Fix up autoloads in vc-rcs.el and vc-sccs.el.
[emacs.git] / lisp / org / ob-R.el
blobb97fd912eae248c1324b70718eb4ddf42a8e6758
1 ;;; ob-R.el --- org-babel functions for R code evaluation
3 ;; Copyright (C) 2009-2014 Free Software Foundation, Inc.
5 ;; Author: Eric Schulte
6 ;; Dan Davison
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/>.
25 ;;; Commentary:
27 ;; Org-Babel support for evaluating R code
29 ;;; Code:
30 (require 'ob)
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
42 '((width . :any)
43 (height . :any)
44 (bg . :any)
45 (units . :any)
46 (pointsize . :any)
47 (antialias . :any)
48 (quality . :any)
49 (compression . :any)
50 (res . :any)
51 (type . :any)
52 (family . :any)
53 (title . :any)
54 (fonts . :any)
55 (version . :any)
56 (paper . :any)
57 (encoding . :any)
58 (pagecentre . :any)
59 (colormodel . :any)
60 (useDingbats . :any)
61 (horizontal . :any)
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."
72 :group 'org-babel
73 :version "24.1"
74 :type 'string)
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."
84 (let ((graphics-file
85 (or graphics-file (org-babel-R-graphical-output-file params))))
86 (mapconcat
87 #'identity
88 (let ((inside
89 (append
90 (when (cdr (assoc :prologue params))
91 (list (cdr (assoc :prologue params))))
92 (org-babel-variable-assignments:R params)
93 (list body)
94 (when (cdr (assoc :epilogue params))
95 (list (cdr (assoc :epilogue params)))))))
96 (if graphics-file
97 (append
98 (list (org-babel-R-construct-graphics-device-call
99 graphics-file params))
100 inside
101 (list "dev.off()"))
102 inside))
103 "\n")))
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'."
108 (save-excursion
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))
117 (result
118 (org-babel-R-evaluate
119 session full-body result-type result-params
120 (or (equal "yes" colnames-p)
121 (org-babel-pick-name
122 (cdr (assoc :colname-names params)) colnames-p))
123 (or (equal "yes" rownames-p)
124 (org-babel-pick-name
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
133 (mapc (lambda (var)
134 (end-of-line 1) (insert var) (comint-send-input nil t)
135 (org-babel-comint-wait-for-output session)) var-lines))
136 session))
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)))
145 buffer)))
147 ;; helper functions
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))))
152 (mapcar
153 (lambda (pair)
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)))))
158 (mapcar
159 (lambda (i)
160 (cons (car (nth i vars))
161 (org-babel-reassemble-table
162 (cdr (nth i vars))
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."
169 (if (stringp s)
170 (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
171 (format "%S" 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."
175 (if (listp value)
176 (let* ((lengths (mapcar 'length (org-remove-if-not 'sequencep value)))
177 (max (if lengths (apply 'max lengths) 0))
178 (min (if lengths (apply 'min lengths) 0))
179 (transition-file (org-babel-temp-file "R-import-")))
180 ;; Ensure VALUE has an orgtbl structure (depth of at least 2).
181 (unless (listp (car value)) (setq value (list value)))
182 (with-temp-file transition-file
183 (insert
184 (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field))
185 "\n"))
186 (let ((file (org-babel-process-file-name transition-file 'noquote))
187 (header (if (or (eq (nth 1 value) 'hline) colnames-p)
188 "TRUE" "FALSE"))
189 (row-names (if rownames-p "1" "NULL")))
190 (if (= max min)
191 (format "%s <- read.table(\"%s\",
192 header=%s,
193 row.names=%s,
194 sep=\"\\t\",
195 as.is=TRUE)" name file header row-names)
196 (format "%s <- read.table(\"%s\",
197 header=%s,
198 row.names=%s,
199 sep=\"\\t\",
200 as.is=TRUE,
201 fill=TRUE,
202 col.names = paste(\"V\", seq_len(%d), sep =\"\"))"
203 name file header row-names max))))
204 (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
206 (defvar ess-ask-for-ess-directory) ; dynamically scoped
207 (defun org-babel-R-initiate-session (session params)
208 "If there is not a current R process then create one."
209 (unless (string= session "none")
210 (let ((session (or session "*R*"))
211 (ess-ask-for-ess-directory
212 (and (and (boundp 'ess-ask-for-ess-directory) ess-ask-for-ess-directory)
213 (not (cdr (assoc :dir params))))))
214 (if (org-babel-comint-buffer-livep session)
215 session
216 (save-window-excursion
217 (when (get-buffer session)
218 ;; Session buffer exists, but with dead process
219 (set-buffer session))
220 (require 'ess) (R)
221 (rename-buffer
222 (if (bufferp session)
223 (buffer-name session)
224 (if (stringp session)
225 session
226 (buffer-name))))
227 (current-buffer))))))
229 (defun org-babel-R-associate-session (session)
230 "Associate R code buffer with an R session.
231 Make SESSION be the inferior ESS process associated with the
232 current code buffer."
233 (setq ess-local-process-name
234 (process-name (get-buffer-process session)))
235 (ess-make-buffer-current))
237 (defun org-babel-R-graphical-output-file (params)
238 "Name of file to which R should send graphical output."
239 (and (member "graphics" (cdr (assq :result-params params)))
240 (cdr (assq :file params))))
242 (defvar org-babel-R-graphics-devices
243 '((:bmp "bmp" "filename")
244 (:jpg "jpeg" "filename")
245 (:jpeg "jpeg" "filename")
246 (:tikz "tikz" "file")
247 (:tiff "tiff" "filename")
248 (:png "png" "filename")
249 (:svg "svg" "file")
250 (:pdf "pdf" "file")
251 (:ps "postscript" "file")
252 (:postscript "postscript" "file"))
253 "An alist mapping graphics file types to R functions.
