lisp/ob-R.el

   1 ;;; ob-R.el --- org-babel functions for R code evaluation
   2
   3 ;; Copyright (C) 2009-2013 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 (eval-when-compile (require 'cl))
  32
  33 (declare-function orgtbl-to-tsv "org-table" (table params))
  34 (declare-function R "ext:essd-r" (&optional start-args))
  35 (declare-function inferior-ess-send-input "ext:ess-inf" ())
  36 (declare-function ess-make-buffer-current "ext:ess-inf" ())
  37 (declare-function ess-eval-buffer "ext:ess-inf" (vis))
  38 (declare-function org-number-sequence "org-compat" (from &optional to inc))
  39 (declare-function org-remove-if-not "org" (predicate seq))
  40 (declare-function org-every "org" (pred seq))
  41
  42 (defconst org-babel-header-args:R
  43   '((width               . :any)
  44     (height              . :any)
  45     (bg                  . :any)
  46     (units               . :any)
  47     (pointsize           . :any)
  48     (antialias           . :any)
  49     (quality             . :any)
  50     (compression         . :any)
  51     (res                 . :any)
  52     (type                . :any)
  53     (family              . :any)
  54     (title               . :any)
  55     (fonts               . :any)
  56     (version             . :any)
  57     (paper               . :any)
  58     (encoding            . :any)
  59     (pagecentre          . :any)
  60     (colormodel          . :any)
  61     (useDingbats         . :any)
  62     (horizontal          . :any)
  63     (results             . ((file list vector table scalar verbatim)
  64                             (raw org html latex code pp wrap)
  65                             (replace silent append prepend)
  66                             (output value graphics))))
  67   "R-specific header arguments.")
  68
  69 (defconst ob-R-safe-header-args
  70   (append org-babel-safe-header-args
  71           '(:width :height :bg :units :pointsize :antialias :quality
  72                    :compression :res :type :family :title :fonts
  73                    :version :paper :encoding :pagecentre :colormodel
  74                    :useDingbats :horizontal))
  75   "Header args which are safe for R babel blocks.
  76
  77 See `org-babel-safe-header-args' for documentation of the format of
  78 this variable.")
  79
  80 (defvar org-babel-default-header-args:R '())
  81 (put 'org-babel-default-header-args:R 'safe-local-variable
  82      (org-babel-header-args-safe-fn ob-R-safe-header-args))
  83
  84 (defcustom org-babel-R-command "R --slave --no-save"
  85   "Name of command to use for executing R code."
  86   :group 'org-babel
  87   :version "24.1"
  88   :type 'string)
  89
  90 (defvar ess-local-process-name) ; dynamically scoped
  91 (defun org-babel-edit-prep:R (info)
  92   (let ((session (cdr (assoc :session (nth 2 info)))))
  93     (when (and session (string-match "^\\*\\(.+?\\)\\*$" session))
  94       (save-match-data (org-babel-R-initiate-session session nil)))))
  95
  96 (defun org-babel-expand-body:R (body params &optional graphics-file)
  97   "Expand BODY according to PARAMS, return the expanded body."
  98   (let ((graphics-file
  99          (or graphics-file (org-babel-R-graphical-output-file params))))
 100     (mapconcat
 101      #'identity
 102      (let ((inside
 103             (append
 104              (when (cdr (assoc :prologue params))
 105                (list (cdr (assoc :prologue params))))
 106              (org-babel-variable-assignments:R params)
 107              (list body)
 108              (when (cdr (assoc :epilogue params))
 109                (list (cdr (assoc :epilogue params)))))))
 110        (if graphics-file
 111            (append
 112             (list (org-babel-R-construct-graphics-device-call
 113                    graphics-file params))
 114             inside
 115             (list "dev.off()"))
 116          inside))
 117      "\n")))
 118
 119 (defun org-babel-execute:R (body params)
 120   "Execute a block of R code.
