lisp/ob-R.el

   1 ;;; ob-R.el --- org-babel functions for R code evaluation
   2
   3 ;; Copyright (C) 2009-2011  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
   9 ;; This file is part of GNU Emacs.
  10
  11 ;; GNU Emacs is free software: you can redistribute it and/or modify
  12 ;; it under the terms of the GNU General Public License as published by
  13 ;; the Free Software Foundation, either version 3 of the License, or
  14 ;; (at your option) any later version.
  15
  16 ;; GNU Emacs is distributed in the hope that it will be useful,
  17 ;; but WITHOUT ANY WARRANTY; without even the implied warranty of
  18 ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  19 ;; GNU General Public License for more details.
  20
  21 ;; You should have received a copy of the GNU General Public License
  22 ;; along with GNU Emacs.  If not, see <http://www.gnu.org/licenses/>.
  23
  24 ;;; Commentary:
  25
  26 ;; Org-Babel support for evaluating R code
  27
  28 ;;; Code:
  29 (require 'ob)
  30 (require 'ob-ref)
  31 (require 'ob-comint)
  32 (require 'ob-eval)
  33 (eval-when-compile (require 'cl))
  34
  35 (declare-function orgtbl-to-tsv "org-table" (table params))
  36 (declare-function R "ext:essd-r" (&optional start-args))
  37 (declare-function inferior-ess-send-input "ext:ess-inf" ())
  38 (declare-function ess-make-buffer-current "ext:ess-inf" ())
  39 (declare-function ess-eval-buffer "ext:ess-inf" (vis))
  40 (declare-function org-number-sequence "org-compat" (from &optional to inc))
  41
  42 (defconst org-babel-header-arg-names:R
  43   '(width height bg units pointsize antialias quality compression
  44           res type family title fonts version paper encoding
  45           pagecentre colormodel useDingbats horizontal)
  46   "R-specific header arguments.")
  47
  48 (defvar org-babel-default-header-args:R '())
  49
  50 (defvar org-babel-R-command "R --slave --no-save"
  51   "Name of command to use for executing R code.")
  52
  53 (defvar ess-local-process-name)
  54 (defun org-babel-edit-prep:R (info)
  55   (let ((session (cdr (assoc :session (nth 2 info)))))
  56     (when (and session (string-match "^\\*\\(.+?\\)\\*$" session))
  57       (save-match-data (org-babel-R-initiate-session session nil))
  58       (setq ess-local-process-name (match-string 1 session)))))
  59
  60 (defun org-babel-expand-body:R (body params &optional graphics-file)
  61   "Expand BODY according to PARAMS, return the expanded body."
  62   (let ((graphics-file
  63          (or graphics-file (org-babel-R-graphical-output-file params))))
  64     (mapconcat
  65      #'identity
  66      ((lambda (inside)
  67         (if graphics-file
  68             (append
  69              (list (org-babel-R-construct-graphics-device-call
  70                     graphics-file params))
  71              inside
  72              (list "dev.off()"))
  73           inside))
  74       (append (org-babel-variable-assignments:R params)
  75               (list body))) "\n")))
  76
  77 (defun org-babel-execute:R (body params)
  78   "Execute a block of R code.
  79 This function is called by `org-babel-execute-src-block'."
  80   (save-excursion
  81     (let* ((result-type (cdr (assoc :result-type params)))
  82            (session (org-babel-R-initiate-session
  83                      (cdr (assoc :session params)) params))
  84            (colnames-p (cdr (assoc :colnames params)))
  85            (rownames-p (cdr (assoc :rownames params)))
  86            (graphics-file (org-babel-R-graphical-output-file params))
  87            (full-body (org-babel-expand-body:R body params graphics-file))
  88            (result
  89             (org-babel-R-evaluate
  90              session full-body result-type
  91              (or (equal "yes" colnames-p)
  92                  (org-babel-pick-name
  93                   (cdr (assoc :colname-names params)) colnames-p))
  94              (or (equal "yes" rownames-p)
  95                  (org-babel-pick-name
  96                   (cdr (assoc :rowname-names params)) rownames-p)))))
  97       (if graphics-file nil result))))
  98
  99 (defun org-babel-prep-session:R (session params)
 100   "Prepare SESSION according to the header arguments specified in PARAMS."
 101   (let* ((session (org-babel-R-initiate-session session params))
 102          (var-lines (org-babel-variable-assignments:R params)))
 103     (org-babel-comint-in-buffer session
 104       (mapc (lambda (var)
 105               (end-of-line 1) (insert var) (comint-send-input nil t)
 106               (org-babel-comint-wait-for-output session)) var-lines))
 107     session))
 108
 109 (defun org-babel-load-session:R (session body params)
 110   "Load BODY into SESSION."
