lisp/ob-R.el

   1 ;;; ob-R.el --- org-babel functions for R code evaluation
   2
   3 ;; Copyright (C) 2009, 2010  Free Software Foundation, Inc.
   4
   5 ;; Author: Eric Schulte, Dan Davison
   6 ;; Keywords: literate programming, reproducible research, R, statistics
   7 ;; Homepage: http://orgmode.org
   8 ;; Version: 0.01
   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 (eval-when-compile (require 'cl))
  33
  34 (declare-function org-babel-comint-in-buffer "ob-comint" (buffer &rest body))
  35 (declare-function comint-send-input "ob-comint" (el'.))
  36 (declare-function org-babel-comint-wait-for-output "ob-comint" (buffer))
  37 (declare-function org-babel-comint-buffer-livep "ob-comint" (buffer))
  38 (declare-function org-babel-comint-with-output "ob-comint" (meta &rest body))
  39 (declare-function orgtbl-to-tsv "ob-table" (table params))
  40 (declare-function R "ext:essd-r" (&optional start-args))
  41 (declare-function inferior-ess-send-input "ext:ess-inf" ())
  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 (defun org-babel-expand-body:R (body params &optional processed-params)
  55   "Expand BODY according to PARAMS, return the expanded body."
  56   (let* ((processed-params (or processed-params
  57                                (org-babel-process-params params)))
  58          (vars (mapcar
  59                 (lambda (i)
  60                   (cons (car (nth i (nth 1 processed-params)))
  61                         (org-babel-reassemble-table
  62                          (cdr (nth i (nth 1 processed-params)))
  63                          (cdr (nth i (nth 4 processed-params)))
  64                          (cdr (nth i (nth 5 processed-params))))))
  65                 (number-sequence 0 (1- (length (nth 1 processed-params))))))
  66          (out-file (cdr (assoc :file params))))
  67     (mapconcat ;; define any variables
  68      #'org-babel-trim
  69      ((lambda (inside)
  70         (if out-file
  71             (append
  72              (org-babel-R-construct-graphics-device-call out-file params)
  73              inside
  74              (list "dev.off()"))
  75           inside))
  76       (append
  77        (mapcar
  78         (lambda (pair)
  79           (org-babel-R-assign-elisp
  80            (car pair) (cdr pair)
  81            (equal "yes" (cdr (assoc :colnames params)))
  82            (equal "yes" (cdr (assoc :rownames params)))))
  83         vars)
  84        (list body))) "\n")))
  85
  86 (defun org-babel-execute:R (body params)
  87   "Execute a block of R code with org-babel.  This function is
  88 called by `org-babel-execute-src-block'."
  89   (message "executing R source code block...")
  90   (save-excursion
  91     (let* ((processed-params (org-babel-process-params params))
  92            (result-type (nth 3 processed-params))
  93            (session (org-babel-R-initiate-session
  94                      (first processed-params) params))
  95            (colnames-p (cdr (assoc :colnames params)))
  96            (rownames-p (cdr (assoc :rownames params)))
  97            (out-file (cdr (assoc :file params)))
  98            (full-body (org-babel-expand-body:R body params processed-params))
  99            (result
 100             (org-babel-R-evaluate
 101              session full-body result-type
 102              (or (equal "yes" colnames-p)
 103                  (org-babel-pick-name (nth 4 processed-params) colnames-p))
 104              (or (equal "yes" rownames-p)
 105                  (org-babel-pick-name (nth 5 processed-params) rownames-p)))))
 106       (message "result is %S" result)
 107       (or out-file result))))
 108
 109 (defun org-babel-prep-session:R (session params)
 110   "Prepare SESSION according to the header arguments specified in PARAMS."
 111   (let* ((session (org-babel-R-initiate-session session params))
 112          (vars (org-babel-ref-variables params))
 113          (var-lines
 114           (mapcar
 115            (lambda (pair) (org-babel-R-assign-elisp
 116                       (car pair) (cdr pair)
 117                       (equal (cdr (assoc :colnames params)) "yes")
 118                       (equal (cdr (assoc :rownames params)) "yes")))
 119            vars)))
 120     (org-babel-comint-in-buffer session
 121       (mapc (lambda (var)
 122               (end-of-line 1) (insert var) (comint-send-input nil t)
 123               (org-babel-comint-wait-for-output session)) var-lines))
 124     session))
 125
 126 (defun org-babel-load-session:R (session body params)
 127   "Load BODY into SESSION."
 128   (save-window-excursion
 129     (let ((buffer (org-babel-prep-session:R session params)))
 130       (with-current-buffer buffer
 131         (goto-char (process-mark (get-buffer-process (current-buffer))))
 132         (insert (org-babel-chomp body)))
 133       buffer)))
 134
 135 ;; helper functions
 136
 137 (defun org-babel-R-quote-tsv-field (s)
 138   "Quote field S for export to R."
 139   (if (stringp s)
 140       (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
 141     (format "%S" s)))
 142
 143 (defun org-babel-R-assign-elisp (name value colnames-p rownames-p)
 144   "Construct R code assigning the elisp VALUE to a variable named NAME."
 145   (if (listp value)
 146       (let ((transition-file (make-temp-file "org-babel-R-import")))
 147         ;; ensure VALUE has an orgtbl structure (depth of at least 2)
 148         (unless (listp (car value)) (setq value (list value)))
 149         (with-temp-file (org-babel-maybe-remote-file transition-file)
 150           (insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
 151           (insert "\n"))
 152         (format "%s <- read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE)"
 153                 name transition-file
 154                 (if (or (eq (nth 1 value) 'hline) colnames-p) "TRUE" "FALSE")
 155                 (if rownames-p "1" "NULL")))
 156     (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
 157
 158 (defun org-babel-R-initiate-session (session params)
 159   "If there is not a current R process then create one."
