;;; 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" "#!/usr/bin/env Rscript")) (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-excursion (let* ((processed-params (org-babel-process-params params)) (result-type (fourth processed-params)) (session (org-babel-R-initiate-session (first processed-params))) (vars (second processed-params)) (column-names-p (cdr (assoc :colnames params))) (out-file (cdr (assoc :file params))) (augmented-body (concat (if out-file (concat (org-babel-R-construct-graphics-device-call out-file params) "\n") "") (mapconcat ;; define any variables (lambda (pair) (org-babel-R-assign-elisp (car pair) (cdr pair))) vars "\n") "\n" body "\n" (if out-file "dev.off()\n" ""))) (result (org-babel-R-evaluate session augmented-body result-type column-names-p))) (or out-file result)))) (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) session)) (defun org-babel-load-session:R (session body params) "Load BODY into SESSION." (save-window-excursion (let ((buffer (org-babel-prep-session:R session params))) (with-current-buffer buffer (goto-char (process-mark (get-buffer-process (current-buffer)))) (insert (org-babel-chomp body))) buffer))) ;; 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))))) (defun org-babel-R-construct-graphics-device-call (out-file params) "Construct the call to the graphics device" (let ((devices '((:bmp . "bmp") (:jpg . "jpeg") (:jpeg . "jpeg") (:tiff . "tiff") (:png . "png") (:pdf . "pdf") (:ps . "postscript") (:postscript . "postscript"))) (allowed-args '(:width :height :bg :units :pointsize :antialias :quality :compression :res :type :family :title :fonts :version :paper :encoding :pagecentre :colormodel :useDingbats :horizontal)) (device (and (string-match ".+\\.\\([^.]+\\)" out-file) (match-string 1 out-file))) (extra-args (cdr (assq :R-dev-args params))) filearg args) (setq device (or (and device (cdr (assq (intern (concat ":" device)) devices))) "png")) (setq filearg (if (member device '("pdf" "postscript")) "file" "filename")) (setq args (mapconcat (lambda (pair) (if (member (car pair) allowed-args) (format ",%s=%s" (substring (symbol-name (car pair)) 1) (cdr pair)) "")) params "")) (format "%s(%s=\"%s\"%s%s%s)\n" device filearg out-file args (if extra-args "," "") (or extra-args "")))) (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 (session body result-type column-names-p) "Pass BODY to the R process in SESSION. 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 session (let* ((tmp-file (make-temp-file "org-babel-R")) (full-body (case result-type (value (mapconcat #'org-babel-chomp (list body (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")) org-babel-R-eoe-indicator) "\n")) (output (mapconcat #'org-babel-chomp (list body org-babel-R-eoe-indicator) "\n")))) (raw (org-babel-comint-with-output session org-babel-R-eoe-output nil (insert full-body) (inferior-ess-send-input))) (comint-prompt-regexp (concat "^\\(" inferior-ess-primary-prompt "\\|" inferior-ess-secondary-prompt "\\)*")) 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