1 ;;; ob-R.el --- org-babel functions for R code evaluation
3 ;; Copyright (C) 2009-2014 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 ess-wait-for-process
"ext:ess-inf"
39 (proc &optional sec-prompt wait force-redisplay
))
40 (declare-function org-number-sequence
"org-compat" (from &optional to inc
))
41 (declare-function org-remove-if-not
"org" (predicate seq
))
42 (declare-function org-every
"org" (pred seq
))
44 (defconst org-babel-header-args
:R
65 (results .
((file list vector table scalar verbatim
)
66 (raw org html latex code pp wrap
)
67 (replace silent append prepend
)
68 (output value graphics
))))
69 "R-specific header arguments.")
71 (defconst ob-R-safe-header-args
72 (append org-babel-safe-header-args
73 '(:width
:height
:bg
:units
:pointsize
:antialias
:quality
74 :compression
:res
:type
:family
:title
:fonts
75 :version
:paper
:encoding
:pagecentre
:colormodel
76 :useDingbats
:horizontal
))
77 "Header args which are safe for R babel blocks.
79 See `org-babel-safe-header-args' for documentation of the format of
82 (defvar org-babel-default-header-args
:R
'())
83 (put 'org-babel-default-header-args
:R
'safe-local-variable
84 (org-babel-header-args-safe-fn ob-R-safe-header-args
))
86 (defcustom org-babel-R-command
"R --slave --no-save"
87 "Name of command to use for executing R code."
92 (defvar ess-local-process-name
) ; dynamically scoped
93 (defun org-babel-edit-prep:R
(info)
94 (let ((session (cdr (assoc :session
(nth 2 info
)))))
95 (when (and session
(string-match "^\\*\\(.+?\\)\\*$" session
))
96 (save-match-data (org-babel-R-initiate-session session nil
)))))
98 (defconst ob-R-transfer-variable-table-with-header
100 con <- textConnection(
113 "R code used to transfer a table defined as a variable from org to R.
114 This function is used when the table contains a header.")
116 (defconst ob-R-transfer-variable-table-without-header
118 con <- textConnection(
128 col.names = paste(\"V\", seq_len(%d), sep =\"\")
133 "R code used to transfer a table defined as a variable from org to R.
134 This function is used when the table does not contain a header.")
136 (defun org-babel-expand-body:R
(body params
&optional graphics-file
)
137 "Expand BODY according to PARAMS, return the expanded body."
140 (when (cdr (assoc :prologue params
))
141 (list (cdr (assoc :prologue params
))))
142 (org-babel-variable-assignments:R params
)
144 (when (cdr (assoc :epilogue params
))
145 (list (cdr (assoc :epilogue params
)))))
148 (defun org-babel-execute:R
(body params
)
149 "Execute a block of R code.
150 This function is called by `org-babel-execute-src-block'."
152 (let* ((result-params (cdr (assoc :result-params params
)))
153 (result-type (cdr (assoc :result-type params
)))
154 (session (org-babel-R-initiate-session
155 (cdr (assoc :session params
)) params
))
156 (colnames-p (cdr (assoc :colnames params
)))
157 (rownames-p (cdr (assoc :rownames params
)))
158 (graphics-file (and (member "graphics" (assq :result-params params
))
159 (org-babel-graphical-output-file params
)))
162 (list (org-babel-expand-body:R body params graphics-file
))))
166 (list (org-babel-R-construct-graphics-device-call
167 graphics-file params
))
169 (list "},error=function(e){plot(x=-1:1, y=-1:1, type='n', xlab='', ylab='', axes=FALSE); text(x=0, y=0, labels=e$message, col='red'); paste('ERROR', e$message, sep=' : ')}); dev.off()"))
173 (org-babel-R-evaluate
174 session full-body result-type result-params
175 (or (equal "yes" colnames-p
)
177 (cdr (assoc :colname-names params
)) colnames-p
))
178 (or (equal "yes" rownames-p
)
180 (cdr (assoc :rowname-names params
)) rownames-p
)))))
181 (if graphics-file nil result
))))
183 (defun org-babel-prep-session:R
(session params
)
184 "Prepare SESSION according to the header arguments specified in PARAMS."
185 (let* ((session (org-babel-R-initiate-session session params
))
186 (var-lines (org-babel-variable-assignments:R params
)))
187 (org-babel-comint-in-buffer session
189 (end-of-line 1) (insert var
) (comint-send-input nil t
)
190 (org-babel-comint-wait-for-output session
)) var-lines
))
193 (defun org-babel-load-session:R
(session body params
)
194 "Load BODY into SESSION."