 121 This function is called by `org-babel-execute-src-block'."
 122   (save-excursion
 123     (let* ((result-params (cdr (assoc :result-params params)))
 124            (result-type (cdr (assoc :result-type params)))
 125            (session (org-babel-R-initiate-session
 126                      (cdr (assoc :session params)) params))
 127            (colnames-p (cdr (assoc :colnames params)))
 128            (rownames-p (cdr (assoc :rownames params)))
 129            (graphics-file (org-babel-R-graphical-output-file params))
 130            (full-body (org-babel-expand-body:R body params graphics-file))
 131            (result
 132             (org-babel-R-evaluate
 133              session full-body result-type result-params
 134              (or (equal "yes" colnames-p)
 135                  (org-babel-pick-name
 136                   (cdr (assoc :colname-names params)) colnames-p))
 137              (or (equal "yes" rownames-p)
 138                  (org-babel-pick-name
 139                   (cdr (assoc :rowname-names params)) rownames-p)))))
 140       (if graphics-file nil result))))
 141
 142 (defun org-babel-prep-session:R (session params)
 143   "Prepare SESSION according to the header arguments specified in PARAMS."
 144   (let* ((session (org-babel-R-initiate-session session params))
 145          (var-lines (org-babel-variable-assignments:R params)))
 146     (org-babel-comint-in-buffer session
 147       (mapc (lambda (var)
 148               (end-of-line 1) (insert var) (comint-send-input nil t)
 149               (org-babel-comint-wait-for-output session)) var-lines))
 150     session))
 151
 152 (defun org-babel-load-session:R (session body params)
 153   "Load BODY into SESSION."
 154   (save-window-excursion
 155     (let ((buffer (org-babel-prep-session:R session params)))
 156       (with-current-buffer buffer
 157         (goto-char (process-mark (get-buffer-process (current-buffer))))
 158         (insert (org-babel-chomp body)))
 159       buffer)))
 160
 161 ;; helper functions
 162
 163 (defun org-babel-variable-assignments:R (params)
 164   "Return list of R statements assigning the block's variables."
 165   (let ((vars (mapcar #'cdr (org-babel-get-header params :var))))
 166     (mapcar
 167      (lambda (pair)
 168        (org-babel-R-assign-elisp
 169         (car pair) (cdr pair)
 170         (equal "yes" (cdr (assoc :colnames params)))
 171         (equal "yes" (cdr (assoc :rownames params)))))
 172      (mapcar
 173       (lambda (i)
 174         (cons (car (nth i vars))
 175               (org-babel-reassemble-table
 176                (cdr (nth i vars))
 177                (cdr (nth i (cdr (assoc :colname-names params))))
 178                (cdr (nth i (cdr (assoc :rowname-names params)))))))
 179       (org-number-sequence 0 (1- (length vars)))))))
 180
 181 (defun org-babel-R-quote-tsv-field (s)
 182   "Quote field S for export to R."
 183   (if (stringp s)
 184       (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
 185     (format "%S" s)))
 186
 187 (defun org-babel-R-assign-elisp (name value colnames-p rownames-p)
 188   "Construct R code assigning the elisp VALUE to a variable named NAME."
 189   (if (listp value)
 190       (let ((max (apply #'max (mapcar #'length (org-remove-if-not
 191                                                 #'sequencep value))))
 192             (min (apply #'min (mapcar #'length (org-remove-if-not
 193                                                 #'sequencep value))))
 194             (transition-file (org-babel-temp-file "R-import-")))
 195         ;; ensure VALUE has an orgtbl structure (depth of at least 2)
 196         (unless (listp (car value)) (setq value (list value)))
 197         (with-temp-file transition-file
 198           (insert
 199            (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field))
 200            "\n"))
 201         (let ((file (org-babel-process-file-name transition-file 'noquote))
 202               (header (if (or (eq (nth 1 value) 'hline) colnames-p)
 203                           "TRUE" "FALSE"))
 204               (row-names (if rownames-p "1" "NULL")))
 205           (if (= max min)
 206               (format "%s <- read.table(\"%s\",
 207                       header=%s,
 208                       row.names=%s,
 209                       sep=\"\\t\",
 210                       as.is=TRUE)" name file header row-names)
 211             (format "%s <- read.table(\"%s\",
 212                    header=%s,
 213                    row.names=%s,
 214                    sep=\"\\t\",
 215                    as.is=TRUE,
 216                    fill=TRUE,
 217                    col.names = paste(\"V\", seq_len(%d), sep =\"\"))"
 218                     name file header row-names max))))
 219     (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
 220
 221 (defvar ess-ask-for-ess-directory) ; dynamically scoped
 222 (defun org-babel-R-initiate-session (session params)
 223   "If there is not a current R process then create one."
