9. Help for Statistical Packages

9.1 Help for the S family
9.9 Help for SAS

9.1 Help for the S family

9.2 ESS[S]--Editing files
9.3 iESS[S]--Inferior ESS processes
9.4 Handling and Reusing Transcripts
9.5 ESS-help--assistance with viewing help
9.6 Philosophies for using ESS[S]
9.7 Scenarios for use (possibilities--based on actual usage)
9.8 Customization Examples and Solutions to Problems

9.2 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.

9.3 iESS[S]--Inferior ESS processes

• - 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 R

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

M-x S

Note that R has some extremely useful command line arguments, -v and -n. To enter these, call R using a "prefix argument", by

C-u M-x R

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

-v 10000 -n 5000

Then that R process will be started up using "R -v 10000 -n 5000".

New for ESS 5.1.2 (and later): "S-elsewhere" command

The idea of "M-x S-elsewhere" is that we open a telnet (or rlogin) to another machine, call the buffer "*S-elsewhere*", and then run S on the other machine in that buffer. We do that by defining "sh" as the inferior-S-elsewhere-program-name. Emacs sets it up in a "*S-elsewhere*" iESS buffer. The user does a telnet or login from that buffer to the other machine and then starts S on the other machine. The usual C-c C-n commands from myfile.s on the local machine get sent through the buffer "*S-elsewhere*" to be executed by S on the other machine.

9.4 Handling and Reusing Transcripts

9.5 ESS-help--assistance with viewing help

• move between help sections
• send examples to S for evaluation

9.6 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.

9.7 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")

9.8 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-s+3.el and essd-s4.el files to be "S" instead of "S4" and "S+3". This will insure 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.

9.9 Help for SAS

9.10 ESS[SAS]--Design philosophy
9.11 ESS[SAS]--Recommended autoexec.sas
9.12 ESS[SAS]--Editing files
9.13 iESS[SAS]--Inferior ESS processes
9.14 ESS[SAS]--Batch processes
9.15 ESS[SAS]--Function keys for batch processing
9.16 ESS[SAS]--TAB key
9.17 ESS[SAS]--Usage scenarios
9.18 ESS[SAS]--Common problems

ESS[SAS] (originally SAS-mode) was designed for use with SAS. SAS-mode was developed by Cook ftp://ftp.biostat.wisc.edu/pub/cook/sas-mode/sas.tar.gz. Those editing features and new advanced features are part of ESS[SAS]. The user interface of ESS[SAS] has similarities with ESS[S], the ESS interface for S, and to the SAS Display Manager. By _emacs_ we mean either GNU Emacs from the Free Software Foundation or XEmacs from the XEmacs Project.

9.10 ESS[SAS]--Design philosophy

ESS[SAS] mode was designed to aid the user in writing and maintaining input command files, such as myfile.sas, for SAS. These are files containing SAS statements. In a batch environment such files would be submitted to SAS by the operating system command:

sas myfile.sas

In a SAS window environment, these files would be brought into the "SAS: PROGRAM EDITOR" window and then submitted with the 'Local' 'Submit' menu commands.

The *SAS:1.log* buffer in ESStr mode corresponds to the file myfile.log in SAS batch usage and to the "SAS: LOG" window in the SAS window environment. All commands submitted to SAS, informative messages, warnings, and errors appear here.

The *SAS:1.lst* buffer in ESSlst mode corresponds to the file myfile.lst in SAS batch usage and to the "SAS: OUTPUT" window in the SAS window environment. All data related printed output from the PROCs appear in this window.

The iESS [SAS:1] buffer exists solely as a communications buffer. Files are edited in the myfile.sas buffer. The C-c C-r key in ESS[SAS] mode is the functional equivalent of bringing a file into the "SAS: PROGRAM EDITOR" window followed by the 'Local' 'Submit' menu commands. The user should never use this buffer directly.

The ESS[SAS] mode was written with two primary goals.

1. Using the emacs environment is desirable for users accessing a remote computer via a network or dial-up who can not use the native SAS window environment.

2. Using the emacs environment is desirable for local users as well due to the inherent efficiency of using the same superior interface all of the time.

9.11 ESS[SAS]--Recommended autoexec.sas

The default settings of the inferior-SAS-args in essd-sas.el are

-stdio -linesize 80 -noovp -nosyntaxcheck

with the interpretations:

-stdio required to make the redirection of stdio work -linesize 80 keeps output lines from folding on standard terminals -noovp prevents error messages from printing 3 times -nosyntaxcheck permits recovery after syntax errors

In addition there are several parameters that can't be set in the command line. For these, we recommend the following line appear in your autoexec.sas in your home directory:

options noovp pagesize=60 linesize=80 formdlim=' ';

Interpretations

noovp prevents error messages from printing 3 time pagesize=60 standard printed page length instead of window length linesize=80 keeps output lines from folding on standard terminals formdlim=' ' blank replaces "C-l" formfeeds to prevent mostly empty pages

The noovp and linesize=80 appear in both the inferior-SAS-args and in the autoexec.sas. The redundancy means that these options are in effect for both SAS interactive and batch jobs.

