ESS -7.IR Manuel d'utilisateur

ESS – Emacs Speaks StatisticsESS version 15.09-develThe ESS Developers (A.J. Rossini, R.M. Heiberger, K. Hornik,M. Maechler, R.A. Sparapani, S.J. Egle

Chapter 1: Introduction to ESS 6• font-lock in process buffers doesn’t "spill" over prompts. Missing closing string delim-iters should not ca

Chapter 1: Introduction to ESS 7• ESS: process output display is 4-10 times faster due to new caching and only occa-sional emacs re-display (for the m

Chapter 1: Introduction to ESS 8• ESS[tracebug]: A better handling of “Selection” prompts and debug related singlekeycommands.• ESS: fix a bug in ess-s

Chapter 1: Introduction to ESS 9• ESS: New “Process” menu entry with process related commands and configuration• iESS: Process buffer is now automatical

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 re

Chapter 1: Introduction to ESS 11• ESS[R]: R AC sources are no longer auto-starting at 0 characters but at the defaultac-auto-start characters.• ESS n

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:• iE

Chapter 1: Introduction to ESS 13a <- some.function(arg1,arg2)This variable should be set as part of indentation style lists, or in ess-mode hook.•

Chapter 1: Introduction to ESS 14normal fashion. Variable ess-tracebug-inject-source-p controls this behavior- if t, always inject source reference, i

Chapter 1: Introduction to ESS 15• ESS[S]: “,“ is bound to ess-smart-comma: If comma is invoked at the process marker ofan ESS inferior buffer, request

iTable of Contents1 Introduction to ESS . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11.1 Why should I use ESS?. . . . . . . . . . . . . .

Chapter 1: Introduction to ESS 16• ESS: new functions to manipulate process plists: ess-process-get and ess-process-set.• ESS: Internal process waitin

Chapter 1: Introduction to ESS 17• Thanks to Martin Maechler for reporting and fixing bugs, providing many useful com-ments and suggestions, and for ma

Chapter 1: Introduction to ESS 18a consistent user interface within emacs, regardless of the details of which programminglanguage is being edited, or

Chapter 2: Installing ESS on your system 192 Installing ESS on your systemThe following section details those steps necessary to get ESS running on yo

Chapter 2: Installing ESS on your system 20ESS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;without even the implied wa

Chapter 3: Interacting with statistical programs 213 Interacting with statistical programsAs well as using ESS to edit your source files for statistica

Chapter 3: Interacting with statistical programs 22Alternatively you can start your process normally (M-x R). After you are asked forstarting director

Chapter 3: Interacting with statistical programs 23We have two older commands, now deprecated, for accessing ESS processes on remotecomputers. See Sec

Chapter 3: Interacting with statistical programs 242. Otherwise, if the variable ess-directory stores the name of a directory (ending in aslash), this

Chapter 4: Interacting with the ESS process 254 Interacting with the ESS processThe primary function of the ESS package is to provide an easy-to-use f

ii7 Editing objects and functions . . . . . . . . . . . . . . . . 377.1 Creating or modifying S objects . . . . . . . . . . . . . . . . . . . . . . .

Chapter 4: Interacting with the ESS process 26Thus, for example, you may use C-x [ and C-x ] to move backward and forwards throughESS sessions in a si

Chapter 4: Interacting with the ESS process 27whenever the cursor is within a command line in the transcript (if the cursor is within somecommand outp

Chapter 4: Interacting with the ESS process 284.3 Command HistoryESS provides easy-to-use facilities for re-executing or editing previous commands. An

Chapter 4: Interacting with the ESS process 29(setq comint-scroll-to-bottom-on-output ’others)(setq comint-scroll-show-maximum-output t);; somewhat ex

Chapter 4: Interacting with the ESS process 30‘n ’ The nth word, where n is a number‘^’ The first word (i.e. the second one on the command line)‘$’ The

Chapter 4: Interacting with the ESS process 31working directory. A prefix argument of 2 or more means get objects for that position.A negative prefix ar

Chapter 4: Interacting with the ESS process 324.6 Is the Statistical Process running under ESS?For the S languages (S, S-Plus, R) ESS sets an option i

Chapter 4: Interacting with the ESS process 33Other commands available in Inferior S mode are discussed in Section “Shell Mode” inThe Gnu Emacs Refere

Chapter 5: Sending code to the ESS process 345 Sending code to the ESS processOther commands are also available for evaluating portions of code in the

