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ESS – Emacs Speaks Statistics

1. 41 ess eldoc abbreviation style 55 ess eldoc show on symbol sss 55 ess eval visibly sacldA t REIP IAS 33 ess execute in process buffer 30 ess fancy comments 0 eee cece eee 37 Concept Index E ER 41 A aborting S commande 32 arguments to 8 program oooocccccccccccccoo o 24 AU UDOIB 86 6adepadudon eee IRR ERO PE 16 auto complete cece cece eee ee eens 46 AULOSAVING cic dese ciate a neh dent eae 40 B DUE TOPS EEN 79 84 Q INTE 31 S Dira cda sar e rd Re gives pea 21 Search obras beonbenpie epu eh epa MESI E HS 31 45 SOU lus sot etigono Song OP eo vagas 33 36 SIBERM I anb cae eats Mae nod ONDE RIVE IS 31 ess first tab never complete 38 45 ess Zont Lock mode 000005 56 ess function template sss 36 ess handy commands 000000ee 55 ess keep dump files 40 ess R font lock keywords ooooccococococooo 56 Oss Search list EE 41 ess source directory lees 41 ess style alist i i x e ia Jb 38 ess switch to end of proc buffer 32 ess swv pdflatex commands 60 ess tab complete in script 37 EE 55 I Jnferior ese DrogTram oo 24 inferior R font lock keywords 56 R Rd indent level 0 eee eee eee 50 Re mode hook iiss sis isos REESEN re 50 Rd to help command ssssseses 50 eut 79 C cleaning e EE 31 COMME eit wr
2. 39 7 6 Maintaining S source Des 39 7 7 Names and locations of dump les 41 8 Reading help files oooooooo o 43 9 Completon eese 45 9 1 Completion of Object namen 45 9 2 Completion of function arguments 0c eee eee eee 46 9 3 Minibuffer completion 00 cece eee nee 46 9 4 Integration with auto complete package susrsrrurnnnna 46 9 5 Teiler pi EES E RR RE Shana ER Rr des 46 10 Developing with ESS 48 IO ESS tracebug aa e extr o santi deb 48 10 2 Editing documentation 49 10 2 1 Editing R documentation Rd Dies 49 10 2 2 Editing Roxygen documentation 51 10 3 ESS developer 52 11 Other ESS features and tools 55 IL JBIDOG cistitis des 55 11 2 Handy commande 55 11 3 Syntactic highlighting of buffers 02000 e eee 56 11 4 Parenthesis matchng eee eee eens 56 11 5 Using graphics with bp 57 11 5 1 Using ESS with the printer driver 57 11 5 2 Using ESS with windowing devices ooooccccooom o 57 11 5 3 Java Graphics Device 0 0 0 cece eee eee eens 57 E Imenus sca a 57 llo Toolbarzliiszie e dis 5T ILS KEE 58 W9 ele 58 11 10 Rutils oreet etm aaa 59 11 11 Interaction with Org mode 60 11 12 Support for Sweave in ESS and AUCTeX usuusuuu 60 ii 12 Overview of ESS features for the S family See Eeer 61 12 1 EE 61 12 2 iESS S Inferior ESS processes 0 e
3. to function arguments e ESS Menus for ESS and iESS have been reorganized and enriched with Tracebug and Developer submenus e ESS R ess developer and ess tracebug commands are available by default in ess dev map which is bound to C c d in ESS and iESS maps e ESS R eldoc truncates long lines whenever eldoc echo area use multiline p is non nil the default Set this variable to t if you insist on multiline eldoc See also ess eldoc abbreviation style e ESS R completion code pre caches arguments of heavy generics such as plot and print to eliminated the undesirable delay on first request e iESS Prompts in inferior buffers are now highlighted uniformly with comint highlight prompt face e ESS R R process no longer wait for the completion of input in inferior buffer Thus long running commands like Sys sleep 5 no longer stall emacs e ESS R S Stata Julia have specialized ess X post run hooks which are run at the end of subprocess initialization e ESS Stata All interactive evaluation commands work as expected On line comments are removed before the evaluation and multiline comments are skipped on C c C c and other interactive commands e ESS no longer auto connects to a subprocess with a different dialect than the current buffer s one e ESS ess arg function offset new line is now a list for all the ESS indentation styles which results in the following indentation after an open a lt s
4. ess eval region start end toggle message Command C c C r Sends the current region to the ESS process ess eval region and go start end vis Command C c M r Like ess eval region but additionally switches point to the ESS process Chapter 5 Sending code to the ESS process 34 ess eval buffer vis Command C c C b Sends the current buffer to the ESS process ess eval buffer and go vis Command C c M b Like ess eval buffer but additionally switches point to the ESS process All the above ess eval commands are useful for evaluating small amounts of code and observing the results in the process buffer for debugging purposes or for generating transcripts from source files When editing S functions it is generally preferable to use C c C 1 to update the function s value In particular ess eval buffer is now largely obsolete A useful way to work is to divide the frame into two windows one containing the source code and the other containing the process buffer If you wish to make the process buffer scroll automatically when the output reaches the bottom of the window you will need to set the variable comint scroll to bottom on output to others or t Chapter 6 Manipulating saved transcript files 35 6 Manipulating saved transcript files Inferior S mode records the transcript the list of all commands executed and their output in the process buffer which can be saved as a transcript file which should normally have the suffi
5. Chapter 4 Interacting with the ESS process 32 ESS sets options STERM ddeESS for independent S Plus for Windows processes run ning in the GUI and communicating with ESS via the DDE Microsoft Dynamic Data Exchange protocol through a ddeESS S buffer Other values of options STERM that we recommend are e length Fixed length xterm or telnet window e scrollable Unlimited length xterm or telnet window e server S Plus Stat Server e BATCH BATCH e Rgui R GUI e Commands S Plus GUI without DDE interface to ESS Additional values may be recommended in the future as new interaction protocols are created Unlike the values iESS and ddeESS ESS can t set these other values since the S language program is not under the control of ESS 4 7 Using emacsclient When starting R or S under Unix ESS sets options editor emacsclient Under Microsoft Windows it will use gnuclient exe rather than emacsclient but the same principle applies Within your R session for example if you have a function called iterator typing fix iterator will show that function in a temporary Emacs buffer You can then correct the function When you kill the buffer the definition of the function is updated Using edit rather than fix means that the function is not updated Finally the S function page x will also show a text representation of the object x in a temporary Emacs buffer 4 8 Other commands provided by inferior ESS The following
6. e ESS R Auto completion new variable ess ac R argument suffix to customize the Di Di insertion of trailing Defaults to e ESS Julia Added index apropos and web search to julia e ESS help More evaluation commands were added to ess help mode C c C c C M x etc Bug Fixes in 12 09 1 e ESShelp Multiple help pages with the same name are properly handled on C c C v e iESSremote Evaluation with ESS remote no longer freezes emacs e iESS comint previous prompt C c C p no longer stops on secondary prompt e ESS R iESS Sqpe S on Windows The options editor is now initialized to emacsclient instead of the previous gnuclient The user may need to add the line server start to the emacs initialization file enacsclient has been included with emacs since GNU Emacs 22 1 e ESS Rnw Fixed connection to R bug in 12 09 only e ESS Rnw Explicit ess swv stangle and ess swv sweave functions e ESS Rnw Fixed completion and smart underscore problems cause by unmatched e ESS R is more careful with the R code injection It now happens only once at the start of the session e ESS R Fixed auto scrolling the comint buffer on evaluation e ESS Julia Solve several indentation and word navigation problems Chapter 1 Introduction to ESS 10 ESS Julia Help system works again Changes New Features in 12 09 Due to XEmacs lacking some features that ESS requires ESS support of X Emac
7. nil will cause the truncation of doc string indifferent of the value of ess eldoc abbreviation style This way you can combine different filter levels with the truncation 11 2 Handy commands ess handy commands Command Request and execute a command from ess handy commands list ess handy commands User Option An alist of custom ESS commands available for call by ess handy commands and ess smart comma function Currently contains change directory ess change directory help index ess display index help object ess display help on object vignettes ess display vignettes objects ls ess execute objects Chapter 11 Other ESS features and tools 56 search ess execute search set width ess execute screen options install packages ess install packages library ess library setRepos ess setRepositories SOS ss sos Handy commands ess library ess install packages etc ask for item with com pletion and execute the correspond command ess sos is a interface to findFn function in package sos If package sos is not found ask user for interactive install 11 3 Syntactic highlighting of buffers ESS provides Font Lock see Section Using Multiple Typefaces in The Gnu Emacs Ref erence Manual patterns for Inferior S Mode S Mode and S Transcript Mode buffers Syntax highlighting within ESS buffers is controlled by ess font lock mode User Option Non nil means we use font lock support for ESS bu
8. Hook to be run when Rd mode is entered Rd indent level User Option The indentation of Rd code with respect to containing blocks Default is 2 Rd to help command User Option The shell command used for converting Rd source to help text Default is R CMD Rd2txt To automatically turn on the abbrev and font lock features of Rd mode add the following lines to one of your Emacs startup files Chapter 10 Developing with ESS 51 add hook Rd mode hook lambda abbrev mode 1 font lock mode 1 10 2 2 Editing Roxygen documentation The Roxygen R package makes it possible to keep the intended contents for Rd files as structured comments in the R source files Roxygen can then parse R files and generate appropriate Rd files from these comments fill the usage fields as well as updating NAMESPACE files See the Roxygen documentation found via http roxygen org for more information on its usage An example of an Roxygen entry for a simple R function can look like this Description of the function Further details about this function HH Otitle A title it param me all parameters must be listed and documented return Description of the return value 1H author The author myfun lt function me cat Hello me n The entry is immediately preceding the object to document and all lines start with the Roxygen prefix string in this case ESS provides support to edit these documentation entries by
9. Note for Windows and Mac OS X users The most straightforward way to install Emacs on your machine is by downloading all in one Emacs binary by Vincent Goulet Note for XEmacs users Due to XEmacs lacking some features that ESS requires ESS support of XEmacs ends with ESS 12 04 4 This decision will be re visited in the future as XEmacs continues to sync with GNU Emacs 2 2 License The source and documentation of 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 Chapter 2 Installing ESS on your system 20 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 PAR TICULAR PURPOSE See the GNU General Public License in the file COPYING in the same directory as this file for more details 2 3 Stability All recent released versions are meant to be release quality versions While some new fea tures are being introduced we are cleaning up and improving the interface We know that there are many remaining opportunities for documentation improvements but all contrib utors are volunteers and time is precious Patches or suggested fixes with bug reports are much appreciated 2 4 Requirements ESS is most likely to work with current recent versions of the following statistical
10. concatenated together and the resulting command is sent to the ESS process currently this is the only way to resubmit a multi line command to the ESS process in one go If the current line does not begin with prompt an error is signalled This feature coupled with the command based motion commands described above could be used as a primitive history mechanism ESS provides a more sophisticated mechanism however which is described in Section 4 3 Command History page 27 4 2 4 Keeping a record of your S session To keep a record of your S session in a disk file use the Emacs command C x C w write file to attach a file to the ESS process buffer The name of the process buffer will probably change to the name of the file but this is not a problem You can still use S as usual just remember to save the file before you quit Emacs with C x C s You can make ESS prompt you for a filename in which to save the transcript every time you start S by setting the variable ess ask about transfile to t See Section 3 5 Customizing startup page 23 We recommend you save your transcripts with filenames that end in St There is a special mode ESS transcript mode see Chapter 6 Transcript Mode page 35 for editing transcript files which is automatically selected for files with this suffix S transcripts can get very large so some judicious editing is appropriate if you are saving it in a file Use C c C o whenever a command produces exce
11. customization group to t Alternatively the same can be achieved by activating the entry AUCTeX Interface from the Sweaving Tangling submenu which toggles this variable on or off When the interface is activated new entries for Sweave ing and LaTeX ing thereafter are available from AUCTeX s Command menu Sweave ing can thus be done by C c C c Sweave RET without an inferior ESS process Similarly LaTeX ing can be done by C c C c LaTeXSweave RET In both cases the process can be monitored with C c C 1 TeX recenter output buffer Open the viewer with C c C v TeX view as usual in AUCTeX Chapter 12 Overview of ESS features for the S family 61 12 Overview of ESS features for the S family 12 1 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
12. 1 both refer to the first word of the previous command while and both refer to the last word in the previous command The format of word designators is as follows 0 The zeroth word i e the first one on the command line n The nth word where n is a number The first word i e the second one on the command line Chapter 4 Interacting with the ESS process 30 The last word xy A range of words y abbreviates 0 y Ld All the words except the zeroth word or nothing if the command had just one word the zeroth Peu Abbreviates x xx Like x but omitting the last word In addition you may surround the entire reference except for the first by braces to allow it to be followed by other non whitespace characters which will be appended to the expanded reference Finally ESS also provides quick substitution a reference like old new means the last command but with the first occurrence of the string old replaced with the string new the last is optional Similarly old means the last command with the first occurrence of the string old deleted again the last is optional To convert a history reference as described above to an input suitable for S you need to expand the history reference using the TAB key For this to work the cursor must be preceded by a space otherwise it would try to complete an object name and not be within a s
13. 1 ESS will inform you of this fact In this case you can jump directly to the line in the source file which caused the error by typing C c ess parse errors You will be returned to the offending file loading it into a buffer if necessary with point at the line S reported as containing the error You may then correct the error and reload the file Note that none of the commands in an S source file will take effect if any part of the file contains errors Sometimes the error is not caused by a syntax error loading a non existent file for example In this case typing C c will simply display a buffer containing S s error message You can force this behavior and avoid jumping to the file when there is a syntax error by passing a prefix argument to ess parse errors with C u C c 7 4 Indenting and formatting S code ESS provides a sophisticated mechanism for indenting S source code thanks to Ken ichi Shibayama Compound statements delimited by and are indented relative to their enclosing block In addition the braces have been electrified to automatically indent to the correct position when inserted and optionally insert a newline at the appropriate place as well Lines which continue an incomplete expression are indented relative to the first line of the expression Function definitions if statements calls to expression and loop constructs are all recognized and indented appropriately User variables are prov
14. For controlling the SAS batch commands you have the global variables ess sas data view libname and ess sas data view fsview command as well as the buffer local variable ess sas data view fsview statement If you have your SAS LIBNAME defined in autoexec sas then the defaults for these variables should be suffi cient Similarly C F9 will prompt you for the name of a permanent SAS dataset near point to be opened for viewing by PROC INSIGHT You can control the SAS batch command line with ess sas data view submit options For controlling the SAS batch commands you have the global variables ess sas data view libname and ess sas data view insight command as well as the buffer local variable ess sas data view insight statement 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 may take a long time to highlight F11 is the same as filetype 1 except it is dat by default F12 will prompt you for the name of a GSASFILE near the point in Log to be opened 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 variables for your own situation ess sas graph view suffix regexp is a regular expression of supported file t
15. Variable ess handy commands stores an alist of useful commands which are called by ess smart comma in the inferior buffer Currently containing change directory ess change directory help index ess display index help object ess display help on object vignettes ess display vignettes objects ls ess execute objects search ess execute search set width ess execute screen options install packages ess install packages library ess library setRepos ess setRepositories SOS ess sos Handy commands ess library ess install packages etc ask for item with com pletion and execute the correspond command ess sos is a interface to f indFn function in package sos If package sos is not found ask user for interactive install e ESS New dynamic mode line indicator Process status is automatically reflected in all mode lines of associated with the process buffers Particularly useful for displaying debug status of ess tracebug and developer status of ess developer in all associated buffers e ESS New ess completing read mechanism ESS uses ido completions whenever possible Variable ess use ido controls whether to use ido completion or not Active by default e ESS now supports comint fields for output and input detection This feature is not used by default but might be useful in the future e ESS S New custom variable inferior ess S prompt to customize prompt detection regular expression in the inferior ESS buffers You can cu
16. a buffer to work with C c C d my function HH a new buffer named yourloginname my function S will be created with an editable copy of the object The buffer is associated with the HH pathname tmp yourloginname my function S and will amlost certainly not exist after you log off HH enter program functions and code into work buffer and send HH 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 HH Return to the work buffer may may not be prefixed C x C b yourloginname my function S HH Fix the function that didn t work and resubmit by placing the HH cursor somewhere in the function and C c C f HH Or you could ve selected a region using the mouse or keyboard HH via setting point mark and C c C r HH Or you could step through line by line using C c C n HH Or just send a single line without moving to the next using C c C j HH To fix that error in syntax for the rchisq command get help 7H by C c C v rchisq 4 Data Analysis S object is real HH Start up S PLUS 3 x in a process buffer this will be S43 1 M x S 3 Work in the process buffer When you find an object that needs HH to be changed this could be a data frame or a variable or a 3 4 function dump it to a buffer Chapter 12 Overview of ESS features for the S family 66 C c C d my cool
17. as a dialect of the BUGS language via ESS JAGS Since BUGS and JAGS are quite similar ESS BUGS and ESS JAGS are necessarily similar ESS JAGS provides 4 features First JAGS syntax is described to allow for proper fontification of statements distributions functions commands and comments in JAGS model files command files and log files Second ESS creates templates for the command file from the model file so that a JAGS batch process can be defined by a single file Third ESS provides a JAGS batch script that allows ESS to set JAGS batch parameters Fourth key sequences are defined to create a command file and submit a JAGS batch process 15 1 ESS JAGS Model files Model files with the bug extension are edited in ESS BUGS mode if require ess bugs d was performed or edited in ESS JAGS mode if require ess jags d Three keys are bound for your use in ESS BUGS F2 C c C c and F2 performs the same action as it does in ESS SAS See Section 13 5 ESS SAS Function keys for batch processing page 70 C c C c performs the function ess bugs next action which you will use a lot Pressing it in an empty buffer for a model file will produce a template for you inserts the set operator lt ESS JAGS does not support replacement variables which were part of ESS BUGS Although replacement variables are an extremely convenient feature creating the elisp code for their operation was challenging So a more elisp ish approach wa
18. can be processed into a variety of formats including LaTEX HTML and plain text Rd format is described in section Rd format of the Writing R Extensions manual in the R distribution ESS has several features that facilitate editing Rd files Visiting an Rd file as characterized by its extension Rd will activate Rd Mode which provides several facilities for making editing R documentation files more convenient by helping with indentation insertions even doing some of the typing for you with Abbrev Mode and by showing Rd keywords strings etc in different faces with Font Lock Mode Note that R also accepts Rd files with extension rd to activate ESS Rd support for this extension you may need to add add to list auto mode alist rd Rd mode to one of your Emacs startup files Chapter 10 Developing with ESS 50 In Rd mode the following special Emacs commands can be used in addition to the standard Emacs commands C h m Describe the features of Rd mode LFD RET Reindent the current line insert a newline and indent the new line reindent then newline and indent An abbrev before point is expanded if abbrev mode is non nil TAB Indent current line based on its contents and on previous lines indent according to mode C c C e Insert a skeleton with Rd markup for at least all mandatory entries in Rd files Rd mode insert skeleton Note that many users might prefer to use the R function pro