195 (save-window-excursion
196 (let ((buffer (org-babel-prep-session:R session params
)))
197 (with-current-buffer buffer
198 (goto-char (process-mark (get-buffer-process (current-buffer))))
199 (insert (org-babel-chomp body
)))
204 (defun org-babel-variable-assignments:R
(params)
205 "Return list of R statements assigning the block's variables."
206 (let ((vars (mapcar 'cdr
(org-babel-get-header params
:var
))))
209 (org-babel-R-assign-elisp
210 (car pair
) (cdr pair
)
211 (equal "yes" (cdr (assoc :colnames params
)))
212 (equal "yes" (cdr (assoc :rownames params
)))))
215 (cons (car (nth i vars
))
216 (org-babel-reassemble-table
218 (cdr (nth i
(cdr (assoc :colname-names params
))))
219 (cdr (nth i
(cdr (assoc :rowname-names params
)))))))
220 (org-number-sequence 0 (1- (length vars
)))))))
222 (defun org-babel-R-quote-tsv-field (s)
223 "Quote field S for export to R."
225 (concat "\"" (mapconcat 'identity
(split-string s
"\"") "\"\"") "\"")
228 (defun org-babel-R-assign-elisp (name value colnames-p rownames-p
)
229 "Construct R code assigning the elisp VALUE to a variable named NAME."
231 (let* ((lengths (mapcar 'length
(org-remove-if-not 'sequencep value
)))
232 (max (if lengths
(apply 'max lengths
) 0))
233 (min (if lengths
(apply 'min lengths
) 0)))
234 ;; Ensure VALUE has an orgtbl structure (depth of at least 2).
235 (unless (listp (car value
)) (setq value
(list value
)))
236 (let ((file (orgtbl-to-tsv value
'(:fmt org-babel-R-quote-tsv-field
)))
237 (header (if (or (eq (nth 1 value
) 'hline
) colnames-p
)
239 (row-names (if rownames-p
"1" "NULL")))
241 (format ob-R-transfer-variable-table-with-header
242 name file header row-names
)
243 (format ob-R-transfer-variable-table-without-header
244 name file header row-names max
))))
245 (cond ((integerp value
) (format "%s <- %s" name
(concat (number-to-string value
) "L")))
246 ((floatp value
) (format "%s <- %s" name value
))
247 ((stringp value
) (format "%s <- %S" name
(org-no-properties value
)))
248 (t (format "%s <- %S" name
(prin1-to-string value
))))))
251 (defvar ess-ask-for-ess-directory
) ; dynamically scoped
252 (defun org-babel-R-initiate-session (session params
)
253 "If there is not a current R process then create one."
254 (unless (string= session
"none")
255 (let ((session (or session
"*R*"))
256 (ess-ask-for-ess-directory
257 (and (boundp 'ess-ask-for-ess-directory
)
258 ess-ask-for-ess-directory
259 (not (cdr (assoc :dir params
))))))
260 (if (org-babel-comint-buffer-livep session
)
262 (save-window-excursion
263 (when (get-buffer session
)
264 ;; Session buffer exists, but with dead process
265 (set-buffer session
))
267 (ess-wait-for-process
268 (get-process (or ess-local-process-name
269 ess-current-process-name
)))
271 (if (bufferp session
)
272 (buffer-name session
)
273 (if (stringp session
)
276 (current-buffer))))))
278 (defun org-babel-R-associate-session (session)
279 "Associate R code buffer with an R session.
280 Make SESSION be the inferior ESS process associated with the
281 current code buffer."
282 (setq ess-local-process-name
283 (process-name (get-buffer-process session
)))
284 (ess-make-buffer-current))
286 (defvar org-babel-R-graphics-devices
287 '((:bmp
"bmp" "filename")
288 (:jpg
"jpeg" "filename")
289 (:jpeg
"jpeg" "filename")
290 (:tikz
"tikz" "file")
291 (:tiff
"tiff" "filename")
292 (:png
"png" "filename")
295 (:ps
"postscript" "file")
296 (:postscript
"postscript" "file"))
297 "An alist mapping graphics file types to R functions.
299 Each member of this list is a list with three members:
300 1. the file extension of the graphics file, as an elisp :keyword
301 2. the R graphics device function to call to generate such a file
302 3. the name of the argument to this function which specifies the
303 file to write to (typically \"file\" or \"filename\")")
305 (defun org-babel-R-construct-graphics-device-call (out-file params
)
306 "Construct the call to the graphics device."