255 Each member of this list is a list with three members:
256 1. the file extension of the graphics file, as an elisp :keyword
257 2. the R graphics device function to call to generate such a file
258 3. the name of the argument to this function which specifies the
259 file to write to (typically \"file\" or \"filename\")")
261 (defun org-babel-R-construct-graphics-device-call (out-file params)
262 "Construct the call to the graphics device."
263 (let* ((allowed-args '(:width :height :bg :units :pointsize
264 :antialias :quality :compression :res
265 :type :family :title :fonts :version
266 :paper :encoding :pagecentre :colormodel
267 :useDingbats :horizontal))
268 (device (and (string-match ".+\\.\\([^.]+\\)" out-file)
269 (match-string 1 out-file)))
270 (device-info (or (assq (intern (concat ":" device))
271 org-babel-R-graphics-devices)
272 (assq :png org-babel-R-graphics-devices)))
273 (extra-args (cdr (assq :R-dev-args params))) filearg args)
274 (setq device (nth 1 device-info))
275 (setq filearg (nth 2 device-info))
276 (setq args (mapconcat
277 (lambda (pair)
278 (if (member (car pair) allowed-args)
279 (format ",%s=%S"
280 (substring (symbol-name (car pair)) 1)
281 (cdr pair)) ""))
282 params ""))
283 (format "%s(%s=\"%s\"%s%s%s)"
284 device filearg out-file args
285 (if extra-args "," "") (or extra-args ""))))
287 (defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
288 (defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
290 (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\")")
292 (defun org-babel-R-evaluate
293 (session body result-type result-params column-names-p row-names-p)
294 "Evaluate R code in BODY."
295 (if session
296 (org-babel-R-evaluate-session
297 session body result-type result-params column-names-p row-names-p)
298 (org-babel-R-evaluate-external-process
299 body result-type result-params column-names-p row-names-p)))
301 (defun org-babel-R-evaluate-external-process
302 (body result-type result-params column-names-p row-names-p)
303 "Evaluate BODY in external R process.
304 If RESULT-TYPE equals 'output then return standard output as a
305 string. If RESULT-TYPE equals 'value then return the value of the
306 last statement in BODY, as elisp."
307 (case result-type
308 (value
309 (let ((tmp-file (org-babel-temp-file "R-")))
310 (org-babel-eval org-babel-R-command
311 (format org-babel-R-write-object-command
312 (if row-names-p "TRUE" "FALSE")
313 (if column-names-p
314 (if row-names-p "NA" "TRUE")
315 "FALSE")
316 (format "{function ()\n{\n%s\n}}()" body)
317 (org-babel-process-file-name tmp-file 'noquote)))
318 (org-babel-R-process-value-result
319 (org-babel-result-cond result-params
320 (with-temp-buffer
321 (insert-file-contents tmp-file)
322 (buffer-string))
323 (org-babel-import-elisp-from-file tmp-file '(16)))
324 column-names-p)))
325 (output (org-babel-eval org-babel-R-command body))))
327 (defvar ess-eval-visibly-p)
329 (defun org-babel-R-evaluate-session
330 (session body result-type result-params column-names-p row-names-p)
331 "Evaluate BODY in SESSION.
332 If RESULT-TYPE equals 'output then return standard output as a
333 string. If RESULT-TYPE equals 'value then return the value of the
334 last statement in BODY, as elisp."
335 (case result-type
336 (value
337 (with-temp-buffer
338 (insert (org-babel-chomp body))
339 (let ((ess-local-process-name
340 (process-name (get-buffer-process session)))
341 (ess-eval-visibly-p nil))
342 (ess-eval-buffer nil)))
343 (let ((tmp-file (org-babel-temp-file "R-")))
344 (org-babel-comint-eval-invisibly-and-wait-for-file
345 session tmp-file
346 (format org-babel-R-write-object-command
347 (if row-names-p "TRUE" "FALSE")
348 (if column-names-p
349 (if row-names-p "NA" "TRUE")
350 "FALSE")
351 ".Last.value" (org-babel-process-file-name tmp-file 'noquote)))
352 (org-babel-R-process-value-result
353 (org-babel-result-cond result-params
354 (with-temp-buffer
355 (insert-file-contents tmp-file)
356 (buffer-string))
357 (org-babel-import-elisp-from-file tmp-file '(16)))
358 column-names-p)))
359 (output
360 (mapconcat
361 #'org-babel-chomp
362 (butlast
363 (delq nil
364 (mapcar
365 (lambda (line) (when (> (length line) 0) line))
366 (mapcar
367 (lambda (line) ;; cleanup extra prompts left in output
368 (if (string-match
369 "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
370 (substring line (match-end 1))
371 line))
372 (org-babel-comint-with-output (session org-babel-R-eoe-output)
373 (insert (mapconcat #'org-babel-chomp
374 (list body org-babel-R-eoe-indicator)
375 "\n"))
376 (inferior-ess-send-input)))))) "\n"))))
378 (defun org-babel-R-process-value-result (result column-names-p)
379 "R-specific processing of return value.
380 Insert hline if column names in output have been requested."
381 (if column-names-p
382 (cons (car result) (cons 'hline (cdr result)))
383 result))
385 (provide 'ob-R)
389 ;;; ob-R.el ends here