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 ((full-body (concat
  44                       (mapconcat ;; define any variables
  45                        (lambda (pair)
  46                          (org-babel-R-assign-elisp (car pair) (cdr pair)))
  47                        vars "\n") "\n" body "\n"))
  48           (session (org-babel-R-initiate-session session))
  49           (colnames (cdr (assoc :colnames params))))
  50       (org-babel-R-evaluate session full-body result-type colnames))))
  51
  52 (defun org-babel-prep-session:R (session params)
  53   "Prepare SESSION according to the header arguments specified in PARAMS."
  54   (let* ((session (org-babel-R-initiate-session session))
  55          (vars (org-babel-ref-variables params)))
  56     (mapc (lambda (pair) (org-babel-R-assign-elisp session (car pair) (cdr pair))) vars)))
  57
  58 ;; helper functions
  59
  60 (defun org-babel-R-quote-tsv-field (s)
  61   "Quote field S for export to R."
  62   (if (stringp s)
  63       (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
  64     (format "%S" s)))
  65
  66 (defun org-babel-R-assign-elisp (name value)
  67   "Read the elisp VALUE into a variable named NAME."
  68   (if (listp value)
  69       (let ((transition-file (make-temp-file "org-babel-R-import")))
  70         ;; ensure VALUE has an orgtbl structure (depth of at least 2)
  71         (unless (listp (car value)) (setq value (list value)))
  72         (with-temp-file transition-file
  73           (insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
  74           (insert "\n"))
  75         (format "%s <- read.table(\"%s\", header=%s, sep=\"\\t\", as.is=TRUE)"
  76                 name transition-file (if (eq (second value) 'hline) "TRUE" "FALSE")))
  77     (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
  78
  79 (defun org-babel-R-initiate-session (session)
  80   "If there is not a current R process then create one."
  81   (unless (string= session "none")
  82     (setq session (or session "*R*"))
  83     (if (org-babel-comint-buffer-livep session)
  84         session
  85       (save-window-excursion
  86         (R)
  87         (rename-buffer (if (bufferp session) (buffer-name session)
  88                          (if (stringp session) session (buffer-name)))) (current-buffer)))))
  89
  90 (defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
  91 (defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
  92 (defvar org-babel-R-wrapper-method "main <- function ()\n{\n%s\n}
  93 write.table(main(), file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=FALSE, col.names=%s, quote=FALSE)")
  94
  95 (defun org-babel-R-evaluate (buffer body result-type colnames)
  96   "Pass BODY to the R process in BUFFER.  If RESULT-TYPE equals
  97 'output then return a list of the outputs of the statements in
  98 BODY, if RESULT-TYPE equals 'value then return the value of the
  99 last statement in BODY, as elisp."
 100   (if (not session)
 101       ;; external process evaluation
 102       (let ((in-tmp-file (make-temp-file "R-in-functional-results"))
 103             (out-tmp-file (make-temp-file "R-out-functional-results")))
 104         (case result-type
 105           (output
 106            (with-temp-file in-tmp-file (insert body))
 107            (shell-command-to-string (format "R --slave --no-save < '%s' > '%s'"
 108                                             in-tmp-file out-tmp-file))
 109            (with-temp-buffer (insert-file-contents out-tmp-file) (buffer-string)))
 110           (value
 111            (with-temp-file in-tmp-file
 112              (insert (format org-babel-R-wrapper-method
 113                              body out-tmp-file (if colnames "TRUE" "FALSE"))))
 114            (shell-command (format "R --no-save < '%s'" in-tmp-file))
 115            (org-babel-import-elisp-from-file out-tmp-file colnames))))
 116     ;; comint session evaluation
 117     (org-babel-comint-in-buffer buffer
 118       (let* ((tmp-file (make-temp-file "org-babel-R"))
 119              (last-value-eval
 120               (format "write.table(.Last.value, file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=FALSE, col.names=%s, quote=FALSE)" tmp-file (if colnames "TRUE" "FALSE")))
 121              (full-body (mapconcat #'org-babel-chomp
 122                                    (list body last-value-eval org-babel-R-eoe-indicator) "\n"))
 123              (raw (org-babel-comint-with-output buffer org-babel-R-eoe-output nil
 124                     (insert full-body) (inferior-ess-send-input)))
 125              (results
 126               (let ((broke nil))
 127                 (delete
 128                  nil
 129                  (mapcar (lambda (el)
 130                            (if (or broke
 131                                    (and (string-match (regexp-quote org-babel-R-eoe-output)
 132                                                       el) (setq broke t)))
 133                                nil
 134                              (if (= (length el) 0)
 135                                  nil
 136                                (if (string-match comint-prompt-regexp el)
 137                                    (substring el (match-end 0))
 138                                  el))))
 139                          (mapcar #'org-babel-trim raw))))))
 140         (case result-type
 141           (output (org-babel-chomp (mapconcat #'identity results "\n")))
 142           (value (org-babel-import-elisp-from-file tmp-file colnames)))))))
 143
 144
 145 (provide 'org-babel-R)
 146 ;;; org-babel-R.el ends here