1 ;;; ob-R.el --- org-babel functions for R code evaluation
3 ;; Copyright (C) 2009-2013 Free Software Foundation, Inc.
5 ;; Author: Eric Schulte
7 ;; Keywords: literate programming, reproducible research, R, statistics
8 ;; Homepage: http://orgmode.org
10 ;; This file is part of GNU Emacs.
12 ;; GNU Emacs is free software: you can redistribute it and/or modify
13 ;; it under the terms of the GNU General Public License as published by
14 ;; the Free Software Foundation, either version 3 of the License, or
15 ;; (at your option) any later version.
17 ;; GNU Emacs is distributed in the hope that it will be useful,
18 ;; but WITHOUT ANY WARRANTY; without even the implied warranty of
19 ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
20 ;; GNU General Public License for more details.
22 ;; You should have received a copy of the GNU General Public License
23 ;; along with GNU Emacs. If not, see <http://www.gnu.org/licenses/>.
27 ;; Org-Babel support for evaluating R code
31 (eval-when-compile (require 'cl))
33 (declare-function orgtbl-to-tsv "org-table" (table params))
34 (declare-function R "ext:essd-r" (&optional start-args))
35 (declare-function inferior-ess-send-input "ext:ess-inf" ())
36 (declare-function ess-make-buffer-current "ext:ess-inf" ())
37 (declare-function ess-eval-buffer "ext:ess-inf" (vis))
38 (declare-function org-number-sequence "org-compat" (from &optional to inc))
39 (declare-function org-remove-if-not "org" (predicate seq))
41 (defconst org-babel-header-args:R
62 (results . ((file list vector table scalar verbatim)
63 (raw org html latex code pp wrap)
64 (replace silent append prepend)
65 (output value graphics))))
66 "R-specific header arguments.")
68 (defvar org-babel-default-header-args:R '())
70 (defcustom org-babel-R-command "R --slave --no-save"
71 "Name of command to use for executing R code."
76 (defvar ess-local-process-name) ; dynamically scoped
77 (defun org-babel-edit-prep:R (info)
78 (let ((session (cdr (assoc :session (nth 2 info)))))
79 (when (and session (string-match "^\\*\\(.+?\\)\\*$" session))
80 (save-match-data (org-babel-R-initiate-session session nil)))))
82 (defun org-babel-expand-body:R (body params &optional graphics-file)
83 "Expand BODY according to PARAMS, return the expanded body."
85 (or graphics-file (org-babel-R-graphical-output-file params))))
90 (when (cdr (assoc :prologue params))
91 (list (cdr (assoc :prologue params))))
92 (org-babel-variable-assignments:R params)
94 (when (cdr (assoc :epilogue params))
95 (list (cdr (assoc :epilogue params)))))))
98 (list (org-babel-R-construct-graphics-device-call
99 graphics-file params))
105 (defun org-babel-execute:R (body params)
106 "Execute a block of R code.
107 This function is called by `org-babel-execute-src-block'."
109 (let* ((result-params (cdr (assoc :result-params params)))
110 (result-type (cdr (assoc :result-type params)))
111 (session (org-babel-R-initiate-session
112 (cdr (assoc :session params)) params))
113 (colnames-p (cdr (assoc :colnames params)))
114 (rownames-p (cdr (assoc :rownames params)))
115 (graphics-file (org-babel-R-graphical-output-file params))
116 (full-body (org-babel-expand-body:R body params graphics-file))
118 (org-babel-R-evaluate
119 session full-body result-type result-params
120 (or (equal "yes" colnames-p)
122 (cdr (assoc :colname-names params)) colnames-p))
123 (or (equal "yes" rownames-p)
125 (cdr (assoc :rowname-names params)) rownames-p)))))
126 (if graphics-file nil result))))
128 (defun org-babel-prep-session:R (session params)
129 "Prepare SESSION according to the header arguments specified in PARAMS."
130 (let* ((session (org-babel-R-initiate-session session params))
131 (var-lines (org-babel-variable-assignments:R params)))
132 (org-babel-comint-in-buffer session
134 (end-of-line 1) (insert var) (comint-send-input nil t)
135 (org-babel-comint-wait-for-output session)) var-lines))
138 (defun org-babel-load-session:R (session body params)
139 "Load BODY into SESSION."
