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 org-number-sequence
"org-compat" (from &optional to inc
))
39 (declare-function org-remove-if-not
"org" (predicate seq
))
40 (declare-function org-every
"org" (pred seq
))
42 (defconst org-babel-header-args
:R
63 (results .
((file list vector table scalar verbatim
)
64 (raw org html latex code pp wrap
)
65 (replace silent append prepend
)
66 (output value graphics
))))
67 "R-specific header arguments.")
69 (defconst ob-R-safe-header-args
70 (append org-babel-safe-header-args
71 '(:width
:height
:bg
:units
:pointsize
:antialias
:quality
72 :compression
:res
:type
:family
:title
:fonts
73 :version
:paper
:encoding
:pagecentre
:colormodel
74 :useDingbats
:horizontal
))
75 "Header args which are safe for R babel blocks.
77 See `org-babel-safe-header-args' for documentation of the format of
80 (defvar org-babel-default-header-args
:R
'())
81 (put 'org-babel-default-header-args
:R
'safe-local-variable
82 (org-babel-header-args-safe-fn ob-R-safe-header-args
))
84 (defcustom org-babel-R-command
"R --slave --no-save"
85 "Name of command to use for executing R code."
90 (defvar ess-local-process-name
) ; dynamically scoped
91 (defun org-babel-edit-prep:R
(info)
92 (let ((session (cdr (assoc :session
(nth 2 info
)))))
93 (when (and session
(string-match "^\\*\\(.+?\\)\\*$" session
))
94 (save-match-data (org-babel-R-initiate-session session nil
)))))
96 (defconst ob-R-transfer-variable-table-with-header
98 con <- textConnection(
111 "R code used to transfer a table defined as a variable from org to R.
112 This function is used when the table contains a header.")
114 (defconst ob-R-transfer-variable-table-without-header
116 con <- textConnection(
126 col.names = paste(\"V\", seq_len(%d), sep =\"\")
131 "R code used to transfer a table defined as a variable from org to R.
132 This function is used when the table does not contain a header.")
134 (defun org-babel-expand-body:R
(body params
&optional graphics-file
)
135 "Expand BODY according to PARAMS, return the expanded body."
138 (when (cdr (assoc :prologue params
))
139 (list (cdr (assoc :prologue params
))))
140 (org-babel-variable-assignments:R params
)
142 (when (cdr (assoc :epilogue params
))
143 (list (cdr (assoc :epilogue params
)))))
146 (defun org-babel-execute:R
(body params
)
147 "Execute a block of R code.
148 This function is called by `org-babel-execute-src-block'."
150 (let* ((result-params (cdr (assoc :result-params params
)))
151 (result-type (cdr (assoc :result-type params
)))
152 (session (org-babel-R-initiate-session
153 (cdr (assoc :session params
)) params
))
154 (colnames-p (cdr (assoc :colnames params
)))
155 (rownames-p (cdr (assoc :rownames params
)))
156 (graphics-file (and (member "graphics" (assq :result-params params
))
157 (org-babel-graphical-output-file params
)))
160 (list (org-babel-expand-body:R body params graphics-file
))))
164 (list (org-babel-R-construct-graphics-device-call
165 graphics-file params
))
167 (list "},error=function(e){plot(x=-1:1, y=-1:1, type='n', xlab='', ylab='', axes=FALSE); text(x=0, y=0, labels=e$message, col='red'); paste('ERROR', e$message, sep=' : ')}); dev.off()"))
171 (org-babel-R-evaluate
172 session full-body result-type result-params
173 (or (equal "yes" colnames-p
)
175 (cdr (assoc :colname-names params
)) colnames-p
))
176 (or (equal "yes" rownames-p
)
178 (cdr (assoc :rowname-names params
)) rownames-p
)))))
179 (if graphics-file nil result
))))
181 (defun org-babel-prep-session:R
(session params
)
182 "Prepare SESSION according to the header arguments specified in PARAMS."
183 (let* ((session (org-babel-R-initiate-session session params
))
184 (var-lines (org-babel-variable-assignments:R params
)))
185 (org-babel-comint-in-buffer session
187 (end-of-line 1) (insert var
) (comint-send-input nil t
)
188 (org-babel-comint-wait-for-output session
)) var-lines
))
191 (defun org-babel-load-session:R
(session body params
)
192 "Load BODY into SESSION."
