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1 | ;;; ob-R.el --- org-babel functions for R code evaluation |
2 | ||
3ab2c837 | 3 | ;; Copyright (C) 2009, 2010 Free Software Foundation, Inc. |
86fbb8ca | 4 | |
acedf35c | 5 | ;; Author: Eric Schulte, Dan Davison |
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6 | ;; Keywords: literate programming, reproducible research, R, statistics |
7 | ;; Homepage: http://orgmode.org | |
3ab2c837 | 8 | ;; Version: 7.7 |
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9 | |
10 | ;; This file is part of GNU Emacs. | |
11 | ||
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. | |
16 | ||
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. | |
21 | ||
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/>. | |
24 | ||
25 | ;;; Commentary: | |
26 | ||
27 | ;; Org-Babel support for evaluating R code | |
28 | ||
29 | ;;; Code: | |
30 | (require 'ob) | |
31 | (require 'ob-ref) | |
32 | (require 'ob-comint) | |
33 | (require 'ob-eval) | |
34 | (eval-when-compile (require 'cl)) | |
35 | ||
f1eee0b6 | 36 | (declare-function orgtbl-to-tsv "org-table" (table params)) |
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37 | (declare-function R "ext:essd-r" (&optional start-args)) |
38 | (declare-function inferior-ess-send-input "ext:ess-inf" ()) | |
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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)) | |
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42 | |
43 | (defconst org-babel-header-arg-names:R | |
44 | '(width height bg units pointsize antialias quality compression | |
45 | res type family title fonts version paper encoding | |
46 | pagecentre colormodel useDingbats horizontal) | |
47 | "R-specific header arguments.") | |
48 | ||
49 | (defvar org-babel-default-header-args:R '()) | |
50 | ||
51 | (defvar org-babel-R-command "R --slave --no-save" | |
52 | "Name of command to use for executing R code.") | |
53 | ||
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54 | (defvar ess-local-process-name) |
55 | (defun org-babel-edit-prep:R (info) | |
56 | (let ((session (cdr (assoc :session (nth 2 info))))) | |
57 | (when (and session (string-match "^\\*\\(.+?\\)\\*$" session)) | |
58 | (save-match-data (org-babel-R-initiate-session session nil)) | |
59 | (setq ess-local-process-name (match-string 1 session))))) | |
60 | ||
61 | (defun org-babel-expand-body:R (body params &optional graphics-file) | |
86fbb8ca | 62 | "Expand BODY according to PARAMS, return the expanded body." |
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63 | (let ((graphics-file |
64 | (or graphics-file (org-babel-R-graphical-output-file params)))) | |
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65 | (mapconcat |
66 | #'identity | |
86fbb8ca | 67 | ((lambda (inside) |
3ab2c837 | 68 | (if graphics-file |
86fbb8ca | 69 | (append |
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70 | (list (org-babel-R-construct-graphics-device-call |
71 | graphics-file params)) | |
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72 | inside |
73 | (list "dev.off()")) | |
74 | inside)) | |
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75 | (append (org-babel-variable-assignments:R params) |
76 | (list body))) "\n"))) | |
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77 | |
78 | (defun org-babel-execute:R (body params) | |
79 | "Execute a block of R code. | |
80 | This function is called by `org-babel-execute-src-block'." | |
81 | (save-excursion | |
afe98dfa | 82 | (let* ((result-type (cdr (assoc :result-type params))) |
86fbb8ca | 83 | (session (org-babel-R-initiate-session |
afe98dfa | 84 | (cdr (assoc :session params)) params)) |
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85 | (colnames-p (cdr (assoc :colnames params))) |
86 | (rownames-p (cdr (assoc :rownames params))) | |
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87 | (graphics-file (org-babel-R-graphical-output-file params)) |
88 | (full-body (org-babel-expand-body:R body params graphics-file)) | |
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89 | (result |
90 | (org-babel-R-evaluate | |
91 | session full-body result-type | |
92 | (or (equal "yes" colnames-p) | |
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93 | (org-babel-pick-name |
94 | (cdr (assoc :colname-names params)) colnames-p)) | |
86fbb8ca | 95 | (or (equal "yes" rownames-p) |
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96 | (org-babel-pick-name |
97 | (cdr (assoc :rowname-names params)) rownames-p))))) | |
3ab2c837 | 98 | (if graphics-file nil result)))) |
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99 | |
100 | (defun org-babel-prep-session:R (session params) | |
101 | "Prepare SESSION according to the header arguments specified in PARAMS." | |
102 | (let* ((session (org-babel-R-initiate-session session params)) | |
afe98dfa | 103 | (var-lines (org-babel-variable-assignments:R params))) |
