org-mode/lisp/org-babel-R.el

;;; org-babel-R.el --- org-babel functions for R code evaluation

;; Copyright (C) 2009 Eric Schulte

;; Author: Eric Schulte
;; Keywords: literate programming, reproducible research, R, statistics
;; Homepage: http://orgmode.org
;; Version: 0.01

;;; License:

;; This program is free software; you can redistribute it and/or modify
;; it under the terms of the GNU General Public License as published by
;; the Free Software Foundation; either version 3, or (at your option)
;; any later version.
;;
;; This program is distributed in the hope that it will be useful,
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;; GNU General Public License for more details.
;;
;; You should have received a copy of the GNU General Public License
;; along with GNU Emacs; see the file COPYING.  If not, write to the
;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
;; Boston, MA 02110-1301, USA.

;;; Commentary:

;; Org-Babel support for evaluating R code

;;; Code:
(require 'org-babel)

(org-babel-add-interpreter "R")

(defun org-babel-execute:R (body params)
  "Execute a block of R code with org-babel.  This function is
called by `org-babel-execute-src-block'."
  (message "executing R source code block...")
  (save-window-excursion
    (let* ((vars (org-babel-ref-variables params))
           (result-params (split-string (or (cdr (assoc :results params)) "")))
           (result-type (cond ((member "output" result-params) 'output)
                              ((member "value" result-params) 'value)
                              (t 'value)))
           (session (org-babel-R-initiate-session ;; (cdr (assoc :session params))
                                                  (get-buffer "*R*")))
           results)
      ;; assign variables
      (mapc (lambda (pair) (org-babel-R-assign-elisp session (car pair) (cdr pair))) vars)
      ;; ;;; debugging statements
      ;; (message (format "result-type=%S" result-type))
      ;; (message (format "body=%S" body))
      ;; (message (format "session=%S" session))
      ;; (message (format "result-params=%S" result-params))
      ;; evaluate body and convert the results to ruby
      (setq results (org-babel-R-evaluate session body result-type))
      (setq results (if (member "scalar" result-params)
                        results
                      (let ((tmp-file (make-temp-file "org-babel-R")))
                        (with-temp-file tmp-file (insert results))
                        (org-babel-import-elisp-from-file tmp-file))))
      (if (and (member "vector" result-params) (not (listp results)))
          (list (list results))
        results))))

(defun org-babel-R-quote-tsv-field (s)
  "Quote field S for export to R."
  (if (stringp s)
      (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
    (format "%S" s)))

(defun org-babel-R-assign-elisp (session name value)
  "Read the elisp VALUE into a variable named NAME in the current
R process in `org-babel-R-buffer'."
  (unless session (error "No active R buffer"))
  (org-babel-comint-input-command
   session
   (if (listp value)
       (let ((transition-file (make-temp-file "org-babel-R-import")))
	 ;; ensure VALUE has an orgtbl structure (depth of at least 2)
	 (unless (listp (car value)) (setq value (list value)))
	 (with-temp-file transition-file
	   (insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
	   (insert "\n"))
	 (format "%s <- read.table(\"%s\", header=FALSE, sep=\"\\t\", as.is=TRUE)"
		 name transition-file))
     (format "%s <- %s" name (org-babel-R-quote-tsv-field value)))))

;; functions for comint evaluation

(defun org-babel-R-initiate-session (session)
  "If there is not a current R process then create one."
  (if (org-babel-comint-buffer-livep session)
      session
    (save-window-excursion (R) (current-buffer))))

(defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
(defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")

(defun org-babel-R-evaluate (buffer body result-type)
  "Pass BODY to the R process in BUFFER.  If RESULT-TYPE equals
'output then return a list of the outputs of the statements in
BODY, if RESULT-TYPE equals 'value then return the value of the
last statement in BODY."
  (org-babel-comint-in-buffer buffer
    (let* ((string-buffer "")
           (tmp-file (make-temp-file "org-babel-R"))
           (last-value-eval
            (format "write.table(.Last.value, file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=FALSE, col.names=FALSE, quote=FALSE)"
                    tmp-file))
           (full-body (mapconcat #'org-babel-chomp (list body last-value-eval org-babel-R-eoe-indicator) "\n"))
           results)
      (flet ((my-filt (text) (setq string-buffer (concat string-buffer text))))
        ;; setup filter
        (add-hook 'comint-output-filter-functions 'my-filt)
        ;; pass FULL-BODY to process
        (goto-char (process-mark (get-buffer-process buffer)))
        (insert full-body)
        (comint-send-input)
        ;; wait for end-of-evaluation indicator
        (while (progn
                 (goto-char comint-last-input-end)
                 (not (save-excursion (and (re-search-forward comint-prompt-regexp nil t)
                                           (re-search-forward (regexp-quote org-babel-R-eoe-output) nil t)))))
          (accept-process-output (get-buffer-process buffer)))
        ;; remove filter
        (remove-hook 'comint-output-filter-functions 'my-filt))
      ;; ;;; debugging
      ;; ;; echo raw results
      ;; (message (format "raw-results=%S" string-buffer))
      ;; ;; split results
      (message (format "split-results=%S" (split-string string-buffer comint-prompt-regexp)))
      ;; split results with `comint-prompt-regexp'
      (setq results (let ((broke nil))
                      (delete nil (mapcar (lambda (el)
                                                  (if (or broke
                                                          (and (string-match (regexp-quote org-babel-R-eoe-output) el) (setq broke t)))
                                                      nil
                                                    (if (= (length el) 0)
                                                        nil
                                                      (if (string-match comint-prompt-regexp el)
                                                          (substring el (match-end 0))
                                                        el))))
                                          (mapcar #'org-babel-trim (split-string string-buffer comint-prompt-regexp))))))
      (case result-type
        (output (mapconcat #'identity results "\n"))
        (value (with-temp-buffer (insert-file-contents tmp-file) (buffer-string)))
        (t (reverse results))))))

(provide 'org-babel-R)
;;; org-babel-R.el ends here