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-current-process-name
) ; dynamically scoped
93 (defvar ess-local-process-name
) ; dynamically scoped
94 (defun org-babel-edit-prep:R
(info)
95 (let ((session (cdr (assoc :session
(nth 2 info
)))))
96 (when (and session
(string-match "^\\*\\(.+?\\)\\*$" session
))
97 (save-match-data (org-babel-R-initiate-session session nil
)))))
99 (defconst ob-R-transfer-variable-table-with-header
101 con <- textConnection(
114 "R code used to transfer a table defined as a variable from org to R.
115 This function is used when the table contains a header.")
117 (defconst ob-R-transfer-variable-table-without-header
119 con <- textConnection(
129 col.names = paste(\"V\", seq_len(%d), sep =\"\")
134 "R code used to transfer a table defined as a variable from org to R.
135 This function is used when the table does not contain a header.")
137 (defun org-babel-expand-body:R
(body params
&optional graphics-file
)
138 "Expand BODY according to PARAMS, return the expanded body."
141 (when (cdr (assoc :prologue params
))
142 (list (cdr (assoc :prologue params
))))
143 (org-babel-variable-assignments:R params
)
145 (when (cdr (assoc :epilogue params
))
146 (list (cdr (assoc :epilogue params
)))))
149 (defun org-babel-execute:R
(body params
)
150 "Execute a block of R code.
151 This function is called by `org-babel-execute-src-block'."
153 (let* ((result-params (cdr (assoc :result-params params
)))
154 (result-type (cdr (assoc :result-type params
)))
155 (session (org-babel-R-initiate-session
156 (cdr (assoc :session params
)) params
))
157 (colnames-p (cdr (assoc :colnames params
)))
158 (rownames-p (cdr (assoc :rownames params
)))
159 (graphics-file (and (member "graphics" (assq :result-params params
))
160 (org-babel-graphical-output-file params
)))
163 (list (org-babel-expand-body:R body params graphics-file
))))
167 (list (org-babel-R-construct-graphics-device-call
168 graphics-file params
))
170 (list "},error=function(e){plot(x=-1:1, y=-1:1, type='n', xlab='', ylab='', axes=FALSE); text(x=0, y=0, labels=e$message, col='red'); paste('ERROR', e$message, sep=' : ')}); dev.off()"))
174 (org-babel-R-evaluate
175 session full-body result-type result-params
176 (or (equal "yes" colnames-p
)
178 (cdr (assoc :colname-names params
)) colnames-p
))
179 (or (equal "yes" rownames-p
)
181 (cdr (assoc :rowname-names params
)) rownames-p
)))))
182 (if graphics-file nil result
))))
184 (defun org-babel-prep-session:R
(session params
)
185 "Prepare SESSION according to the header arguments specified in PARAMS."
186 (let* ((session (org-babel-R-initiate-session session params
))
187 (var-lines (org-babel-variable-assignments:R params
)))
188 (org-babel-comint-in-buffer session
190 (end-of-line 1) (insert var
) (comint-send-input nil t
)
191 (org-babel-comint-wait-for-output session
)) var-lines
))
194 (defun org-babel-load-session:R
(session body params
)
195 "Load BODY into SESSION."
196 (save-window-excursion
197 (let ((buffer (org-babel-prep-session:R session params
)))
198 (with-current-buffer buffer
199 (goto-char (process-mark (get-buffer-process (current-buffer))))
200 (insert (org-babel-chomp body
)))
205 (defun org-babel-variable-assignments:R
(params)
206 "Return list of R statements assigning the block's variables."
207 (let ((vars (mapcar 'cdr
(org-babel-get-header params
:var
))))
210 (org-babel-R-assign-elisp
211 (car pair
) (cdr pair
)
212 (equal "yes" (cdr (assoc :colnames params
)))
213 (equal "yes" (cdr (assoc :rownames params
)))))
216 (cons (car (nth i vars
))
217 (org-babel-reassemble-table
219 (cdr (nth i
(cdr (assoc :colname-names params
))))
220 (cdr (nth i
(cdr (assoc :rowname-names params
)))))))
221 (org-number-sequence 0 (1- (length vars
)))))))
223 (defun org-babel-R-quote-tsv-field (s)
224 "Quote field S for export to R."
