS provides a number of features to make life easier. There is an easy to use command history mechanism, including a quick prefix-search history. To reduce typing, command-line completion is provided for all S objects and "hot keys" are provided for common S function calls. Help files are easily accessible, and a paging mechanism is provided to view them. Finally, an incidental (but very useful) side-effect of ESS is that a transcript of your session is kept for later saving or editing. No special knowledge of Emacs is necessary when using S interactively under ESS. For those that use S in the typical edit-test-revise cycle when programming S functions, ESS provides for editing of S functions in Emacs edit buffers. Unlike the typical use of S where the editor is restarted every time an object is edited, ESS uses the current Emacs session for editing. In practical terms, this means that you can edit more than one function at once, and that the ESS process is still available for use while editing. Error checking is performed on functions loaded back into S, and a mechanism to jump directly to the error is provided. ESS also provides for maintaining text versions of your S functions in specified source directories. * Menu: * Features:: Why should I use ESS? * New features:: * Credits:: Authors of and contributors to ESS * Latest version:: Getting the latest version of ESS * Manual:: How to read this manual  File: ess.info, Node: Features, Next: New features, Prev: Introduction, Up: Introduction Why should I use ESS? ===================== S is a powerful system for manipulating and analyzing data, but its user interface -- particularly on Unix platforms -- leaves something to be desired. ESS is a package which is designed to make S easier to use. ESS provides several features which make it easier to interact with the ESS process (i.e. enter commands and view the output). These include: * Command-line editing for fixing mistakes in commands before they are entered. The `-e' flag for S-plus provides something similar to this, but here you have the full range of Emacs commands rather than a limited subset. However, other packages such as XLisp-Stat and S3 do not necessarily have features like this built-in. *Note Command-line editing::. * Searchable command history for recalling previously-submitted commands. This provides all the features of the `Splus -e' history mechanism, plus added features such as history searching. *Note Command History::. * Command-line completion of both object and file names for quick entry. This is similar to `tcsh''s facility for filenames; here it also applies to object names and list components. *Note Completion::. * Hot-keys for quick entry of commonly-used commands in `S' such as `objects()' and `search()'. *Note Hot keys::. * Transcript recording for a complete record of all the actions in an S session. *Note Transcript::. * Interface to the help system, with a specialized mode for viewing S help files. *Note Help::. If you commonly create or modify S functions, you will have found the standard facilities for this (the `fix()' function, for example) severely limiting. Using S's standard features, one can only edit one function at a time, and you can't continue to use S while editing. ESS corrects these problems by introducing the following features: * 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. *Note Edit buffer::. * A specialized editing mode for S code, which provides syntactic indentation and highlighting. *Note 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. *Note Error Checking::. * Source code revision maintenance, which allows you to keep historic versions of S source files. *Note Source Files::. * Facilities for evaluating S code such as portions of source files, or line-by-line evaluation of files (useful for debugging). *Note Evaluating code::. Finally, ESS provides features for re-submitting commands from saved transcript files, including: * Evaluation of previously entered commands, stripping away unnecessary prompts. *Note Transcript resubmit::.  File: ess.info, Node: New features, Next: Credits, Prev: Features, Up: Introduction New features in ESS =================== Changes/New Features in 5.2.2: * ESS[R]: If you have other versions of R on your exec-path, such as "R-1.8.1" with Unix or "rw1081" with Windows, ESS will find them and create appropriate functions, such as M-x R-1.8.1 or M-x rw1081, for calling them. By default only Unix programs beginning "R-1" and "R-2" and Windows programs parallel to the version of R in your exec-path will be found, but see ess-r-versions and ess-rterm-versions for ways to find other versions of R. * ESS[R]: Other versions of R, such as "R-1.8.1" on Unix and "rw1081" on Windows, are added to the "ESS / Start Process / Other" menu. * ESS[S]: If you have other versions of S-Plus on your Windows computer, such as S-Plus 6.1 or S-Plus 