 111   (save-window-excursion
 112     (let ((buffer (org-babel-prep-session:R session params)))
 113       (with-current-buffer buffer
 114         (goto-char (process-mark (get-buffer-process (current-buffer))))
 115         (insert (org-babel-chomp body)))
 116       buffer)))
 117
 118 ;; helper functions
 119
 120 (defun org-babel-variable-assignments:R (params)
 121   "Return list of R statements assigning the block's variables"
 122   (let ((vars (mapcar #'cdr (org-babel-get-header params :var))))
 123     (mapcar
 124      (lambda (pair)
 125        (org-babel-R-assign-elisp
 126         (car pair) (cdr pair)
 127         (equal "yes" (cdr (assoc :colnames params)))
 128         (equal "yes" (cdr (assoc :rownames params)))))
 129      (mapcar
 130       (lambda (i)
 131         (cons (car (nth i vars))
 132               (org-babel-reassemble-table
 133                (cdr (nth i vars))
 134                (cdr (nth i (cdr (assoc :colname-names params))))
 135                (cdr (nth i (cdr (assoc :rowname-names params)))))))
 136       (org-number-sequence 0 (1- (length vars)))))))
 137
 138 (defun org-babel-R-quote-tsv-field (s)
 139   "Quote field S for export to R."
 140   (if (stringp s)
 141       (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
 142     (format "%S" s)))
 143
 144 (defun org-babel-R-assign-elisp (name value colnames-p rownames-p)
 145   "Construct R code assigning the elisp VALUE to a variable named NAME."
 146   (if (listp value)
 147       (let ((transition-file (org-babel-temp-file "R-import-")))
 148         ;; ensure VALUE has an orgtbl structure (depth of at least 2)
 149         (unless (listp (car value)) (setq value (list value)))
 150         (with-temp-file transition-file
 151           (insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
 152           (insert "\n"))
 153         (format "%s <- read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE)"
 154                 name (org-babel-process-file-name transition-file 'noquote)
 155                 (if (or (eq (nth 1 value) 'hline) colnames-p) "TRUE" "FALSE")
 156                 (if rownames-p "1" "NULL")))
 157     (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
 158
 159 (defvar ess-ask-for-ess-directory nil)
 160 (defun org-babel-R-initiate-session (session params)
 161   "If there is not a current R process then create one."
 162   (unless (string= session "none")
 163     (let ((session (or session "*R*"))
 164           (ess-ask-for-ess-directory
 165            (and ess-ask-for-ess-directory (not (cdr (assoc :dir params))))))
 166       (if (org-babel-comint-buffer-livep session)
 167           session
 168         (save-window-excursion
 169           (require 'ess) (R)
 170           (rename-buffer
 171            (if (bufferp session)
 172                (buffer-name session)
 173              (if (stringp session)
 174                  session
 175                (buffer-name))))
 176           (current-buffer))))))
 177
 178 (defvar ess-local-process-name nil)
 179 (defun org-babel-R-associate-session (session)
 180   "Associate R code buffer with an R session.
 181 Make SESSION be the inferior ESS process associated with the
 182 current code buffer."
 183   (setq ess-local-process-name
 184         (process-name (get-buffer-process session)))
 185   (ess-make-buffer-current))
 186
 187 (defun org-babel-R-graphical-output-file (params)
 188   "Name of file to which R should send graphical output."
 189   (and (member "graphics" (cdr (assq :result-params params)))
 190        (cdr (assq :file params))))
 191
 192 (defun org-babel-R-construct-graphics-device-call (out-file params)
 193   "Construct the call to the graphics device."
