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
   6 ;;      Dan Davison
   7 ;; Keywords: literate programming, reproducible research, R, statistics
   8 ;; Homepage: http://orgmode.org
   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-params (cdr (assoc :result-params params)))
  83            (result-type (cdr (assoc :result-type params)))
  84            (session (org-babel-R-initiate-session
  85                      (cdr (assoc :session params)) params))
  86            (colnames-p (cdr (assoc :colnames params)))
  87            (rownames-p (cdr (assoc :rownames params)))
  88            (graphics-file (org-babel-R-graphical-output-file params))
  89            (full-body (org-babel-expand-body:R body params graphics-file))
  90            (result
  91             (org-babel-R-evaluate
  92              session full-body result-type result-params
  93              (or (equal "yes" colnames-p)
  94                  (org-babel-pick-name
  95                   (cdr (assoc :colname-names params)) colnames-p))
  96              (or (equal "yes" rownames-p)
  97                  (org-babel-pick-name
  98                   (cdr (assoc :rowname-names params)) rownames-p)))))
  99       (if graphics-file nil result))))
 100
 101 (defun org-babel-prep-session:R (session params)
 102   "Prepare SESSION according to the header arguments specified in PARAMS."
 103   (let* ((session (org-babel-R-initiate-session session params))
 104          (var-lines (org-babel-variable-assignments:R params)))
 105     (org-babel-comint-in-buffer session
 106       (mapc (lambda (var)
 107               (end-of-line 1) (insert var) (comint-send-input nil t)
 108               (org-babel-comint-wait-for-output session)) var-lines))
 109     session))
 110
 111 (defun org-babel-load-session:R (session body params)
 112   "Load BODY into SESSION."
 113   (save-window-excursion
 114     (let ((buffer (org-babel-prep-session:R session params)))
 115       (with-current-buffer buffer
 116         (goto-char (process-mark (get-buffer-process (current-buffer))))
 117         (insert (org-babel-chomp body)))
 118       buffer)))
 119
 120 ;; helper functions
 121
 122 (defun org-babel-variable-assignments:R (params)
 123   "Return list of R statements assigning the block's variables"
 124   (let ((vars (mapcar #'cdr (org-babel-get-header params :var))))
 125     (mapcar
 126      (lambda (pair)
 127        (org-babel-R-assign-elisp
 128         (car pair) (cdr pair)
 129         (equal "yes" (cdr (assoc :colnames params)))
 130         (equal "yes" (cdr (assoc :rownames params)))))
 131      (mapcar
 132       (lambda (i)
 133         (cons (car (nth i vars))
 134               (org-babel-reassemble-table
 135                (cdr (nth i vars))
 136                (cdr (nth i (cdr (assoc :colname-names params))))
 137                (cdr (nth i (cdr (assoc :rowname-names params)))))))
 138       (org-number-sequence 0 (1- (length vars)))))))
 139
 140 (defun org-babel-R-quote-tsv-field (s)
 141   "Quote field S for export to R."
 142   (if (stringp s)
 143       (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
 144     (format "%S" s)))
 145
 146 (defun org-babel-R-assign-elisp (name value colnames-p rownames-p)
 147   "Construct R code assigning the elisp VALUE to a variable named NAME."
 148   (if (listp value)
 149       (let ((transition-file (org-babel-temp-file "R-import-")))
 150         ;; ensure VALUE has an orgtbl structure (depth of at least 2)
 151         (unless (listp (car value)) (setq value (list value)))
 152         (with-temp-file transition-file
 153           (insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
 154           (insert "\n"))
 155         (format "%s <- read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE)"
 156                 name (org-babel-process-file-name transition-file 'noquote)
 157                 (if (or (eq (nth 1 value) 'hline) colnames-p) "TRUE" "FALSE")
 158                 (if rownames-p "1" "NULL")))
 159     (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
 160
 161 (defvar ess-ask-for-ess-directory nil)
 162 (defun org-babel-R-initiate-session (session params)
 163   "If there is not a current R process then create one."
 164   (unless (string= session "none")
 165     (let ((session (or session "*R*"))
 166           (ess-ask-for-ess-directory
 167            (and ess-ask-for-ess-directory (not (cdr (assoc :dir params))))))
 168       (if (org-babel-comint-buffer-livep session)
 169           session
 170         (save-window-excursion
 171           (require 'ess) (R)
 172           (rename-buffer
 173            (if (bufferp session)
 174                (buffer-name session)
 175              (if (stringp session)
 176                  session
 177                (buffer-name))))
 178           (current-buffer))))))
 179
 180 (defvar ess-local-process-name nil)
 181 (defun org-babel-R-associate-session (session)
 182   "Associate R code buffer with an R session.
 183 Make SESSION be the inferior ESS process associated with the
 184 current code buffer."
 185   (setq ess-local-process-name
 186         (process-name (get-buffer-process session)))
 187   (ess-make-buffer-current))
 188
 189 (defun org-babel-R-graphical-output-file (params)
 190   "Name of file to which R should send graphical output."
 191   (and (member "graphics" (cdr (assq :result-params params)))
 192        (cdr (assq :file params))))
 193
 194 (defun org-babel-R-construct-graphics-device-call (out-file params)
 195   "Construct the call to the graphics device."
