lisp/org/ob-R.el

   1 ;;; ob-R.el --- org-babel functions for R code evaluation
   2
   3 ;; Copyright (C) 2009-2016 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
  41 (defconst org-babel-header-args:R
  42   '((width               . :any)
  43     (height              . :any)
  44     (bg                  . :any)
  45     (units               . :any)
  46     (pointsize           . :any)
  47     (antialias           . :any)
  48     (quality             . :any)
  49     (compression         . :any)
  50     (res                 . :any)
  51     (type                . :any)
  52     (family              . :any)
  53     (title               . :any)
  54     (fonts               . :any)
  55     (version             . :any)
  56     (paper               . :any)
  57     (encoding            . :any)
  58     (pagecentre          . :any)
  59     (colormodel          . :any)
  60     (useDingbats         . :any)
  61     (horizontal          . :any)
  62     (results             . ((file list vector table scalar verbatim)
  63                             (raw org html latex code pp wrap)
  64                             (replace silent append prepend)
  65                             (output value graphics))))
  66   "R-specific header arguments.")
  67
  68 (defvar org-babel-default-header-args:R '())
  69
  70 (defcustom org-babel-R-command "R --slave --no-save"
  71   "Name of command to use for executing R code."
  72   :group 'org-babel
  73   :version "24.1"
  74   :type 'string)
  75
  76 (defvar ess-local-process-name) ; dynamically scoped
  77 (defun org-babel-edit-prep:R (info)
  78   (let ((session (cdr (assoc :session (nth 2 info)))))
  79     (when (and session (string-match "^\\*\\(.+?\\)\\*$" session))
  80       (save-match-data (org-babel-R-initiate-session session nil)))))
  81
  82 (defun org-babel-expand-body:R (body params &optional graphics-file)
  83   "Expand BODY according to PARAMS, return the expanded body."
  84   (let ((graphics-file
  85          (or graphics-file (org-babel-R-graphical-output-file params))))
  86     (mapconcat
  87      #'identity
  88      (let ((inside
  89             (append
  90              (when (cdr (assoc :prologue params))
  91                (list (cdr (assoc :prologue params))))
  92              (org-babel-variable-assignments:R params)
  93              (list body)
  94              (when (cdr (assoc :epilogue params))
  95                (list (cdr (assoc :epilogue params)))))))
  96        (if graphics-file
  97            (append
  98             (list (org-babel-R-construct-graphics-device-call
  99                    graphics-file params))
 100             inside
 101             (list "dev.off()"))
 102          inside))
 103      "\n")))
 104
 105 (defun org-babel-execute:R (body params)
 106   "Execute a block of R code.
 107 This function is called by `org-babel-execute-src-block'."
 108   (save-excursion
 109     (let* ((result-params (cdr (assoc :result-params params)))
 110            (result-type (cdr (assoc :result-type params)))
 111            (session (org-babel-R-initiate-session
 112                      (cdr (assoc :session params)) params))
 113            (colnames-p (cdr (assoc :colnames params)))
 114            (rownames-p (cdr (assoc :rownames params)))
 115            (graphics-file (org-babel-R-graphical-output-file params))
 116            (full-body (org-babel-expand-body:R body params graphics-file))
 117            (result
 118             (org-babel-R-evaluate
 119              session full-body result-type result-params
 120              (or (equal "yes" colnames-p)
 121                  (org-babel-pick-name
 122                   (cdr (assoc :colname-names params)) colnames-p))
 123              (or (equal "yes" rownames-p)
 124                  (org-babel-pick-name
 125                   (cdr (assoc :rowname-names params)) rownames-p)))))
 126       (if graphics-file nil result))))
 127
 128 (defun org-babel-prep-session:R (session params)
 129   "Prepare SESSION according to the header arguments specified in PARAMS."
 130   (let* ((session (org-babel-R-initiate-session session params))
 131          (var-lines (org-babel-variable-assignments:R params)))
 132     (org-babel-comint-in-buffer session
 133       (mapc (lambda (var)
 134               (end-of-line 1) (insert var) (comint-send-input nil t)
 135               (org-babel-comint-wait-for-output session)) var-lines))
 136     session))
 137
 138 (defun org-babel-load-session:R (session body params)
 139   "Load BODY into SESSION."
 140   (save-window-excursion
 141     (let ((buffer (org-babel-prep-session:R session params)))
 142       (with-current-buffer buffer
 143         (goto-char (process-mark (get-buffer-process (current-buffer))))
 144         (insert (org-babel-chomp body)))
 145       buffer)))
 146
 147 ;; helper functions
 148
 149 (defun org-babel-variable-assignments:R (params)
 150   "Return list of R statements assigning the block's variables."