4.5, ESS will find them and create appropriate functions, such as M-x splus61, for calling the console version (Sqpe) inside an emacs buffer. By default only programs installed in the default location will be found, but see ess-SHOME-versions for ways to find other versions of S-Plus. * ESS[S]: Other versions of Sqpe on Windows, such as "splus61", are added to the "ESS / Start Process / Other" menu. * ESS[R]: (bug fix) ess-quit (bound to C-c C-q) should now quit the inferior R process, when issued from either the inferior buffer, or from a .R buffer. Changes/New Features in 5.2.1: * ESS[S] (R and S-plus): now have toolbar support with icons to evaluate code in the inferior process or to switch there. This code is experimental and likely to change as XEmacs/Emacs issues get resolved. The toolbar should be enabled if your Emacs displays images, but can be disabled with the variable ess-use-toolbar. Thanks to David Smith from Insightful for the S-plus logo. * ESS[SAS]: ess-sas-graph-view (F12) enhanced; you can specify external file viewers for each graphics file type via the alist ess-sas-graph-view-viewer-alist; also .jpg/.gif are now handled by image-mode on XEmacs, if available, otherwise by graphics primitives as before Changes/New Features in 5.2.0: * ESS[BUGS]: new info documentation! now supports interactive processing thanks to Aki Vehtari (mailto:Aki.Vehtari@hut.fi); new architecture-independent unix support as well as support for BUGS v. 0.5 * ESS[SAS]: convert .log to .sas with ess-sas-transcript; info documentation improved; Local Variable bug fixes; SAS/IML statements/functions now highlighted; files edited remotely by ange-ftp/EFS/tramp are recognized and pressing SUBMIT opens a buffer on the remote host via the local variable ess-sas-shell-buffer-remote-init which defaults to "ssh"; changed the definition of the variable ess-sas-edit-keys-toggle to boolean rather than 0/1; added the function ess-electric-run-semicolon which automatically reverse indents lines containing only "run;"; C-F1 creates MS RTF portrait from the current buffer; C-F2 creates MS RTF landscape from the current buffer; C-F9 opens a SAS DATASET with PROC INSIGHT rather than PROC FSVIEW; C-F10 kills all buffers associated with .sas program; "inferior" aliases for SAS batch: C-c C-r for submit region, C-c C-b for submit buffer, C-c C-x for goto .log; C-c C-y for goto .lst * ESS[S]: Pressing underscore ("_") once inserts " <- " (as before); pressing underscore twice inserts a literal underscore. To stop this smart behaviour, add "(ess-smart-underscore nil)" to your .emacs after ess-site has been loaded; ess-dump-filename-template-proto (new name!) now can be customized successfully (for S language dialects); Support for Imenu has been improved; set ess-imenu-use-S to non-nil to get an "Imenu-S" item on your menubar; ess-help: Now using nice underlines (instead of `nuke-* ^H_') * ESS[R]: After (require 'essa-r), M-x ess-r-var allows to load numbers from any Emacs buffer into an existing *R* process; M-x ess-rdired gives a "directory editor" of R objects; fixed ess-retr-lastvalue-command, i.e. .Last.value bug (thanks to David Brahm) * ESS: Support for creating new window frames has been added to ESS. Inferior ESS processes can be created in dedicated frames by setting inferior-ess-own-frame to t. ESS help buffers can also open in new frames; see the documentation for ess-help-own-frame for details. (Thanks to Kevin Rodgers for contributing code.) Changes/New Features in 5.1.24: * The version number is now correct even inside ESS/Emacs Changes/New Features in 5.1.23: * Minor more Makefile clean up. Changes/New Features in 5.1.22: * Besides info documentation, PDF and HTML documentation are also provided (instead of built using "make") and available on the web as well; see ESS web page (http://software.biostat.washington.edu/ess/doc) and StatLib (http://lib.stat.cmu.edu/general/ESS/doc) * Now that info documentation is available, the README.* files are no longer supported. However, they are still distributed for what it's worth. * ESS is now an XEmacs package! See XEmacs Installation HOWTO (http://www.xemacs.org/Install/index.html) for details (specifically, items 10-15). * ESS[SAS]: more user-friendly enhancements for remote SAS batch jobs with Kermit file transfers (LOG and OUTPUT function key features now supported). Multiple shells now supported so you can run SAS on different computers from different buffers by setting the buffer-local variable ess-sas-shell-buffer to unique buffer names. * Major re-vamping of Makefile/Makeconf. Changes/New Features in 5.1.21: * ESS[SAS]: info documentation now available!, see ESS->Help for SAS; F12 opens GSASFILE nearest point for viewing either within emacs, when available, or via an external viewer; more syntax highlighting keywords; more enhancements for remote SAS batch jobs with Kermit; new framework