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 "^\\*\\(.+?\\)\\*$" session
))
94 (save-match-data (org-babel-R-initiate-session session nil
)))))
96 (defun org-babel-expand-body:R
(body params
&optional graphics-file
)
97 "Expand BODY according to PARAMS, return the expanded body."
100 (when (cdr (assoc :prologue params
))
101 (list (cdr (assoc :prologue params
))))
102 (org-babel-variable-assignments:R params
)
104 (when (cdr (assoc :epilogue params
))
105 (list (cdr (assoc :epilogue params
)))))
108 (defun org-babel-execute:R
(body params
)
109 "Execute a block of R code.
110 This function is called by `org-babel-execute-src-block'."
112 (let* ((result-params (cdr (assoc :result-params params
)))
113 (result-type (cdr (assoc :result-type params
)))
114 (session (org-babel-R-initiate-session
115 (cdr (assoc :session params
)) params
))
116 (colnames-p (cdr (assoc :colnames params
)))
117 (rownames-p (cdr (assoc :rownames params
)))
118 (graphics-file (and (member "graphics" (assq :result-params params
))
119 (org-babel-graphical-output-file params
)))
122 (list (org-babel-expand-body:R body params graphics-file
))))
126 (list (org-babel-R-construct-graphics-device-call
127 graphics-file params
))
129 (list "},error=function(e){plot(x=-1:1, y=-1:1, type='n', xlab='', ylab='', axes=FALSE); text(x=0, y=0, labels=e$message, col='red'); paste('ERROR', e$message, sep=' : ')}); dev.off()"))
133 (org-babel-R-evaluate
134 session full-body result-type result-params
135 (or (equal "yes" colnames-p
)
137 (cdr (assoc :colname-names params
)) colnames-p
))
138 (or (equal "yes" rownames-p
)
140 (cdr (assoc :rowname-names params
)) rownames-p
)))))
141 (if graphics-file nil result
))))
143 (defun org-babel-prep-session:R
(session params
)
144 "Prepare SESSION according to the header arguments specified in PARAMS."
145 (let* ((session (org-babel-R-initiate-session session params
))
146 (var-lines (org-babel-variable-assignments:R params
)))
147 (org-babel-comint-in-buffer session
149 (end-of-line 1) (insert var
) (comint-send-input nil t
)
150 (org-babel-comint-wait-for-output session
)) var-lines
))
153 (defun org-babel-load-session:R
(session body params
)
154 "Load BODY into SESSION."
155 (save-window-excursion
156 (let ((buffer (org-babel-prep-session:R session params
)))
157 (with-current-buffer buffer
158 (goto-char (process-mark (get-buffer-process (current-buffer))))
159 (insert (org-babel-chomp body
)))
164 (defun org-babel-variable-assignments:R
(params)
165 "Return list of R statements assigning the block's variables."
166 (let ((vars (mapcar 'cdr
(org-babel-get-header params
:var
))))
169 (org-babel-R-assign-elisp
170 (car pair
) (cdr pair
)
171 (equal "yes" (cdr (assoc :colnames params
)))
172 (equal "yes" (cdr (assoc :rownames params
)))))
175 (cons (car (nth i vars
))
176 (org-babel-reassemble-table
178 (cdr (nth i
(cdr (assoc :colname-names params
))))
179 (cdr (nth i
(cdr (assoc :rowname-names params
)))))))
180 (org-number-sequence 0 (1- (length vars
)))))))
182 (defun org-babel-R-quote-tsv-field (s)
183 "Quote field S for export to R."
185 (concat "\"" (mapconcat 'identity
(split-string s
"\"") "\"\"") "\"")
188 (defun org-babel-R-assign-elisp (name value colnames-p rownames-p
)
189 "Construct R code assigning the elisp VALUE to a variable named NAME."
191 (let* ((lengths (mapcar 'length
(org-remove-if-not 'sequencep value
)))
192 (max (if lengths
(apply 'max lengths
) 0))
193 (min (if lengths
(apply 'min lengths
) 0))
194 (transition-file (org-babel-temp-file "R-import-")))
195 ;; Ensure VALUE has an orgtbl structure (depth of at least 2).
196 (unless (listp (car value
)) (setq value
(list value
)))
197 (with-temp-file transition-file
199 (orgtbl-to-tsv value
'(:fmt org-babel-R-quote-tsv-field
))
201 (let ((file (org-babel-process-file-name transition-file
'noquote
))
202 (header (if (or (eq (nth 1 value
) 'hline
) colnames-p
)
204 (row-names (if rownames-p
"1" "NULL")))
206 (format "%s <- read.table(\"%s\",
210 as.is=TRUE)" name file header row-names
)
211 (format "%s <- read.table(\"%s\",
217 col.names = paste(\"V\", seq_len(%d), sep =\"\"))"
218 name file header row-names max
))))
219 (format "%s <- %s" name
(org-babel-R-quote-tsv-field value
))))
221 (defvar ess-ask-for-ess-directory
) ; dynamically scoped
222 (defun org-babel-R-initiate-session (session params
)
223 "If there is not a current R process then create one."
224 (unless (string= session
"none")
225 (let ((session (or session
"*R*"))
226 (ess-ask-for-ess-directory
227 (and (and (boundp 'ess-ask-for-ess-directory
) ess-ask-for-ess-directory
)
228 (not (cdr (assoc :dir params
))))))
229 (if (org-babel-comint-buffer-livep session
)
231 (save-window-excursion
232 (when (get-buffer session
)
233 ;; Session buffer exists, but with dead process
234 (set-buffer session
))
237 (if (bufferp session
)
238 (buffer-name session
)
239 (if (stringp session
)
242 (current-buffer))))))
244 (defun org-babel-R-associate-session (session)
245 "Associate R code buffer with an R session.