9.12 ESS[SAS]--Editing files

ESS[SAS] is the mode for editing SAS 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, or a single line to an inferior SAS process. - ability to switch between processes which would be the target of the buffer (for the above). - ability to save and submit the file you are working on as a batch SAS process with a single keypress and to continue editing while it is runs in the background. - capability of killing the batch SAS process through the shell buffer or allow the SAS process to keep on running after you exit emacs. - single keypress navigation of .sas, .log and .lst files (.log and .lst files are automatically refreshed with each keypress).

ESS[SAS], the mode for editing SAS language files, is automatically turned on when editing a file with a ".sas" suffix (or other, if specified in ess-site). The batch processing keypress commands are enabled by default to use the same function keys that the SAS Display Manager uses. The interactive capabilities of ESS require you to start an inferior SAS process with M-x SAS (described below).

At this writing (5.1.21), the indenting and syntactic highlighting are usually correct.

9.13 iESS[SAS]--Inferior ESS processes

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

To start up iESS[SAS] mode, use:

M-x SAS

We plan to add

- The ability to request help from a process for variables and functions, and to have the results sent into a separate buffer. - completion of object names and file names.

9.14 ESS[SAS]--Batch processes

The default command used by the Submit function key (F3 or F8) to submit a batch SAS job is simply "sas". If necessary, you can over-ride this in your .emacs file something like one of the following:

;;; (setq ess-sas-submit-command "nohup nice sas") ;; Unix ;;; (setq ess-sas-submit-command "c:/progra~1/sas/sas.exe") ;; Windows ;;; (setq ess-sas-submit-command "invoke SAS using program file") ;; Mac

Note that when you are specifying a path under Windows, you should avoid spaces (that is use "progra~1", not "Program Files") and you should use forward slashes "/". There may be occasions when you want to run a particular buffer under a different version of SAS or specify different options on the command line. In that case, you can over-ride ess-sas-submit-command in your local buffer with file variables or other means.

There is a built-in delay before a batch SAS job is submitted when using a Unix shell under either Unix or Windows. This is necessary in many cases since the shell might not be ready to receive a command. This delay is currently set high enough so as not to be a problem on any system. But, there may be cases when it needs to be set higher, or could be set much lower to speed things up. You can over-ride the default in your .emacs file by (the default of 5 seconds is shown):

(setq ess-sleep-for 5)

9.15 ESS[SAS]--Function keys for batch processing

The description of the setup for function keys for batch processing of SAS files is unavoidably more complex than we wish it were. The actual use of the function keys is simple. There are five distinct options:

1. (default) Function keys in ESS[SAS] modes do whatever they normally do in other emacs modes. Many users will have defined some of the keys [f2]-[f12] in their .emacs or _emacs file, or will have installation-wide definitions in their site-start.el file. By default, ESS does not override those definitions. This default is intended to make ESS[SAS] mode behave similarly to other emacs modes.

2,3,4,5. Users who are primarily familiar with SAS, and who are learning emacs as a way to approach SAS, will likely want to duplicate the function key capabilities that SAS Institute provides with its Display Manager. There are still options.

1. SAS provides different function key definitions with its PC and Unix products; ESS can use either.
2. The ESS[SAS] function key definitions can be active in all buffers (global) or limited (local) only to buffers that have SAS-related file extensions: .sas, .log, .lst, filetype-1 (which defaults to .txt), and filetype-2 which defaults to .dat.

The distinction between local and global appears subtle. If you want the ESS[SAS] definitions to work when you are in *shell* or when editing files other than the file extensions that SAS recognizes, you will most likely want to use the global definitions. If you want your function keys to understand SAS batch commands when you are editing SAS files, and to behave normally when editing other files, then you will choose the local definitions.

The option can be chosen by the person installing ESS for a site or by an individual.

1. The site manager can uncomment only one of the following lines. ESS[SAS] Function keys are available in ESS[SAS] and related modes if you uncomment either of the following lines in your ess-site.el:

   ;;2; (setq ess-sas-local-unix-keys t) ;;3; (setq ess-sas-local-pc-keys t)

   ESS[SAS] Function keys are available in all emacs modes if you uncomment either of the following lines in your ess-site.el:

   ;;4; (setq ess-sas-global-unix-keys t) ;;5; (setq ess-sas-global-pc-keys t)

   The names -unix- and -pc- have nothing to do with the operating system that you are running. Rather they mimic the definitions that the SAS Display Manager uses by default on those platforms.

