diff options
Diffstat (limited to 'lisp/org/ob-R.el')
| -rw-r--r-- | lisp/org/ob-R.el | 279 |
1 files changed, 279 insertions, 0 deletions
diff --git a/lisp/org/ob-R.el b/lisp/org/ob-R.el new file mode 100644 index 00000000000..105862c1571 --- /dev/null +++ b/lisp/org/ob-R.el @@ -0,0 +1,279 @@ +;;; ob-R.el --- org-babel functions for R code evaluation + +;; Copyright (C) 2009, 2010 Free Software Foundation, Inc. + +;; Author: Eric Schulte, Dan Davison +;; Keywords: literate programming, reproducible research, R, statistics +;; Homepage: http://orgmode.org +;; Version: 7.01 + +;; This file is part of GNU Emacs. + +;; GNU Emacs 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 of the License, or +;; (at your option) any later version. + +;; GNU Emacs 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. If not, see <http://www.gnu.org/licenses/>. + +;;; Commentary: + +;; Org-Babel support for evaluating R code + +;;; Code: +(require 'ob) +(require 'ob-ref) +(require 'ob-comint) +(require 'ob-eval) +(eval-when-compile (require 'cl)) + +(declare-function orgtbl-to-tsv "ob-table" (table params)) +(declare-function R "ext:essd-r" (&optional start-args)) +(declare-function inferior-ess-send-input "ext:ess-inf" ()) + +(defconst org-babel-header-arg-names:R + '(width height bg units pointsize antialias quality compression + res type family title fonts version paper encoding + pagecentre colormodel useDingbats horizontal) + "R-specific header arguments.") + +(defvar org-babel-default-header-args:R '()) + +(defvar org-babel-R-command "R --slave --no-save" + "Name of command to use for executing R code.") + +(defun org-babel-expand-body:R (body params &optional processed-params) + "Expand BODY according to PARAMS, return the expanded body." + (let* ((processed-params (or processed-params + (org-babel-process-params params))) + (vars (mapcar + (lambda (i) + (cons (car (nth i (nth 1 processed-params))) + (org-babel-reassemble-table + (cdr (nth i (nth 1 processed-params))) + (cdr (nth i (nth 4 processed-params))) + (cdr (nth i (nth 5 processed-params)))))) + (number-sequence 0 (1- (length (nth 1 processed-params)))))) + (out-file (cdr (assoc :file params)))) + (mapconcat ;; define any variables + #'org-babel-trim + ((lambda (inside) + (if out-file + (append + (list (org-babel-R-construct-graphics-device-call out-file params)) + inside + (list "dev.off()")) + inside)) + (append + (mapcar + (lambda (pair) + (org-babel-R-assign-elisp + (car pair) (cdr pair) + (equal "yes" (cdr (assoc :colnames params))) + (equal "yes" (cdr (assoc :rownames params))))) + vars) + (list body))) "\n"))) + +(defun org-babel-execute:R (body params) + "Execute a block of R code. +This function is called by `org-babel-execute-src-block'." + (save-excursion + (let* ((processed-params (org-babel-process-params params)) + (result-type (nth 3 processed-params)) + (session (org-babel-R-initiate-session + (first processed-params) params)) + (colnames-p (cdr (assoc :colnames params))) + (rownames-p (cdr (assoc :rownames params))) + (out-file (cdr (assoc :file params))) + (full-body (org-babel-expand-body:R body params processed-params)) + (result + (org-babel-R-evaluate + session full-body result-type + (or (equal "yes" colnames-p) + (org-babel-pick-name (nth 4 processed-params) colnames-p)) + (or (equal "yes" rownames-p) + (org-babel-pick-name (nth 5 processed-params) rownames-p))))) + (message "result is %S" result) + (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 params)) + (vars (org-babel-ref-variables params)) + (var-lines + (mapcar + (lambda (pair) (org-babel-R-assign-elisp + (car pair) (cdr pair) + (equal (cdr (assoc :colnames params)) "yes") + (equal (cdr (assoc :rownames params)) "yes"))) + vars))) + (org-babel-comint-in-buffer session + (mapc (lambda (var) + (end-of-line 1) (insert var) (comint-send-input nil t) + (org-babel-comint-wait-for-output session)) var-lines)) + 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 colnames-p rownames-p) + "Construct R code assigning the elisp VALUE to 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 (org-babel-maybe-remote-file transition-file) + (insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field))) + (insert "\n")) + (format "%s <- read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE)" + name transition-file + (if (or (eq (nth 1 value) 'hline) colnames-p) "TRUE" "FALSE") + (if rownames-p "1" "NULL"))) + (format "%s <- %s" name (org-babel-R-quote-tsv-field value)))) + +(defun org-babel-R-initiate-session (session params) + "If there is not a current R process then create one." + (unless (string= session "none") + (let ((session (or session "*R*")) + (ess-ask-for-ess-directory (not (cdr (assoc :dir params))))) + (if (org-babel-comint-buffer-livep session) + session + (save-window-excursion + (require 'ess) (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") + (:svg . "svg") + (: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" "svg")) "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)" + 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=%s, col.names=%s, quote=FALSE)") +(defvar org-babel-R-wrapper-lastvar "write.table(.Last.value, file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=%s, col.names=%s, quote=FALSE)") + +(defun org-babel-R-evaluate + (session body result-type column-names-p row-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 + (case result-type + (output (org-babel-eval org-babel-R-command body)) + (value + (let ((tmp-file (make-temp-file "org-babel-R-results-"))) + (org-babel-eval org-babel-R-command + (format org-babel-R-wrapper-method + body tmp-file + (if row-names-p "TRUE" "FALSE") + (if column-names-p + (if row-names-p "NA" "TRUE") + "FALSE"))) + (org-babel-R-process-value-result + (org-babel-import-elisp-from-file + (org-babel-maybe-remote-file tmp-file)) column-names-p)))) + ;; comint session evaluation + (case result-type + (value + (let ((tmp-file (make-temp-file "org-babel-R")) + broke) + (org-babel-comint-with-output (session org-babel-R-eoe-output) + (insert (mapconcat + #'org-babel-chomp + (list + body + (format org-babel-R-wrapper-lastvar + tmp-file + (if row-names-p "TRUE" "FALSE") + (if column-names-p + (if row-names-p "NA" "TRUE") + "FALSE")) + org-babel-R-eoe-indicator) "\n")) + (inferior-ess-send-input)) + (org-babel-R-process-value-result + (org-babel-import-elisp-from-file + (org-babel-maybe-remote-file tmp-file)) column-names-p))) + (output + (mapconcat + #'org-babel-chomp + (butlast + (delq nil + (mapcar + #'identity + (org-babel-comint-with-output (session org-babel-R-eoe-output) + (insert (mapconcat #'org-babel-chomp + (list body org-babel-R-eoe-indicator) + "\n")) + (inferior-ess-send-input)))) 2) "\n"))))) + +(defun org-babel-R-process-value-result (result column-names-p) + "R-specific processing of return value. +Insert hline if column names in output have been requested." + (if column-names-p + (cons (car result) (cons 'hline (cdr result))) + result)) + +(provide 'ob-R) + +;; arch-tag: cd4c7298-503b-450f-a3c2-f3e74b630237 + +;;; ob-R.el ends here |