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
  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 ((max (apply #'max (mapcar #'length (org-remove-if-not
 177                                                 #'sequencep value))))
 178             (min (apply #'min (mapcar #'length (org-remove-if-not
 179                                                 #'sequencep value))))
 180             (transition-file (org-babel-temp-file "R-import-")))
 181         ;; ensure VALUE has an orgtbl structure (depth of at least 2)
 182         (unless (listp (car value)) (setq value (list value)))
 183         (with-temp-file transition-file
 184           (insert
 185            (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field))
 186            "\n"))
 187         (let ((file (org-babel-process-file-name transition-file 'noquote))
 188               (header (if (or (eq (nth 1 value) 'hline) colnames-p)
 189                           "TRUE" "FALSE"))
 190               (row-names (if rownames-p "1" "NULL")))
 191           (if (= max min)
 192               (format "%s <- read.table(\"%s\",
 193                       header=%s,
 194                       row.names=%s,
 195                       sep=\"\\t\",
 196                       as.is=TRUE)" name file header row-names)
 197             (format "%s <- read.table(\"%s\",
 198                    header=%s,
 199                    row.names=%s,
 200                    sep=\"\\t\",
 201                    as.is=TRUE,
 202                    fill=TRUE,
 203                    col.names = paste(\"V\", seq_len(%d), sep =\"\"))"
 204                     name file header row-names max))))
 205     (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
 206
 207 (defvar ess-ask-for-ess-directory) ; dynamically scoped
 208 (defun org-babel-R-initiate-session (session params)
 209   "If there is not a current R process then create one."
 210   (unless (string= session "none")
 211     (let ((session (or session "*R*"))
 212           (ess-ask-for-ess-directory
 213            (and (and (boundp 'ess-ask-for-ess-directory) ess-ask-for-ess-directory)
 214                 (not (cdr (assoc :dir params))))))
 215       (if (org-babel-comint-buffer-livep session)
 216           session
 217         (save-window-excursion
 218           (when (get-buffer session)
 219             ;; Session buffer exists, but with dead process
 220             (set-buffer session))
 221           (require 'ess) (R)
 222           (rename-buffer
 223            (if (bufferp session)
 224                (buffer-name session)
 225              (if (stringp session)
 226                  session
 227                (buffer-name))))
 228           (current-buffer))))))
 229
 230 (defun org-babel-R-associate-session (session)
 231   "Associate R code buffer with an R session.
 232 Make SESSION be the inferior ESS process associated with the
 233 current code buffer."
 234   (setq ess-local-process-name
 235         (process-name (get-buffer-process session)))
 236   (ess-make-buffer-current))
 237
 238 (defun org-babel-R-graphical-output-file (params)
 239   "Name of file to which R should send graphical output."
 240   (and (member "graphics" (cdr (assq :result-params params)))
 241        (cdr (assq :file params))))
 242
 243 (defvar org-babel-R-graphics-devices
 244   '((:bmp "bmp" "filename")
 245     (:jpg "jpeg" "filename")
 246     (:jpeg "jpeg" "filename")
 247     (:tikz "tikz" "file")
 248     (:tiff "tiff" "filename")
 249     (:png "png" "filename")
 250     (:svg "svg" "file")
 251     (:pdf "pdf" "file")
 252     (:ps "postscript" "file")
 253     (:postscript "postscript" "file"))
 254   "An alist mapping graphics file types to R functions.
 255
 256 Each member of this list is a list with three members:
 257 1. the file extension of the graphics file, as an elisp :keyword
 258 2. the R graphics device function to call to generate such a file
 259 3. the name of the argument to this function which specifies the
 260    file to write to (typically \"file\" or \"filename\")")
 261
 262 (defun org-babel-R-construct-graphics-device-call (out-file params)
 263   "Construct the call to the graphics device."
 264   (let* ((allowed-args '(:width :height :bg :units :pointsize
 265                                 :antialias :quality :compression :res
 266                                 :type :family :title :fonts :version
 267                                 :paper :encoding :pagecentre :colormodel
 268                                 :useDingbats :horizontal))
 269          (device (and (string-match ".+\\.\\([^.]+\\)" out-file)
 270                       (match-string 1 out-file)))
 271          (device-info (or (assq (intern (concat ":" device))
 272                                 org-babel-R-graphics-devices)
 273                           (assq :png org-babel-R-graphics-devices)))
 274         (extra-args (cdr (assq :R-dev-args params))) filearg args)
 275     (setq device (nth 1 device-info))
 276     (setq filearg (nth 2 device-info))
 277     (setq args (mapconcat
 278                 (lambda (pair)
 279                   (if (member (car pair) allowed-args)
 280                       (format ",%s=%S"
 281                               (substring (symbol-name (car pair)) 1)
 282                               (cdr pair)) ""))
 283                 params ""))
 284     (format "%s(%s=\"%s\"%s%s%s)"
 285             device filearg out-file args
 286             (if extra-args "," "") (or extra-args ""))))
 287
 288 (defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
 289 (defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
 290
 291 (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\")")
 292
 293 (defun org-babel-R-evaluate
 294   (session body result-type result-params column-names-p row-names-p)
 295   "Evaluate R code in BODY."
