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d128662fa3
This proposal for code tidying uses multiple-value-bind to satisfy:
1. The various parsed/resolved components of the param list (session,
vars, result-type) are available in the org-babel-execute:LANG
functions.
2. Those functions don't duplicate the code for parsing the params
list and resolving references
3. The functions still have the params list available to them, should
they need to implement language-specific behaviour using it.
If the org-babel-execute:LANG functions need to be called directly,
then that would now have to be via
(multiple-value-bind (session vars result-params result-type)
(org-babel-process-params params) (funcall cmd body params))
as in org-babel-exp.el. (But is it actually necessary to by-pass
org-babel-execute-src-block?)
146 lines
5.7 KiB
EmacsLisp
146 lines
5.7 KiB
EmacsLisp
;;; org-babel-R.el --- org-babel functions for R code evaluation
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;; Copyright (C) 2009 Eric Schulte
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;; Author: Eric Schulte
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;; Keywords: literate programming, reproducible research, R, statistics
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;; Homepage: http://orgmode.org
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;; Version: 0.01
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;;; License:
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;; This program is free software; you can redistribute it and/or modify
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;; it under the terms of the GNU General Public License as published by
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;; the Free Software Foundation; either version 3, or (at your option)
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;; any later version.
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;;
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;; This program is distributed in the hope that it will be useful,
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;; but WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;; GNU General Public License for more details.
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;;
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;; You should have received a copy of the GNU General Public License
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;; along with GNU Emacs; see the file COPYING. If not, write to the
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;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
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;; Boston, MA 02110-1301, USA.
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;;; Commentary:
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;; Org-Babel support for evaluating R code
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;;; Code:
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(require 'org-babel)
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(org-babel-add-interpreter "R")
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(add-to-list 'org-babel-tangle-langs '("R" "r"))
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(defun org-babel-execute:R (body params)
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"Execute a block of R code with org-babel. This function is
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called by `org-babel-execute-src-block' via multiple-value-bind."
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(message "executing R source code block...")
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(save-window-excursion
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(let ((full-body (concat
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(mapconcat ;; define any variables
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(lambda (pair)
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(org-babel-R-assign-elisp (car pair) (cdr pair)))
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vars "\n") "\n" body "\n"))
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(session (org-babel-R-initiate-session session)))
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(org-babel-R-evaluate session full-body result-type))))
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(defun org-babel-prep-session:R (session params)
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"Prepare SESSION according to the header arguments specified in PARAMS."
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(let* ((session (org-babel-R-initiate-session session))
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(vars (org-babel-ref-variables params)))
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(mapc (lambda (pair) (org-babel-R-assign-elisp session (car pair) (cdr pair))) vars)))
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;; helper functions
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(defun org-babel-R-quote-tsv-field (s)
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"Quote field S for export to R."
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(if (stringp s)
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(concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
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(format "%S" s)))
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(defun org-babel-R-assign-elisp (name value)
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"Read the elisp VALUE into a variable named NAME."
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(if (listp value)
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(let ((transition-file (make-temp-file "org-babel-R-import")))
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;; ensure VALUE has an orgtbl structure (depth of at least 2)
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(unless (listp (car value)) (setq value (list value)))
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(with-temp-file transition-file
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(insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
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(insert "\n"))
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(format "%s <- read.table(\"%s\", header=FALSE, sep=\"\\t\", as.is=TRUE)"
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name transition-file))
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(format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
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(defun org-babel-R-initiate-session (session)
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"If there is not a current R process then create one."
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(unless (string= session "none")
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(setq session (or session "*R*"))
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(if (org-babel-comint-buffer-livep session)
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session
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(save-window-excursion
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(R)
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(rename-buffer (if (bufferp session) (buffer-name session)
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(if (stringp session) session (buffer-name)))) (current-buffer)))))
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(defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
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(defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
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(defvar org-babel-R-wrapper-method "main <- function ()\n{\n%s\n}
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write.table(main(), file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=FALSE, col.names=FALSE, quote=FALSE)")
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(defun org-babel-R-evaluate (buffer body result-type)
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"Pass BODY to the R process in BUFFER. If RESULT-TYPE equals
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'output then return a list of the outputs of the statements in
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BODY, if RESULT-TYPE equals 'value then return the value of the
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last statement in BODY, as elisp."
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(if (not session)
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;; external process evaluation
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(let ((in-tmp-file (make-temp-file "R-in-functional-results"))
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(out-tmp-file (make-temp-file "R-out-functional-results")))
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(case result-type
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(output
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(with-temp-file in-tmp-file (insert body))
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(shell-command-to-string (format "R --slave --no-save < '%s' > '%s'"
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in-tmp-file out-tmp-file))
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(with-temp-buffer (insert-file-contents out-tmp-file) (buffer-string)))
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(value
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(with-temp-file in-tmp-file
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(insert (format org-babel-R-wrapper-method body out-tmp-file)))
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(shell-command (format "R --no-save < '%s'" in-tmp-file))
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(org-babel-import-elisp-from-file out-tmp-file))))
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;; comint session evaluation
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(org-babel-comint-in-buffer buffer
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(let* ((tmp-file (make-temp-file "org-babel-R"))
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(last-value-eval
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(format "write.table(.Last.value, file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=FALSE, col.names=FALSE, quote=FALSE)"
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tmp-file))
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(full-body (mapconcat #'org-babel-chomp
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(list body last-value-eval org-babel-R-eoe-indicator) "\n"))
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(raw (org-babel-comint-with-output buffer org-babel-R-eoe-output nil
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(insert full-body) (inferior-ess-send-input)))
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(results
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(let ((broke nil))
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(delete
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nil
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(mapcar (lambda (el)
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(if (or broke
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(and (string-match (regexp-quote org-babel-R-eoe-output)
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el) (setq broke t)))
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nil
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(if (= (length el) 0)
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nil
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(if (string-match comint-prompt-regexp el)
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(substring el (match-end 0))
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el))))
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(mapcar #'org-babel-trim raw))))))
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(case result-type
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(output (org-babel-trim (mapconcat #'identity results "\n")))
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(value (org-babel-import-elisp-from-file tmp-file)))))))
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(provide 'org-babel-R)
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;;; org-babel-R.el ends here
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