 196   (let ((devices
 197          '((:bmp . "bmp")
 198            (:jpg . "jpeg")
 199            (:jpeg . "jpeg")
 200            (:tex . "tikz")
 201            (:tiff . "tiff")
 202            (:png . "png")
 203            (:svg . "svg")
 204            (:pdf . "pdf")
 205            (:ps . "postscript")
 206            (:postscript . "postscript")))
 207         (allowed-args '(:width :height :bg :units :pointsize
 208                                :antialias :quality :compression :res
 209                                :type :family :title :fonts :version
 210                                :paper :encoding :pagecentre :colormodel
 211                                :useDingbats :horizontal))
 212         (device (and (string-match ".+\\.\\([^.]+\\)" out-file)
 213                      (match-string 1 out-file)))
 214         (extra-args (cdr (assq :R-dev-args params))) filearg args)
 215     (setq device (or (and device (cdr (assq (intern (concat ":" device))
 216                                             devices))) "png"))
 217     (setq filearg
 218           (if (member device '("pdf" "postscript" "svg" "tikz")) "file" "filename"))
 219     (setq args (mapconcat
 220                 (lambda (pair)
 221                   (if (member (car pair) allowed-args)
 222                       (format ",%s=%s"
 223                               (substring (symbol-name (car pair)) 1)
 224                               (cdr pair)) ""))
 225                 params ""))
 226     (format "%s(%s=\"%s\"%s%s%s)"
 227             device filearg out-file args
 228             (if extra-args "," "") (or extra-args ""))))
 229
 230 (defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
 231 (defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
 232
 233 (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\")")
 234
 235 (defun org-babel-R-evaluate
 236   (session body result-type result-params column-names-p row-names-p)
 237   "Evaluate R code in BODY."
 238   (if session
 239       (org-babel-R-evaluate-session
 240        session body result-type result-params column-names-p row-names-p)
 241     (org-babel-R-evaluate-external-process
 242      body result-type result-params column-names-p row-names-p)))
 243
 244 (defun org-babel-R-evaluate-external-process
 245   (body result-type result-params column-names-p row-names-p)
 246   "Evaluate BODY in external R process.
 247 If RESULT-TYPE equals 'output then return standard output as a
 248 string. If RESULT-TYPE equals 'value then return the value of the
 249 last statement in BODY, as elisp."
 250   (case result-type
 251     (value
 252      (let ((tmp-file (org-babel-temp-file "R-")))
 253        (org-babel-eval org-babel-R-command
 254                        (format org-babel-R-write-object-command
 255                                (if row-names-p "TRUE" "FALSE")
 256                                (if column-names-p
 257                                    (if row-names-p "NA" "TRUE")
 258                                  "FALSE")
 259                                (format "{function ()\n{\n%s\n}}()" body)
 260                                (org-babel-process-file-name tmp-file 'noquote)))
 261        (org-babel-R-process-value-result
 262         (if (or (member "scalar" result-params)
 263                 (member "verbatim" result-params))
 264             (with-temp-buffer
 265               (insert-file-contents tmp-file)
 266               (buffer-string))
 267           (org-babel-import-elisp-from-file tmp-file '(16)))
 268         column-names-p)))
 269     (output (org-babel-eval org-babel-R-command body))))
 270
 271 (defun org-babel-R-evaluate-session
 272   (session body result-type result-params column-names-p row-names-p)
 273   "Evaluate BODY in SESSION.
 274 If RESULT-TYPE equals 'output then return standard output as a
 275 string. If RESULT-TYPE equals 'value then return the value of the
 276 last statement in BODY, as elisp."
 277   (case result-type
 278     (value
 279      (with-temp-buffer
 280        (insert (org-babel-chomp body))
 281        (let ((ess-local-process-name
 282               (process-name (get-buffer-process session))))
 283          (ess-eval-buffer nil)))
 284      (let ((tmp-file (org-babel-temp-file "R-")))
 285        (org-babel-comint-eval-invisibly-and-wait-for-file
 286         session tmp-file
 287         (format org-babel-R-write-object-command
 288                 (if row-names-p "TRUE" "FALSE")
 289                 (if column-names-p
 290                     (if row-names-p "NA" "TRUE")
 291                   "FALSE")
 292                 ".Last.value" (org-babel-process-file-name tmp-file 'noquote)))
 293        (org-babel-R-process-value-result
 294         (if (or (member "scalar" result-params)
 295                 (member "verbatim" result-params))
 296             (with-temp-buffer
 297               (insert-file-contents tmp-file)
 298               (buffer-string))
 299           (org-babel-import-elisp-from-file tmp-file '(16)))
 300         column-names-p)))
 301     (output
 302      (mapconcat
 303       #'org-babel-chomp
 304       (butlast
 305        (delq nil
 306              (mapcar
 307               (lambda (line) (when (> (length line) 0) line))
 308               (mapcar
 309                (lambda (line) ;; cleanup extra prompts left in output
 310                  (if (string-match
 311                       "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
 312                      (substring line (match-end 1))
 313                    line))
 314                (org-babel-comint-with-output (session org-babel-R-eoe-output)
 315                  (insert (mapconcat #'org-babel-chomp
 316                                     (list body org-babel-R-eoe-indicator)
 317                                     "\n"))
 318                  (inferior-ess-send-input)))))) "\n"))))
 319
 320 (defun org-babel-R-process-value-result (result column-names-p)
 321   "R-specific processing of return value.
 322 Insert hline if column names in output have been requested."
 323   (if column-names-p
 324       (cons (car result) (cons 'hline (cdr result)))
 325     result))
 326
 327 (provide 'ob-R)
 328
 329
 330
 331 ;;; ob-R.el ends here