193 (save-window-excursion
194 (let ((buffer (org-babel-prep-session:R session params
)))
195 (with-current-buffer buffer
196 (goto-char (process-mark (get-buffer-process (current-buffer))))
197 (insert (org-babel-chomp body
)))
202 (defun org-babel-variable-assignments:R
(params)
203 "Return list of R statements assigning the block's variables."
204 (let ((vars (mapcar 'cdr
(org-babel-get-header params
:var
))))
207 (org-babel-R-assign-elisp
208 (car pair
) (cdr pair
)
209 (equal "yes" (cdr (assoc :colnames params
)))
210 (equal "yes" (cdr (assoc :rownames params
)))))
213 (cons (car (nth i vars
))
214 (org-babel-reassemble-table
216 (cdr (nth i
(cdr (assoc :colname-names params
))))
217 (cdr (nth i
(cdr (assoc :rowname-names params
)))))))
218 (org-number-sequence 0 (1- (length vars
)))))))
220 (defun org-babel-R-quote-tsv-field (s)
221 "Quote field S for export to R."
223 (concat "\"" (mapconcat 'identity
(split-string s
"\"") "\"\"") "\"")
226 (defun org-babel-R-assign-elisp (name value colnames-p rownames-p
)
227 "Construct R code assigning the elisp VALUE to a variable named NAME."
229 (let* ((lengths (mapcar 'length
(org-remove-if-not 'sequencep value
)))
230 (max (if lengths
(apply 'max lengths
) 0))
231 (min (if lengths
(apply 'min lengths
) 0)))
232 ;; Ensure VALUE has an orgtbl structure (depth of at least 2).
233 (unless (listp (car value
)) (setq value
(list value
)))
234 (let ((file (orgtbl-to-tsv value
'(:fmt org-babel-R-quote-tsv-field
)))
235 (header (if (or (eq (nth 1 value
) 'hline
) colnames-p
)
237 (row-names (if rownames-p
"1" "NULL")))
239 (format ob-R-transfer-variable-table-with-header
240 name file header row-names
)
241 (format ob-R-transfer-variable-table-without-header
242 name file header row-names max
))))
243 (cond ((integerp value
) (format "%s <- %s" name
(concat (number-to-string value
) "L")))
244 ((floatp value
) (format "%s <- %s" name value
))
245 ((stringp value
) (format "%s <- %S" name
(org-no-properties value
)))
246 (t (format "%s <- %S" name
(prin1-to-string value
))))))
249 (defvar ess-ask-for-ess-directory
) ; dynamically scoped
250 (defun org-babel-R-initiate-session (session params
)
251 "If there is not a current R process then create one."
252 (unless (string= session
"none")
253 (let ((session (or session
"*R*"))
254 (ess-ask-for-ess-directory
255 (and (boundp 'ess-ask-for-ess-directory
)
256 ess-ask-for-ess-directory
257 (not (cdr (assoc :dir params
))))))
258 (if (org-babel-comint-buffer-livep session
)
260 (save-window-excursion
261 (when (get-buffer session
)
262 ;; Session buffer exists, but with dead process
263 (set-buffer session
))
266 (if (bufferp session
)
267 (buffer-name session
)
268 (if (stringp session
)
271 (current-buffer))))))
273 (defun org-babel-R-associate-session (session)
274 "Associate R code buffer with an R session.
275 Make SESSION be the inferior ESS process associated with the
276 current code buffer."
277 (setq ess-local-process-name
278 (process-name (get-buffer-process session
)))
279 (ess-make-buffer-current))
281 (defvar org-babel-R-graphics-devices
282 '((:bmp
"bmp" "filename")
283 (:jpg
"jpeg" "filename")
284 (:jpeg
"jpeg" "filename")
285 (:tikz
"tikz" "file")
286 (:tiff
"tiff" "filename")
287 (:png
"png" "filename")
290 (:ps
"postscript" "file")
291 (:postscript
"postscript" "file"))
292 "An alist mapping graphics file types to R functions.
294 Each member of this list is a list with three members:
295 1. the file extension of the graphics file, as an elisp :keyword
296 2. the R graphics device function to call to generate such a file
297 3. the name of the argument to this function which specifies the
298 file to write to (typically \"file\" or \"filename\")")
300 (defun org-babel-R-construct-graphics-device-call (out-file params
)
301 "Construct the call to the graphics device."