226 (concat "\"" (mapconcat 'identity
(split-string s
"\"") "\"\"") "\"")
229 (defun org-babel-R-assign-elisp (name value colnames-p rownames-p
)
230 "Construct R code assigning the elisp VALUE to a variable named NAME."
232 (let* ((lengths (mapcar 'length
(org-remove-if-not 'sequencep value
)))
233 (max (if lengths
(apply 'max lengths
) 0))
234 (min (if lengths
(apply 'min lengths
) 0)))
235 ;; Ensure VALUE has an orgtbl structure (depth of at least 2).
236 (unless (listp (car value
)) (setq value
(list value
)))
237 (let ((file (orgtbl-to-tsv value
'(:fmt org-babel-R-quote-tsv-field
)))
238 (header (if (or (eq (nth 1 value
) 'hline
) colnames-p
)
240 (row-names (if rownames-p
"1" "NULL")))
242 (format ob-R-transfer-variable-table-with-header
243 name file header row-names
)
244 (format ob-R-transfer-variable-table-without-header
245 name file header row-names max
))))
246 (cond ((integerp value
) (format "%s <- %s" name
(concat (number-to-string value
) "L")))
247 ((floatp value
) (format "%s <- %s" name value
))
248 ((stringp value
) (format "%s <- %S" name
(org-no-properties value
)))
249 (t (format "%s <- %S" name
(prin1-to-string value
))))))
252 (defvar ess-ask-for-ess-directory
) ; dynamically scoped
253 (defun org-babel-R-initiate-session (session params
)
254 "If there is not a current R process then create one."
255 (unless (string= session
"none")
256 (let ((session (or session
"*R*"))
257 (ess-ask-for-ess-directory
258 (and (boundp 'ess-ask-for-ess-directory
)
259 ess-ask-for-ess-directory
260 (not (cdr (assoc :dir params
))))))
261 (if (org-babel-comint-buffer-livep session
)
263 (save-window-excursion
264 (when (get-buffer session
)
265 ;; Session buffer exists, but with dead process
266 (set-buffer session
))
268 (ess-wait-for-process
269 (get-process (or ess-local-process-name
270 ess-current-process-name
)))
272 (if (bufferp session
)
273 (buffer-name session
)
274 (if (stringp session
)
277 (current-buffer))))))
279 (defun org-babel-R-associate-session (session)
280 "Associate R code buffer with an R session.
281 Make SESSION be the inferior ESS process associated with the
282 current code buffer."
283 (setq ess-local-process-name
284 (process-name (get-buffer-process session
)))
285 (ess-make-buffer-current))
287 (defvar org-babel-R-graphics-devices
288 '((:bmp
"bmp" "filename")
289 (:jpg
"jpeg" "filename")
290 (:jpeg
"jpeg" "filename")
291 (:tikz
"tikz" "file")
292 (:tiff
"tiff" "filename")
293 (:png
"png" "filename")
296 (:ps
"postscript" "file")
297 (:postscript
"postscript" "file"))
298 "An alist mapping graphics file types to R functions.
300 Each member of this list is a list with three members:
301 1. the file extension of the graphics file, as an elisp :keyword
302 2. the R graphics device function to call to generate such a file
303 3. the name of the argument to this function which specifies the
304 file to write to (typically \"file\" or \"filename\")")
306 (defun org-babel-R-construct-graphics-device-call (out-file params
)
307 "Construct the call to the graphics device."