 224   (unless (string= session "none")
 225     (let ((session (or session "*R*"))
 226           (ess-ask-for-ess-directory
 227            (and (and (boundp 'ess-ask-for-ess-directory) ess-ask-for-ess-directory)
 228                 (not (cdr (assoc :dir params))))))
 229       (if (org-babel-comint-buffer-livep session)
 230           session
 231         (save-window-excursion
 232           (when (get-buffer session)
 233             ;; Session buffer exists, but with dead process
 234             (set-buffer session))
 235           (require 'ess) (R)
 236           (rename-buffer
 237            (if (bufferp session)
 238                (buffer-name session)
 239              (if (stringp session)
 240                  session
 241                (buffer-name))))
 242           (current-buffer))))))
 243
 244 (defun org-babel-R-associate-session (session)
 245   "Associate R code buffer with an R session.
 246 Make SESSION be the inferior ESS process associated with the
 247 current code buffer."
 248   (setq ess-local-process-name
 249         (process-name (get-buffer-process session)))
 250   (ess-make-buffer-current))
 251
 252 (defun org-babel-R-graphical-output-file (params)
 253   "Name of file to which R should send graphical output."
 254   (and (member "graphics" (cdr (assq :result-params params)))
 255        (cdr (assq :file params))))
 256
 257 (defvar org-babel-R-graphics-devices
 258   '((:bmp "bmp" "filename")
 259     (:jpg "jpeg" "filename")
 260     (:jpeg "jpeg" "filename")
 261     (:tikz "tikz" "file")
 262     (:tiff "tiff" "filename")
 263     (:png "png" "filename")
 264     (:svg "svg" "file")
 265     (:pdf "pdf" "file")
 266     (:ps "postscript" "file")
 267     (:postscript "postscript" "file"))
 268   "An alist mapping graphics file types to R functions.
 269
 270 Each member of this list is a list with three members:
 271 1. the file extension of the graphics file, as an elisp :keyword
 272 2. the R graphics device function to call to generate such a file
 273 3. the name of the argument to this function which specifies the
 274    file to write to (typically \"file\" or \"filename\")")
 275
 276 (defun org-babel-R-construct-graphics-device-call (out-file params)
 277   "Construct the call to the graphics device."
 278   (let* ((allowed-args '(:width :height :bg :units :pointsize
 279                                 :antialias :quality :compression :res
 280                                 :type :family :title :fonts :version
 281                                 :paper :encoding :pagecentre :colormodel
 282                                 :useDingbats :horizontal))
 283          (device (and (string-match ".+\\.\\([^.]+\\)" out-file)
 284                       (match-string 1 out-file)))
 285          (device-info (or (assq (intern (concat ":" device))
 286                                 org-babel-R-graphics-devices)
 287                           (assq :png org-babel-R-graphics-devices)))
 288         (extra-args (cdr (assq :R-dev-args params))) filearg args)
 289     (setq device (nth 1 device-info))
 290     (setq filearg (nth 2 device-info))
 291     (setq args (mapconcat
 292                 (lambda (pair)
 293                   (if (member (car pair) allowed-args)
 294                       (format ",%s=%S"
 295                               (substring (symbol-name (car pair)) 1)
 296                               (cdr pair)) ""))
 297                 params ""))
 298     (format "%s(%s=\"%s\"%s%s%s)"
 299             device filearg out-file args
 300             (if extra-args "," "") (or extra-args ""))))
 301
 302 (defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
 303 (defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
 304
 305 (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\")")
 306
 307 (defun org-babel-R-evaluate
 308   (session body result-type result-params column-names-p row-names-p)
 309   "Evaluate R code in BODY."