for remote SAS interactive jobs, see ess-remote * ESS[S]: info documentation now available!, see ESS->Help for the S family * Makefile: tag now independent of rel; info files made by doc/Makefile and installed in new info sub-directory Changes/New Features in 5.1.20: * New `options()$STERM' in the S dialects (S, S-Plus, R). The S program can determine the environment in which it is currently running. ESS sets the option to `iESS' or `ddeESS' when it starts an S language process. We recommend other specific values for S language processes that ESS does not start. * New `ess-mouse-me' function, assigned to S-mouse-3 by default. User may click on a word or region and then choose from the menu to display the item, or a summary, or a plot, etc. This feature is still under development. * GNU Emacs 21.1 is now supported (fixed for S dialects, SAS & BUGS), (some from Stephen Eglen). * XEmacs 21.x is now supported (fixed w32-using-nt bug) * XEmacs on Win (NT) is better supported. * Workaround for bug in Sqpe+6 (S-PLUS 6 for Win). * should now work even when imenu is not available (for old Xemacsen). * ESS[SAS]: XEmacs-Imenu fix; C-TAB is globalized along with your function-key definitions, if specified; you can specify your SAS library definitions outside of autoexec.sas for ess-sas-data-view with SAS code placed in the variable ess-sas-data-view-libname, also the dataset name is defaulted to the nearest permanent dataset to point; Speedbar support now works for permanent datasets, please ignore first./last.; new font-locking is now the default with more improvements for font-locking PROCs, macro statements, * ; and %* ; comments; you can toggle sas-log-mode with F10 which will font-lock your .log (if it isn't too big); submit remote .sas files accessed with ange-ftp, EFS or Tramp (Kermit is experimental) by setting ess-sas-submit-method to 'sh; ess-sas-submit-command and ess-sas-submit-command-options are buffer-local so you can have local file variable sections at the end of your .sas files to request different executables or specify special options and the local file variables are re-read at submit instead of only at file open so that if you make a change it is picked up immediately; * ESS[BUGS]: font-lock with `in' fixed. * for STATA: font-lock bug fixed. * for Rd mode: C-c C-v and `switch-process' in menu. further, C-c C-f prefix (Rd-font) for inserting or surrounding a word by things such as \code{.}, \code{\link{.}}, \emph{.} etc. * new functions (ess-directory-function) and (ess-narrow-to-defun) ess-directory <-> default-directory logic (Jeff Mincy). * Re-organized Makefile and fixed a few bugs. Changes/New Features in 5.1.19: * S+6 now supported (Tony Rossini (Unix) and Rich Heiberger (Windows)) * 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) * 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) * Many small (and large) fixes/contributions (MMaechler) * 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) 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 and Rodney Sparapani) * Customize support (for most Emacsen which support it) (AJRossini) * ARC and ViSta support out of the box, and fixes for XLispStat (AJRossini) 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. 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 and Rich Heiberger. Changes/New Features in 5.1.11: * More fixes to Stata mode, thanks to Brendan Halpin (mailto: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 (mailto:brahm@alum.mit.edu). * Fixes to SAS mode, thanks to Rodney Sparapani 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.  File: ess.info, Node: Credits, Next: Latest version, Prev: New features, Up: Introduction Authors of and contributors to ESS ================================== The ESS environment is built on the open-source projects of many contributors, dating back nearly 15 years. Doug Bates and Ed Kademan wrote S-mode in 1989 to edit S and Splus files in GNU Emacs. Frank Ritter and Mike Meyer added features, creating version 2. Meyer and David Smith made further contributions, creating version 3. For version 4, David Smith provided process interaction based on Olin Shivers' comint package. John Sall wrote GNU Emacs macros for SAS source code around 1990. Tom Cook added more functionality creating SAS-mode which was distributed in 1994. Also in 1994, A.J. Rossini extended S-mode to support XEmacs. Together with extensions written by Martin Maechler, this became version 4.7 and supported S, Splus, and R. In 1995, Rossini extended SAS-mode to work with XEmacs. In 1997, Rossini merged S-mode and SAS-mode into a single Emacs package for statistical programming; the product of this marriage was called ESS version 5. * The multiple process code, and the idea for `ess-eval-line-and-next-line' are by Rod Ball. * Thanks to Doug Bates for many useful suggestions. * Thanks to Martin Maechler for reporting and fixing