19. causing emacs to hang during R debugging with ess eval visibly equal to t ESS fix in ess eval linewise that was causing emacs to recenter the prompt in visible window Chapter 1 Introduction to ESS 8 e ESS tracebug A better handling of Selection prompts and debug related singlekey commands e ESS fix a bug in ess switch process that was causing new selection to fail e ESS R Solve missing ess local process name bug in R dired e ESS SWV ess swv PDF doesn t ask for a command to run if there is only one command in ess swv pdflatex commands e ESS SWV ess swv weave gained an universal argument to allow for an interactive choice between available weavers sweave knitr e ESS ess eval and step functions go to next empty line at eob instead of staying at the last line Changes New Features in 12 09 1 e ESS Breaking Changes in Keys New keymaps ess doc map bound to C c C d ess extra map bound to C c C e ess dump object into edit buffer was moved on C c C e C d roxygen map was moved on C c C o and ess roxy update entry now resides on C c C o C o ess handy commands is not bound anymore ess dev map including ess tracebug and ess developer moved on C c C t C c C y is deprecated in favor of C c C z C z e ESS R new command ess describe object at point bound to C c C d C e repeat C e or eto cycle It was inspired by Erik Iverson s ess R object tooltip Customize ess describe at point met
20. deletion x will actually perform the deletion Chapter 11 Other ESS features and tools 59 11 10 Rutils Ess rutils builds up on ess rdired providing key bindings for performing basic R functions in the inferior ESS process buffer such as loading and managing packages object manipulation listing viewing and deleting and alternatives to help start and RSiteSearch that use the browse url Emacs function The library can be loaded using M x load file but the easiest is to include require ess rutils in your emacs Once R is started with M x R and if the value of the customizable variable ess rutils keys is true several key bindings become available in iESS process buffers ess rutils local pkgs Command C c C 1 List all packages in all available libraries ess rutils repos pkgs Command C c C r List available packages from repositories listed by getOptions repos in the current R session ess rutils update pkgs lib repos Command C c C u Update packages in a particular library lib and repository repos ess rutils apropos Command C c C a Search for a string using apropos ess rutils rm all Command C c C m Remove all R objects ess rutils objs Command C c C o Manipulate R objects wrapper for ess rdired ess rutils load wkspc Command C c C w Load a workspace file into R ess rutils save wkspc Command C c C s Save a workspace file ess change directory Command C c C d Chang
21. device ps gsfname gsasfile gsfmode append 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 proc plot plot a b vpos 25 run 13 9 ESS SAS Windows e ESS SAS does not work on Windows See Section 13 7 iESS SAS Common prob lems page 74 e ESS SAS mode for editing SAS language files works very well See Section 13 2 ESS SAS Editing files page 67 e There are two execution options for SAS on Windows You can use batch See Section 13 4 ESS SAS Batch SAS processes page 68 Or you can mark regions with the mouse and submit the code with submit region or paste them into SAS Display Manager Chapter 14 ESS for BUGS 76 14 ESS for BUGS ESS BUGS was originally designed for use with BUGS software Later it evolved to support JAGS as a dialect of the BUGS language via ESS JAGS however ESS JAGS is documented in the section Help for JAGS ESS BUGS provides 5 features First BUGS syntax is de scribed to allow for proper fontification of statements distributions functions commands and comments in BUGS model files command files and log files Second ESS creates tem plates for the command file from the model file so that a BUGS batch process can be defined by a single file Third ESS provides a BUGS batch script that allows ESS to set BUGS batch parameters Fourth key sequences are defined to creat
22. 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 12 5 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 44 Data Analysis Example source code is real Load the file you want to work with C x C f myfile s Chapter 12 Overview of ESS features for the S family 64 Edit as appropriate and then start up S PLUS 3 x M x S 3 A new buffer S43 1 will appear Splus will have been started HH in this buffe
23. ess default style C ess default style User Option The default value of ess style See the variable ess style alist for how these groups DEFAULT OWN GNU BSD map onto different settings for variables ess style alist User Option Predefined formatting styles for ESS code Values for all groups except OWN are fixed To change the value of variables in the OWN group customize the variable ess own style list The default style in use is controlled by ess default style The styles DEFAULT and OWN are initially identical If you wish to edit some of the default values set ess default style to OWN and change ess own style list See Appendix A Customization page 81 for convenient ways to set both these variables If you prefer not to use the custom facility you can change individual indentation vari ables within a hook for example Chapter 7 Editing objects and functions 39 defun myindent ess hook setq ess indent level 4 add hook ess mode hook myindent ess hook In the rare case that you d like to add an entire new indentation style of your own copy the definition of ess own style list to a new variable and ensure that the last line of the set declaration calls ess add style with a unique name for your style e g MINE Finally add setq ess default style MINE to use your new style 7 5 Commands for motion completion and more A number of commands are provided to move across function def
24. features for dealing with such plots 11 5 1 Using ESS with the printer driver This is the simplest and least desirable method of using graphics within ESS S s printer device driver produces crude character based plots which can be contained within the ESS process buffer itself To start using character graphics issue the S command printer width 79 the width 79 argument prevents Emacs line wrapping at column 80 on an 80 column terminal Use a different value for a terminal with a different number of columns Plotting commands do not generate graphics immediately but are stored until the show command is issued which displays the current figure 11 5 2 Using ESS with windowing devices Of course the ideal way to use graphics with ESS is to use a windowing system Under X Windows or X11 this requires that the DISPLAY environment variable be appropriately set 11 5 3 Java Graphics Device S 6 1 and newer on Windows contains a java library that supports graphics Send the commands library winjava java graph to start the graphics driver This allows you to use ESS for both interaction and graphics within S PLUS Thanks to Tim Hesterberg for this information 11 6 Imenu Imenu is an Emacs tool for providing mode specific buffer indexes In some of the ESS editing modes currently SAS and S support for Imenu is provided For example in S mode buffers the menubar should display an item called Imenu S Within
25. 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 Chapter 16 Bugs and Bug Reporting Mailing Lists 80 e helping users of ESS to get along with it e discussing aspects of using ESS on Emacs and XEmacs e suggestions for improvements e announcements of new releases of ESS e posting small patches to ESS 16 4 Help with emacs Emacs is a complex editor with many abilities that we do not have space to describe here If you have problems with other features of emacs e g printing there are several sources to consult including the emacs FAQs try M x xemacs www faq or M x view emacs FAQ and EmacsWiki http www emacswiki org Please consult them before asking on the mailing list about issues that are not specific to ESS Appendix A Customizing ESS 81 Appendix A Customizing ESS ESS can be easily customized to your taste simply by including the appropriate lines in your emacs file There are numerous variables which affect the behavior of ESS in certain situations which can be modified to your liking Keybindings may be set or changed to your preferences and for per buffer customizations hooks are also available Most of these variables ca
26. found in ess site R S s etc Alternatively type M x R mode to put the current buffer into R mode However one will have to start up an inferior process to take advantage of the interactive features 12 2 ESS S Inferior ESS processes ESS inferior ESS is the mode for interfacing with active statistical processes programs This mode handles proper indenting generated by both Tab and Return color and font highlighting based on syntax ability to resubmit the contents of a multi line command to the executing process with a single keystroke RET The ability to request help from the current process for variables and functions and to have the results sent into a separate buffer completion of object names and file names interactive history mechanism transcript recording and editing To start up iESS mode use M x S 3 M x S4 M x S 5 M x S 6 M x R for S PLUS 3 x S4 S 5 S 6 or S47 and R respectively This assumes that you have access to each Usually the site will have defined one of these programs by default S46 to the simpler name M x S Chapter 12 Overview of ESS features for the S family 62 In the rare case that you wish to pass command line arguments to the starting S 6 process set the variable inferior Splus args Note that R has some extremely useful command line arguments For example vanilla will ensure R starts up without loading in any init fil
27. not want to save any history files and hence have setq ess history file nil or will only want one global command history file and have setq ess history directory R in your emacs file 4 4 References to historical commands Instead of searching through the command history using the command described in the pre vious section you can alternatively refer to a historical command directly using a notation very similar to that used in csh History references are introduced by a or character and have meanings as follows ur The immediately previous command IN The Nth previous command Itext The last command beginning with the string text I text The last command containing the string text In addition you may follow the reference with a word designator to select particular words of the input A word is defined as a sequence of characters separated by whitespace You can modify this definition by setting the value of comint delimiter argument list to a list of characters that are allowed to separate words and themselves form words Words are numbered beginning with zero The word designator usually begins with a colon character however it may be omitted if the word reference begins with a or If the word is to be selected from the previous command the second character can be omitted from the event specification For instance 1 and
28. package New command ess developer load package calls 1oad all on the package containing current file ess developer add package now offers IDO menu completions with available loading methods currently library and load all Loading command can be customized with ess developer load on add commands e TAB now indents region if region is active a contribution of Matthew Fidler in pull 41 e M x ess version now reports full loading path and recognizes git and ELPA versions e warning and error keyword are now highlighted with font lock warning face as they should be for quite some time these keywords have been hijacked by compilation mode fontification e eldoc Eldoc now recognizes multiple processes If current process is busy or cur rent buffer is not associated with a process eldoc picks its completions from the first available free process e org babel evaluation is now org friendly e help new help buffers now try to reuse ess help buffers This behavior is controlled by ess help reuse window custom variable e help foo pops IDO menu on multiple help files so far it worked only for C c C v e remote evaluation is considerably faster now on slow connections e ESS R tracebug R source references regular expressions are mostly language agnostic e ess function call face inherits from font lock function name face rather than font lock builtin face e ess inject source now accepts function and buffer option e Documenta
29. q reci ag EE 82 Function and program index 0 00 e cece tee eee 82 Variable index isos HEEN ENEE deed ia KEE 84 ii Chapter 1 Introduction to ESS 1 1 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 JAGS and Stata 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 4 S 3 S 4 S 5 S 6 S 7 R XLS VST SAS Currently the documentation contains many references to S where actually any sup ported statistics language is meant i e S could also mean R or SAS For exclusively interactive users of S ESS provides a n
30. the process buffer Default is t Passing a prefix C u vis to any of the following commands however reverses the mean ing of ess eval visibly for that command only for example C u C c C j suppresses the current line of S or other code in the ESS process buffer This method of evaluation is an alternative to S s source function when you want the input as well as the output to be displayed You can sort of do this with source when the option echo T is set except that prompts do not get displayed ESS puts prompts in the right places Primary commands for evaluating code are ess eval region or line and step vis Command Send the highlighted region or current line and step to next line of code ess eval region or function or paragraph vis Command C M x Sends the current selected region or function or paragraph ess eval region or function or paragraph and step vis Command C c C c Like ess eval region or function or paragraph but steps to next line of code Other not so often used evaluation commands are ess eval line vis Command C c C j Sends the current line to the ESS process ess eval line and go vis Command C c M j Like ess eval line but additionally switches point to the ESS process ess eval function vis no error Command C c C f Sends the S function containing point to the ESS process ess eval function and go vis Command C c M f Like ess eval function but additionally switches point to the ESS process
31. to ESS The ESS environment is built on the open source projects of many contributors dating back to 1989 where Doug Bates and Ed Kademan wrote S mode 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 significant enhancements to allow for powerful process interaction John Sall wrote GNU Emacs macros for SAS source code around 1990 Tom Cook added functions to submit jobs review listing and log files and produce basic views of a dataset thus creating a SAS mode which was distributed in 1994 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 Richard M Heiberger designed the inferior mode for interactive SAS and SAS mode was further integrated into ESS Thomas Lumley s Stata mode written around 1996 was also folded into ESS More changes were made to support additional statistical languages particularly XLispStat ESS initially worked only with Unix statistics packages that used standard input and standard output for both the command line interface and batch proces
32. want to discard the last command output altogether use C c C o comint kill output which deletes everything from the last command to the current prompt Use this command judiciously to keep your transcript to a more manageable size 4 2 2 Viewing older commands If you want to view the output from more historic commands than the previous command commands are also provided to move backwards and forwards through previously entered commands in the process buffer C c C p comint previous input Moves point to the preceding command in the process buffer C c C n comint next input Moves point to the next command in the process buffer Note that these two commands are analogous to C p and C n but apply to command lines rather than text lines And just like C p and C n passing a prefix argument to these com mands means to move to the ARG th next or previous command These commands are also discussed in Section Shell History Copying in The GNU Emacs Reference Manual There are also two similar commands not bound to any keys by default which move to preceding or succeeding commands but which first prompt for a regular expression see Section Syntax of Regular Expression in The GNU Emacs Reference Manual and then moves to the next previous command matching the pattern comint backward matching input regexp arg comint forward matching input regexp arg Search backward forward through the transcript buffer for the arg th p
33. with C c C 1 the disk file again corresponds exactly well almost see below to S s record of the object s definition and so some people prefer to delete the disk file rather than unnecessarily use up space This option allows you to do just that If the value of ess keep dump files is t dump files are never deleted after they are loaded Thus you can maintain a complete text record of the functions you have edited within ESS Backup files are kept as usual and so by using the Emacs numbered backup facility see Section Single or Numbered Backups in The Gnu Emacs Reference Manual you can keep a historic record of function definitions Another possibility is to maintain the files with a version control system such as RCS See Section Version Control in The Gnu Emacs Reference Manual As long as a dump file exists in the appropriate place for a particular object editing that object with C c C e C d finds that file for editing unless a prefix argument is given the ESS process is not consulted Thus you can keep comments outside the function definition as a means of documentation that does not clutter the S object itself Another useful feature is that you may format the code in any fashion you please without S re indenting the code every time you edit it These features are particularly useful for project based work If the value of ess keep dump f iles is nil the dump file is always silently deleted after a successful load with
34. 39 ESCOTE Ria 39 ESCOCIA 39 II roire rrr rrrrrnn 38 M M 38 Main aid 45 MEC o dan 38 Masas osito bed 60 Mn lt P O A 60 MSN Sas oie es HE ade sd 60 MRE WEEN 30 R O 25 35 T VE oT comint backward matching input 26 comint bol 5 2 2 212 xe RER TRES ze 25 Comint copv old Amput ooo 27 Indices Comint denamnilc complete sss 45 comint forward matching input 26 comint history isearch backward regexp 28 comint interrupt subjob 32 EE et he EE 25 EE Get RE OR 26 COMINt NeXt input EE 26 28 comint next matching input from input 28 comint previous input 26 28 comint previous matching input from input Em 28 comint show output occ cee mee 26 D Dinan LER 36 E esg Change directorg cece cece eee 59 GE EE 31 44 ess desctibe help mode so 43 gss developar i EEN 53 ess developer add package 53 ess developer load package 53 ess developer remove package 53 ess display help on object 31 43 ess dump object into edit buffer 36 ess electric brace eee 38 ess eval bu ffer ce ecce denise 34 ess eval buffer and go 0005 34 ess eval function s cele nl tae trees 33 ess eval function and go 33 ess eval line a e ea 33 ess eual Line andgo rrn 33 ess eval Line and etenp 44 ess eval region cece cece penina 33 44 ess eval re
35. C c C 1 While this is useful for files that were created with C c C e C d it also applies to any other file you load say a source file of function definitions and so can be dangerous to use unless you are careful Note that since ess keep dump files is buffer local you can make sure particular files are not deleted by setting it to t in the Local Variables section of the file See Section Local Variables in Files in The Gnu Emacs Reference Manual A safer option is to set ess keep dump files to ask this means that ESS will always ask for confirmation before deleting the file Since this can get annoying if you always want to delete dump files created with C c C e C d but not any other files setting ess keep dump files to check the default value will silently delete dump files created with C c C e C d in the current Emacs session but query for any other file Note that in any case you will only be asked for confirmation once per file and your answer is remembered for the rest of the Emacs session Note that in all cases if an error such as a syntax error is detected while loading the file with C c C 1 the dump file is never deleted This is so that you can edit the file in a new Emacs session if you happen to quit Emacs before correcting the error Dump buffers are always autosaved regardless of the value of ess keep dump f iles Chapter 7 Editing objects and functions Al 7 7 Names and locations of dump files Every dump f
36. DEER 21 ed NH EE EE 31 EE 45 temporary buffers 00 0 0000 44 temporary buffers killing 31 lranscrlpt siiissirebebRbee e io eh A 25 transcript le ide E EXER EO RP s 24 transcript file names oo 27 86 transcript mode Motion eee 35 transcripts of S sessions ee eee ee eee d using S interactively 0000 1 NA n 5T working directory 008 21 41 X WindOWB clicenerieet e pietre Rudd 57
37. ESS Emacs Speaks Statistics ESS version 15 03 1 The ESS Developers A J Rossini R M Heiberger K Hornik M Maechler R A Sparapani S J Eglen S P Luque H Redestig and V Spinu Current Documentation by The ESS Developers Copyright 2002 2014 The ESS Developers Copyright 1996 2001 A J Rossini Original Documentation by David M Smith Copyright 1992 1995 David M Smith Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are preserved on all copies Permission is granted to copy and distribute modified versions of this manual under the conditions for verbatim copying provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one Table of Contents 1 Introduction to ESS 1 1 1 Why should I use En dl 1 1 1 Features Overview ccc cence cence eee eens 1 1 2 New features mn 3 1 3 Authors of and contributors to bn 16 1 4 Getting the latest version of ap 17 1 4 1 Git for ESS development 17 1 5 How to read this manual 17 2 Installing ESS on your system 19 2 1 Step by step mstruchonsg 00 e eee eens 19 2 2 Ee EE 19 2S eebe 20 2 4 Requirements ce ccc eee hm nn 20 3 Interacting with statistical programs 21 3 1 Starting an ESS process 00 ee cece eee eee eee ees 21 3 2 Running more than one ESS