 194   (let ((devices
 195          '((:bmp . "bmp")
 196            (:jpg . "jpeg")
 197            (:jpeg . "jpeg")
 198            (:tiff . "tiff")
 199            (:png . "png")
 200            (:svg . "svg")
 201            (:pdf . "pdf")
 202            (:ps . "postscript")
 203            (:postscript . "postscript")))
 204         (allowed-args '(:width :height :bg :units :pointsize
 205                                :antialias :quality :compression :res
 206                                :type :family :title :fonts :version
 207                                :paper :encoding :pagecentre :colormodel
 208                                :useDingbats :horizontal))
 209         (device (and (string-match ".+\\.\\([^.]+\\)" out-file)
 210                      (match-string 1 out-file)))
 211         (extra-args (cdr (assq :R-dev-args params))) filearg args)
 212     (setq device (or (and device (cdr (assq (intern (concat ":" device))
 213                                             devices))) "png"))
 214     (setq filearg
 215           (if (member device '("pdf" "postscript" "svg")) "file" "filename"))
 216     (setq args (mapconcat
 217                 (lambda (pair)
 218                   (if (member (car pair) allowed-args)
 219                       (format ",%s=%s"
 220                               (substring (symbol-name (car pair)) 1)
 221                               (cdr pair)) ""))
 222                 params ""))
 223     (format "%s(%s=\"%s\"%s%s%s)"
 224             device filearg out-file args
 225             (if extra-args "," "") (or extra-args ""))))
 226
 227 (defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
 228 (defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
 229
 230 (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\")")
 231
 232 (defun org-babel-R-evaluate
 233   (session body result-type column-names-p row-names-p)
 234   "Evaluate R code in BODY."
 235   (if session
 236       (org-babel-R-evaluate-session
 237        session body result-type column-names-p row-names-p)
 238     (org-babel-R-evaluate-external-process
 239      body result-type column-names-p row-names-p)))
 240
 241 (defun org-babel-R-evaluate-external-process
 242   (body result-type column-names-p row-names-p)
 243   "Evaluate BODY in external R process.
 244 If RESULT-TYPE equals 'output then return standard output as a
 245 string. If RESULT-TYPE equals 'value then return the value of the
 246 last statement in BODY, as elisp."
 247   (case result-type
 248     (value
 249      (let ((tmp-file (org-babel-temp-file "R-")))
 250        (org-babel-eval org-babel-R-command
 251                        (format org-babel-R-write-object-command
 252                                (if row-names-p "TRUE" "FALSE")
 253                                (if column-names-p
 254                                    (if row-names-p "NA" "TRUE")
 255                                  "FALSE")
 256                                (format "{function ()\n{\n%s\n}}()" body)
 257                                (org-babel-process-file-name tmp-file 'noquote)))
 258        (org-babel-R-process-value-result
 259         (org-babel-import-elisp-from-file tmp-file '(16)) column-names-p)))
 260     (output (org-babel-eval org-babel-R-command body))))
 261
 262 (defun org-babel-R-evaluate-session
 263   (session body result-type column-names-p row-names-p)
 264   "Evaluate BODY in SESSION.
 265 If RESULT-TYPE equals 'output then return standard output as a
 266 string. If RESULT-TYPE equals 'value then return the value of the
 267 last statement in BODY, as elisp."
 268   (case result-type
 269     (value
 270      (with-temp-buffer
 271        (insert (org-babel-chomp body))
 272        (let ((ess-local-process-name
 273               (process-name (get-buffer-process session))))
 274          (ess-eval-buffer nil)))
 275      (let ((tmp-file (org-babel-temp-file "R-")))
 276        (org-babel-comint-eval-invisibly-and-wait-for-file
 277         session tmp-file
 278         (format org-babel-R-write-object-command
 279                 (if row-names-p "TRUE" "FALSE")
 280                 (if column-names-p
 281                     (if row-names-p "NA" "TRUE")
 282                   "FALSE")
 283                 ".Last.value" (org-babel-process-file-name tmp-file 'noquote)))
 284        (org-babel-R-process-value-result
 285         (org-babel-import-elisp-from-file tmp-file '(16))  column-names-p)))
 286     (output
 287      (mapconcat
 288       #'org-babel-chomp
 289       (butlast
 290        (delq nil
 291              (mapcar
 292               (lambda (line) (when (> (length line) 0) line))
 293               (mapcar
 294                (lambda (line) ;; cleanup extra prompts left in output
 295                  (if (string-match
 296                       "^\\([ ]*[>+][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
 297                      (substring line (match-end 1))
 298                    line))
 299                (org-babel-comint-with-output (session org-babel-R-eoe-output)
 300                  (insert (mapconcat #'org-babel-chomp
 301                                     (list body org-babel-R-eoe-indicator)
 302                                     "\n"))
 303                  (inferior-ess-send-input)))))) "\n"))))
 304
 305 (defun org-babel-R-process-value-result (result column-names-p)
 306   "R-specific processing of return value.
 307 Insert hline if column names in output have been requested."
 308   (if column-names-p
 309       (cons (car result) (cons 'hline (cdr result)))
 310     result))
 311
 312 (provide 'ob-R)
 313
 314
 315
 316 ;;; ob-R.el ends here