contrib/babel/lisp/langs/org-babel-R.el

   1 ;;; org-babel-R.el --- org-babel functions for R code evaluation
   2
   3 ;; Copyright (C) 2009 Eric Schulte
   4
   5 ;; Author: Eric Schulte
   6 ;; Keywords: literate programming, reproducible research, R, statistics
   7 ;; Homepage: http://orgmode.org
   8 ;; Version: 0.01
   9
  10 ;;; License:
  11
  12 ;; This program 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, or (at your option)
  15 ;; any later version.
  16 ;;
  17 ;; This program 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; see the file COPYING.  If not, write to the
  24 ;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
  25 ;; Boston, MA 02110-1301, USA.
  26
  27 ;;; Commentary:
  28
  29 ;; Org-Babel support for evaluating R code
  30
  31 ;;; Code:
  32 (require 'org-babel)
  33
  34 (org-babel-add-interpreter "R")
  35
  36 (add-to-list 'org-babel-tangle-langs '("R" "r"))
  37
  38 (defun org-babel-execute:R (body params)
  39   "Execute a block of R code with org-babel.  This function is
  40 called by `org-babel-execute-src-block' via multiple-value-bind."
  41   (message "executing R source code block...")
  42   (save-window-excursion
  43     (let* ((session (org-babel-R-initiate-session session))
  44            (column-names-p (cdr (assoc :colnames params)))
  45            (out-file (cdr (assoc :file params)))
  46            (augmented-body
  47             (concat
  48              (if out-file (concat (org-babel-R-construct-graphics-device-call out-file params) "\n") "")
  49              (mapconcat ;; define any variables
  50               (lambda (pair) (org-babel-R-assign-elisp (car pair) (cdr pair))) vars "\n")
  51              "\n" body "\n" (if out-file "dev.off()\n" "")))
  52            (result (org-babel-R-evaluate session augmented-body result-type column-names-p)))
  53       (or out-file result))))
  54
  55 (defun org-babel-prep-session:R (session params)
  56   "Prepare SESSION according to the header arguments specified in PARAMS."
  57   (let* ((session (org-babel-R-initiate-session session))
  58          (vars (org-babel-ref-variables params)))
  59     (mapc (lambda (pair) (org-babel-R-assign-elisp session (car pair) (cdr pair))) vars)))
  60
  61 ;; helper functions
  62
  63 (defun org-babel-R-quote-tsv-field (s)
  64   "Quote field S for export to R."
  65   (if (stringp s)
  66       (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
  67     (format "%S" s)))
  68
  69 (defun org-babel-R-assign-elisp (name value)
  70   "Read the elisp VALUE into a variable named NAME."
  71   (if (listp value)
  72       (let ((transition-file (make-temp-file "org-babel-R-import")))
  73         ;; ensure VALUE has an orgtbl structure (depth of at least 2)
  74         (unless (listp (car value)) (setq value (list value)))
  75         (with-temp-file transition-file
  76           (insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
  77           (insert "\n"))
  78         (format "%s <- read.table(\"%s\", header=%s, sep=\"\\t\", as.is=TRUE)"
  79                 name transition-file (if (eq (second value) 'hline) "TRUE" "FALSE")))
  80     (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
  81
  82 (defun org-babel-R-initiate-session (session)
  83   "If there is not a current R process then create one."