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104 | (org-babel-comint-in-buffer session |
105 | (mapc (lambda (var) | |
106 | (end-of-line 1) (insert var) (comint-send-input nil t) | |
107 | (org-babel-comint-wait-for-output session)) var-lines)) | |
108 | session)) | |
109 | ||
110 | (defun org-babel-load-session:R (session body params) | |
111 | "Load BODY into SESSION." | |
112 | (save-window-excursion | |
113 | (let ((buffer (org-babel-prep-session:R session params))) | |
114 | (with-current-buffer buffer | |
115 | (goto-char (process-mark (get-buffer-process (current-buffer)))) | |
116 | (insert (org-babel-chomp body))) | |
117 | buffer))) | |
118 | ||
119 | ;; helper functions | |
120 | ||
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121 | (defun org-babel-variable-assignments:R (params) |
122 | "Return list of R statements assigning the block's variables" | |
123 | (let ((vars (mapcar #'cdr (org-babel-get-header params :var)))) | |
124 | (mapcar | |
125 | (lambda (pair) | |
126 | (org-babel-R-assign-elisp | |
127 | (car pair) (cdr pair) | |
128 | (equal "yes" (cdr (assoc :colnames params))) | |
129 | (equal "yes" (cdr (assoc :rownames params))))) | |
130 | (mapcar | |
131 | (lambda (i) | |
132 | (cons (car (nth i vars)) | |
133 | (org-babel-reassemble-table | |
134 | (cdr (nth i vars)) | |
135 | (cdr (nth i (cdr (assoc :colname-names params)))) | |
136 | (cdr (nth i (cdr (assoc :rowname-names params))))))) | |
137 | (org-number-sequence 0 (1- (length vars))))))) | |
138 | ||
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139 | (defun org-babel-R-quote-tsv-field (s) |
140 | "Quote field S for export to R." | |
141 | (if (stringp s) | |
142 | (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"") | |
143 | (format "%S" s))) | |
144 | ||
145 | (defun org-babel-R-assign-elisp (name value colnames-p rownames-p) | |
146 | "Construct R code assigning the elisp VALUE to a variable named NAME." | |
147 | (if (listp value) | |
afe98dfa | 148 | (let ((transition-file (org-babel-temp-file "R-import-"))) |
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149 | ;; ensure VALUE has an orgtbl structure (depth of at least 2) |
150 | (unless (listp (car value)) (setq value (list value))) | |
afe98dfa | 151 | (with-temp-file transition-file |
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152 | (insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field))) |
153 | (insert "\n")) | |
154 | (format "%s <- read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE)" | |
afe98dfa | 155 | name (org-babel-process-file-name transition-file 'noquote) |
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156 | (if (or (eq (nth 1 value) 'hline) colnames-p) "TRUE" "FALSE") |
157 | (if rownames-p "1" "NULL"))) | |
158 | (format "%s <- %s" name (org-babel-R-quote-tsv-field value)))) | |
159 | ||
afe98dfa | 160 | (defvar ess-ask-for-ess-directory nil) |
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161 | (defun org-babel-R-initiate-session (session params) |
162 | "If there is not a current R process then create one." | |
163 | (unless (string= session "none") | |
164 | (let ((session (or session "*R*")) | |
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165 | (ess-ask-for-ess-directory |
166 | (and ess-ask-for-ess-directory (not (cdr (assoc :dir params)))))) | |
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167 | (if (org-babel-comint-buffer-livep session) |
168 | session | |
169 | (save-window-excursion | |
170 | (require 'ess) (R) | |
171 | (rename-buffer | |
172 | (if (bufferp session) | |
173 | (buffer-name session) | |
174 | (if (stringp session) | |
175 | session | |
176 | (buffer-name)))) | |
177 | (current-buffer)))))) | |
178 | ||
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179 | (defvar ess-local-process-name nil) |
180 | (defun org-babel-R-associate-session (session) | |
181 | "Associate R code buffer with an R session. | |
182 | Make SESSION be the inferior ESS process associated with the | |
183 | current code buffer." | |
184 | (setq ess-local-process-name | |
185 | (process-name (get-buffer-process session))) | |
186 | (ess-make-buffer-current)) | |
187 | ||
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188 | (defun org-babel-R-graphical-output-file (params) |
189 | "Name of file to which R should send graphical output." | |
190 | (and (member "graphics" (cdr (assq :result-params params))) | |
191 | (cdr (assq :file params)))) | |
192 | ||
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193 | (defun org-babel-R-construct-graphics-device-call (out-file params) |
194 | "Construct the call to the graphics device." | |
195 | (let ((devices | |
196 | '((:bmp . "bmp") | |
197 | (:jpg . "jpeg") | |
198 | (:jpeg . "jpeg") | |
199 | (:tiff . "tiff") | |
200 | (:png . "png") | |
201 | (:svg . "svg") | |
202 | (:pdf . "pdf") | |
203 | (:ps . "postscript") | |
204 | (:postscript . "postscript"))) | |
205 | (allowed-args '(:width :height :bg :units :pointsize | |
206 | :antialias :quality :compression :res | |