Chapter 5: Sending code to the ESS process 35[Command]ess-eval-buffer visC-c C-b Sends the current buffer to the ESS process.[Command]ess-eval-buffer-a

iii12 Overview of ESS features for the S family. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6212.1

Chapter 6: Manipulating saved transcript files 366 Manipulating saved transcript filesInferior S mode records the transcript (the list of all commands e

Chapter 7: Editing objects and functions 377 Editing objects and functionsESS provides facilities for editing S objects within your Emacs session. Mos

Chapter 7: Editing objects and functions 38automatically if the buffer was generated with C-c C-e C-d). The file will then be loaded,and if it loads suc

Chapter 7: Editing objects and functions 39[User Option]ess-first-tab-never-completeIf non-nil, TAB never tries to complete in ess-mode. The default ’

Chapter 7: Editing objects and functions 40(defun myindent-ess-hook ()(setq ess-indent-level 4))(add-hook ’ess-mode-hook ’myindent-ess-hook)In the rar

Chapter 7: Editing objects and functions 41wanted to look at the definition of one of the standard S functions) the source dump filewon’t be left around

Chapter 7: Editing objects and functions 427.7 Names and locations of dump filesEvery dump file should be given a unique file name, usually the dumped ob

Chapter 7: Editing objects and functions 43If the directory generated by the lambda function does not exist but can be created,you will be asked wheth

Chapter 8: Reading help files 448 Reading help filesESS provides an easy-to-use facility for reading S help files from within Emacs. From withinthe ESS p

Chapter 8: Reading help files 45‘R’ REQUIRED ARGUMENTS:‘r’ REFERENCES:‘s’ SEE ALSO:‘S’ SIDE EFFECTS:‘u’ USAGE:‘v’ VALUE:‘<’ Jumps to beginning of fil

Chapter 1: Introduction to ESS 11 Introduction to ESSThe S family (S, Splus and R) and SAS statistical analysis packages provide sophisticatedstatisti

Chapter 9: Completion 469 Completion9.1 Completion of object namesThe TAB key is for completion. The value of the variable ess-first-tab-never-complet

Chapter 9: Completion 479.2 Completion of function argumentsWhen inside a function call (i.e. following ‘(’), TAB completion also provides functionarg

Chapter 9: Completion 48Once installed, Icicles can be activated by evaluating (maybe place in ‘~/.emacs’):(require ’icicles)(icy-mode 1)Icicles can b

Chapter 10: Developing with ESS 4910 Developing with ESSESS provides several tools to help you with the development of your R packages:10.1 ESS traceb

Chapter 10: Developing with ESS 50w . Watch window . ‘ess-watch’(C- prefixed equivalents are also defined)* Navigation to errors (general emacs functi

Chapter 10: Developing with ESS 51C-h m Describe the features of Rd mode.LFDRET Reindent the current line, insert a newline and indent the new line (r

Chapter 10: Developing with ESS 5210.2.2 Editing Roxygen documentationThe Roxygen R package makes it possible to keep the intended contents for Rd file

Chapter 10: Developing with ESS 53of-open, i.e. C-u C-c C-e C-t, visit the generated HTML file instead. Requires theRoxygen and tools packages to be in

Chapter 10: Developing with ESS 54In order to use ess-developer you must add names of the packages that you are developingto ess-developer-packages. Y

Chapter 10: Developing with ESS 55Class "boo" is defined (with package slot foo) but no metadata objectfound to revise subclass information-

Chapter 1: Introduction to ESS 2• SAS• OpenBUGS/JAGS• Stata• Julia• Editing source code (S family, SAS, OpenBUGS/JAGS, Stata, Julia)• Syntactic indent

Chapter 11: Other ESS features and tools 5611 Other ESS features and toolsESS has a few extra features, which didn’t fit anywhere else.11.1 ElDocIn ElD

Chapter 11: Other ESS features and tools 57search ess-execute-searchset-width ess-execute-screen-optionsinstall.packagesess-install.packageslibrary es

Chapter 11: Other ESS features and tools 5811.5 Using graphics with ESSOne of the main features of the S package is its ability to generate high-resol

Chapter 11: Other ESS features and tools 5911.8 TAGSThe Emacs tags facility can be used to navigate around your files containing definitions ofS functio

Chapter 11: Other ESS features and tools 6011.10 RutilsEss-rutils builds up on ess-rdired, providing key bindings for performing basic R functions int

Chapter 11: Other ESS features and tools 6111.11 Interaction with Org modeOrg-mode (http://orgmode.org) now supports reproducible research and literat

Chapter 12: Overview of ESS features for the S family 6212 Overview of ESS features for the S family12.1 ESS[S]–Editing filesESS[S] is the mode for edi

Chapter 12: Overview of ESS features for the S family 63In the (rare) case that you wish to pass command line arguments to the starting S+6process, se

Chapter 12: Overview of ESS features for the S family 64’( ("Splus64" "/usr/local/bin/Splus64")("Splus64-j" "/usr/l

Chapter 12: Overview of ESS features for the S family 65## Edit as appropriate, and then start up S-PLUS 3.xM-x S+3## A new buffer *S+3:1* will appear.