bugs, providing many useful comments and suggestions, and for maintaining the S-mode mailing list. * Thanks to Frank Ritter for updates from the previous version, the menu code, and invaluable comments on the manual. * Thanks to Ken'ichi Shibayama for his excellent indenting code, and many comments and suggestions. * Last but definitely not least, thanks to the many beta testers of the S-mode and ESS mailing lists. _ESS_ version 5 is being developed and currently maintained by * A.J. Rossini (mailto:rossini@u.washington.edu) * Richard M. Heiberger (mailto:rmh@temple.edu) * Kurt Hornik (mailto:hornik@ci.tuwien.ac.at) * Martin Maechler (mailto:maechler@stat.math.ethz.ch) * Rodney A. Sparapani (mailto:rsparapa@mcw.edu) * Stephen Eglen (mailto:stephen@gnu.org)  File: ess.info, Node: Latest version, Next: Manual, Prev: Credits, Up: Introduction Getting the latest version of ESS ================================= The latest version of ESS is always available on the web at: ESS web page (http://www.analytics.washington.edu/downloads/ess/) or StatLib (http://lib.stat.cmu.edu/general/ESS/) There no longer is an anonymous CVS repository for ESS, due to lack of interest, little demand, and problems with security.  File: ess.info, Node: Manual, Prev: Latest version, Up: Introduction How to read this manual ======================= If you need to install ESS, read *Note Installation:: for details on what needs to be done before proceeding to the next chapter. In this manual we use the standard notation for describing the keystrokes used to invoke certain commands. `C-' means hold the CONTROL key while typing the character . `M-' means hold the META or EDIT or ALT key down while typing . If there is no META, EDIT or ALT key, instead press and release the ESC key and then type . All ESS commands can be invoked by typing `M-x command'. Most of the useful commands are bound to keystrokes for ease of use. Also, the most popular commands are also available through the emacs menubar, and finally, if available, a small subset are provided on the toolbar. Where possible, keybindings are similar to other modes in emacs to strive for a consistent user interface within emacs, regardless of the details of which programming language is being edited, or process being run. Some commands, such as `M-x R' can accept an optional `prefix' argument. To specify the prefix argument, you would type `C-u' before giving the command. e.g. If you type `C-u M-x R', you will be asked for command line options that you wish to invoke the R process with. Emacs is often referred to as a `self-documenting' text editor. This applies to ESS in two ways. First, limited documentation about each ESS command can be obtained by typing `C-h f'. For example, if you type `C-h f ess-eval-region', documentation for that command will appear in a separate *Help* buffer. Second, a complete list of keybindings that are available in each ESS mode and brief description of that mode is available by typing `C-h m' within an ESS buffer. Emacs is a versatile editor written in both C and lisp; ESS is written in the Emacs lisp dialect (termed `elisp') and thus benefits from the flexible nature of lisp. In particular, many aspects of ESS behaviour can be changed by suitable customization of lisp variables. This manual mentions some of the most frequent variables. A full list of them however is available by using the Custom facility within emacs. (Type `M-x customize-group RET ess RET' to get started.) *Note 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.  File: ess.info, Node: Installation, Next: Interactive ESS, Prev: Introduction, Up: Top Installing ESS on your system ***************************** The following section details those steps necessary to get ESS running on your system. * Menu: * Unix installation:: Installing ESS on your Unix system * Microsoft Windows installation:: Installing ESS on your MS Windows system * Requirements:: emacs, Operating Systems and Statistical Packages * System dependent:: Variables you may need to change We now discuss installation, which might happen under Unix or Microsoft Windows. First, we discuss Unix installation. *Note Unix installation::. For Microsoft Windows Installation please skip to the *Note Microsoft Windows installation::.  File: ess.info, Node: Unix installation, Next: Microsoft Windows installation, Up: Installation Unix installation ================= 1. cd to a directory where you want to install ESS, creating it if necessary. This directory will be referred to below as ESSDIR. 2. Retrieve the latest version from gzipped tar file (http://www.analytics.washington.edu/downloads/ess/ess-VERSION.tar.gz) to ESSDIR. 