246 Make SESSION be the inferior ESS process associated with the
247 current code buffer."
248 (setq ess-local-process-name
249 (process-name (get-buffer-process session
)))
250 (ess-make-buffer-current))
252 (defvar org-babel-R-graphics-devices
253 '((:bmp
"bmp" "filename")
254 (:jpg
"jpeg" "filename")
255 (:jpeg
"jpeg" "filename")
256 (:tikz
"tikz" "file")
257 (:tiff
"tiff" "filename")
258 (:png
"png" "filename")
261 (:ps
"postscript" "file")
262 (:postscript
"postscript" "file"))
263 "An alist mapping graphics file types to R functions.
265 Each member of this list is a list with three members:
266 1. the file extension of the graphics file, as an elisp :keyword
267 2. the R graphics device function to call to generate such a file
268 3. the name of the argument to this function which specifies the
269 file to write to (typically \"file\" or \"filename\")")
271 (defun org-babel-R-construct-graphics-device-call (out-file params
)
272 "Construct the call to the graphics device."
273 (let* ((allowed-args '(:width
:height
:bg
:units
:pointsize
274 :antialias
:quality
:compression
:res
275 :type
:family
:title
:fonts
:version
276 :paper
:encoding
:pagecentre
:colormodel
277 :useDingbats
:horizontal
))
278 (device (and (string-match ".+\\.\\([^.]+\\)" out-file
)
279 (match-string 1 out-file
)))
280 (device-info (or (assq (intern (concat ":" device
))
281 org-babel-R-graphics-devices
)
282 (assq :png org-babel-R-graphics-devices
)))
283 (extra-args (cdr (assq :R-dev-args params
))) filearg args
)
284 (setq device
(nth 1 device-info
))
285 (setq filearg
(nth 2 device-info
))
286 (setq args
(mapconcat
288 (if (member (car pair
) allowed-args
)
290 (substring (symbol-name (car pair
)) 1)
293 (format "%s(%s=\"%s\"%s%s%s); tryCatch({"
294 device filearg out-file args
295 (if extra-args
"," "") (or extra-args
""))))
297 (defvar org-babel-R-eoe-indicator
"'org_babel_R_eoe'")
298 (defvar org-babel-R-eoe-output
"[1] \"org_babel_R_eoe\"")
300 (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\")")
302 (defun org-babel-R-evaluate
303 (session body result-type result-params column-names-p row-names-p
)
304 "Evaluate R code in BODY."
306 (org-babel-R-evaluate-session
307 session body result-type result-params column-names-p row-names-p
)
308 (org-babel-R-evaluate-external-process
309 body result-type result-params column-names-p row-names-p
)))
311 (defun org-babel-R-evaluate-external-process
312 (body result-type result-params column-names-p row-names-p
)
313 "Evaluate BODY in external R process.
314 If RESULT-TYPE equals 'output then return standard output as a
315 string. If RESULT-TYPE equals 'value then return the value of the
316 last statement in BODY, as elisp."
319 (let ((tmp-file (org-babel-temp-file "R-")))
320 (org-babel-eval org-babel-R-command
321 (format org-babel-R-write-object-command
322 (if row-names-p
"TRUE" "FALSE")
324 (if row-names-p
"NA" "TRUE")
326 (format "{function ()\n{\n%s\n}}()" body
)
327 (org-babel-process-file-name tmp-file
'noquote
)))
328 (org-babel-R-process-value-result
329 (org-babel-result-cond result-params
331 (insert-file-contents tmp-file
)
333 (org-babel-import-elisp-from-file tmp-file
'(16)))
335 (output (org-babel-eval org-babel-R-command body
))))
337 (defvar ess-eval-visibly-p
)
339 (defun org-babel-R-evaluate-session
340 (session body result-type result-params column-names-p row-names-p
)
341 "Evaluate BODY in SESSION.
342 If RESULT-TYPE equals 'output then return standard output as a
343 string. If RESULT-TYPE equals 'value then return the value of the
344 last statement in BODY, as elisp."
348 (insert (org-babel-chomp body
))
349 (let ((ess-local-process-name
350 (process-name (get-buffer-process session
)))
351 (ess-eval-visibly-p nil
))
352 (ess-eval-buffer nil
)))
353 (let ((tmp-file (org-babel-temp-file "R-")))
354 (org-babel-comint-eval-invisibly-and-wait-for-file
356 (format org-babel-R-write-object-command
357 (if row-names-p
"TRUE" "FALSE")
359 (if row-names-p
"NA" "TRUE")
361 ".Last.value" (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)))
375 (lambda (line) (when (> (length line
) 0) line
))
377 (lambda (line) ;; cleanup extra prompts left in output
379 "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line
)
380 (substring line
(match-end 1))
382 (org-babel-comint-with-output (session org-babel-R-eoe-output
)
383 (insert (mapconcat 'org-babel-chomp
384 (list body org-babel-R-eoe-indicator
)
386 (inferior-ess-send-input)))))) "\n"))))
388 (defun org-babel-R-process-value-result (result column-names-p
)
389 "R-specific processing of return value.
390 Insert hline if column names in output have been requested."
392 (cons (car result
) (cons 'hline
(cdr result
)))
399 ;;; ob-R.el ends here