 296   (if session
 297       (org-babel-R-evaluate-session
 298        session body result-type result-params column-names-p row-names-p)
 299     (org-babel-R-evaluate-external-process
 300      body result-type result-params column-names-p row-names-p)))
 301
 302 (defun org-babel-R-evaluate-external-process
 303   (body result-type result-params column-names-p row-names-p)
 304   "Evaluate BODY in external R process.
 305 If RESULT-TYPE equals 'output then return standard output as a
 306 string.  If RESULT-TYPE equals 'value then return the value of the
 307 last statement in BODY, as elisp."
 308   (case result-type
 309     (value
 310      (let ((tmp-file (org-babel-temp-file "R-")))
 311        (org-babel-eval org-babel-R-command
 312                        (format org-babel-R-write-object-command
 313                                (if row-names-p "TRUE" "FALSE")
 314                                (if column-names-p
 315                                    (if row-names-p "NA" "TRUE")
 316                                  "FALSE")
 317                                (format "{function ()\n{\n%s\n}}()" body)
 318                                (org-babel-process-file-name tmp-file 'noquote)))
 319        (org-babel-R-process-value-result
 320         (org-babel-result-cond result-params
 321           (with-temp-buffer
 322             (insert-file-contents tmp-file)
 323             (buffer-string))
 324           (org-babel-import-elisp-from-file tmp-file '(16)))
 325         column-names-p)))
 326     (output (org-babel-eval org-babel-R-command body))))
 327
 328 (defvar ess-eval-visibly-p)
 329
 330 (defun org-babel-R-evaluate-session
 331   (session body result-type result-params column-names-p row-names-p)
 332   "Evaluate BODY in SESSION.
 333 If RESULT-TYPE equals 'output then return standard output as a
 334 string.  If RESULT-TYPE equals 'value then return the value of the
 335 last statement in BODY, as elisp."
 336   (case result-type
 337     (value
 338      (with-temp-buffer
 339        (insert (org-babel-chomp body))
 340        (let ((ess-local-process-name
 341               (process-name (get-buffer-process session)))
 342              (ess-eval-visibly-p nil))
 343          (ess-eval-buffer nil)))
 344      (let ((tmp-file (org-babel-temp-file "R-")))
 345        (org-babel-comint-eval-invisibly-and-wait-for-file
 346         session tmp-file
 347         (format org-babel-R-write-object-command
 348                 (if row-names-p "TRUE" "FALSE")
 349                 (if column-names-p
 350                     (if row-names-p "NA" "TRUE")
 351                   "FALSE")
 352                 ".Last.value" (org-babel-process-file-name tmp-file 'noquote)))
 353        (org-babel-R-process-value-result
 354         (org-babel-result-cond result-params
 355           (with-temp-buffer
 356             (insert-file-contents tmp-file)
 357             (buffer-string))
 358           (org-babel-import-elisp-from-file tmp-file '(16)))
 359         column-names-p)))
 360     (output
 361      (mapconcat
 362       #'org-babel-chomp
 363       (butlast
 364        (delq nil
 365              (mapcar
 366               (lambda (line) (when (> (length line) 0) line))
 367               (mapcar
 368                (lambda (line) ;; cleanup extra prompts left in output
 369                  (if (string-match
 370                       "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
 371                      (substring line (match-end 1))
 372                    line))
 373                (org-babel-comint-with-output (session org-babel-R-eoe-output)
 374                  (insert (mapconcat #'org-babel-chomp
 375                                     (list body org-babel-R-eoe-indicator)
 376                                     "\n"))
 377                  (inferior-ess-send-input)))))) "\n"))))
 378
 379 (defun org-babel-R-process-value-result (result column-names-p)
 380   "R-specific processing of return value.
 381 Insert hline if column names in output have been requested."
 382   (if column-names-p
 383       (cons (car result) (cons 'hline (cdr result)))
 384     result))
 385
 386 (provide 'ob-R)
 387
 388
 389
 390 ;;; ob-R.el ends here