3. Decompress/unarchive the files from the disribution. gunzip ess-VERSION.tar.gz tar xvf ess-VERSION.tar (or: `gunzip < ess-VERSION.tar.gz | tar xvf -' ). (or using GNU tar: `tar zxvf ess-VERSION.tar.gz'). The `tar' command will create the subdirectory ess-VERSION and unarchive the files there. If you are using GNU Emacs 19.29, decompress/unarchive `ESSDIR/ess-VERSION/lisp/19.29.tar.gz', read `ESSDIR/ess-VERSION/lisp/19.29/README', follow the instructions and you might be able to get ESS to work. _Please note that GNU Emacs 19.29 is no longer supported_. For a list of supported versions of emacs, see *Note Requirements::. 4. Edit the file `ESSDIR/ess-VERSION/lisp/ess-site.el' as explained in the comments section of that file. 5. Add the line (load "ESSDIR/ess-VERSION/lisp/ess-site") to your user or system installation file (GNU Emacs uses `$HOME/.emacs' and XEmacs uses `$HOME/.xemacs/init.el' for the user initialization file. GNU Emacs uses default.el or site-init.el and XEmacs uses site-start.el for the system installation file). Alternatively, if ess-site.el is in your current Lisp path, you can do: (require 'ess-site) to configure emacs for ESS. 6. That's it! 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). 7. (OPTIONAL) If you are running S-PLUS or R, you might consider installing the database files. From within emacs, `C-x d' to the directory containing ESS. Now: M-x S+6 to get S running. Once you see the SPLUS prompt, do: M-x ess-create-object-name-db (this will create the file `ess-s+6-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. (OPTIONAL) READ THIS ITEM THOROUGHLY BEFORE STARTING: If you want to place the compiled files in other locations edit the LISPDIR and INFODIR entries in `Makeconf' in the ESSDIR/ess-VERSION directory (if you are using XEmacs, then you also need to edit the EMACS entry as follows: EMACS=xemacs). You can compile those files by: make all When that completes successfully, install the compiled files: make install This will install the compiled info files and lisp files. If you are an XEmacs user, then you should be done. If not, then you may have to edit/create the file `dir' that is found in the directory specified by `INFODIR': see the sample `dir' in ESSDIR/ess-VERSION/doc/info. If `dir' does not exist in `INFODIR', then the sample `dir' will be installed. _Note 1:_ It is assumed that GNU make will be used; otherwise, edit the ESSVERSION and ESSVERSIONTAG entries in `Makeconf' appropriately, e.g.: ESSVERSION=5.2.0 and ESSVERSIONTAG=ESS-5-2-0 _Note 2:_ ESS can be installed for XEmacs as an XEmacs package much more easily than what has been described anywhere above. However, the latest ESS version will not be available at the same time as an XEmacs package; generally, it can take weeks or months to appear in the latter format. For more information on installing ESS as an XEmacs package see Quickstart Package Guide (http://www.xemacs.org/Documentation/packageGuide.html).  File: ess.info, Node: Microsoft Windows installation, Next: Requirements, Prev: Unix installation, Up: Installation Microsoft Windows installation ============================== For Microsoft Windows installation, please follow the next steps: (see separate instructions above for UNIX *Note Unix installation::. 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-VERSION.tar.gz' or the zip file `ess-VERSION.zip', and a directory for the ESS source, which will be termed "the ESS-VERSION source directory". 2. Retrieve the compressed tar file `ess-VERSION.tar.gz' or the zipped file `ess-VERSION.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-VERSION.tar.gz' to the location where you want the ess-VERSION directory, for example to `c:\emacs\ess-VERSION.tar.gz', and cd there. For example, cd c:\emacs Extract the files from the distribution, which will unpack into a subdirectory, `ess-VERSION'. gunzip ess-VERSION.tar.gz tar xvf ess-VERSION.tar (or: `gunzip < ess-VERSION.tar.gz | tar xvf -' ). (or: from the zip file: `unzip ess-VERSION.zip') The `tar' command will extract files into the current directory. Do not create `ess-VERSION' 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/XP, add the directories to the PATH using the `My Computer/Control Panel/System/Advanced/Environment Variables' 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 `/'. (GNU Emacs uses the filename `%HOME%/.emacs' and XEmacs uses the filename `%HOME%/.xemacs/init.el' for the initialization file.) 7. 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). 8. To run statistical processes under emacs: To start the S-PLUS 6.x GUI from ESS under emacs: M-x S (or `M-x S+6'). 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. ESS will start the S-PLUS GUI. There will be slight delay during which emacs is temporarily frozen. ESS will arrange for communication with the S-PLUS GUI using the DDE protocol. 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. (If you are still using S-PLUS 4.x or 2000, then use `M-x S+4'.) To start an S-PLUS 6.x session inside an emacs buffer--and without the S-PLUS GUI: M-x Sqpe (or `M-x Sqpe+6'). 