Chapter 1: Introduction to ESS 3• Command-line completion of both object and file names for quick entry. This is similarto tcsh’s facility for filenames

Chapter 12: Overview of ESS features for the S family 663: ## Program revision example (S object is real)## Start up S-PLUS 3.x in a process buffer (th

Chapter 12: Overview of ESS features for the S family 67C-c C-d my.cool.function## Edit the function as appropriate, and dump back in to the## process

Chapter 13: ESS for SAS 6813 ESS for SASESS[SAS] was designed for use with SAS. It is descended from emacs macros developed byJohn Sall for editing SA

Chapter 13: ESS for SAS 6913.3 ESS[SAS]–TAB keyTwo options. The TAB key is bound by default to sas-indent-line. This function is usedto syntactically

Chapter 13: ESS for SAS 70ess-sas-submit-command: "sas8"End:The command line is also made of ess-sas-submit-pre-command, ess-sas-submit-post

Chapter 13: ESS for SAS 71F5 (F6)Now, ‘refresh’ the ‘.lst’ and go to it’s buffer.F6 (F7)If you wish to make changes, go to the ‘.sas’ file with.F4 (F5)M

Chapter 13: ESS for SAS 72Finally, we get to what the function keys actually do. You may recognize some of thenicknames as SAS Display Manager command

Chapter 13: ESS for SAS 73open an interactive PROC INSIGHT session on the SAS dataset nearpointC-F10 C-F10 toggle-listingtoggle ESS[SAS] for ‘.lst’ fil

Chapter 13: ESS for SAS 74(setq ess-sas-graph-view-suffix-regexp (concat "[.]\\([eE]?[pP][sS]\\|""[pP][dD][fF]\\|[gG][iI][fF]\\|[jJ][pP

Chapter 13: ESS for SAS 75M-x SASFour buffers will appear on screen:Buffer Mode Description‘foo.sas’ ESS[SAS] your source file‘*SAS:1*’ iESS[SAS:1] iESS

Chapter 1: Introduction to ESS 4• ESS[R]: Detect library and require calls for better completion caching.• Buffer display is now customizable (ess-show

Chapter 13: ESS for SAS 76find / -name sas -printNow place a soft link to the real sas executable in your ~/bin directory, with forexamplecd ~/binln -

Chapter 14: ESS for BUGS 7714 ESS for BUGSESS[BUGS] was originally designed for use with BUGS software. Later, it evolved to supportJAGS as a dialect

Chapter 15: ESS for JAGS 7815 ESS for JAGSESS[BUGS] was originally designed for use with BUGS software. Later, it evolved to supportJAGS as a dialect

Chapter 15: ESS for JAGS 79C-c C-c, a command file is created if one does not already exist. When you are finishedediting your command file, pressing C-c

Chapter 16: Bugs and Bug Reporting, Mailing Lists 8016 Bugs and Bug Reporting, Mailing Lists16.1 Bugs• Commands like ess-display-help-on-object and li

Chapter 16: Bugs and Bug Reporting, Mailing Lists 81• helping users of ESS to get along with it.• discussing aspects of using ESS on Emacs and XEmacs.

Appendix A: Customizing ESS 82Appendix A Customizing ESSESS can be easily customized to your taste simply by including the appropriate lines inyour ‘.

Indices 83IndicesKey index,, . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56{{ . . . . . . . . . . . .

Indices 84comint-bol. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25comint-copy-old-input . . . . . . . . . . . . . . . . .

Indices 85Oobjects() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30Pprinter(). . . . . . . . . . . . . . . . . . . . .

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 gi

Indices 86completion on file names . . . . . . . . . . . . . . . . . . . . . . . 46completion on lists. . . . . . . . . . . . . . . . . . . . . . . . .

Indices 87SS+elsewhere . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21search list. . . . . . . . . . . . . . . . . . . . . .