 310   (if session
 311       (org-babel-R-evaluate-session
 312        session body result-type result-params column-names-p row-names-p)
 313     (org-babel-R-evaluate-external-process
 314      body result-type result-params column-names-p row-names-p)))
 315
 316 (defun org-babel-R-evaluate-external-process
 317   (body result-type result-params column-names-p row-names-p)
 318   "Evaluate BODY in external R process.
 319 If RESULT-TYPE equals 'output then return standard output as a
 320 string.  If RESULT-TYPE equals 'value then return the value of the
 321 last statement in BODY, as elisp."
 322   (case result-type
 323     (value
 324      (let ((tmp-file (org-babel-temp-file "R-")))
 325        (org-babel-eval org-babel-R-command
 326                        (format org-babel-R-write-object-command
 327                                (if row-names-p "TRUE" "FALSE")
 328                                (if column-names-p
 329                                    (if row-names-p "NA" "TRUE")
 330                                  "FALSE")
 331                                (format "{function ()\n{\n%s\n}}()" body)
 332                                (org-babel-process-file-name tmp-file 'noquote)))
 333        (org-babel-R-process-value-result
 334         (org-babel-result-cond result-params
 335           (with-temp-buffer
 336             (insert-file-contents tmp-file)
 337             (buffer-string))
 338           (org-babel-import-elisp-from-file tmp-file '(16)))
 339         column-names-p)))
 340     (output (org-babel-eval org-babel-R-command body))))
 341
 342 (defvar ess-eval-visibly-p)
 343
 344 (defun org-babel-R-evaluate-session
 345   (session body result-type result-params column-names-p row-names-p)
 346   "Evaluate BODY in SESSION.
 347 If RESULT-TYPE equals 'output then return standard output as a
 348 string.  If RESULT-TYPE equals 'value then return the value of the
 349 last statement in BODY, as elisp."
 350   (case result-type
 351     (value
 352      (with-temp-buffer
 353        (insert (org-babel-chomp body))
 354        (let ((ess-local-process-name
 355               (process-name (get-buffer-process session)))
 356              (ess-eval-visibly-p nil))
 357          (ess-eval-buffer nil)))
 358      (let ((tmp-file (org-babel-temp-file "R-")))
 359        (org-babel-comint-eval-invisibly-and-wait-for-file
 360         session tmp-file
 361         (format org-babel-R-write-object-command
 362                 (if row-names-p "TRUE" "FALSE")
 363                 (if column-names-p
 364                     (if row-names-p "NA" "TRUE")
 365                   "FALSE")
 366                 ".Last.value" (org-babel-process-file-name tmp-file 'noquote)))
 367        (org-babel-R-process-value-result
 368         (org-babel-result-cond result-params
 369           (with-temp-buffer
 370             (insert-file-contents tmp-file)
 371             (buffer-string))
 372           (org-babel-import-elisp-from-file tmp-file '(16)))
 373         column-names-p)))
 374     (output
 375      (mapconcat
 376       #'org-babel-chomp
 377       (butlast
 378        (delq nil
 379              (mapcar
 380               (lambda (line) (when (> (length line) 0) line))
 381               (mapcar
 382                (lambda (line) ;; cleanup extra prompts left in output
 383                  (if (string-match
 384                       "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
 385                      (substring line (match-end 1))
 386                    line))
 387                (org-babel-comint-with-output (session org-babel-R-eoe-output)
 388                  (insert (mapconcat #'org-babel-chomp
 389                                     (list body org-babel-R-eoe-indicator)
 390                                     "\n"))
 391                  (inferior-ess-send-input)))))) "\n"))))
 392
 393 (defun org-babel-R-process-value-result (result column-names-p)
 394   "R-specific processing of return value.
 395 Insert hline if column names in output have been requested."
 396   (if column-names-p
 397       (cons (car result) (cons 'hline (cdr result)))
 398     result))
 399
 400 (provide 'ob-R)
 401
 402
 403
 404 ;;; ob-R.el ends here