 151   (let ((vars (mapcar #'cdr (org-babel-get-header params :var))))
 152     (mapcar
 153      (lambda (pair)
 154        (org-babel-R-assign-elisp
 155         (car pair) (cdr pair)
 156         (equal "yes" (cdr (assoc :colnames params)))
 157         (equal "yes" (cdr (assoc :rownames params)))))
 158      (mapcar
 159       (lambda (i)
 160         (cons (car (nth i vars))
 161               (org-babel-reassemble-table
 162                (cdr (nth i vars))
 163                (cdr (nth i (cdr (assoc :colname-names params))))
 164                (cdr (nth i (cdr (assoc :rowname-names params)))))))
 165       (org-number-sequence 0 (1- (length vars)))))))
 166
 167 (defun org-babel-R-quote-tsv-field (s)
 168   "Quote field S for export to R."
 169   (if (stringp s)
 170       (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
 171     (format "%S" s)))
 172
 173 (defun org-babel-R-assign-elisp (name value colnames-p rownames-p)
 174   "Construct R code assigning the elisp VALUE to a variable named NAME."
 175   (if (listp value)
 176       (let* ((lengths (mapcar 'length (org-remove-if-not 'sequencep value)))
 177              (max (if lengths (apply 'max lengths) 0))
 178              (min (if lengths (apply 'min lengths) 0))
 179              (transition-file (org-babel-temp-file "R-import-")))
 180         ;; Ensure VALUE has an orgtbl structure (depth of at least 2).
 181         (unless (listp (car value)) (setq value (list value)))
 182         (with-temp-file transition-file
 183           (insert
 184            (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field))
 185            "\n"))
 186         (let ((file (org-babel-process-file-name transition-file 'noquote))
 187               (header (if (or (eq (nth 1 value) 'hline) colnames-p)
 188                           "TRUE" "FALSE"))
 189               (row-names (if rownames-p "1" "NULL")))
 190           (if (= max min)
 191               (format "%s <- read.table(\"%s\",
 192                       header=%s,
 193                       row.names=%s,
 194                       sep=\"\\t\",
 195                       as.is=TRUE)" name file header row-names)
 196             (format "%s <- read.table(\"%s\",
 197                    header=%s,
 198                    row.names=%s,
 199                    sep=\"\\t\",
 200                    as.is=TRUE,
 201                    fill=TRUE,
 202                    col.names = paste(\"V\", seq_len(%d), sep =\"\"))"
 203                     name file header row-names max))))
 204     (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
 205
 206 (defvar ess-ask-for-ess-directory) ; dynamically scoped
 207 (defun org-babel-R-initiate-session (session params)
 208   "If there is not a current R process then create one."
 209   (unless (string= session "none")
 210     (let ((session (or session "*R*"))
 211           (ess-ask-for-ess-directory
 212            (and (and (boundp 'ess-ask-for-ess-directory) ess-ask-for-ess-directory)
 213                 (not (cdr (assoc :dir params))))))
 214       (if (org-babel-comint-buffer-livep session)
 215           session
 216         (save-window-excursion
 217           (when (get-buffer session)
 218             ;; Session buffer exists, but with dead process
 219             (set-buffer session))
 220           (require 'ess) (R)
 221           (rename-buffer
 222            (if (bufferp session)
 223                (buffer-name session)
 224              (if (stringp session)
 225                  session
 226                (buffer-name))))
 227           (current-buffer))))))
 228
 229 (defun org-babel-R-associate-session (session)
 230   "Associate R code buffer with an R session.
 231 Make SESSION be the inferior ESS process associated with the
 232 current code buffer."
 233   (setq ess-local-process-name
 234         (process-name (get-buffer-process session)))
 235   (ess-make-buffer-current))
 236
 237 (defun org-babel-R-graphical-output-file (params)
 238   "Name of file to which R should send graphical output."
 239   (and (member "graphics" (cdr (assq :result-params params)))
 240        (cdr (assq :file params))))
 241
 242 (defvar org-babel-R-graphics-devices
 243   '((:bmp "bmp" "filename")
 244     (:jpg "jpeg" "filename")
 245     (:jpeg "jpeg" "filename")
 246     (:tikz "tikz" "file")
 247     (:tiff "tiff" "filename")
 248     (:png "png" "filename")
 249     (:svg "svg" "file")
 250     (:pdf "pdf" "file")
 251     (:ps "postscript" "file")
 252     (:postscript "postscript" "file"))
 253   "An alist mapping graphics file types to R functions.
 254
 255 Each member of this list is a list with three members:
 256 1. the file extension of the graphics file, as an elisp :keyword
 257 2. the R graphics device function to call to generate such a file
 258 3. the name of the argument to this function which specifies the
 259    file to write to (typically \"file\" or \"filename\")")
 260
 261 (defun org-babel-R-construct-graphics-device-call (out-file params)
 262   "Construct the call to the graphics device."
