1 ;;; ob-R.el --- org-babel functions for R code evaluation
3 ;; Copyright (C) 2009-2012 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
34 (eval-when-compile (require 'cl
))
36 (declare-function orgtbl-to-tsv
"org-table" (table params
))
37 (declare-function R
"ext:essd-r" (&optional start-args
))
38 (declare-function inferior-ess-send-input
"ext:ess-inf" ())
39 (declare-function ess-make-buffer-current
"ext:ess-inf" ())
40 (declare-function ess-eval-buffer
"ext:ess-inf" (vis))
41 (declare-function org-number-sequence
"org-compat" (from &optional to inc
))
43 (defconst org-babel-header-args
:R
64 (results .
((file list vector table scalar verbatim
)
65 (raw org html latex code pp wrap
)
66 (replace silent append prepend
)
67 (output value graphics
))))
68 "R-specific header arguments.")
70 (defvar org-babel-default-header-args
:R
'())
72 (defvar org-babel-R-command
"R --slave --no-save"
73 "Name of command to use for executing R code.")
75 (defvar ess-local-process-name
)
76 (defun org-babel-edit-prep:R
(info)
77 (let ((session (cdr (assoc :session
(nth 2 info
)))))
78 (when (and session
(string-match "^\\*\\(.+?\\)\\*$" session
))
79 (save-match-data (org-babel-R-initiate-session session nil
))
80 (setq ess-local-process-name
(match-string 1 session
)))))
82 (defun org-babel-expand-body:R
(body params
&optional graphics-file
)
83 "Expand BODY according to PARAMS, return the expanded body."
85 (or graphics-file
(org-babel-R-graphical-output-file params
))))
91 (list (org-babel-R-construct-graphics-device-call
92 graphics-file params
))
96 (append (org-babel-variable-assignments:R params
)
99 (defun org-babel-execute:R
(body params
)
100 "Execute a block of R code.
101 This function is called by `org-babel-execute-src-block'."
103 (let* ((result-params (cdr (assoc :result-params params
)))
104 (result-type (cdr (assoc :result-type params
)))
105 (session (org-babel-R-initiate-session
106 (cdr (assoc :session params
)) params
))
107 (colnames-p (cdr (assoc :colnames params
)))
108 (rownames-p (cdr (assoc :rownames params
)))
109 (graphics-file (org-babel-R-graphical-output-file params
))
110 (full-body (org-babel-expand-body:R body params graphics-file
))
112 (org-babel-R-evaluate
113 session full-body result-type result-params
114 (or (equal "yes" colnames-p
)
116 (cdr (assoc :colname-names params
)) colnames-p
))
117 (or (equal "yes" rownames-p
)
119 (cdr (assoc :rowname-names params
)) rownames-p
)))))
120 (if graphics-file nil result
))))
122 (defun org-babel-prep-session:R
(session params
)
123 "Prepare SESSION according to the header arguments specified in PARAMS."
124 (let* ((session (org-babel-R-initiate-session session params
))
125 (var-lines (org-babel-variable-assignments:R params
)))
126 (org-babel-comint-in-buffer session
128 (end-of-line 1) (insert var
) (comint-send-input nil t
)
129 (org-babel-comint-wait-for-output session
)) var-lines
))
132 (defun org-babel-load-session:R
(session body params
)
133 "Load BODY into SESSION."
134 (save-window-excursion
135 (let ((buffer (org-babel-prep-session:R session params
)))
136 (with-current-buffer buffer
137 (goto-char (process-mark (get-buffer-process (current-buffer))))
138 (insert (org-babel-chomp body
)))
143 (defun org-babel-variable-assignments:R
(params)
144 "Return list of R statements assigning the block's variables"
145 (let ((vars (mapcar #'cdr
(org-babel-get-header params
:var
))))
148 (org-babel-R-assign-elisp
149 (car pair
) (cdr pair
)
150 (equal "yes" (cdr (assoc :colnames params
)))
151 (equal "yes" (cdr (assoc :rownames params
)))))
154 (cons (car (nth i vars
))
155 (org-babel-reassemble-table
157 (cdr (nth i
(cdr (assoc :colname-names params
))))
158 (cdr (nth i
(cdr (assoc :rowname-names params
)))))))
159 (org-number-sequence 0 (1- (length vars
)))))))
161 (defun org-babel-R-quote-tsv-field (s)
162 "Quote field S for export to R."
164 (concat "\"" (mapconcat 'identity
(split-string s
"\"") "\"\"") "\"")
167 (defun org-babel-R-assign-elisp (name value colnames-p rownames-p
)
168 "Construct R code assigning the elisp VALUE to a variable named NAME."
170 (let ((max (apply #'max
(mapcar #'length value
)))
171 (min (apply #'min
(mapcar #'length value
)))
172 (transition-file (org-babel-temp-file "R-import-")))
173 ;; ensure VALUE has an orgtbl structure (depth of at least 2)
174 (unless (listp (car value
)) (setq value
(list value
)))
175 (with-temp-file transition-file
177 (orgtbl-to-tsv value
'(:fmt org-babel-R-quote-tsv-field
))
179 (let ((file (org-babel-process-file-name transition-file
'noquote
))
180 (header (if (or (eq (nth 1 value
) 'hline
) colnames-p
)
182 (row-names (if rownames-p
"1" "NULL")))
184 (format "%s <- read.table(\"%s\",
188 as.is=TRUE)" name file header row-names
)
189 (format "%s <- read.table(\"%s\",
195 col.names = paste(\"V\", seq_len(%d), sep =\"\"))"
196 name file header row-names max
))))
197 (format "%s <- %s" name
(org-babel-R-quote-tsv-field value
))))
199 (defvar ess-ask-for-ess-directory nil
)
200 (defun org-babel-R-initiate-session (session params
)
201 "If there is not a current R process then create one."