140 (save-window-excursion
141 (let ((buffer (org-babel-prep-session:R session params)))
142 (with-current-buffer buffer
143 (goto-char (process-mark (get-buffer-process (current-buffer))))
144 (insert (org-babel-chomp body)))
149 (defun org-babel-variable-assignments:R (params)
150 "Return list of R statements assigning the block's variables."
151 (let ((vars (mapcar #'cdr (org-babel-get-header params :var))))
154 (org-babel-R-assign-elisp
155 (car pair) (cdr pair)
156 (equal "yes" (cdr (assoc :colnames params)))
157 (equal "yes" (cdr (assoc :rownames params)))))
160 (cons (car (nth i vars))
161 (org-babel-reassemble-table
163 (cdr (nth i (cdr (assoc :colname-names params))))
164 (cdr (nth i (cdr (assoc :rowname-names params)))))))
165 (org-number-sequence 0 (1- (length vars)))))))
167 (defun org-babel-R-quote-tsv-field (s)
168 "Quote field S for export to R."
170 (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
173 (defun org-babel-R-assign-elisp (name value colnames-p rownames-p)
174 "Construct R code assigning the elisp VALUE to a variable named NAME."
176 (let ((max (apply #'max (mapcar #'length (org-remove-if-not
177 #'sequencep value))))
178 (min (apply #'min (mapcar #'length (org-remove-if-not
179 #'sequencep value))))
180 (transition-file (org-babel-temp-file "R-import-")))
181 ;; ensure VALUE has an orgtbl structure (depth of at least 2)
182 (unless (listp (car value)) (setq value (list value)))
183 (with-temp-file transition-file
185 (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field))
187 (let ((file (org-babel-process-file-name transition-file 'noquote))
188 (header (if (or (eq (nth 1 value) 'hline) colnames-p)
190 (row-names (if rownames-p "1" "NULL")))
192 (format "%s <- read.table(\"%s\",
196 as.is=TRUE)" name file header row-names)
197 (format "%s <- read.table(\"%s\",
203 col.names = paste(\"V\", seq_len(%d), sep =\"\"))"
204 name file header row-names max))))
205 (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
207 (defvar ess-ask-for-ess-directory) ; dynamically scoped
208 (defun org-babel-R-initiate-session (session params)
209 "If there is not a current R process then create one."
210 (unless (string= session "none")
211 (let ((session (or session "*R*"))
212 (ess-ask-for-ess-directory
213 (and (and (boundp 'ess-ask-for-ess-directory) ess-ask-for-ess-directory)
214 (not (cdr (assoc :dir params))))))
215 (if (org-babel-comint-buffer-livep session)
217 (save-window-excursion
218 (when (get-buffer session)
219 ;; Session buffer exists, but with dead process
220 (set-buffer session))
223 (if (bufferp session)
224 (buffer-name session)
225 (if (stringp session)
228 (current-buffer))))))
230 (defun org-babel-R-associate-session (session)
231 "Associate R code buffer with an R session.
232 Make SESSION be the inferior ESS process associated with the
233 current code buffer."
234 (setq ess-local-process-name
235 (process-name (get-buffer-process session)))
236 (ess-make-buffer-current))
238 (defun org-babel-R-graphical-output-file (params)
239 "Name of file to which R should send graphical output."
240 (and (member "graphics" (cdr (assq :result-params params)))
241 (cdr (assq :file params))))
243 (defvar org-babel-R-graphics-devices
244 '((:bmp "bmp" "filename")
245 (:jpg "jpeg" "filename")
246 (:jpeg "jpeg" "filename")
247 (:tikz "tikz" "file")
248 (:tiff "tiff" "filename")
249 (:png "png" "filename")
252 (:ps "postscript" "file")
253 (:postscript "postscript" "file"))
254 "An alist mapping graphics file types to R functions.
256 Each member of this list is a list with three members:
257 1. the file extension of the graphics file, as an elisp :keyword
258 2. the R graphics device function to call to generate such a file
259 3. the name of the argument to this function which specifies the
260 file to write to (typically \"file\" or \"filename\")")
262 (defun org-babel-R-construct-graphics-device-call (out-file params)
263 "Construct the call to the graphics device."
