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

171 lines
6.2 KiB
EmacsLisp

;;; 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")
(defvar org-babel-R-func-name "org_babel_R_main"
"This is the main function which wraps each R source code
block.")
(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))
results)
(org-babel-R-initiate-R-buffer)
(mapc (lambda (pair) (org-babel-R-assign-elisp (car pair) (cdr pair))) vars)
(org-babel-R-input-command
(format "%s <- function ()\n{\n%s\n}" org-babel-R-func-name body))
(org-babel-R-to-elisp org-babel-R-func-name))))
(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 (name value)
"Read the elisp VALUE into a variable named NAME in the current
R process in `org-babel-R-buffer'."
(unless org-babel-R-buffer (error "No active R buffer"))
(org-babel-R-input-command
(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\", sep=\"\\t\", as.is=TRUE)" name transition-file))
(format "%s <- %s" name (org-babel-R-quote-tsv-field value)))))
(defun org-babel-R-to-elisp (func-name)
"Return the result of calling the function named FUNC-NAME in
`org-babel-R-buffer' as Emacs lisp."
(let ((tmp-file (make-temp-file "org-babel-R")) result)
(org-babel-R-input-command
(format "write.table(%s(), \"%s\", , ,\"\\t\", ,\"nil\", , FALSE, FALSE)" func-name tmp-file))
(with-temp-buffer
(message "before condition")
(condition-case nil
(progn
(org-table-import tmp-file nil)
(delete-file tmp-file)
(setq result (mapcar (lambda (row)
(mapcar #'org-babel-R-read row))
(org-table-to-lisp))))
(error nil))
(message "after condition")
(if (null (cdr result)) ;; if result is trivial vector, then scalarize it
(if (consp (car result))
(if (null (cdr (car result)))
(caar result)
result)
(car result))
result))))
(defun org-babel-R-read (cell)
"Strip nested \"s from around strings in exported R values."
(org-babel-read (or (and (stringp cell)
(string-match "\\\"\\(.+\\)\\\"" cell)
(match-string 1 cell))
cell)))
;; functions for evaluation of R code
(defvar org-babel-R-buffer nil
"Holds the buffer for the current R process")
(defun org-babel-R-initiate-R-buffer ()
"If there is not a current R process then create one."
;; DED: Ideally I think we should use ESS mechanisms for this sort
;; of thing. See ess-force-buffer-current.
(unless (and (buffer-live-p org-babel-R-buffer) (get-buffer org-babel-R-buffer))
(save-excursion
(R)
(setf org-babel-R-buffer (current-buffer))
(org-babel-R-wait-for-output)
(org-babel-R-input-command ""))))
(defun org-babel-R-command-to-string (command)
"Send a command to R, and return the results as a string."
(org-babel-R-input-command command)
(org-babel-R-last-output))
(defun org-babel-R-input-command (command)
"Pass COMMAND to the R process running in `org-babel-R-buffer'."
(save-excursion
(save-match-data
(set-buffer org-babel-R-buffer)
(goto-char (process-mark (get-buffer-process (current-buffer))))
(insert command)
(comint-send-input)
(org-babel-R-wait-for-output))))
(defun org-babel-R-wait-for-output ()
"Wait until output arrives"
(save-excursion
(save-match-data
(set-buffer org-babel-R-buffer)
(while (progn
(goto-char comint-last-input-end)
(not (re-search-forward comint-prompt-regexp nil t)))
(accept-process-output (get-buffer-process (current-buffer)))))))
(defun org-babel-R-last-output ()
"Return the last R output as a string"
(save-excursion
(save-match-data
(set-buffer org-babel-R-buffer)
(goto-char (process-mark (get-buffer-process (current-buffer))))
(forward-line 0)
(let ((raw (buffer-substring comint-last-input-end (- (point) 1)))
output output-flag)
(mapconcat
(lambda (el)
(if (stringp el)
(format "%s" el)
(format "%S" el)))
(delq nil
(mapcar
(lambda (line)
(unless (string-match "^>" line)
(and (string-match "\\[[[:digit:]]+\\] *\\(.*\\)$" line)
(match-string 1 line))))
;; drop first, because it's the last line of input
(cdr (split-string raw "[\n\r]")))) "\n")))))
(provide 'org-babel-R)
;;; org-babel-R.el ends here