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. You get Unix-like behavior, in particular the entire transcript is available for emacs-style search commands. Send lines or regions from the emacs buffer containing your S program (for example, `myfile.s') to the *S+6* buffer with the `C-c C-n' or `C-c C-r' keys. Interactive graphics are available with Sqpe by using the java library supplied with S-PLUS 6.1 and newer releases. Enter the commands: library(winjava) java.graph() Graphs can be saved from the `java.graph' device in several formats, but not PostScript. If you need a PostScript file you will need to open a separate `postscript' device. (If you are still using S-PLUS 4.x or 2000, then use `M-x Sqpe+4'.) To connect to an already running S-PLUS GUI (started, for example, from the S-PLUS icon): M-x S+6-existing 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. ESS will arrange for communication with the already running S-PLUS GUI using the DDE protocol. 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. (If you are still using S-PLUS 4.x or 2000, then use `M-x S+4-existing'.) 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 *Note ESS(SAS)--MS Windows::. The user can also edit SAS files in an `ESS[SAS]' buffer and than manually copy and paste them into an Editor window in the SAS Display Manager. For Windows, inferior SAS in an `iESS[SAS]' buffer does not work on the local machine. It does work over a network connection to SAS running on a remote Unix computer. Reason: we use ddeclient to interface with programs and SAS doesn't provide the corresponding ddeserver capability. 9. (OPTIONAL) If you are running Sqpe or R, you might consider installing the database files. From within emacs, `C-x d' to the directory containing ESS. Now: M-x Sqpe+6 to get S running. Once you see the SPLUS prompt, do: M-x ess-create-object-name-db (this will create the file `ess-s+6-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). 10. That's it!  File: ess.info, Node: Requirements, Prev: Microsoft Windows installation, Up: Installation Requirements ============ ESS has been tested with * S-PLUS 3.3, 3.4, 4.5, 2000, 5.0, 5.1, 6.0, 6.1, 6.2 * R >=0.49 * S4 * SAS >=6.12 * BUGS 0.5, 0.603 * Stata >=6.0 * XLispStat >=3.50 on the following platforms * Linux (all) * Solaris/SunOS (all) * Microsoft Windows 95/98/NT/2000/XP (SPLUS 4.5/2000/6.*, R, SAS and BUGS) * Apple Mac OS (SAS for OS 9 and X11 R for OS X) with the following versions of emacs * GNU Emacs 20.3, 20.4, 20.5, 20.6, 20.7, 21.1, 21.3 * XEmacs 21.0, 21.1.13-14, 21.4.0-8, 21.4.9-13/21.5.17(1), 21.4.14-15; as of June 2004, ESS does not work with XEmacs Betas such as 21.5.17 * GNU Emacs <20.3 and XEmacs <21.0(2) ---------- Footnotes ---------- (1) requires the files.el patch to revert-buffer for the Local Variables updating problem (2) These releases of emacs are no longer supported, so an upgrade is recommended if you plan to use ESS. If you have GNU Emacs 19.29, see *Note Unix installation::. Also, note that the `custom' library bundled with Emacs 19.34 is too _old_, its API is incompatible with the `new custom' bundled with recent Emacsen. The `new custom' for Emacs 19.34 is available for download here (ftp://ftp.dina.kvl.dk/pub/Staff/Per.Abrahamsen/custom/custom-1.9962.tar.gz).  File: ess.info, Node: System dependent, Prev: Installation, Up: Installation Variables you may need to change ================================ If you run the S program (from the shell) with a command other than `Splus' you will need to set the variable `inferior-ess-program' to the name of the appropriate program by including a line such as (setq inferior-ess-program "S+") in your `.emacs' file (substituting `S+' for the name of your S program.) If you need to call this program with any arguments, the variable you need to set is dependent on the value of `inferior-ess-program'; for example if it is `"Splus"', set the variable `inferior-Splus-args' to a string of arguments to the `Splus' program. If `inferior-ess-program' has some other value, substitute the `Splus' part of `inferior-Splus-args' with the appropriate program name. There aren't many instances where you need to call S with arguments, however: in particular do not call the S program with the `-e' command-line editor argument since ESS provides this feature for you. If you are running Splus (the enhanced version of S from Statsci) you may also need to set the variable `S-plus' to `t'. If your value of `inferior-ess-program' is `"S+"' or `Splus' this will not be necessary, however; `S-plus' defaults to `t' in this case. Finally, if you use a non-standard prompt within S, you will need to set the variable `inferior-ess-prompt' to a regular expression which will match both the primary prompt (`"> "' by default) and the continuing prompt (default of `"+ "'.) The default value of this variable matches S's default prompts. For example, if you use (`"$ "') as your primary prompt (you have `options(prompt="$ ")' in your `.First' function), add the following line to your `.emacs': (setq inferior-ess-prompt "^\\(\\+\\|[^\\$]*\\$\\) *") You will also need to set the variable `inferior-ess-primary-prompt' to a regular expression which matches the primary prompt only. Do not anchor the regexp to the beginning of the line with `^'. Once again, the default value matches S's default prompt; in the example above the appropriate value would be `"[^\\$]*\\$ *"'. Once these variables are set appropriately, ESS should work on any system.  