38. ESS on your system The following section details those steps necessary to get ESS running on your system 2 1 Step by step instructions 19 1 Download the latest zip or tgz archive from ESS downloads area and unpack it into a directory where you would like ESS to reside We will denote this directory as path to ESS hereafter Alternatively you can use git to fetch the most recent development version to your local machine with git clone https github com emacs ess ESS git path to ESS 2 Optionally compile elisp files and build the documentation with cd path to ESS make Without this step info pdf and html documentation and reference card will not be available 3 Optionally install into your local machine with make install You might need ad ministrative privileges make install The files are installed into usr share emacs directory For this step to run correctly on Mac OS X you will need to adjust the PREFIX path in Makeconf The necessary code and instructions are commented in that file 4 If you have performed the make install step from above just add require ess site q to your emacs file Otherwise you should add path to ESS lisp to your emacs load path and then load ESS with the following lines in your emacs add to list load path path to ESS lisp load ess site 5 Restart your Emacs and check that ESS was loaded from a correct location with M x ess version
39. ESS process To start an S session on Unix or on Windows when you use the Cygwin bash shell simply type M x S RET To start an S session on Windows when you use the MSDOS prompt shell simply type M x S 6 msdos 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 subdi rectory 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 3 2 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 com pletion is provided over the names of all running S processes This is a good command to consid
40. SS process thus allowing editing or correction of the command before the ESS process sees it Once corrections have been made press RET to send the edited command to the ESS process If you want to select a particular command from the history by matching it against a regular expression see Section Syntax of Regular Expression in The GNU Emacs Refer ence Manual to search for a particular variable name for example these commands are also available M r comint history isearch backward regexp Prompt for a regular expression and search backwards through the input history for a command matching the expression A common type of search is to find the last command that began with a particular sequence of characters the following two commands provide an easy way to do this C c M r comint previous matching input from input Select the previous command in the history which matches the string typed so far C c M s comint next matching input from input Select the next command in the history which matches the string typed so far Instead of prompting for a regular expression to match against as they instead select commands starting with those characters already entered For instance if you wanted to re execute the last attach command you may only need to type att and then C c M r and RET See Section Shell History Ring in The GNU Emacs Reference Manual for a more detailed discussion of the history mechanism and do experiment with
41. 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 Appendix A Customization page 81 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 Chapter 2 Installing ESS on your system 2 Installing
42. T function key F3 or F8 to submit a batch SAS job whether local or remote is ess sas submit command which defaults to sas program sas program is invoke SAS using program file for Mac Classic and sas otherwise However you may have to alter ess sas submit command for a particular program so it is defined as buffer local Conveniently it can be set at the end of the program endsas Chapter 13 ESS for SAS 69 Local variables ess sas submit command sas8 End The command line is also made of ess sas submit pre command ess sas submit post command and ess sas submit command options the last of which is also buffer local Here are some examples for your emacs or xemacs init el file you may also use M x customize variable sh default setq ess sas submit pre command nohup sh default setq ess sas submit post command rsasuser amp sh example setq default ess sas submit command usr local sas sas ms dos default setq ess sas submit pre command start ms dos default setq ess sas submit post command rsasuser icon Windows example setq default ess sas submit command c progra 1 sas sas exe Windows example setq default ess sas submit command c progra 1 sas sas exe There is a built in delay before a batch SAS job is submitted when using a UNIX imitating shell under Windows This is necessary in many cases since the shell might not be ready to receive a command Th
43. ady the message buffer is checked for new ones A prefix arg specifies how many error messages to move negative means move back to previous error messages Just C u as a prefix means reparse the error message buffer and start at the first error The reset argument specifies restarting from the beginning See Section 7 3 Error Checking page 37 for more details ess display help on object object command Command C c C v Pops up a help buffer for an S object or function If command is supplied it is used instead of inferior ess help command See Chapter 8 Help page 43 for more details ess quit Command C c C q Issue an exiting command to the inferior process additionally also running ess cleanup for disposing of any temporary buffers such as help buffers and edit buffers that may have been created Use this command when you have finished your S session instead of simply quitting at the inferior process prompt otherwise you will need to issue the command ess cleanup explicitly to make sure that all the files that need to be saved have been saved and that all the temporary buffers have been killed 4 6 Is the Statistical Process running under ESS For the S languages S S Plus R ESS sets an option in the current process that programs in the language can check to determine the environment in which they are currently running ESS sets options STERM iESS for S language processes running in an inferior iESS S or iESS R buffer
44. an arrange for that Place the cursor in the buffer displaying foo sas Enter the sequence C c C w The cursor will normally be in buffer foo sas If not put it there and C x b foo sas Send regions lines or the entire file contents to SAS regions are most useful a high lighted region will normally begin with the keywords DATA or PROC and end with RUN C C r Information appears in the log buffer analysis results in the listing buffer In case of errors make the corrections in the foo sas buffer and resubmit with another C c C r 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 foo log and foo 1st 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 foo 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 1st and Log buffers for monitoring output Troubleshooting See Section 13 7 ESS SAS Common problems page 74 13 7 iESS SAS Common problems 1 ESS SAS does not work on Windows In order to run SAS insi
45. appear in The lambda expression is evaluated with the process buffer as the current buffer and so you can use the variables local to that buffer to make your choice For example the following expression causes source files to be saved in the subdirectory Src of the directory the ESS process was run in setq ess source directory lambda concat ess directory Src ess directory is a buffer local variable in process buffers which records the directory the ESS process was run from This is useful if you keep your dump files and you often edit objects with the same name in different ESS processes Alternatively if you often change your S working directory during an S session you may like to keep dump files in some subdirectory of the directory pointed to by the first element of the current search list This way you can edit objects of the same name in different directories during the one S session setq ess source directory lambda file name as directory expand file name concat car ess search list Src Chapter 7 Editing objects and functions 42 If the directory generated by the lambda function does not exist but can be created you will be asked whether you wish to create the directory If you choose not to or the directory cannot be created you will not be able to edit functions Chapter 8 Reading help files 43 8 Reading help files ESS provides an easy to use facility for reading S help files from with
46. appears after the output from the first ESS process separated by a form feed L character Thus pages in the ESS process buffer correspond to ESS sessions Chapter 4 Interacting with the ESS process 26 Thus for example you may use C x and C x to move backward and forwards through ESS sessions in a single ESS process buffer For more information about page commands see Section Pages in The GNU Emacs Reference Manual 4 2 1 Manipulating the output from the last command Viewing the output of the command you have just entered is a common occurrence and ESS provides a number of facilities for doing this Whenever a command produces a longish output it is possible that the window will scroll leaving the next prompt near the middle of the window The first part of the command output may have scrolled off the top of the window even though the entire output would fit in the window if the prompt were near the bottom of the window If this happens you can use the following comint commands comint show maximum output to move to the end of the buffer and place cursor on bottom line of window to make more of the last output visible To make this happen automatically for all inputs set the variable comint scroll to bottom on input to t or this If the first part of the output is still not visible use C c C r comint show output which moves cursor to the previous command line and places it at the top of the window Finally if you
47. assic Under Windows it will default to ab if you are using a UNIX imitating shell otherwise ms dos for an MS DOS shell On Mac OS X it will default to sh but under Mac Classic it defaults to apple script You will also set this to sh if the SAS batch job needs to run on a remote machine rather than your local machine This works transparently if you are editing the remote file via ange ftp EFS or tramp Note that ess sas shell buffer remote init is a Local Variable that defaults to ssh which will be used to open the buffer on the remote host and it is assumed that no password is necessary i e you are using ssh agent ssh add or the equivalent see the discussion about Local Variables below if you need to change the default However if you are editing the file locally and transferring it back and forth with Kermit you need some additional steps First start Kermit locally before remotely logging in Open a local copy of the file with the ess kermit prefix character prepended the default is Execute the command M x ess kermit get which automatically brings the contents of the remote file into your local copy If you transfer files with Kermit manually in a shell buffer then note that the Kermit escape sequence is C q C c rather than C c which it would be in an ordinary terminal application i e not in an emacs buffer Lastly note that the remote Kermit command is specified by ess kermit command The command used by the SUBMI
48. ay and hyperlinks were broken in 13 09 1 ESS Julia recognize function names ending with ESS Julia fix indentation of for comprehension syntax within brackets Changes Selected Bug Fixes in 13 09 1 ess remote and TRAMP R support code is now downloaded in binary form instead of being injected from local machine The R code is stored in config ESSR directory on the remote machine TRAMP PAGER environment variable is now correctly set to inferior ess pager retrieval of help topics on remote machines is fixed org babel source references of R code executed from org files correctly point to source references in original org files version 8 2 1 or higher of org mode is required for this feature ess execute is now bound to C c C e C e in ess extra map completion works again in ess execute ESS R head and tail methods were replaced by htsummary in ess R describe object at point commands ESS roxygen evaluation commands now work in roxygen blocks Leading comments are automatically removed before the evaluation ESS transcript Clean Region now works with multiline statements ess transcript clean region etc correctly treat multiline statements i e no longer forgets the lines typically preceded by ESS SAS Three features fixes with special thanks to Matthew Fidler https github com emacs ess ESS pulls mlf176f2 Turn on SAS log mode when appropriate Indent comments and CARDS statement more appropr
49. 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 a For a site installation or an individual place ONLY ONE of the following lines in your initialization file prior to a require load ESS SAS function keys are available in ESS SAS if you choose either 2 or 3 and in all modes if you choose 4 or 5 332 setq ess sas local unix keys t 333 setq ess sas local pc keys t 334 setq ess sas global unix keys t 335 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 b If your site installation has configured the keys contrary to your liking then you must call the appropriate function load ess site local unix keys ess sas global pc keys Chapter 13 ESS for SAS 71 Finally we get to what the function keys actually do You may recognize some of the nicknames as SAS Display Manager commands they are in all capitals UNIX PC Nickname 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 1st or Log file in the current buffer and submit the file a
50. bmd is used for BUGS command files and jmd for JAGS command files For your jmd file there is only one variable ess jags command in the Local Variables section When you have finished editing your model file and press C c Chapter 15 ESS for JAGS 78 C c a command file is created if one does not already exist When you are finished editing your command file pressing C c C c again will submit your command file as a batch job The ess jags command variable allows you to specify a different JAGS program to use to run your model defaults to jags 15 3 ESS JAGS Log files The jog extension is used for JAGS log files You may find F2 useful to refresh the jog if the batch process over writes or appends it Chapter 16 Bugs and Bug Reporting Mailing Lists 79 16 Bugs and Bug Reporting Mailing Lists 16 1 Bugs e Commands like ess display help on object and list completion cannot be used while the user is entering a multi line command The only real fix in this situation is to use another ESS process e The ess eval commands can leave point in the ESS process buffer in the wrong place when point is at the same position as the last process output This proves difficult to fix in general as we need to consider all windows with window point at the right place e It s possible to clear the modification flag say by saving the buffer with the edit buffer not having been loaded into S e Backup files can sometimes be lef
51. cally removed before the command is submitted 6 2 Cleaning transcript files Yet another use for transcript files is to extract the command lines for inclusion in an S source file or function Transcript mode provides one command which does just this ess transcript clean region beg end even if read only Command C c C w Strip the transcript in the region given by beg and end leaving only com mands Deletes any lines not beginning with a prompt and then removes the prompt from those lines that remain Prefix argument even if read only means to clean even if the buffer is read only Don t forget to remove any erroneous commands first The remaining command lines may then be copied to a source file or edit buffer for inclusion in a function definition or may be evaluated directly see Chapter 5 Evaluating code page 33 using the code evaluation commands from S mode also available in S Transcript Mode Chapter 7 Editing objects and functions 36 7 Editing objects and functions ESS provides facilities for editing S objects within your Emacs session Most editing is performed on functions although in theory you may edit datasets as well Edit buffers are always associated with files although you may choose to make these files temporary if you wish Alternatively you may make use of a simple yet powerful mechanism for maintaining backups of text representations of S functions Error checking is performed when S code is loaded into
52. ckage to be installed Chapter 10 Developing with ESS 52 ess roxy preview HTML visit instead of open Command C c C o C t Use the attached R process to parse the entry at to generate HTML for the entry and open it in a browser When used with the prefix argument visit instead of open i e C u C c C e C t visit the generated HTML file instead Requires the Roxygen and tools packages to be installed ess roxy previous entry Command C c C o p Go to start of the Roxygen entry above point ess roxy next entry Command C c C o n Go to end of the Roxygen entry above point ess roxy hide all Command C c C o C h Use the hideshow mode to fold away the visibility of all Roxygen entries Hide show support must be enabled for this binding to get defined ESS also advises the following standard editing functions in order to make Roxygen editing more intuitive TAB ess R complete object name Complete Roxygen tag at point E g doing TAB when the point is at the end of par completes to param M h mark paragraph If the transient mark mode is active place mark and point at start end end of the field at point and activate the mark TAB ess indent command If hide show support is enabled fold away the visibility of the Roxygen entry at point M q fill paragraph Fill the Roxygen field at point C a move beginning of line Move to the point directly to the right of the Rox ygen start string RET newline and indent Insert a new line and
53. commands and related function key definitions However six other keys have been provided for convenience and are described below shell switches you to the shell buffer where you can interact with your operating system This is especially helpful if you would like to kill a SAS batch job You can specify a different buffer name to associate with a SAS batch job besides shell with the buffer local variable ess sas shell buffer This allows you to have multiple buffers running SAS batch jobs on multiple local remote computers that may rely on different methods specified by the buffer local variable ess sas submit method F2 performs the refresh operation on the current buffer refresh compares the buffer s last modified date time with the file s last modified date time 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 F11 are pressed filetype 1 switches you to a file with the same file name as your sas file but with a different extension txt by default and performs refresh You can over ride the default extension for example in your emacs or xemacs init el file setq ess sas suffix 1 csv for example F9 will prompt you for the name of a permanent SAS dataset near point to be opened for viewing by PROC FSEDIT You can control the SAS batch command line with ess sas data view submit options
54. commands are also available in the process buffer comint interrupt subjob Command C c C c Sends a Control C signal to the ESS process This has the effect of aborting the current command ess switch to inferior or script buffer toggle eob Command C c C z When in process buffer return to the most recent script buffer When in a script buffer pop to the associated process buffer This is a single key command that is C c C z C z from a script buffer returns to the original buffer If toggle eob is given the value of ess switch to end of proc buffer is toggled ess switch to end of proc buffer User Option If non nil ess switch to inferior or script buffer goes to end of process buffer Other commands available in Inferior S mode are discussed in Section Shell Mode in The Gnu Emacs Reference Manual Chapter 5 Sending code to the ESS process 33 5 Sending code to the ESS process Other commands are also available for evaluating portions of code in the S process These commands cause the selected code to be evaluated directly by the ESS process as if you had typed them in at the command line the source function is not used You may choose whether both the commands and their output appear in the process buffer as if you had typed in the commands yourself or if the output alone is echoed The behavior is controlled by the variable ess eval visibly User Option Non nil means ess eval commands display commands and output in
55. connection 6 Once you get the S or R or SAS prompt then you are completely connected All the C c C n and related commands work correctly in sending commands from myfile s or myfile r on the PC to the S 3 buffer running the S or R or SAS program on the remote machine 7 Graphics on the remote machine works fine If you run the X window system on the remote unix machine you should be able to display them in xfree86 on your PC If you don t run X Windows or X11 then you can write graphics to the postscript device and copy it to your PC with dired and display it with ghostscript 3 5 Changing the startup actions If you do not wish ESS to prompt for a starting directory when starting a new process set the variable ess ask for ess directory to nil In this case the starting directory will be set using one of the following methods 1 If the variable ess directory function stores the name of a function the value re turned by this function is used The default for this variable is nil Chapter 3 Interacting with statistical programs 24 2 Otherwise if the variable ess directory stores the name of a directory ending in a slash this value is used The default for this variable is nil 3 Otherwise the working directory of the current buffer is used If ess ask for ess directory has a non nil value as it does by default then the value determined by the above rules provides the default when prompti
56. created whenever you type C c C e C d ess dump object into edit buffer and may either be deleted after use or kept as a backup file or as a means of keeping several versions of an S function ess delete dump files User Option If non nil dump files created with C c C e C d are deleted immediately after they are created by the ess process Since immediately after S dumps an object s definition to a disk file the source code on disk corresponds exactly to S s idea of the object s definition the disk file isn t needed deleting it now has the advantage that if you don t modify the file say because you just Chapter 7 Editing objects and functions 40 wanted to look at the definition of one of the standard S functions the source dump file won t be left around when you kill the buffer Note that this variable only applies to files generated with S s dump function it doesn t apply to source files which already exist The default value is t ess keep dump files User Option Variable controlling whether to delete dump files after a successful load If nil always delete If ask confirm to delete If check confirm to delete except for files created with ess dump object into edit buffer Anything else never delete This variable only affects the behaviour of ess load file Dump files are never deleted if an error occurs during the load After an object has been successfully i e without error loaded back into S