308 (let* ((allowed-args '(:width
:height
:bg
:units
:pointsize
309 :antialias
:quality
:compression
:res
310 :type
:family
:title
:fonts
:version
311 :paper
:encoding
:pagecentre
:colormodel
312 :useDingbats
:horizontal
))
313 (device (and (string-match ".+\\.\\([^.]+\\)" out-file
)
314 (match-string 1 out-file
)))
315 (device-info (or (assq (intern (concat ":" device
))
316 org-babel-R-graphics-devices
)
317 (assq :png org-babel-R-graphics-devices
)))
318 (extra-args (cdr (assq :R-dev-args params
))) filearg args
)
319 (setq device
(nth 1 device-info
))
320 (setq filearg
(nth 2 device-info
))
321 (setq args
(mapconcat
323 (if (member (car pair
) allowed-args
)
325 (substring (symbol-name (car pair
)) 1)
328 (format "%s(%s=\"%s\"%s%s%s); tryCatch({"
329 device filearg out-file args
330 (if extra-args
"," "") (or extra-args
""))))
332 (defvar org-babel-R-eoe-indicator
"'org_babel_R_eoe'")
333 (defvar org-babel-R-eoe-output
"[1] \"org_babel_R_eoe\"")
335 (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\")")
337 (defun org-babel-R-evaluate
338 (session body result-type result-params column-names-p row-names-p
)
339 "Evaluate R code in BODY."
341 (org-babel-R-evaluate-session
342 session body result-type result-params column-names-p row-names-p
)
343 (org-babel-R-evaluate-external-process
344 body result-type result-params column-names-p row-names-p
)))
346 (defun org-babel-R-evaluate-external-process
347 (body result-type result-params column-names-p row-names-p
)
348 "Evaluate BODY in external R process.
349 If RESULT-TYPE equals 'output then return standard output as a
350 string. If RESULT-TYPE equals 'value then return the value of the
351 last statement in BODY, as elisp."
354 (let ((tmp-file (org-babel-temp-file "R-")))
355 (org-babel-eval org-babel-R-command
356 (format org-babel-R-write-object-command
357 (if row-names-p
"TRUE" "FALSE")
359 (if row-names-p
"NA" "TRUE")
361 (format "{function ()\n{\n%s\n}}()" body
)
362 (org-babel-process-file-name tmp-file
'noquote
)))
363 (org-babel-R-process-value-result
364 (org-babel-result-cond result-params
366 (insert-file-contents tmp-file
)
368 (org-babel-import-elisp-from-file tmp-file
'(16)))
370 (output (org-babel-eval org-babel-R-command body
))))
372 (defvar ess-eval-visibly-p
)
374 (defun org-babel-R-evaluate-session
375 (session body result-type result-params column-names-p row-names-p
)
376 "Evaluate BODY in SESSION.
377 If RESULT-TYPE equals 'output then return standard output as a
378 string. If RESULT-TYPE equals 'value then return the value of the
379 last statement in BODY, as elisp."
383 (insert (org-babel-chomp body
))
384 (let ((ess-local-process-name
385 (process-name (get-buffer-process session
)))
386 (ess-eval-visibly-p nil
))
387 (ess-eval-buffer nil
)))
388 (let ((tmp-file (org-babel-temp-file "R-")))
389 (org-babel-comint-eval-invisibly-and-wait-for-file
391 (format org-babel-R-write-object-command
392 (if row-names-p
"TRUE" "FALSE")
394 (if row-names-p
"NA" "TRUE")
396 ".Last.value" (org-babel-process-file-name tmp-file
'noquote
)))
397 (org-babel-R-process-value-result
398 (org-babel-result-cond result-params
400 (insert-file-contents tmp-file
)
402 (org-babel-import-elisp-from-file tmp-file
'(16)))
410 (lambda (line) (when (> (length line
) 0) line
))
412 (lambda (line) ;; cleanup extra prompts left in output
414 "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line
)
415 (substring line
(match-end 1))
417 (org-babel-comint-with-output (session org-babel-R-eoe-output
)
418 (insert (mapconcat 'org-babel-chomp
419 (list body org-babel-R-eoe-indicator
)
421 (inferior-ess-send-input)))))) "\n"))))
423 (defun org-babel-R-process-value-result (result column-names-p
)
424 "R-specific processing of return value.
425 Insert hline if column names in output have been requested."
427 (cons (car result
) (cons 'hline
(cdr result
)))
434 ;;; ob-R.el ends here