107 lines
4.2 KiB
EmacsLisp
107 lines
4.2 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-buffer "org-babel-R"
|
|
"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."
|
|
(unless (org-babel-comint-buffer-livep org-babel-R-buffer)
|
|
(save-window-excursion (R) (setf org-babel-R-buffer (current-buffer)))))
|
|
|
|
(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-params (split-string (or (cdr (assoc :results params)) "")))
|
|
results)
|
|
;; (message (format "%S" results-params))
|
|
(org-babel-R-initiate-R-buffer)
|
|
(mapc (lambda (pair) (org-babel-R-assign-elisp (car pair) (cdr pair))) vars)
|
|
(cond
|
|
((member "script" results-params) ;; collect all output
|
|
(let ((tmp-file (make-temp-file "org-babel-R-script-output")))
|
|
(org-babel-comint-input-command org-babel-R-buffer (format "sink(%S)" tmp-file))
|
|
(org-babel-comint-input-command org-babel-R-buffer body)
|
|
(org-babel-comint-input-command org-babel-R-buffer "sink()")
|
|
(with-temp-buffer (insert-file-contents tmp-file) (buffer-string))))
|
|
((member "last" results-params) ;; the value of the last statement
|
|
(org-babel-comint-input-command org-babel-R-buffer body)
|
|
(org-babel-R-last-value-as-elisp))))))
|
|
|
|
(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-comint-input-command
|
|
org-babel-R-buffer
|
|
(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)))))
|
|
|
|
(defun org-babel-R-last-value-as-elisp ()
|
|
"Return the last value returned by R as Emacs lisp."
|
|
(let ((tmp-file (make-temp-file "org-babel-R")) result)
|
|
(org-babel-comint-input-command
|
|
org-babel-R-buffer
|
|
(format "write.table(.Last.value, file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=FALSE, col.names=FALSE, quote=FALSE)"
|
|
tmp-file))
|
|
(org-babel-import-elisp-from-file tmp-file)))
|
|
|
|
(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)))
|
|
|
|
(provide 'org-babel-R)
|
|
;;; org-babel-R.el ends here
|