302 (let* ((allowed-args '(:width
:height
:bg
:units
:pointsize
303 :antialias
:quality
:compression
:res
304 :type
:family
:title
:fonts
:version
305 :paper
:encoding
:pagecentre
:colormodel
306 :useDingbats
:horizontal
))
307 (device (and (string-match ".+\\.\\([^.]+\\)" out-file
)
308 (match-string 1 out-file
)))
309 (device-info (or (assq (intern (concat ":" device
))
310 org-babel-R-graphics-devices
)
311 (assq :png org-babel-R-graphics-devices
)))
312 (extra-args (cdr (assq :R-dev-args params
))) filearg args
)
313 (setq device
(nth 1 device-info
))
314 (setq filearg
(nth 2 device-info
))
315 (setq args
(mapconcat
317 (if (member (car pair
) allowed-args
)
319 (substring (symbol-name (car pair
)) 1)
322 (format "%s(%s=\"%s\"%s%s%s); tryCatch({"
323 device filearg out-file args
324 (if extra-args
"," "") (or extra-args
""))))
326 (defvar org-babel-R-eoe-indicator
"'org_babel_R_eoe'")
327 (defvar org-babel-R-eoe-output
"[1] \"org_babel_R_eoe\"")
329 (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\")")
331 (defun org-babel-R-evaluate
332 (session body result-type result-params column-names-p row-names-p
)
333 "Evaluate R code in BODY."
335 (org-babel-R-evaluate-session
336 session body result-type result-params column-names-p row-names-p
)
337 (org-babel-R-evaluate-external-process
338 body result-type result-params column-names-p row-names-p
)))
340 (defun org-babel-R-evaluate-external-process
341 (body result-type result-params column-names-p row-names-p
)
342 "Evaluate BODY in external R process.
343 If RESULT-TYPE equals 'output then return standard output as a
344 string. If RESULT-TYPE equals 'value then return the value of the
345 last statement in BODY, as elisp."
348 (let ((tmp-file (org-babel-temp-file "R-")))
349 (org-babel-eval org-babel-R-command
350 (format org-babel-R-write-object-command
351 (if row-names-p
"TRUE" "FALSE")
353 (if row-names-p
"NA" "TRUE")
355 (format "{function ()\n{\n%s\n}}()" body
)
356 (org-babel-process-file-name tmp-file
'noquote
)))
357 (org-babel-R-process-value-result
358 (org-babel-result-cond result-params
360 (insert-file-contents tmp-file
)
362 (org-babel-import-elisp-from-file tmp-file
'(16)))
364 (output (org-babel-eval org-babel-R-command body
))))
366 (defvar ess-eval-visibly-p
)
368 (defun org-babel-R-evaluate-session
369 (session body result-type result-params column-names-p row-names-p
)
370 "Evaluate BODY in SESSION.
371 If RESULT-TYPE equals 'output then return standard output as a
372 string. If RESULT-TYPE equals 'value then return the value of the
373 last statement in BODY, as elisp."
377 (insert (org-babel-chomp body
))
378 (let ((ess-local-process-name
379 (process-name (get-buffer-process session
)))
380 (ess-eval-visibly-p nil
))
381 (ess-eval-buffer nil
)))
382 (let ((tmp-file (org-babel-temp-file "R-")))
383 (org-babel-comint-eval-invisibly-and-wait-for-file
385 (format org-babel-R-write-object-command
386 (if row-names-p
"TRUE" "FALSE")
388 (if row-names-p
"NA" "TRUE")
390 ".Last.value" (org-babel-process-file-name tmp-file
'noquote
)))
391 (org-babel-R-process-value-result
392 (org-babel-result-cond result-params
394 (insert-file-contents tmp-file
)
396 (org-babel-import-elisp-from-file tmp-file
'(16)))
404 (lambda (line) (when (> (length line
) 0) line
))
406 (lambda (line) ;; cleanup extra prompts left in output
408 "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line
)
409 (substring line
(match-end 1))
411 (org-babel-comint-with-output (session org-babel-R-eoe-output
)
412 (insert (mapconcat 'org-babel-chomp
413 (list body org-babel-R-eoe-indicator
)
415 (inferior-ess-send-input)))))) "\n"))))
417 (defun org-babel-R-process-value-result (result column-names-p
)
418 "R-specific processing of return value.
419 Insert hline if column names in output have been requested."
421 (cons (car result
) (cons 'hline
(cdr result
)))
428 ;;; ob-R.el ends here