202 (unless (string= session
"none")
203 (let ((session (or session
"*R*"))
204 (ess-ask-for-ess-directory
205 (and ess-ask-for-ess-directory
(not (cdr (assoc :dir params
))))))
206 (if (org-babel-comint-buffer-livep session
)
208 (save-window-excursion
211 (if (bufferp session
)
212 (buffer-name session
)
213 (if (stringp session
)
216 (current-buffer))))))
218 (defvar ess-local-process-name nil
)
219 (defun org-babel-R-associate-session (session)
220 "Associate R code buffer with an R session.
221 Make SESSION be the inferior ESS process associated with the
222 current code buffer."
223 (setq ess-local-process-name
224 (process-name (get-buffer-process session
)))
225 (ess-make-buffer-current))
227 (defun org-babel-R-graphical-output-file (params)
228 "Name of file to which R should send graphical output."
229 (and (member "graphics" (cdr (assq :result-params params
)))
230 (cdr (assq :file params
))))
232 (defun org-babel-R-construct-graphics-device-call (out-file params
)
233 "Construct the call to the graphics device."
244 (:postscript .
"postscript")))
245 (allowed-args '(:width
:height
:bg
:units
:pointsize
246 :antialias
:quality
:compression
:res
247 :type
:family
:title
:fonts
:version
248 :paper
:encoding
:pagecentre
:colormodel
249 :useDingbats
:horizontal
))
250 (device (and (string-match ".+\\.\\([^.]+\\)" out-file
)
251 (match-string 1 out-file
)))
252 (extra-args (cdr (assq :R-dev-args params
))) filearg args
)
253 (setq device
(or (and device
(cdr (assq (intern (concat ":" device
))
256 (if (member device
'("pdf" "postscript" "svg" "tikz")) "file" "filename"))
257 (setq args
(mapconcat
259 (if (member (car pair
) allowed-args
)
261 (substring (symbol-name (car pair
)) 1)
264 (format "%s(%s=\"%s\"%s%s%s)"
265 device filearg out-file args
266 (if extra-args
"," "") (or extra-args
""))))
268 (defvar org-babel-R-eoe-indicator
"'org_babel_R_eoe'")
269 (defvar org-babel-R-eoe-output
"[1] \"org_babel_R_eoe\"")
271 (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\")")
273 (defun org-babel-R-evaluate
274 (session body result-type result-params column-names-p row-names-p
)
275 "Evaluate R code in BODY."
277 (org-babel-R-evaluate-session
278 session body result-type result-params column-names-p row-names-p
)
279 (org-babel-R-evaluate-external-process
280 body result-type result-params column-names-p row-names-p
)))
282 (defun org-babel-R-evaluate-external-process
283 (body result-type result-params column-names-p row-names-p
)
284 "Evaluate BODY in external R process.
285 If RESULT-TYPE equals 'output then return standard output as a
286 string. If RESULT-TYPE equals 'value then return the value of the
287 last statement in BODY, as elisp."
290 (let ((tmp-file (org-babel-temp-file "R-")))
291 (org-babel-eval org-babel-R-command
292 (format org-babel-R-write-object-command
293 (if row-names-p
"TRUE" "FALSE")
295 (if row-names-p
"NA" "TRUE")
297 (format "{function ()\n{\n%s\n}}()" body
)
298 (org-babel-process-file-name tmp-file
'noquote
)))
299 (org-babel-R-process-value-result
300 (if (or (member "scalar" result-params
)
301 (member "verbatim" result-params
))
303 (insert-file-contents tmp-file
)
305 (org-babel-import-elisp-from-file tmp-file
'(16)))
307 (output (org-babel-eval org-babel-R-command body
))))
309 (defun org-babel-R-evaluate-session
310 (session body result-type result-params column-names-p row-names-p
)
311 "Evaluate BODY in SESSION.
312 If RESULT-TYPE equals 'output then return standard output as a
313 string. If RESULT-TYPE equals 'value then return the value of the
314 last statement in BODY, as elisp."
318 (insert (org-babel-chomp body
))
319 (let ((ess-local-process-name
320 (process-name (get-buffer-process session
)))
321 (ess-eval-visibly-p nil
))
322 (ess-eval-buffer nil
)))
323 (let ((tmp-file (org-babel-temp-file "R-")))
324 (org-babel-comint-eval-invisibly-and-wait-for-file
326 (format org-babel-R-write-object-command
327 (if row-names-p
"TRUE" "FALSE")
329 (if row-names-p
"NA" "TRUE")
331 ".Last.value" (org-babel-process-file-name tmp-file
'noquote
)))
332 (org-babel-R-process-value-result
333 (if (or (member "scalar" result-params
)
334 (member "verbatim" result-params
))
336 (insert-file-contents tmp-file
)
338 (org-babel-import-elisp-from-file tmp-file
'(16)))
346 (lambda (line) (when (> (length line
) 0) line
))
348 (lambda (line) ;; cleanup extra prompts left in output
350 "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line
)
351 (substring line
(match-end 1))
353 (org-babel-comint-with-output (session org-babel-R-eoe-output
)
354 (insert (mapconcat #'org-babel-chomp
355 (list body org-babel-R-eoe-indicator
)
357 (inferior-ess-send-input)))))) "\n"))))
359 (defun org-babel-R-process-value-result (result column-names-p
)
360 "R-specific processing of return value.
361 Insert hline if column names in output have been requested."
363 (cons (car result
) (cons 'hline
(cdr result
)))
370 ;;; ob-R.el ends here