264 (let* ((allowed-args '(:width :height :bg :units :pointsize
265 :antialias :quality :compression :res
266 :type :family :title :fonts :version
267 :paper :encoding :pagecentre :colormodel
268 :useDingbats :horizontal))
269 (device (and (string-match ".+\\.\\([^.]+\\)" out-file)
270 (match-string 1 out-file)))
271 (device-info (or (assq (intern (concat ":" device))
272 org-babel-R-graphics-devices)
273 (assq :png org-babel-R-graphics-devices)))
274 (extra-args (cdr (assq :R-dev-args params))) filearg args)
275 (setq device (nth 1 device-info))
276 (setq filearg (nth 2 device-info))
277 (setq args (mapconcat
279 (if (member (car pair) allowed-args)
281 (substring (symbol-name (car pair)) 1)
284 (format "%s(%s=\"%s\"%s%s%s)"
285 device filearg out-file args
286 (if extra-args "," "") (or extra-args ""))))
288 (defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
289 (defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
291 (defvar org-babel-R-write-object-command "{function(object,transfer.file){object;invisible(if(inherits(try({tfile<-tempfile();write.table(object,file=tfile,sep=\"\\t\",na=\"nil\",row.names=%s,col.names=%s,quote=FALSE);file.rename(tfile,transfer.file)},silent=TRUE),\"try-error\")){if(!file.exists(transfer.file))file.create(transfer.file)})}}(object=%s,transfer.file=\"%s\")")
293 (defun org-babel-R-evaluate
294 (session body result-type result-params column-names-p row-names-p)
295 "Evaluate R code in BODY."
297 (org-babel-R-evaluate-session
298 session body result-type result-params column-names-p row-names-p)
299 (org-babel-R-evaluate-external-process
300 body result-type result-params column-names-p row-names-p)))
302 (defun org-babel-R-evaluate-external-process
303 (body result-type result-params column-names-p row-names-p)
304 "Evaluate BODY in external R process.
305 If RESULT-TYPE equals 'output then return standard output as a
306 string. If RESULT-TYPE equals 'value then return the value of the
307 last statement in BODY, as elisp."
310 (let ((tmp-file (org-babel-temp-file "R-")))
311 (org-babel-eval org-babel-R-command
312 (format org-babel-R-write-object-command
313 (if row-names-p "TRUE" "FALSE")
315 (if row-names-p "NA" "TRUE")
317 (format "{function ()\n{\n%s\n}}()" body)
318 (org-babel-process-file-name tmp-file 'noquote)))
319 (org-babel-R-process-value-result
320 (org-babel-result-cond result-params
322 (insert-file-contents tmp-file)
324 (org-babel-import-elisp-from-file tmp-file '(16)))
326 (output (org-babel-eval org-babel-R-command body))))
328 (defvar ess-eval-visibly-p)
330 (defun org-babel-R-evaluate-session
331 (session body result-type result-params column-names-p row-names-p)
332 "Evaluate BODY in SESSION.
333 If RESULT-TYPE equals 'output then return standard output as a
334 string. If RESULT-TYPE equals 'value then return the value of the
335 last statement in BODY, as elisp."
339 (insert (org-babel-chomp body))
340 (let ((ess-local-process-name
341 (process-name (get-buffer-process session)))
342 (ess-eval-visibly-p nil))
343 (ess-eval-buffer nil)))
344 (let ((tmp-file (org-babel-temp-file "R-")))
345 (org-babel-comint-eval-invisibly-and-wait-for-file
347 (format org-babel-R-write-object-command
348 (if row-names-p "TRUE" "FALSE")
350 (if row-names-p "NA" "TRUE")
352 ".Last.value" (org-babel-process-file-name tmp-file 'noquote)))
353 (org-babel-R-process-value-result
354 (org-babel-result-cond result-params
356 (insert-file-contents tmp-file)
358 (org-babel-import-elisp-from-file tmp-file '(16)))
366 (lambda (line) (when (> (length line) 0) line))
368 (lambda (line) ;; cleanup extra prompts left in output
370 "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
371 (substring line (match-end 1))
373 (org-babel-comint-with-output (session org-babel-R-eoe-output)
374 (insert (mapconcat #'org-babel-chomp
375 (list body org-babel-R-eoe-indicator)
377 (inferior-ess-send-input)))))) "\n"))))
379 (defun org-babel-R-process-value-result (result column-names-p)
380 "R-specific processing of return value.
381 Insert hline if column names in output have been requested."
383 (cons (car result) (cons 'hline (cdr result)))
390 ;;; ob-R.el ends here