57. de an emacs buffer it is necessary to start SAS with the stdio option SAS does not support the stdio option on Windows 2 If M x SAS gives errors upon startup check the following e you are running Windows see 1 e ess sas sh command from the ESS etc directory needs to be executable too check type M x dired if not fix it as follows type M then at the minibuffer prompt Eval type set file modes ess sas sh command 493 e sas isn t in your executable path to verify type M and at the minibuffer prompt Eval type executable find sas 3 M x SAS starts SAS Display Manager Probably the command sas on your system calls a shell script In that case you will need to locate the real sas executable and link to it You can execute the UNIX command find name sas print Now place a soft link to the real sas executable in your bin directory with for example Chapter 13 ESS for SAS 75 cd bin ln s usr local sas9 sas sas Check your PATH environment variable to confirm that bin appears before the directory in which the sas shell script appears 13 8 ESS SAS Graphics Output from a SAS GRAPH PROC can be displayed in a SAS GRAPH window for SAS batch on Windows or for both SAS batch and interactive with XWindows on UNIX If you need to create graphics files and view them with F12 then include the following either in foo sas or in autoexec sas filename gsasfile graphics ps goptions
58. e DEE 59 ess utille reitesearch 59 ess r tils save WKSpC ee nues 59 ess utills update pkes 59 Gg EE 38 ess Skip Lo help section s 43 ess Skip Lo nezt section es 43 ess skip to previous section 43 ess smart comms oserelbedu deg ee cR pe aes 55 ess submit bug report sess 79 ess switch to end of ESS 44 ess switch to inferior or script buffer 32 A EE 60 OSS SWVHPDE cooper eed 60 e watered aes ue bau 60 S8 SWV WOABVO cria ltd 60 A 0 RPPbebEe be nere e e Ped 48 ess transcript clean region 35 ess transcript copy command 35 ess transcript send command 35 ess transcript send command and move 35 ess use ido ess completing read 46 F E E E EE 52 I inferior ess send input 25 M mark paragraph siseibecewbRRR ica 52 move beginning of Line eee 52 N newline and indent eee eee 52 Indices O Objects EE 30 P printer EEN 57 Variable index A EE 46 AC SOULCE R AL ES iia re 46 ac source R objects 2 cece eee eee 46 C comint delimiter argument list 29 comint input ring size sss 28 comment Columm ii id2i larger br dg aea 37 E ess ask about transfile 24 27 ess ask for ese directorg 23 e ss default style pepe i nene 38 ess delete dump Tiles 39 ess die Ci ios 41 ess dump filename template
59. e a command file and submit a BUGS batch process Lastly interactive submission of BUGS commands is also supported 14 1 ESS BUGS Model files Model files with the bug extension are edited in ESS BUGS mode if require ess bugs d was performed Model files with the jag extension are edited in ESS JAGS mode if require ess jags d was performed Three keys are bound for your use in ESS BUGS F2 C c C c and F2 performs the same action as it does in ESS SAS See Section 13 5 ESS SAS Function keys for batch processing page 70 C c C c performs the function ess bugs next action which you will use a lot Pressing it in an empty buffer for a model file will produce a template for you inserts the set operator lt 14 2 ESS BUGS Command files To avoid extension name collision bmd is used for BUGS command files and jmd for JAGS command files When you have finished editing your model file and press C c C c a command file is created if one does not already exist When you are finished editing your command file pressing C c C c again will submit your command file as a batch job 14 3 ESS BUGS Log files To avoid extension name collision bog is used for BUGS log files The command line generated by ESS creates the bog transcript file Similarly jog is used for JAGS log files Chapter 15 ESS for JAGS 77 15 ESS for JAGS ESS BUGS was originally designed for use with BUGS software Later it evolved to support JAGS
60. e handles e proper indenting generated by both TAB and RET e color and font choices based on syntax e 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 e capability of killing the batch SAS process through the shell buffer or allow the SAS process to keep on running after you exit emacs e single keypress navigation of sas 10g and 1st files log and 1st files are refreshed with each keypress e ability to send the contents of an entire buffer a highlighted region or a single line to an interactive SAS process e ability to switch between processes which would be the target of the buffer for the above ESS SAS is automatically turned on when editing a file with a sas suffix or other extension if specified via auto mode alist The function keys can be enabled to use the same function keys that the SAS Display Manager does The interactive capabilities of ESS require you to start an inferior SAS process with M x SAS See Section 13 6 ESS SAS Interactive SAS processes page 73 At this writing the indenting and syntax highlighting are generally correct Known issues for multiple line or 4 comments only the first line is highlighted for log files only the first line of a NOTE WARNING or ERROR message is highlighted unmatched single double quotes in CARDS data lines are NOT ignored in an iterat
61. e myproject Or enter M x ESS elsewhere You will be prompted for an ESS program and for a starting directory I usually give it my project directory on the local machine say myname myproject 2 The S 3 buffer will appear with a prompt from the local operating system the unix prompt on a unix workstation or with cygwin bash on a PC or the msdos prompt on a PC without bash emacs may freeze because the cursor is at the wrong place Unfreeze it with C g then move the cursor to the end with M gt With Stelsewhere the buffer name is based on the name of the ESS program 3 Enter telnet myname other machine or ssh myname other machine You will be prompted for your password on the remote machine Use M x send invisible before typing the password itself 4 Before starting the ESS process type stty echo nl at the unix prompt The echo turns off the echo the n1 turns off the newline that you see as M 5 You are now talking to the unix prompt on the other machine in the S 3 buffer cd into the directory for the current project and start the ESS process by entering Splus or R or sas stdio as appropriate If you can login remotely to your Windows 2000 then you should be able to run Sqpe on the Windows machine I haven t tested this and no one has reported their tests to me You will not be able to run the GUI through this text only
62. e old one the function is assigned into that namespace If not found it is assigned into GlobalEnv Chapter 11 Other ESS features and tools 55 11 Other ESS features and tools ESS has a few extra features which didn t fit anywhere else 11 1 ElDoc In ElDoc mode the echo area displays function s arguments at point From ESS version 12 03 ElDoc is active by default in ess mode and inferior ess mode buffers To activate it only in ess mode buffers place the following into your init file setq ess use eldoc script only q P y ess use eldoc User Option If t activate eldoc in ess mode and inferior ess mode buffers If script only activate in ess mode buffers only Set ess use eldoc to nil to stop using ElDoc altogether ess eldoc show on symbol User Option This variable controls whether the help is shown only inside function calls If set to t ElDoc shows help string whenever the point is on a symbol otherwise the default shows only when the point is in a function call i e after ess eldoc abbreviation style User Option The variable determines how the doc string should be abbreviated to fit into mini buffer Posible values are nil mild normal strong and aggressive Please see the documentation of the variable for more details The default filter is normal Ess eldoc also honors the value of eldoc echo area use multiline p which if set to
63. e the working directory for the current R session ess rutils html docs Command C c C H Use browse url to navigate R html documentation See the submenu Rutils under the iESS menu for alternative access to these functions The function ess rutils rsitesearch is provided without a particular key binding This function is useful in any Emacs buffer so can be bound to a user defined key eval after load ess rutils global set key control c f6 ess rutils rsitesearch Functions for listing objects and packages ess rutils local pkgs ess rutils repos pkgs and ess rutils objs show results in a separate buffer and window in ess rutils mode providing useful key bindings in this mode type in this buffer for a description Chapter 11 Other ESS features and tools 60 11 11 Interaction with Org mode Org mode http orgmode org now supports reproducible research and literate program ming in many languages including R see chapter 14 of the Org manual http orgmode org org html Working With Source Code For ESS users this offers a document based work environment within which to embed ESS usage R code lives in code blocks of an Org document from which it can be edited in ess mode evaluated extracted tangled to pure code files The code can also be exported woven with the surrounding text to several formats including HTML and LaTeX Results of evaluation including figures can be captured in
64. eat to cycle ess debug toggle error action d Flag for debugging ess debug flag for debugging u Unflag for debugging tess debug unflag for debugging g Chapter 10 Developing with ESS 49 W Watch window ess watch C prefixed equivalents are also defined Navigation to errors general emacs functionality C x M gn next error M g p previous error Misc Show this help ess tracebug show help To configure how electric watch window splits the display see ess watch width threshold and ess watch height threshold variables A more detailed ess tracebug documentation with screenshots is available at http code google com p ess tracebug A short tutorial is at http code google com p ess tracebug wiki GettingStarted Note Currently ess tracebug does not detect some of R s debug related messages in non English locales To set your R messages to English add the following line to your Rprofile init file Sys setlocale LC MESSAGES C 10 2 Editing documentation ESS provides two ways of writing documentation for R objects Either using the standard R documentation system or using in source documentation written as structured comment fields for use with the Roxygen package 10 2 1 Editing R documentation Rd files R objects are documented in files written in the R documentation Rd a simple markup language closely resembling La TEX which
65. ebugging From ESS13 05 ess tracebug is on by default You can toggle it on and off with M x ess tracebug To disable startup activation of ess tracebug set ess use tracebug to nil Tracebug functionality can be found on ess dev map bound to C c C t Additionally when subprocess is in a debugging state ess debug minor mode is active and the following additional shortcuts are available Interactive Debugging ess debug minor mode map M C Continue ess debug command continue M C C Continue multi ess debug command continue multi M N Next step ess debug command next M C N Next step multi ess debug command next multi M U Up frame ess debug command up M Q Quit debugging ess debug command quit These are all the tracebug commands defined in ess dev map C c C t to show this table Breakpoints ess dev map b Set BP repeat to cycle BP type ess bp set B Set conditional BP ess bp set conditional k Kill BP ess bp ki1 K Kill all BPs ess bp kill all o Toggle BP state ess bp toggle state 1 Set logger BP ess bp set logger n Goto next BP ess bp next p Goto previous BP ess bp previous C prefixed equivalents are also defined Debugging ess dev map D Show traceback ess show traceback also on C c UM si Show callstack ess show call stack also on C c N e Toggle error action rep
66. ed github issue 163 ESS R On windows if ess prefer higher bit is non nil the default then R newest will try to run a 64 bit rather than 32 bit version of R Changes and New Features in 15 03 ESS R Full native support for company mode ESS R More efficient caching algorithm for R completion ESS New offset variable ess close paren offset to control the indentation of the closing parentheses ESS R Ask for CRAN mirror only once per emacs session Chapter 1 Introduction to ESS 4 e ESS R Detect library and require calls for better completion caching e Buffer display is now customizable ess show buffer action e Use y or n p instead of yes or no p throughout e More support for ODS in ess sas graph view e Makefiles are now both UNIX and GNU friendly e ESS R Simplify directory lookup in ess developer 137 e Make closed paren indentation consistent Bug Fixes in 15 03 e Fix open brace indentation bug 27 in ess R ESS bugs R e lix git version lookup e Don t check directory modtime in R dialect e Declare all ess macros for edebug e Add ess smart comma to eldoc message functions e Inform users when retrieving RDA aliases e Line ending in is also a continuation line e Filing roxy paragraphs works as expected now e In ess developer add package remove incorrect wait argument from ess get words from vector call e Fix 96 117 120 125 134 137 e Fix ess quit r Call base q e
67. edit buffers are also available in S help mode see Section 7 1 Edit buffer page 36 Of course the usual non editing Emacs commands are available and for convenience the digits and act as prefix arguments If a help buffer already exists for an object for which help is requested that buffer is popped to immediately the ESS process is not consulted at all If the contents of the help file have changed you either need to kill the help buffer first or pass a prefix argument with C u to ess display help on object Help buffers are marked as temporary buffers in ESS and are deleted when ess quit or ess cleanup are called Help buffers normally appear in another window within the current frame If you wish help buffers to appear in their own frame either one per help buffer or one for all help buffers you can customize the variable ess help own frame Chapter 9 Completion 45 9 Completion 9 1 Completion of object names The TAB key is for completion The value of the variable ess first tab never complete controls when completion is allowed controls when completion is allowed to occur In ess mode TAB first tries to indent and if there is nothing to indent complete the object name instead TAB comint dynamic complete Complete the S object name or filename before point When the cursor is just after a partially completed object name pressing TAB provides completion in a similar fashion to tcsh except that completion is per
68. ee eee eee eres 61 12 3 ESS help assistance with viewing bein 63 12 4 Philosophies for using ESS O E RR vous 63 12 5 Scenarios for use possibilities based on actual usage 63 12 6 Customization Examples and Solutions to Problems 66 13 ESS for SAS sidad ERA 67 13 1 ESS SAS Design philosophy 0 0 e eee eee eee 67 18 2 ESS SAS Editing leg gen cec ort terr ieee BEER 67 13 3 ESS SAS TAB ke 68 13 4 ESS SAS Batch SAS processes 0 00 cece eee eee ees 68 13 5 ESS SAS Function keys for batch processing 70 13 6 ESS SAS Interactive SAS processes eee e ee 73 13 7 IESS SAS Common problems 2 224 3e ka or RR aS 74 13 8 ESS SAS Graphics 2 0 0 0 cece cece eee ee 75 139 ESS SAS Windows ccc cece cece ene 75 14 ESS for BUGS occas Erde re dE Be reg 76 141 ESS BUGS Model Bleser LR E e rh ER ERR 76 14 2 ESS BUGS Command files eese n 76 14 3 ESS BUGS Log Blees eet ae e St RE 76 15 ESS for ACID Aeren d EN EEN os TT 15 1 ESS JAGS Model 58 pda o EP 71 15 2 ESS JAGS Command Diles occitano ENEE 77 15 3 ESS JAGS Log UE 78 16 Bugs and Bug Reporting Mailing Lists 79 16 1 age eege hee ge du idend p SR S RE Eege e 79 16 2 Reporting Bugs 79 16 3 Mailing Listin SNE a eR IRE e phe deer 79 16 4 Help with emacg 0 0 cece cece nee m 80 Appendix A Customizing ESS 81 o A ER ee EE 82 Key 1hd6xz fos egeie rk Ed ca heer eee
69. elp in HTML browser new function ess display help in browser bound to w in help mode map It depends on R s browser option New custom variable ess help pop to buffer if non nil ESS help buffers are given focus on display The default is t breaking change New menu entries for the above functions Bogus help buffers are no longer generated by default i e buffers of the form No documentation for foo in specified packages and libraries you could try foo ess help kill bogus buffers now defaults to t Beware there may be instances where the default is unsatisfactory such as debugging and or during R development Thanks to Ross Boylan for making the suggestion Sam Steingold for reminding us of this variable and Martin Maechler for the warning e ESS now uses IDO completing read functionality for all the interactive requests It uses ido completion mechanism whenever available and falls back on classical completing read otherwise You can set ess use ido to nil if you don t want the IDO completion See the documentation string of ess use ido for more information about IDO and ESS configuration Chapter 1 Introduction to ESS 15 e ESS S is bound to ess smart comma If comma is invoked at the process marker of an ESS inferior buffer request and execute a command from ess handy commands list If ess R smart operators is t ess smart comma also inserts after comma e ESS S notably R
70. er binding to a global key 3 3 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 with tramp Require tramp in your emacs file require tramp Now start an ssh session with C x f ssh user host RET Tramp should open a dired buffer in your remote home directory Now call your favorite ESS process R Julia stata etc as you would usually do on local machine M x R Chapter 3 Interacting with statistical programs 22 Alternatively you can start your process normally M x R After you are asked for starting directory simply type ssh userGhost RET R process will be started on the remote machine To simplify the process even further create a config file in your ssh folder and add an account For example if you use amazon EC2 it might look like following Host amazon Hostname ec2 54 215 203 181 us west 1 compute amazonaws com User ubuntu IdentityFile ssh my_amazon_key pem ForwardX11 yes With this configuration ssh amazon is enough to start a connection The ForwardX11 is needed if you want to see R graphic device showing on the current machine Other ways to setup a remote ESS connection are through ess remote 1 Start a new shell telnet or ssh buffer and connect to the remote computer e g use M x shell M x telnet or M
71. es To enter a command line argument call R using a prefix argument by C u M x R and when ESS prompts for Starting Args enter for example vanilla Then that R process will be started up using R vanilla If you wish to always call R with certain arguments set the variable inferior R args accordingly If you have other versions of R or S Plus available on the system ESS is also able to start those versions How this exactly works depend on which OS you are using as described in the following paragraphs The general principle regardless of OS is that ESS searches the paths listed in the variable exec path for R binaries If ESS cannot find your R binaries on Unix you can change the unix environment variable PATH as this variable is used to set exec path R on Unix systems If you have R 1 8 1 on your exec path it can be started using M x R 1 8 1 By default ESS will find versions of R beginning R 1 or R 2 If your versions of R are called other names consider renaming them with a symbolic link or change the variable ess r versions To see which functions have been created for starting different versions of R type M x R and then hit Tab These other versions of R can also be started from the ESS gt Start Process gt Other menu R on Windows systems If you have rw1081 on your exec path it can be started using M x rw1081 By default ESS will find versions of R located in directories parallel to the version o
72. ese a Werke us 56 historic backups cece eee ee eee eee 40 e WEE 31 I lee 46 IDO completions 0 0 rreren rrena 46 85 eh EE 37 installation ceras rta 19 interactive use of So eee eee eee eee 1 interrupting S commande 32 introduction c sees ARTE SE apace cob laid wee arse Sie rn 1 K keyboard short oute oo 31 killing temporary butter 31 killing the ESS process 00 00 31 L lists completion op 45 M motion in transcript mode 35 multi line commands resubmitting 21 multiple ESS processes sssssseess 21 N new objects creating 0 008 8 36 el 30 P pages in the process buffer oooo o oooooo 25 paging commands in help buffers 43 paragraphs in the process buffer 25 parsing EE 37 process buffer Lise eeu I cea be nee 21 process nalH68 cesiex ek e aeree RE Re Ee aar 21 programming TM A DEE Steed 1 Project work 1n 94 er Re eee BEY 40 quitting from Fan 31 re executing Commande 27 reading long command outputs 26 remote Computers 21 reverting function definitions 36 TORY A EE ol ROX GON ioco Social et eecht We dee P 51 TUNING Serraria iadnn R4 pexbebebpr e eva Res 21 Indices S otelsewh ere erbe wer eves heute ses cee 21 search lists 3 atb dcdweetaceeeeeetadaeas 31 41 sendiug INPUbi EE 25 starting directory 2 A des maca rd 21 Sarna
73. etions shown temporar ily in the standard Completions buffer and interactively select completion candidates using several methods As of version 2013 04 04 Icicles provides support for completion in ESS Please consult Icicles documentation which is easily accessible via customize group Icicles for more details on installation and customization options Once installed Icicles can be activated by evaluating maybe place in emacs Chapter 9 Completion 4T require icicles icy mode 1 Icicles can be toggled at any moment by typing M x icy When Icicles is on TAB offers completion provided the conditions determined by ess first tab never complete allow it Typing M TAB will attempt completion regardless Typing M in ESS or iESS modes brings up the relevant completion candidates from which to choose Minibuffer input filters the available candidates Use TAB for prefix completion or S TAB for substring or regexp completion Use S SPC to match an additional pattern repeatable You can cycle among the matching candidates choosing with RET or mouse 2 Chapter 10 Developing with ESS 48 10 Developing with ESS ESS provides several tools to help you with the development of your R packages 10 1 ESS tracebug ESS tracebug offers visual debugging interactive error navigation interactive backtrace breakpoint manipulation control over R error actions watch window and interactive flag ging unflagging of functions for d