  84   (unless (string= session "none")
  85     (setq session (or session "*R*"))
  86     (if (org-babel-comint-buffer-livep session)
  87         session
  88       (save-window-excursion
  89         (R)
  90         (rename-buffer (if (bufferp session) (buffer-name session)
  91                          (if (stringp session) session (buffer-name)))) (current-buffer)))))
  92
  93 (defun org-babel-R-construct-graphics-device-call (out-file params)
  94   "Construct the call to the graphics device"
  95   (let ((devices
  96          '((:bmp . "bmp")
  97            (:jpg . "jpeg")
  98            (:jpeg . "jpeg")
  99            (:tiff . "tiff")
 100            (:png . "png")
 101            (:pdf . "pdf")
 102            (:ps . "postscript")
 103            (:postscript . "postscript")))
 104         (allowed-args '(:width :height :bg :units :pointsize
 105                                :antialias :quality :compression :res :type
 106                                :family :title :fonts :version :paper :encoding
 107                                :pagecentre :colormodel :useDingbats :horizontal))
 108         (device (and (string-match ".+\\.\\([^.]+\\)" out-file) (match-string 1 out-file)))
 109         (extra-args (cdr (assq :R-dev-args params))) filearg args)
 110     (setq device (or (and device (cdr (assq (intern (concat ":" device)) devices))) "png"))
 111     (setq filearg (if (member device '("pdf" "postscript")) "file" "filename"))
 112     (setq args (mapconcat (lambda (pair)
 113                             (if (member (car pair) allowed-args)
 114                                 (format ",%s=%s" (substring (symbol-name (car pair)) 1) (cdr pair)) ""))
 115                           params ""))
 116     (format "%s(%s=\"%s\"%s%s%s)\n" device filearg out-file args (if extra-args "," "") (or extra-args ""))))
 117
 118 (defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
 119 (defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
 120 (defvar org-babel-R-wrapper-method "main <- function ()\n{\n%s\n}
 121 write.table(main(), file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=FALSE, col.names=%s, quote=FALSE)")
 122
 123 (defun org-babel-R-evaluate (buffer body result-type column-names-p)
 124   "Pass BODY to the R process in BUFFER.  If RESULT-TYPE equals
 125 'output then return a list of the outputs of the statements in
 126 BODY, if RESULT-TYPE equals 'value then return the value of the
 127 last statement in BODY, as elisp."
 128   (if (not session)
 129       ;; external process evaluation
 130       (let ((in-tmp-file (make-temp-file "R-in-functional-results"))
 131             (out-tmp-file (make-temp-file "R-out-functional-results")))
 132         (case result-type
 133           (output
 134            (with-temp-file in-tmp-file (insert body))
 135            (shell-command-to-string (format "R --slave --no-save < '%s' > '%s'"
 136                                             in-tmp-file out-tmp-file))
 137            (with-temp-buffer (insert-file-contents out-tmp-file) (buffer-string)))
 138           (value
 139            (with-temp-file in-tmp-file
 140              (insert (format org-babel-R-wrapper-method
 141                              body out-tmp-file (if column-names-p "TRUE" "FALSE"))))
 142            (shell-command (format "R --no-save < '%s'" in-tmp-file))
 143            (org-babel-R-process-value-result
 144             (org-babel-import-elisp-from-file out-tmp-file) column-names-p))))
 145     ;; comint session evaluation
 146     (org-babel-comint-in-buffer buffer
 147       (let* ((tmp-file (make-temp-file "org-babel-R"))
 148              (full-body
 149               (case result-type
 150                 (value
 151                  (mapconcat #'org-babel-chomp (list body
 152                                                     (format "write.table(.Last.value, file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=FALSE, col.names=%s, quote=FALSE)" tmp-file (if column-names-p "TRUE" "FALSE"))
 153                                                     org-babel-R-eoe-indicator) "\n"))
 154                 (output
 155                  (mapconcat #'org-babel-chomp (list body org-babel-R-eoe-indicator) "\n"))))
 156              (raw (org-babel-comint-with-output buffer org-babel-R-eoe-output nil
 157                     (insert full-body) (inferior-ess-send-input)))
 158              broke results)
 159         (case result-type
 160           (value (org-babel-R-process-value-result
 161                   (org-babel-import-elisp-from-file tmp-file) column-names-p))
 162           (output
 163            (flet ((extractor
 164                    (el)
 165                    (if (or broke
 166                            (and (string-match (regexp-quote org-babel-R-eoe-output) el)
 167                                 (setq broke t)))
 168                        nil
 169                      (if (= (length el) 0)
 170                          nil
 171                        (if (string-match comint-prompt-regexp el)
 172                            (substring el (match-end 0))
 173                          el)))))
 174              (mapconcat
 175               #'identity
 176               (delete nil (mapcar #'extractor (mapcar #'org-babel-chomp raw))) "\n"))))))))
 177
 178 (defun org-babel-R-process-value-result (result column-names-p)
 179   "R-specific processing of return value prior to return to org-babel.
 180
 181 Currently, insert hline if column names in output have been requested."
 182   (if column-names-p
 183       (cons (car result) (cons 'hline (cdr result)))
 184     result))
 185
 186
 187 (provide 'org-babel-R)
 188 ;;; org-babel-R.el ends here