lisp/org/ob-R.el

   1 ;;; ob-R.el --- org-babel functions for R code evaluation
   2
   3 ;; Copyright (C) 2009, 2010  Free Software Foundation, Inc.
   4
   5 ;; Author: Eric Schulte, Dan Davison
   6 ;; Keywords: literate programming, reproducible research, R, statistics
   7 ;; Homepage: http://orgmode.org
   8 ;; Version: 7.7
   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
  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))
  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
  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)
  62   "Expand BODY according to PARAMS, return the expanded body."
  63   (let ((graphics-file
  64          (or graphics-file (org-babel-R-graphical-output-file params))))
  65     (mapconcat
  66      #'identity
  67      ((lambda (inside)
  68         (if graphics-file
  69             (append
  70              (list (org-babel-R-construct-graphics-device-call
  71                     graphics-file params))
  72              inside
  73              (list "dev.off()"))
  74           inside))
  75       (append (org-babel-variable-assignments:R params)
  76               (list body))) "\n")))
  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
  82     (let* ((result-type (cdr (assoc :result-type params)))
  83            (session (org-babel-R-initiate-session
  84                      (cdr (assoc :session params)) params))
  85            (colnames-p (cdr (assoc :colnames params)))
  86            (rownames-p (cdr (assoc :rownames params)))
  87            (graphics-file (org-babel-R-graphical-output-file params))
  88            (full-body (org-babel-expand-body:R body params graphics-file))
  89            (result
  90             (org-babel-R-evaluate
  91              session full-body result-type
  92              (or (equal "yes" colnames-p)
  93                  (org-babel-pick-name
  94                   (cdr (assoc :colname-names params)) colnames-p))
  95              (or (equal "yes" rownames-p)
  96                  (org-babel-pick-name
  97                   (cdr (assoc :rowname-names params)) rownames-p)))))
  98       (if graphics-file nil result))))
  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))
 103          (var-lines (org-babel-variable-assignments:R params)))
 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
 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
 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)
 148       (let ((transition-file (org-babel-temp-file "R-import-")))
 149         ;; ensure VALUE has an orgtbl structure (depth of at least 2)
 150         (unless (listp (car value)) (setq value (list value)))
 151         (with-temp-file transition-file
 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)"
 155                 name (org-babel-process-file-name transition-file 'noquote)
 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
 160 (defvar ess-ask-for-ess-directory nil)
 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*"))
 165           (ess-ask-for-ess-directory
 166            (and ess-ask-for-ess-directory (not (cdr (assoc :dir params))))))
 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
 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
 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
 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\"")
 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\")")
 232
 233 (defun org-babel-R-evaluate
 234   (session body result-type column-names-p row-names-p)
 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
 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"))))
 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
 315 ;; arch-tag: cd4c7298-503b-450f-a3c2-f3e74b630237
 316
 317 ;;; ob-R.el ends here