74. f R in your PATH If your versions of R are called other names you will need to change the variable ess rterm versions To see which functions have been created for starting different versions of R type M x rw and then hit Tab These other versions of R can also be started from the ESS gt Start Process gt Other menu Once ESS has found these extra versions of R 1t will then create a new function called M x R newest which will call the newest version of R that it found ESS examines the date in the first line of information from R version to determine which is newest S on Unix systems If you have Splus7 on your exec path it can be started using M x Splus7 By default ESS will find all executables beginning Splus on your path If your versions of S are called other names consider renaming them with a symbolic link or change the variable ess s versions To see which functions have been created for starting different versions of Splus type M x Splus and then hit Tab These other versions of Splus can also be started from the ESS gt Start Process gt Other menu A second mechanism is also available for running other versions of Splus The variable ess s versions list is a list of lists each sublist should be of the form DEFUN NAME PATH ARGS DEFUN NAME is the name of the new emacs function you wish to create to start the new S process PATH is the full path to the version of S you want to run ARGS is an optional string of c
75. ffers Default is t to use font lock support If you change the value of this variable restart Emacs for it to take effect The font lock patterns are defined by the following variables which you may modify if desired inferior R font lock keywords User Option Font lock patterns for inferior R processes There is a corresponding inferior S font lock keywords for S processes The default value highlights prompts in puts assignments output messages vector and matrix labels and literals such as NA and TRUE ess R font lock keywords User Option Font lock patterns for ESS R programming mode There is a corresponding ess S font lock keywords for S buffers The default value highlights function names literals assignments source functions and reserved words 11 4 Parenthesis matching Emacs and XEmacs have facilities for highlighting the parenthesis matching the parenthesis at point This feature is very useful when trying to examine which parentheses match each other This highlighting also indicates when parentheses are not matching Depending on what version of emacs you use one of the following should work in your initialisation file paren set mode paren for XEmacs show paren mode t for Emacs Chapter 11 Other ESS features and tools 57 11 5 Using graphics with ESS One of the main features of the S package is its ability to generate high resolution graphics plots and ESS provides a number of
76. for fixing mistakes C c C w backward kill word Deletes the previous word such as an object name on the command line C c C u comint kill input Deletes everything from the prompt to point Use this to abandon a command you have not yet sent to the ESS process C c C a comint bol Move to the beginning of the line and then skip forwards past the prompt if any See Section Shell Mode in The Gnu Emacs Reference Manual for other commands relevant to entering input 4 2 Manipulating the transcript Most of the time the cursor spends most of its time at the bottom of the ESS process buffer entering commands However all the input and output from the current and previous ESS sessions is stored in the process buffer we call this the transcript and often we want to move back up through the buffer to look at the output from previous commands for example Within the process buffer a paragraph is defined as the prompt the command after the prompt and the output from the command Thus M 4 and M move you backwards and forwards respectively through commands in the transcript A particularly useful command is M h mark paragraph which will allow you to mark a command and its entire output for deletion perhaps For more information about paragraph commands see Section Paragraphs in The GNU Emacs Reference Manual If an ESS process finishes and you restart it in the same process buffer the output from the new ESS process
77. for the directory to change to It will then change directory within the S buffer and also update the emacs variable default directory Alternatively if you have already executed setwd press M RET within the S buffer so that Emacs can update default directory Chapter 13 ESS for SAS 67 13 ESS for SAS ESS SAS was designed for use with SAS It is descended from emacs macros developed by John Sall for editing SAS programs and SAS mode by Tom Cook Those editing features and new advanced features are part of ESS SAS The user interface of ESS SAS has similarities with ESS S and the SAS Display Manager 13 1 ESS SAS Design philosophy ESS SAS was designed to aid the user in writing and maintaining SAS programs such as foo sas Both interactive and batch submission of SAS programs is supported ESS SAS was written with two primary goals 1 The emacs text editor provides a powerful and flexible development environment for programming languages These features are a boon to all programmers and with the help of ESS SAS to SAS users as well 2 Although a departure from SAS Display Manager ESS SAS provides similar key def initions to give novice ESS SAS users a head start Also inconvenient SAS Display Manager features like remote submission and syntax highlighting are provided trans parently appealing to advanced ESS SAS users 13 2 ESS SAS Editing files ESS SAS is the mode for editing SAS language files This mod
78. formed over all known S object names instead of file names ESS maintains a list of all objects known to S at any given time which basically consists of all objects functions and datasets in every attached directory listed by the search command along with the component objects of attached data frames if your version of S supports them For example consider the three functions available in Splus version 3 0 called binomplot binom test and binomial Typing bin TAB after the S prompt will insert the characters om completing the longest prefix binom which distinguishes these three commands Pressing TAB once more provides a list of the three commands which have this prefix allowing you to add more characters say which specify the function you desire After entering more characters pressing TAB yet again will complete the object name up to uniqueness etc If you just wish to see what completions exist without adding any extra characters type M ess list object completions Command M List all possible completions of the object name at point ESS also provides completion over the components of named lists and environments after S4 classes slots after package and namespace objects after and Completion is also provided over file names which is particularly useful when using S functions such as get or scan which require fully expanded file names In the Inferior ESS buffer
79. function Edit the function as appropriate and dump back in to the HH process buffer C c C b Return to the S PLUS process buffer C c C y Continue working 4 When you need help use C c C v rchisq instead of entering help rchisq 12 6 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 S43 we ve stuck you with Simply edit the ess dialect alist entry in the ess sp3 d el and ess s4 d el files to be S instead of S4 and S43 This will ensure that all the inferior process buffer names are S 2 Suppose that you WANT to have the first buffer name indexed by 1 in the same manner as your S PLUS processes 2 3 4 and 5 for you heavy simulation people Then 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 4 When you change directory within a R or S session using the setwd command emacs does not recognise that you have changed the current directory Solution Use M x ess change directory his will prompt you
80. gion and go suus 33 ess eval region or function or paragraph T intone 33 ess eval region or function or paragraph A A ep reU Spe eee pp 33 ess eval region or line and step 33 ess execute objects 6c cece eee eee 30 ess execute search eee eee eee eee 31 ess goto beginning of function or para 39 ess goto end of function or para 39 ess handy commands eee eens 55 ess indent command 0 cece eee 52 A lo AAA dae pee lee ppt 38 ess indent or complete suse 3T ess list object completions 45 ess Ioad file oc cine nr Rr eR 31 36 ess mark function sess 39 ess parse errOorS e ees 31 37 A EE 31 44 ess R complete object name 52 o AA 2 83 ess request a procesS s seeeesse 21 G8S reSynch 2 36 2 ocaneim waders Re Ded LIESS 45 ess roxy hide all i dee dog e eeIy be S 52 ess roxy next entry s sss eee d eee 52 ess roxy preview HTML oooooooooo o 52 ess roxy preview Rd sss 51 ess roxy previous entry eee 52 ess roxy toggle roxy region 51 ess roxy update entry esee 51 ess rutils apropos sees 59 ess rutils html docs eee 59 ess rutils load WKSpC cepere eg 59 ess Cutile Local pkee 59 e NEE 59 ess rutils repos pkgs ee 59 e RE
81. he prompt from those lines that remain Useful to paste code from emails documentation inferior ESS buffers or transcript files e Documentation ESS user manual has been rearranged and completed with several new chapters and sections to reflect newly added features Completion Developing with ESS ESS tracebug ESS developer ESS ElDoc IDO Completion and Evaluating Code e RefCard Reference card was updated to include new features e Eldoc Eldoc was rewritten and is activated by default See ess use eldoc ess eldoc show on symbol ess eldoc abbreviation style variables for how to change the default behavior Note skeleton pair insert maybe prohibits eldoc display on insertion e ESS R Eldoc shows arguments of a generic function whenever found e ESS TAB in ess mode now indents and completes if there is nothing to indent Set ess first tab never completes p to t to make TAB never complete on first invoca tion Completion mechanism is similar to the completion in the inferior ess mode a filename expansion is tried if not found ESS completes the symbol by querying the process e ESS for emacs version 24 or higher ESS is fully compatible with the emacs 24 com pletion scheme i e all the completion is done by completion at point Also in accordance with emacs conventions ESS doesn t bind M TAB for emacs 24 or higher M TAB calls the default complete symbol e ESS R Out of the box integrati
82. hod to use tooltip instead of an electric buffer e ESS New command ess build tags for directory bound to C c C e C t for build ing dialect specific tag tables After building tags use M to navigate to function and objects definitions By default C c C e C t builds tags based on imenu regular ex pressions and also include other common languages c o cpp etc But it relies on external find and etags commands If ess build tags command is defined for R the inferior process is asked to build tags instead e ESS ess switch process offers new alternative to start a new process instead of switching to one of the currently running processes e ESS Switching between processes C c C s uses buffer names instead of the internal process names Use M x rename buffer command to conveniently rename your process buffers e ESS Process buffers can be automatically named on process creation according to user specified scheme Default schemes are proc proc dir and proc abbr long dir where proc stands for the internal process name and dir stands for the directory where the process was started in The default is proc For customization see ess gen proc buffer name function e ESS ess eval visibly p is deprecated in favor of ess eval visibly e ESS New evaluation pattern nowait In addition to old nil and t values ess eval visibly accepts nowait for a visible evaluation with no waiting for the process See ess eval visibly for deta
83. iately ESS SAS ess sas edit keys toggle default returns to nil ESS R support for prettify symbols mode contribution from Rudiger Sonderfeld https github com emacs ess ESS pu11 65 ESS SW V knitr now evaluates in the current frame ESS developer ess developer doesn t kill open DESCRIPTION files anymore ESS roxygen ess roxy preview HTML is now on C c C o C w and ess roxy preview text is now on C c C o C t ESS installation with make install was simplified and should work out of the box on most nix systems ESS installation instructions simplified fixed font lock bug introduced in 13 09 that was causing very slow process output Changes New Features in 13 09 Chapter 1 Introduction to ESS 6 e font lock in process buffers doesn t spill over prompts Missing closing string delim iters should not cause wrong fontification of the following command input e ESS julia full features M TAB completion and auto complete support which now works for modules structures and data types e ESS julia a much better eldoc showing arguments of methods and data type construc tors e ESS developer ESS developer work flow pattern has been streamlined ESS developer is now au tomatically activated on per file basis if the file is part of a developed package ess developer packages The old behavior activation on per process basis is still available on M x ess developer in a process buffer integration with devtools
84. ided to control the amount of indentation in each case and there are also a number of predefined indentation styles to choose from Comments are also handled specially by ESS using an idea borrowed from the Emacs Lisp indentation style By default comments beginning with are aligned to the begin ning of the line Comments beginning with are aligned to the current level of indentation for the block containing the comment Finally comments beginning with are aligned to a column on the right the 40th column by default but this value is controlled by the variable comnent column or just after the expression on the line containing the comment if it extends beyond the indentation column You turn off the default behavior by adding the line setq ess fancy comments nil to your emacs file ESS also supports Roxygen entries which is R documentation maintained in the source code as comments See Section 10 2 2 Roxygen page 51 The indentation commands provided by ESS are ess indent or complete Command TAB Indents the current line as S code Try to indent first and if code is already properly indented complete instead In ess mode only tries completion if ess tab complete in script is non nil See also ess first tab never complete ess tab complete in script User Option If non nil TAB in script buffers tries to complete if there is nothing to indent Chapter 7 Editing objects and functions 38 ess fir
85. if the cursor is not in a string and does not follow a partial object name the TAB key has a third use it expands history references See Section 4 4 History expansion page 29 Efficiency in completion is gained by maintaining a cache of objects currently known to S when a new object becomes available or is deleted only one component of the cache corresponding to the associated directory needs to be refreshed If ESS ever becomes con fused about what objects are available for completion such as when if refuses to complete an object you know is there the command M x ess resynch forces the entire cache to be refreshed which should fix the problem Chapter 9 Completion 46 9 2 Completion of function arguments When inside a function call i e following TAB completion also provides function arguments If function is a generic completion will provide all the arguments of S3 methods known to R A related functionality is See Section 11 1 ESS ElDoc page 55 which displays function arguments in the echo area whenever the point is inside a function call 9 3 Minibuffer completion From version 12 03 ESS uses IDO mechanism part of default emacs for minibuffer com pletion if ido el package is available and the value of ess use ido it t the default The completion command ess completing read falls back on classic completion read interface if this feature is not available for whatever reason 9 4 Integration with auto c
86. ile should be given a unique file name usually the dumped object name with some additions ess dump filename template User Option Template for filenames of dumped objects s is replaced by the object name By default dump file names are the user name followed by and the object and end ing with S Thus if user joe dumps the object myfun the dump file will have name joe myfun S The username part is included to avoid clashes when dumping into a publicly writable directory such as tmp you may wish to remove this part if you are dumping into a directory owned by you You may also specify the directory in which dump files are written ess source directory User Option Directory name ending in a slash where S dump files are to be written By default dump files are always written to tmp which is fine when ess keep dump files is nil If you are keeping dump files then you will probably want to keep them somewhere in your home directory say S source This could be achieved by including the following line in your emacs file setq ess source directory expand file name S source If you would prefer to keep your dump files in separate directories depending on the value of some variable ESS provides a facility for this also By setting ess source directory to a lambda expression which evaluates to a directory name you have a great deal of flexibility in selecting the directory for a particular source file to
87. ils on evaluation patterns Chapter 1 Introduction to ESS 9 e ESS New Process menu entry with process related commands and configuration e iESS Process buffer is now automatically shown on errors e ESS New ess switch to inferior or script buffer command bound to C c C z in both script and process buffers If invoked form process buffer it switches to the most recent buffer of the same dialect It is a single key command e ESSR help On multiple help pages with the same name C c C v now asks for user resolution directly in emacs e ESS R ess roxy new variable ess roxy re for fontification of cases where the number of leading differs from ess roxy str e ESS R Eldoc was considerably enhanced It now finds hidden default 53 methods and displays non default methods arguments after trailing e ESS R New ess display demos command bound to C c C d o and C c C d C o e ESS New ess help web search command bound to C c C d w and C c C d C w to facilitate interactive search of web resources Implemented for R Stata and Julia See also ess help web search command e ESS ess pdf viewer pref accepts now command line arguments e ESS Rnw Add knitr support Customize ess swv processor for the default proces sor e ESS Rnw More thorough renaming of remaining noweb to ess noweb e ESS Rnw new commands ess eval chunk and step and ess eval chunk bound to M n C c and M n C M x to mirror standard ess commands in C c map
88. in Emacs From within the ESS process buffer or any ESS edit buffer typing C c C v ess display help on object will prompt you for the name of an object for which you would like documentation Completion is provided over all objects which have help files If the requested object has documentation you will be popped into a buffer named help obj name containing the help file This buffer is placed in a special S Help mode which disables the usual editing commands but which provides a number of keys for paging through the help file Help commands ess describe help mode Pops up a help buffer with a list of the commands available in S help mode h ess display help on object Pop up a help buffer for a different object Paging commands b DEL scroll down Move one page backwards through the help file SPC scroll up Move one page forwards through the help file gt lt end of buffer Move to the beginning and end of the help file respectively Section based motion commands D ess skip to previous section and ess skip to next section Move to the next and previous section header in the help file respectively A section header consists of a number of capitalized words followed by a colon In addition the s key followed by one of the following letters will jump to a particular section in the help file Note that R uses capitalized instead of all capital section headers e g Description instead of DESCRIPTION and a
89. ing buffer C c and jumps through this buffers if still alive or in original org buffer otherwise New keys in watch mode and d wo new hooks ess tracebug enter hook and ess tracebug exit hook e ESS R New package ess developer to evaluate R code directly in the package environ ment and namespace It can be toggled on and off with C c d t When ess developer is on all ESS evaluation commands are redefined to evaluate code in appropriate en vironments Add package names to the list of your development packages with C d a and remove with C d r Source the current file with C d s Evaluation function which depend on ess eval region ask for the package to source the code into ess eval function and alternatives search for the function name in the development packages environment and namespace and insert the definition accordingly See the documenta tion section Developing with ESS ESS developer for more details e ESS R help system New Features qquits window instead of calling ess switch to end of ESS This is consistent with emacs behavior help and other special buffers breaking change k kills window without asking for the name pointed by Sam Steingold Help map inherits from special mode map as sugested by Sam Steingold Package index new function ess display index bound to iin help mode map Package vignettes new function ess display vignettes bound to vin help mode map Display h
90. initions in the edit buffer ess goto beginning of function or para Command ESC C a aka C M a If inside a function go to the beginning of it otherwise go to the beginning of paragraph ess goto end of function or para Command ESC C e aka C M e Move point to the end of the function containing point ess mark function Command ESC C h aka C M h Place point at the beginning of the S function containing point and mark at the end Don t forget the usual Emacs commands for moving over balanced expressions and paren theses See Section Lists and Sexps in The GNU Emacs Reference Manual Completion is provided in the edit buffer in a similar fashion to the process buffer TAB first indents and if there is nothing to indent completes the object or file name M lists file completions See See Chapter 9 Completion page 45 for more Finally C c C z ess switch to inferior or script buffer returns you to the iESS process buffer if done from a script buffer placing point at the end of the buffer If this is done from the iESS process buffer point is taken to the script buffer In addition some commands available in the process buffer are also available in the script buffer You can still read help files with C c C v edit another function with C c C e C d and of course C c C 1 can be used to load a source file into 7 6 Maintaining S source files Every edit buffer in ESS is associated with a dump file on disk Dump files are
