lisp/ob-R.el

   1 ;;; ob-R.el --- org-babel functions for R code evaluation
   2
   3 ;; Copyright (C) 2009-2014 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 "^\\*\\(.+?\\)\\*$" session))
  94       (save-match-data (org-babel-R-initiate-session session nil)))))
  95
  96 (defun org-babel-expand-body:R (body params &optional graphics-file)
  97   "Expand BODY according to PARAMS, return the expanded body."
  98   (mapconcat 'identity
  99              (append
 100               (when (cdr (assoc :prologue params))
 101                 (list (cdr (assoc :prologue params))))
 102               (org-babel-variable-assignments:R params)
 103               (list body)
 104               (when (cdr (assoc :epilogue params))
 105                 (list (cdr (assoc :epilogue params)))))
 106              "\n"))
 107
 108 (defun org-babel-execute:R (body params)
 109   "Execute a block of R code.
 110 This function is called by `org-babel-execute-src-block'."
 111   (save-excursion
 112     (let* ((result-params (cdr (assoc :result-params params)))
 113            (result-type (cdr (assoc :result-type params)))
 114            (session (org-babel-R-initiate-session
 115                      (cdr (assoc :session params)) params))
 116            (colnames-p (cdr (assoc :colnames params)))
 117            (rownames-p (cdr (assoc :rownames params)))
 118            (graphics-file (and (member "graphics" (assq :result-params params))
 119                                (org-babel-graphical-output-file params)))
 120            (full-body
 121             (let ((inside
 122                    (list (org-babel-expand-body:R body params graphics-file))))
 123               (mapconcat 'identity
 124                          (if graphics-file
 125                              (append
 126                               (list (org-babel-R-construct-graphics-device-call
 127                                      graphics-file params))
 128                               inside
 129                               (list "},error=function(e){plot(x=-1:1, y=-1:1, type='n', xlab='', ylab='', axes=FALSE); text(x=0, y=0, labels=e$message, col='red'); paste('ERROR', e$message, sep=' : ')}); dev.off()"))
 130                            inside)
 131                          "\n")))
 132            (result
 133             (org-babel-R-evaluate
 134              session full-body result-type result-params
 135              (or (equal "yes" colnames-p)
 136                  (org-babel-pick-name
 137                   (cdr (assoc :colname-names params)) colnames-p))
 138              (or (equal "yes" rownames-p)
 139                  (org-babel-pick-name
 140                   (cdr (assoc :rowname-names params)) rownames-p)))))
 141       (if graphics-file nil result))))
 142
 143 (defun org-babel-prep-session:R (session params)
 144   "Prepare SESSION according to the header arguments specified in PARAMS."
 145   (let* ((session (org-babel-R-initiate-session session params))
 146          (var-lines (org-babel-variable-assignments:R params)))
 147     (org-babel-comint-in-buffer session
 148       (mapc (lambda (var)
 149               (end-of-line 1) (insert var) (comint-send-input nil t)
 150               (org-babel-comint-wait-for-output session)) var-lines))
 151     session))
 152
 153 (defun org-babel-load-session:R (session body params)
 154   "Load BODY into SESSION."
 155   (save-window-excursion
 156     (let ((buffer (org-babel-prep-session:R session params)))
 157       (with-current-buffer buffer
 158         (goto-char (process-mark (get-buffer-process (current-buffer))))
 159         (insert (org-babel-chomp body)))
 160       buffer)))
 161
 162 ;; helper functions
 163
 164 (defun org-babel-variable-assignments:R (params)
 165   "Return list of R statements assigning the block's variables."
 166   (let ((vars (mapcar 'cdr (org-babel-get-header params :var))))
 167     (mapcar
 168      (lambda (pair)
 169        (org-babel-R-assign-elisp
 170         (car pair) (cdr pair)
 171         (equal "yes" (cdr (assoc :colnames params)))
 172         (equal "yes" (cdr (assoc :rownames params)))))
 173      (mapcar
 174       (lambda (i)
 175         (cons (car (nth i vars))
 176               (org-babel-reassemble-table
 177                (cdr (nth i vars))
 178                (cdr (nth i (cdr (assoc :colname-names params))))
 179                (cdr (nth i (cdr (assoc :rowname-names params)))))))
 180       (org-number-sequence 0 (1- (length vars)))))))
 181
 182 (defun org-babel-R-quote-tsv-field (s)
 183   "Quote field S for export to R."
 184   (if (stringp s)
 185       (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
 186     (format "%S" s)))
 187
 188 (defun org-babel-R-assign-elisp (name value colnames-p rownames-p)
 189   "Construct R code assigning the elisp VALUE to a variable named NAME."
 190   (if (listp value)
 191       (let* ((lengths (mapcar 'length (org-remove-if-not 'sequencep value)))
 192              (max (if lengths (apply 'max lengths) 0))
 193              (min (if lengths (apply 'min lengths) 0))
 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 (defvar org-babel-R-graphics-devices
 253   '((:bmp "bmp" "filename")
 254     (:jpg "jpeg" "filename")
 255     (:jpeg "jpeg" "filename")
 256     (:tikz "tikz" "file")
 257     (:tiff "tiff" "filename")
 258     (:png "png" "filename")
 259     (:svg "svg" "file")
 260     (:pdf "pdf" "file")
 261     (:ps "postscript" "file")
 262     (:postscript "postscript" "file"))
 263   "An alist mapping graphics file types to R functions.