File: ess.info, Node: Interactive ESS, Next: Help for the S family, Prev: Installation, Up: Top Interacting with statistical programs ************************************* As well as using ESS to edit your source files for statistical programs, you can ESS to run these statistical programs. In this chapter, we mostly will refer by example to running S from within emacs. The emacs convention is to name such proceses running under its control as `inferior processes'. This term can be slightly misleading, in which case these processes can be thought of `interactive processes'. Either way, we use the term `iESS' to refer to the Emacs mode used to interact with statistical programs. * Menu: * Starting up:: * Multiple ESS processes:: * ESS processes on Remote Computers:: * S+elsewhere and ESS-elsewhere:: * Customizing startup::  File: ess.info, Node: Starting up, Next: Multiple ESS processes, Up: Interactive ESS Starting an ESS process ======================= To start an S session, simply type `M-x S RET'. S will then (by default) ask the question S starting data directory? Enter the name of the directory you wish to start S from (that is, the directory you would have `cd''d to before starting S from the shell). This directory should have a `.Data' subdirectory. You will then be popped into a buffer with name `*S*' which will be used for interacting with the ESS process, and you can start entering commands.  File: ess.info, Node: Multiple ESS processes, Next: ESS processes on Remote Computers, Prev: Starting up, Up: Interactive ESS Running more than one ESS process ================================= ESS allows you to run more than one ESS process simultaneously in the same session. Each process has a name and a number; the initial process (process 1) is simply named (using S-PLUS as an example) `S+3:1'. The name of the process is shown in the mode line in square brackets (for example, `[S+3:2]'); this is useful if the process buffer is renamed. Without a prefix argument, `M-x S' starts a new ESS process, using the first available process number. With a prefix argument (for R), `C-u M-x R' allows for the specification of command line options. You can switch to any active ESS process with the command `M-x ess-request-a-process'. Just enter the name of the process you require; completion is provided over the names of all running S processes. This is a good command to consider binding to a global key.  File: ess.info, Node: ESS processes on Remote Computers, Next: Customizing startup, Prev: Multiple ESS processes, Up: Interactive ESS ESS processes on Remote Computers ================================= ESS works with processes on remote computers as easily as with processes on the local machine. The recommended way to access a statistical program on remote computer is to start it from a telnet or ssh buffer and then connect ESS to that buffer. 1. Start a new telnet or ssh buffer and connect to the remote computer (e.g. use `M-x telnet' or `M-x ssh'; ssh.el is available at `ftp://ftp.splode.com/pub/users/friedman/emacs-lisp/ssh.el'). 2. Start the ESS process on the remote machine, for example with one of the commands `Splus', or `R', or `sas -stdio'. 3. Enter the ESS command `M-x ess-remote'. You will be prompted for a program name. Enter `sp6' or `r' or `sas' or another valid name. Your telnet process is now known to ESS. All the usual ESS commands (`C-c C-n' and its relatives) now work with the S language processes. For SAS you need to use a different command `C-c i' (that is a regular `i', not a `C-i') to send lines from your `myfile.sas' to the remote SAS process. `C-c i' sends lines over invisibly and lets SAS display them formatted correctly as in a SAS log file. 4. Graphics (interactive) on the remote machine. If you run X11 (*Note 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. *Note ESS(SAS)--Function keys for batch processing::, for more information on using the F12 key for displaying graphics files with SAS. Should you or a colleague inadvertently start a statistical process in an ordinary `*shell*' buffer, the `ess-remote' command can be used to convert it to an ESS buffer and allow you to use the ESS commands with it. We have two older commands, now deprecated, for accessing ESS processes on remote computers. *Note S+elsewhere and ESS-elsewhere::.