307 (let* ((allowed-args '(:width
:height
:bg
:units
:pointsize
308 :antialias
:quality
:compression
:res
309 :type
:family
:title
:fonts
:version
310 :paper
:encoding
:pagecentre
:colormodel
311 :useDingbats
:horizontal
))
312 (device (and (string-match ".+\\.\\([^.]+\\)" out-file
)
313 (match-string 1 out-file
)))
314 (device-info (or (assq (intern (concat ":" device
))
315 org-babel-R-graphics-devices
)
316 (assq :png org-babel-R-graphics-devices
)))
317 (extra-args (cdr (assq :R-dev-args params
))) filearg args
)
318 (setq device
(nth 1 device-info
))
319 (setq filearg
(nth 2 device-info
))
320 (setq args
(mapconcat
322 (if (member (car pair
) allowed-args
)
324 (substring (symbol-name (car pair
)) 1)
327 (format "%s(%s=\"%s\"%s%s%s); tryCatch({"
328 device filearg out-file args
329 (if extra-args
"," "") (or extra-args
""))))
331 (defvar org-babel-R-eoe-indicator
"'org_babel_R_eoe'")
332 (defvar org-babel-R-eoe-output
"[1] \"org_babel_R_eoe\"")
334 (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\")")
336 (defun org-babel-R-evaluate
337 (session body result-type result-params column-names-p row-names-p
)
338 "Evaluate R code in BODY."
340 (org-babel-R-evaluate-session
341 session body result-type result-params column-names-p row-names-p
)
342 (org-babel-R-evaluate-external-process
343 body result-type result-params column-names-p row-names-p
)))
345 (defun org-babel-R-evaluate-external-process
346 (body result-type result-params column-names-p row-names-p
)
347 "Evaluate BODY in external R process.
348 If RESULT-TYPE equals 'output then return standard output as a
349 string. If RESULT-TYPE equals 'value then return the value of the
350 last statement in BODY, as elisp."
353 (let ((tmp-file (org-babel-temp-file "R-")))
354 (org-babel-eval org-babel-R-command
355 (format org-babel-R-write-object-command
356 (if row-names-p
"TRUE" "FALSE")
358 (if row-names-p
"NA" "TRUE")
360 (format "{function ()\n{\n%s\n}}()" body
)
361 (org-babel-process-file-name tmp-file
'noquote
)))
362 (org-babel-R-process-value-result
363 (org-babel-result-cond result-params
365 (insert-file-contents tmp-file
)
367 (org-babel-import-elisp-from-file tmp-file
'(16)))
369 (output (org-babel-eval org-babel-R-command body
))))
371 (defvar ess-eval-visibly-p
)
373 (defun org-babel-R-evaluate-session
374 (session body result-type result-params column-names-p row-names-p
)
375 "Evaluate BODY in SESSION.
376 If RESULT-TYPE equals 'output then return standard output as a
377 string. If RESULT-TYPE equals 'value then return the value of the
378 last statement in BODY, as elisp."
382 (insert (org-babel-chomp body
))
383 (let ((ess-local-process-name
384 (process-name (get-buffer-process session
)))
385 (ess-eval-visibly-p nil
))
386 (ess-eval-buffer nil
)))
387 (let ((tmp-file (org-babel-temp-file "R-")))
388 (org-babel-comint-eval-invisibly-and-wait-for-file
390 (format org-babel-R-write-object-command
391 (if row-names-p
"TRUE" "FALSE")
393 (if row-names-p
"NA" "TRUE")
395 ".Last.value" (org-babel-process-file-name tmp-file
'noquote
)))
396 (org-babel-R-process-value-result
397 (org-babel-result-cond result-params
399 (insert-file-contents tmp-file
)
401 (org-babel-import-elisp-from-file tmp-file
'(16)))
409 (lambda (line) (when (> (length line
) 0) line
))
411 (lambda (line) ;; cleanup extra prompts left in output
413 "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line
)
414 (substring line
(match-end 1))
416 (org-babel-comint-with-output (session org-babel-R-eoe-output
)
417 (insert (mapconcat 'org-babel-chomp
418 (list body org-babel-R-eoe-indicator
)
420 (inferior-ess-send-input)))))) "\n"))))
422 (defun org-babel-R-process-value-result (result column-names-p
)
423 "R-specific processing of return value.
424 Insert hline if column names in output have been requested."
426 (cons (car result
) (cons 'hline
(cdr result
)))
433 ;;; ob-R.el ends here