91. is delay is currently set high enough so as not to be a problem 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 or xemacs init el file by setq ess sleep for 0 2 For example setq ess sas global unix keys t keys shown setq ess sas global pc keys t in parentheses ESS SAS function keys are presented in the next section Open the file you want to work with C x C f foo sas foo sas will be in ESS SAS mode Edit as appropriate then save and submit the batch SAS job F3 F8 The job runs in the shell buffer while you continue to edit foo sas If ess sas submit method is sh then the message buffer will display the shell notification when the job is complete The sh setting also allows you to terminate the SAS batch job before it is finished F8 F3 Terminating a SAS batch in the shell buffer kill PID You may want to visit the log whether the job is still running or it is finished and check for error messages The Log will be refreshed and you will be placed in it s buffer You will be taken to the first error message if any F5 F6 Goto the next error message if any Chapter 13 ESS for SAS 70 F5 F6 Now refresh the 1st and go to it s buffer F6 F7 If you wish to make changes go to the sas file with F4 F5 Make your editing changes and submit again F3 F8 13 5 ESS SAS Function key
92. it Rey een tidak ER 16 command history a K EN ed 27 command line arguments 0 61 command line completion sssssrsrereru 45 command line edt ng 25 ege te EE 25 COMMENTS siii dins 40 comments 1n Beien owner enk ee EE EEN 37 completion in edit buffer o o ooooooomm m 39 completion of object name 45 Indices completion on file names sssssrurreren 45 completion on lists 45 completion when prompted for object names 36 creating new obiects 0 200 36 CROCUS derre AE a ras 16 customization EEN 81 D data Tames e ENEE EE RENE 45 deleting output 00 e eee 26 directories sess A tn 21 dump file d rectories eee eee 41 dump file names esses ee E ER eere 41 dump files 22 esed or edu ardid 36 39 E echoing commands when evaluating 33 edit o 36 editing commande 27 editing Dunctions skirti tsue 36 editing transcripts 27 BID OC eer staan bere cite meee dee 55 EE 32 entering Commande 25 EE 37 ess developer 52 ESS process butter 21 ESS process directory 0008 21 ESS tracebug o set a rete e Aber de 48 ESS elsewhere 00 0 eee e eee eee ee 21 ESS TORY EE 51 evaluating code with echoed commands 33 evaluating S expressions 005 33 F font lock mode 56 formatting source Code 3T G ee iii E aR 57 H Handy commande 55 help fileg z 1 eine tene eger er pem sa eps 43 highlighting e
93. ive DO statement TO and BY are not highlighted Chapter 13 ESS for SAS 68 13 3 ESS SAS TAB key 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 sas indent width spaces from the margin continuation lines are indented sas indent width 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 activated by placing the following line in your initialization file prior to a require load setq ess sas edit keys toggle nil ESS provides an alternate behavior for TAB that makes it behave as it does in SAS Display Manager i e move the cursor to the next stop The alternate behavior also provides a TAB backwards C TAB that moves the cursor to the stop to the left and deletes any characters between them This functionality is obtained by placing the following line in your initialization file prior to a require load setq ess sas edit keys toggle t Under the alternate behavior TAB is bound to M x tab to tab stop and the stops are defined by ess sas tab stop list 13 4 ESS SAS Batch SAS processes Submission of a SAS batch job is dependent on your environment ess sas submit method is determined by your operating system and your shell It defaults to sh unless you are running Windows or Mac Cl
94. ject you were editing in a previous session and which possibly was never loaded to the S session Finally if both these tests fail the ESS process is consulted and a dump O command issued If you want to force ESS to ask the ESS process for the object s definition say to reformat an unmodified buffer or to revert back to S s idea of the object s definition pass a prefix argument to ess dump object into edit buffer by typing C u C c C e C d 7 2 Loading source files into the ESS process The best way to get information particularly function definitions into S is to load them in as source file using S s source function You have already seen how to create source files using C c C e C d ESS provides a complementary command for loading source files even files not created with ESS into the ESS process namely ess load file C c C 1 see Section 4 5 Hot keys page 30 After typing C c C 1 you will prompt for the name of the file to load into S usually this is the current buffer s file which is the default value selected by simply pressing RET at the prompt You will be asked to save the buffer first if it has been modified this happens Chapter 7 Editing objects and functions 37 automatically if the buffer was generated with C c C e C d The file will then be loaded and if it loads successfully you will be returned to the ESS process 7 3 Detecting errors in source files If any errors occur when loading a file with C c C
95. ll get eventually to package foo Thus all methods and functions de fined in GlobalEnv can see objects in package foo environment See also http cran r project org doc manuals R ints html Namespaces In order to use ess developer you must add names of the packages that you are developing to ess developer packages You can also do that interactively with C c C t C a To remove packages from ess developer packages use C c C t C r When developer mode is on the process mode line indicator displays a small or capital letter d If variable ess developer activate in package is t the default R mode will check after visiting the file whether or not the file is part of the package If visited file is part of a package listed in ess developer packages developer mode is activated automatically Developer mode is usually activated on per file basis and a small d appears in the modeline You can also activate ess developer for all buffers connected to current process This is done by toggling ess developer in subprocess buffer In this case a big D will appear in the modeline ess developer val Command C c C t C t Toggle developer mode on and off If called from script buffer toggle developer on file by file basis When called from process buffer toggle developer on per process basis ess developer add package from attached remove Command C c C t C a Add a package to your development list ess developer packages ess devel
96. lso only some versions of S plus have sections BACKGROUND BUGS OPTIONAL ARGUMENTS REQUIRED ARGUMENTS and SIDE EFFECTS Do use s to get the current list of active key bindings a ARGUMENTS bi BACKGROUND B BUGS d DESCRIPTION D DETAILS ei EXAMPLES n NOTE 0 OPTIONAL ARGUMENTS Chapter 8 Reading help files 44 R REQUIRED ARGUMENTS Y REFERENCES tg SEE ALSO d SIDE EFFECTS y USAGE y VALUE e Jumps to beginning of file gt Jumps to end of file q Pops up a help buffer with a list of the defined section motion keys Evaluation 1 ess eval line and step Evaluates the current line in the ESS process and moves to the next line Useful for running examples in help files f ess eval region Send the contents of the current region to the ESS process Useful for running examples in help files Quit commands q ess help quit Return to previously selected buffer and bury the help buffer kill buffer Return to previously selected buffer and kills the help buffer x ess kill buffer and go Return to the ESS process killing this help buffer Miscellaneous i ess display index Prompt for a package and display it s help index v ess display vignettes Display all available vignettes Ww ess display help in browser Display current help page with the web browser isearch forward Same as C s In addition all of the ESS commands available in the
97. mpt on an existing R object to generate a non empty Rd shell documenting the object which already has all information filled in which can be obtained from the object C c C f Insert font specifiers for some of the Rd markup commands markup available for emphasizing or quoting text including markup for URLs and email addresses Rd font C c C f is only a prefix see e g C c C f TAB for the available bindings Note that currently not all of the Rd text markup as described in section Marking text of Writing R Extensions can be accessed via C c C f C c C j Insert a suitably indented item on the next line Rd mode insert item C c C p Preview a plain text version help file see Chapter 8 Help page 43 gener ated from the Rd file Rd preview help In addition when editing Rd files one can interact with a running R process in a similar way as when editing R language files E g C c C v provides access to on line help and C c C n sends the current line to the R process for evaluation This interaction is particularly useful when editing the examples in the Rd file See C h m for all available commands Rd mode also provides access to abbreviations for most of the Rd markup commands Type M x list abbrevs with Abbrev mode turned on to list all available abbrevs Note that all Rd abbrevs start with a grave accent Rd mode can be customized via the following variables Rd mode hook User Option
98. n a graphics viewer on the local machine Most statistical software can write one or more of postscript GIF or JPEG files Depending on the versions of emacs and the operating system that you are running emacs itself may display gif and jpg files Otherwise a graphics file viewer will be needed Ghostscript ghostview may be downloaded to display ps and eps files Viewers for GIF and JPEG are usually included with operating systems See Section 13 5 ESS SAS Function keys for batch processing page 70 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 Chapter 3 Interacting with statistical programs 23 We have two older commands now deprecated for accessing ESS processes on remote computers See Section 3 4 S elsewhere and ESS elsewhere page 23 3 4 S elsewhere and ESS elsewhere These commands are now deprecated We recommend ess remote We have two versions of the elsewhere function Stelsewhere is specific for the S Plus program The more general function ESS elsewhere is not as stable 1 Enter M x Stelsewhere You will be prompted for a starting directory I usually give it my project directory on the local machine say mynam
99. n be viewed and set using the Custom facility within Emacs Type M x customize group RET ess RET to see all the ESS variables that can be cus tomized Variables are grouped by subject to make it easy to find related variables Indices Indices Key index 9 da tano 55 EEN 38 RE 38 C GHGs des EE 38 GEG unie I ELA Sat ot tn ets Beaten tase 31 37 SS Rm 59 PII ME WEE 59 EI IO QE ADR 59 Uc UP uerbo aun MP CPC RE EIN MK P RET 59 GCF EE 59 76 CAs EE 59 Q 6 Uo EE 59 adc steam 59 el E 59 luxu O A E e E E h 59 sa 34 e ENER 32 e 33 GHC CH EE 36 C C CHE cp el Oe pM 33 xor E 33 CHC CH ci ars Oks eee ened EEG RES ERG E 31 A Dade Did sumpnbNs d n Td 51 A egppi tacui pepe ELE ed 52 G36 C 0 EE EE 51 CAC CROC EE e CHC 0 0 Cu ri ad id 52 6 0 0 EE 52 Ce CHO Dussni ensi redu bone Pre uM DURS 52 pae pm n 31 n Ee EE 33 ee EET od CO DEPUES 53 A dade supe bue ied 53 C C b DL 5 550555 IAE EA 53 Function and program index B backward kill word esee sss 25 82 eg A eee ae EP Es 53 gc 31 Oc CHW ciuis a cies 35 UG CX Lbs piod v adea Po oO MO edP 30 eo E 32 COM Dier suite epit eben a 34 GAG MSP rd saint ete cob Sok ae ap UNE 39 DM E E DUE AIT LEER ES 33 GAG Mar o orem ep In tos 39 CC RET cerak gessi ut uus E EST EM I Pis Eres 35 O Po E EEE 38 E EE 39 ed E a ccna dag Seah eee sb Rn Qed 39 CAM DEE 39 et o EE 38 E EE 33 EEN 31 E ESCOTE
100. n your working directory A prefix argument of 2 or more means get objects for that position A negative prefix argument posn gets the objects for that position as well as toggling ess execute in process buffer Chapter 4 Interacting with the ESS process 31 ess execute search invert Command C c C s Sends the inferior ess search list command command to the ess language process search in S Prefix invert toggles ess execute in process buffer ess execute may seem pointless when you could just type the command in anyway but it proves useful for spot calculations which would otherwise clutter your transcript or for evaluating an expression while partway through entering a command You can also use this command to generate new hot keys using the Emacs keyboard macro facilities see Section Keyboard Macros in The GNU Emacs Reference Manual The following hot keys do not use ess execute in process buffer to decide where to display the output they either always display in the process buffer or in a separate buffer as indicated ess load file filename Command C c C 1 Prompts for a file filename to load into the ESS process using source If there is an error during loading you can jump to the error in the file with the following function ess parse errors arg reset Command C c or C x Visits next next error message and corresponding source code If all the error messages parsed so far have been processed alre
101. ng for the starting directory Incidentally ess directory is an ideal variable to set in ess pre run hook If you like to keep a record of your S sessions set the variable ess ask about transfile to t and you will be asked for a filename for the transcript before the ESS process starts ess ask about transfile User Option If non nil as for a file name in which to save the session transcript Enter the name of a file in which to save the transcript at the prompt If the file doesn t exist it will be created and you should give it a file name ending in St if the file already exists the transcript will be appended to the file Note if you don t set this variable but you still want to save the transcript you can still do it later see Section 4 2 4 Saving transcripts page 27 Once these questions are answered if they are asked at all the S process itself is started by calling the program name specified in the variable inferior ess program If you need to pass any arguments to this program they may be specified in the variable inferior S_ program name args e g if inferior ess program is S then the variable to set is inferior S args It is not normally necessary to pass arguments to the S program in particular do not pass the e option to Splus since ESS provides its own command history mechanism By default the new process will be displayed in the same window in the current frame If you wish your S proce
102. nged to t Set it to nil if you want to keep the previous behavior ESS tracebug Electric debug keys have been removed breaking change The function ality was replaced with ess debug minor mode and ess debug minor mode map ESS tracebug ess tracebug map is an alias to ess dev map C c C t ESS tracebug ess bp toggle state C c C t o can now be used during the debug session to toggle breakpoints on the fly suggestion by Ross Boylan ESS tracebug ess debug flag for debugging and ess debug unflag for debugging work correctly from the debugging contexts These commands also recognize non exported functions for the packages listed in ess developer packages C c C t C a ESS R Eldoc activated by ess use eldoc has become more sophisticated and hence also more intruding in the interface between the Statistics softare e g R and the user Note that you can turn off ElDoc by placing setq ess use eldoc nil in your emacs file prior to loading ESS ESS SAS long over looked SAS mode hook appears ESS SAS ess sas edit keys toggle now defaults to t since sas indent line is still broken i e TAB is now bound to ess sas tab to tab stop by default Changes Bug Fixes in 12 09 2 ESS new ess switch to end of proc buffer variable that controls whether C c C z switches to the end of process buffer The default is t You can use prefix argument to C c C z to toggle this variable ESS fix in ess eval linewise that was
103. ni e Stephen Eglen e Sebastian P Luque e Henning Redestig e Vitalie Spinu 1 4 Getting the latest version of ESS The latest released version of ESS is always available on the web at ESS web page or StatLib 1 4 1 Git for ESS development For development and experimentation on new ESS features there is now a GitHub branch for ESS available at https github com emacs ess ESS 1 5 How to read this manual If you need to install ESS read Chapter 2 Installation page 19 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 lt chr gt means hold the CONTROL key while typing the character lt chr gt M lt chr gt means hold the META or EDIT or ALT key down while typing lt chr gt If there is no META EDIT or ALT key instead press and release the ESC key and then type lt chr gt 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 Chapter 1 Introduction to ESS 18 a consistent user interface within emacs regardless of the details of which programming language is being edited or process being run
104. none regex AC t E Mtl lt t function 1 R This will find entries in your source file of the form some name lt function with the function name starting in column 0 Windows users may need to change the single quotes to double quotes R version 2 9 0 introduced a front end script for finding R tags which calls the rtags function By default this script will recursively search the directories for relevant tags in R C Rd files To use this script from the command line try the following to get started R CMD rtags help For further details see http developer r project org rtags html 11 9 Rdired Ess rdired provides a dired like buffer for viewing editing and plotting objects in your current R session If you are used to using the dired directory editor facility in Emacs this mode gives you similar functionality for R objects Start an R session with M x R and then store a few variables such as s lt sin seq from 0 to 8 pi length 100 x lt c 1 4 9 y lt rnorm 20 z lt TRUE Then use M x ess rdired to create a buffer listing the objects in your current environ ment and display it in a new window mode length s numeric 100 x numeric 3 y numeric 20 Z logical 1 Type C h m or to get a list of the keybindings for this mode For example with your point on the line of a variable p will plot the object v will view it and d will mark the object for
105. ome function other function argl arg2 e ESS SAS Improved MS RTF support for GNU Emacs try ess sas rtf portrait and ess sas rtf landscape Changes Bug Fixes in 12 04 3 e ESS basic support for package el compatibility e ESS R correct indentation of amp and continuation lines e M x ess version shows the svn revision even after make install e ESS SAS improved XEmacs support e ESS R better finding of previous prompt e ESS Stata adjusted prompt for mata mode e ESS R resolved name clashes with cl el e ESS R removed dependence on obsolete package assoc Chapter 1 Introduction to ESS 12 New make target lisp to build the lisp only part i e not building the docs Changes New Features in 12 04 1 iESS Stata New interactive help invocation iESS Stata New custom variable inferior STA start file iESS Stata inferior STA program name is now stata and can be customized ESS Stata New sections in stata help files Syntax s S Remarks r Title t Bug Fixes in 12 04 1 ESS R Better ess tracebug error handling ESS R Corrected ess eldoc help string filtering and improved argument caching ESS R Indentation of non block if else for while lines fixed M x ess version should work better ESS Filename completion now again works inside strings iESS Stata Fixed prompt detection issue ESS Rd R is autostarted also from here when needed Changes New Features in 12 04 ESS Reverting new behavi
106. ommand line arguments to pass to the S process Here is an example setting setq ess s versions list Chapter 12 Overview of ESS features for the S family 63 Splus64 usr local bin Splus64 Splus64 j usr local bin Splus64 j which will then allow you to do M x Splus64 j to start Splus64 with the corresponding command line arguments If you change the value of either ess s versions or ess s versions list you should put them in your emacs before ess site is loaded since the new emacs functions are created when ESS is loaded Sqpe S Plus running inside an emacs buffer on Windows systems If you have an older version of S Plus S Plus 6 1 for example on your system ir can be started inside an emacs buffer with M x splus61 By default ESS will find versions of S Plus located in the installation directories that Insightful uses by default If your versions of S Plus are anywhere else you will need to change the variable ess SHOME versions To see which functions have been created for starting different versions of S Plus type M x spl and then hit Tab These other versions of S Plus can also be started from the ESS gt Start Process gt Other menu 12 3 ESS help assistance with viewing help ESS has built in facilities for viewing help files from S See Chapter 8 Help page 43 12 4 Philosophies for using ESS S The first is preferred and configured for T he second one can be retrieved again by changing
107. omplete package ESS provides three sources for Auto Completion mode ac source R args ac source R objects and ac source R The last one combines the previous two and makes them play nicely together See auto complete package documentation http cx4a org software auto complete for how to modify and install your own completion sources For the default auto complete ESS configuration install the latest version of auto complete package ESS automatically detect the package and activates auto complete in ESS buffers To deactivate AC place the following into your init file setq ess use auto complete nil Or to activate auto completion only in the ess mode buffers setq ess use auto complete script only ESS provides AC help both for arguments and objects default keys C or lt f1 gt You can bind M h to display quick help pop ups define key ac completing map kbd M h ac quick help AC binds M n and M p for the navigation in the completion menu which might be inconvenient if you want it to use in the inferior R Bind it to something else define key ac completing map M n nil was ac next define key ac completing map M p nil was ac previous define key ac completing map M ac next define key ac completing map M k ac previous 9 5 Icicles Another option for comprehensively handling completion in Emacs is via Icicles http www emacswiki org emacs Icicles It allows users to have compl
108. on with Auto Completion mode http cx4a org software auto completeff Three AC sources ac source R args ac source R objects and ac source R are provided The last one combines the previous two and makes them play nicely together Set ess use auto complete to t to start using it Refer to documentation string of ac use auto complete for further information e ESS R New unified and fast argument completion system comprised of ess funname start ess function arguments ess get object at point Eldoc and auto completion integration are using this system e ESS ess switch to end of ESS C c C z and ess switch to ESS C c C y Au tomatically start the process whenever needed e ESS R roxy knows about previewing text version of the documentation Bound to C c C e t e ESS R Solved the nil filename bug in roxygen support e ESS R ess tracebug is now part of ESS New Features Source injection Tracebug now can inject source references on the fly during code evaluation i e you don t have to source your file but just evaluate your code in Chapter 1 Introduction to ESS 14 normal fashion Variable ess tracebug inject source p controls this behavior if t always inject source reference if function inject only for functions this is the default if nil never inject During the source injection the value of ess eval visibly is ignored Org mode support Visual debugger is now aware of the temporary org source edit
