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

156 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")
(add-to-list 'org-babel-tangle-langs '("R" "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' via multiple-value-bind."
(message "executing R source code block...")
(save-window-excursion
(let ((full-body (concat
(mapconcat ;; define any variables
(lambda (pair)
(org-babel-R-assign-elisp (car pair) (cdr pair)))
vars "\n") "\n" body "\n"))
(session (org-babel-R-initiate-session session))
(column-names-p (cdr (assoc :colnames params))))
(org-babel-R-evaluate session full-body result-type column-names-p))))
(defun org-babel-prep-session:R (session params)
"Prepare SESSION according to the header arguments specified in PARAMS."
(let* ((session (org-babel-R-initiate-session session))
(vars (org-babel-ref-variables params)))
(mapc (lambda (pair) (org-babel-R-assign-elisp session (car pair) (cdr pair))) vars)))
;; helper functions
(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."
(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=%s, sep=\"\\t\", as.is=TRUE)"
name transition-file (if (eq (second value) 'hline) "TRUE" "FALSE")))
(format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
(defun org-babel-R-initiate-session (session)
"If there is not a current R process then create one."
(unless (string= session "none")
(setq session (or session "*R*"))
(if (org-babel-comint-buffer-livep session)
session
(save-window-excursion
(R)
(rename-buffer (if (bufferp session) (buffer-name session)
(if (stringp session) session (buffer-name)))) (current-buffer)))))
(defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
(defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
(defvar org-babel-R-wrapper-method "main <- function ()\n{\n%s\n}
write.table(main(), file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=FALSE, col.names=%s, quote=FALSE)")
(defun org-babel-R-evaluate (buffer body result-type column-names-p)
"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, as elisp."
(if (not session)
;; external process evaluation
(let ((in-tmp-file (make-temp-file "R-in-functional-results"))
(out-tmp-file (make-temp-file "R-out-functional-results")))
(case result-type
(output
(with-temp-file in-tmp-file (insert body))
(shell-command-to-string (format "R --slave --no-save < '%s' > '%s'"
in-tmp-file out-tmp-file))
(with-temp-buffer (insert-file-contents out-tmp-file) (buffer-string)))
(value
(with-temp-file in-tmp-file
(insert (format org-babel-R-wrapper-method
body out-tmp-file (if column-names-p "TRUE" "FALSE"))))
(shell-command (format "R --no-save < '%s'" in-tmp-file))
(org-babel-R-process-value-result
(org-babel-import-elisp-from-file out-tmp-file) column-names-p))))
;; comint session evaluation
(org-babel-comint-in-buffer buffer
(let* ((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=%s, quote=FALSE)" tmp-file (if column-names-p "TRUE" "FALSE")))
(full-body (mapconcat #'org-babel-chomp
(list body last-value-eval org-babel-R-eoe-indicator) "\n"))
(raw (org-babel-comint-with-output buffer org-babel-R-eoe-output nil
(insert full-body) (inferior-ess-send-input))) broke results)
(case result-type
(value (org-babel-R-process-value-result
(org-babel-import-elisp-from-file tmp-file) column-names-p))
(output
(flet ((extractor
(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)))))
(mapconcat
#'identity
(delete nil (mapcar #'extractor (mapcar #'org-babel-chomp raw))) "\n"))))))))
(defun org-babel-R-process-value-result (result column-names-p)
"R-specific processing of return value prior to return to org-babel.
Currently, insert hline if column names in output have been requested."
(if column-names-p
(cons (car result) (cons 'hline (cdr result)))
result))
(provide 'org-babel-R)
;;; org-babel-R.el ends here