2. The option can be selected by an individual by adding a line to the .emacs (or _emacs) file, immediately following the

   (load "ess-site")

   line. If your site manager has chosen an option 2,3,4,5 you don't want, you must turn it off before selecting a different option. To turn off an option, add the appropriate line (uncommented) to your .emacs (_emacs) file.

   ;;2; (setq ess-sas-local-unix-keys nil) ;;3; (setq ess-sas-local-pc-keys nil) ;;4; (setq ess-sas-global-unix-keys nil) ;;5; (setq ess-sas-global-pc-keys nil)

Finally, we get to what the function keys actually do. You may recognize some of the Short Names as SAS Display Manager commands (they are in all capitals).

Unix PC Short Name Long Description F2 F2 refresh revert the current buffer with the file of the same name if the file is newer than the buffer. F3 F8 SUBMIT save the current .sas file (which is either the .sas file in the current buffer or the .sas file associated with the .lst or .log file in the current buffer) and submit the file as a batch SAS job. C-F3 C-F8 SUBMIT-REGION Write region to temporary file, and submit to SAS. F4 F5 PROGRAM switch buffer to .sas file. F5 F6 LOG switch buffer to .log file, `refresh' and goto next error message, if any. C-F5 C-F6 APPEND-TO-LOG Append ess-temp.log to the current .log file. F6 F7 OUTPUT switch buffer to .lst file and `refresh'. C-F6 C-F7 APPEND-TO-OUTPUT Append ess-temp.lst to the current .lst file. F7 F4 filetype-1 switch buffer to filetype-1 (defaults to .txt) file and `refresh'. F8 F3 shell switch buffer to shell. F9 F9 VIEWTABLE open an interactive FSEDIT/FSBROWSE session on the SAS dataset near point F10 F10 toggle-log toggle ESS[SAS] for .log files; may be useful for certain debugging situations F11 F11 filetype-2 switch buffer to filetype-2 (defaults to .dat) file and refresh. F12 F12 viewgraph open a GSASFILE near point for viewing either in emacs or with an external viewer

Besides the keys that mimic SAS Display Manager commands, five other keys have been provided for convenience. `shell' switches you to the *shell* buffer where you can type operating system commands. This is especially helpful if you would like to kill a SAS batch job. F2 performs the `refresh' operation on the current buffer. `refresh' compares the buffer date/time stamp with the file date/time stamp and replaces the buffer with the file if the file is newer. This is the same operation that is automatically performed when LOG, OUTPUT, `filetype-1' or `filetype-2' are pressed. `filetype-1' switches you to a file with the same file root as your .sas file, but with a different extension; .txt by default. `filetype-2' is similar, except it is .dat by default. You can over-ride the default, by specifying a different extension in your .emacs file. For example, for `filetype-1':

(setq ess-sas-suffix-1 "txt")

F10 toggles ESS[SAS] mode for .log files which is off by default (technically, it is SAS-log-mode, but it looks the same). The syntax highlighting can be helpful in certain debugging situations, but large .log files will take a long time to render. F12 will open a GSASFILE near point for viewing either with emacs or with an external viewer. Depending on your version of emacs and the operating system you are using, emacs may support .gif and .jpg files internally. You may need to change the following two variables for your own situation:

(setq ess-sas-graph-suffix-regexp "[.]\\(e?ps\\|gif\\|jpe?g\\|tiff?\\)") (setq ess-sas-image-viewer "kodakimg") ;; external viewer

9.16 ESS[SAS]--TAB key

Again, two options.

The TAB key is bound by default to sas-indent-line. This function is used to syntactically indent SAS code so PROC and RUN are in the left margin, other statements are indented 4 spaces from the margin, continuation lines are indented 4 spaces in from the beginning column of that statement. This is the type of functionality that emacs provides in most programming language modes. This functionality is equivalent to uncommenting the following line in ess-site.el:

;;; (setq ess-sas-edit-keys-toggle 0)

ESS provides an alternate behavior for the TAB key that makes it behave as it does on non-emacs terminals, i.e. move the cursor to the next tab stop. The alternate behavior also provides a backwards TAB key: C-TAB. This functionality is obtained by uncommenting the following line in ess-site.el:

;;; (setq ess-sas-edit-keys-toggle 1)

Under the alternate behavior, the TAB key is bound to tab-to-tab-stop and the tab stops are set by default at multiples of 4.

9.17 ESS[SAS]--Usage scenarios

We present one scenario for using ESS to interact with SAS. 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 "##").