109. oper remove package Command C c C t C r Remove a package from your development list When you add a package to ess developer packages ESS will ask for loading com mand By default there are two options library and load_all from devtools package You can configure this behavior in ess developer load on add commands To explisitely load the package containing current file use C c C t 1 ess developer load package Command C c C t 1 Load package with Load all utility from devtools package When developer mode is on ESS evaluation commands behave differently e C c C 1 ess load file asks for the package to source into and inserts all redefined objects into the package foo or namespace foo accordingly PLAIN OBJECTS and FUNCTIONS If the object is found in an environment package foo or namespace foo and differs from the old one it is assigned into the corresponding environment If the object is not found it is assigned into GlobalEnv The environment of functions is set to namespace foo CLASSES Same as plain objects with the difference that even if the class definition is assigned into GlobalEnv it is still associated with the package foo Thus if you issue getClassDeff foo you will get a class definition with the slot package pointing to package foo Chapter 10 Developing with ESS 54 Note Occasionally after adding new classes you might get warnings from setClass This is especially true if new class inheri
110. or of 12 03 TAB in ess mode no longer completes by default If you want smart TAB completion in R and S scripts similarly to iESS behavior set the variable ess tab complete in script to t Also see ess first tab never complete for how to customize where first TAB is allowed to complete ESS completion is consistently bound to M TAB aka M C i in both Emacs23 and Emacs24 ESS The variable ess arg function offset new line introduced in ESS 12 03 now accepts a list with the first element a number to indicate that the offset should be computed from the indent of the previous line For example setting it to 2 results in a lt some function argl arg2 Changes New Features in 12 03 ESS indentation new offset variable ess arg function offset new line controlling for the indentation of lines immediately following open This is useful to shift backwards function arguments after a long function call expression a lt some function argl arg2 instead of the old a lt some function argl arg2 If is not followed by new line the behavior is unchanged Chapter 1 Introduction to ESS 13 a lt some function arg1 arg2 This variable should be set as part of indentation style lists or in ess mode hook e ESS R C c sets indentation style e ESS In ESS buffers yank C y command accepts double argument C u C u to paste commands only It deletes any lines not beginning with a prompt and then removes t
111. packages R S PLUS SAS Stata OpenBUGS and JAGS ESS supports current and recent stable versions of GNU Emacs currently specifically the 23 x and 24 x series alpha beta pre release versions are NOT SUPPORTED Non Windows users beware GNU Emacs 24 3 is preferable to 24 1 or 24 2 these broken builds suffer from bug 12463 http debbugs gnu org cgi bugreport cgi bug 12463 which will cause emacs and ESS to get progressively slower over time Due to XEmacs lacking some features that ESS requires ESS support of XEmacs ends with ESS 12 04 4 This decision will be re visited in the future as XEmacs continues to sync with GNU Emacs To build the PDF documentation you will need a version of TeX Live or texinfo that includes texi2dvi BEWARE recent TeX Live and some texinfo RPMs do NOT include texi2dvi Chapter 3 Interacting with statistical programs 21 3 Interacting with statistical programs As well as using ESS to edit your source files for statistical programs you can use ESS to run these statistical programs In this chapter we mostly will refer by example to running S from within emacs The emacs convention is to name such processes 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 3 1 Starting an
112. process eee e ee 21 3 3 ESS processes on Remote Computers 21 3 4 S elsewhere and ESS elsewhere 2000 e eee eee ee eee 23 3 5 Changing the startup actions 23 4 Interacting with the ESS process 25 4 1 Entering commands and fixing mistakes ooooomooo o o 25 4 2 Manipulating the transcnnpt eee 25 4 2 1 Manipulating the output from the last command 26 4 2 2 Viewing older commande 26 4 2 3 Re submitting commands from the transcript 26 4 2 4 Keeping a record of your S session 000s eee eee 27 4 3 Command History 27 4 3 1 Saving the command store 29 4 4 References to historical commande 29 4 5 Hot keys for common commande 30 4 6 Is the Statistical Process running under ESS 31 4 7 Using emacsclient eee eee eens 32 4 8 Other commands provided by mifertor k p 32 5 Sending code to the ESS process 33 6 Manipulating saved transcript files 35 6 1 Resubmitting commands from the transcript file 35 6 2 Cleaning transcript Des 35 7 Editing objects and functions 36 7 1 Creating or modifying S objects 0 cece eee eee ee 36 7 2 Loading source files into the ESS process 2000005 36 7 3 Detecting errors in source Des 37 7 4 Indenting and formatting S code o 7 4 1 Changing indentation styles ec cee eee eee 38 7 5 Commands for motion completion and more
113. provides several features which make it easier to interact with the ESS process a connection between your buffer and the statistical package which is waiting for you to input commands These include e 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 do not necessarily have features like this built in See Section 4 1 Command line editing page 25 e Searchable command history for recalling previously submitted commands This pro vides all the features of the Splus e history mechanism plus added features such as history searching See Section 4 3 Command History page 27 Chapter 1 Introduction to ESS 3 for 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 See Chapter 9 Completion page 45 Hot keys for quick entry of commonly used commands in S such as objects and search See Section 4 5 Hot keys page 30 Transcript recording for a complete record of all the actions in an S session See Section 4 2 Transcript page 25 Interface to the help system with a specialized mode for viewing S help files See Chapter 8 Help page 43 If you commonly create or modify S functions you will ha
114. providing line filling navigation template generation etc Syntax highlighting is provided for Emacs but not for XEmacs Roxygen is customized by the variables in the customization group Ess Roxy Cus tomizables include the Roxygen prefix use of folding to toggle visibility of Roxygen entries and the Roxygen template All ESS Roxygen support is defined in ess roxy el which is loaded by default in ESS The following special Emacs commands are provided ess roxy update entry Command C c C o C o Generate a Roxygen template or update the parameter list in Roxygen entry at point or above the function at the point Documented parameters that are not in the function are placed last in the list parameters that are not documented and not in the definition are dropped Parameter descriptions are filled if ess roxy fill param p is non nil ess roxy toggle roxy region beg end Command C c C o C c Toggle the presence of the leading Roxygen string on all lines in the marked region between beg and end Convenient for transferring text to Roxygen entries and to evaluate example fields ess roxy preview Rd name file Command C c C o C r Use the attached R process to parse the entry at point to obtain the Rd code Convenient for previewing and checking syntax When used with the prefix argument name file i e C u C c C e C r place the content in a buffer associated with a Rd file with the same name as the documentation Requires the Roxygen pa
115. r The buffer is in iESS S 3 1 mode HH Split the screen and go back to the file editing buffer C x 2 C x b myfile s HH 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 HH one line at a time with C c C n HH Save the revised myfile s with C x C s Save the entire S43 1 interaction buffer with C c C s You will be prompted for a file name The recommended name is ij 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 HH 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 HH edit program functions and code in myfile s and send revised HH 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 HH or load the entire buffer with C c C 1 HH save the revised myfile s when you have finished C c C s Chapter 12 Overview of ESS features for the S family 65 3 Program revision example S object is real HH 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
116. r and don t step to end of buffer or end of chunk code 0 when at the end of the code ESS ess handy commands function is bound to C c h ESS ESS is now blinking the evaluated region Set ess blink region to nil to deacti vate ess blink delay gives the duration of the blink Evaluated region is blinked in highlight face ESS R help New key a for apropos in help buffers Also available through C c h ESS R help All R commands of type foo bar and foo bar are recognized and redirected into appropriate ESS help buffers ESS R New customization interface for font lock ESS font lock operates with predefined keywords Default keywords are listed in ess R font lock keywords and inferior R font lock keywords which see The user can easily customize those by adding new keywords These variables can also be interac tively accessed and saved through ESS Font lock submenu Several new fontification keywords have been added Most notably the keywords for highlighting of function calls numbers and operators ESS R auto complete is now activated by default whenever auto complete package is detected Set ess use auto complete to nil to deactivate Chapter 1 Introduction to ESS 11 e ESS R R AC sources are no longer auto starting at 0 characters but at the default ac auto start characters e ESS no longer redefines default ac sources but only appends ac source filename to it e ESS ac source R now concatenates
117. revi ous next command matching regexp arg is the prefix argument regexp is prompted for in the minibuffer 4 2 3 Re submitting commands from the transcript When moving through the transcript you may wish to re execute some of the commands you find there ESS provides three commands to do this these commands may be used Chapter 4 Interacting with the ESS process 27 whenever the cursor is within a command line in the transcript if the cursor is within some command output an error is signalled Note all three commands involve the RETURN key RET inferior ess send input See Section 4 1 Command line editing page 25 C c RET comint copy old input Copy the command under the cursor to the current command line but don t execute it Leaves the cursor on the command line so that the copied command may be edited When the cursor is not after the current prompt the RETURN key has a slightly different behavior than usual Pressing RET on any line containing a command that you entered i e a line beginning with a prompt sends that command to the ESS process once again If you wish to edit the command before executing it use C c RET instead it copies the command to the current prompt but does not execute it allowing you to edit it before submitting it These commands work even if the current line is a continuation line i e the prompt is instead of gt in this case all the lines that form the multi line command are
118. s a batch SAS job F4 F5 PROGRAM switch buffer to sas file F5 F6 LOG switch buffer to Log file refresh and goto next error message if any F6 F7 OUTPUT switch buffer to 1st file and refresh 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 PROC FSEDIT session on the SAS dataset near point F10 F10 toggle log toggle ESS SAS for 1log files 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 C F1 C F1 rtf portrait create an MS RTF portrait file from the current buffer with a file extension of rtf C F2 C F2 rtf landscape create an MS RTF landscape file from the current buffer with a file extension of rtf C F3 C F8 submit region write region to ess temp sas and submit C F5 C F6 append to log append ess temp log to the current Log file C F6 C F7 append to output append ess temp 1st to the current 1st file C F9 C F9 INSIGHT open an interactive PROC INSIGHT session on the SAS dataset near point Chapter 13 ESS for SAS 72 C F10 C F10 toggle listing toggle ESS SAS for 1st files useful for toggling read only SUBMIT PROGRAM LOG and OUTPUT need no further explanation since they mimic the SAS Display Manager
119. s adopted for ESS JAGS elisp local variables These variables are created as part of the template i e with the first press of C c C c in an empty buffer For your bug file they are named ess jags chains ess jags monitor ess jags thin ess jags burnin and ess jags update they appear in the Local Variables section When you are finished editing your model file pressing C c C c will perform the necessary actions to build your command file for you The ess jags chains variable is the number of chains that you want to initialize and sample from defaults to 1 The ess jags monitor variable is a list of variables that you want monitored encase each variable in double quotes When you press C c C c the appropriate statements are created in the command file to monitor the list of variables By default no variables are explicitly monitored which means JAGS will implicitly monitor all default variables The ess jags thin variable is the thinning parameter By default the thinning parameter is set to 1 i e no thinning The ess jags burnin variable is the number of initial samples to discard By default the burnin parameter is set to 10000 The ess jags update variable is the number of post burnin samples to keep By default the update parameter is set to 10000 Both ess jags burnin and ess jags update are multiplied by ess jags thin since JAGS does not do it automatically 15 2 ESS JAGS Command files To avoid extension name collision
120. s ends with ESS 12 04 4 This decision will be re visited in the future as XEmacs continues to syne with GNU Emacs ESS R On Windows there is now a new customizable variable currently called ess directory containing R to tell ESS where to look for the Rterm exe executa bles The name of the variable and the values it can take are both in beta and subject to change Prior to this variable ESS searched only in the default installation direc tory Setting this variable now tells ESS how to find Rterm exe executables when they are installed somewhere else ESS julia new mode for editing julia code j1 Start with M x julia Full interaction interface imenu and basic error referencing are available ESS R noweb noweb mode and noweb font lock mode have been renamed to ess noweb mode and ess noweb font lock mode to avoid conflicts with the real noweb mode ESS R noweb The long standing font lock bug has been solved in ess noweb interface ESS Basic evaluation keys are now bound to ess eval region functions C M x is bound to ess eval region or function or paragraph C c C c is bound to ess eval region or function or paragraph and step C RET is bound to ess eval region or line and step Each of these functions first evaluates the region whenever the region is active ESS C M a C M e now step to beginning end of paragraph if no function has been detected ESS ess eval and step family of functions are now smarte
121. s for batch processing The setup of function keys for SAS batch processing is unavoidably complex but the usage of function keys is simple There are five distinct options Option 1 default Function keys in ESS SAS are not bound to elisp commands This is in accordance with the GNU Elisp Coding Standards GECS which do not allow function keys to be bound so that they are available to the user Options 2 5 Since GECS does not allow function keys to be bound by modes these keys are often unused So ESS SAS provides users with the option of binding elisp commands to these keys Users who are familiar with SAS will most likely want to duplicate the function key capabilities of the SAS Display Manager There are four options noted in parentheses a SAS Display Manager has different function key definitions for UNIX 2 4 and Windows 3 5 ESS SAS can use either b The ESS SAS function key definitions can be active in all buffers global 4 5 or limited local 2 3 only to buffers with files that are associated with ESS SAS as specified in your auto mode alist The distinction between local and global is subtle If you want the ESS SAS definitions to work when you are in the shel1 buffer or when editing files other than the file extensions that ESS 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
122. s from folding on standard terminals noovp prevents error messages from printing 3 times nosyntaxcheck permits recovery after syntax errors To start up iESS SAS mode use M x SAS The SAS 1 log buffer in ESStr mode corresponds to the file foo log in SAS batch usage and to the SAS LOG window in the SAS Display Manager All commands submitted to SAS informative messages warnings and errors appear here The SAS 1 1st buffer in ESS1st mode corresponds to the file foo 1st in SAS batch usage and to the SAS OUTPUT window in the SAS Display Manager All printed output appears in this window The SAS 1 buffer exists solely as a communications buffer The user should never use this buffer directly Files are edited in the foo sas buffer The C c C r key in ESS SAS is the functional equivalent of bringing a file into the SAS PROGRAM EDITOR window followed by SUBMIT For example open the file you want to work with C x C f foo sas foo sas will be in ESS SAS mode Edit as appropriate and then start up SAS with the cursor in the foo sas buffer M x SAS Chapter 13 ESS for SAS 74 Four buffers will appear on screen Buffer Mode Description foo sas ESS SAS your source file SAS 1 iESS SAS 1 iESS communication buffer SAS 1 log Shell ESStr SAS log information SAS 1 1st Shell ESSlst SAS listing information If you would prefer each of the four buffers to appear in its own individual frame you c
123. sing ESS could not communicate with statistical packages that did not use this protocol T his changed in 1998 when Brian Ripley demonstrated use of the Windows Dynamic Data Exchange DDE protocol with ESS Heiberger then used DDE to provide interactive interfaces for Windows versions of Splus In 1999 Rodney A Sparapani and Heiberger implemented SAS batch for ESS relying on files rather than standard input standard output for Unix Windows and Mac In 2001 Sparapani added BUGS batch file processing to ESS for Unix and Windows e The multiple process code and the idea for ess eval line and next line are by Rod Ball e Thanks to Doug Bates for many useful suggestions Chapter 1 Introduction to ESS 17 e Thanks to Martin Maechler for reporting and fixing bugs providing many useful com ments and suggestions and for maintaining the ESS mailing lists e Thanks to Frank Ritter for updates particularly the menu code and invaluable com ments on the manual e Thanks to Ken ichi Shibayama for his excellent indenting code and many comments and suggestions e Thanks to Aki Vehtari for adding interactive BUGS support e Thanks to Brendan Halpin for bug fixes and updates to Stata mode e Last but definitely not least thanks to the many ESS users and contributors to the ESS mailing lists ESS is being developed and currently maintained by e A J Rossini e Richard M Heiberger e Kurt Hornik e Martin Maechler e Rodney A Sparapa
124. ss to appear in a separate variable customize the variable inferior ess own frame Alternatively change inferior ess same window if you wish the process to appear within another window of the current frame Chapter 4 Interacting with the ESS process 25 A Interacting with the ESS process The primary function of the ESS package is to provide an easy to use front end to the S interpreter This is achieved by running the S process from within an Emacs buffer called hereafter inferior buffer which has an active inferior ess mode The features of Inferior S mode are similar to those provided by the standard Emacs shell mode see Section Shell Mode in The Gnu Emacs Reference Manual Command line completion of S objects and a number of hot keys for commonly used S commands are also provided for ease of typing 4 1 Entering commands and fixing mistakes Sending a command to the ESS process is as simple as typing it in and pressing the RETURN key inferior ess send input Command RET Send the command on the current line to the ESS process If you make a typing error before pressing RET all the usual Emacs editing commands are available to correct it see Section Basic editing commands in The GNU Emacs Reference Manual Once the command has been corrected you can press RETURN even if the cursor is not at the end of the line to send the corrected command to the ESS process Emacs provides some other commands which are useful
125. ssively long output printing large arrays for example Delete erroneous commands and the resulting error messages or other output by moving to the command or its output and typing M h C w Also remember that C c C x and other hot keys may be used for commands whose output you do not wish to appear in the transcript These suggestions are appropriate even if you are not saving your transcript to disk since the larger the transcript the more memory your Emacs process will use on the host machine Finally if you intend to produce S source code suitable for using with source or inclusion in an S function from a transcript then the command ess transcript clean region may be of use see Section 6 2 Clean page 35 4 3 Command History ESS provides easy to use facilities for re executing or editing previous commands An input history of the last few commands is maintained by default the last 500 commands are Chapter 4 Interacting with the ESS process 28 stored although this can be changed by setting the variable comint input ring size in inferior ess mode hook The simplest history commands simply select the next and previous commands in the input history M p comint previous input Select the previous command in the input history M n comint next input Select the next command in the input history For example pressing M p once will re enter the last command into the process buffer after the prompt but does not send it to the E