 160   (unless (string= session "none")
 161     (let ((session (or session "*R*"))
 162           (ess-ask-for-ess-directory (not (cdr (assoc :dir params)))))
 163       (if (org-babel-comint-buffer-livep session)
 164           session
 165         (save-window-excursion
 166           (require 'ess) (R)
 167           (rename-buffer
 168            (if (bufferp session)
 169                (buffer-name session)
 170              (if (stringp session)
 171                  session
 172                (buffer-name))))
 173           (current-buffer))))))
 174
 175 (defun org-babel-R-construct-graphics-device-call (out-file params)
 176   "Construct the call to the graphics device."
 177   (let ((devices
 178          '((:bmp . "bmp")
 179            (:jpg . "jpeg")
 180            (:jpeg . "jpeg")
 181            (:tiff . "tiff")
 182            (:png . "png")
 183            (:svg . "svg")
 184            (:pdf . "pdf")
 185            (:ps . "postscript")
 186            (:postscript . "postscript")))
 187         (allowed-args '(:width :height :bg :units :pointsize
 188                                :antialias :quality :compression :res
 189                                :type :family :title :fonts :version
 190                                :paper :encoding :pagecentre :colormodel
 191                                :useDingbats :horizontal))
 192         (device (and (string-match ".+\\.\\([^.]+\\)" out-file)
 193                      (match-string 1 out-file)))
 194         (extra-args (cdr (assq :R-dev-args params))) filearg args)
 195     (setq device (or (and device (cdr (assq (intern (concat ":" device))
 196                                             devices))) "png"))
 197     (setq filearg
 198           (if (member device '("pdf" "postscript" "svg")) "file" "filename"))
 199     (setq args (mapconcat
 200                 (lambda (pair)
 201                   (if (member (car pair) allowed-args)
 202                       (format ",%s=%s"
 203                               (substring (symbol-name (car pair)) 1)
 204                               (cdr pair)) ""))
 205                 params ""))
 206     (format "%s(%s=\"%s\"%s%s%s)"
 207             device filearg out-file args
 208             (if extra-args "," "") (or extra-args ""))))
 209
 210 (defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
 211 (defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
 212 (defvar org-babel-R-wrapper-method "main <- function ()\n{\n%s\n}
 213 write.table(main(), file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=%s, col.names=%s, quote=FALSE)")
 214 (defvar org-babel-R-wrapper-lastvar "write.table(.Last.value, file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=%s, col.names=%s, quote=FALSE)")
 215
 216 (defun org-babel-R-evaluate
 217   (session body result-type column-names-p row-names-p)
 218   "Pass BODY to the R process in SESSION.  If RESULT-TYPE equals
 219 'output then return a list of the outputs of the statements in
 220 BODY, if RESULT-TYPE equals 'value then return the value of the
 221 last statement in BODY, as elisp."
 222   (if (not session)
 223       ;; external process evaluation
 224       (case result-type
 225         (output (org-babel-eval org-babel-R-command body))
 226         (value
 227          (let ((tmp-file (make-temp-file "org-babel-R-results-")))
 228            (org-babel-eval org-babel-R-command
 229                            (format org-babel-R-wrapper-method
 230                                    body tmp-file
 231                                    (if row-names-p "TRUE" "FALSE")
 232                                    (if column-names-p
 233                                        (if row-names-p "NA" "TRUE")
 234                                      "FALSE")))
 235            (org-babel-R-process-value-result
 236             (org-babel-import-elisp-from-file
 237              (org-babel-maybe-remote-file tmp-file))  column-names-p))))
 238     ;; comint session evaluation
 239     (case result-type
 240       (value
 241        (let ((tmp-file (make-temp-file "org-babel-R"))
 242              broke)
 243          (org-babel-comint-with-output (session org-babel-R-eoe-output)
 244            (insert (mapconcat
 245                     #'org-babel-chomp
 246                     (list
 247                      body
 248                      (format org-babel-R-wrapper-lastvar
 249                              tmp-file
 250                              (if row-names-p "TRUE" "FALSE")
 251                              (if column-names-p
 252                                  (if row-names-p "NA" "TRUE")
 253                                "FALSE"))
 254                      org-babel-R-eoe-indicator) "\n"))
 255            (inferior-ess-send-input))
 256          (org-babel-R-process-value-result
 257           (org-babel-import-elisp-from-file
 258            (org-babel-maybe-remote-file tmp-file))  column-names-p)))
 259       (output
 260        (mapconcat
 261         #'org-babel-chomp
 262         (butlast
 263          (delq nil
 264                (mapcar
 265                 #'identity
 266                 (org-babel-comint-with-output (session org-babel-R-eoe-output)
 267                   (insert (mapconcat #'org-babel-chomp
 268                                      (list body org-babel-R-eoe-indicator)
 269                                      "\n"))
 270                   (inferior-ess-send-input)))) 2) "\n")))))
 271
 272 (defun org-babel-R-process-value-result (result column-names-p)
 273   "R-specific processing of return value prior to return to
 274 org-babel.  Insert hline if column names in output have been
 275 requested."
 276   (if column-names-p
 277       (cons (car result) (cons 'hline (cdr result)))
 278     result))
 279
 280
 281 (provide 'ob-R)
 282
 283 ;; arch-tag: cd4c7298-503b-450f-a3c2-f3e74b630237
 284
 285 ;;; ob-R.el ends here