 263   (let* ((allowed-args '(:width :height :bg :units :pointsize
 264                                 :antialias :quality :compression :res
 265                                 :type :family :title :fonts :version
 266                                 :paper :encoding :pagecentre :colormodel
 267                                 :useDingbats :horizontal))
 268          (device (and (string-match ".+\\.\\([^.]+\\)" out-file)
 269                       (match-string 1 out-file)))
 270          (device-info (or (assq (intern (concat ":" device))
 271                                 org-babel-R-graphics-devices)
 272                           (assq :png org-babel-R-graphics-devices)))
 273         (extra-args (cdr (assq :R-dev-args params))) filearg args)
 274     (setq device (nth 1 device-info))
 275     (setq filearg (nth 2 device-info))
 276     (setq args (mapconcat
 277                 (lambda (pair)
 278                   (if (member (car pair) allowed-args)
 279                       (format ",%s=%S"
 280                               (substring (symbol-name (car pair)) 1)
 281                               (cdr pair)) ""))
 282                 params ""))
 283     (format "%s(%s=\"%s\"%s%s%s)"
 284             device filearg out-file args
 285             (if extra-args "," "") (or extra-args ""))))
 286
 287 (defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
 288 (defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
 289
 290 (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\")")
 291
 292 (defun org-babel-R-evaluate
 293   (session body result-type result-params column-names-p row-names-p)
 294   "Evaluate R code in BODY."
 295   (if session
 296       (org-babel-R-evaluate-session
 297        session body result-type result-params column-names-p row-names-p)
 298     (org-babel-R-evaluate-external-process
 299      body result-type result-params column-names-p row-names-p)))
 300
 301 (defun org-babel-R-evaluate-external-process
 302   (body result-type result-params column-names-p row-names-p)
 303   "Evaluate BODY in external R process.
 304 If RESULT-TYPE equals 'output then return standard output as a
 305 string.  If RESULT-TYPE equals 'value then return the value of the
 306 last statement in BODY, as elisp."
 307   (case result-type
 308     (value
 309      (let ((tmp-file (org-babel-temp-file "R-")))
 310        (org-babel-eval org-babel-R-command
 311                        (format org-babel-R-write-object-command
 312                                (if row-names-p "TRUE" "FALSE")
 313                                (if column-names-p
 314                                    (if row-names-p "NA" "TRUE")
 315                                  "FALSE")
 316                                (format "{function ()\n{\n%s\n}}()" body)
 317                                (org-babel-process-file-name tmp-file 'noquote)))
 318        (org-babel-R-process-value-result
 319         (org-babel-result-cond result-params
 320           (with-temp-buffer
 321             (insert-file-contents tmp-file)
 322             (buffer-string))
 323           (org-babel-import-elisp-from-file tmp-file '(16)))
 324         column-names-p)))
 325     (output (org-babel-eval org-babel-R-command body))))
 326
 327 (defvar ess-eval-visibly-p)
 328
 329 (defun org-babel-R-evaluate-session
 330   (session body result-type result-params column-names-p row-names-p)
 331   "Evaluate BODY in SESSION.
 332 If RESULT-TYPE equals 'output then return standard output as a
 333 string.  If RESULT-TYPE equals 'value then return the value of the
 334 last statement in BODY, as elisp."
 335   (case result-type
 336     (value
 337      (with-temp-buffer
 338        (insert (org-babel-chomp body))
 339        (let ((ess-local-process-name
 340               (process-name (get-buffer-process session)))
 341              (ess-eval-visibly-p nil))
 342          (ess-eval-buffer nil)))
 343      (let ((tmp-file (org-babel-temp-file "R-")))
 344        (org-babel-comint-eval-invisibly-and-wait-for-file
 345         session tmp-file
 346         (format org-babel-R-write-object-command
 347                 (if row-names-p "TRUE" "FALSE")
 348                 (if column-names-p
 349                     (if row-names-p "NA" "TRUE")
 350                   "FALSE")
 351                 ".Last.value" (org-babel-process-file-name tmp-file 'noquote)))
 352        (org-babel-R-process-value-result
 353         (org-babel-result-cond result-params
 354           (with-temp-buffer
 355             (insert-file-contents tmp-file)
 356             (buffer-string))
 357           (org-babel-import-elisp-from-file tmp-file '(16)))
 358         column-names-p)))
 359     (output
 360      (mapconcat
 361       #'org-babel-chomp
 362       (butlast
 363        (delq nil
 364              (mapcar
 365               (lambda (line) (when (> (length line) 0) line))
 366               (mapcar
 367                (lambda (line) ;; cleanup extra prompts left in output
 368                  (if (string-match
 369                       "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
 370                      (substring line (match-end 1))
 371                    line))
 372                (org-babel-comint-with-output (session org-babel-R-eoe-output)
 373                  (insert (mapconcat #'org-babel-chomp
 374                                     (list body org-babel-R-eoe-indicator)
 375                                     "\n"))
 376                  (inferior-ess-send-input)))))) "\n"))))
 377
 378 (defun org-babel-R-process-value-result (result column-names-p)
 379   "R-specific processing of return value.
 380 Insert hline if column names in output have been requested."
 381   (if column-names-p
 382       (cons (car result) (cons 'hline (cdr result)))
 383     result))
 384
 385 (provide 'ob-R)
 386
 387
 388
 389 ;;; ob-R.el ends here