126. st tab never complete User Option If non nil TAB never tries to complete in ess mode The default symbol does not try to complete if the next char is a valid symbol constituent There are more options see the help C h v ess indent exp Command TAB Indents each line in the S compound expression which follows point Very useful for beautifying your S code ess electric brace Command The braces automatically indent to the correct position when typed The following Emacs command are also helpful RET LFD newline and indent Insert a newline and indent the next line Note that most keyboards nowadays do not have a LINEFEED key but RET and C j are equivalent M indent for comment Indents an existing comment line appropriately or inserts an appropriate comment marker 7 4 1 Changing indentation styles The combined value of nine variables that control indentation are collectively termed a style ESS provides several styles covering the common styles of indentation DEFAULT OWN GNU BSD K amp R C RRR CLB The variable ess style alist lists the value of each indentation variable per style ess set style Command C c Sets the formatting style in this buffer to be one of the predefined styles including GNU BSD K amp R CLB and C The DEFAULT style uses the default values for the indenting variables The OWN style allows you to use your own private values of the indentation variable see below setq
127. stomize this variable to enhance comint navigation comint previous prompt and comint next prompt the inferior buffers e ESS R Internal R completion retrieval ess R complete object name was rewritten and is faster now e ESS is using process plist to store process specific variables as opposed to buffer local variables as it was using before The use of buffer local variables to store process variables is discouraged Chapter 1 Introduction to ESS 16 e ESS new functions to manipulate process plists ess process get and ess process set e ESS Internal process waiting mechanism was completely rewritten ESS no more relies on prompt regular expressions for the prompt detection The only requirement on the primary process prompt is to end in gt This could be overwritten by setting inferor ess primary prompt e ESS S notably R Saved command history ess history file now accepts t default nil or a file name By setting it to nil no command line history is saved anymore ess history directory now allows to have the history all saved in one central file e ESS R more Roxygen improvements e ESS R C c to set indentation style e ESS R Functions with non standard names for example aaa bbb cc are properly handled by font lock and evaluation routines e ESS R Several regexp bugs described in etc R ESS bugs el were fixed in ess get words from vector and ess command 1 3 Authors of and contributors
128. t behind even when ess keep dump files is nil e Passing an incomplete S expression to ess execute causes ESS to hang e The function based commands don t always work as expected on functions whose body is not a parenthesized or compound expression and don t even recognize anonymous functions i e functions not assigned to any variable e Multi line commands could be handled better by the command history mechanism e Changes to the continutation prompt in R e g options continue are not automatically detected by ESS Hence for now the best thing is not to change the continuation prompt If you do change the continuation prompt you will need to change accordingly the value of inferior ess secondary prompt in R customize alist 16 2 Reporting Bugs Please send bug reports suggestions etc to ESS bugsOstat 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 If Emacs reports an error backtraces can help us debug the problem Type M x set variable RET debug on error RET t RET Then run the command that causes the error and you should see a Backtrace buffer containing debug information send us that buffer Note that comments suggestions words of praise and large cash donations are also more than welcome 16 3 Mailing Lists There is a mailing list
129. the ESS process 7 1 Creating or modifying S objects To edit an S object type ess dump object into edit buffer object Command C c C e C d Edit an S object in its own edit buffer from within the ESS process buffer S You will then be prompted for an object to edit you may either type in the name of an existing object for which completion is available using the TAB key or you may enter the name of a new object A buffer will be created containing the text representation of the requested object or if you entered the name of a non existent object at the prompt and the variable ess function template is non nil you will be presented with a template defined by that variable which defaults to a skeleton function construct You may then edit the function as required The edit buffer generated by ess dump object into edit buffer is placed in the ESS major mode which provides a number of commands to facilitate editing S source code Commands are provided to intelligently indent S code evaluate portions of S code and to move around S code constructs Note when you dump a file with C c C e C d ESS first checks to see whether there already exists an edit buffer containing that object and if so pops you directly to that buffer If not ESS next checks whether there is a file in the appropriate place with the appropriate name see Section 7 6 Source Files page 39 and if so reads in that file You can use this facility to return to an ob
130. the In Out menu to explore the possibilities Many ESS users like to have even easier access to these and recommend to add something like eval after load comint progn define key comint mode map upl gt comint previous matching input from input define key comint mode map down gt comint next matching input from input also recommended for ESS use setq comint scroll to bottom on output others setq comint scroll show maximum output t somewhat extreme almost disabling writing in R shell buffers above prom Chapter 4 Interacting with the ESS process 29 setq comint scroll to bottom on input this to your emacs file where the last two settings are typically desirable for the situation where you work with a script e g code R and send code chunks to the process buffer e g R Note however that these settings influence all comint using emacs modes not just the ESS ones and for that reason these customization cannot be part of ESS itself 4 3 1 Saving the command history The ess history file variable which is t by default together with ess history directory governs if and where the command history is saved and restored between sessions By default ess history directory is nil and the command history will be stored as text file in the ess directory e g as Rhistory Experienced ESS users often work exclusively with script files rather than in a e g R console session and may
131. the Org document and data can be passed from the Org document e g from a table to the ESS R process This section contributed by Dan Davison and Eric Schulte 11 12 Support for Sweave in ESS and AUCTeX ESS provides support for writing and processing Sweave http www statistik lmu de leisch Sweave building up on Emacs ess noweb mode for literate programming When working on an Sweave document the following key bindings are available ess swv weave choose Command M n s Run Sweave on the current Rnw file If choose is non nil offer a menu of available weavers ess swv latex Command M n 1 Run LaTeX after Sweave ing ess swv PS Command M n p Generate and display a postscript file after LaTeX ing ess swv PDF pdflatex cmd Command M n P Generate and display a PDF file after LaTeX ing Optional argument pdflatex cmd is the command to use which by default is the command used to generate the PDF file is the first element of ess swv pdflatex commands ess swv pdflatex commands User Option Commands used by ess swv PDF to run a version of pdflatex the first entry is the default command Sweave ing with ess swv weave starts an inferior ESS process if one is not available Other commands are available from the Sweaving Tangling submenu of the Noweb menu AUCTeX http www gnu org software auctex users may prefer to set the variable ess swv plug into AUCTeX p available from the ESS Sweave
132. the Roxygen prefix string 10 3 ESS developer Usual ESS evaluation commands See Chapter 5 Evaluating code page 33 send portions of the current buffer for the evaluation in the current environment usually R_GlobalEnv Often in process of the developing packages with namespaces it is necessary to evaluate code directly in the package s environment or its namespace The ess developer utility provides such a functionality with minimal disruption of the usual ESS work flow To understand how ess developer works you must be familiar with namespace system in R In a nutshell all objects defined in a package foo are stored in an environment called namespace foo Parent environment of namespace foo is an environment imports foo which contains copies of all objects from other packages which foo imports Parent envi ronment of imports foo is the namespace base Parent environment of namespace base is GlobalEnv Thus functions and methods stored in namespace foo see all the objects in GlobalEnv unless shadowed by objects in imports foo namespace base or names pace foo itself There is another environment associated with foo package foo This environment stores copies of exported objects from namespace foo and is placed on the search path i e if foo is loaded and if you start with GlobalEnv and iteratively call Chapter 10 Developing with ESS 53 parent env you wi
133. this menubar you will then be offered bookmarks to particular parts of your source file such as the starting point of each function definition Imenu works by searching your buffer for lines that match what ESS thinks is the begin ning of a suitable entry e g the beginning of a function definition To examine the regular expression that ESS uses check the value of imenu generic expression This value is set by various ESS variables such as ess imenu S generic expression 11 7 Toolbar The R and editing modes have support for a toolbar This toolbar provides icons to act as shortcuts for starting new S R processes or for evaluating regions of your source buffers The toolbar should be present if your emacs can display images See Appendix A Customization page 81 for ways to change the toolbar Chapter 11 Other ESS features and tools 58 11 8 TAGS The Emacs tags facility can be used to navigate around your files containing definitions of S functions This facility is independent of ESS usage but is written here since ESS users may wish to take advantage of TAGS facility Read more about emacs tags in an emacs manual Etags the program that generates the TAGS file does not yet know the syntax to recognise function definitions in S files Hence you will need to provide a regexp that matches your function definitions Here is an example call broken over two lines type as one line that should be appropriate etags language
134. tion The New Features section and NEWS now represent recent changes within the last year or so All changes can be found in the new news html or NEWS and ONEWS e ESS R ess rep regexp should no longer inf loop rarely and hence M x ess fix miscellaneous should neither Changes New Features in 13 05 e ESS gretl Support for gret1 both editing and sub process interaction A contribu tion of Ahmadou Dicko Chapter 1 Introduction to ESS 7 ESS process output display is 4 10 times faster due to new caching and only oc casional emacs re display for the moment this functionality is available only when ess tracebug is active ESS C c is now bound to ess show traceback and C c is bound to ess show call stack ESS R ESS stores function in ESSR environment to avoid kludging users global environment and accidental deletion ESS R new variable ess swv processing command to control weaving and tangling ESS R ess default style has been changed from DEFAULT to RRR Use some thing like setq ess default style DEFAULT or setq ess indent level 2 in your emacs equivalent before loading ESS if you do not like this new incompati ble default style ESS julia ESS stores its functions in ESS module ESS julia Eldoc is now supported in julia modes ESS julial Adjusted error reference detection and interactive help to julia internal changes ESS R ess use tracebug s default has been cha
135. tring otherwise it would try to complete a filename So to expand the history reference type SPC TAB This will convert the history reference into an S command from the history which you can then edit or press RET to execute For example to execute the last command that referenced the variable data type data SPC TAB RET 4 5 Hot keys for common commands ESS provides a number of commands for executing the commonly used functions These commands below are basically information gaining commands such as objectsO or search which tend to clutter up your transcript and for this reason some of the hot keys display their output in a temporary buffer instead of the process buffer by default This behavior is controlled by the following option ess execute in process buffer User Option If non nil means that these commands will produce their output in the process buffer instead In any case passing a prefix argument to the commands with C u will reverse the meaning of ess execute in process buffer for that command i e the output will be displayed in the process buffer if it usually goes to a temporary buffer and vice versa These are the hot keys that behave in this way ess execute objects posn Command C c C x Sends the objects command to the ESS process A prefix argument spec ifies the position on the search list use a negative argument to toggle ess execute in process buffer as well A quick way to see what objects are i
136. ts or is inherited by a class whose definition is not exported You might get something like Warning Class boo is defined with package slot foo but no metadata object found to revise subclass information not exported You can safely ignore this warnings 84 METHODS Similarly to function definitions modified methods are assigned in the local method table in the namespace foo New methods are assigned into GlobalEnv but with the environment pointing to namespace foo There is a suttle catch with method caching in R though See the code in etc ESSR developer R for more details 83 METHODS S3 methods are not automatically registered You can register them manually after you have inserted method name me class into your package environment using ess developer like follows registerS3method method name my class my package method_name my class If you don t register your 3 method R will call the registered aka cached S3 method instead of the new method that ess developer inserted in the package environment e C c C r ess eval region and functions that depend on it ess eval paragraph ess eval buffer etc behave as ess load file but restrict the evaluation to the cor responding region e C c C f ess eval function and friends check if the current function s name can be found in a namespace foo or package foo for a foo from ess developer packages If found and new function definition differs from th
137. umber 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 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 1 1 Why should I use ESS Statistical packages are powerful software systems for manipulating and analyzing data but their user interfaces often leave something something to be desired they offer weak editor functionality and they differ among themsel
138. ve found the standard facilities this the ixO 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 See Section 7 1 Edit buffer page 36 A specialized editing mode for S code which provides syntactic indentation and high lighting See Section 7 4 Indenting page 37 Facilities for loading and error checking source files including a keystroke to jump straight to the position of an error in a source file See Section 7 3 Error Checking page 37 Source code revision maintenance which allows you to keep historic versions of S source files See Section 7 6 Source Files page 39 Facilities for evaluating S code such as portions of source files or line by line evaluation of files useful for debugging See Chapter 5 Evaluating code page 33 Finally ESS provides features for re submitting commands from saved transcript files including Evaluation of previously entered commands stripping away unnecessary prompts See Section 4 2 3 Transcript resubmit page 26 1 2 New features in ESS Ch e anges and New Features in 15 03 1 ESS R An indentation bug has been fix
139. ven if it is masked e Fix ess show buffer to always display the buffer in another window e Makefile Fix cd bug for directories with spaces in them e ess kill buffer and go modified to not restart R Changes Selected Bug Fixes in 14 09 e ESS Julia Executable is changed to julia e ESS Julia Completion and help system was adjusted to Julia v 0 3 0 Julia v 0 2 x is no more supported e ESS R Running R with gdb debugger now works as expected e iESS Inferior ESS buffers are now derived from comint mode e ESS R ess execute screen options uses correct screen width in terminal sessions e ESS ess build tags for directory works when no TAGS file name was provided e ESS ess continued statement offset is now respected everywhere except inside of the if test condition e ESS New variable ess first continued statement offset for indentation of the first line in multiline statements e ESSR Starting in multiline statements indentation is now ignored to achieve a more pleasant alignment e ESSR Improved behavior of RET in roxygen blocks e ESS R command cleaning with C u C u C y was broken with lines containing Chapter 1 Introduction to ESS 5 ESS R fixed empty watch window bug ESS R don t ask for help location on ac quick help request of github 81 R ESS importClassesFrom and importMethodsFrom were added to the list of two parameter roxygen commands ESS R fix vignetes displ
140. ves so markedly that you have to re learn how to do those things for each package ESS is a package which is designed to make editing and interacting with statistical packages more uniform user friendly and give you the power of emacs as well 1 1 1 Features Overview e Languages Supported e S family R and S AKA S PLUS Chapter 1 Introduction to ESS 2 SAS OpenBUGS JAGS Stata Julia e Editing source code S family SAS OpenBUGS JAGS Stata Julia Syntactic indentation and highlighting of source code Partial evaluation of code Loading and error checking of code Source code revision maintenance Batch execution SAS OpenBUGS JAGS Use of imenu to provide links to appropriate functions e Interacting with the process S family SAS Stata Julia Command line editing Searchable Command history Command line completion of S family object names and file names Quick access to object lists and search lists Transcript recording Interface to the help system e Transcript manipulation S family Stata Recording and saving transcript files Manipulating and editing saved transcripts Re evaluating commands from transcript files e Interaction with Help Pages and other Documentation R Fast Navigation Sending Examples to running ESS process Fast Transfer to Further Help Pages e Help File Editing R Syntactic indentation and highlighting of source code Sending Examples to running ESS process Previewing ESS
141. x St The most obvious use for a transcript file is as a static record of the actions you have performed in a particular S session Sometimes however you may wish to re execute commands recorded in the transcript file by submitting them to a running ESS process This is what Transcript Mode is for If you load file a with the suffix St into Emacs it is placed in S Transcript Mode Transcript Mode is similar to Inferior S mode see Chapter 4 Entering commands page 25 paragraphs are defined as a command and its output and you can move though commands either with the paragraph commands or with C c C p and C c C n 6 1 Resubmitting commands from the transcript file Three commands are provided to re submit command lines from the transcript file to a running ESS process They are ess transcript send command Command M RET Sends the current command line to the ESS process and execute it ess transcript copy command Command C c RET Copy the current command to the ESS process and switch to it ready to edit the copied command ess transcript send command and move Command RET Sends the current command to the ESS process and move to the next command line This command is useful for submitting a series of commands Note that the first two commands are similar to those on the same keys in inferior 5 Mode In all three cases the commands should be executed when the cursor is on a command line in the transcript the prompt is automati
142. x ssh ssh el is available at http www splode com friedman software emacs lisp src ssh el 2 Start the ESS process on the remote machine for example with one of the commands Splus or R or sas stdio 3 Start M x ess remote You will be prompted for a program name with completion Choose one Your process is now known to ESS All the usual ESS commands C c C n and its relatives now work with the 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 With ess remote you get teletype behavior the data input the log and the listing all appear in the same buffer To make this work you need to end every PROC and DATA step with a RUN statement The RUN statement is what tells SAS that it should process the preceding input statements 4 Graphics interactive on the remote machine If you run X11 See Section 11 5 2 X11 page 57 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 i
143. ypes defined via file name extensions ess sas graph view viewer default is the default external viewer for your platform ess sas graph view viewer alist is an alist of exceptions to the default i e file types and their associated viewers which will be used rather than the default viewer setq ess sas graph view suffix regexp concat NNC eE pP sS NN Chapter 13 ESS for SAS 73 pP aD F NM gG iI F NV jJ pP eE gG NN tT iI F F 7 default setq ess sas graph view viewer default kodakimg Windows default setq ess sas graph view viewer default sdtimage Solaris default setq ess sas graph view viewer alist eE pP sS gv pP aD F gv default w gv C F2 produces US landscape by default however it can produce A4 landscape first line for global key mapping second for local global set key control f2 ess sas rtf a4 landscape define key sas mode local map control f2 ess sas rtf a4 landscape 13 6 iESS SAS Interactive SAS processes Inferior ESS iESS is the method for interfacing with interactive statistical processes programs iESS SAS is what is needed for interactive SAS programming iESS SAS works best with the SAS command line option settings stdio linesize 80 noovp nosyntaxcheck the default of inferior SAS args stdio required to make the redirection of stdio work linesize 80 keeps output line

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ESS – Emacs Speaks Statistics