 264
 265 Each member of this list is a list with three members:
 266 1. the file extension of the graphics file, as an elisp :keyword
 267 2. the R graphics device function to call to generate such a file
 268 3. the name of the argument to this function which specifies the
 269    file to write to (typically \"file\" or \"filename\")")
 270
 271 (defun org-babel-R-construct-graphics-device-call (out-file params)
 272   "Construct the call to the graphics device."
 273   (let* ((allowed-args '(:width :height :bg :units :pointsize
 274                                 :antialias :quality :compression :res
 275                                 :type :family :title :fonts :version
 276                                 :paper :encoding :pagecentre :colormodel
 277                                 :useDingbats :horizontal))
 278          (device (and (string-match ".+\\.\\([^.]+\\)" out-file)
 279                       (match-string 1 out-file)))
 280          (device-info (or (assq (intern (concat ":" device))
 281                                 org-babel-R-graphics-devices)
 282                           (assq :png org-babel-R-graphics-devices)))
 283         (extra-args (cdr (assq :R-dev-args params))) filearg args)
 284     (setq device (nth 1 device-info))
 285     (setq filearg (nth 2 device-info))
 286     (setq args (mapconcat
 287                 (lambda (pair)
 288                   (if (member (car pair) allowed-args)
 289                       (format ",%s=%S"
 290                               (substring (symbol-name (car pair)) 1)
 291                               (cdr pair)) ""))
 292                 params ""))
 293     (format "%s(%s=\"%s\"%s%s%s); tryCatch({"
 294             device filearg out-file args
 295             (if extra-args "," "") (or extra-args ""))))
 296
 297 (defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
 298 (defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
 299
 300 (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\")")
 301
 302 (defun org-babel-R-evaluate
 303   (session body result-type result-params column-names-p row-names-p)
 304   "Evaluate R code in BODY."
 305   (if session
 306       (org-babel-R-evaluate-session
 307        session body result-type result-params column-names-p row-names-p)
 308     (org-babel-R-evaluate-external-process
 309      body result-type result-params column-names-p row-names-p)))
 310
 311 (defun org-babel-R-evaluate-external-process
 312   (body result-type result-params column-names-p row-names-p)
 313   "Evaluate BODY in external R process.
 314 If RESULT-TYPE equals 'output then return standard output as a
 315 string.  If RESULT-TYPE equals 'value then return the value of the
 316 last statement in BODY, as elisp."
 317   (case result-type
 318     (value
 319      (let ((tmp-file (org-babel-temp-file "R-")))
 320        (org-babel-eval org-babel-R-command
 321                        (format org-babel-R-write-object-command
 322                                (if row-names-p "TRUE" "FALSE")
 323                                (if column-names-p
 324                                    (if row-names-p "NA" "TRUE")
 325                                  "FALSE")
 326                                (format "{function ()\n{\n%s\n}}()" body)
 327                                (org-babel-process-file-name tmp-file 'noquote)))
 328        (org-babel-R-process-value-result
 329         (org-babel-result-cond result-params
 330           (with-temp-buffer
 331             (insert-file-contents tmp-file)
 332             (buffer-string))
 333           (org-babel-import-elisp-from-file tmp-file '(16)))
 334         column-names-p)))
 335     (output (org-babel-eval org-babel-R-command body))))
 336
 337 (defvar ess-eval-visibly-p)
 338
 339 (defun org-babel-R-evaluate-session
 340   (session body result-type result-params column-names-p row-names-p)
 341   "Evaluate BODY in SESSION.
 342 If RESULT-TYPE equals 'output then return standard output as a
 343 string.  If RESULT-TYPE equals 'value then return the value of the
 344 last statement in BODY, as elisp."
 345   (case result-type
 346     (value
 347      (with-temp-buffer
 348        (insert (org-babel-chomp body))
 349        (let ((ess-local-process-name
 350               (process-name (get-buffer-process session)))
 351              (ess-eval-visibly-p nil))
 352          (ess-eval-buffer nil)))
 353      (let ((tmp-file (org-babel-temp-file "R-")))
 354        (org-babel-comint-eval-invisibly-and-wait-for-file
 355         session tmp-file
 356         (format org-babel-R-write-object-command
 357                 (if row-names-p "TRUE" "FALSE")
 358                 (if column-names-p
 359                     (if row-names-p "NA" "TRUE")
 360                   "FALSE")
 361                 ".Last.value" (org-babel-process-file-name tmp-file 'noquote)))
 362        (org-babel-R-process-value-result
 363         (org-babel-result-cond result-params
 364           (with-temp-buffer
 365             (insert-file-contents tmp-file)
 366             (buffer-string))
 367           (org-babel-import-elisp-from-file tmp-file '(16)))
 368         column-names-p)))
 369     (output
 370      (mapconcat
 371       'org-babel-chomp
 372       (butlast
 373        (delq nil
 374              (mapcar
 375               (lambda (line) (when (> (length line) 0) line))
 376               (mapcar
 377                (lambda (line) ;; cleanup extra prompts left in output
 378                  (if (string-match
 379                       "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
 380                      (substring line (match-end 1))
 381                    line))
 382                (org-babel-comint-with-output (session org-babel-R-eoe-output)
 383                  (insert (mapconcat 'org-babel-chomp
 384                                     (list body org-babel-R-eoe-indicator)
 385                                     "\n"))
 386                  (inferior-ess-send-input)))))) "\n"))))
 387
 388 (defun org-babel-R-process-value-result (result column-names-p)
 389   "R-specific processing of return value.
 390 Insert hline if column names in output have been requested."
 391   (if column-names-p
 392       (cons (car result) (cons 'hline (cdr result)))
 393     result))
 394
 395 (provide 'ob-R)
 396
 397
 398
 399 ;;; ob-R.el ends here