Batch SAS (-unix-keys illustrated, pc-keys in the comments)

## Find the file you want to work with C-x C-f myfile.sas ## myfile.sas will be in ESS[SAS] mode ## Edit as appropriate, then save and submit the batch SAS job. ## -pc- F8 F3 ## The job runs in the shell buffer while you continue to edit ## myfile.sas. If you are running a Unix shell under Unix or ## Windows, the message buffer will notify you with a shell ## notification when the job is complete. If so, then you ## will also have the option of terminating the batch job ## before it is finished. ## -pc- F3 F8 ## In any case, you may want to visit the .log while the process ## is still running (unix only) or when it is done and check for ## error messages ## (you will be taken to the next error message, if any). ## The .log will be refreshed and you will be placed in it's buffer. ## -pc- F6 F5 ## Now, refresh the .lst and go to it's buffer. ## -pc- F7 F6 ## If you wish to make changes, go to the .sas file with ## -pc- F5 F4 ## make your editing changes and then submit again.

Interactive SAS

## Find the file you want to work with C-x C-f myfile.sas ## myfile.sas will be in ESS[SAS] mode ## Edit as appropriate, and then start up SAS with the cursor in ## the myfile.sas buffer M-x SAS ## Four buffers will appear on screen: ## myfile.sas in ESS[SAS] mode # your source file ## *SAS:1* in iESS [SAS:1] mode # ESS communication buffer ## *SAS:1.log* in Shell [] ESStr mode # SAS log information ## *SAS:1.lst* in Shell [] ESSlst mode # SAS listing information ## If you would prefer each of the four buffers to appear in its ## own individual frame, you can arrange for that. Place the ## cursor in the buffer displaying myfile.sas. Enter the ## sequence: C-c C-w ## The cursor will normally be in buffer myfile.sas. ## If not, put it there: C-x b myfile.sas ## Send regions, lines, or the entire file contents to SAS ## (regions are most useful). A highlighted region will normally ## begin with the keywords 'DATA' or 'PROC' and end with the ## keyword 'RUN;' C-c C-r ## Information appears in the log buffer, analysis results in the ## listing buffer. In case of errors, make the corrections in the ## myfile.sas buffer and resubmit with another C-c C-r ## PROC GPLOT graphs will normally be produced in a postscript ## file and be viewed later. Include the lines /* required gsoptions for batch files */ /* comment out these lines for interactive use on X-terminals*/ filename grafout 'temp.ps'; goptions device=ps gsfname=grafout gsfmode=append gaccess=sasgastd; ## in myfile.sas. ## PROC PLOT graphs can be viewed in the listing buffer. You may ## wish to control the vertical spacing to allow the entire plot ## to be visible on screen, for example, by proc plot; plot a*b / vpos=25; ## At the end of the session you may save the log and listing ## buffers with the usual C-x C-s commands. You will be prompted ## for a file name. Typically, the names myfile.log and mfile.lst ## will be used. You will almost certainly want to edit the saved ## files before including them in a report. The files are ## read-only by default. You can make them writable by the emacs ## command C-x C-q. ## At the end of the session, the input file myfile.sas will ## typically have been revised. You can save it. It can be used ## later as the beginning of another iESS[SAS] session. It can ## also be used as a batch input file to SAS. ## The *SAS:1* buffer is strictly for ESS use. The user should ## never need to read it or write to it. Refer to the .lst and ## .log buffers for monitoring output!

Here is a typical myfile.sas:

title 'Analysis of Case 0502'; data case0502; infile '/home/public/stat/Data/case0502.asc' firstobs=2; input percent code; run; proc glm; class code; model percent=code /ss1; run;

9.18 ESS[SAS]--Common problems

1. If M-x SAS gives weird errors upon startup, check the following: - you are running Windows: SAS does not support stdio on Windows - ess-sas-sh-command (in the ESS source directory) needs to be executable (solution: "chmod ugo+rx ess-sas-sh-command"). - sas isn't in your executable path (verify using "which sas" from a shell command-line) - you need a copy of SAS (we can't solve this) 2. M-x SAS starts up SAS in the window system (motif, for example), instead of starting it up in the emacs buffers. Probably the unix command "sas" on your system calls a local script which in turn calls the sas executable. The fix is to call the sas executable directly. Change the line in ess-sas-sh command from:   sas </dev/tty 1>$stdout 2>$stderr $  to a call to the complete path name of the sas executable on your system, for example:   /usr/local/sas612/sas </dev/tty 1>$stdout 2>$stderr $  To find the complete path name on your system, you can execute the line (from the unix prompt):   find / -name 'sas' -exec ls -ld {} \; and expect a response similar to the following   -rwxr-xr-x 1 sas sas 2441216 Sep 9 1997 /usr/local/sas612/sas