207 | :type :family :title :fonts :version | |
208 | :paper :encoding :pagecentre :colormodel | |
209 | :useDingbats :horizontal)) | |
210 | (device (and (string-match ".+\\.\\([^.]+\\)" out-file) | |
211 | (match-string 1 out-file))) | |
212 | (extra-args (cdr (assq :R-dev-args params))) filearg args) | |
213 | (setq device (or (and device (cdr (assq (intern (concat ":" device)) | |
214 | devices))) "png")) | |
215 | (setq filearg | |
216 | (if (member device '("pdf" "postscript" "svg")) "file" "filename")) | |
217 | (setq args (mapconcat | |
218 | (lambda (pair) | |
219 | (if (member (car pair) allowed-args) | |
220 | (format ",%s=%s" | |
221 | (substring (symbol-name (car pair)) 1) | |
222 | (cdr pair)) "")) | |
223 | params "")) | |
224 | (format "%s(%s=\"%s\"%s%s%s)" | |
225 | device filearg out-file args | |
226 | (if extra-args "," "") (or extra-args "")))) | |
227 | ||
228 | (defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'") | |
229 | (defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"") | |
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230 | |
231 | (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\")") | |
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232 | |
233 | (defun org-babel-R-evaluate | |
234 | (session body result-type column-names-p row-names-p) | |
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235 | "Evaluate R code in BODY." |
236 | (if session | |
237 | (org-babel-R-evaluate-session | |
238 | session body result-type column-names-p row-names-p) | |
239 | (org-babel-R-evaluate-external-process | |
240 | body result-type column-names-p row-names-p))) | |
241 | ||
242 | (defun org-babel-R-evaluate-external-process | |
243 | (body result-type column-names-p row-names-p) | |
244 | "Evaluate BODY in external R process. | |
245 | If RESULT-TYPE equals 'output then return standard output as a | |
246 | string. If RESULT-TYPE equals 'value then return the value of the | |
247 | last statement in BODY, as elisp." | |
248 | (case result-type | |
249 | (value | |
250 | (let ((tmp-file (org-babel-temp-file "R-"))) | |
251 | (org-babel-eval org-babel-R-command | |
252 | (format org-babel-R-write-object-command | |
253 | (if row-names-p "TRUE" "FALSE") | |
254 | (if column-names-p | |
255 | (if row-names-p "NA" "TRUE") | |
256 | "FALSE") | |
257 | (format "{function ()\n{\n%s\n}}()" body) | |
258 | (org-babel-process-file-name tmp-file 'noquote))) | |
259 | (org-babel-R-process-value-result | |
260 | (org-babel-import-elisp-from-file tmp-file '(16)) column-names-p))) | |
261 | (output (org-babel-eval org-babel-R-command body)))) | |
262 | ||
263 | (defun org-babel-R-evaluate-session | |
264 | (session body result-type column-names-p row-names-p) | |
265 | "Evaluate BODY in SESSION. | |
266 | If RESULT-TYPE equals 'output then return standard output as a | |
267 | string. If RESULT-TYPE equals 'value then return the value of the | |
268 | last statement in BODY, as elisp." | |
269 | (case result-type | |
270 | (value | |
271 | (with-temp-buffer | |
272 | (insert (org-babel-chomp body)) | |
273 | (let ((ess-local-process-name | |
274 | (process-name (get-buffer-process session)))) | |
275 | (ess-eval-buffer nil))) | |
276 | (let ((tmp-file (org-babel-temp-file "R-"))) | |
277 | (org-babel-comint-eval-invisibly-and-wait-for-file | |
278 | session tmp-file | |
279 | (format org-babel-R-write-object-command | |
280 | (if row-names-p "TRUE" "FALSE") | |
281 | (if column-names-p | |
282 | (if row-names-p "NA" "TRUE") | |
283 | "FALSE") | |
284 | ".Last.value" (org-babel-process-file-name tmp-file 'noquote))) | |
285 | (org-babel-R-process-value-result | |
286 | (org-babel-import-elisp-from-file tmp-file '(16)) column-names-p))) | |
287 | (output | |
288 | (mapconcat | |
289 | #'org-babel-chomp | |
290 | (butlast | |
291 | (delq nil | |
292 | (mapcar | |
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293 | (lambda (line) (when (> (length line) 0) line)) |
294 | (mapcar | |
295 | (lambda (line) ;; cleanup extra prompts left in output | |
296 | (if (string-match | |
297 | "^\\([ ]*[>+][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line) | |
298 | (substring line (match-end 1)) | |
299 | line)) | |
300 | (org-babel-comint-with-output (session org-babel-R-eoe-output) | |
301 | (insert (mapconcat #'org-babel-chomp | |
302 | (list body org-babel-R-eoe-indicator) | |
303 | "\n")) | |
304 | (inferior-ess-send-input)))))) "\n")))) | |
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305 | |
306 | (defun org-babel-R-process-value-result (result column-names-p) | |
307 | "R-specific processing of return value. | |
308 | Insert hline if column names in output have been requested." | |
309 | (if column-names-p | |
310 | (cons (car result) (cons 'hline (cdr result))) | |
311 | result)) | |
312 | ||
313 | (provide 'ob-R) | |
314 | ||
5b409b39 | 315 | |
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316 | |
317 | ;;; ob-R.el ends here |